Abstract 73: Blockade of p38 MAPK reduces the tumor-induced immune suppressive microenvironment in metastatic breast cancer

The ability of CD8+ T cells to mount an anti-tumor immune response is compromised by immune suppression in the tumor microenvironment (TME). Tumor Associated Macrophages (TAMs) and Myeloid Derived Suppressor Cells (MDSCs) are a major part of this immune suppressive network. Targeting these populations remains challenging. Previously, we have reported that pharmacological and genetic blockade of p38 MAPK impeded the expansion and mobilization of monocytic and granulocytic MDSCs in mouse mammary carcinoma models. We also found that blockade of p38 or depletion of MDSCs reduced tumor growth and metastasis while enhancing the levels of CD8+ T cells in the primary tumors. In the present study, we asked whether CD8+ T cells contribute to the anti-metastatic activity of p38 inhibitor (p38i) and how p38 blockade affects the functional status of T cells and MDSCs. By using the mouse mammary carcinoma 4T1 model, we found that depletion of CD8+ T cells negated the effects of p38i on tumor growth and metastasis, indicating that CD8+ T cells contribute to the anti-tumor and anti-metastatic effects of p38 blockade. Next, we examined whether p38i exhibits a direct effect on T cells. The results of the T cell proliferation in vitro assays revealed that p38 blockade did not have a direct impact on T cell proliferation in response to αCD3/αCD28 stimulation. To determine the effect of p38 blockade on T cells in vivo, we performed single cell RNA-seq on the 4T1 tumor models treated with p38i and the 4T1 model with p38α (Mapk14) knockout (p38ko). This study revealed that p38 blockade by p38i or by inactivation of p38 in tumor cells decreased the amount of exhausted T cells and increased Th1 cells in the TME, indicating a positive effect on T cell functions. Furthermore, we observed a significant decrease in inflammatory signaling in granulocytes and monocytes upon p38 blockade. Our previous study showed that p38i did not affect generation of MDSCs in vitro in response to G-CSF & GM-CSF. To determine whether p38i alters MDSCs in vivo, we assessed MDSC gene signature in monocytic and granulocytic MDSCs isolated from spleens of tumor-bearing mice subjected to p38 blockade. This work revealed that the MDSC gene signature was reduced in both p38i and p38ko groups compared to tumor bearing mice treated with vehicle-control. These results indicated a reduction in the MDSC generation in the in vivo model. Our study revealed that blockade of p38 reduces tumor induced immune suppression and may enhance anti-tumor immune response in metastatic breast cancer.

Citation Format: Priyanka Rajan, Justin Zonneville, Robert Zollo, Mackenzie Honikel, Sofija Raudins, Sean Colligan, Brian Morreale, Mohammed Alruwaili, Mohammed Alqarni, Scott Olejniczak, Joseph Barbi, Scott Abrams, Andrei Bakin. Blockade of p38 MAPK reduces the tumor-induced immune suppressive microenvironment in metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 73.

Abstract 3397: Evaluation of a novel two-drug combination strategy for p53-deficient colorectal and pancreatic cancers

Colorectal Cancer (CRC) and Pancreatic Ductal Adenocarcinoma (PDAC) are the most lethal cancers worldwide. Despite initial response to standard-of-care therapy, a significant proportion of CRC/PDAC cancers relapse and progress to metastatic disease with poor overall survival (OS). Thus, better treatment options are urgently needed. Genetic alterations in the tumor suppressor p53 gene (TP53) are found in most CRC and PDAC cases and contribute to cancer relapse, progression, and metastasis. Even though the functional consequences of p53 mutations have been extensively studied, there are no FDA approved drug or their combination targeting p53 mutant (p53mut) cancers. Here we present a novel inducer-amplifier strategy for selective targeting p53-deficient CRC and PDAC. The Cancer Genome Atlas (TCGA) data showed elevated tumor mutational burden (TMB) and high expression levels of Base-Excision Repair (BER) in p53mut CRC and PADC. Assessment of the BER activity in CRC and PADC cells by a new methodology with deoxyuridine analogues ethynyl-deoxyuridine (EdU) and trifluorothymidine (TFT) revealed a significant delay in removal of genomic EdU and TFT in p53-deficient cells compared to isogenic p53 wildtype (p53wt) cells. Notably, p53-deficient cells accumulated in late S/G2 phase. Further, deoxyuridine analogues such as TFT-containing TAS102 induced buildup of DNA damage in p53-deficient cancer cells. Mechanistically, TAS102 did not block DNA replication but rather provoked activation of DNA Damage Response (DDR) resulting in DNA breaks in p53-deficient cells, while p53wt repaired the DNA lesion. This response was further enhanced by poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) leading to elevated cell death selectively in p53-deficient cancer cells, along with accumulation of cells in G2 phase. PARPi alone did not induce DNA damage in cancer cells. In preclinical in vivo models, the TAS102-PARPi combination was far more effective than either drug alone in the p53mut Cell-Derived Xenograft (CDX) and Patient-Derived xenograft (PDX) models. Immunohistochemistry data showed that the two-drug combination increased DNA damage and cell death while decreasing cell proliferation in p53-mutant models. In comparison, the two-drug combination and TAS102 exhibited comparable effectiveness in p53wt PDX model. Notably, the two-drug therapy did not exhibit significant toxicity in mouse models. In summary, this work demonstrates that our novel inducer-amplifier strategy provides effective treatment option for aggressive p53-deficient CRC and PDAC cancers while limiting adverse toxic events and improving the quality of life for cancer patients.

