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  1. Article ; Online: N-Glycosylation as a Modulator of Protein Conformation and Assembly in Disease.

    Pasala, Chiranjeevi / Sharma, Sahil / Roychowdhury, Tanaya / Moroni, Elisabetta / Colombo, Giorgio / Chiosis, Gabriela

    Biomolecules

    2024  Volume 14, Issue 3

    Abstract: Glycosylation, a prevalent post-translational modification, plays a pivotal role in regulating intricate cellular processes by covalently attaching glycans to macromolecules. Dysregulated glycosylation is linked to a spectrum of diseases, encompassing ... ...

    Abstract Glycosylation, a prevalent post-translational modification, plays a pivotal role in regulating intricate cellular processes by covalently attaching glycans to macromolecules. Dysregulated glycosylation is linked to a spectrum of diseases, encompassing cancer, neurodegenerative disorders, congenital disorders, infections, and inflammation. This review delves into the intricate interplay between glycosylation and protein conformation, with a specific focus on the profound impact of N-glycans on the selection of distinct protein conformations characterized by distinct interactomes-namely, protein assemblies-under normal and pathological conditions across various diseases. We begin by examining the spike protein of the SARS virus, illustrating how N-glycans regulate the infectivity of pathogenic agents. Subsequently, we utilize the prion protein and the chaperone glucose-regulated protein 94 as examples, exploring instances where N-glycosylation transforms physiological protein structures into disease-associated forms. Unraveling these connections provides valuable insights into potential therapeutic avenues and a deeper comprehension of the molecular intricacies that underlie disease conditions. This exploration of glycosylation's influence on protein conformation effectively bridges the gap between the glycome and disease, offering a comprehensive perspective on the therapeutic implications of targeting conformational mutants and their pathologic assemblies in various diseases. The goal is to unravel the nuances of these post-translational modifications, shedding light on how they contribute to the intricate interplay between protein conformation, assembly, and disease.
    MeSH term(s) Glycosylation ; Protein Processing, Post-Translational ; Polysaccharides/chemistry ; Protein Conformation ; Prions/metabolism
    Chemical Substances Polysaccharides ; Prions
    Language English
    Publishing date 2024-02-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom14030282
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation.

    Roychowdhury, Tanaya / Chattopadhyay, Samit

    Frontiers in cell and developmental biology

    2020  Volume 8, Page(s) 602994

    Abstract: Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved ... ...

    Abstract Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure-function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein-protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA-protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.
    Language English
    Publishing date 2020-12-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2020.602994
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Use of Native-PAGE for the Identification of Epichaperomes in Cell Lines.

    Roychowdhury, Tanaya / Santhaseela, Anand R / Sharma, Sahil / Panchal, Palak / Rodina, Anna / Chiosis, Gabriela

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2693, Page(s) 175–191

    Abstract: Epichaperomes are disease-associated pathologic scaffolds, composed of tightly bound chaperones, co-chaperones, and other factors. They mediate anomalous protein-protein interactions inside cells, which aberrantly affects the function of protein networks, ...

    Abstract Epichaperomes are disease-associated pathologic scaffolds, composed of tightly bound chaperones, co-chaperones, and other factors. They mediate anomalous protein-protein interactions inside cells, which aberrantly affects the function of protein networks, and in turn, cellular phenotypes. Epichaperome study necessitates the implementation of methods that retain these protein complexes in their native cellular states for analysis. Here we describe a protocol for detection and composition analysis of epichaperomes in cell homogenates through native polyacrylamide gel electrophoresis.
    MeSH term(s) Native Polyacrylamide Gel Electrophoresis ; Molecular Chaperones ; Cell Line ; Electrophoresis, Gel, Two-Dimensional/methods ; Electrophoresis, Polyacrylamide Gel
    Chemical Substances Molecular Chaperones
    Language English
    Publishing date 2023-08-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3342-7_14
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: MicroRNA-324-5p-CUEDC2 Axis Mediates Gain-of-Function Mutant p53-Driven Cancer Stemness.

    Ghatak, Dishari / Datta, Arindam / Roychowdhury, Tanaya / Chattopadhyay, Samit / Roychoudhury, Susanta

    Molecular cancer research : MCR

    2021  Volume 19, Issue 10, Page(s) 1635–1650

    Abstract: Regulation of cancer stemness has recently emerged as a new gain-of-function (GOF) property of mutant p53. In this study, we identify miR-324-5p as a critical epigenetic regulator of cancer stemness and demonstrate its role in mediating GOF-mutant p53- ... ...

