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Bitarafan S, Pybus AF, Rivera Moctezuma FG, Adibi M, Franklin TC, Singer AC, Wood LB. Frequency and duration of sensory flicker controls astrocyte and neuron specific transcriptional profiles in 5xFAD mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.594705. [PMID: 38826251 PMCID: PMC11142106 DOI: 10.1101/2024.05.20.594705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Current clinical trials are investigating gamma frequency sensory stimulation as a potential therapeutic strategy for Alzheimer's disease, yet we lack a comprehensive picture of the effects of this stimulation on multiple aspects of brain function. While most prior research has focused on gamma frequency sensory stimulation, we previously showed that exposing mice to visual flickering stimulation increased MAPK and NFκB signaling in the visual cortex in a manner dependent on duration and frequency of sensory stimulation exposure. Because these pathways control multiple neuronal and glial functions and are differentially activated based on the duration and frequency of flicker stimulation, we aimed to define the transcriptional effects of different frequencies and durations of flicker stimulation on multiple brain functions. Methods We exposed 5xFAD mice to different frequencies of audio/visual flicker stimulation (constant light, 10Hz, 20Hz, 40Hz) for durations of 0.5hr, 1hr, or 4hr, then used bulk RNAseq to profile transcriptional changes within the visual cortex and hippocampus tissues. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes controlled by frequency and/or duration of stimulation. Results Within the visual cortex, we found that all stimulation frequencies caused fast activation of a module of immune genes within 1hr and slower suppression of synaptic genes after 4hrs of stimulation. Interestingly, all frequencies of stimulation led to slow suppression of astrocyte specific gene sets, while activation of neuronal gene sets was frequency and duration specific. In contrast, in the hippocampus, immune and synaptic modules were suppressed based on the frequency of stimulation. Specifically,10Hz activated a module of genes associated with mitochondrial function, metabolism, and synaptic translation while 10Hz rapidly suppressed a module of genes linked to neurotransmitter activity. Conclusion Collectively, our data indicate that the frequency and duration of flicker stimulation controls immune, neuronal, and metabolic genes in multiple regions of the brain affected by Alzheimer's disease. Flicker stimulation may thus represent a potential therapeutic strategy that can be tuned based on the brain region and the specific cellular process to be modulated.
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2
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Ram A, Pargett M, Choi Y, Murphy D, Cabel M, Kosaisawe N, Quon G, Albeck J. Deciphering the History of ERK Activity from Fixed-Cell Immunofluorescence Measurements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580760. [PMID: 38405841 PMCID: PMC10889026 DOI: 10.1101/2024.02.16.580760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The Ras/ERK pathway drives cell proliferation and other oncogenic behaviors, and quantifying its activity in situ is of high interest in cancer diagnosis and therapy. Pathway activation is often assayed by measuring phosphorylated ERK. However, this form of measurement overlooks dynamic aspects of signaling that can only be observed over time. In this study, we combine a live, single-cell ERK biosensor approach with multiplexed immunofluorescence staining of downstream target proteins to ask how well immunostaining captures the dynamic history of ERK activity. Combining linear regression, machine learning, and differential equation models, we develop an interpretive framework for immunostains, in which Fra-1 and pRb levels imply long term activation of ERK signaling, while Egr-1 and c-Myc indicate recent activation. We show that this framework can distinguish different classes of ERK dynamics within a heterogeneous population, providing a tool for annotating ERK dynamics within fixed tissues.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Yongin Choi
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Markhus Cabel
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, Davis
| | - John Albeck
- Department of Molecular and Cellular Biology, University of California, Davis
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3
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Ginley-Hidinger M, Abewe H, Osborne K, Richey A, Kitchen N, Mortenson KL, Wissink EM, Lis J, Zhang X, Gertz J. Cis-regulatory control of transcriptional timing and noise in response to estrogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.14.532457. [PMID: 36993565 PMCID: PMC10054948 DOI: 10.1101/2023.03.14.532457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cis-regulatory elements control transcription levels, temporal dynamics, and cell-cell variation or transcriptional noise. However, the combination of regulatory features that control these different attributes is not fully understood. Here, we used single cell RNA-seq during an estrogen treatment time course and machine learning to identify predictors of expression timing and noise. We find that genes with multiple active enhancers exhibit faster temporal responses. We verified this finding by showing that manipulation of enhancer activity changes the temporal response of estrogen target genes. Analysis of transcriptional noise uncovered a relationship between promoter and enhancer activity, with active promoters associated with low noise and active enhancers linked to high noise. Finally, we observed that co-expression across single cells is an emergent property associated with chromatin looping, timing, and noise. Overall, our results indicate a fundamental tradeoff between a gene's ability to quickly respond to incoming signals and maintain low variation across cells.
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Affiliation(s)
- Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Hosiana Abewe
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kyle Osborne
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandra Richey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Noel Kitchen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Katelyn L. Mortenson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Erin M. Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xiaoyang Zhang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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4
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 2: downstream decoding. Biochem J 2023; 480:1909-1928. [PMID: 38038975 PMCID: PMC10754290 DOI: 10.1042/bcj20230277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Signaling by the extracellular signal-regulated kinase (ERK) pathway controls many cellular processes, including cell division, death, and differentiation. In this second installment of a two-part review, we address the question of how the ERK pathway exerts distinct and context-specific effects on multiple processes. We discuss how the dynamics of ERK activity induce selective changes in gene expression programs, with insights from both experiments and computational models. With a focus on single-cell biosensor-based studies, we summarize four major functional modes for ERK signaling in tissues: adjusting the size of cell populations, gradient-based patterning, wave propagation of morphological changes, and diversification of cellular gene expression states. These modes of operation are disrupted in cancer and other related diseases and represent potential targets for therapeutic intervention. By understanding the dynamic mechanisms involved in ERK signaling, there is potential for pharmacological strategies that not only simply inhibit ERK, but also restore functional activity patterns and improve disease outcomes.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
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5
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Azizi SA, Qiu T, Brookes NE, Dickinson BC. Regulation of ERK2 activity by dynamic S-acylation. Cell Rep 2023; 42:113135. [PMID: 37715953 PMCID: PMC10591828 DOI: 10.1016/j.celrep.2023.113135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023] Open
Abstract
Extracellular signal-regulated kinases (ERK1/2) are key effector proteins of the mitogen-activated protein kinase pathway, choreographing essential processes of cellular physiology. Here, we discover that ERK1/2 are subject to S-acylation, a reversible lipid modification of cysteine residues, at C271/C254. The levels of ERK1/2 S-acylation are modulated by epidermal growth factor (EGF) signaling, mirroring its phosphorylation dynamics, and acylation-deficient ERK2 displays altered phosphorylation patterns. We show that ERK1/2 S-acylation is mediated by "writer" protein acyl transferases (PATs) and "eraser" acyl protein thioesterases (APTs) and that chemical inhibition of either lipid addition or removal alters ERK1/2's EGF-triggered transcriptional program. Finally, in a mouse model of metabolic syndrome, we find that ERK1/2 lipidation levels correlate with alterations in ERK1/2 lipidation writer/eraser expression, solidifying a link between ERK1/2 activity, ERK1/2 lipidation, and organismal health. This study describes how lipidation regulates ERK1/2 and offers insight into the role of dynamic S-acylation in cell signaling more broadly.