Citation Format: Mohammed M. Alruwaili, Justin Zonneville, Mohammed A. Alqarni, Priyanka Rajan, Hannah Serio, Robert Straubinger, Christos Fountzilas, Andrei Bakin. Evaluation of a novel two-drug combination strategy for p53-deficient colorectal and pancreatic cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3397.

Abstract B039: Development of a selective therapeutic intervention for p53 mutant for pancreatic adenocarcinoma

Genetic alterations in the tumor suppressor p53 gene (TP53) are found in over 70% of Pancreatic Adenocarcinoma (PAAD) and contribute to poor prognosis, cancer progression and metastasis. Existing treatment options for p53 mutant (p53mut) cancer are limited and there is an urgent need for better therapeutic interventions that can be greatly beneficial to a large proportion of patients with PAAD. Here we present a novel therapeutic strategy for selective targeting p53mut pancreatic tumors. Genomic data revealed that p53-deficient PAADs express high levels of DNA replication genes as well as genes involved in Base Excision (BER) and Mismatch (MMR) Repair, indicating activation of these mechanisms. Evaluation of BER activity by a novel methodology with a modified deoxyuridine analogue showed a significant dysregulation in BER mediated repair in p53mut cancer cells leading to accumulation of p53mut tumor cells in late S/G2 phase. By exploiting this defect, we found that treatment with a deoxyuridine analogue such as trifluorothymidine (TFT, a component of TAS102) resulted in accumulation of DNA breaks selectively in p53mut cells. A deoxyuridine analogue (TFT) did not block DNA replication but rather activated DNA repair leading to DNA breaks in p53mut cells whereas p53 wild type cells accumulated in G1 with minimal DNA damage. Further, we found that inhibition of poly (ADP) ribose polymerase (PARP) enhanced DNA damage and increased cell death selectively in p53mut tumor cells although PARP inhibitor alone was not effective. In contrast, the TAS102-PARPi did not induce DNA damage in the normal cells such as hTERT-immortalized Human Pancreatic Nestin Expressing cells (HPNE). A new TAS102-PARPi combination regimen demonstrated greater inhibition of tumor growth and improved the survival rates in p53mut PAAD xenograft models including Cell-Derived Xenograft (CDX) and Patient-Derived xenograft (PDX) models, compared to either drug alone without adverse effects in mice. Thus, this preclinical work identified a novel and immediately feasible strategy for p53mut disease that may improve treatment and the quality of life for a significant proportion of patients with PAAD while limiting toxic effects on normal tissues.

Citation Format: Mohammed M. Alruwaili, Justin Zonneville, Mohammed A. Alqarni, Priyanka Rajan, Hannah Serio, Robert Straubinger, Christos Fountzilas, Andrei Bakin. Development of a selective therapeutic intervention for p53 mutant for pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B039.

Abstract P5-17-06: P38 kinase as a therapeutic target to reverse an immune suppressive tumor microenvironment in metastatic breast cancer

The immune suppressive tumor microenvironment (TME) in metastatic breast cancer (MBC) limits the benefits of immunotherapy with immune checkpoint inhibitors (ICIs). In particular, the primary TME drives the expansion and recruitment of immune suppressive myeloid cell populations, such as tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs). Treatments targeting these populations can potentially improve the efficacy of ICI therapy. To that end, our published and new findings have revealed that the p38 Mitogen-Activated Protein Kinase (MAPK) contributes to the expansion and mobilization of TAMs and MDSCs. Further, we found that pharmacological blockade of p38 decreased metastasis and increased the levels of CD8+ T cells while decreasing TAMs in the primary TME. Depletion of PMN-MDSCs, a major MDSC subset, was accompanied by reduced TAM infiltration and phenocopied the anti-metastatic effects of p38 blockade. Next, we explored the impact of p38 blockade on the composition and functionality of the immune populations in the primary TME by using single-cell RNA-sequencing. We found that p38 blockade increased levels of Irf8+ monocytic populations, indicating a decrease in immune-suppressive properties of the TME. Notably, p38 blockade increased the expression of factors related to the activation of CD8+ cytotoxic T lymphocytes, i.e., Jchain, Icos, and Cd137. Thus, our data indicate that p38 blockade alters the immune landscape within the primary TME and favors an antitumor immune response. Our data also suggest that the p38 kinase controls the production of tumor-derived factors (TDFs) which facilitate the recruitment of those pro-tumor myeloid populations. Thus, we explored this p38-TDF-myeloid axis by using trans-well migration assays. We tested the migration of the monocyte-like cell line RAW 264.7 in response to tumor-conditioned media prepared from tumor cells treated with or without the p38 inhibitor, Ralimetinib. Our data showed that the migration of RAW 264.7 cells was significantly diminished towards the conditioned media from tumor cells treated with the p38 inhibitor or from tumor cells with a genetic inactivation of p38α by CRISPR/Cas9 compared to the corresponding controls. Altogether, our studies demonstrate that p38 kinase is a potential therapeutic target, which reshapes the immune suppressive contexture of TME in MBC to improve antitumor immunity.

Citation Format: Priyanka Rajan, Justin Zonneville, Sean Colligan, Scott Abrams, Andrei Bakin. P38 kinase as a therapeutic target to reverse an immune suppressive tumor microenvironment in metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-17-06.