    Abstract Regulation of cancer stemness has recently emerged as a new gain-of-function (GOF) property of mutant p53. In this study, we identify miR-324-5p as a critical epigenetic regulator of cancer stemness and demonstrate its role in mediating GOF-mutant p53-driven stemness phenotypes. We report that miR-324-5p is upregulated in human cancer cell lines and non-small cell lung carcinoma (NSCLC) tumors carrying
    Language English
    Publishing date 2021-07-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2098788-2
    ISSN 1557-3125 ; 1541-7786
    ISSN (online) 1557-3125
    ISSN 1541-7786
    DOI 10.1158/1541-7786.MCR-20-0717
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: G-quadruplex structural dynamics at MAPK12 promoter dictates transcriptional switch to determine stemness in breast cancer.

    Sengupta, Pallabi / Dutta, Anindya / Suseela, Y V / Roychowdhury, Tanaya / Banerjee, Nilanjan / Dutta, Ananya / Halder, Satyajit / Jana, Kuladip / Mukherjee, Gopeswar / Chattopadhyay, Samit / Govindaraju, Thimmaiah / Chatterjee, Subhrangsu

    Cellular and molecular life sciences : CMLS

    2024  Volume 81, Issue 1, Page(s) 33

    Abstract: P38γ (MAPK12) is predominantly expressed in triple negative breast cancer cells (TNBC) and induces stem cell (CSC) expansion resulting in decreased survival of the patients due to metastasis. Abundance of G-rich sequences at MAPK12 promoter implied the ... ...

    Abstract P38γ (MAPK12) is predominantly expressed in triple negative breast cancer cells (TNBC) and induces stem cell (CSC) expansion resulting in decreased survival of the patients due to metastasis. Abundance of G-rich sequences at MAPK12 promoter implied the functional probability to reverse tumorigenesis, though the formation of G-Quadruplex (G4) structures at MAPK12 promoter is elusive. Here, we identified two evolutionary consensus adjacent G4 motifs upstream of the MAPK12 promoter, forming parallel G4 structures. They exist in an equilibria between G4 and duplex, regulated by the binding turnover of Sp1 and Nucleolin that bind to these G4 motifs and regulate MAPK12 transcriptional homeostasis. To underscore the gene-regulatory functions of G4 motifs, we employed CRISPR-Cas9 system to eliminate G4s from TNBC cells and synthesized a naphthalene diimide (NDI) derivative (TGS24) which shows high-affinity binding to MAPK12-G4 and inhibits MAPK12 transcription. Deletion of G4 motifs and NDI compound interfere with the recruitment of the transcription factors, inhibiting MAPK12 expression in cancer cells. The molecular basis of NDI-induced G4 transcriptional regulation was analysed by RNA-seq analyses, which revealed that MAPK12-G4 inhibits oncogenic RAS transformation and trans-activation of NANOG. MAPK12-G4 also reduces CD44
    MeSH term(s) Humans ; G-Quadruplexes ; Gene Expression Regulation ; Promoter Regions, Genetic ; Triple Negative Breast Neoplasms/genetics ; Mitogen-Activated Protein Kinase 12/genetics
    Chemical Substances Mitogen-Activated Protein Kinase 12 (EC 2.7.1.-)
    Language English
    Publishing date 2024-01-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1358415-7
    ISSN 1420-9071 ; 1420-682X
    ISSN (online) 1420-9071
    ISSN 1420-682X
    DOI 10.1007/s00018-023-05046-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Curcumin arrests G-quadruplex in the nuclear hyper-sensitive III

    Roy, Ananya / Chatterjee, Oishika / Banerjee, Nilanjan / Roychowdhury, Tanaya / Dhar, Gopa / Mukherjee, Gopeswar / Chatterjee, Subhrangsu

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 20, Page(s) 10203–10219

    Abstract: ... c- ... ...

    Abstract c-MYC
    MeSH term(s) Female ; Humans ; Apoptosis ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Curcumin/pharmacology ; G-Quadruplexes ; Genes, myc ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Proto-Oncogene Proteins c-myc/genetics ; Proto-Oncogene Proteins c-myc/chemistry ; Proto-Oncogene Proteins c-myc/metabolism ; MDA-MB-231 Cells
    Chemical Substances Curcumin (IT942ZTH98) ; Proto-Oncogene Proteins c-bcl-2 ; Proto-Oncogene Proteins c-myc
    Language English
    Publishing date 2021-06-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.1940284
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  7. Article ; Online: Sequence driven interaction of amino acids in de-novo designed peptides determines c-Myc G-quadruplex unfolding inducing apoptosis in cancer cells.

    Banerjee, Nilanjan / Chatterjee, Oishika / Roychowdhury, Tanaya / Basu, Debadrita / Dutta, Anindya / Chowdhury, Madhurima / Dastidar, Shubhra Ghosh / Chatterjee, Subhrangsu

    Biochimica et biophysica acta. General subjects

    2022  Volume 1867, Issue 2, Page(s) 130267

    Abstract: c-MYC proto-oncogene harbors a putative G-quadruplex structure (Pu27) at the ... ...

