{"entity": "researcher", "timestamp": "2026-07-12T08:42:09.942Z", "family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "affiliations": ["Department of Medical Biochemistry and Biophysics, Ume\u00e5 University, SE-901 87, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796"}}, "publications": [{"entity": "publication", "iuid": "b05f9a8302e1405588f93dc3cb79e0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5"}}, "title": "Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection.", "authors": [{"family": "Peters", "given": "Marie B A", "initials": "MBA", "orcid": "0000-0001-8994-0864", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4733590d054742b732c2028a8f5e8a.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Yau", "given": "Wai-Lok", "initials": "WL"}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Niedermoser", "given": "Isabell", "initials": "I", "orcid": "0000-0002-5301-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b5c11f4f945a5a273c9fd040bee6f.json"}}, {"family": "Gerold", "given": "Gisa", "initials": "G", "orcid": "0000-0002-1326-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6353493de47c4ec58831f79ed94045f4.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}, {"family": "Lundmark", "given": "Richard", "initials": "R", "orcid": "0000-0001-9104-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1b756caa79468dab0f960e43cd61d3.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Orthoflaviviruses are RNA viruses that cause serious diseases in humans, with currently no antivirals available. Targeting host factors is emerging as an attractive antiviral approach. However, as a first step, there is a need to understand which host proteins are hijacked and for what purpose. Here, using a combination of fluorescence microscopy, knock-down, crosslinking immunoprecipitation sequencing, mass spectrometry, and in vitro and biophysical assays, we identify nucleoporin-153 (NUP153) as a proviral factor during orthoflavivirus infection. We show that NUP153 is recruited to the virus amplification site on the endoplasmic reticulum to impact the structural to nonstructural viral protein ratios. We find that NUP153 interacts with both the viral proteins NS3 and NS5, and a highly conserved G-rich motif on the viral RNA. These interactions specifically promote the production of viral structural proteins, leading to an efficient virion assembly, virus release and spread to new cells. We propose that NUP153 acts as a key regulator in viral protein ratios, a mechanism that appears conserved among orthoflaviviruses.", "doi": "10.1038/s41467-026-71449-1", "pmid": "41951628", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71449-1"}], "notes": [], "created": "2026-04-10T12:13:07.525Z", "modified": "2026-04-10T12:13:08.280Z"}, {"entity": "publication", "iuid": "a537001d14d34f14b3048bdf35e0b950", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a537001d14d34f14b3048bdf35e0b950.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a537001d14d34f14b3048bdf35e0b950"}}, "title": "Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at G1/S checkpoint.", "authors": [{"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Gillet", "given": "Natacha", "initials": "N", "orcid": "0000-0002-7657-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce5b43ffd5e44fbe926a3d26064b6760.json"}}, {"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2026-02-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "1149", "issn-l": "2041-1723"}, "abstract": "I-motifs are non-canonical, four-stranded DNA structures in cytosine-rich genomic regions, yet their protein-mediated regulation remains underexplored. Here, we identify PCBP1 (Poly(rC)-binding protein 1) as a selective i-motif-binding protein that unfolds specific i-motifs depending on their protonation and hairpin-forming propensities. Systematic truncation reveals that individual K-homology (KH) domains of PCBP1 cannot selectively bind or unfold i-motifs, but their coordinated actions restore wild-type PCBP1 functions. Using biochemical, biophysical, and molecular dynamics studies, we demonstrate that KH1+2 domains remodel i-motifs, recruiting KH3 to facilitate unfolding and efficient DNA replication. Chromatin and cell-based investigations reveal that PCBP1-knockdown increases i-motif formation at specific genomic loci, coinciding with G1/S arrest and elevated \u03b3H2AX, indicative of genomic instability. During G1/S transition, PCBP1 occupancy peaks at these i-motif loci, ensuring i-motif resolution in early S phase. These findings establish PCBP1 as a critical regulator of i-motif dynamics, directly linking its unfolding activity to G1/S transition and genome stability.", "doi": "10.1038/s41467-026-68822-5", "pmid": "41629296", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-68822-5"}, {"db": "pmc", "key": "PMC12865031"}], "notes": [], "created": "2026-02-04T15:32:08.919Z", "modified": "2026-02-04T15:32:09.419Z"}, {"entity": "publication", "iuid": "7dde054c9c0243a18bbb34e6abd3167f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7dde054c9c0243a18bbb34e6abd3167f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7dde054c9c0243a18bbb34e6abd3167f"}}, "title": "CRISPR-Cas9 targeting of G-Quadruplex DNA in ADH1 promoter highlights its role in transcriptome and metabolome regulation.", "authors": [{"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.json"}}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2025-09-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "17", "issn-l": "0305-1048"}, "abstract": "G-quadruplex (G4) structures are critical regulators of gene expression, yet the role of an individual G4 within its native chromatin remains underexplored, especially outside human systems. Here, we used CRISPR-Cas9 to introduce guanine-to-thymine mutations at a G4-forming motif within the adh1+ promoter in yeast