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Yang JM, Chi WY, Liang J, Takayanagi S, Iglesias PA, Huang CH. Deciphering cell signaling networks with massively multiplexed biosensor barcoding. Cell 2021; 184:6193-6206.e14. [PMID: 34838160 PMCID: PMC8686192 DOI: 10.1016/j.cell.2021.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.
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Affiliation(s)
- Jr-Ming Yang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
| | - Wei-Yu Chi
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jessica Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Saki Takayanagi
- XDBio Graduate Program, Johns Hopkins School of Medicine, MD 21205, USA
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chuan-Hsiang Huang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
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Palma-Vera SE, Einspanier R. Experimental and bioinformatic analysis of cultured Bovine Endometrial Cells (BEND) responding to interferon tau (IFNT). Reprod Biol Endocrinol 2016; 14:22. [PMID: 27091464 PMCID: PMC4835850 DOI: 10.1186/s12958-016-0156-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/10/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In ruminants, embryo implantation depends on progesterone (P4) and interferon tau (IFNT) controlling endometrial function. IFNT antagonizes bovine endometrial cells (BEND) response to phorbol 12,13-dibutyrate (PDBU) through posttranscriptional regulation of gene expression. We have previously described microRNAs (miRNAs) profiles in bovine endometrium, detecting miR-106a, relevant for embryo maternal communication. In this study, we investigated the expression miR-106a and genes for prostaglandin-endoperoxide synthase 2 (PTGS2), phospholipase A2, group IVA (PLA2G4A), estrogen receptor 1 (ESR1) and progesterone receptor (PR) in response to IFNT in BEND cells and searched for interferon responsive factors (IRFs) binding sites in their promoter genomic regions. The aim of this study was to unravel the molecular mechanisms involved in IFNT signalling and its regulation of miR-106a. FINDINGS PTGS2 showed increased expression under PDBU, which was antagonized by IFNT. IFNT induced expression of PR and miR-106a and downregulation of ESR1 and PR. Bioinformatic analyses detected that PLA2G4A was associated to IRF-1 and IRF-6, while ESR1, PR and PTGS2 were associated to only IRF-6. All genes exhibit one motif per IRF, except miR-106a that had three binding sites for IRF-6. CONCLUSIONS We report the IFNT regulatory effect on miR-106a expression through IRF-6 in bovine endometrial cells. We identified a set of potential binding sites for IRF-1 and IRF-6 within the bovine genome. A set of candidate gene regions could be characterized where IFNT can act via IRFs to regulate the expression of proteins and miRNAs. Future studies will use these data to detect new IFNT regulatory mechanisms in the endometrium.
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Affiliation(s)
- Sergio E. Palma-Vera
- Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
- Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Ralf Einspanier
- Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
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Radi ZA, Marusak RA, Morris DL. Species Comparison of the Role of p38 MAP Kinase in the Female Reproductive System. J Toxicol Pathol 2009; 22:109-24. [PMID: 22271984 PMCID: PMC3246056 DOI: 10.1293/tox.22.109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 04/14/2009] [Indexed: 12/11/2022] Open
Abstract
The p38 mitogen-activated protein kinases (MAPKs) are members of discrete signal
transduction pathways that have significant regulatory roles in a variety of biological
processes, depending on the cell, tissue and organ type. p38 MAPKs are involved in
inflammation, cell growth and differentiation and cell cycle. In the female reproductive
system, p38 MAPKs are known to regulate various aspects of the reproductive process such
as mammalian estrous and menstrual cycles as well as early pregnancy and parturition. p38
MAPKs have also been implicated in alterations and pathologies observed in the female
reproductive system. Therefore, pharmacologic modulation of p38 MAPKs, and inter-connected
signaling pathways (e.g., estrogen receptor signaling, c-fos, c-jun), may influence
reproductive physiology and function. This article provides a critical, comparative review
of available data on the roles of p38 MAPKs in the mammalian female reproductive system
and in reproductive pathophysiology in humans and preclinical species. We first introduce
fundamental differences and similarities of the mammalian female reproductive system that
should be considered by toxicologists and toxicologic pathologists when assessing the
effects of new pharmacologic agents on the female reproductive system. We then explore in
detail the known roles for p38 MAPKs and related molecules in female reproduction. This
foundation is then extended to pathological conditions in which p38 MAPKs are thought to
play an integral role.
