{"entity": "researcher", "timestamp": "2026-07-14T01:22:07.064Z", "family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "affiliations": ["Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.", "Proteomics Biomedicum, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d"}}, "publications": [{"entity": "publication", "iuid": "cc47692d5ce54490b075f561042eafa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc47692d5ce54490b075f561042eafa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc47692d5ce54490b075f561042eafa5"}}, "title": "Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells", "authors": [{"family": "Deligiannis", "given": "Spyridon Panagiotis", "initials": "SP"}, {"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2359-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a0f932253042239c1d38ea00ca0018.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "Akos", "initials": "A", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Lavogina", "given": "Darja", "initials": "D"}, {"family": "Papaikonomou", "given": "Kiriaki", "initials": "K"}, {"family": "Zubarev", "given": "Roman", "initials": "R", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Acharya", "given": "Ganesh", "initials": "G"}, {"family": "Velthut-Meikas", "given": "Agne", "initials": "A", "orcid": "0000-0003-1927-9016", "researcher": {"href": "https://publications.scilifelab.se/researcher/3371af7256714f478d42af5cf868134d.json"}}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}, {"family": "Salumets", "given": "Andres", "initials": "A", "orcid": "0000-0002-1251-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dcf4bacf5c4792bbfd111495d43595.json"}}, {"family": "Di Nisio", "given": "Valentina", "initials": "V", "orcid": "0000-0002-8435-7925", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee1509ba58840f597b7fccc778a0a20.json"}}], "type": "journal-article", "published": "2026-01-02", "journal": {"title": "J Ovarian Res", "issn": "1757-2215", "issn-l": null, "volume": "19", "issue": "1", "pages": null}, "abstract": "Radiotherapy is a cornerstone of cancer treatment; however, its effects on healthy ovarian somatic cells remain largely unexplored. This study addresses this gap by investigating how human cortical and medullary primary ovarian cells (cPOCs and mPOCs, respectively) respond to acute, high-dose X-ray exposure in vitro.\n\nOvarian tissue was obtained from eight patients (aged 23\u201336 years) undergoing gender-affirming surgery at Karolinska University Hospital in Huddinge, Sweden. The tissue was separated into cortex and medulla and dissociated into cPOCs and mPOCs. Monolayer cultures of cPOCs and mPOCs were exposed to 10 Gy X-rays upon reaching confluency, or left unexposed as paired controls. Following irradiation, cells were assessed for ATP content and mitochondrial dehydrogenase activity, followed by immunofluorescence staining, bulk RNA sequencing (Illumina Stranded mRNA Prep Ligation protocol; sequencing on the Illumina NovaSeq 6000 platform), bulk proteomic analysis (liquid chromatography\u2013tandem mass spectrometry), and a functional assay for assessing their ability to form 3D Silk-Ovarioids.\n\nWhile irradiation did not significantly affect cell viability, immunofluorescence analyses revealed alterations in DNA damage response, apoptosis, and cell cycle regulation. Transcriptomic analysis showed minimal changes at 1 h post-irradiation in both cPOCs and mPOCs. However, marked shifts in transcriptomic profiles were observed at 4 h (2,810 and 2,540 DEGs in cPOCs and mPOCs, respectively) and at 24 h (2,462 and 2,802 DEGs, respectively), including upregulation of the p53 pathway and downregulation of MYC targets, E2F targets, the G2/M checkpoint, and the mTORC1 pathway. At the proteomic level, differentially expressed proteins associated with cell adhesion, focal adhesion, and cadherin binding were detected at 24 h post-irradiation. Functionally, irradiated cells demonstrated an impaired capacity to self-organize into 3D Silk-Ovarioids, indicating compromised cell\u2013cell adhesion.\n\nThese findings reveal a novel mechanism by which radiotherapy may damage ovarian tissue independently of follicular loss, underscoring the need for targeted strategies to preserve somatic cell function in fertility preservation protocols.\n\nThe online version contains supplementary material available at 10.1186/s13048-025-01932-8.", "doi": "10.1186/s13048-025-01932-8", "pmid": "41485059", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC12930946"}, {"db": "pii", "key": "10.1186/s13048-025-01932-8"}], "notes": [], "created": "2026-01-07T10:51:06.159Z", "modified": "2026-03-24T09:15:33.835Z"}, {"entity": "publication", "iuid": "c998995ead0244f1b2aa6425b4c94d94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c998995ead0244f1b2aa6425b4c94d94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c998995ead0244f1b2aa6425b4c94d94"}}, "title": "Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting", "authors": [{"family": "Al-Radi", "given": "Omayma", "initials": "O"}, {"family": "Ingelshed", "given": "Katrine", "initials": "K"}, {"family": "Eichhorn", "given": "Lisa", "initials": "L"}, {"family": "Josefsson", "given": "Heidi", "initials": "H", "orcid": "0009-0001-0493-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba8b17ae27f45ceb95d633757087213.json"}}, {"family": "Krkoska", "given": "Martin", "initials": "M"}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Lindstr\u00f6m", "given": "Susanne", "initials": "S", "orcid": "0009-0009-7396-9529", "researcher": {"href": "https://publications.scilifelab.se/researcher/fed14c3020094d9a8ca1ace96cbbe7b2.