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Affiliation(s)
- Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Tian Qiu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Noah E Brookes
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
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6
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Cuevas-Navarro A, Wagner M, Van R, Swain M, Mo S, Columbus J, Allison MR, Cheng A, Messing S, Turbyville TJ, Simanshu DK, Sale MJ, McCormick F, Stephen AG, Castel P. RAS-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy. SCIENCE ADVANCES 2023; 9:eadf4766. [PMID: 37450595 PMCID: PMC10348673 DOI: 10.1126/sciadv.adf4766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
RIT1 is a RAS guanosine triphosphatase (GTPase) that regulates different aspects of signal transduction and is mutated in lung cancer, leukemia, and in the germline of individuals with Noonan syndrome. Pathogenic RIT1 proteins promote mitogen-activated protein kinase (MAPK) hyperactivation; however, this mechanism remains poorly understood. Here, we show that RAF kinases are direct effectors of membrane-bound mutant RIT1 necessary for MAPK activation. We identify critical residues in RIT1 that facilitate interaction with membrane lipids and show that these are necessary for association with RAF kinases and MAPK activation. Although mutant RIT1 binds to RAF kinases directly, it fails to activate MAPK signaling in the absence of classical RAS proteins. Consistent with aberrant RAF/MAPK activation as a driver of disease, we show that pathway inhibition alleviates cardiac hypertrophy in a mouse model of RIT1 mutant Noonan syndrome. These data shed light on the function of pathogenic RIT1 and identify avenues for therapeutic intervention.
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Affiliation(s)
- Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Morgan Wagner
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Richard Van
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monalisa Swain
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Stephanie Mo
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Madeline R. Allison
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Thomas J. Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Matthew J. Sale
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrew G. Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
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7
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Juul NH, Yoon JK, Martinez MC, Rishi N, Kazadaeva YI, Morri M, Neff NF, Trope WL, Shrager JB, Sinha R, Desai TJ. KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming. Nature 2023; 619:860-867. [PMID: 37468622 PMCID: PMC10423036 DOI: 10.1038/s41586-023-06324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
Many cancers originate from stem or progenitor cells hijacked by somatic mutations that drive replication, exemplified by adenomatous transformation of pulmonary alveolar epithelial type II (AT2) cells1. Here we demonstrate a different scenario: expression of KRAS(G12D) in differentiated AT1 cells reprograms them slowly and asynchronously back into AT2 stem cells that go on to generate indolent tumours. Like human lepidic adenocarcinoma, the tumour cells slowly spread along alveolar walls in a non-destructive manner and have low ERK activity. We find that AT1 and AT2 cells act as distinct cells of origin and manifest divergent responses to concomitant WNT activation and KRAS(G12D) induction, which accelerates AT2-derived but inhibits AT1-derived adenoma proliferation. Augmentation of ERK activity in KRAS(G12D)-induced AT1 cells increases transformation efficiency, proliferation and progression from lepidic to mixed tumour histology. Overall, we have identified a new cell of origin for lung adenocarcinoma, the AT1 cell, which recapitulates features of human lepidic cancer. In so doing, we also uncover a capacity for oncogenic KRAS to reprogram a differentiated and quiescent cell back into its parent stem cell en route to adenomatous transformation. Our work further reveals that irrespective of a given cancer's current molecular profile and driver oncogene, the cell of origin exerts a pervasive and perduring influence on its subsequent behaviour.
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Affiliation(s)
- Nicholas H Juul
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jung-Ki Yoon
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina C Martinez
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Neha Rishi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yana I Kazadaeva
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Winston L Trope
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B Shrager
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Lyon A, Tripathi R, Meeks C, He D, Wu Y, Liu J, Wang C, Chen J, Zhu H, Mukherjee S, Ganguly S, Plattner R. ABL1/2 and DDR1 Drive MEKi Resistance in NRAS-Mutant Melanomas by Stabilizing RAF/MYC/ETS1 and Promoting RAF Homodimerization. Cancers (Basel) 2023; 15:954. [PMID: 36765910 PMCID: PMC9913232 DOI: 10.3390/cancers15030954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Melanomas harboring NRAS mutations are a particularly aggressive and deadly subtype. If patients cannot tolerate or the melanomas are insensitive to immune checkpoint blockade, there are no effective 2nd-line treatment options. Drugs targeting the RAF/MEK/ERK pathway, which are used for BRAF-mutant melanomas, do little to increase progression-free survival (PFS). Here, using both loss-of-function and gain-of-function approaches, we show that ABL1/2 and DDR1 are critical nodes during NRAS-mutant melanoma intrinsic and acquired MEK inhibitor (MEKi) resistance. In some acquired resistance cells, ABL1/2 and DDR1 cooperate to stabilize RAF proteins, activate ERK cytoplasmic and nuclear signaling, repress p27/KIP1 expression, and drive RAF homodimerization. In contrast, other acquired resistance cells depend solely on ABL1/2 for their survival, and are sensitive to highly specific allosteric ABL1/2 inhibitors, which prevent β-catenin nuclear localization and destabilize MYC and ETS1 in an ERK-independent manner. Significantly, targeting ABL1/2 and DDR1 with an FDA-approved anti-leukemic drug, reverses intrinsic MEKi resistance, delays acquisition of acquired resistance, and doubles the survival time in a NRAS-mutant mouse model. These data indicate that repurposing FDA-approved drugs targeting ABL1/2 and DDR1 may be a novel and effective strategy for treating patients with treatment-refractory NRAS-driven melanomas.
