Transcriptome analysis and connectivity mapping of Cissampelos pareira L. provides molecular links of ESR1 modulation to viral inhibition

  1. Madiha Haider
  2. Dhwani Dholakia
  3. Aleksha Panwar
  4. Parth Garg
  5. Atish Gheware
  6. Dayanidhi Singh
  7. Khushboo Singhal
  8. Shaunak A Burse
  9. Surekha Kumari
  10. Anmol
  11. Arjun Ray
  12. Guruprasad R. Medigeshi
  13. Upendra Sharma
  14. Bhavana Prasher
  15. Mitali Mukerji

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Abstract

Bioactive fractions or compounds obtained from medicinal plants have been used for the treatment of multiple diseases. This effect could be due to common pathways underlying these conditions that are targeted by such medicines. In this study, we explored the molecular basis of action of one such herbal formulation Cissampelos pareira , used for the treatment of female hormone disorders and fever. Genome-wide expression studies on MCF7 cell lines treated with Cipa extract were carried out using Affymetrix arrays. Transcriptome analysis revealed a downregulation of signatures of estrogen response governed by estrogen receptor α (ERα). Molecular docking analysis identified 38 constituent molecules in Cipa that potentially bind (ΔG< -7.5) with ERα at the same site as estrogen. Cipa transcriptome signatures show high positive connectivity ( https://clue.io/ ) scores with protein translation inhibitors such as emetine (score: 99.61) and knockdown signatures of genes linked to the antiviral response such as ribosomal protein RPL7 (score: 99.92), which is also an ERα coactivator. Cipa exhibits antiviral activity in dengue infected MCF7 cells that is decreased upon ESR1 (estrogen receptor 1) gene knockdown. This approach reveals a novel pathway involving ESR1-RPL7 axis that could be a potential target in dengue viral infection.

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  1. Version published to 10.1101/2021.02.17.431579v2 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2021.02.17.431579: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Connectivity map analysis for identifying similarities with known perturbations: The connectivity map dataset currently contains 1,319,138 gene expression profiles, resulting in 473,647 signatures, generated against approximately 27,000 perturbations in 9 cell lines including MCF7, HEPG2, A549, A375, PC3, HCC515, HT29, HA1E and VCAP.
    HEPG2
    suggested: None
    A549
    suggested: None
    A375
    suggested: None
    HCC515
    suggested: RRID:CVCL_5136)
    Cipa treatment in DENV infection: MCF-7 were seeded at 100,000 cells per well in 24 well plate and were maintained for 24 hours (37 degrees; 5% CO2).
    MCF-7
    suggested: None
    50,000 BHK-21 cells were plated per well in 24-well plate.
    BHK-21
    suggested: None
    siRNA-mediated knockdown of ESR1 in MCF7 cells: 1 μM concentration of siRNA targeting ESR1 gene and non-targeting control (NTC) were mixed with Opti-MEM (Life Technologies) and 1 μl of Lipofectamine RNAiMax to a total volume of 100 μl in a 24-well plate.
    MCF7
    suggested: None
    Software and Algorithms
    SentencesResources
    Batch effects were removed and differential gene expression analysis was done using the limma package in R.
    limma
    suggested: (LIMMA, RRID:SCR_010943)
    After correcting for FDR<5%, enrichments were analyzed for GO: Molecular Function, Cellular Compartment, Biological Processes, KEGG and Reactome.
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    In order to identify the specific sets of genes modulated by Cipa, we used Gene set enrichment analysis.
    Gene set enrichment analysis
    suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)
    ERE analysis: Sequence of 5KB upstream region of genes were downloaded from UCSC genome browser for Human genome GRCh38 build.
    UCSC genome browser
    suggested: (UCSC Genome Browser, RRID:SCR_005780)
    The CIPA ligands available in the PubChem database were downloaded from there, the 3D structures of the rest of the ligands were drawn using Marvin Sketch, a computational tool for drawing 3 and 2 dimensional chemical structures.
    PubChem
    suggested: (PubChem, RRID:SCR_004284)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

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  3. Version published to 10.1101/2021.02.17.431579v1 on bioRxiv