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Chen Y, Qin Y, Fu Y, Gao Z, Deng Y. Integrated Analysis of Bulk RNA-Seq and Single-Cell RNA-Seq Unravels the Influences of SARS-CoV-2 Infections to Cancer Patients. Int J Mol Sci 2022; 23:15698. [PMID: 36555339 PMCID: PMC9779348 DOI: 10.3390/ijms232415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious and pathogenic coronavirus that emerged in late 2019 and caused a pandemic of respiratory illness termed as coronavirus disease 2019 (COVID-19). Cancer patients are more susceptible to SARS-CoV-2 infection. The treatment of cancer patients infected with SARS-CoV-2 is more complicated, and the patients are at risk of poor prognosis compared to other populations. Patients infected with SARS-CoV-2 are prone to rapid development of acute respiratory distress syndrome (ARDS) of which pulmonary fibrosis (PF) is considered a sequelae. Both ARDS and PF are factors that contribute to poor prognosis in COVID-19 patients. However, the molecular mechanisms among COVID-19, ARDS and PF in COVID-19 patients with cancer are not well-understood. In this study, the common differentially expressed genes (DEGs) between COVID-19 patients with and without cancer were identified. Based on the common DEGs, a series of analyses were performed, including Gene Ontology (GO) and pathway analysis, protein-protein interaction (PPI) network construction and hub gene extraction, transcription factor (TF)-DEG regulatory network construction, TF-DEG-miRNA coregulatory network construction and drug molecule identification. The candidate drug molecules (e.g., Tamibarotene CTD 00002527) obtained by this study might be helpful for effective therapeutic targets in COVID-19 patients with cancer. In addition, the common DEGs among ARDS, PF and COVID-19 patients with and without cancer are TNFSF10 and IFITM2. These two genes may serve as potential therapeutic targets in the treatment of COVID-19 patients with cancer. Changes in the expression levels of TNFSF10 and IFITM2 in CD14+/CD16+ monocytes may affect the immune response of COVID-19 patients. Specifically, changes in the expression level of TNFSF10 in monocytes can be considered as an immune signature in COVID-19 patients with hematologic cancer. Targeting N6-methyladenosine (m6A) pathways (e.g., METTL3/SERPINA1 axis) to restrict SARS-CoV-2 reproduction has therapeutic potential for COVID-19 patients.
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Affiliation(s)
- Yu Chen
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Yujia Qin
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Yuanyuan Fu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Zitong Gao
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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Kedei N, Telek A, Michalowski AM, Kraft MB, Li W, Poudel YB, Rudra A, Petersen ME, Keck GE, Blumberg PM. Comparison of transcriptional response to phorbol ester, bryostatin 1, and bryostatin analogs in LNCaP and U937 cancer cell lines provides insight into their differential mechanism of action. Biochem Pharmacol 2013; 85:313-24. [PMID: 23146662 PMCID: PMC3553297 DOI: 10.1016/j.bcp.2012.10.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 10/03/2012] [Accepted: 10/05/2012] [Indexed: 11/23/2022]
Abstract
Bryostatin 1, like the phorbol esters, binds to and activates protein kinase C (PKC) but paradoxically antagonizes many but not all phorbol ester responses. Previously, we have compared patterns of biological response to bryostatin 1, phorbol ester, and the bryostatin 1 derivative Merle 23 in two human cancer cell lines, LNCaP and U937. Bryostatin 1 fails to induce a typical phorbol ester biological response in either cell line, whereas Merle 23 resembles phorbol ester in the U937 cells and bryostatin 1 in the LNCaP cells. Here, we have compared the pattern of their transcriptional response in both cell lines. We examined by qPCR the transcriptional response as a function of dose and time for a series of genes regulated by PKCs. In both cell lines bryostatin 1 differed primarily from phorbol ester in having a shorter duration of transcriptional modulation. This was not due to bryostatin 1 instability, since bryostatin 1 suppressed the phorbol ester response. In both cell lines Merle 23 induced a pattern of transcription largely like that of phorbol ester although with a modest reduction at later times in the LNCaP cells, suggesting that the difference in biological response of the two cell lines to Merle 23 lies downstream of this transcriptional regulation. For a series of bryostatins and analogs which ranged from bryostatin 1-like to phorbol ester-like in activity on the U937 cells, the duration of transcriptional response correlated with the pattern of biological activity, suggesting that this may provide a robust platform for structure activity analysis.