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Kheder", "given": "Sania", "initials": "S"}, {"family": "Cerrato", "given": "Carmine P", "initials": "CP"}, {"family": "Ferm\u00e9", "given": "Suzon", "initials": "S"}, {"family": "Bosdotter", "given": "Cecilia", "initials": "C"}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications.scilifelab.se/researcher/98fffa8e99254fb597bf07dea61d8e37.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Vojtesek", "given": "Borivoj", "initials": "B"}, {"family": "Lane", "given": "David P", "initials": "DP"}, {"family": "Kannan", "given": "Pavitra", "initials": "P", "orcid": "0000-0002-9170-6062", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4f0b833cc604caf8dcff52dcbaa4fb9.json"}}], "type": "journal-article", "published": "2025-12-08", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "16", "issue": "1", "pages": "883", "issn-l": "2041-4889"}, "abstract": "The cell cycle is a key regulator of endothelial cell specification into tip and stalk cell phenotypes, which are essential for angiogenesis in both normal development and pathological conditions. While the tumor suppressor p53 is known to regulate the cell cycle and influence cell fate, its role in modulating the cell fate of these phenotypes remains unclear. Using non-genotoxic small molecule and stapled peptide compounds to pharmacologically activate p53 via MDM2 inhibition, we demonstrate that graded levels of p53 induce distinct cellular fates in normal endothelial cells. Low levels of p53 induce reversible cell cycle arrest by reducing DNA replication, while high levels induce senescence and cell death. Surprisingly, all tested levels of p53 activation reduced the growth of venous blood vessels in vitro and in zebrafish embryo models. This reduction in sprouting may stem from distinct cellular responses in tip-like and non-tip-like cells to pharmacological p53 activation: low p53 levels primarily reduced proliferation in non-tip-like cells, whereas high levels decreased the frequency of tip-like cells and the expression of genes associated with tip and stalk cell identities. Our findings show for the first time that pharmacological p53 activation modulates endothelial cell fate in a dose-dependent manner during sprouting angiogenesis. They also highlight the potential of using graded p53 modulation as a therapeutic strategy to target abnormal tip or stalk cell development in pathological angiogenesis, such as in cancer.", "doi": "10.1038/s41419-025-08292-7", "pmid": "41360924", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12698774"}, {"db": "pii", "key": "10.1038/s41419-025-08292-7"}], "notes": [], "created": "2025-12-12T12:24:13.109Z", "modified": "2026-01-09T07:55:39.395Z"}, {"entity": "publication", "iuid": "c783ffc03b364c5c97b3c8c519bf55a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c783ffc03b364c5c97b3c8c519bf55a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c783ffc03b364c5c97b3c8c519bf55a7"}}, "title": "Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility.", "authors": [{"family": "Tr\u0161eli\u010d", "given": "Tilen", "initials": "T", "orcid": "0009-0006-0316-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d50c0b7e88d4033b14afdc5ea254801.json"}}, {"family": "Pelo", "given": "Nathalie", "initials": "N"}, {"family": "Martin de Fremont", "given": "Gregoire", "initials": "G", "orcid": "0000-0003-3393-3969", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e1b9b6db64f4fdb9ab8b6eab5eb59ba.json"}}, {"family": "Iyer", "given": "Vaishnavi S", "initials": "VS"}, {"family": "Richardsdotter Andersson", "given": "Elina", "initials": "E", "orcid": "0009-0003-7008-529X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ff0a7a67ed4fdfb5135c2e33c429ab.json"}}, {"family": "Ottosson", "given": "Vijole", "initials": "V", "orcid": "0009-0003-6530-9033", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f0ee7dd68e3411db6975ec7aac67b16.json"}}, {"family": "Frei", "given": "David Alexander", "initials": "DA"}, {"family": "Baas", "given": "Elisa", "initials": "E", "orcid": "0009-0002-0587-7242", "researcher": {"href": "https://publications.scilifelab.se/researcher/a658fbfac5c74616ac5797b2330ae50a.json"}}, {"family": "Nyberg", "given": "William A", "initials": "WA"}, {"family": "Thorlacius", "given": "Gu\u00f0n\u00fd Ella", "initials": "GE"}, {"family": "Mentlein", "given": "Lara", "initials": "L"}, {"family": "Boddul", "given": "Sanjaykumar V", "initials": "SV", "orcid": "0000-0002-0711-1147", "researcher": {"href": "https://publications.scilifelab.se/researcher/312d8252d0c24f0583512c950504afa9.json"}}, {"family": "Sandu", "given": "Ioana", "initials": "I"}, {"family": "Velasquez Pulgarin", "given": "Diego", "initials": "D"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gerlach", "given": "Carmen", "initials": "C", "orcid": "0000-0001-7889-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/893fad4751a6411392488c5e37c0aa13.json"}}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Espinosa", "given": "Alexander", "initials": "A"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "40", "pages": "e2426917122", "issn-l": "0027-8424"}, "abstract": "Genetic association links disordered autoimmunity 1 (DIORA1) to numerous autoimmune rheumatic diseases, including systemic lupus erythematosus, Sj\u00f6gren's disease, rheumatoid arthritis, polymyositis, and systemic sclerosis. However, its cellular function has remained unknown. Here, we identify the Myotonic Dystrophy Kinase-Related Cdc42-Binding Kinases (MRCK kinases) family of serine/threonine kinases-key regulators of actomyosin contractility and cell motility-as direct