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  • Conrads, Thomas P.  (111)
  • 1
    In: Journal of Virology, American Society for Microbiology, Vol. 80, No. 18 ( 2006-09-15), p. 9039-9052
    Abstract: Human immunodeficiency virus type 1 (HIV-1) infects CD4 + T lymphocytes and monocytes/macrophages, incorporating host proteins in the process of assembly and budding. Analysis of the host cell proteins incorporated into virions can provide insights into viral biology. We characterized proteins in highly purified HIV-1 virions produced from human monocyte-derived macrophages (MDM), within which virus buds predominantly into intracytoplasmic vesicles, in contrast to the plasmalemmal budding of HIV-1 typically seen with infected T cells. Liquid chromatography-linked tandem mass spectrometry of highly purified virions identified many cellular proteins, including 33 previously described proteins in HIV-1 preparations from other cell types. Proteins involved in many different cellular structures and functions were present, including those from the cytoskeleton, adhesion, signaling, intracellular trafficking, chaperone, metabolic, ubiquitin/proteasomal, and immune response systems. We also identified annexins, annexin-binding proteins, Rab proteins, and other proteins involved in membrane organization, vesicular trafficking, and late endosomal function, as well as apolipoprotein E, which participates in cholesterol transport, immunoregulation, and modulation of cell growth and differentiation. Several tetraspanins, markers of the late endosomal compartment, were also identified. MDM-derived HIV contained 26 of 37 proteins previously found in exosomes, consistent with the idea that HIV uses the late endosome/multivesicular body pathway during virion budding from macrophages.
    Type of Medium: Online Resource
    ISSN: 0022-538X , 1098-5514
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 1495529-5
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  • 2
    In: PROTEOMICS, Wiley, Vol. 4, No. 11 ( 2004-11), p. 3401-3412
    Abstract: Heavy alcohol consumption can damage various cells and organs partly through production of reactive oxygen species (ROS) and mitochondrial dysfunction. Treatment with antioxidants can significantly reduce the degree of damage. Despite well established roles of ROS in alcohol‐induced cell injury, the proteins that are selectively oxidized by ROS are poorly characterized. We hypothesized that certain cysteinyl residues of target proteins are oxidized by ROS upon alcohol exposure, and these modified proteins may play roles in mitochondrial dysfunction. A targeted proteomics approach utilizing biotin‐ N ‐maleimide (biotin‐NM) as a specific probe to label oxidized cysteinyl residues was employed to investigate which mitochondrial proteins are modified during and after alcohol exposure. Human hepatoma HepG2 cells with transduced CYP2E1 (E47 cells) were used as a model to generate ROS through CYP2E1‐mediated ethanol metabolism. Following exposure to 100 m M ethanol for 4 and 8 h, the biotin‐NM‐labeled oxidized proteins were purified with agarose coupled to either streptavidin or monoclonal antibody against biotin. The purified proteins were resolved by two‐dimensional gel electrophoresis and protein spots that displayed differential abundances were excised from the gel, in‐gel digested with trypsin and analyzed for identity utilizing either matrix‐assisted laser desorption‐time of flight mass spectrometry or microcapillary reversed‐phase liquid chromatography‐tandem mass spectrometry. The results demonstrate that heat shock protein 60, protein disulfide isomerase, mitochondrial aldehyde dehydrogenases, prohibitin, and other proteins were oxidized after alcohol exposure. The identity of some of the proteins purified with streptavidin‐agarose was also confirmed by immunoblot analyses using the specific antibody to each target protein. This method was also used to identify oxidized mitochondrial proteins in the alcohol‐fed mouse liver. These results suggest that exposure to ethanol causes oxidation of various mitochondrial proteins that may negatively affect their function and contribute to alcohol‐induced mitochondrial dysfunction and cellular injury.