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Affiliation(s)
- Anastasia Lyon
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Rakshamani Tripathi
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Christina Meeks
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Yuanyuan Wu
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Jinpeng Liu
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Chi Wang
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Sujata Mukherjee
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Saptadwipa Ganguly
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Rina Plattner
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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9
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Wang Y, Wang HM, Zhou Y, Hu LH, Wan JM, Yang JH, Niu HB, Hong XP, Hu P, Chen LB, Hu P, Chen LB. Dusp1 regulates thermal tolerance limits in zebrafish by maintaining mitochondrial integrity. Zool Res 2023; 44:126-141. [PMID: 36419379 PMCID: PMC9841188 DOI: 10.24272/j.issn.2095-8137.2022.397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Temperature tolerance restricts the distribution of a species. However, the molecular and cellular mechanisms that set the thermal tolerance limits of an organism are poorly understood. Here, we report on the function of dual-specificity phosphatase 1 (DUSP1) in thermal tolerance regulation. Notably, we found that dusp1 -/- zebrafish grew normally but survived within a narrowed temperature range. The higher susceptibility of these mutant fish to both cold and heat challenges was attributed to accelerated cell death caused by aggravated mitochondrial dysfunction and over-production of reactive oxygen species in the gills. The DUSP1-MAPK-DRP1 axis was identified as a key pathway regulating these processes in both fish and human cells. These observations suggest that DUSP1 may play a role in maintaining mitochondrial integrity and redox homeostasis. We therefore propose that maintenance of cellular redox homeostasis may be a key mechanism for coping with cellular thermal stress and that the interplay between signaling pathways regulating redox homeostasis in the most thermosensitive tissue (i.e., gills) may play an important role in setting the thermal tolerance limit of zebrafish.
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Affiliation(s)
- Ying Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Hua-Min Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Yan Zhou
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Ling-Hong Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Jing-Ming Wan
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Ji-Hui Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Hong-Bo Niu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Xiu-Ping Hong
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Peng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Liang-Biao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China,E-mail:
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10
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Tislevoll BS, Hellesøy M, Fagerholt OHE, Gullaksen SE, Srivastava A, Birkeland E, Kleftogiannis D, Ayuda-Durán P, Piechaczyk L, Tadele DS, Skavland J, Panagiotis B, Hovland R, Andresen V, Seternes OM, Tvedt THA, Aghaeepour N, Gavasso S, Porkka K, Jonassen I, Fløisand Y, Enserink J, Blaser N, Gjertsen BT. Early response evaluation by single cell signaling profiling in acute myeloid leukemia. Nat Commun 2023; 14:115. [PMID: 36611026 PMCID: PMC9825407 DOI: 10.1038/s41467-022-35624-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24 h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing shows induction of MAPK target gene expression in patients with high phospho-ERK1/2 24 h post-chemotherapy, while proteomics confirm an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.
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Affiliation(s)
- Benedicte Sjo Tislevoll
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Monica Hellesøy
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway
| | - Oda Helen Eck Fagerholt
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stein-Erik Gullaksen
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway
| | - Aashish Srivastava
- Genome Core Facility, Clinical Laboratory, K2 Haukeland University Hospital, Bergen, Norway
| | - Even Birkeland
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, Bergen, Norway
| | - Dimitrios Kleftogiannis
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Cancer Biomarkers and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway
| | - Laure Piechaczyk
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Dagim Shiferaw Tadele
- Department of Molecular Genetics, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway.,Department of Translational Hematology and Oncology Research, Cleveland Clinic, OH, 44106, USA
| | - Jørn Skavland
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Baliakas Panagiotis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Randi Hovland
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Vibeke Andresen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | | | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, 94121, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94121, USA.,Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, 94121, USA
| | - Sonia Gavasso
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Clinical Treatment Research (NeuroSysMed), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Inge Jonassen
- Centre for Cancer Biomarkers and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Yngvar Fløisand
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Jorrit Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0037, Oslo, Norway
| | - Nello Blaser
- Department of Informatics, University of Bergen, Bergen, Norway.
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway.
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11
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ERK-mediated NELF-A phosphorylation promotes transcription elongation of immediate-early genes by releasing promoter-proximal pausing of RNA polymerase II. Nat Commun 2022; 13:7476. [PMID: 36463234 PMCID: PMC9719515 DOI: 10.1038/s41467-022-35230-4] [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: 07/09/2021] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Growth factor-induced, ERK-mediated induction of immediate-early genes (IEGs) is crucial for cell growth and tumorigenesis. Although IEG expression is mainly regulated at the level of transcription elongation by RNA polymerase-II (Pol-II) promoter-proximal pausing and its release, the role of ERK in this process remains unknown. Here, we identified negative elongation factor (NELF)-A as an ERK substrate. Upon growth factor stimulation, ERK phosphorylates NELF-A, which dissociates NELF from paused Pol-II at the promoter-proximal regions of IEGs, allowing Pol-II to resume elongation and produce full-length transcripts. Furthermore, we found that in cancer cells, PP2A efficiently dephosphorylates NELF-A, thereby preventing aberrant IEG expression induced by ERK-activating oncogenes. However, when PP2A inhibitor proteins are overexpressed, as is frequently observed in cancers, decreased PP2A activity combined with oncogene-mediated ERK activation conspire to induce NELF-A phosphorylation and IEG upregulation, resulting in tumor progression. Our data delineate previously unexplored roles of ERK and PP2A inhibitor proteins in carcinogenesis.
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12
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Stern AD, Smith GR, Santos LC, Sarmah D, Zhang X, Lu X, Iuricich F, Pandey G, Iyengar R, Birtwistle MR. Relating individual cell division events to single-cell ERK and Akt activity time courses. Sci Rep 2022; 12:18077. [PMID: 36302844 PMCID: PMC9613772 DOI: 10.1038/s41598-022-23071-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/25/2022] [Indexed: 02/01/2023] Open
Abstract
Biochemical correlates of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to division events in the same single cells using the non-transformed MCF10A epithelial line. Following growth factor treatment, in cells that divide both ERK and Akt activities are significantly higher within the S-G2 time window (~ 8.5-40 h). Such differences were much smaller in the pre-S-phase, restriction point window which is traditionally associated with ERK and Akt activity dependence, suggesting unappreciated roles for ERK and Akt in S through G2. Simple metrics of central tendency in this time window are associated with subsequent cell division fates. ERK activity was more strongly associated with division fates than Akt activity, suggesting Akt activity dynamics may contribute less to the decision driving cell division in this context. We also find that ERK and Akt activities are less correlated with each other in cells that divide. Network reconstruction experiments demonstrated that this correlation behavior was likely not due to crosstalk, as ERK and Akt do not interact in this context, in contrast to other transformed cell types. Overall, our findings support roles for ERK and Akt activity throughout the cell cycle as opposed to just before the restriction point, and suggest ERK activity dynamics may be more important than Akt activity dynamics for driving cell division in this non-transformed context.
