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  1. Article ; Online: Analytical validation of the PROphet test for treatment decision-making guidance in metastatic non-small cell lung cancer.

    Ben Yellin / Lahav, Coren / Sela, Itamar / Yahalom, Galit / Shoval, Shani Raveh / Elon, Yehonatan / Fuller, James / Harel, Michal

    Journal of pharmaceutical and biomedical analysis

    2023  Volume 238, Page(s) 115803

    Abstract: The blood proteome, consisting of thousands of proteins engaged in various biological processes, acts as a valuable source of potential biomarkers for various medical applications. PROphet is a plasma proteomics-based test that serves as a decision- ... ...

    Abstract The blood proteome, consisting of thousands of proteins engaged in various biological processes, acts as a valuable source of potential biomarkers for various medical applications. PROphet is a plasma proteomics-based test that serves as a decision-support tool for non-small cell lung cancer (NSCLC) patients, combining proteomic profiling using SomaScan technology and subsequent computational algorithm. PROphet was implemented as a laboratory developed test (LDT). Under the Clinical Laboratory Improvement Amendments (CLIA) and Commission on Office Laboratory Accreditation (COLA) regulations, prior to releasing patient test results, a clinical laboratory located in the United States employing an LDT must examine its performance characteristics with regard to analytical validity. This study describes the experimental and computational analytical validity of the PROphet test, as required by CLIA/COLA regulations. Experimental precision analysis displayed a median coefficient of variation (CV) of 3.9 % and 4.7 % for intra-plate and inter-plate examination, respectively, and the median accuracy rate between sites was 88 %. Computational precision exhibited a high accuracy rate, with 93 % of samples displaying complete concordance in results. A cross-platform comparison between SomaScan and other proteomics platforms yielded a median Spearman's rank correlation coefficient of 0.51, affirming the consistency and reliability of the SomaScan platform as used under the PROphet test. Our study presents a robust framework for evaluating the analytical validity of a platform that combines an experimental assay with subsequent computational algorithms. When applied to the PROphet test, strong analytical performance of the test was demonstrated.
    MeSH term(s) Humans ; United States ; Carcinoma, Non-Small-Cell Lung/metabolism ; Proteomics/methods ; Lung Neoplasms/diagnosis ; Lung Neoplasms/metabolism ; Reproducibility of Results ; Biomarkers/metabolism
    Chemical Substances Biomarkers
    Language English
    Publishing date 2023-10-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 604917-5
    ISSN 1873-264X ; 0731-7085
    ISSN (online) 1873-264X
    ISSN 0731-7085
    DOI 10.1016/j.jpba.2023.115803
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1850: Show issues Location:
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  2. Article ; Online: Longitudinal plasma proteomic profiling of patients with non-small cell lung cancer undergoing immune checkpoint blockade.

    Harel, Michal / Lahav, Coren / Jacob, Eyal / Dahan, Nili / Sela, Itamar / Elon, Yehonatan / Raveh Shoval, Shani / Yahalom, Galit / Kamer, Iris / Zer, Alona / Sharon, Ofer / Carbone, David P / Dicker, Adam P / Bar, Jair / Shaked, Yuval

    Journal for immunotherapy of cancer

    2022  Volume 10, Issue 6

    Abstract: Background: Immune checkpoint inhibitors (ICIs) have revolutionized the cancer therapy landscape due to long-term benefits in patients with advanced metastatic disease. However, robust predictive biomarkers for response are still lacking and treatment ... ...

    Abstract Background: Immune checkpoint inhibitors (ICIs) have revolutionized the cancer therapy landscape due to long-term benefits in patients with advanced metastatic disease. However, robust predictive biomarkers for response are still lacking and treatment resistance is not fully understood.
    Methods: We profiled approximately 800 pre-treatment and on-treatment plasma proteins from 143 ICI-treated patients with non-small cell lung cancer (NSCLC) using ELISA-based arrays. Different clinical parameters were collected from the patients including specific mutations, smoking habits, and body mass index, among others. Machine learning algorithms were used to identify a predictive signature for response. Bioinformatics tools were used for the identification of patient subtypes and analysis of differentially expressed proteins and pathways in each response group.
    Results: We identified a predictive signature for response to treatment comprizing two proteins (CXCL8 and CXCL10) and two clinical parameters (age and sex). Bioinformatic analysis of the proteomic profiles identified three distinct patient clusters that correlated with multiple parameters such as response, sex and TNM (tumors, nodes, and metastasis) staging. Patients who did not benefit from ICI therapy exhibited significantly higher plasma levels of several proteins on-treatment, and enrichment in neutrophil-related proteins.
    Conclusions: Our study reveals potential biomarkers in blood plasma for predicting response to ICI therapy in patients with NSCLC and sheds light on mechanisms underlying therapy resistance.
    MeSH term(s) Antineoplastic Agents, Immunological/adverse effects ; Biomarkers ; Carcinoma, Non-Small-Cell Lung/pathology ; Humans ; Immune Checkpoint Inhibitors ; Lung Neoplasms/pathology ; Plasma ; Proteomics
    Chemical Substances Antineoplastic Agents, Immunological ; Biomarkers ; Immune Checkpoint Inhibitors
    Language English
    Publishing date 2022-06-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2719863-7
    ISSN 2051-1426 ; 2051-1426
    ISSN (online) 2051-1426
    ISSN 2051-1426
    DOI 10.1136/jitc-2022-004582
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Circulating autoantibodies to LGALS3BP: a novel biomarker for cancer.