    Type of Medium: Online Resource
    ISSN: 1615-9853 , 1615-9861
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2004
    detail.hit.zdb_id: 2037674-1
    SSG: 12
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  • 3
    In: Nitric Oxide, Elsevier BV, Vol. 14, No. 2 ( 2006-3), p. 144-151
    Type of Medium: Online Resource
    ISSN: 1089-8603
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2006
    detail.hit.zdb_id: 1471433-4
    SSG: 12
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  • 4
    In: Nitric Oxide, Elsevier BV, Vol. 14, No. 4 ( 2006-6), p. 41-
    Type of Medium: Online Resource
    ISSN: 1089-8603
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2006
    detail.hit.zdb_id: 1471433-4
    SSG: 12
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  • 5
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2017-11-09)
    Abstract: ATR kinase activity slows replication forks and prevents origin firing in damaged cells. Here we describe proteomic analyses that identified mechanisms through which ATR kinase inhibitors induce unscheduled origin firing in undamaged cells. ATR-Chk1 inhibitor-induced origin firing is mediated by Cdc7 kinase through previously undescribed phosphorylations on GINS that induce an association between GINS and And-1. ATR-Chk1 inhibitor-induced origin firing is blocked by prior exposure to DNA damaging agents showing that the prevention of origin firing does not require ongoing ATR activity. In contrast, ATR-Chk1 inhibitor-induced origins generate additional replication forks that are targeted by subsequent exposure to DNA damaging agents. Thus, the sequence of administration of an ATR kinase inhibitor and a DNA damaging agent impacts the DNA damage induced by the combination. Our experiments identify competing ATR and Cdc7 kinase-dependent mechanisms at replication origins in human cells.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2553671-0
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  • 6
    In: JAMA Network Open, American Medical Association (AMA), Vol. 5, No. 10 ( 2022-10-14), p. e2236626-
    Abstract: Despite similar histologic appearance among high-grade serous ovarian cancers (HGSOCs), clinical observations suggest vast differences in gross appearance. There is currently no systematic framework by which to classify HGSOCs according to their gross morphologic characteristics. Objective To develop and characterize a gross morphologic classification system for HGSOC. Design, Setting, and Participants This cohort study included patients with suspected advanced-stage ovarian cancer who presented between April 1, 2013, and August 5, 2016, to the University of Texas MD Anderson Cancer Center, a large referral center. Patients underwent laparoscopic assessment of disease burden before treatment and received a histopathologic diagnosis of HGSOC. Researchers assigning morphologic subtype and performing molecular analyses were blinded to clinical outcomes. Data analysis was performed between April 2020 and November 2021. Exposures Gross tumor morphologic characteristics. Main Outcomes and Measures Clinical outcomes and multiomic profiles of representative tumor samples of type I or type II morphologic subtypes were compared. Results Of 112 women (mean [SD] age 62.7 [9.7] years) included in the study, most patients (84% [94]) exhibited a predominant morphologic subtype and many (63% [71] ) had a uniform morphologic subtype at all involved sites. Compared with those with uniform type I morphologic subtype, patients with uniform type II morphologic subtype were more likely to have a favorable Fagotti score (83% [19 of 23] vs 46% [22 of 48] ; P  = .004) and thus to be triaged to primary tumor reductive surgery. Similarly, patients with uniform type II morphologic subtype also had significantly higher mean (SD) estimated blood loss (639 [559; 95% CI, 391-887] mL vs 415 [527; 95% CI, 253-577] mL; P  = .006) and longer mean (SD) operative time (408 [130; 95% CI, 350-466] minutes vs 333 [113; 95% CI, 298-367] minutes; P  = .03) during tumor reductive surgery. Type I tumors had enrichment of epithelial-mesenchymal transition (false discovery rate [FDR] q-value, 3.10 × 10 −24 ), hypoxia (FDR q-value, 1.52 × 10 −5 ), and angiogenesis pathways (FDR q-value, 2.11 × 10 −2 ), whereas type II tumors had enrichment of pathways related to MYC signaling (FDR q-value, 2.04 × 10 −9 ) and cell cycle progression (FDR q-value, 1.10 × 10 −5 ) by integrated proteomic and transcriptomic analysis. Abundances of metabolites and lipids also differed between the 2 morphologic subtypes. Conclusions and Relevance This study identified 2 novel, gross morphologic subtypes of HGSOC, each with unique clinical features and molecular signatures. The findings may have implications for triaging patients to surgery or chemotherapy, identifying outcomes, and developing tailored therapeutic strategies.