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Affiliation(s)
- N Kedei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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Kedei N, Lubart E, Lewin NE, Telek A, Lim L, Mannan P, Garfield SH, Kraft MB, Keck GE, Kolusheva S, Jelinek R, Blumberg PM. Some phorbol esters might partially resemble bryostatin 1 in their actions on LNCaP prostate cancer cells and U937 leukemia cells. Chembiochem 2011; 12:1242-51. [PMID: 21542090 PMCID: PMC3313843 DOI: 10.1002/cbic.201100064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Indexed: 11/11/2022]
Abstract
Phorbol 12-myristate 13-acetate (PMA) and bryostatin 1 are both potent protein kinase C (PKC) activators. In LNCaP human prostate cancer cells, PMA induces tumor necrosis factor alpha (TNFα) secretion and inhibits proliferation; bryostatin 1 does not, and indeed blocks the response to PMA. This difference has been attributed to bryostatin 1 not localizing PKCδ to the plasma membrane. Since phorbol ester lipophilicity influences PKCδ localization, we have examined in LNCaP cells a series of phorbol esters and related derivatives spanning some eight logs in lipophilicity (logP) to see if any behave like bryostatin 1. The compounds showed marked differences in their effects on proliferation and TNFα secretion. For example, maximal responses for TNFα secretion relative to PMA ranged from 97 % for octyl-indolactam V to 24 % for phorbol 12,13-dibenzoate. Dose-response curves ranged from monophasic for indolactam V to markedly biphasic for sapintoxin D. The divergent patterns of response, however, correlated neither to lipophilicity, to plasma membrane translocation of PKCδ, nor to the ability to interact with model membranes. In U937 human leukemia cells, a second system in which PMA and bryostatin 1 have divergent effects, viz. PMA but not bryostatin 1 inhibits proliferation and induces attachment, all the compounds acted like PMA for proliferation, but several induced a reduced level or a biphasic dose-response curve for attachment. We conclude that active phorbol esters are not all equivalent. Depending on the system, some might partially resemble bryostatin 1 in their behavior; this encourages the concept that bryostatin-like behavior may be obtained from other structural templates.
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Affiliation(s)
- Noemi Kedei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Emanuel Lubart
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Nancy E. Lewin
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Andrea Telek
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Langston Lim
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Poonam Mannan
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Susan H. Garfield
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
| | - Matthew B. Kraft
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, U.S.A
| | - Gary E. Keck
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, U.S.A
| | - Sofiya Kolusheva
- Department of Chemistry, Ben Gurion University, Beer Sheva 84105, Israel
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University, Beer Sheva 84105, Israel
| | - Peter M. Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, U.S.A
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Vrana JA, Kramer LB, Saunders AM, Zhang XF, Dent P, Povirk LF, Grant S. Inhibition of protein kinase C activator-mediated induction of p21CIP1 and p27KIP1 by deoxycytidine analogs in human leukemia cells: relationship to apoptosis and differentiation. Biochem Pharmacol 1999; 58:121-31. [PMID: 10403525 DOI: 10.1016/s0006-2952(99)00077-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Events accompanying sequential exposure of U937 leukemic cells to the deoxycytidine (dCyd) analogs 1-[beta-D-arabinofuranosyl]cytosine (ara-C) or 2',2'-difluorodeoxycytidine (gemcitabine; dFdC) followed by two protein kinase C (PKC) activators [bryostatin 1 (BRY) or phorbol 12'-myristate 13'-acetate (PMA)] exhibiting disparate differentiation-inducing abilities were characterized. A 