Abstract PS19-21: Tak1 signaling regulates p53 through a mechanism involving ribosomal stress

Triple-negative breast cancer (TNBC) is among the most aggressive forms of breast cancer with limited therapeutic options. TAK1 is implicated in aggressive behavior of TNBC, while means are not fully understood. Here, we report that pharmacological blockade of TAK1 signaling hampered ribosome biogenesis (RBG) by reducing expression of RBG regulators such as RRS1, while not changing expression of ribosomal core proteins. Importantly, TAK1 blockade upregulated expression of p53 target genes in cell lines carrying wild type (wt) TP53 but not in p53-mutant cells. By examining involvement of the ribosomal stress response, we found that p53 activation by blockade of TAK1 was prevented by depletion of ribosomal protein RPL11. Further, siRNA-mediated depletion of TAK1 or RELA resulted in activation of p53 signaling and this response was dependent on RPL11. Knockdown of RRS1 disrupted nucleolar organization and resulted in activation of p53. Genomic TCGA data showed that TNBCs express high levels of ribosome biogenesis regulators, and elevated RRS1 levels correlate with unfavorable prognosis. Cytotoxicity data showed that TNBC cell lines are more sensitive to TAK1 inhibitor compared to luminal and HER2+ cell lines. Together, the data indicate that TAK1 regulates p53 activation by controlling ribosome biogenesis factors, and the TAK1-ribosome axis is a potential therapeutic target in TNBC.

Citation Format: Andrei Bakin, Justin Zonneville. Tak1 signaling regulates p53 through a mechanism involving ribosomal stress [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-21.

Modelling plexcitons of periodic gold nanorod arrays with molecular components

Plasmonic or exciton/plasmon (plexcitonic) systems are presently described based on electromagnetic models, ignoring the need for an improved microscopic understanding. This is based on the fact that a full quantum mechanical approach on a micrometer scale still represents a considerable challenge. In this paper we report on the experimental observation of plexcitons in 2D gold nanorod array systems coupled to dye molecules and we provide a description of the experimental data using a quantum model. We show that treating the collective behavior in the array as being represented by a single quasiparticle is a suitable approximation that offers the opportunity to avoid the complicated calculation of long-distance interactions between the individual nanoparticles of the plexcitonic, periodic system. This enables us to model the optical response of plasmons in nanostructured arrays in contact with quantum emitters and to derive microscopic informations. Our work provides a potential tool for the design of plexcitonic devices, which rely on periodic metallic nanostructures.

Androgen-responsive serum response factor target genes regulate prostate cancer cell migration

Progression of prostate cancer (CaP) relies on androgen receptor (AR) signaling, but AR-dependent events that underlie the lethal phenotype remain unknown. Recently, an indirect mechanism of androgen action in which effects of AR on CaP cells are mediated by Serum Response Factor (SRF) has been identified. This is the first mode of androgen action to be associated with aggressive CaP and disease recurrence. The manner in which androgen-responsive SRF activity controls aggressive CaP cell behavior is unknown. Here, the contribution of two representative SRF effector genes that are underexpressed, calponin 2 (CNN2), or overexpressed, sidekick-homolog 1 (SDK1), in clinical CaP specimens is studied. AR- and SRF- dependency of CNN2 and SDK1 expression was verified using synthetic and natural androgens, antiandrogens, and small interfering RNAs targeting AR or SRF, and evaluating the kinetics of androgen induction and SRF binding to endogenously and exogenously expressed regulatory gene regions in AR-positive CaP model systems that mimic the transition from androgen-stimulated to castration-recurrent disease. Small interfering RNA-mediated deregulation of CNN2 or SDK1 expression did not affect CaP cell proliferation or apoptosis but had marked effects on CaP cell morphology and actin cytoskeleton organization. Loss of CNN2 induced cellular protrusions and increased CaP cell migration, whereas silencing of SDK1 led to cell rounding and blunted CaP cell migration. Changes in cell migration did not involve epithelial-mesenchymal transition but correlated with altered β1-integrin expression. Taken together, individual androgen-responsive SRF target genes affect CaP cell behavior by modulating cell migration, which may have implications for therapeutic intervention downstream of AR and SRF.

Magneto-Stark effect of excitons as the origin of second harmonic generation in ZnO

The magneto-Stark effect of excitons is demonstrated to be an efficient source of optical nonlinearity in hexagonal ZnO. Strong resonant second harmonic generation signals induced by an external magnetic field are observed in the spectral range of 2s and 2p excitons. The microscopic theoretical analysis shows that for excitons with a finite wave vector, exciton states of opposite parity are mixed by an effective odd parity electric field induced by the magnetic field despite its even parity. The field, spectral, and polarization dependencies of the second harmonic generation intensity validate the proposed mechanism. The observed phenomenon is not limited to a certain symmetry class and therefore must be effective in other semiconductors.