    Type of Medium: Online Resource
    ISSN: 2574-3805
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2022
    detail.hit.zdb_id: 2931249-8
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  • 7
    In: Clinical Proteomics, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2022-12)
    Abstract: Optimal cytoreduction to no residual disease (R0) correlates with improved disease outcome for high-grade serous ovarian cancer (HGSOC) patients. Treatment of HGSOC patients with neoadjuvant chemotherapy, however, may select for tumor cells harboring alterations in hallmark cancer pathways including metastatic potential. This study assessed this hypothesis by performing proteomic analysis of matched, chemotherapy naïve and neoadjuvant chemotherapy (NACT)-treated HGSOC tumors obtained from patients who had suboptimal (R1, n = 6) versus optimal (R0, n = 14) debulking at interval debulking surgery (IDS). Methods Tumor epithelium was harvested by laser microdissection from formalin-fixed, paraffin-embedded tissues from matched, pre- and post-NACT treated tumors for twenty HGSOC patients and analyzed by quantitative mass spectrometry-based proteomics. Results Differential analysis of patient matched pre- and post-NACT treated tumors revealed proteins associated with cell survival and metabolic signaling to be significantly altered in post-NACT treated tumor cells. Comparison of pre-NACT treated tumors from suboptimal (R1) versus optimally (R0) debulked patients identified proteins associated with tumor cell viability and invasion signaling enriched in R1 patients. We identified five proteins altered between R1 and R0 patients in pre- NACT treated tumors that significantly correlated with PFS in an independent cohort of HGSOC patients, including Fermitin family homolog 2 (FERMT2), a protein elevated in R1 that correlated with disease progression in HGSOC patients (multivariate Cox HR = 1.65, Wald p = 0.022) and increased metastatic potential in solid-tumor malignancies. Conclusions This study identified distinct proteome profiles in patient matched pre- and post-NACT HGSOC tumors that correlate with NACT resistance and that may predict residual disease status at IDS that collectively warrant further pre-clinical investigation.
    Type of Medium: Online Resource
    ISSN: 1542-6416 , 1559-0275
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2163624-2
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  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2015
    In:  Molecular Cancer Therapeutics Vol. 14, No. 12_Supplement_2 ( 2015-12-01), p. C10-C10
    In: Molecular Cancer Therapeutics, American Association for Cancer Research (AACR), Vol. 14, No. 12_Supplement_2 ( 2015-12-01), p. C10-C10
    Abstract: Triple-negative breast cancer (TNBC) represents a major subtype of breast cancer (BC) and no biomarkers or targeted treatments are available. Retrospective proteomic analysis of formalin-fixed paraffin-embedded (FFPE) BC tissue has the potential to identify novel biomarkers and pathways associated with disease recurrence in TNBC, since sample data can be coupled with clinical data, including treatment and patient outcome. Primary TNBC tissue of patients who experienced distant metastasis or no recurrence within a 10 year follow-up period was retrieved to investigate whether proteomics using liquid chromatography tandem mass spectrometry (LC-MS/MS) can identify proteins and pathways associated with their metastatic potential. FFPE material on PEN-membrane slides were deparaffinized according to standard procedure with xylene/ethanol and stained with hematoxylin and eosin. Cancer cells were dissected by UV laser capture microdissection (LCM) and subjected to protein extraction in triethylammonium bicarbonate/acetonitrile buffer by heat-induced antigen retrieval. Extracted proteins were trypsinized and generated peptides were isobarically labelled with 6-plex tandem mass tags, combined 1:1 and subjected to hydrophilic interaction liquid chromatography LC-MS/MS. Preliminary experiments identified & gt;500 unique proteins from BC FFPE tissue, verifying a robust setup. Cancer cells from primary TNBC FFPE tissues of 15 patients who experienced distant metastatic and 20 patients who did not have recurrence within ten years were isolated by UV-LCM and analyzed according to the above setup. The patients were stratified into four working groups based upon their menopausal status (pre or post) and their recurrence (recurrence or no-recurrence) outcome. The median aged varied from 42.2 to 63.4 years between the four groups with most tumors being diagnosed as T1 or T2 (TNM classification system). All tumors were grade 2 or higher at diagnosis, with no distant metastasis present prior to removal of the primary tumor. We identified 2564 high-confident proteins across the 35 patient samples with ≥2 unique peptides. Statistical analysis was done in RStudio and GproX and revealed distinct molecular profiles capable of separating metastatic from non-metastatic patients with a p-value ≤0.05. Furthermore three proteins were found to be differentially regulated between the two groups with a p-value & lt;0.001 making these highly interesting targets in the prevention of metastatic lesions in TNBC. Research funded by the Danish Research Council, the A.P. Møller foundation and The Regional Strategically Research Council of Southern Denmark Citation Format: Martin H. Pedersen, Brian L. Hood, Thomas P. Conrads, Henrik J. Ditzel, Rikke Leth-Larsen. Quantitative proteomics of formalin-fixed paraffin-embedded, primary triple-negative breast cancer tissues of patients who experienced distant metastasis or no recurrence. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C10.