    Grassadonia, Antonino / Tinari, Nicola / Natoli, Clara / Yahalom, Galit / Iacobelli, Stefano

    Disease markers

    2013  Volume 35, Issue 6, Page(s) 747–752

    Abstract: Purpose: Circulating autoantibodies have been extensively investigated as possible markers for early diagnosis of cancer. The present study was carried out to investigate whether anti-LGALS3BP IgG autoantibodies could be classified as a biomarker for ... ...

    Abstract Purpose: Circulating autoantibodies have been extensively investigated as possible markers for early diagnosis of cancer. The present study was carried out to investigate whether anti-LGALS3BP IgG autoantibodies could be classified as a biomarker for malignant tumors.
    Methods: An in-house developed enzyme-linked immunosorbent assay was used to detect autoantibodies to LGALS3BP in sera from 71 patients with various types of cancers and 54 healthy subjects matched by age and gender.
    Results: Patients with cancer have significant higher circulating levels of anti-LGALS3BP antibodies as compared to control subjects (P < 0.001). The test has a sensitivity of 33% and a specificity of 98%.
    Conclusions: Anti-LGALS3BP IgG autoantibodies are a promising biomarker for malignant tumors and could play a role in the development of a multimarker assay for the early detection of cancer.
    MeSH term(s) Adult ; Aged ; Aged, 80 and over ; Antigens, Neoplasm/blood ; Antigens, Neoplasm/immunology ; Autoantibodies/blood ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/immunology ; Carrier Proteins/blood ; Carrier Proteins/immunology ; Case-Control Studies ; Enzyme-Linked Immunosorbent Assay ; Female ; Glycoproteins/blood ; Glycoproteins/immunology ; Humans ; Immunoglobulin G/blood ; Male ; Middle Aged ; Neoplasms/blood ; Neoplasms/diagnosis ; Neoplasms/immunology ; Sensitivity and Specificity
    Chemical Substances Antigens, Neoplasm ; Autoantibodies ; Biomarkers, Tumor ; Carrier Proteins ; Glycoproteins ; Immunoglobulin G ; LGALS3BP protein, human
    Language English
    Publishing date 2013-11-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 604951-5
    ISSN 1875-8630 ; 0278-0240
    ISSN (online) 1875-8630
    ISSN 0278-0240
    DOI 10.1155/2013/214595
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1856: Show issues Location:
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    Einzelsignatur: Show issues

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  4. Article ; Online: AUG sequences are required to sustain nonsense-codon-mediated suppression of splicing.

    Kamhi, Eyal / Yahalom, Galit / Kass, Gideon / Hacham, Yael / Sperling, Ruth / Sperling, Joseph

    Nucleic acids research

    2006  Volume 34, Issue 12, Page(s) 3421–3433

    Abstract: More than 90% of human genes are rich in intronic latent 5' splice sites whose utilization in pre-mRNA splicing would introduce in-frame stop codons into the resultant mRNAs. We have therefore hypothesized that suppression of splicing (SOS) at latent 5' ... ...