Cellular model of Warburg effect identifies tumor promoting function of UCP2 in breast cancer and its suppression by genipin

The Warburg Effect is characterized by an irreversible injury to mitochondrial oxidative phosphorylation (OXPHOS) and an increased rate of aerobic glycolysis. In this study, we utilized a breast epithelial cell line lacking mitochondrial DNA (rho⁰) that exhibits the Warburg Effect associated with breast cancer. We developed a MitoExpress array for rapid analysis of all known nuclear genes encoding the mitochondrial proteome. The gene-expression pattern was compared among a normal breast epithelial cell line, its rho⁰ derivative, breast cancer cell lines and primary breast tumors. Among several genes, our study revealed that over-expression of mitochondrial uncoupling protein UCP2 in rho⁰ breast epithelial cells reflects gene expression changes in breast cancer cell lines and in primary breast tumors. Furthermore, over-expression of UCP2 was also found in leukemia, ovarian, bladder, esophagus, testicular, colorectal, kidney, pancreatic, lung and prostate tumors. Ectopic expression of UCP2 in MCF7 breast cancer cells led to a decreased mitochondrial membrane potential and increased tumorigenic properties as measured by cell migration, in vitro invasion and anchorage independent growth. Consistent with in vitro studies, we demonstrate that UCP2 over-expression leads to development of tumors in vivo in an orthotopic model of breast cancer. Genipin, a plant derived small molecule, suppressed the UCP2 led tumorigenic properties, which were mediated by decreased reactive oxygen species and down-regulation of UCP2. However, UCP1, 3, 4 and 5 gene expression was unaffected. UCP2 transcription was controlled by SMAD4. Together, these studies suggest a tumor-promoting function of UCP2 in breast cancer. In summary, our studies demonstrate that i) the Warburg Effect is mediated by UCP2; ii) UCP2 is over-expressed in breast and many other cancers; iii) UCP2 promotes tumorigenic properties in vitro and in vivo and iv) genipin suppresses the tumor promoting function of UCP2.

Role of β5-integrin in epithelial-mesenchymal transition in response to TGF-β

Epithelial-mesenchymal-transition (EMT) in response to TGFβ contributes to normal development, wound healing and tumor progression. The present study provides evidence for a critical role of β5-integrin in the TGFβ-induced EMT and the tumorigenic potential of carcinoma cells. We show that the αvβ-integrin subunits are upregulated during the TGFβ-induced EMT and this response requires Smad transcription factors. Depletion of αv-integrin by siRNA blocked the EMT response whereas knock-down of β1-integrin had no effect. Importantly, depletion of β5-integrin blocked the TGFβ-induced EMT impairing adhesion to cell-matrix and integrin signaling, but did not change expression of E-cadherin and TGFβ-target genes. Accordingly, the EMT process and integrin signaling were blocked by cRGD peptide interfering with cell-matrix adhesion or by inhibition of focal adhesion kinase, indicating the importance of β5-integrin-mediated adhesions in EMT. Finally, depletion of β5-integrin significantly reduced invasiveness of breast carcinoma cells. Thus, the β5-integrin adhesions contribute to the TGFβ-induced EMT and the tumorigenic potential of carcinoma cells.

Swelling Phenomena in Sintered Silver Die Attach Structures at High Temperatures: Reliability Problems and Solutions for an Operation above 350°C

A very effective method to bond an electronic device to a substrate is the pressure assisted sintering of a sub-micron silver paste at temperatures between 150°C and 300°C. This technique-sometimes called “Silver-Sintering” or “Low Temperature Joining Technique (LTJT)” is already used in many power electronics industry applications. It provides die attach layers with excellent pull-strength of more than 100 MPa at room temperature and 30 MPa at 300°C. Additionally the electrical and thermal conductivity is nearly as good as it is in pure silver. Such sintered die attach layers are said to be stable up to temperatures above 500°C, but no detailed investigations in this temperature range are available up to now. Our recent investigations by shear- tests on monometallic chip/substrate-samples and dilatometer measurements showed a non-linear thermal expansion of the sintered structures above 350°C including a strong irreversible expansion of the whole sintered structure after long term heat treatments. Beyond the investigations on the swelling effect itself we present studies on the relationship between the expansion of the sintered layer and the resulting layer properties. Finally we discuss possibilities to take advantage out of this effect and additionally analyze options to reduce the swelling by adding SiC-particles to the silver paste. As a result, we demonstrate that swelling of the silver paste has to be taken into consideration when silver sintering is to be used for device operation temperatures above 350°C.

Zinc oxide nanorod based photonic devices: recent progress in growth, light emitting diodes and lasers

Zinc oxide (ZnO), with its excellent luminescent properties and the ease of growth of its nanostructures, holds promise for the development of photonic devices. The recent advances in growth of ZnO nanorods are discussed. Results from both low temperature and high temperature growth approaches are presented. The techniques which are presented include metal-organic chemical vapour deposition (MOCVD), vapour phase epitaxy (VPE), pulse laser deposition (PLD), vapour-liquid-solid (VLS), aqueous chemical growth (ACG) and finally the electrodeposition technique as an example of a selective growth approach. Results from structural as well as optical properties of a variety of ZnO nanorods are shown and analysed using different techniques, including high resolution transmission electron microscopy (HR-TEM), scanning electron microscopy (SEM), photoluminescence (PL) and cathodoluminescence (CL), for both room temperature and for low temperature performance. These results indicate that the grown ZnO nanorods possess reproducible and interesting optical properties. Results on obtaining p-type doping in ZnO micro- and nanorods are also demonstrated using PLD. Three independent indications were found for p-type conducting, phosphorus-doped ZnO nanorods: first, acceptor-related CL peaks, second, opposite transfer characteristics of back-gate field effect transistors using undoped and phosphorus doped wire channels, and finally, rectifying I-V characteristics of ZnO:P nanowire/ZnO:Ga p-n junctions. Then light emitting diodes (LEDs) based on n-ZnO nanorods combined with different technologies (hybrid technologies) are suggested and the recent electrical, as well as electro-optical, characteristics of these LEDs are shown and discussed. The hybrid LEDs reviewed and discussed here are mainly presented for two groups: those based on n-ZnO nanorods and p-type crystalline substrates, and those based on n-ZnO nanorods and p-type amorphous substrates. Promising electroluminescence characteristics aimed at the development of white LEDs are demonstrated. Although some of the presented LEDs show visible emission for applied biases in excess of 10 V, optimized structures are expected to provide the same emission at much lower voltage. Finally, lasing from ZnO nanorods is briefly reviewed. An example of a recent whispering gallery mode (WGM) lasing from ZnO is demonstrated as a way to enhance the stimulated emission from small size structures.