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Affiliation(s)
- Alan D Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luis C Santos
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepraj Sarmah
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Xiang Zhang
- School of Computing, Clemson University, Clemson, SC, USA
| | - Xiaoming Lu
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | | | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc R Birtwistle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
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13
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Sen-Kilic E, Huckaby AB, Damron FH, Barbier M. P. aeruginosa type III and type VI secretion systems modulate early response gene expression in type II pneumocytes in vitro. BMC Genomics 2022; 23:345. [PMID: 35508983 PMCID: PMC9068226 DOI: 10.1186/s12864-022-08554-0] [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: 12/23/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lung airway epithelial cells are part of innate immunity and the frontline of defense against bacterial infections. During infection, airway epithelial cells secrete proinflammatory mediators that participate in the recruitment of immune cells. Virulence factors expressed by bacterial pathogens can alter epithelial cell gene expression and modulate this response. Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, expresses numerous virulence factors to facilitate establishment of infection and evade the host immune response. This study focused on identifying the role of two major P. aeruginosa virulence factors, type III (T3SS) and type VI (T6SS) secretion systems, on the early transcriptome response of airway epithelial cells in vitro. RESULTS We performed RNA-seq analysis of the transcriptome response of type II pneumocytes during infection with P. aeruginosa in vitro. We observed that P. aeruginosa differentially upregulates immediate-early response genes and transcription factors that induce proinflammatory responses in type II pneumocytes. P. aeruginosa infection of type II pneumocytes was characterized by up-regulation of proinflammatory networks, including MAPK, TNF, and IL-17 signaling pathways. We also identified early response genes and proinflammatory signaling pathways whose expression change in response to infection with P. aeruginosa T3SS and T6SS mutants in type II pneumocytes. We determined that T3SS and T6SS modulate the expression of EGR1, FOS, and numerous genes that are involved in proinflammatory responses in epithelial cells during infection. T3SS and T6SS were associated with two distinct transcriptomic signatures related to the activation of transcription factors such as AP1, STAT1, and SP1, and the secretion of pro-inflammatory cytokines such as IL-6 and IL-8. CONCLUSIONS Taken together, transcriptomic analysis of epithelial cells indicates that the expression of immediate-early response genes quickly changes upon infection with P. aeruginosa and this response varies depending on bacterial viability and injectosomes. These data shed light on how P. aeruginosa modulates host epithelial transcriptome response during infection using T3SS and T6SS.
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Affiliation(s)
- Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.,Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Annalisa B Huckaby
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.,Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.,Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA. .,Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, USA.
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14
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Valls PO, Esposito A. Signalling dynamics, cell decisions, and homeostatic control in health and disease. Curr Opin Cell Biol 2022; 75:102066. [PMID: 35245783 PMCID: PMC9097822 DOI: 10.1016/j.ceb.2022.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/13/2022]
Abstract
Cell signalling engenders cells with the capability to receive and process information from the intracellular and extracellular environments, trigger and execute biological responses, and communicate with each other. Ultimately, cell signalling is responsible for maintaining homeostasis at the cellular, tissue and systemic level. For this reason, cell signalling is a topic of intense research efforts aimed to elucidate how cells coordinate transitions between states in developing and adult organisms in physiological and pathological conditions. Here, we review current knowledge of how cell signalling operates at multiple spatial and temporal scales, focusing on how single-cell analytical techniques reveal mechanisms underpinning cell-to-cell variability, signalling plasticity, and collective cellular responses.
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Affiliation(s)
- Pablo Oriol Valls
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
| | - Alessandro Esposito
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom; Centre for Genome Engineering and Maintenance, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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15
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Davidian D, LeGro M, Barghouth PG, Rojas S, Ziman B, Maciel EI, Ardell D, Escobar AL, Oviedo NJ. Restoration of DNA integrity and cell cycle by electric stimulation in planarian tissues damaged by ionizing radiation. J Cell Sci 2022; 135:274829. [PMID: 35322853 PMCID: PMC9264365 DOI: 10.1242/jcs.259304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/05/2022] [Indexed: 10/18/2022] Open
Abstract
Exposure to high levels of ionizing γ-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally γ-irradiated tissues of the planarian flatworm Schmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+ stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse the damaging effects of high dose γ-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.
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Affiliation(s)
- Devon Davidian
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Melanie LeGro
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Paul G Barghouth
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Salvador Rojas
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Benjamin Ziman
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Eli Isael Maciel
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - David Ardell
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Health Sciences Research Institute, University of California, Merced, USA
| | - Ariel L Escobar
- Department of Bioengineering, University of California, Merced, USA.,Health Sciences Research Institute, University of California, Merced, USA
| | - Néstor J Oviedo
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Health Sciences Research Institute, University of California, Merced, USA
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16
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Analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling in the activation of neural stem progenitor cells. NPJ Regen Med 2021; 6:68. [PMID: 34686684 PMCID: PMC8536777 DOI: 10.1038/s41536-021-00179-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPCs). Here we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, aiming to identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC-specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration and proliferation of NSPC through the downregulation of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.
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17
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Häger SC, Dias C, Sønder SL, Olsen AV, da Piedade I, Heitmann ASB, Papaleo E, Nylandsted J. Short-term transcriptomic response to plasma membrane injury. Sci Rep 2021; 11:19141. [PMID: 34580330 PMCID: PMC8476590 DOI: 10.1038/s41598-021-98420-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Plasma membrane repair mechanisms are activated within seconds post-injury to promote rapid membrane resealing in eukaryotic cells and prevent cell death. However, less is known about the regeneration phase that follows and how cells respond to injury in the short-term. Here, we provide a genome-wide study into the mRNA expression profile of MCF-7 breast cancer cells exposed to injury by digitonin, a mild non-ionic detergent that permeabilizes the plasma membrane. We focused on the early transcriptional signature and found a time-dependent increase in the number of differentially expressed (> twofold, P < 0.05) genes (34, 114 and 236 genes at 20-, 40- and 60-min post-injury, respectively). Pathway analysis highlighted a robust and gradual three-part transcriptional response: (1) prompt activation of immediate-early response genes, (2) activation of specific MAPK cascades and (3) induction of inflammatory and immune pathways. Therefore, plasma membrane injury triggers a rapid and strong stress and immunogenic response. Our meta-analysis suggests that this is a conserved transcriptome response to plasma membrane injury across different cell and injury types. Taken together, our study shows that injury has profound effects on the transcriptome of wounded cells in the regeneration phase (subsequent to membrane resealing), which is likely to influence cellular status and has been previously overlooked.
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Affiliation(s)
- Swantje Christin Häger
- Membrane Integrity, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Catarina Dias
- Membrane Integrity, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Stine Lauritzen Sønder
- Membrane Integrity, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - André Vidas Olsen
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Isabelle da Piedade
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Anne Sofie Busk Heitmann
- Membrane Integrity, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Jesper Nylandsted
- Membrane Integrity, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen N, Denmark.