24-hr exposure to 10 nM BRY or PMA after a 6-hr incubation with 1 microM ara-C or 100 nM dFdC resulted in equivalent increases in apoptosis, caspase-3 activation, and polyADP-ribose polymerase degradation, as well as identical DNA cleavage patterns. BRY and PMA did not modify retention of the lethal ara-C metabolite ara-CTP or alter ara-CTP/dCTP ratios. Unexpectedly, pretreatment of cells with ara-C or dFdC opposed BRY- and PMA-related induction of the cyclin-dependent kinase inhibitors (CDKIs) p21CIP1 and/or p27KIP1. These effects were not mimicked by the DNA polymerase inhibitor aphidicolin or by VP-16, a potent inducer of apoptosis. Inhibition of PKC activator-induced CDKI expression by ara-C and dFdC did not lead to redistribution of proliferating cell nuclear antigen but was accompanied by sub-additive or antagonistic effects on leukemic cell differentiation. Sequential exposure of cells to ara-C followed by BRY or PMA led to substantial reductions in clonogenicity that could not be attributed solely to apoptosis. Finally, pretreatment of cells with ara-C attenuated PMA- and BRY-mediated activation of mitogen-activated protein kinase, an enzyme implicated in CDKI induction. Collectively, these findings suggest that pretreatment of leukemic cells with certain dCyd analogs interferes with CDKI induction by the PKC activators PMA and BRY, and that this action may contribute to modulation of apoptosis and differentiation in cells exposed sequentially to these agents.
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Affiliation(s)
- J A Vrana
- Department of Medicine, Medical College of Virginia, Richmond 23298-0230, USA
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Wang Z, Su ZZ, Fisher PB, Wang S, VanTuyle G, Grant S. Evidence of a functional role for the cyclin-dependent kinase inhibitor p21(WAF1/CIP1/MDA6) in the reciprocal regulation of PKC activator-induced apoptosis and differentation in human myelomonocytic leukemia cells. Exp Cell Res 1998; 244:105-16. [PMID: 9770354 DOI: 10.1006/excr.1998.4191] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The functional role of the cyclin-dependent kinase inhibitor p21(WAF1/CIP1) in leukemic cell G1 arrest, differentiation, and apoptosis induced by two PKC activators (PMA and bryostatin 1) was examined using antisense-expressing lines [U937/p21AS(F4) and U937/p21AS(B8)]. Following incubation with 10 nM PMA (24 h), antisense-expressing cells displayed induction of p27(KIP1) but not of p21, whereas empty vector-containing cells (U937/pREP4) exhibited induction of both p21 and p27. Antisense-expressing cells were impaired in G1 arrest, dephosphorylation of the retinoblastoma protein, dephosphorylation and reduction in activity of cyclin-dependent kinase 2, and acquisition of differentiated features (e.g., plastic adherence). Bryostatin 1 induced p27 but not p21 in control cells and was less effective than PMA in initiating G1 arrest and related events. Nevertheless, disruption of p21 expression abrogated the effects of bryostatin 1 on cell cycle arrest and cellular maturation. Dysregulation of p21 did not, however, modify PMA- or bryostatin 1-mediated down-regulation of c-Myc protein. Unexpectedly, disruption of p21 failed to attenuate the net reduction in viable cell number following PMA or bryostatin 1 treatment inasmuch as impaired differentiation was accompanied by a lowered threshold for PMA- and bryostatin 1-induced apoptosis. Inhibition of p21 expression also promoted PMA- and bryostatin 1-mediated loss of mitochondrial transmembrane potential (DeltaPsim ) and release of cytochrome c into the cytosol. Together, these findings demonstrate a critical functional role for p21 in regulating myelomonocytic leukemic cell G1 arrest and differentiation following exposure to two PKC activators exhibiting disparate patterns of activity. They also suggest that following treatment with these agents, dysregulation of p21 prevents leukemic cells from engaging a normal differentiation program through a c-Myc-independent mechanism, and instead directs cells along an apoptotic pathway.
