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  1. AU="Vlasenkova, Ramilia"
  2. AU="Taheri, Fateme"
  3. AU="Berman, Robert F"
  4. AU="Resnick, Cory M"
  5. AU=Freeman Gordon J AU=Freeman Gordon J
  6. AU="Fangru Zhou"

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  1. Artikel: Characterization of Cancer/Testis Antigens as Prognostic Markers of Ovarian Cancer.

    Vlasenkova, Ramilia / Konysheva, Daliya / Nurgalieva, Alsina / Kiyamova, Ramziya

    Diagnostics (Basel, Switzerland)

    2023  Band 13, Heft 19

    Abstract: The main goal of this study was to characterize cancer/testis antigens (CTAs) as potential molecular markers of ovarian cancer. First, we gathered and analyzed a significantly large dataset of 21 selected CTAs that are encoded by 32 genes; the dataset ... ...

    Abstract The main goal of this study was to characterize cancer/testis antigens (CTAs) as potential molecular markers of ovarian cancer. First, we gathered and analyzed a significantly large dataset of 21 selected CTAs that are encoded by 32 genes; the dataset consisted of the mutation data, expression data, and survival data of patients with ovarian cancer (n = 15,665). The 19 functionally significant missense mutations were identified in 9 CTA genes: ACRBP, CCT4, KDM5B, MAGEA1, MAGEA4, PIWIL1, PIWIL2, PRAME, and SPA17. The analysis of the mRNA expression levels of 21 CTAs in healthy and tumor ovarian tissue showed an up-regulation in the expression level of AKAP3, MAGEA4, PIWIL1, and PRAME in tumor samples and a down-regulation in the expression level of CTAG1A, CTAG1B, MAGEC1, and PIWIL2. The CCT4 up-regulation and PRAME mutations were correlated with a good prognosis for ovarian cancer, while higher levels of GAGE2A and CT45A1 mRNAs were correlated with a poor prognosis for ovarian cancer patients. Thus, GAGE2, CT45, CCT4, and PRAME cancer/testis antigens can be considered as potential prognostic markers for ovarian tumors, and GAGE2, CCT4, and PRAME were revealed to be correlated with the prognosis for ovarian cancer patients for the first time.
    Sprache Englisch
    Erscheinungsdatum 2023-09-29
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2662336-5
    ISSN 2075-4418
    ISSN 2075-4418
    DOI 10.3390/diagnostics13193092
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Identification of New Regulators of Pancreatic Cancer Cell Sensitivity to Oxaliplatin and Cisplatin.

    Skripova, Vera / Vlasenkova, Ramilia / Zhou, Yan / Astsaturov, Igor / Kiyamova, Ramziya

    Molecules (Basel, Switzerland)

    2022  Band 27, Heft 4

    Abstract: The chemoresistance of tumor cells is one of the most urgent challenges in modern oncology and in pancreatic cancer, in which this problem is the most prominent. Therefore, the identification of new chemosensitizing co-targets may be a path toward ... ...

    Abstract The chemoresistance of tumor cells is one of the most urgent challenges in modern oncology and in pancreatic cancer, in which this problem is the most prominent. Therefore, the identification of new chemosensitizing co-targets may be a path toward increasing chemotherapy efficacy. In this work, we performed high-performance in vitro knockout CRISPR/Cas9 screening to find potential regulators of the sensitivity of pancreatic cancer. For this purpose, MIA PaCa-2 cells transduced with two sgRNA libraries ("cell cycle/nuclear proteins genes" and "genome-wide") were screened by oxaliplatin and cisplatin. In total, 173 candidate genes were identified as potential regulators of pancreatic cancer cell sensitivity to oxaliplatin and/or cisplatin; among these, 25 genes have previously been reported, while 148 genes were identified for the first time as potential platinum drug sensitivity regulators. We found seven candidate genes involved in pancreatic cancer cell sensitivity to both cisplatin and oxaliplatin. Gene ontology enrichment analysis reveals the enrichment of single-stranded DNA binding, damaged DNA binding pathways, and four associated with NADH dehydrogenase activity. Further investigation and validation of the obtained results by in vitro, in vivo, and bioinformatics approaches, as well as literature analysis, will help to identify novel pancreatic cancer platinum sensitivity regulators.
    Mesh-Begriff(e) Antineoplastic Agents/pharmacology ; Biomarkers, Tumor ; CRISPR-Cas Systems ; Cell Line, Tumor ; Cisplatin/pharmacology ; Computational Biology/methods ; Drug Resistance, Neoplasm/drug effects ; Drug Resistance, Neoplasm/genetics ; Drug Screening Assays, Antitumor ; Gene Expression Profiling ; Gene Knockdown Techniques ; Gene Ontology ; Gene Regulatory Networks ; Humans ; Oxaliplatin/pharmacology ; Pancreatic Neoplasms ; Synthetic Lethal Mutations
    Chemische Substanzen Antineoplastic Agents ; Biomarkers, Tumor ; Oxaliplatin (04ZR38536J) ; Cisplatin (Q20Q21Q62J)
    Sprache Englisch
    Erscheinungsdatum 2022-02-14
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules27041289
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.MO 81: Hefte anzeigen

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  3. Artikel ; Online: Characterization of

    Vlasenkova, Ramilia / Nurgalieva, Alsina / Akberova, Natalia / Bogdanov, Mikhail / Kiyamova, Ramziya

    Biomolecules

    2021  Band 11, Heft 12

    Abstract: The main goal of this study is to ... ...

