Transformation-specific Protein Research Articles

High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma

Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription.

ETS Binding Sites are Critical for Activity of the LHX2‐Associated Sub‐AER Regulatory Module 1 (LASARM1)

Fibroblast growth factors (FGFs) secreted from the apical ectodermal ridge (AER) coordinate proximal-distal patterning, while sonic hedgehog (SHH) from the zone of polarizing activity (ZPA) directs anterior-posterior growth of the limb. These signaling centers maintain each other's expression in a reciprocal feedback loop; however, the molecular intermediates involved are only partially characterized. LIM homeobox 2 (LHX2) has been identified as an intermediate regulator downstream of FGF in the reciprocal loop. We have identified a cis-regulatory module (CRM) located upstream of the LHX2 promoter that is active in the sub-AER LHX2 expression domain. Overexpression of FGF in Hamburger-Hamilton stage 24 (HH24) chicken limb buds, resulted in increased expression of several FGF-associated transcription factors, including E26 transformation-specific proteins (ETS). Members of the ETS family have been known to regulate the expression of SHH via an enhancer known as the Zone of Polarizing Activity Regulatory Sequence (ZRS). We wondered whether the regulation of LHX2 was mediated through this LHX2-associated sub-AER Regulatory Module 1 (LASARM1) via ETS transcription factors. In silico analysis of LASARM1 revealed three ETS binding sites within LASARM1 and hypothesized that mutation of all three binding sites would disrupt FGF-mediated enhancer activity. To determine whether these ETS transcription factor binding sites contribute to LASARM1 activity, we performed site directed mutagenesis on all three ETS binding sites (triple∆ETS) within a LASARM1-ptk-eGFP reporter construct, followed by targeted regional electroporation (TREP) into the limb buds of HH24 chick embryos. Transfection efficiency was determined by co-transfection with a β-actin promoter-driven RFP construct. After 24 hours of incubation, LASARM1 activity was determined by fluorescence microscopy. We found that mutation of all three ETS binding sites within LASARM1 resulted in fluorescence that was undetectable, suggesting reduced LASARM1 activity. Our findings suggest that FGF signaling utilizes ETS transcription factors to regulate LHX2 expression through the LASARM1 enhancer. Further work is needed to confirm this connection. Investigations regarding the relationship between FGF and LHX2 will provide important insights into the mechanisms underlying the FGF-SHH regulatory loop.

FLI1 and ERG protein degradation is regulated via Cathepsin B lysosomal pathway in human dermal microvascular endothelial cells.

ObjectivesFriend leukemia integration 1 and erythroblast transformation‐specific, important regulators of endothelial cell homeostasis, are reduced in microvascular endothelial cells in scleroderma patients, and their deficiency has been implicated in disease pathogenesis. The goal of this study was to identify the mechanisms involved in the protein turnover of friend leukemia integration 1 and erythroblast transformation‐specific in microvascular endothelial cells.MethodsThe effects of lysosome and proteosome inhibitors on friend leukemia integration 1 and erythroblast transformation‐specific levels were assessed by Western blotting and capillary morphogenesis. The effect of scleroderma and control sera on the levels of friend leukemia integration 1 and erythroblast transformation‐specific was examined.ResultsThe reduction in the protein levels of friend leukemia integration 1 and erythroblast transformation‐specific in response to interferon α or Poly:(IC) was reversed by blocking either lysosomal (leupeptin and Cathepsin B inhibitor) or proteosomal degradation (MG132). MG132, leupeptin or CTSB‐(i) also counteracted the anti‐angiogenic effects of Poly:(IC) or interferon α. Scleroderma sera reduced protein levels of friend leukemia integration 1 and erythroblast transformation‐specific in comparison to control sera. Treatment with CTSB(i) increased the levels of friend leukemia integration 1 and erythroblast transformation‐specific in a majority of serum‐treated samples.ConclusionsInhibition of cathepsin B was effective in reversing the reduction of friend leukemia integration 1 and erythroblast transformation‐specific protein levels after treatment with interferon α or scleroderma sera, suggesting that targeting cathepsin B may have a beneficial effect in SSc vascular disease.