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18
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Klotz-Noack K, Klinger B, Rivera M, Bublitz N, Uhlitz F, Riemer P, Lüthen M, Sell T, Kasack K, Gastl B, Ispasanie SSS, Simon T, Janssen N, Schwab M, Zuber J, Horst D, Blüthgen N, Schäfer R, Morkel M, Sers C. SFPQ Depletion Is Synthetically Lethal with BRAF V600E in Colorectal Cancer Cells. Cell Rep 2021; 32:108184. [PMID: 32966782 DOI: 10.1016/j.celrep.2020.108184] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 04/28/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022] Open
Abstract
Oncoproteins such as the BRAFV600E kinase endow cancer cells with malignant properties, but they also create unique vulnerabilities. Targeting of BRAFV600E-driven cytoplasmic signaling networks has proved ineffective, as patients regularly relapse with reactivation of the targeted pathways. We identify the nuclear protein SFPQ to be synthetically lethal with BRAFV600E in a loss-of-function shRNA screen. SFPQ depletion decreases proliferation and specifically induces S-phase arrest and apoptosis in BRAFV600E-driven colorectal and melanoma cells. Mechanistically, SFPQ loss in BRAF-mutant cancer cells triggers the Chk1-dependent replication checkpoint, results in decreased numbers and reduced activities of replication factories, and increases collision between replication and transcription. We find that BRAFV600E-mutant cancer cells and organoids are sensitive to combinations of Chk1 inhibitors and chemically induced replication stress, pointing toward future therapeutic approaches exploiting nuclear vulnerabilities induced by BRAFV600E.
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Affiliation(s)
- Kathleen Klotz-Noack
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bertram Klinger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Maria Rivera
- EPO Experimentelle Pharmakologie und Onkologie Berlin-Buch GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Natalie Bublitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Uhlitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Pamela Riemer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Mareen Lüthen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Sell
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Katharina Kasack
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bastian Gastl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Sylvia S S Ispasanie
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Tincy Simon
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany; University of Tuebingen, 72074 Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany; Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Auf der Morgenstelle 8, 72074 Tuebingen, Germany; German Cancer Consortium (DKTK), Partner Site Tuebingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; Medical University of Vienna, VBC, 1030 Vienna, Austria
| | - David Horst
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nils Blüthgen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reinhold Schäfer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany; Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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19
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Lormeau C, Rudolf F, Stelling J. A rationally engineered decoder of transient intracellular signals. Nat Commun 2021; 12:1886. [PMID: 33767179 PMCID: PMC7994635 DOI: 10.1038/s41467-021-22190-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/05/2021] [Indexed: 12/20/2022] Open
Abstract
Cells can encode information about their environment by modulating signaling dynamics and responding accordingly. Yet, the mechanisms cells use to decode these dynamics remain unknown when cells respond exclusively to transient signals. Here, we approach design principles underlying such decoding by rationally engineering a synthetic short-pulse decoder in budding yeast. A computational method for rapid prototyping, TopoDesign, allowed us to explore 4122 possible circuit architectures, design targeted experiments, and then rationally select a single circuit for implementation. This circuit demonstrates short-pulse decoding through incoherent feedforward and positive feedback. We predict incoherent feedforward to be essential for decoding transient signals, thereby complementing proposed design principles of temporal filtering, the ability to respond to sustained signals, but not to transient signals. More generally, we anticipate TopoDesign to help designing other synthetic circuits with non-intuitive dynamics, simply by assembling available biological components.
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Affiliation(s)
- Claude Lormeau
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Mattenstrasse 26, CH 4058, Basel, Switzerland
- Life Science Zurich Graduate School, Interdisciplinary PhD Program Systems Biology, Zurich, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Mattenstrasse 26, CH 4058, Basel, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Mattenstrasse 26, CH 4058, Basel, Switzerland.
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20
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Sharma S, Sharma M, Rana AK, Joshi R, Swarnkar MK, Acharya V, Singh D. Deciphering key regulators involved in epilepsy-induced cardiac damage through whole transcriptome and proteome analysis in a rat model. Epilepsia 2020; 62:504-516. [PMID: 33341939 DOI: 10.1111/epi.16794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 11/27/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Sudden unexpected death in epilepsy (SUDEP) is a major outcome of cardiac dysfunction in patients with epilepsy. In continuation of our previous work, the present study was envisaged to explore the key regulators responsible for cardiac damage associated with chronic seizures using whole transcriptome and proteome analysis in a rat model of temporal lobe epilepsy. METHODS A standard lithium-pilocarpine protocol was used to induce recurrent seizures in rats. The isolated rat heart tissue was subjected to transcriptomic and proteomic analysis. An integrated approach of RNA-Seq, proteomics, and system biology analysis was used to identify key regulators involved in seizure-linked cardiac changes. The analyzed differential expression patterns and network interactions were supported by gene and protein expression studies. RESULTS Altogether, 1157 differentially expressed genes and 1264 proteins were identified in the cardiac tissue of epileptic animals through RNA-Seq and liquid chromatography with tandem mass spectrometry-based proteomic analysis, respectively. The network analysis revealed seven critical genes-STAT3, Myc, Fos, Erbb2, Erbb3, Notch1, and Mapk8-that could play a role in seizure-mediated cardiac changes. The LC-MS/MS analysis supported the activation of the transforming growth factor β (TGF-β) pathway in the heart of epileptic animals. Furthermore, our gene and protein expression studies established a key role of STAT3, Erbb, and Mapk8 to develop cardiac changes linked with recurrent seizures. SIGNIFICANCE The present multi-omics study identified STAT3, Mapk8, and Erbb as key regulators involved in seizure-associated cardiac changes. It provided a deeper understanding of molecular, cellular, and network-level operations of the identified regulators that lead to cardiac changes in epilepsy.
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Affiliation(s)
- Supriya Sharma
- Pharmacology and Toxicology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Meetal Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Functional Genomics and Complex System Laboratory, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Anil Kumar Rana
- Pharmacology and Toxicology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Robin Joshi
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Mohit Kumar Swarnkar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vishal Acharya
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Functional Genomics and Complex System Laboratory, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Damanpreet Singh
- Pharmacology and Toxicology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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21
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Meisig J, Dreser N, Kapitza M, Henry M, Rotshteyn T, Rahnenführer J, Hengstler J, Sachinidis A, Waldmann T, Leist M, Blüthgen N. Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation. Nucleic Acids Res 2020; 48:12577-12592. [PMID: 33245762 PMCID: PMC7736781 DOI: 10.1093/nar/gkaa1089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
Thousands of transcriptome data sets are available, but approaches for their use in dynamic cell response modelling are few, especially for processes affected simultaneously by two orthogonal influencing variables. We approached this problem for neuroepithelial development of human pluripotent stem cells (differentiation variable), in the presence or absence of valproic acid (signaling variable). Using few basic assumptions (sequential differentiation states of cells; discrete on/off states for individual genes in these states), and time-resolved transcriptome data, a comprehensive model of spontaneous and perturbed gene expression dynamics was developed. The model made reliable predictions (average correlation of 0.85 between predicted and subsequently tested expression values). Even regulations predicted to be non-monotonic were successfully validated by PCR in new sets of experiments. Transient patterns of gene regulation were identified from model predictions. They pointed towards activation of Wnt signaling as a candidate pathway leading to a redirection of differentiation away from neuroepithelial cells towards neural crest. Intervention experiments, using a Wnt/beta-catenin antagonist, led to a phenotypic rescue of this disturbed differentiation. Thus, our broadly applicable model allows the analysis of transcriptome changes in complex time/perturbation matrices.