interactors of DIORA1. Through interaction mapping, we show that DIORA1 binds three distinct modules of MRCK kinases, including the conserved kinase inhibitory motif, C1-PH, and citron homology domains. DIORA1 knockdown in human cells altered cellular phosphorylation patterns and reduced phosphorylation of known MRCK targets. RNA-sequencing and proteomic analyses revealed upregulation of epithelial-mesenchymal transition genes and proteins, and functional analyses confirmed increased cell invasion, following knockdown of DIORA1. Together, these findings identify the autoimmunity-associated DIORA1 protein as an interactor of MRCK kinases and a regulator of cell motility.", "doi": "10.1073/pnas.2426917122", "pmid": "41042840", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12519202"}], "notes": [], "created": "2025-11-21T17:57:08.724Z", "modified": "2025-11-21T17:57:09.957Z"}, {"entity": "publication", "iuid": "276f9dc9c9074208b65c0d97631c4af2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/276f9dc9c9074208b65c0d97631c4af2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/276f9dc9c9074208b65c0d97631c4af2"}}, "title": "Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data.", "authors": [{"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Chernobrovkin", "given": "Alexey L", "initials": "AL"}, {"family": "Lundstrom", "given": "Susanna L", "initials": "SL"}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/de932cbcb2c341f7a6544104026c7b1c.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b3f220ebf947779d4b2638d2ccef1c.json"}}, {"family": "Vegvari", "given": "Akos", "initials": "A", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gaetani", "given": "Massimilliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "12", "issue": "40", "pages": "e03963", "issn-l": null}, "abstract": "DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, a first approximation of the species search engine (SSE) is introduced. SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. The advantages and limitations of the proposed approach, and the possibility of extending it to other tissues is discussed.", "doi": "10.1002/advs.202503963", "pmid": "40787835", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12561455"}], "notes": [], "created": "2025-11-25T16:41:57.206Z", "modified": "2025-11-25T16:41:57.260Z"}, {"entity": "publication", "iuid": "57fc3379fa7d498cbf6dfb3d1a9a5af0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57fc3379fa7d498cbf6dfb3d1a9a5af0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57fc3379fa7d498cbf6dfb3d1a9a5af0"}}, "title": "The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.", "authors": [{"family": "Rekha", "given": "Rokeya Sultana", "initials": "RS"}, {"family": "Padhi", "given": "Avinash", "initials": "A"}, {"family": "Frengen", "given": "Nicolai", "initials": "N", "orcid": "0000-0003-1834-7638", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623.json"}}, {"family": "Hauenstein", "given": "Julia", "initials": "J", "orcid": "0000-0001-6674-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bda375874844045bd86d62d3b25e071.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Agerberth", "given": "Birgitta", "initials": "B"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}, {"family": "Gu\u00f0mundsson", "given": "Gu\u00f0mundur H", "initials": "GH"}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}], "type": "journal article", "published": "2025-01-28", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "44", "issue": "1", "pages": "115031", "issn-l": null}, "abstract": "The human cathelicidin peptide LL-37 induces autophagy in human macrophages. Different post-translational modifications (PTMs) such as citrullination, acetylation, and formylation impact LL-37, yet their effect on autophagy remains unknown. Thus, we set out to study how the cellular source could impact PTM of LL-37 and subsequent effects on autophagy initiation. Neutrophil-released LL-37 failed to induce autophagy, unlike macrophage-released LL-37. Mass spectrometry analysis revealed modifications on neutrophil-derived LL-37, especially at the N terminus, while macrophage-derived LL-37 remained mostly native. Native LL-37 initiated autophagy, while formylated and acetylated versions did not. Truncated peptides lacking the N-terminal di-leucine motif or substituted with di-alanine did not initiate autophagy. Native LL-37 failed to initiate autophagy in macrophages with genetic inactivation of dipeptidyl peptidase-1. An intact N-terminal di-leucine motif in LL-37 was crucial for autophagy initiation, and modifications abrogated the effects. This pathway presents a novel way to regulate the effects of LL-37 in infection or inflammation.", "doi": "10.1016/j.celrep.2024.115031", "pmid": "39708316", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(24)01382-2"}], "notes": [], "created": "2025-02-28T14:11:56.119Z", "modified": "2025-11-28T10:42:15.993Z"}, {"entity": "publication", "iuid": "ac19adf0d3404aa687ad8a49eb00c6fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac19adf0d3404aa687ad8a49eb00c6fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac19adf0d3404aa687ad8a49eb00c6fe"}}, "title": "Network analysis reveals age- and virus-specific circuits in nasal epithelial cells of extremely premature infants.", "authors": [{"family": "Wisgrill", "given": "Lukas", "initials": "L", "orcid": "0000-0001-9833-9499", "researcher": {"href": "https://publications.scilifelab.se/researcher/32c01d645e1946f4a7174c8f8878d54d.json"}}, {"family": "Martens", "given": "Anke", "initials": "A", "orcid": "0000-0001-5774-5650", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff034529539a47eeb0548c5ceff5a365.json"}}, {"family": "Kasbauer", "given": "Rajmund", "initials": "R"}, {"family": "Eigenschink", "given": "Michael", "initials": "M", "orcid": "0000-0001-6469-5014", "researcher": {"href": "https://publications.scilifelab.se/researcher/937c22ecea85475fb8dde2b2ca8aa883.json"}}, {"family": "Pummer", "given": "Linda", "initials": "L"}, {"family": "Redlberger-Fritz", "given": "Monika", "initials": "M", "orcid": "0000-0001-6265-557X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a23b5e0c68f4633acae557350ba6a53.