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Affiliation(s)
- Zaher A. Radi
- Drug Safety Research & Development, Pfizer Global
R&D, 700 Chesterfield Parkway West, St. Louis, MO 63017, USA
| | | | - Dale L. Morris
- Drug Safety Research & Development, Pfizer Global
R&D, 700 Chesterfield Parkway West, St. Louis, MO 63017, USA
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Godkin JD, Roberts MP, Elgayyar M, Guan W, Tithof PK. Phospholipase A2 regulation of bovine endometrial (BEND) cell prostaglandin production. Reprod Biol Endocrinol 2008; 6:44. [PMID: 18811942 PMCID: PMC2563010 DOI: 10.1186/1477-7827-6-44] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/23/2008] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Prostaglandins (PG), produced by the uterine endometrium, are key regulators of several reproductive events, including estrous cyclicity, implantation, pregnancy maintenance and parturition. Phospholipase A2 (PLA2) catalyzes the release of arachidonic acid from membrane phospholipids, the rate-limiting step in PG biosynthesis. The bovine endometrial (BEND) cell line has served as a model system for investigating regulation of signaling mechanisms involved in uterine PG production but information concerning the specific PLA2 enzymes involved and their role in regulation of this process is limited. The objectives of this investigation were to evaluate the expression and activities of calcium-dependent group IVA (PLA2G4A) and calcium-independent group VI (PLA2G6) enzymes in the regulation of BEND cell PG production. METHODS Cells were grown to near-confluence and treated with phorbol 12, 13 dibutyrate (PDBu), interferon-tau (IFNT), the PLA2G4A inhibitor pyrrolidine-1 (PYR-1), the PLA2G6 inhibitor bromoenol lactone (BEL) and combinations of each. Concentrations of PGF2alpha and PGE2 released into the medium were determined. Western blot analysis was performed on cellular protein to determine effects of treatment on expression of PLA2G4A, PLA2G6 and PLA2G4C. PLA2 assays were performed on intact cells by measuring arachidonic acid and linoleic acid release and group-specific PLA2 activity assays were performed on cell lysates. RESULTS BEND cells produced about 10-fold more PGE2 than PGF2alpha under resting conditions. Production of both PGs increased significantly in response to PDBu-stimulation. PYR-1 significantly diminished production of both PGs by resting cells and abolished the stimulatory effect of PDBu. BEL stimulated production of both PGs. IFNT reduced both PGE2 and PGF2alpha production by resting cells and diminished PDBu stimulation of PG production. Conversely, IFNT did not significantly reduce BEL stimulation of PG production. Cellular expression of PLA2G4A was enhanced by PDBu and this response was diminished by IFNT. Expression of PLA2G6 was not observed to be affected by treatments and no PLA2G4C expression was observed. Arachidonic acid release from intact cells was significantly increased by PDBu and this effect was attenuated by PYR-1 but not by BEL. Release of linoleic acid from intact cells was stimulated by PDBu and inhibited by BEL but not PYR-1. Group specific PLA2-activity assays demonstrated both PLA2G4A and PLA2G6 activity. CONCLUSION Results from this study demonstrate that PGE2 and PGF2-alpha production by BEND cells is mediated by the activity and expression of PLA2G4A. Interferon-tau treatment diminished expression of PLA2G4A and PG production. BEND cells were shown to express PLA2G6 but, unlike primary or early passage luminal bovine endometrial cells, stimulation of PLA2G6 activity was not associated with increased PG production.
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Affiliation(s)
- James D Godkin
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
| | - Mary P Roberts
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
| | - Mona Elgayyar
- The University of Tennessee College of Veterinary Medicine, Department of Pathology, Knoxville, TN, USA
| | - Wei Guan
- The University of Tennessee College of Veterinary Medicine, Department of Pathology, Knoxville, TN, USA
| | - Patricia K Tithof
- The University of Tennessee College of Veterinary Medicine, Department of Pathology, Knoxville, TN, USA
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Wang SZ, Roberts RM. Interaction of stress-activated protein kinase-interacting protein-1 with the interferon receptor subunit IFNAR2 in uterine endometrium. Endocrinology 2004; 145:5820-31. [PMID: 15345682 DOI: 10.1210/en.2004-0991] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During early pregnancy in ruminants, a type I interferon (IFN-tau) signals from the conceptus to the mother to ensure the functional survival of the corpus luteum. IFN-tau operates through binding to the type I IFN receptor (IFNR). Here we have explored the possibility that IFNAR2, one of the two subunits of the receptor, might interact with hitherto unknown signal transduction factors in the uterus that link IFN action to pathways other than the well established Janus kinase-signal transducer and activator of transcription pathways. A yeast two-hybrid screen of an ovine (ov) endometrial cDNA library with the carboxyl-terminal 185 amino acids of ovIFNAR2 as bait identified stress-activated protein kinase-interacting protein 1 (ovSin1) as a protein that bound constitutively through its own carboxyl terminus to the receptor. ovSin1 is a little studied, 522-amino acid-long polypeptide (molecular weight, 59,200) that is highly conserved across vertebrates, but has identifiable orthologs in Drosophila and yeast. It appears to be expressed ubiquitously in mammals, although in low abundance, in a wide range of mammalian tissues in addition to endometrium. Sin1 mRNA occurs in at least two alternatively spliced forms, the smaller of which lacks a 108-bp internal exon. ovSin1, although not exhibiting features of a membrane-spanning protein, such as IFNAR2, is concentrated predominantly in luminal and glandular epithelial cells of the uterine endometrium. When ovSin1 and ovIFNAR2 are coexpressed, the two proteins can be coimmunoprecipitated and colocalized to the plasma membrane and to perinuclear structures. Sin1 provides a possible link among type I IFN action, stress-activated signaling pathways, and control of prostaglandin production.