Raymond L. Erikson, PhD: In Memoriam (1936–2020)

![][1] > I hoed and trenched and weeded, And took the flowers to fair. > > The Shropshire Lad by A. E. Houseman In 2016, Ray started a personal reflection on his career in science titled “Four Decades of Protein Phosphorylation and Cancer Research.” Nothing more aptly fit his

MRTFA augments megakaryocyte maturation by enhancing the SRF regulatory axis

AbstractSerum response factor (SRF) is a ubiquitously expressed transcription factor that binds DNA at CArG (CC[A/T]6GG) domains in association with myocardin-family proteins (eg, myocardin-related transcription factor A [MRTFA]) or the ternary complex factor family of E26 transformation-specific (ETS) proteins. In primary hematopoietic cells, knockout of either SRF or MRTFA decreases megakaryocyte (Mk) maturation causing thrombocytopenia. The human erythroleukemia (HEL) cell line mimics the effects of MRTFA on Mk maturation, and MRTFA overexpression (MRTFAOE) in HEL cells enhances megakaryopoiesis. To identify the mechanisms underlying these effects, we performed integrated analyses of anti-SRF chromatin immunoprecipitation (ChIP) and RNA-sequencing data from noninduced and phorbol ester (12-O-tetradecanoylphorbol-13-acetate [TPA])–induced HEL cells, with and without MRTFAOE. We found that 11% of genes were upregulated with TPA induction, which was enhanced by MRTFAOE, resulting in an upregulation of 25% of genes. MRTFAOE increased binding of SRF to genomic sites and enhanced TPA-induced expression of SRF target genes. The TPA-induced genes are predicted to be regulated by SRF and ETS factors, whereas those upregulated by TPA plus MRTFAOE lack ETS binding motifs, and MRTFAOE skews SRF binding to genomic regions with CArG sites in regions relatively lacking in ETS binding motifs. Finally, ChIP–polymerase chain reaction using HEL cells and primary human CD34+ cell–derived subpopulations confirms that both SRF and MRTFA have increased binding during megakaryopoiesis at upregulated target genes (eg, CORO1A). We show for the first time that MRTFA increases both the genomic association and activity of SRF and upregulates genes that enhance primary human megakaryopoiesis.

Proteasomal Degradation of the EWS-FLI1 Fusion Protein Is Regulated by a Single Lysine Residue

E-26 transformation-specific (ETS) proteins are transcription factors directing gene expression through their conserved DNA binding domain. They are implicated as truncated forms or interchromosomal rearrangements in a variety of tumors including Ewing sarcoma, a pediatric tumor of the bone. Tumor cells express the chimeric oncoprotein EWS-FLI1 from a specific t(22;11)(q24;12) translocation. EWS-FLI1 harbors a strong transactivation domain from EWSR1 and the DNA-binding ETS domain of FLI1 in the C-terminal part of the protein. Although Ewing cells are crucially dependent on continuous expression of EWS-FLI1, its regulation of turnover has not been characterized in detail. Here, we identify the EWS-FLI1 protein as a substrate of the ubiquitin-proteasome system with a characteristic polyubiquitination pattern. Using a global protein stability approach, we determined the half-life of EWS-FLI1 to lie between 2 and 4 h, whereas full-length EWSR1 and FLI1 were more stable. By mass spectrometry, we identified two ubiquitin acceptor lysine residues of which only mutation of Lys-380 in the ETS domain of the FLI1 part abolished EWS-FLI1 ubiquitination and stabilized the protein posttranslationally. Expression of this highly stable mutant protein in Ewing cells while simultaneously depleting the endogenous wild type protein differentially modulates two subgroups of target genes to be either EWS-FLI1 protein-dependent or turnover-dependent. The majority of target genes are in an unaltered state and cannot be further activated. Our study provides novel insights into EWS-FLI1 turnover, a critical pathway in Ewing sarcoma pathogenesis, and lays new ground to develop novel therapeutic strategies in Ewing sarcoma.