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Warth", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-6104-0706", "researcher": {"href": "https://publications.scilifelab.se/researcher/51d385ac37f442a5b1fb8fe64ce23dbb.json"}}, {"family": "Berger", "given": "Angelika", "initials": "A", "orcid": "0000-0001-6876-5497", "researcher": {"href": "https://publications.scilifelab.se/researcher/e108926b03184a55aa8a187af987c8ee.json"}}, {"family": "Fyhrquist", "given": "Nanna", "initials": "N", "orcid": "0000-0002-5408-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/b072b498b2014b12930d1fa1dbb3f30a.json"}}, {"family": "Alenius", "given": "Harri", "initials": "H", "orcid": "0000-0003-0106-8923", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f88b2c54fe044a1b76ed7107677c11a.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Allergy", "issn": "1398-9995", "volume": "79", "issue": "11", "pages": "3062-3081", "issn-l": "0105-4538"}, "abstract": "Viral respiratory infections significantly affect young children, particularly extremely premature infants, resulting in high hospitalization rates and increased health-care burdens. Nasal epithelial cells, the primary defense against respiratory infections, are vital for understanding nasal immune responses and serve as a promising target for uncovering underlying molecular and cellular mechanisms.\n\nUsing a trans-well pseudostratified nasal epithelial cell system, we examined age-dependent developmental differences and antiviral responses to influenza A and respiratory syncytial virus through systems biology approaches.\n\nOur studies revealed differences in innate-receptor repertoires, distinct developmental pathways, and differentially connected antiviral network circuits between neonatal and adult nasal epithelial cells. Consensus network analysis identified unique and shared cellular-viral networks, emphasizing highly relevant virus-specific pathways, independent of viral replication kinetics.\n\nThis research highlights the importance of nasal epithelial cells in innate antiviral immune responses and offers crucial insights that allow for a deeper understanding of age-related differences in nasal epithelial cell immunity following respiratory virus infections.", "doi": "10.1111/all.16196", "pmid": "38898695", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-25T10:26:43.233Z", "modified": "2025-02-28T14:20:05.193Z"}, {"entity": "publication", "iuid": "7469a2b8bd88408a99fdf9074d6dce9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7469a2b8bd88408a99fdf9074d6dce9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7469a2b8bd88408a99fdf9074d6dce9e"}}, "title": "Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates.", "authors": [{"family": "Meng", "given": "Zhaowei", "initials": "Z"}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Zhang", "given": "Xuepei", "initials": "X"}, {"family": "Lyu", "given": "Hezheng", "initials": "H"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2024-08-20", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "96", "issue": "33", "pages": "13533-13541", "issn-l": "0003-2700"}, "abstract": "Here, we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics and demonstrates its utility in studying proteolytic events in programmed cell death. With gel-assisted proteome position integral shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 84 proteins exhibiting in a statistically significant manner at least two of the following features: (i) a negative MW shift; (ii) an elevated ratio in a pair of a semitryptic and tryptic peptide, (iii) a negative shift in the standard deviation of MW estimated for different peptides, and (iv) a negative shift in skewness of the same data. Of these proteins, 58 molecules were previously unreported caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, the GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.", "doi": "10.1021/acs.analchem.4c02051", "pmid": "39110629", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2024-08-21T16:03:52.664Z", "modified": "2024-08-21T16:03:52.890Z"}, {"entity": "publication", "iuid": "b2cb8fa709924974859cd7b23995e51b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2cb8fa709924974859cd7b23995e51b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2cb8fa709924974859cd7b23995e51b"}}, "title": "Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.", "authors": [{"family": "ElBeck", "given": "Zaher", "initials": "Z", "orcid": "0000-0002-2073-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abd18865bda4f53a1521974e6f9e46b.json"}}, {"family": "Hossain", "given": "Mohammad Bakhtiar", "initials": "MB", "orcid": "0000-0002-4251-1912", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7e91850afd945dfb91a396d843194f4.