    Abstract The main goal of this study is to consider
    Mesh-Begriff(e) Biomarkers, Tumor/genetics ; Databases, Genetic ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; INDEL Mutation ; Male ; Mutation ; Mutation, Missense ; Neoplasms/genetics ; Prognosis ; Sodium-Phosphate Cotransporter Proteins, Type IIb/genetics ; Survival Analysis
    Chemische Substanzen Biomarkers, Tumor ; SLC34A2 protein, human ; Sodium-Phosphate Cotransporter Proteins, Type IIb
    Sprache Englisch
    Erscheinungsdatum 2021-12-14
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom11121878
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.

    Demidova, Elena V / Serebriiskii, Ilya G / Vlasenkova, Ramilia / Kelow, Simon / Andrake, Mark D / Hartman, Tiffiney R / Kent, Tatiana / Virtucio, James / Rosen, Gail L / Pomerantz, Richard T / Dunbrack, Roland L / Golemis, Erica A / Hall, Michael J / Chen, David Y T / Daly, Mary B / Arora, Sanjeevani

    BMC genomics

    2023  Band 24, Heft 1, Seite(n) 388

    Sprache Englisch
    Erscheinungsdatum 2023-07-10
    Erscheinungsland England
    Dokumenttyp Published Erratum
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-023-09486-z
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  5. Artikel ; Online: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.

    Demidova, Elena V / Serebriiskii, Ilya G / Vlasenkova, Ramilia / Kelow, Simon / Andrake, Mark D / Hartman, Tiffiney R / Kent, Tatiana / Virtucio, James / Rosen, Gail L / Pomerantz, Richard T / Dunbrack, Roland L / Golemis, Erica A / Hall, Michael J / Chen, David Y T / Daly, Mary B / Arora, Sanjeevani

    BMC genomics

    2023  Band 24, Heft 1, Seite(n) 212

    Abstract: Background: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.!# ...

    Abstract Background: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.
    Methods: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.
    Results: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities.
    Conclusions: Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.
    Mesh-Begriff(e) Humans ; Carcinoma, Renal Cell ; Genetic Predisposition to Disease ; DNA Replication ; Germ-Line Mutation ; Kidney Neoplasms ; Germ Cells
    Sprache Englisch
    Erscheinungsdatum 2023-04-24
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-023-09310-8
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma.

    Nicolas, Emmanuelle / Demidova, Elena V / Iqbal, Waleed / Serebriiskii, Ilya G / Vlasenkova, Ramilia / Ghatalia, Pooja / Zhou, Yan / Rainey, Kim / Forman, Andrea F / Dunbrack, Roland L / Golemis, Erica A / Hall, Michael J / Daly, Mary B / Arora, Sanjeevani

    Molecular genetics & genomic medicine

    2019  Band 7, Heft 3, Seite(n) e556

    Abstract: Background: Identification of genetic factors causing predisposition to renal cell carcinoma has helped improve screening, early detection, and patient survival.: Methods: We report the characterization of a proband with renal and thyroid cancers and ...

    Abstract Background: Identification of genetic factors causing predisposition to renal cell carcinoma has helped improve screening, early detection, and patient survival.
    Methods: We report the characterization of a proband with renal and thyroid cancers and a family history of renal and other cancers by whole-exome sequencing (WES), coupled with WES analysis of germline DNA from additional affected and unaffected family members.
    Results: This work identified multiple predicted protein-damaging variants relevant to the pattern of inherited cancer risk. Among these, the proband and an affected brother each had a heterozygous Ala45Thr variant in SDHA, a component of the succinate dehydrogenase (SDH) complex. SDH defects are associated with mitochondrial disorders and risk for various cancers; immunochemical analysis indicated loss of SDHB protein expression in the patient's tumor, compatible with SDH deficiency. Integrated analysis of public databases and structural predictions indicated that the two affected individuals also had additional variants in genes including TGFB2, TRAP1, PARP1, and EGF, each potentially relevant to cancer risk alone or in conjunction with the SDHA variant. In addition, allelic imbalances of PARP1 and TGFB2 were detected in the tumor of the proband.
    Conclusion: Together, these data suggest the possibility of risk associated with interaction of two or more variants.
    Mesh-Begriff(e) Adult ; Aged ; Carcinoma, Renal Cell/genetics ; Electron Transport Complex II/genetics ; Epistasis, Genetic ; Female ; Germ-Line Mutation ; HSP90 Heat-Shock Proteins/genetics ; Humans ; Kidney Neoplasms/genetics ; Male ; Middle Aged ; Pedigree ; Poly (ADP-Ribose) Polymerase-1/genetics ; Transforming Growth Factor beta2/genetics
    Chemische Substanzen HSP90 Heat-Shock Proteins ; TGFB2 protein, human ; TRAP1 protein, human ; Transforming Growth Factor beta2 ; Electron Transport Complex II (EC 1.3.5.1) ; SDHA protein, human (EC 1.3.5.1) ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30)
    Sprache Englisch
    Erscheinungsdatum 2019-01-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2734884-2
    ISSN 2324-9269 ; 2324-9269
    ISSN (online) 2324-9269
    ISSN 2324-9269
    DOI 10.1002/mgg3.556
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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