Transcription Factors Oct-1 and GATA-3 Cooperatively Regulate Th2 Cytokine Gene Expression via the RHS5 within the Th2 Locus Control Region.

The T helper type 2 (Th2) locus control region (LCR) regulates Th2 cell differentiation. Several transcription factors bind to the LCR to modulate the expression of Th2 cytokine genes, but the molecular mechanisms behind Th2 cytokine gene regulation are incompletely understood. Here, we used database analysis and an oligonucleotide competition/electrophoretic mobility shift assays to search for transcription factors binding to RHS5, a DNase I hypersensitive site (DHS) within the Th2 LCR. Consequently, we demonstrated that GATA-binding protein-3 (GATA-3), E26 transformation-specific protein 1 (Ets-1), octamer transcription factor-1 (Oct-1), and Oct-2 selectively associate with RHS5. Furthermore, chromatin immunoprecipitation and luciferase reporter assays showed that Oct-1 and Oct-2 bound within the Il4 promoter region and the Th2 LCR, and that Oct-1 and GATA-3 or Oct-2 synergistically triggered the transactivational activity of the Il4 promoter through RHS5. These results suggest that Oct-1 and GATA-3/Oct-2 direct Th2 cytokine gene expression in a cooperative manner.

Long-term effect of curcumin down-regulates expression of tumor necrosis factor-α and interleukin-6 via modulation of E26 transformation-specific protein and nuclear factor-κB transcription factors in livers of lymphoma bearing mice

Tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) are typical multifunctional proinflammatory cytokines involved actively in the regulation of immunity, hematopoiesis, inflammation and carcinogenesis. Coordinated regulation of these cytokines could be required for effective regulation of early phase inflammation and cancer progression. The present work was aimed to analyze the anti-carcinogenic action of curcumin on the expression of TNF-α and IL-6 even after withdrawal of treatment. Up-regulated expressions of TNF-α and IL-6 in terms of mRNA and protein levels in lymphoma bearing mice were significantly down-regulated by curcumin as compared to normal. Electrophoretic mobility shift assay (EMSA) results revealed that curcumin reduced binding of nuclear protein with ETS and NF-κB binding elements of TNF-α and IL-6 promoters, respectively. The anti-carcinogenic effect of curcumin against lymphoma progression has been reported previously. In continuation, the present study suggests that the long-term effect of curcumin may contribute to attenuate cancer progression via the down-regulation of TNF-α and IL-6 modulated by E26 transformation-specific protein (ETS) and nuclear factor-κB (NF-κB), respectively.

Downregulation of Friend Leukemia Virus Integration 1 as a Feedback Mechanism That Restrains Lipopolysaccharide Induction of Matrix Metalloproteases and Interleukin-10 in Human Macrophages

The E26 transformation-specific (Ets) proteins are a family of transcription factors with important roles in a variety of cellular processes ranging from proliferation and differentiation to transformation and metastasis. Tissue-specific expression of Ets proteins and their ability to interact with other families of transcription factors contribute to their versatility. In this study, we investigated the regulation of Ets factors in primary human monocytes and macrophages, and their role in matrix metalloprotease (MMP) and cytokine production. The macrophage-activating Toll-like receptor ligand, lipopolysaccharide (LPS), induced the expression of Ets family members epithelium-specific Ets factor 3 (ESE-3) and TEL-2 but rapidly suppressed Friend leukemia virus integration 1 (FLI-1) expression. Modulation of FLI-1 expression using either RNA interference or forced expression identified a positive role for FLI-1 in contributing to LPS-induced expression of MMP-1, MMP-3, MMP-10, and interleukin-10 (IL-10). Thus, the rapid downregulation of FLI-1 expression after LPS stimulation attenuates the induction of various MMPs and IL-10 under inflammatory conditions. In contrast, the expression of IL-6 and TNFα and the effects of interferon (IFN)γ on LPS responses were not dependent on FLI-1. Our results define a novel FLI-1-mediated self-regulatory feedback loop that limits MMP expression and thus may attenuate extent of tissue destruction associated with inflammatory responses.