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Lindgren", "given": "Julia", "initials": "J", "orcid": "0000-0002-3566-2069", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3c465ab67924de69b7248e3acff0978.json"}}, {"family": "Walentinsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-8100-6866", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f835d5cb84de6ad619c50d81d5dd1.json"}}, {"family": "Koppenh\u00f6fer", "given": "Dominique", "initials": "D", "orcid": "0000-0001-5807-9645", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ab61b179f940a8853619f5a817e06a.json"}}, {"family": "Jarvis", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-7583-6548", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bfea4b88ef64bebbcdf8839e4428864.json"}}, {"family": "B\u00fcrli", "given": "Roland", "initials": "R"}, {"family": "Jamier", "given": "Tanguy", "initials": "T", "orcid": "0000-0003-3014-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/eab91541aeb24d9face573899b25b19c.json"}}, {"family": "Franssen", "given": "Elske", "initials": "E"}, {"family": "Firth", "given": "Mike", "initials": "M"}, {"family": "Degasperi", "given": "Andrea", "initials": "A", "orcid": "0000-0001-6879-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/c074b0dc07bb4b779a4c20e190854594.json"}}, {"family": "Bendtsen", "given": "Claus", "initials": "C", "orcid": "0000-0002-8338-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21acfbf749d4f1ca0a8be226d4696ce.json"}}, {"family": "Menzies", "given": "Robert I", "initials": "RI"}, {"family": "Streckfuss-B\u00f6meke", "given": "Katrin", "initials": "K"}, {"family": "Kohlhaas", "given": "Michael", "initials": "M"}, {"family": "Nickel", "given": "Alexander G", "initials": "AG"}, {"family": "Lund", "given": "Lars H", "initials": "LH"}, {"family": "Maack", "given": "Christoph", "initials": "C", "orcid": "0000-0003-3694-4559", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3dedbf152c4f24847d6d83b15ed1c3.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a00cfe9d521047f280978d84d7dcf1b3.json"}}], "type": "journal article", "published": "2024-03-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "2358"}, "abstract": "While excessive production of reactive oxygen species (ROS) is a characteristic hallmark of numerous diseases, clinical approaches that ameliorate oxidative stress have been unsuccessful. Here, utilizing multi-omics, we demonstrate that in cardiomyocytes, mitochondrial isocitrate dehydrogenase (IDH2) constitutes a major antioxidative defense mechanism. Paradoxically reduced expression of IDH2 associated with ventricular eccentric hypertrophy is counterbalanced by an increase in the enzyme activity. We unveil redox-dependent sex dimorphism, and extensive mutual regulation of the antioxidative activities of IDH2 and NRF2 by a feedforward network that involves 2-oxoglutarate and L-2-hydroxyglutarate and mediated in part through unconventional hydroxy-methylation of cytosine residues present in introns. Consequently, conditional targeting of ROS in a murine model of heart failure improves cardiac function in sex- and phenotype-dependent manners. Together, these insights may explain why previous attempts to treat heart failure with antioxidants have been unsuccessful and open new approaches to personalizing and, thereby, improving such treatment.", "doi": "10.1038/s41467-024-46384-8", "pmid": "38509128", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10954618"}, {"db": "pii", "key": "10.1038/s41467-024-46384-8"}], "notes": [], "created": "2024-03-21T08:13:07.086Z", "modified": "2024-11-13T10:25:41.474Z"}, {"entity": "publication", "iuid": "6978cc74d9584c42a41d0f3bb5c79dea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6978cc74d9584c42a41d0f3bb5c79dea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6978cc74d9584c42a41d0f3bb5c79dea"}}, "title": "Mapping the GALNT1 substrate landscape with versatile proteomics tools", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL", "orcid": "0000-0003-2363-4287", "researcher": {"href": "https://publications.scilifelab.se/researcher/916e190e150e465c9e6afc11911bae04.json"}}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/de932cbcb2c341f7a6544104026c7b1c.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Lu", "given": "Weiqi", "initials": "W"}, {"family": "Fang", "given": "Pan", "initials": "P"}, {"family": "Zhang", "given": "Xuepei", "initials": "X"}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b3f220ebf947779d4b2638d2ccef1c.json"}}, {"family": "Wang", "given": "Jijing", "initials": "J"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gygi", "given": "Steven P", "initials": "SP", "orcid": "0000-0001-7626-0034", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7237a4242ad47d795a1a2741f32071f.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "posted-content", "published": "2022-08-24", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.08.24.505189", "pmid": null, "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-11-29T20:07:08.693Z", "modified": "2025-12-18T18:23:30.185Z"}, {"entity": "publication", "iuid": "3faa49c2fd47420e8ad82ec59836faea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3faa49c2fd47420e8ad82ec59836faea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3faa49c2fd47420e8ad82ec59836faea"}}, "title": "Hepatocyte Thorns, A Novel Drug-Induced Stress Response in Human and Mouse Liver Spheroids.", "authors": [{"family": "Pridgeon", "given": "Chris S", "initials": "CS", "orcid": "0000-0003-4414-8544", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef4e848f8a82437792fcd073268388c7.json"}}, {"family": "Bolhuis", "given": "Dian P", "initials": "DP", "orcid": "0000-0003-3862-8621", "researcher": {"href": "https://publications.scilifelab.se/researcher/18f838548b224467af8a0b6e1527002e.json"}}, {"family": "Milosavljevi\u0107", "given": "Filip", "initials": "F"}, {"family": "Manojlovi\u0107", "given": "Marina", "initials": "M"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M"}, {"family": "Juki\u0107", "given": "Marin