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Affiliation(s)
- Johannes Meisig
- Institute of Pathology, Charité-Universitätsmedizin, 10117 Berlin, Germany
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Nadine Dreser
- In Vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden Chair foundation, University of Konstanz, 78457 Konstanz, Germany
| | - Marion Kapitza
- In Vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden Chair foundation, University of Konstanz, 78457 Konstanz, Germany
| | - Margit Henry
- Faculty of Medicine, Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Tamara Rotshteyn
- Faculty of Medicine, Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Jörg Rahnenführer
- Department of Statistics, TU Dortmund University, 44221 Dortmund, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), TU Dortmund University, 44139 Dortmund, Germany
| | - Agapios Sachinidis
- Faculty of Medicine, Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Tanja Waldmann
- In Vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden Chair foundation, University of Konstanz, 78457 Konstanz, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Dept inaugurated by the Doerenkamp-Zbinden Chair foundation, University of Konstanz, 78457 Konstanz, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité-Universitätsmedizin, 10117 Berlin, Germany
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
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22
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Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020; 81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Genetic predisposition affects the penetrance of tumor-initiating mutations, such as APC mutations that stabilize β-catenin and cause intestinal tumors in mice and humans. However, the mechanisms involved in genetically predisposed penetrance are not well understood. Here, we analyzed tumor multiplicity and gene expression in tumor-prone Apc Min/+ mice on highly variant C57BL/6J (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 × PWD) F1 APC Min offspring mice were largely free of intestinal adenoma, and several chromosome substitution (consomic) strains carrying single PWD chromosomes on the B6 genetic background displayed reduced adenoma numbers. Multiple dosage-dependent modifier loci on PWD chromosome 5 each contributed to tumor suppression. Activation of β-catenin-driven and stem cell-specific gene expression in the presence of Apc Min or following APC loss remained moderate in intestines carrying PWD chromosome 5, suggesting that PWD variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 were predominantly cis controlled and largely reflected parental patterns, providing a genetic basis for inheritance of tumor susceptibility. Human SNP variants of several modifier candidates were depleted in colorectal cancer genomes, suggesting that similar mechanisms may also affect the penetrance of cancer driver mutations in humans. Overall, our analysis highlights the strong impact that multiple genetic variants acting in networks can exert on tumor development. SIGNIFICANCE: These findings in mice show that, in addition to accidental mutations, cancer risk is determined by networks of individual gene variants.
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Affiliation(s)
- Alexandra L Farrall
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Christina Grimm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecophysiology and Aquaculture, Berlin, Germany
| | | | - Marta Caparros
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Prague, Czech Republic
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
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23
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Rydenfelt M, Klinger B, Klünemann M, Blüthgen N. SPEED2: inferring upstream pathway activity from differential gene expression. Nucleic Acids Res 2020; 48:W307-W312. [PMID: 32313938 PMCID: PMC7319438 DOI: 10.1093/nar/gkaa236] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/25/2020] [Accepted: 04/16/2020] [Indexed: 12/13/2022] Open
Abstract
Extracting signalling pathway activities from transcriptome data is important to infer mechanistic origins of transcriptomic dysregulation, for example in disease. A popular method to do so is by enrichment analysis of signature genes in e.g. differentially regulated genes. Previously, we derived signatures for signalling pathways by integrating public perturbation transcriptome data and generated a signature database called SPEED (Signalling Pathway Enrichment using Experimental Datasets), for which we here present a substantial upgrade as SPEED2. This web server hosts consensus signatures for 16 signalling pathways that are derived from a large number of transcriptomic signalling perturbation experiments. When providing a gene list of e.g. differentially expressed genes, the web server allows to infer signalling pathways that likely caused these genes to be deregulated. In addition to signature lists, we derive ‘continuous’ gene signatures, in a transparent and automated fashion without any fine-tuning, and describe a new algorithm to score these signatures.
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Affiliation(s)
- Mattias Rydenfelt
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin 10117, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin 10115, Germany
| | - Bertram Klinger
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin 10117, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin 10115, Germany
| | - Martina Klünemann
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin 10117, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin 10115, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin 10117, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin 10115, Germany
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24
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Furlan M, Galeota E, Gaudio ND, Dassi E, Caselle M, de Pretis S, Pelizzola M. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Res 2020; 30:1492-1507. [PMID: 32978246 PMCID: PMC7605262 DOI: 10.1101/gr.260984.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT−, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled. Finally, we applied INSPEcT− to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA.
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Affiliation(s)
- Mattia Furlan
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy.,Physics Department and INFN, University of Turin, 10125 Turin, Italy
| | - Eugenia Galeota
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Nunzio Del Gaudio
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Erik Dassi
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Michele Caselle
- Physics Department and INFN, University of Turin, 10125 Turin, Italy
| | - Stefano de Pretis
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
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25
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Davies AE, Pargett M, Siebert S, Gillies TE, Choi Y, Tobin SJ, Ram AR, Murthy V, Juliano C, Quon G, Bissell MJ, Albeck JG. Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity. Cell Syst 2020; 11:161-175.e5. [PMID: 32726596 PMCID: PMC7856305 DOI: 10.1016/j.cels.2020.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/06/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023]
Abstract
Intratumoral heterogeneity is associated with aggressive tumor behavior, therapy resistance, and poor patient outcomes. Such heterogeneity is thought to be dynamic, shifting over periods of minutes to hours in response to signaling inputs from the tumor microenvironment. However, models of this process have been inferred from indirect or post-hoc measurements of cell state, leaving the temporal details of signaling-driven heterogeneity undefined. Here, we developed a live-cell model system in which microenvironment-driven signaling dynamics can be directly observed and linked to variation in gene expression. Our analysis reveals that paracrine signaling between two cell types is sufficient to drive continual diversification of gene expression programs. This diversification emerges from systems-level properties of the EGFR-RAS-ERK signaling cascade, including intracellular amplification of amphiregulin-mediated paracrine signals and differential kinetic filtering by target genes including Fra-1, c-Myc, and Egr1. Our data enable more precise modeling of paracrine-driven transcriptional variation as a generator of gene expression heterogeneity. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Alexander E Davies
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Yongin Choi
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Savannah J Tobin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA; Department of Veterinary Biosciences, College of Veterinary Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Abhineet R Ram
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Vaibhav Murthy
- Department of Veterinary Biosciences, College of Veterinary Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Celina Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Mina J Bissell
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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26
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Blum Y, Mikelson J, Dobrzyński M, Ryu H, Jacques MA, Jeon NL, Khammash M, Pertz O. Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling. Mol Syst Biol 2020; 15:e8947. [PMID: 31777174 PMCID: PMC6864398 DOI: 10.15252/msb.20198947] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/27/2019] [Accepted: 10/21/2019] [Indexed: 01/09/2023] Open
Abstract
Stimulation of PC-12 cells with epidermal (EGF) versus nerve (NGF) growth factors (GFs) biases the distribution between transient and sustained single-cell ERK activity states, and between proliferation and differentiation fates within a cell population. We report that fibroblast GF (FGF2) evokes a distinct behavior that consists of a gradually changing population distribution of transient/sustained ERK signaling states in response to increasing inputs in a dose response. Temporally controlled GF perturbations of MAPK signaling dynamics applied using microfluidics reveal that this wider mix of ERK states emerges through the combination of an intracellular feedback, and competition of FGF2 binding to FGF receptors (FGFRs) and heparan sulfate proteoglycan (HSPG) co-receptors. We show that the latter experimental modality is instructive for model selection using a Bayesian parameter inference. Our results provide novel insights into how different receptor tyrosine kinase (RTK) systems differentially wire the MAPK network to fine-tune fate decisions at the cell population level.