An enhancer with cell-type dependent activity is located between the myeloid and epithelial aminopeptidase N (CD 13) promoters.

The 5' flanking region of the gene encoding the small intestinal brush-border peptidase aminopeptidase N (APN) was screened for the presence of enhancer regions. A 300 bp region with enhancer activity was identified 2.7 kb upstream of the transcriptional start site which is used in epithelial cells. The enhancer stimulated transcription from a heterologous promoter (the simian virus 40 early promoter) in a position- and orientation-independent manner. The activity of the enhancer is cell-type dependent and it is active in liver (HepG2), intestinal (Caco-2) and myeloid (K562) cells. As the epithelial APN promoter is active in the first two cell-types and the myeloid APN promoter in the last, the results may suggest that the enhancer, through a cooperation with either of the promoters, is important for the tissue-specific expression of APN. A detailed analysis of the enhancer led to the identification of four functionally important regions that are protected against DNase I digestion by Caco-2 nuclear extract. Sequence analysis suggests that two of the regions may interact with members of the Ets transcription factor family (Ets is a transformation-specific protein first discovered in the E26 avian erythroblastosis virus), one region with a CCAAT enhancer-binding protein and one region with Sp1, a transcriptional activator first described as a factor binding to the simian virus 40 early promoter.

A transformation-specific polypeptide distinct from heat shock proteins is induced by herpes simplex virus type 2 infection.

A tumour-specific polypeptide designated U90 is one of a set of polypeptides which are encoded by the host cell and are specific for the transformed cell state, being immunoprecipitated by the sera of tumour-bearing animals. The interest in these tumour-specific polypeptides centres on the finding that they are also recognized by antisera raised against herpes simplex virus type 2 (HSV-2)-infected cells, implying some role for HSV-2 in tumorigenesis. The peptide map of HSV-2-induced U90 is indistinguishable from that of U90 present in uninfected tumour cells, including mouse cells transformed by human papillomavirus type 16. In tumour cells, U90 is located principally in the plasma membrane fraction and cannot be induced by heat shock, glucose starvation, or treatment with tunicamycin or calcium ionophore. U90 is not related to either the heat shock protein of Mr 90,000 (HSP90) or the glucose-related polypeptide of Mr 94,000 (GRP94) as determined by peptide mapping and the use of monospecific, monoclonal and antipeptide antibodies. This suggests that U90 is a novel transformation-specific protein which can be induced by infection with HSV-2.

Avian sarcoma virus 17 carries the jun oncogene.

Biologically active molecular clones of avian sarcoma virus 17 (ASV 17) contain a replication-defective proviral genome of 3.5 kilobases (kb). The genome retains partial gag and env sequences, which flank a cell-derived putative oncogene of 0.93 kb, termed jun. The jun gene lacks preserved coding domains of tyrosine-specific protein kinases. It also shows no significant nucleic acid homology with other known oncogenes. The probable transformation-specific protein in ASV 17-transformed cells is a 55-kDa gag-jun fusion product.

Leukemogenicity of avian oncovirus S13

Avian oncovirus S13 induces erythroblastic and granulocytic leukemias in line 6 and Spafas chickens. It also causes anemia, sarcomas, and endothelial proliferation. The leukemic cells contain the transformation-specific protein of S13, gp155.

Avian retrovirus S13: Properties of the genome and of the transformation-specific protein

The avian retrovirus S13 codes for an env-linked transformation-specific glycoprotein with a molecular weight of 155,000 (gp155). Treatment of gp155 with endoglycosidase H or growth of S13-infected cells in the presence of tunicamycin reduces the molecular weight of gp155 to about 140K, but these gp155-related molecules may still contain sugar residues. The gp155 protein is not incorporated into virions; it is phosphorylated, but in immunoprecipitates does not show protein kinase activity. The genome of S13 is an 8.5-kilobase (kb) RNA; the helper virus genome is 7.5 kb in size. The putative onc sequences of S13 do not hybridize to DNA probes representing src, erb A, erb B, myc, myb, fps, fms, H- ras, B- lym, abl, rel, and ets.