M", "initials": "MM"}, {"family": "Ingelman-Sundberg", "given": "Magnus", "initials": "M", "orcid": "0000-0002-7255-9079", "researcher": {"href": "https://publications.scilifelab.se/researcher/3095e3b59e4b4f5bb2b74332b4423ab3.json"}}], "type": "journal article", "published": "2022-05-10", "journal": {"title": "Cells", "issn": "2073-4409", "issn-l": "2073-4409", "volume": "11", "issue": "10", "pages": null}, "abstract": "The in vivo-relevant phenotype of 3D liver spheroids allows for long-term studies of, e.g., novel mechanisms of chronic drug-induced liver toxicity. Using this system, we present a novel drug-induced stress response in human and murine hepatocyte spheroids, wherein long slender filaments form after chronic treatment with four different drugs, of which three are PPAR\u03b1 antagonists. The morphology of the thorns varies between donors and the compounds used. They are mainly composed of diverse protein fibres, which are glycosylated. Their formation is inhibited by treatment with fatty acids or antioxidants. Treatment of mice with GW6471 revealed changes in gene and protein expression, such as those in the spheroids. In addition, similar changes in keratin expression were seen following the treatment of hepatotoxic drugs, including aflatoxin B1, paracetamol, chlorpromazine, cyclosporine, and ketoconazole. We suggest that thorn formation may be indicative of hepatocyte metaplasia in response to toxicity and that more focus should be placed on alterations of ECM-derived protein expression as biomarkers of liver disease and chronic drug-induced hepatotoxicity, changes that can be studied in stable in vivo-like hepatic cell systems, such as the spheroids.", "doi": "10.3390/cells11101597", "pmid": "35626634", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "cells11101597"}, {"db": "pmc", "key": "PMC9139950"}], "notes": [], "created": "2022-06-05T20:29:22.197Z", "modified": "2024-01-18T23:31:39.077Z"}, {"entity": "publication", "iuid": "c70668b3d6344353b5fea94523f88e89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c70668b3d6344353b5fea94523f88e89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c70668b3d6344353b5fea94523f88e89"}}, "title": "Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals.", "authors": [{"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S", "orcid": "0000-0002-1086-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3e88a57db14fe0b99dd7b6286f0b81.json"}}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "J\u00fctte", "given": "Bianca B", "initials": "BB"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}, {"family": "Rodriguez", "given": "Jimmy Esneider", "initials": "JE", "orcid": "0000-0002-6735-3332", "researcher": {"href": "https://publications.scilifelab.se/researcher/48d26949ce194599889ee9fb2a819f2d.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Svensson", "given": "J Peter", "initials": "JP", "orcid": "0000-0002-5863-6250", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c226ba652024fdabbbf9203e1edb5d1.json"}}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2022-04-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "357", "issn-l": "2399-3642"}, "abstract": "HIV-1 infection induces a chronic inflammatory environment not restored by suppressive antiretroviral therapy (ART). As of today, the effect of viral suppression and immune reconstitution in people living with HIV-1 (PLWH) has been well described but not completely understood. Herein, we show how PLWH who naturally control the virus (PLWHEC) have a reduced proportion of CD4+CCR6+ and CD8+CCR6+ cells compared to PLWH on suppressive ART (PLWHART) and HIV-1 negative controls (HC). Expression of CCR2 was reduced on both CD4+, CD8+ and classical monocytes in PLWHEC compared to PLWHART and HC. Longer suppressive therapy, measured in the same patients, decreased number of cells expressing CCR2 on all monocytic cell populations while expression on CD8+ T cells increased. Furthermore, the CD4+CCR6+/CCR6- cells exhibited a unique proteomic profile with a modulated energy metabolism in PLWHEC compared to PLWHART independent of CCR6 status. The CD4+CCR6+ cells also showed an enrichment in proteins involved in apoptosis and p53 signalling in PLWHEC compared to PLWHART, indicative of increased sensitivity towards cell death mechanisms. Collectively, this data shows how PLWHEC have a unique chemokine receptor profile that may aid in facilitating natural control of HIV-1 infection.", "doi": "10.1038/s42003-022-03315-x", "pmid": "35418589", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9008025"}, {"db": "pii", "key": "10.1038/s42003-022-03315-x"}], "notes": [], "created": "2022-12-02T08:49:45.869Z", "modified": "2022-12-02T08:49:45.999Z"}, {"entity": "publication", "iuid": "2b5a77cf1023482b9a4307217fcfb0aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b5a77cf1023482b9a4307217fcfb0aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b5a77cf1023482b9a4307217fcfb0aa"}}, "title": "Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection.", "authors": [{"family": "Mikaeloff", "given": "Flora", "initials": "F"}, {"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S", "orcid": "0000-0002-1086-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3e88a57db14fe0b99dd7b6286f0b81.json"}}, {"family": "Ikomey", "given": "George Mondinde", "initials": "GM"}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "Gupta", "given": "Soham", "initials": "S", "orcid": "0000-0003-1136-3010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bbd430437164ba38676d7b94e2189ab.json"}}, {"family": "Magdaleno", "given": "Gustavo