Tumorigenic transformation of human breast epithelial cells induced by mitochondrial DNA depletion

Human mitochondrial DNA (mtDNA) encodes 13 proteins involved in oxidative phosphorylation (OXPHOS). In order to investigate the role of mitochondrial OXPHOS genes in breast tumorigenesis, we have developed a breast epithelial cell line devoid of mtDNA (rho(0) cells). Our analysis revealed that depletion of mtDNA in breast epithelial cells results in in vitro tumorigenic phenotype as well as breast tumorigenesis in a xenograft model. We identified two major gene networks which were differentially regulated between parental and rho(0) epithelial cells. The focal proteins in these networks include (i) FN1 (fibronectin) and (ii) p53. Bioinformatic analyses of FN1 network identified laminin, integrin and 3 of 6 members of peroxiredoxin whose expression were altered in rho(0) epithelial cells. In the p53 network, we identified SMC4 and WRN whose changes in expression suggest that this network may affect chromosomal stability. Consistent with above finding our study revealed an increase in DNA double strand breaks and unique chromosomal rearrangements in rho(0) breast epithelial cells. Additionally, we identified tight junction proteins claudin-1 and claudin-7 in p53 network. To determine the functional relevance of altered gene expression, we focused on detailed analyses of claudin-1 and -7 proteins in breast tumorigenesis. Our study determined that (i) claudin-1 and 7 were indeed downregulated in rho(0) breast epithelial cells, (ii) downregulation of claudin-1 or -7 led to neoplastic transformation of breast epithelial cells, and (iii) claudin-1 and -7 were also downregulated in primary breast tumors. Together, our study suggest that mtDNA encoded OXPHOS genes play a key role in transformation of breast epithelial cells and that multiple pathway involved in mitochondria-to-nucleus retrograde regulation contribute to transformation of breast epithelial cells.

On the difficulties in characterizing ZnO nanowires

The electrical properties of single ZnO nanowires grown by vapor phase transport were investigated. While some samples were contacted by Ti/Au electrodes, another set of samples was investigated using a manipulator tip in a low energy electron point-source microscope. The deduced resistivities range from 1 to 10(3) Ωcm. Additionally, the resistivities of nanowires from multiple publications were brought together and compared to the values obtained from our measurements. The overview of all data shows enormous differences (10(-3)-10(5) Ωcm) in the measured resistivities. In order to reveal the origin of the discrepancies, the influence of growth parameters, measuring methods, contact resistances, crystal structures and ambient conditions are investigated and discussed in detail.

Regulation of galectin-1 expression by transforming growth factor beta1 in metastatic mammary adenocarcinoma cells: implications for tumor-immune escape

Tumors escape from immune surveillance by producing immunosuppressive cytokines and proapototic factors, including TGF-beta and galectin-1 (Gal-1). Since immunosuppressive mechanisms might act in concert to confer tumor-immune privilege, we investigated the potential cross talk between TGF-beta and Gal-1 in highly metastatic mammary adenocarcinoma (LM3) cells. While Gal-1 treatment was not capable of regulating TGF-beta synthesis, a pronounced and dose-dependent increase in Gal-1 expression was observed when tumor cells were treated with TGF-beta(1. )This effect was also observed in the murine lung adenocarcinoma LP07 and in the human breast adenocarcinoma MCF-7 cell lines. TGF-beta1-mediated upregulation of Gal-1 expression was specifically mediated by TbetaRI and TbetaRII, since it was abrogated when LM3 cells were infected with retroviral vectors expressing the dominant negative forms of these receptors. In addition, gal-1 gene sequence analysis revealed the presence of three putative binding sites for Smad4 and Smad3 transcription factors, consistent with the ability of TGF-beta(1) to trigger a Smad-dependent signaling pathway in these cells. Thus, TGF-beta(1) may trigger a Smad-dependent pathway to control Gal-1 expression, suggesting that distinct mechanisms might cooperate in tilting the balance toward an immunosuppressive environment at the tumor site.

Transforming growth factor-beta1 mediates epithelial to mesenchymal transdifferentiation through a RhoA-dependent mechanism

Transforming growth factor-beta1 (TGF-beta) can be tumor suppressive, but it can also enhance tumor progression by stimulating the complex process of epithelial-to-mesenchymal transdifferentiaion (EMT). The signaling pathway(s) that regulate EMT in response to TGF-beta are not well understood. We demonstrate the acquisition of a fibroblastoid morphology, increased N-cadherin expression, loss of junctional E-cadherin localization, and increased cellular motility as markers for TGF-beta-induced EMT. The expression of a dominant-negative Smad3 or the expression of Smad7 to levels that block growth inhibition and transcriptional responses to TGF-beta do not inhibit mesenchymal differentiation of mammary epithelial cells. In contrast, we show that TGF-beta rapidly activates RhoA in epithelial cells, and that blocking RhoA or its downstream target p160(ROCK), by the expression of dominant-negative mutants, inhibited TGF-beta-mediated EMT. The data suggest that TGF-beta rapidly activates RhoA-dependent signaling pathways to induce stress fiber formation and mesenchymal characteristics.

Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD)

All nine pseudouridine (psi) residues in Escherichia coli 23S RNA are in or very near the peptidyl transfer centre (PTC) of the ribosome. Five psi synthases catalyze synthesis of these nine psi's. Deletion of the gene for one psi synthase, RluD, which directs synthesis of three closely clustered psi's in the decoding site of the PTC, has a profound negative impact on cell growth. We describe the isolation, without amplification from a cloned coding element, of the triple-site modifying enzyme, RluD, the N-terminal sequence of which has been used to clone and express the corresponding gene, rluD. Unlike "expressed" RluD, which so far has not been shown to modify one (1911) of the three closely clustered sites (1911, 1915, 1917), "natural" RluD modifies all three sites; and unlike another pai synthase, RluA, natural RluD has greatly expanded modifying activity at low Mg concentrations. These properties of the expressed and natural forms of RluD are discussed.

Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

The pseudouridine (psi) residues present in the high molecular mass RNA from the large ribosomal subunit (LSU) have been sequenced from representative species of the eukaryotes, prokaryotes and archaebacteria, and from mitochondrial and chloroplast organelles. Ribosomes from Bacillus subtilis, Halobacter halobium, Drosphilia melanogaster, Mus musculus, Homo sapiens, mitochondria of M. musculus, H. sapiens and Trypanosoma brucei, and Zea mays chloroplasts were examined, resulting in the exact localization of 190 psi residues. The number of psi residues per RNA varied from one in the mitochondrial RNAs to 57 in the cytoplasmic LSU RNA of D. melanogaster and M. musculus. Despite this, all of the psi residues were found in three domains, II, IV and V. All three are at or have been linked to the peptidyl transferase center according to the literature. Comparison of the sites for psi among the species examined revealed four conserved or semi-conserved segments. One is the region 1911 to 1917, which contains three psi or modified psi in almost all species examined. This site is also juxtaposed to the decoding site of the 30 S subunit in the 70 S ribosome and has been implicated in the fidelity of codon recognition. Three additional sites were at the peptidyl transferase center itself. The juxtaposition of the conserved sites for psi with the two important functions of the ribosome, codon recognition and peptide bond formation, implies an important role for psi in ribosome function. We report some new putative modified nucleosides in LSU RNAs as detected by reverse transcription, correct a segment of the sequence of Z. mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known psi residues in ribosomal RNA, and compare the sites for psi with those known for methylated nucleosides in H. sapiens.

The pseudouridine residues of ribosomal RNA

Pseudouridine (psi), the most common single modified nucleoside in ribosomal RNA, has been positioned in the small subunit (SSU) and large subunit (LSU) RNAs of a number of representative species. Most of the information has been obtained by application of a rapid primed reverse transcriptase sequencing technique. The locations of these psi residues have been compared. Many sites for psi are the same among species, but others are distinct. In general, the percentage psi in multicellular eukaryotes is greater than in prokaryotes. In LSU RNA, the psi residues are strongly clustered in three domains, all of which are near or connected to the peptidyl transferase center. There is no apparent clustering of psi in SSU RNA. The psi sites in LSU RNA overlap those for the methylated nucleosides, but this is not the case in SSU RNA. There are 265 psi sites known to nucleotide resolution, of which 246 are in defined secondary structures, and 112 of these are in nonidentical structural contexts. All 246 psi sites can be classified into five structural types. Two Escherichia coli psi synthases have been cloned and characterized, one for psi 516 in SSU RNA and one for psi 746 in LSU RNA. The psi 746 synthase recognizes free RNA, but the psi 516 enzyme requires an intermediate RNP particle. Possible functional roles for psi in the ribosome are discussed.

Mapping of the 13 pseudouridine residues in Saccharomyces cerevisiae small subunit ribosomal RNA to nucleotide resolution

The number and location of all of the pseudouridine (phi) residues in Saccharomyces cerevisiae small subunit (SSU) ribosomal RNA have been determined by a reverse transcriptase sequencing method [Bakin, A. and Ofengand, J., 1993, Biochemistry, 32, 9754-9762]. Thirteen residues were found in addition to the previously described m1acp3 phi 1189. The residues were scattered throughout the molecule with three being in expansion segments. No phi was found in the three highly conserved single-stranded sequence elements common to all SSU RNAs. Specifically, phi 563, the analog of phi 516 (Escherichia coli) and phi 517 (Bacillus subtilis) were not found. Eight of the phi were located identically to those in mammalian SSU RNA and three were near to mammalian phi residues in the secondary structure. There was no discernible correlation between the sites for phi and the known locations of the methylated nucleosides as exists in large subunit (LSU) RNAs. Comparison of the structural context in which phi was found in SSU RNA with that in LSU RNA showed a differential bias suggestive of possible different roles for phi in the two rRNAs. This work also identified the locations of three putative new modified bases in SSU rRNA, and revealed 15 sequence differences between the yeast strain used here and the reported sequence.

Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli

Pseudouridine (psi) is commonly found in both small and large subunit ribosomal RNAs of prokaryotes and eukaryotes. In Escherichia coli small subunit RNA, there is only one psi, at position 516, in a region of the RNA known to be involved in codon recognition [Bakin et al. (1994) Nucleic Acids Res. 22, 3681-3684]. To assess the function of this single psi residue, the enzyme catalyzing its formation was purified and cloned. The enzyme contains 231 amino acids and has a calculated molecular mass of 25,836 Da. It converts U516 in E. coli 16S RNA transcripts into psi but does not modify any other position in this RNA. It does not react with free unmodified 16S RNA at all, and only poorly with 30S particles containing unmodified RNA. The preferred substrate is an RNA fragment from residues 1 to 678 which has been complexed with 30S ribosomal proteins. The yield varied from 0.6 to 1.0 mol of psi/mol of RNA, depending on the preparation. Free RNA(1-678) was inactive, as was RNA(1-526) and the RNP particle made from it. 23S RNA and tRNAVal transcripts were also inactive. These results suggest that psi formation in vivo occurs at an intermediate stage of 30S assembly. The gene is located at 47.1 min immediately 5' to, and oriented in the same direction as, the bicyclomycin resistance gene. The gene was cloned behind a (His)6 leader for affinity purification. Virtually all of the overexpressed protein was found in inclusion bodies but could be purified to homogeneity on a Ni2+(-) containing resin. Over 200 mg of pure protein could be obtained from a liter of cell culture. Amino acid sequence comparison revealed the existence of a gene in Bacillus subtilis with a similar sequence, and psi sequence analysis established that B. subtilis has the equivalent of psi 516 in its small subunit rRNA. On the other hand, no common sequence motifs could be detected among this enzyme and the two tRNA psi synthases which have been cloned up to now.

A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe)

An Escherichia coli pseudouridine (psi) synthase, which forms both psi 746 in E. coli 23S ribosomal RNA and psi 32 in tRNA(Phe), has been isolated and cloned. The enzyme contains 219 amino acids and has a calculated MW of 24,432 Da. Amino acid sequence comparison with the three other psi synthases that have been cloned to date, two for tRNA and one for 16S RNA, did not reveal any common sequence motifs, despite the catalysis of a common reaction. The gene was cloned behind a (His)6 leader for affinity purification. Upon overexpression, most of the enzyme remained soluble in the cell cytoplasm and could be purified to homogeneity on a Ni(2+)-containing resin. The enzyme reacted with both full-length 23S RNA or a fragment from residues 1-847, forming 1 mol psi/mol RNA at position 746, a normal site for psi. The enzyme has no dependence on Mg2+. The same yield was obtained in 1 mM EDTA as in 10 mM Mg2+, and the rate was faster in EDTA than in Mg2+. Full-length 16S RNA or fragments 1-526 or 1-678, as well as tRNA(Val) transcripts, were not modified in either EDTA or Mg2+. tRNA(Phe) transcripts, however, were modified with a yield of 1 mol psi/mol transcript at a rate in EDTA like that of 23S RNA. Sequencing showed all of the psi to be at position 32, a normal site for psi in this tRNA. Both 23S rRNA psi 746 and tRNA psi 32 occur in single-stranded segments of the same sequence, psi UGAAAA, closed by a stem. Therefore, this synthase may require for recognition only a short stretch of primary sequence 3' to the site of pseudouridylation. This is the first example of a dual-specificity modifying enzyme for RNA, that is, one which is specific for a single site in one RNA, and equally site-specific in a second class of RNA. The essentiality of these psi residues can now be assessed by disruption of the synthase gene.

Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli

tRNA pseudouridine 55 (psi 55) synthase, the enzyme that is specific for the conversion of U55 to psi 55 in the m5U psi CG loop in most tRNAs, has been purified from Escherichia coli and cloned. On SDS gels, a single polypeptide chain with a mass of 39.7 kDa was found. The gene is a previously described open reading frame, p35, located at 68.86 min on the E. coli chromosome between the infB and rpsO genes. The proposed name for this gene is truB. There is very little protein sequence homology between the truB gene product and the hisT (truA) product, which forms psi in the anticodon arm of tRNAs. However, there was high homology with a fragment of a Bacillus subtilis gene that may produce the analogous enzyme in that species. The cloned gene was fused to a 5'-leader coding for a (His)6 tract, and the protein was overexpressed > 400-fold in E. coli. The recombinant protein was purified to homogeneity in one step from a crude cell extract by affinity chromatography using a Ni(2+)-containing matrix. The SDS mass of the recombinant protein was 41.5 kDa, whereas that calculated from the gene was 37.3. The recombinant protein was specific for U55 in tRNA transcripts and reacted neither at other sites for psi in such transcripts nor with transcripts of 16S or 23S ribosomal RNA or subfragments. The enzyme did not require either a renatured RNA structure or Mg2+, and prior formation of m5U was not required. Stoichiometric formation of psi occurred with no requirement for an external source of energy, indicating that psi synthesis is thermodynamically favored.