S13, a rapidly oncogenic replication-defective avian retrovirus

The avian leukemia sarcoma virus S13 transforms chicken and Japanese quail embryo fibroblasts and chicken erythroid cells in tissue culture. S13-induced erythroid transformation requires culture conditions suitable for the growth of normal erythroid precursors (H. Beug and M. J. Hayman (1984), Cell, 36, 963–972). S13-transformed erythroid colonies contain a high percentage of cells that differentiate in absence of erythropoietin. S13 is defective in pol and env functions but can code for a complete set of gag proteins. Nonproducer cell clones transformed by S13 release a noninfectious viral particle containing gag but no functional env or pol proteins. They also synthesize a transformation-specific protein of 155,000 molecular weight. This protein reacts with antibody to viral envelope glycoproteins and appears to represent onc as well as env sequences. The 155,000-molecular weight env-linked protein does not cross react immunologically with an antiserum against the v- erb A and v- erb B gene products.

Cloned DNA of defective avian sarcoma virus mutant LA46 encodes the cis-acting temperature-sensitive defect in replication

Avian defective sarcoma virus mutant LA46 carries a temperature-sensitive defect in replication and transformation. To elucidate this defect, we cloned the integrated provirus of LA46. By DNA-mediated transfection, the cloned DNA induced fusiform-transformed foci in chick embryo fibroblasts without helper virus. LA46-encoded transformation-specific protein p105 was expressed in these transformants in the absence of helper virus-encoded proteins. Superinfection of the transformed cells with different helper viruses resulted in the resue of pseudotypes. All the rescued pseudotypes retained helper viruses resulted in the resue of pseudotypes. All the rescued pseudotypes suggesting that the defect was due to a cis-acting lesion in the LA46 genome. Restriction enzyme comparison between LA46 and wild-type virus revealed sequence differences near the 5′ and 3′ termini of the LA46 genome, including the long terminal repeat regions.

Isolation of three new avian sarcoma viruses: ASV 9, ASV 17, and ASV 25

The newly isolated avian sarcoma viruses, ASV 9, 17, and 25, cause fibrosarcomas in young chickens and induce foci of transformed cells in chick embryo fibroblast cultures. They are defective in replication and belong to envelope subgroup A. The sizes of their genomes are 6 kb (ASV 9), 5 kb (ASV 17), and 6 kb (ASV 25), respectively. All three contain long terminal repeat (LTR) and gag sequences but lack pol. env is absent from ASV 9 and ASV 25, but some env sequences are detectable in ASV 17. None of the defective viral genomes hybridized to selected onc probes representing src, fps, yes, myc, myb, and erb A. erb B appears absent from ASV 9 and ASV 17, but some hybridization between the erb B probe and the RNA of ASV 25 was detected. ASV 9 codes for a transformation-specific gag-linked protein of 130kDa. Multiple gag-linked transformation-specific proteins are seen in ASV 17 and 25; they require further study.

Decreased DNA-binding ability of purified transformation-specific proteins from deletion mutants of the acute avian leukemia virus MC29.