Daniel Vega", "initials": "GDV"}, {"family": "Esc\u00f3s", "given": "Alejandra", "initials": "A", "orcid": "0000-0002-2990-7920", "researcher": {"href": "https://publications.scilifelab.se/researcher/7344a932be1649418f7de419efe98bd3.json"}}, {"family": "Lyonga", "given": "Emilia", "initials": "E"}, {"family": "Okomo", "given": "Marie Claire", "initials": "MC"}, {"family": "Tagne", "given": "Claude Tayou", "initials": "CT"}, {"family": "Babu", "given": "Hemalatha", "initials": "H"}, {"family": "Lorson", "given": "Christian L", "initials": "CL"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Banerjea", "given": "Akhil C", "initials": "AC"}, {"family": "Kele", "given": "Julianna", "initials": "J"}, {"family": "Hanna", "given": "Luke Elizabeth", "initials": "LE"}, {"family": "Singh", "given": "Kamal", "initials": "K", "orcid": "0000-0001-6153-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ce44cd68d68429195bd05741b1a01ac.json"}}, {"family": "de Magalh\u00e3es", "given": "Jo\u00e3o Pedro", "initials": "JP", "orcid": "0000-0002-6363-2465", "researcher": {"href": "https://publications.scilifelab.se/researcher/2008de4aab5e4559891581b28d1b7163.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "27", "issn-l": "2399-3642"}, "abstract": "Despite successful combination antiretroviral therapy (cART), persistent low-grade immune activation together with inflammation and toxic antiretroviral drugs can lead to long-lasting metabolic flexibility and adaptation in people living with HIV (PLWH). Our study investigated alterations in the plasma metabolic profiles by comparing PLWH on long-term cART(>5 years) and matched HIV-negative controls (HC) in two cohorts from low- and middle-income countries (LMIC), Cameroon, and India, respectively, to understand the system-level dysregulation in HIV-infection. Using untargeted and targeted LC-MS/MS-based metabolic profiling and applying advanced system biology methods, an altered amino acid metabolism, more specifically to glutaminolysis in PLWH than HC were reported. A significantly lower level of neurosteroids was observed in both cohorts and could potentiate neurological impairments in PLWH. Further, modulation of cellular glutaminolysis promoted increased cell death and latency reversal in pre-monocytic HIV-1 latent cell model U1, which may be essential for the clearance of the inducible reservoir in HIV-integrated cells.", "doi": "10.1038/s42003-021-02985-3", "pmid": "35017663", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8752762"}, {"db": "pii", "key": "10.1038/s42003-021-02985-3"}], "notes": [], "created": "2022-12-05T08:10:43.650Z", "modified": "2025-10-17T13:03:15.416Z"}, {"entity": "publication", "iuid": "34c177a6bf874180a7803c15a79588ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c177a6bf874180a7803c15a79588ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c177a6bf874180a7803c15a79588ae"}}, "title": "System-wide identification and prioritization of enzyme substrates by thermal analysis.", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Beusch", "given": "Christian M", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/278e50b11a3c4ef69b6e2708f99b5f3e.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a75556311084e2b827ab1f646d7a16c.json"}}, {"family": "Wells", "given": "Juan Astorga", "initials": "JA", "orcid": "0000-0003-1017-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/14530d9aa03747858976b4889e959fe5.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85179acfa7e4916ad40ae478d6dcc0a.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z"}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36b29dc4fd44785b36b9baa9e291757.json"}}, {"family": "Rodin", "given": "Sergey", "initials": "S"}, {"family": "N\u00e4reoja", "given": "Katja", "initials": "K"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "A"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Cheng", "given": "Qing", "initials": "Q"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Arn\u00e9r", "given": "Elias S J", "initials": "ESJ", "orcid": "0000-0002-4807-6114", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a545effced47da8a5192a7472ceb8f.json"}}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H", "orcid": "0000-0003-4059-3501", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49b25ddfc934f3ca41020c3f38c6bfc.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2021-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "1296"}, "abstract": "Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.", "doi": "10.1038/s41467-021-21540-6", "pmid": "33637753", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21540-6"}, {"db": "pmc", "key": "PMC7910609"}], "notes": [], "created": "2020-01-23T10:41:17.194Z", "modified": "2021-12-09T09:37:12.987Z"}, {"entity": "publication", "iuid": "131283b276484c18b504aa4dc0115f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19"}}, "title": "The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.", "authors": [{"family": "Schober", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Moore", "given": "David", "initials": "D"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Moedas", "given": "Marco F", "initials": "MF", "orcid": "0000-0001-5461-0320", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a9cd9caaa014f4280544a243520e18c.json"}}, {"family": "Clemente", "given": "Paula", "initials": "P"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Fissi", "given": "Najla