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Affiliation(s)
- Z Wang
- Medical College of Virginia, Virginia Commonwealth University, Richmond, Virginia, 23298, USA
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Vrana JA, Saunders AM, Chellappan SP, Grant S. Divergent effects of bryostatin 1 and phorbol myristate acetate on cell cycle arrest and maturation in human myelomonocytic leukemia cells (U937). Differentiation 1998; 63:33-42. [PMID: 9615391 DOI: 10.1046/j.1432-0436.1998.6310033.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bryostatin 1 and the phorbol ester, phorbol myristate acetate (PMA), both bind to and activate protein kinase C (PKC) but exhibit divergent biological actions. Bryostatin 1 exerts variable effects on leukemic cell differentiation, and has been reported by some investigators to inhibit the proliferation of the monocytic leukemic cell line U937. In this study, we have compared the efficacy of bryostatin 1 and PMA with respect to U937 cell maturation, with a major emphasis on differential actions on the cell cycle arrest machinery. At equimolar concentrations (10 nM), PMA, in contrast to bryostatin 1, induced cellular differentiation of U937 cells, reflected by growth inhibition, increased plastic adhesion, and expression of the monocytic differentiation marker, CD11b. Consistent with these results, bryostatin 1 was less effective in inducing G0/G1 arrest and inhibiting cyclin-dependent kinase 2 (CDK2) activity. Bryostatin 1, unlike PMA, failed to induce expression of the cyclin-dependent kinase inhibitor (CDKI), p21CIP1/WAF1, and blocked the ability of PMA to induce this protein. Bryostatin 1 exposure resulted in increased expression of the CDKI p27KIP1 in these cells, although the kinetics differed from PMA. In addition, bryostatin 1 was less effective than PMA in dephosphorylating pRb, modifying E2F complexes, and downregulating c-Myc. Co-administration of bryostatin 1 with PMA antagonized the latter's differentiation-inducing capacity and anti-proliferative effects, actions that were accompanied by a reduction in PMA-mediated p21CIP1/WAF1 induction, CDK2 inhibition, pRb dephosphorylation, and c-Myc downregulation. Antagonistic effects of bryostatin 1 on PMA-related cell cycle events were mimicked by the specific PKC inhibitor GF109203X. Together, these studies indicate that bryostatin 1 is a considerably weaker stimulus than PMA for U937 cell differentiation, and raise the possibility that this deficiency arises from its failure to induce p21CIP1/WAF1 and trigger cell cycle arrest.
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Affiliation(s)
- J A Vrana
- Department of Medicine, Medical College of Virgina, Richmond, USA
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Galron D, Tamir A, Gelkop S, Grossman N, Isakov N. The effect of bryostatin on protein kinase C-regulated functions in human T lymphocytes and epidermal keratinocytes. Immunol Lett 1993; 39:17-22. [PMID: 8144186 DOI: 10.1016/0165-2478(93)90159-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The bryostatin (Bryo) is a macrocyclic lactone that binds specifically to protein kinase C (PKC) thereby affecting cell growth and differentiation and inhibits phorbol ester-induced tumor promotion. We used human peripheral blood lymphocytes (PBL) and epidermal cells in order to analyze the action mechanism of Bryo and compare it with that of the phorbol ester PMA. Bryo and PMA activated PBL- or T cell-derived PKC in a similar dose-response and induced a similar time kinetic of cytosol-to-membrane translocation of enzymatically active and immunoreactive PKC. In addition, the 2 drugs induced similar patterns of protein phosphorylation and activated the c-fos and c-jun genes that their protein products regulate transcription of TRE-containing genes. In contrast, long-term (20 h) treatment of cells with Bryo resulted in a marked loss of both cytosolic- and membrane-bound PKC while PMA induced only a slight reduction in the amount of cellular PKC. Inhibition of PMA-induced human T-cell proliferation by Bryo correlated with a reduction in the amount of cellular PKC. An opposite effect was observed in human epidermal cells where Bryo augmented growth and proliferation while PMA induced terminal differentiation and cell death. We propose that at least some of the differences in the biological effects induced by Bryo and PMA are due to distinct regulations of PKC. Thus, although both agents can initially bind to and activate PKC at a later time (approximately 16 h), Bryo, but not PMA, induces rapid PKC degradation and inhibition of PKC-regulated biological responses that are dependent on the continuous presence and/or activation of the enzyme.
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Affiliation(s)
- D Galron
- Department of Microbiology and Immunology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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