    Abstract More than 90% of human genes are rich in intronic latent 5' splice sites whose utilization in pre-mRNA splicing would introduce in-frame stop codons into the resultant mRNAs. We have therefore hypothesized that suppression of splicing (SOS) at latent 5' splice sites regulates alternative 5' splice site selection in a way that prevents the production of toxic nonsense mRNAs and verified this idea by showing that the removal of such in-frame stop codons is sufficient to activate latent splicing. Splicing control by SOS requires recognition of the mRNA reading frame, presumably recognizing the start codon sequence. Here we show that AUG sequences are indeed essential for SOS. Although protein translation does not seem to be required for SOS, the first AUG is shown here to be necessary but not sufficient. We further show that latent splicing can be elicited upon treatment with pactamycin-a drug known to block translation by its ability to recognize an RNA fold-but not by treatment with other drugs that inhibit translation through other mechanisms. The effect of pactamycin on SOS is dependent neither on steady-state translation nor on the pioneer round of translation. This effect is found for both transfected and endogenous genes, indicating that SOS is a natural mechanism.
    MeSH term(s) Animals ; Aspartate Carbamoyltransferase/genetics ; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/genetics ; Cell Line ; Codon, Initiator ; Codon, Nonsense ; Cricetinae ; DNA Primers ; Dihydroorotase/genetics ; Humans ; Mutation ; Pactamycin/pharmacology ; Peptide Chain Initiation, Translational ; Polymerase Chain Reaction ; Protein Synthesis Inhibitors/pharmacology ; RNA Precursors/metabolism ; RNA Splice Sites ; RNA Splicing/drug effects ; RNA, Messenger/metabolism
    Chemical Substances CAD trifunctional enzyme ; Codon, Initiator ; Codon, Nonsense ; DNA Primers ; Protein Synthesis Inhibitors ; RNA Precursors ; RNA Splice Sites ; RNA, Messenger ; Pactamycin (23668-11-3) ; Aspartate Carbamoyltransferase (EC 2.1.3.2) ; Dihydroorotase (EC 3.5.2.3) ; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) (EC 6.3.5.5)
    Language English
    Publishing date 2006-07-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkl390
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1067: Show issues Location:
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  5. Article: An Antibody-based Blood Test Utilizing a Panel of Biomarkers as a New Method for Improved Breast Cancer Diagnosis.

    Yahalom, Galit / Weiss, Daria / Novikov, Ilya / Bevers, Therese B / Radvanyi, Laszlo G / Liu, Mei / Piura, Benjamin / Iacobelli, Stefano / Sandri, Maria T / Cassano, Enrico / Allweis, Tanir M / Bitterman, Arie / Engelman, Pnina / Vence, Luis M / Rosenberg, Marvin M

    Biomarkers in cancer

    2013  Volume 5, Page(s) 71–80

    Abstract: In order to develop a new tool for diagnosis of breast cancer based on autoantibodies against a panel of biomarkers, a clinical trial including blood samples from 507 subjects was conducted. All subjects showed a breast abnormality on exam or breast ... ...

    Abstract In order to develop a new tool for diagnosis of breast cancer based on autoantibodies against a panel of biomarkers, a clinical trial including blood samples from 507 subjects was conducted. All subjects showed a breast abnormality on exam or breast imaging and final biopsy pathology of either breast cancer patients or healthy controls. Using an enzyme-linked immunosorbent assay, the samples were tested for autoantibodies against a predetermined number of biomarkers in various models that were used to determine a diagnosis, which was compared to the clinical status. Our new assay achieved a sensitivity of 95.2% [CI = 92.8-96.8%] at a fixed specificity of 49.5%. Receiver-operator characteristic curve analysis showed an area under the curve of 80.1% [CI = 72.6-87.6%]. These results suggest that a blood test which is based on models comprising several autoantibodies to specific biomarkers may be a new and novel tool for improving the diagnostic evaluation of breast cancer.
    Language English
    Publishing date 2013-11-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2592049-2
    ISSN 1179-299X
    ISSN 1179-299X
    DOI 10.4137/BIC.S13236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Stop codons affect 5' splice site selection by surveillance of splicing.

    Li, Binghui / Wachtel, Chaim / Miriami, Elana / Yahalom, Galit / Friedlander, Gilgi / Sharon, Gil / Sperling, Ruth / Sperling, Joseph

    Proceedings of the National Academy of Sciences of the United States of America

    2002  Volume 99, Issue 8, Page(s) 5277–5282

    Abstract: Pre-mRNA splicing involves recognition of a consensus sequence at the 5' splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for ... ...

    Abstract Pre-mRNA splicing involves recognition of a consensus sequence at the 5' splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for splicing. We noticed that in most cases the utilization of such a latent intronic 5' SS for splicing would introduce an in-frame stop codon into the resultant mRNA. This finding suggested a link between SS selection and maintenance of an ORF within the mRNA. Here we tested this idea by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5' SS were mutated. We found that splicing with the latent site is indeed activated by such mutations. Our findings predict the existence of a checking mechanism, as a component of the nuclear pre-mRNA splicing machine, to ensure the maintenance of an ORF. This notion is highly important for accurate gene expression, as perturbations that would lead to splicing at these latent sites are expected to introduce in-frame stop codons into the majority of mRNAs.
    MeSH term(s) Alternative Splicing ; Animals ; Binding Sites ; Cell Line ; Codon ; Codon, Nonsense ; Codon, Terminator ; Cricetinae ; Fibroblasts/metabolism ; Humans ; Iduronidase/chemistry ; Mesocricetus ; Models, Genetic ; Mutation ; Open Reading Frames ; Plasmids/metabolism ; Point Mutation ; Protein Binding ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Transfection
    Chemical Substances Codon ; Codon, Nonsense ; Codon, Terminator ; RNA, Messenger ; Iduronidase (EC 3.2.1.76)
    Language English
    Publishing date 2002-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.082095299
    Database MEDical Literature Analysis and Retrieval System OnLINE

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