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Affiliation(s)
- Yannick Blum
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jan Mikelson
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hyunryul Ryu
- Institute of Advanced Machinery and Design, Seoul National University, Seoul, Korea
| | | | - Noo Li Jeon
- Institute of Advanced Machinery and Design, Seoul National University, Seoul, Korea
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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27
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Sen S, Cheng Z, Sheu KM, Chen YH, Hoffmann A. Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression. Cell Syst 2020; 10:169-182.e5. [PMID: 31972132 DOI: 10.1016/j.cels.2019.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/20/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022]
Abstract
Pathogen-derived lipopolysaccharide (LPS) and cytokine tumor necrosis factor (TNF) activate NFκB with distinct duration dynamics, but how immune response genes decode NFκB duration to produce stimulus-specific expression remains unclear. Here, detailed transcriptomic profiling of combinatorial and temporal control mutants identified 81 genes that depend on stimulus-specific NFκB duration for their stimulus-specificity. Combining quantitative experimentation with mathematical modeling, we found that for some genes a long mRNA half-life allowed effective decoding, but for many genes this was insufficient to account for the data; instead, we found that chromatin mechanisms, such as a slow transition rate between inactive and RelA-bound enhancer states, could also decode NFκB dynamics. Chromatin-mediated decoding is favored by genes acting as immune effectors (e.g., tissue remodelers and T cell recruiters) rather than immune regulators (e.g., signaling proteins and monocyte recruiters). Overall, our results delineate two gene regulatory strategies that decode stimulus-specific NFκB dynamics and determine distinct biological functions.
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Affiliation(s)
- Supriya Sen
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhang Cheng
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences (QCB), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Katherine M Sheu
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu Hsin Chen
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences (QCB), University of California, Los Angeles, Los Angeles, CA 90095, USA.
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28
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Blum Y, Mikelson J, Dobrzyński M, Ryu H, Jacques MA, Jeon NL, Khammash M, Pertz O. Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling. Mol Syst Biol 2019; 15:e8947. [PMID: 31777174 DOI: 10.1101/629287v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/27/2019] [Accepted: 10/21/2019] [Indexed: 05/24/2023] Open
Abstract
Stimulation of PC-12 cells with epidermal (EGF) versus nerve (NGF) growth factors (GFs) biases the distribution between transient and sustained single-cell ERK activity states, and between proliferation and differentiation fates within a cell population. We report that fibroblast GF (FGF2) evokes a distinct behavior that consists of a gradually changing population distribution of transient/sustained ERK signaling states in response to increasing inputs in a dose response. Temporally controlled GF perturbations of MAPK signaling dynamics applied using microfluidics reveal that this wider mix of ERK states emerges through the combination of an intracellular feedback, and competition of FGF2 binding to FGF receptors (FGFRs) and heparan sulfate proteoglycan (HSPG) co-receptors. We show that the latter experimental modality is instructive for model selection using a Bayesian parameter inference. Our results provide novel insights into how different receptor tyrosine kinase (RTK) systems differentially wire the MAPK network to fine-tune fate decisions at the cell population level.
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Affiliation(s)
- Yannick Blum
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jan Mikelson
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hyunryul Ryu
- Institute of Advanced Machinery and Design, Seoul National University, Seoul, Korea
| | | | - Noo Li Jeon
- Institute of Advanced Machinery and Design, Seoul National University, Seoul, Korea
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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29
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Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium. Nat Commun 2019; 10:2919. [PMID: 31266962 PMCID: PMC6606648 DOI: 10.1038/s41467-019-10954-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/12/2019] [Indexed: 12/26/2022] Open
Abstract
Oncogenic mutations in KRAS or BRAF are frequent in colorectal cancer and activate the ERK kinase. Here, we find graded ERK phosphorylation correlating with cell differentiation in patient-derived colorectal cancer organoids with and without KRAS mutations. Using reporters, single cell transcriptomics and mass cytometry, we observe cell type-specific phosphorylation of ERK in response to transgenic KRASG12V in mouse intestinal organoids, while transgenic BRAFV600E activates ERK in all cells. Quantitative network modelling from perturbation data reveals that activation of ERK is shaped by cell type-specific MEK to ERK feed forward and negative feedback signalling. We identify dual-specificity phosphatases as candidate modulators of ERK in the intestine. Furthermore, we find that oncogenic KRAS, together with β-Catenin, favours expansion of crypt cells with high ERK activity. Our experiments highlight key differences between oncogenic BRAF and KRAS in colorectal cancer and find unexpected heterogeneity in a signalling pathway with fundamental relevance for cancer therapy. KRASG12V and BRAFV600E are oncogenic mutations that activate ERK signalling. Here, the authors use single cell analysis in intestinal organoids and show that BRAFV600E activates ERK in all intestinal cell types, while KRASG12V induces ERK activation in only a subset of cells, depending on cell differentiation state.
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30
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Abstract
A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.
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Affiliation(s)
- Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA .,Howard Hughes Medical Institute, Pasadena, CA 91125, USA
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31
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Imoto H, Okada M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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32
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Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE, Bivona TG, Lim WA. Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway. Science 2018; 361:361/6405/eaao3048. [PMID: 30166458 DOI: 10.1126/science.aao3048] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/16/2018] [Indexed: 12/16/2022]
Abstract
The Ras-Erk (extracellular signal-regulated kinase) pathway encodes information in its dynamics; the duration and frequency of Erk activity can specify distinct cell fates. To enable dynamic encoding, temporal information must be accurately transmitted from the plasma membrane to the nucleus. We used optogenetic profiling to show that both oncogenic B-Raf mutations and B-Raf inhibitors can cause corruption of this transmission, so that short pulses of input Ras activity are distorted into abnormally long Erk outputs. These changes can reshape downstream transcription and cell fates, resulting in improper decisions to proliferate. These findings illustrate how altered dynamic signal transmission properties, and not just constitutively increased signaling, can contribute to cell proliferation and perhaps cancer, and how optogenetic profiling can dissect mechanisms of signaling dysfunction in disease.