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Affiliation(s)
- Shu-Zong Wang
- Department of Veterinary Pathology, University of Missouri, Columbia, Missouri 65211, USA
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Guzeloglu A, Binelli M, Badinga L, Hansen TR, Thatcher WW. Inhibition of phorbol ester-induced PGF2alpha secretion by IFN-tau is not through regulation of protein kinase C. Prostaglandins Other Lipid Mediat 2004; 74:87-99. [PMID: 15560118 DOI: 10.1016/j.prostaglandins.2004.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Inhibitory effect of IFN-tau on phorbol ester (PdBu)-induced PGF2alpha secretion was hypothesized to be manifested by the regulation of protein kinase C (PKC) in bovine endometrial (BEND) cells. Following 12 h stimulation with PdBu, cells were unresponsive to freshly added PdBu. Pretreatment of cells with a PKC inhibitor abolished PGF2alpha secretion in response to PdBu. Therefore, PdBu induction of PGF2alpha secretion is through activation of PKC. The alpha, epsilon, iota and lambda isotypes of the PKC family were identified by Western blotting. Cells were then treated with medium alone (control), PdBu or PdBu + IFN-tau for 3 or 6 h. The PdBu-induced secretion of PGF2alpha was suppressed by IFN-tau. At 3 and 6 h, PKCalpha and PKCepsilon were detected both in the cytosolic and membrane fractions of unstimulated cells. There was a clear reduction of PKCalpha in the cytoplasm induced by PdBu and PdBu + IFN-tau at 3 and 6 h. The total abundance (cytoplasm and membrane fractions) of PKCalpha was lower in the PdBu + IFN-tau than PdBu alone. These temporal responses indicate a PKCalpha responsiveness of BEND cells to PdBu and PDBu + INF-tau with some evidence that IFN-tau causes a slight but detectable reduction in PKCalpha when added with PdBu. However, IFN-tau-induced decrease in the total abundance of PKCalpha was not enough to affect negatively the translocation of the PKCalpha to the membrane. Therefore, IFN-tau's ability to suppress secretion of PGF2alpha is unlikely due to an interference with the PdBu-induced activity of PKC.
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Affiliation(s)
- A Guzeloglu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
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Guzeloglu A, Bilby TR, Meikle A, Kamimura S, Kowalski A, Michel F, MacLaren LA, Thatcher WW. Pregnancy and Bovine Somatotropin in Nonlactating Dairy Cows: II. Endometrial Gene Expression Related to Maintenance of Pregnancy. J Dairy Sci 2004; 87:3268-79. [PMID: 15377606 DOI: 10.3168/jds.s0022-0302(04)73463-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The objective was to evaluate the effects of pregnancy and bovine somatotropin (bST) on endometrial gene and protein expression related to maintenance of pregnancy in nonlactating dairy cows at d 17. In endometrial tissues, treatment with bST increased the steady state concentration of oxytocin receptor (OTR) mRNA; bST-treated cyclic (bST-C) cows had greater OTR mRNA than bST-treated pregnant (bST-P) cows. Estradiol receptor alpha (ERalpha) mRNA was reduced in bST-P cows compared with control P and C (no bST) cows. Western blotting revealed that pregnancy decreased the abundance of ERalpha protein, and bST stimulated an increase in ERalpha protein in C and P cows. Treatment with bST increased steady state concentrations of progesterone receptor (PR) mRNA. No differences were detected in steady state mRNA concentrations of prostaglandin H synthase-2 (PGHS-2), prostaglandin E synthase, and prostaglandin F synthase due to pregnancy or bST treatment. However, PGHS-2 protein was increased in response to pregnancy and bST treatment. Immunostaining indicated that P decreased ERalpha protein in luminal epithelium and increased PR protein in epithelial cells of the uterine glands. The PR protein response in the glands was less in bST-P cows than in P cows. In the stromal layer of the endometrium, bST decreased PR protein abundance in C and P cows. The PGHS-2 protein was localized exclusively in the luminal epithelium cells of endometrium and was increased in P cows. In conclusion, distinctly different mRNA and protein responses were detected between C and P cows related to prostaglandin biosynthesis, and bST-induced changes may potentially impact mechanisms associated with maintenance of pregnancy in nonlactating cows.
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Affiliation(s)
- A Guzeloglu
- Department of Animal Sciences, University of Florida, Gainesville 32611-0910, USA
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