    Abstract c-MYC proto-oncogene harbors a putative G-quadruplex structure (Pu27) at the NHEIII
    MeSH term(s) G-Quadruplexes ; Proto-Oncogene Proteins c-myc/genetics ; Amino Acids ; Promoter Regions, Genetic ; Peptides/pharmacology ; Apoptosis ; Neoplasms
    Chemical Substances Proto-Oncogene Proteins c-myc ; Amino Acids ; Peptides
    Language English
    Publishing date 2022-11-02
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 60-7
    ISSN 1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbagen.2022.130267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Kaempferol with Verapamil impeded panoramic chemoevasion pathways in breast cancer through ROS overproduction and disruption of lysosomal biogenesis.

    Nandi, Sourav Kumar / Chatterjee, Niloy / Roychowdhury, Tanaya / Pradhan, Ayan / Moiz, Sumaiya / Manna, Krishnendu / Sarkar, Diptendra Kumar / Dhar, Pubali / Dutta, Amitava / Mukhopadhyay, Soma / Bhattacharya, Rittwika

    Phytomedicine : international journal of phytotherapy and phytopharmacology

    2023  Volume 113, Page(s) 154689

    Abstract: Background: Reactive oxygen species (ROS) at low level promotes cell survival through lysosome induced autophagy induction. Glucose stress induced acidosis, hypoxia, ROS, upregulates markers related to cancer stemness and multidrug resistance. Also, ... ...

    Abstract Background: Reactive oxygen species (ROS) at low level promotes cell survival through lysosome induced autophagy induction. Glucose stress induced acidosis, hypoxia, ROS, upregulates markers related to cancer stemness and multidrug resistance. Also, lysosomal upregulation is proposed to be one of the important indicators of cell survival under ROS induced stress. Studies supported that, stimulation of Lysosome-TFEB-Ca
    Purpose: To observe the effect of synergistic drug combination, Kaempferol and Verapamil on markers regulating chemoevasion, tumor stemness & acidosis as well as lysosome upregulation pathways, under low as well as high glucose conditions.
    Hypothesis: Based on our earlier observation as well as previous reports, we hypothesized, our drug combination Kaempferol with Verapamil could attenuate markers related to chemoevasion, tumor stemness & acidosis as well as lysosome-TFEB-Ca2+ pathway, all of which have indispensable association and role in chemoresistance.
    Methods: RNA and protein expression of candidate genes, along with ROS production and Ca2+ concentrations were measured in ex vivo models in altered glucose conditions upon treatment with KV. Also, computational approaches were utilized to hypothesize the mechanism of action of the drug combination. PCR, IHC, western blotting and molecular docking approaches were used in this study.
    Results: The overproduction of ROS by our candidate drugs KV, downregulated the chemoresistance and tumor acidosis markers along with ATP1B1 and resulted in lysosomal disruption with reduction of Ca
    Conclusion: Our ex-vivo and in-silico studies revealed that our candidate drug combination KV, could effectively target several pathways regulating chemoresistance, that were not hitherto studied in the same experimental setup and thus may be endorsed for therapeutic purposes.
    MeSH term(s) Humans ; Female ; Reactive Oxygen Species/metabolism ; Breast Neoplasms/pathology ; Verapamil/pharmacology ; Calcium/metabolism ; Kaempferols/pharmacology ; Kaempferols/metabolism ; Molecular Docking Simulation ; Autophagy ; Glucose/metabolism ; Lysosomes
    Chemical Substances Reactive Oxygen Species ; Verapamil (CJ0O37KU29) ; Calcium (SY7Q814VUP) ; Kaempferols ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2023-02-15
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1205240-1
    ISSN 1618-095X ; 0944-7113
    ISSN (online) 1618-095X
    ISSN 0944-7113
    DOI 10.1016/j.phymed.2023.154689
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  9. Article ; Online: Targeting Oncogene Promoters and Ribosomal RNA Biogenesis by G-Quadruplex Binding Ligands Translate to Anticancer Activity.

    Venkata Suseela, Yelisetty / Sengupta, Pallabi / Roychowdhury, Tanaya / Panda, Suman / Talukdar, Sangita / Chattopadhyay, Samit / Chatterjee, Subhrangsu / Govindaraju, Thimmaiah

    ACS bio & med chem Au

    2021  Volume 2, Issue 2, Page(s) 125–139

    Abstract: G-Quadruplex (GQ) nucleic acids are promising therapeutic targets in anticancer research due to their structural robustness, polymorphism, and gene-regulatory functions. Here, we presented the structure-activity relationship of carbazole-based ... ...