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Affiliation(s)
- L J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A J Sabnis
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A Mitchell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Garbarino
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Toettcher
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - T G Bivona
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - W A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
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33
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Davies AE, Albeck JG. Microenvironmental Signals and Biochemical Information Processing: Cooperative Determinants of Intratumoral Plasticity and Heterogeneity. Front Cell Dev Biol 2018; 6:44. [PMID: 29732370 PMCID: PMC5921997 DOI: 10.3389/fcell.2018.00044] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
Intra-tumor cellular heterogeneity is a major challenge in cancer therapy. Tumors are composed of multiple phenotypic subpopulations that vary in their ability to initiate metastatic tumors and in their sensitivity to chemotherapy. In many cases, cells can transition between these subpopulations, not by genetic mutation, but instead through reversible changes in signal transduction or gene expression programs. This plasticity begins at the level of the microenvironment where local autocrine and paracrine signals, exosomes, tumor–stroma interactions, and extracellular matrix (ECM) composition create a signaling landscape that varies over space and time. The integration of this complex array of signals engages signaling pathways that control gene expression. The resulting modulation of gene expression programs causes individual cells to sample a wide array of phenotypic states that support tumor growth, dissemination, and therapeutic resistance. In this review, we discuss how information flows dynamically within the microenvironmental landscape to inform cell state decisions and to create intra-tumoral heterogeneity. We address the role of plasticity in the acquisition of transient and prolonged drug resistant states and discuss how targeted pharmacological modification of the signaling landscape may be able to constrain phenotypic plasticity, leading to improved treatment responses.
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Affiliation(s)
- Alexander E Davies
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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34
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Gillies TE, Pargett M, Minguet M, Davies AE, Albeck JG. Linear Integration of ERK Activity Predominates over Persistence Detection in Fra-1 Regulation. Cell Syst 2017; 5:549-563.e5. [PMID: 29199017 DOI: 10.1016/j.cels.2017.10.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/29/2017] [Accepted: 10/27/2017] [Indexed: 12/14/2022]
Abstract
ERK signaling regulates the expression of target genes, but it is unclear how ERK activity dynamics are interpreted. Here, we investigate this question using simultaneous, live, single-cell imaging of two ERK activity reporters and expression of Fra-1, a target gene controlling epithelial cell identity. We find that Fra-1 is expressed in proportion to the amplitude and duration of ERK activity. In contrast to previous "persistence detector" and "selective filter" models in which Fra-1 expression only occurs when ERK activity persists beyond a threshold duration, our observations demonstrate that the network regulating Fra-1 expression integrates total ERK activity and responds to it linearly. However, exploration of a generalized mathematical model of the Fra-1 coherent feedforward loop demonstrates that it can perform either linear integration or persistence detection, depending on the basal mRNA production rate and protein production delays. Our data indicate that significant basal expression and short delays cause Fra-1 to respond linearly to integrated ERK activity.
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Affiliation(s)
- Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Marta Minguet
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Alex E Davies
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
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35
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Wyler E, Menegatti J, Franke V, Kocks C, Boltengagen A, Hennig T, Theil K, Rutkowski A, Ferrai C, Baer L, Kermas L, Friedel C, Rajewsky N, Akalin A, Dölken L, Grässer F, Landthaler M. Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection. Genome Biol 2017; 18:209. [PMID: 29089033 PMCID: PMC5663069 DOI: 10.1186/s13059-017-1329-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022] Open
Abstract
Background Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ways to adapt the infected cells to their needs, but knowledge about these transcriptional and post-transcriptional modifications is sparse. Results Here, we show that HSV-1 induces the expression of about 1000 antisense transcripts from the human host cell genome. A subset of these is also activated by the closely related varicella zoster virus. Antisense transcripts originate either at gene promoters or within the gene body, and they show different susceptibility to the inhibition of early and immediate early viral gene expression. Overexpression of the major viral transcription factor ICP4 is sufficient to turn on a subset of antisense transcripts. Histone marks around transcription start sites of HSV-1-induced and constitutively transcribed antisense transcripts are highly similar, indicating that the genetic loci are already poised to transcribe these novel RNAs. Furthermore, an antisense transcript overlapping with the BBC3 gene (also known as PUMA) transcriptionally silences this potent inducer of apoptosis in cis. Conclusions We show for the first time that a virus induces widespread antisense transcription of the host cell genome. We provide evidence that HSV-1 uses this to downregulate a strong inducer of apoptosis. Our findings open new perspectives on global and specific alterations of host cell transcription by viruses. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1329-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Jennifer Menegatti
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, 66421, Homburg/Saar, Germany
| | - Vedran Franke
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Christine Kocks
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anastasiya Boltengagen
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Thomas Hennig
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Kathrin Theil
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Andrzej Rutkowski
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge, CB2 0QQ, UK.,Present address: AstraZeneca, Darwin Building, 310 Cambridge Science Park, Cambridge, CB4 0WG, UK
| | - Carmelo Ferrai
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Laura Baer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, 66421, Homburg/Saar, Germany
| | - Lisa Kermas
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Caroline Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333, München, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Friedrich Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, 66421, Homburg/Saar, Germany.
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany. .,IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany.
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36
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Uhlitz F, Sieber A, Wyler E, Fritsche-Guenther R, Meisig J, Landthaler M, Klinger B, Blüthgen N. An immediate-late gene expression module decodes ERK signal duration. Mol Syst Biol 2017; 13:928. [PMID: 28468958 PMCID: PMC5448165 DOI: 10.15252/msb.20177554] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RAF‐MEK‐ERK signalling pathway controls fundamental, often opposing cellular processes such as proliferation and apoptosis. Signal duration has been identified to play a decisive role in these cell fate decisions. However, it remains unclear how the different early and late responding gene expression modules can discriminate short and long signals. We obtained both protein phosphorylation and gene expression time course data from HEK293 cells carrying an inducible construct of the proto‐oncogene RAF. By mathematical modelling, we identified a new gene expression module of immediate–late genes (ILGs) distinct in gene expression dynamics and function. We find that mRNA longevity enables these ILGs to respond late and thus translate ERK signal duration into response amplitude. Despite their late response, their GC‐rich promoter structure suggested and metabolic labelling with 4SU confirmed that transcription of ILGs is induced immediately. A comparative analysis shows that the principle of duration decoding is conserved in PC12 cells and MCF7 cells, two paradigm cell systems for ERK signal duration. Altogether, our findings suggest that ILGs function as a gene expression module to decode ERK signal duration.
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Affiliation(s)
- Florian Uhlitz
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Sieber
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Johannes Meisig
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Bertram Klinger
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany .,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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