El", "initials": "NE", "orcid": "0000-0002-6631-4630", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec87cba920947028856aadb5892f7a6.json"}}, {"family": "Filograna", "given": "Roberta", "initials": "R"}, {"family": "Bucher", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0002-9391-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec4467fb36b44f0a0b1dfa056ec964d.json"}}, {"family": "Hinze", "given": "Yvonne", "initials": "Y", "orcid": "0000-0002-2966-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/a922a71f2fde43908945980353ed595a.json"}}, {"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e90cde879dc41eaade439bcf951a646.json"}}, {"family": "Hedman", "given": "Erik", "initials": "E", "orcid": "0000-0003-4017-9749", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffc752d50a6649248c6809ea5aec803d.json"}}, {"family": "Chernogubova", "given": "Ekaterina", "initials": "E"}, {"family": "Begzati", "given": "Arjana", "initials": "A", "orcid": "0000-0002-8770-8022", "researcher": {"href": "https://publications.scilifelab.se/researcher/a15af0dbd68445538bd92c89f6d901df.json"}}, {"family": "Wibom", "given": "Rolf", "initials": "R", "orcid": "0000-0001-6721-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d5fc666ef84a8784d8b28ecf233146.json"}}, {"family": "Jain", "given": "Mohit", "initials": "M"}, {"family": "Nilsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-6020-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c6d082934d818445fe0187dbb23e.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C", "orcid": "0000-0003-0418-1673", "researcher": {"href": "https://publications.scilifelab.se/researcher/888298d25fb94acca7639063d3592373.json"}}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "8", "issn-l": "2375-2548"}, "abstract": "Induction of the one-carbon cycle is an early hallmark of mitochondrial dysfunction and cancer metabolism. Vital intermediary steps are localized to mitochondria, but it remains unclear how one-carbon availability connects to mitochondrial function. Here, we show that the one-carbon metabolite and methyl group donor S-adenosylmethionine (SAM) is pivotal for energy metabolism. A gradual decline in mitochondrial SAM (mitoSAM) causes hierarchical defects in fly and mouse, comprising loss of mitoSAM-dependent metabolites and impaired assembly of the oxidative phosphorylation system. Complex I stability and iron-sulfur cluster biosynthesis are directly controlled by mitoSAM levels, while other protein targets are predominantly methylated outside of the organelle before import. The mitoSAM pool follows its cytosolic production, establishing mitochondria as responsive receivers of one-carbon units. Thus, we demonstrate that cellular methylation potential is required for energy metabolism, with direct relevance for pathophysiology, aging, and cancer.", "doi": "10.1126/sciadv.abf0717", "pmid": "33608280", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/8/eabf0717"}, {"db": "pmc", "key": "PMC7895438"}], "notes": [], "created": "2021-12-06T13:45:25.780Z", "modified": "2024-01-16T13:48:40.799Z"}, {"entity": "publication", "iuid": "0db4269a42a5414c862b6766046b6288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0db4269a42a5414c862b6766046b6288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0db4269a42a5414c862b6766046b6288"}}, "title": "ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1694ffdcd94a55b6c172a854706e0f.json"}}, {"family": "Beusch", "given": "Christian Michel", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/278e50b11a3c4ef69b6e2708f99b5f3e.json"}}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36b29dc4fd44785b36b9baa9e291757.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a75556311084e2b827ab1f646d7a16c.json"}}, {"family": "Zhang", "given": "Bo", "initials": "B", "orcid": "0000-0001-8890-8416", "researcher": {"href": "https://publications.scilifelab.se/researcher/79097385e3ea4496bb498c981302b344.json"}}, {"family": "Tokat", "given": "\u00dclk\u00fc G\u00fcler", "initials": "\u00dcG"}, {"family": "Stergiou", "given": "Eleni", "initials": "E", "orcid": "0000-0001-9115-4985", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ff5335a69db40848ec6131d4735da18.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal-article", "published": "2019-12-00", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "10", "issue": "1", "pages": "5715"}, "abstract": "Deconvolution of targets and action mechanisms of anticancer compounds is fundamental in drug development. Here, we report on ProTargetMiner as a publicly available expandable proteome signature library of anticancer molecules in cancer cell lines. Based on 287 A549 adenocarcinoma proteomes affected by 56 compounds, the main dataset contains 7,328 proteins and 1,307,859 refined protein-drug pairs. These proteomic signatures cluster by compound targets and action mechanisms. The targets and mechanistic proteins are deconvoluted by partial least square modeling, provided through the website http://protargetminer.genexplain.com. For 9 molecules representing the most diverse mechanisms and the common cancer cell lines MCF-7, RKO and A549, deep proteome datasets are obtained. Combining data from the three cell lines highlights common drug targets and cell-specific differences. The database can be easily extended and merged with new compound signatures. ProTargetMiner serves as a chemical proteomics resource for the cancer research community, and can become a valuable tool in drug discovery.", "doi": "10.1038/s41467-019-13582-8", "pmid": "31844049", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13582-8"}, {"db": "pmc", "key": "PMC6915695"}], "notes": [], "created": "2019-01-10T14:09:06.234Z", "modified": "2021-06-21T14:06:27.659Z"}]}