    Abstract G-Quadruplex (GQ) nucleic acids are promising therapeutic targets in anticancer research due to their structural robustness, polymorphism, and gene-regulatory functions. Here, we presented the structure-activity relationship of carbazole-based monocyanine ligands using region-specific functionalization with benzothiazole (TCA and TCZ), lepidine (LCA and LCZ), and quinaldine (QCA and QCZ) acceptor moieties and evaluated their binding profiles with different oncogenic GQs. Their differential turn-on fluorescence emission upon GQ binding confirmed the GQ-to-duplex selectivity of all carbazole ligands, while the isothermal titration calorimetry results showed selective interactions of TCZ and TCA to
    Language English
    Publishing date 2021-11-22
    Publishing country United States
    Document type Journal Article
    ISSN 2694-2437
    ISSN (online) 2694-2437
    DOI 10.1021/acsbiomedchemau.1c00039
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  10. Article ; Online: Deregulation of the CD44-NANOG-MDR1 associated chemoresistance pathways of breast cancer stem cells potentiates the anti-cancer effect of Kaempferol in synergism with Verapamil.

    Nandi, Sourav Kumar / Roychowdhury, Tanaya / Chattopadhyay, Samit / Basu, Sudarshana / Chatterjee, Krishti / Choudhury, Pritha / Banerjee, Nirmalya / Saha, Prosenjit / Mukhopadhyay, Soma / Mukhopadhyay, Ashis / Bhattacharya, Rittwika

    Toxicology and applied pharmacology

    2022  Volume 437, Page(s) 115887

    Abstract: Chemoresistance is an imminent therapeutic challenge for breast cancer. Previous evidence suggests that breast cancer stem cells (BCSC) develop resistance through upregulation of stemness and chemo-evasion markers viz. SOX2, OCT4, NANOG, MDR1 and CD44, ... ...

    Abstract Chemoresistance is an imminent therapeutic challenge for breast cancer. Previous evidence suggests that breast cancer stem cells (BCSC) develop resistance through upregulation of stemness and chemo-evasion markers viz. SOX2, OCT4, NANOG, MDR1 and CD44, following anticancer chemotherapeutic treatments. Early studies suggest an inhibitory role of Kaempferol in BCSC propagation through downregulation of epithelial to mesenchymal transition. We hypothesized that the pathway involved in chemoresistance could be effectively addressed through Kaempferol (K), alone or in combination with Verapamil (V), which is an inhibitor of MDR1. We used K in combination with V, in multiple assays to determine if there was an inhibitory effect on BCSC. Both K and KV attenuated pH-dependent mammosphere formation in primary BCSC and MDA-MB-231 cells. RNA and protein (immunocytochemistry, western blot) expression of candidate markers viz. SOX2, OCT4, NANOG, MDR1 and CD44 were carried out in the presence or absence of candidate drugs in ex-vivo grown primary BCSC and MDA-MB-231 cell line. Immunoprecipitation assay, cell cycle analysis was carried out in MDA-MB-231. Our candidate drugs were not only anti-proliferative, but also downregulated candidate genes expression at RNA and protein level in both settings, with more robust efficacy in KV treatment than K; induced G2/M dependent cell cycle arrest, and interrupted physical association of CD44 with NANOG as well as MDR1 in MDA-MB-231. In primary tumor explant but not in adjacent normal tissue, our candidate drugs K and KV induced robust γH2AX expression. Thus, our candidate drugs are effective in attenuating BCSC survival.
    MeSH term(s) ATP Binding Cassette Transporter, Subfamily B/genetics ; ATP Binding Cassette Transporter, Subfamily B/metabolism ; Antineoplastic Agents/administration & dosage ; Antineoplastic Agents/pharmacology ; Breast Neoplasms/drug therapy ; Cell Line, Tumor ; Deoxycytidine/analogs & derivatives ; Deoxycytidine/pharmacology ; Drug Resistance, Neoplasm ; Drug Synergism ; Female ; Gene Expression Regulation/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Hyaluronan Receptors/genetics ; Hyaluronan Receptors/metabolism ; Kaempferols/administration & dosage ; Kaempferols/pharmacology ; Nanog Homeobox Protein/genetics ; Nanog Homeobox Protein/metabolism ; Neoplastic Stem Cells/drug effects ; Verapamil/administration & dosage ; Verapamil/pharmacology
    Chemical Substances ABCB1 protein, human ; ATP Binding Cassette Transporter, Subfamily B ; Antineoplastic Agents ; CD44 protein, human ; Hyaluronan Receptors ; Kaempferols ; NANOG protein, human ; Nanog Homeobox Protein ; Deoxycytidine (0W860991D6) ; kaempferol (731P2LE49E) ; gemcitabine (B76N6SBZ8R) ; Verapamil (CJ0O37KU29)
    Language English
    Publishing date 2022-01-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 204477-8
    ISSN 1096-0333 ; 0041-008X
    ISSN (online) 1096-0333
    ISSN 0041-008X
    DOI 10.1016/j.taap.2022.115887
    Database MEDical Literature Analysis and Retrieval System OnLINE

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