Avian myelocytomatosis virus MC29 is a highly oncogenic replication-defective retrovirus that predominantly affects hematopoietic cells and causes acute leukemia in vivo and that transforms hematopoietic cells as well as fibroblasts in vitro. The transformation-specific sequence, v-myc, is expressed as part of a fusion protein that contains the viral structural protein p19. By use of monoclonal antibodies against p19 we showed that the v-myc-encoded protein is located in the nucleus of MC29-transformed fibroblasts and that after purification over an immunoaffinity column the protein binds to double-stranded DNA. In this report we describe the analysis of the v-myc gene product from MC29-transformed bone marrow cells. The immunoaffinity column-purified protein from these cells also bound to DNA and was indistinguishable from the purified protein from MC29-transformed fibroblasts. In addition, the v-myc gene products from fibroblasts transformed by three nonconditional mutants of MC29--which transform hematopoietic cells with a markedly decreased efficiency in vivo and in vitro but still transform fibroblasts in vitro, expressing deleted v-myc proteins--were analyzed. In contrast to the wild-type protein, the purified mutant proteins had decreased DNA-binding abilities. Furthermore, a preferential binding of the wild-type protein to poly(dG) . poly(dC) duplexes was observed. Such a specificity was lost with a mutant protein. These results provide evidence that the interaction of the v-myc protein with DNA may be directly involved in transformation of the hematopoietic target cells. Further, the transformation-specific fusion proteins purified from cells transformed by avian erythroblastosis virus, which belongs to a different class of acute leukemia viruses, and by Fujinami sarcoma virus were found not to be DNA-binding proteins, suggesting the existence of different transformation mechanisms.

Ts transformation mutants of avian sarcoma virus PRCII: Lack of strict correlation between transforming ability and properties of the P105-associated kinase

Three mutants of avian sarcoma virus PRC-II, LA42, LA46, and LA47, have a temperature-sensitive ( ts) lesion affecting cellular transformation in vitro. At the nonpermissive temperature (41.5°) they do not induce focus formation in fibroblast cultures. LA46 also fails to induce colonies in soft agar at 41.5°, while LA42 and LA47 have retained this ability. The mutations appear to be located in the transformation-specific insert of the defective sarcoma virus genomes, since association with different wild-type ( wt) helper viruses does not lead to changes in the transforming phenotypes. The transformation-specific protein P105 of PRCII is detectable at the nonpermissive temperature in moderately reduced quantity in wt- and LA42-infected cells, while the amounts of P105 precipitable from LA47-infected cultures under these conditions are significantly decreased. LA46 made barely detectable quantities of P105 at 41.5°. This temperature sensitivity of LA46 in the synthesis of P105 may reflect the greatly reduced levels of transformation-specific RNA in LA46-infected cells at 41.5°. Intracellular phosphorylation of P105 was not found to be ts in the mutants or in wt PRCII at both serine and tyrosine acceptor sites. P105 extracted from wt-, ts mutant- or wt-revertant-infected cells at permissive and nonpermissive temperatures did not vary significantly in the specific activity of its associated protein kinase as assayed in vitro by phosphorylation of P105 itself. However, preincubation of P105 in vitro at 41.5° revealed greater instability of protein kinase reactions measured in P105 immunoprecipitates from mutant- as compared to wt-infected cells. Also the elevation of cellular phosphotyrosine, characteristics of PRCII-transformed cells, was greatly reduced in ts mutant-infected cells at the nonpermissive temperature but was restored to wt levels in genetic revertants derived from the ts mutants. These observations suggest that there is no direct correlation between in vivo or in vitro phosphorylation of P105 and the induction of all parameters of oncogenic transformation. The increase of total cellular phosphotyrosine appears to be correlated with focus formation, but not with the ability to induce agar colonies.

Detection and localization of a phosphotyrosine-containing onc gene product in feline tumor cells.

Protein phosphorylation by a tyrosine-specific kinase is now recognized as a common event in retrovirus-transformed cells. We report in this communication that the feline sarcoma virus (FeSV) encoded transformation-specific proteins (gag-fes fusion proteins) and their associated protein kinases are also found in the FeSV in vivo induced tumor preparations, either in the form of fresh tumor homogenate or in the form of cultured cells. With the combined use of subcellular fractionation and detergent extraction we found that the protein kinase activity was present in both the membrane fraction (P100) and the cytosol (S100). The gag-fes proteins of two different strains of FeSV were found to associate with the cell framework to different degrees, suggesting that the specific conformational presentation of these proteins may be dictated by the unique portion of each polyprotein. The same gag-fes transformation related proteins could be immunoprecipitated with antiserum to phosphotyrosine.