Clustering of pseudouridine residues around the peptidyltransferase center of yeast cytoplasmic and mitochondrial ribosomes

Analysis of the high molecular weight RNAs of the larger ribosomal subunit of Saccharomyces cerevisiae cytoplasm and mitochondria by a new method [Bakin, A., & Ofengand, J. (1993) Biochemistry 32, 9754-9762] has for the first time located all of the pseudouridine residues present in these two RNAs. Thirty pseudouridines were found in the cytoplasmic RNA, and one was found in the mitochondrial RNA. The 30 cytoplasmic RNA pseudouridines were clustered in three regions of the RNA known to be at or near the peptidyltransferase center. The single pseudouridine in yeast mitochondrial rRNA at position 2819 was also located at the peptidyltransferase center. The localization of pseudouridines at or near the peptidyltransferase center in both cytoplasmic and mitochondrial ribosomes implies a functional role for pseudouridine in peptide bond formation. A correlation was shown to exist between the locations of the pseudouridines determined in this work and the positions of the methylated nucleotides (both 2'-OCH3 and base-methylated) determined previously by others. In addition, this work has tentatively identified the locations of two previously unknown ribothymidine residues, at positions 955 and 2920 in the cytoplasmic rRNA.

The single pseudouridine residue in Escherichia coli 16S RNA is located at position 516

The number and location of pseudouridine residues in Escherichia coli 16S ribosomal RNA has been determined by a combination of direct and indirect methods. Only one residue was found, at position 516. This site is at the 5'-end of one of the three most highly conserved long sequences of this RNA molecule. A number of experimental findings have strongly implicated this loop in the fidelity of codon recognition by A-site bound tRNA. By virtue of its location, we suggest that psi 516 may also play a role in maintaining the fidelity of protein synthesis.

Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique

A new technique has been developed for the facile location of pseudouridylate (psi) residues in any RNA molecule. The method uses two known modification procedures which in combination uniquely identify U residues which have been converted into psi. The first procedure involves reaction of all U-like and G-like residues with N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide p-tosylate (CMC), followed by alkaline removal of all CMC groups except those linked to the N3 of psi. This stops reverse transcription, resulting in a gel band which identifies the U residue. The second procedure is uridine-specific hydrazinolysis which cleaves the RNA chain at all U residues and produces a gel band upon reverse transcription. psi residues, being resistant to hydrazinolysis, are not cleaved and do not stop reverse transcription. This leads to the absence of a band at psi residues. The combined method can also distinguish psi from 5-methyluridine, 4-thiouridine, uridine-5-oxyacetic acid, and 2-thio-5-methylaminomethyluridine as shown by treating rRNA and tRNA species known to contain these modified bases at defined sites. By this procedure, four new sites for psi in Escherichia coli 23S RNA were discovered, and one was disproven. The four new sites are at positions 2457, 2504, 2580, and 2605. The erroneous site is at position 2555. These four new psi residues, which are all in or within 2-3 residues of the peptidyltransferase ring, are thus in a position to play a functional and/or structural role at the peptidyltransferase center.(ABSTRACT TRUNCATED AT 250 WORDS)

Functional effects of a G to U base change at position 530 in a highly conserved loop of Escherichia coli 16S RNA

Any base change at position 530 introduced into Escherichia coli on a multicopy plasmid leads to cell death [Powers & Noller (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 1042-1046]. It was suggested that these mutants cannot carry out chain elongation. To define more precisely the function of base 530, we have studied ribosomes in which G530 was mutated to U530. In vivo, U530 16S rRNA was incorporated into 30S subunits and could combine with 50S to make 70S ribosomes. 16S rRNA in vitro transcripts containing U530 were assembled into 30S ribosomes, and their activity was tested in defined steps of protein synthesis. Mutant 30S ribosomes were as active as wild-type in poly(U)-dependent poly(Phe) synthesis, P- and A-site tRNA binding, and 30S initiation complex formation. 30S initiation complexes, in the presence of 50S, could react with puromycin like the wild-type. The rate, extent, and position of cross-linking of AcVal-tRNA in the P site to 16S RNA were identical in mutant and wild-type ribosomes. Although there appeared to be no defect in 70S initiation complex formation or in direct A-site binding of Phe-tRNA dependent on poly(U), U530 30S ribosomes were nevertheless defective in carrying out synthesis of fMet-Val dipeptide using natural mRNA. Mutant 30S ribosomes were also refractory to streptomycin-induced misreading although no misreading was observed in its absence.(ABSTRACT TRUNCATED AT 250 WORDS)

Interaction between the two conserved single-stranded regions at the decoding site of small subunit ribosomal RNA is essential for ribosome function

Formation of the tertiary base pair G1401:C1501, which brings together two universally present and highly sequence-conserved single-stranded segments of small subunit ribosomal RNA, is essential for ribosome function. It was previously reported that mutation of G1401 inactivated all in vitro functions of the ribosome [Cunningham et al. (1992) Biochemistry 31, 7629-7637]. Here we show that mutation of C1501 to G was equally inactivating but that the double mutant C1401:G1501 with the base pair reversed had virtually full activity for tRNA binding to the P, A, and I sites and for peptide bond formation. Initiation-dependent formation of the first peptide bond remained 70-85% inhibited, despite full 70S initiation complex formation ability as evidenced by the ability to form fMET-puromycin. These results suggest that the defect in formation of the first peptide bond lies in filling the initial A site, Ai, rather than the subsequent elongation A sites, Ae. An increased mobility around the anticodon was detected by UV cross-linking of the anticodon of P-site-bound tRNA to C1399 as well as to the expected C1400. These findings provide the first experimental evidence for the existence of the G1401:C1501 base pair and show that this base pair, located at the decoding site, is essential for function. The structural implications of tertiary base pair formation are discussed.