Schizosaccharomyces pombe, creating two mutant strains: one with G4-only mutations and another with both G4 and TATA-box mutations. Chromatin immunoprecipitation using BG4 antibody confirmed reduced G4 enrichment in both mutants, validating G4 structure formation in the wild-type chromatin. Detailed characterizations demonstrated that the G4 mutations alter its dynamics without fully preventing its formation. These mutations significantly reduce adh1 transcript levels, with G4 TATA-box mutant causing the strongest transcriptional suppression. This indicates a positive regulatory role for the G4 structure in transcription. Furthermore, both mutants displayed altered transcriptomic profiles, particularly impacting the oxidoreductase pathway. Metabolomic analyses by mass spectrometry further highlighted substantial disruptions in NAD+/NADH metabolism, a key energy reservoir for metabolic regulation. These results highlight that tuning G4 dynamics, without abolishing the structure, can still profoundly affect gene expression and metabolism, unlike prior studies on the human MYC promoter that disrupted G4 formation. This represents the first such finding in yeast.", "doi": "10.1093/nar/gkaf853", "pmid": "40966507", "labels": {"Swedish Metabolomics Centre": "Service", "Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12448892"}, {"db": "pii", "key": "8252031"}], "notes": [], "created": "2025-11-18T12:14:00.787Z", "modified": "2025-11-27T12:55:10.572Z"}, {"entity": "publication", "iuid": "b174f9dfdb4a4fc693ef7617a4b88f0f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b174f9dfdb4a4fc693ef7617a4b88f0f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b174f9dfdb4a4fc693ef7617a4b88f0f"}}, "title": "A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression.", "authors": [{"family": "Deiana", "given": "Marco", "initials": "M", "orcid": "0000-0002-7815-4494", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9efbe74ca3940029d782d3ba645fa34.json"}}, {"family": "Andr\u00e9s Cast\u00e1n", "given": "Jos\u00e9 Mar\u00eda", "initials": "JM", "orcid": "0000-0003-1012-9505", "researcher": {"href": "https://publications.scilifelab.se/researcher/72c1e687626d479bb738b734ddd5ffed.json"}}, {"family": "Josse", "given": "Pierre", "initials": "P", "orcid": "0000-0002-4943-5828", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa046fb387846e083ce32f9ae3914d9.json"}}, {"family": "Kahsay", "given": "Abraha", "initials": "A"}, {"family": "S\u00e1nchez", "given": "Dar\u00edo Puch\u00e1n", "initials": "DP"}, {"family": "Morice", "given": "Korentin", "initials": "K"}, {"family": "Gillet", "given": "Natacha", "initials": "N", "orcid": "0000-0002-7657-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce5b43ffd5e44fbe926a3d26064b6760.json"}}, {"family": "Ravindranath", "given": "Ranjitha", "initials": "R"}, {"family": "Patel", "given": "Ankit Kumar", "initials": "AK"}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.json"}}, {"family": "Rodriguez-Marquez", "given": "Eva", "initials": "E"}, {"family": "Khrouz", "given": "Lhoussain", "initials": "L", "orcid": "0000-0001-7098-8534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0b94b97266943628d8e512a2f23c830.json"}}, {"family": "Dumont", "given": "Elise", "initials": "E", "orcid": "0000-0002-2359-111X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f7b8a4b687c4eacaa550a7b0e1824a0.json"}}, {"family": "Abad Gal\u00e1n", "given": "Laura", "initials": "L", "orcid": "0000-0001-6226-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c02dcda84044c899f82b88313f5213.json"}}, {"family": "Allain", "given": "Magali", "initials": "M", "orcid": "0000-0002-0893-6028", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9ae4c3cfe4348d5af5dc69a2bb365b0.json"}}, {"family": "Walker", "given": "Bright", "initials": "B", "orcid": "0000-0002-0613-8866", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f28f9f1a7724dac86ba59c897d1ed48.json"}}, {"family": "Ahn", "given": "Hyun Seo", "initials": "HS", "orcid": "0000-0002-6014-0916", "researcher": {"href": "https://publications.scilifelab.se/researcher/45122ada8d3746e2acebcf805bf16e97.json"}}, {"family": "Maury", "given": "Olivier", "initials": "O", "orcid": "0000-0002-4639-643X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd39f301c4934cf7a3e61b7ba984e63a.json"}}, {"family": "Blanchard", "given": "Philippe", "initials": "P", "orcid": "0000-0002-9408-8108", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b181cd702d54796a6e0058b5facf800.json"}}, {"family": "Le Bahers", "given": "Tangui", "initials": "T", "orcid": "0000-0003-2166-081X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cda268d05eb24dc180332aa1bf3871be.json"}}, {"family": "\u00d6hlund", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5847-2778", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e9e473f68c460098a37e22d0a41369.json"}}, {"family": "von Hofsten", "given": "Jonas", "initials": "J", "orcid": "0000-0003-3730-1790", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee9e4dc7b9a44b818e4c10aea633a934.json"}}, {"family": "Monnereau", "given": "Cyrille", "initials": "C", "orcid": "0000-0002-8928-2416", "researcher": {"href": "https://publications.scilifelab.se/researcher/1712a32086094d52abcac1252d4fd913.json"}}, {"family": "Cabanetos", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0003-3781-887X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a03a47d2558643b4b1bbfd80286e9575.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2023-07-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "12", "pages": "6264-6285", "issn-l": "0305-1048"}, "abstract": "Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.", "doi": "10.1093/nar/gkad365", "pmid": "37191066", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10325911"}, {"db": "pii", "key": "7160217"}], "notes": [], "created": "2024-01-18T13:01:00.383Z", "modified": "2025-10-17T13:03:53.699Z"}]}