    Type of Medium: Online Resource
    ISSN: 1535-7163 , 1538-8514
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
    detail.hit.zdb_id: 2062135-8
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2010
    In:  Cancer Research Vol. 70, No. 8_Supplement ( 2010-04-15), p. 2062-2062
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 70, No. 8_Supplement ( 2010-04-15), p. 2062-2062
    Abstract: MicroRNAs (miRNAs) represent an endogenous, post-transcriptional gene expression regulatory mechanism that is mediated by small, non-coding double-stranded RNAs (dsRNA) which target discrete messenger RNAs (mRNAs) resulting in their degradation or translational repression. Current computational methodologies predict that an average of 200 unique genes may be targeted by a single miRNA with the vast majority remaining, as yet, experimentally unvalidated. Furthermore, as miRNAs regulate their gene targets post-transcriptionally, the application of global, quantitative proteomic analysis to miRNA target discovery will yield a more comprehensive assessment of miRNA activity than gene expression analysis alone. Several miRNAs have been shown to be robustly downregulated in breast cancer, including microRNA-145 (miR-145). Recent investigations of miR-145 in breast cancer have revealed tumor suppressor activities for this miRNA and that loss of miR-145 expression may be associated with early stages of breast cancer pathogenesis. To elucidate targets of miR-145 and its role in breast cancer, we restored expression in the human breast cancer cell lines MDA-MB-231 and SKBR3 and conducted both phenotypic and global, quantitative protein expression analysis utilizing mass spectrometry-based proteomics. Phenotypic analyses indicated that MDA-MB-231 and SKBR3 cells stably expressing miR-145 exhibit a growth advantage relative to control cells. In support of this evidence, GO enrichment analysis of significantly differentially expressed proteins in miR-145-expressing MDA-MB-231 (MDA-145) cells revealed modulation of factors associated with cell cycle regulation, such as increased expression of the G2/M-phase regulatory factors anaphase promoting complex subunit 1 (ANAPC1) and cell division cycle 20 homolog (CDC20) expression and decreased expression of DnaJ (Hsp40) homolog (DNAJA3). Investigation of miR-145-specific effects via sequence analysis of 3’ untranslated regions derived from genes corresponding to proteins which were decreased in abundance in MDA-145 cells revealed 33 target candidates that contained a miR-145 “seed” motif. Of these 33 candidates, 21 have been previously predicted as miR-145 targets (miRNAMap). Target candidates are associated with cell cycle regulation and mitochondrial function and include integrin linked kinase (ILK), the cytokine growth factor chromosome 19 open reading frame 10 (C19ORF10) and microsomal glutathione S-transferase 1 (MGST1). Validation of target candidates and exploration of their role in the miR-145-mediated growth advantage phenotype are currently underway. In conclusion, these results indicate that restoration of stable miR-145 expression in breast cancer cells confers a growth advantage which is underscored by modulation of proteins associated with cell cycle regulation and mitochondrial activity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2062.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2010
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 10
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2014
    In:  Molecular Cancer Research Vol. 12, No. 9 ( 2014-09-01), p. 1283-1291
    In: Molecular Cancer Research, American Association for Cancer Research (AACR), Vol. 12, No. 9 ( 2014-09-01), p. 1283-1291
    Abstract: A subset of acute promyelocytic leukemia (APL) cases has been characterized by the t(5;17)(q35;q21) translocation variant, which fuses nucleophosmin (NPM) to retinoic acid receptor α (RARA). The resultant NPM-RAR fusion protein blocks myeloid differentiation and leads to a leukemic phenotype similar to that caused by the t(15;17)(q22;q21) PML-RAR fusion. The contribution of the N-terminal 117 amino acids of NPM contained within NPM-RAR has not been well studied. As a molecular chaperone, NPM interacts with a variety of proteins implicated in leukemogenesis. Therefore, a proteomic analysis was conducted to identify novel NPM-RAR–associated proteins. TNF receptor type I–associated DEATH domain protein (TRADD) was identified as a relevant binding partner for NPM-RAR. This interaction was validated by coprecipitation and colocalization analysis. Biologic assessment found that NPM-RAR expression impaired TNF-induced signaling through TRADD, blunting TNF-mediated activation of caspase-3 (CASP3) and caspase-8 (CASP8), to ultimately block apoptosis. Implications: This study identifies a novel mechanism through which NPM-RAR affects leukemogenesis. Mol Cancer Res; 12(9); 1283–91. ©2014 AACR.
    Type of Medium: Online Resource
    ISSN: 1541-7786 , 1557-3125
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2014
    detail.hit.zdb_id: 2097884-4
    SSG: 12
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