{"entity": "researcher", "timestamp": "2026-07-13T10:17:09.169Z", "family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "affiliations": ["Bioinformatics, Department of Physics, Chemistry and Biology, Link\u00f6ping University, Link\u00f6ping, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2"}}, "publications": [{"entity": "publication", "iuid": "c1686601bc6b4c808ba31fbb6c6d93d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1686601bc6b4c808ba31fbb6c6d93d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1686601bc6b4c808ba31fbb6c6d93d3"}}, "title": "A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis.", "authors": [{"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Giordano", "given": "Antonino", "initials": "A"}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C", "orcid": "0000-0002-9088-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ead2e8f98754d1586891eda5adb9e1a.json"}}, {"family": "Venkata S Badam", "given": "Tejaswi", "initials": "T"}, {"family": "Samudyata", "given": "Samudyata", "initials": "S"}, {"family": "Lem\u00e9e", "given": "Marianne Victoria", "initials": "MV", "orcid": "0000-0002-4897-0722", "researcher": {"href": "https://publications.scilifelab.se/researcher/361e3a91dc5245e587309759769414c8.json"}}, {"family": "Stridh", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-4855-0039", "researcher": {"href": "https://publications.scilifelab.se/researcher/613e86be4685423093de57bb83be261b.json"}}, {"family": "Gkogka", "given": "Asimenia", "initials": "A"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Harroud", "given": "Adil", "initials": "A", "orcid": "0000-0003-2616-7274", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a769f610fb430e89258c1c30cbd23b.json"}}, {"family": "Gyllenberg", "given": "Alexandra", "initials": "A"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Boddul", "given": "Sanjaykumar", "initials": "S"}, {"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Sorosina", "given": "Melissa", "initials": "M"}, {"family": "Filippi", "given": "Massimo", "initials": "M", "orcid": "0000-0002-5485-0479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8878f32c07334124b8e3bce42c94c076.json"}}, {"family": "Esposito", "given": "Federica", "initials": "F"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}, {"family": "Casaccia", "given": "Patrizia", "initials": "P", "orcid": "0000-0002-4785-9264", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62a7dde40bd454e9072ff43fff8a2ea.json"}}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Sellgren", "given": "Carl M", "initials": "CM", "orcid": "0000-0001-9103-2785", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c0740ddfd6d4c98988b2a19096a9814.json"}}, {"family": "Golzio", "given": "Christelle", "initials": "C"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}], "type": "journal article", "published": "2024-07-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6419", "issn-l": "2041-1723"}, "abstract": "Multiple Sclerosis (MS) is a heterogeneous inflammatory and neurodegenerative disease with an unpredictable course towards progressive disability. Treating progressive MS is challenging due to limited insights into the underlying mechanisms. We examined the molecular changes associated with primary progressive MS (PPMS) using a cross-tissue (blood and post-mortem brain) and multilayered data (genetic, epigenetic, transcriptomic) from independent cohorts. In PPMS, we found hypermethylation of the 1q21.1 locus, controlled by PPMS-specific genetic variations and influencing the expression of proximal genes (CHD1L, PRKAB2) in the brain. Evidence from reporter assay and CRISPR/dCas9 experiments supports a causal link between methylation and expression and correlation network analysis further implicates these genes in PPMS brain processes. Knock-down of CHD1L in human iPSC-derived neurons and knock-out of chd1l in zebrafish led to developmental and functional deficits of neurons. Thus, several lines of evidence suggest a distinct genetic-epigenetic-transcriptional interplay in the 1q21.1 locus potentially contributing to PPMS pathogenesis.", "doi": "10.1038/s41467-024-50794-z", "pmid": "39079955", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11289459"}, {"db": "pii", "key": "10.1038/s41467-024-50794-z"}], "notes": [], "created": "2024-08-15T12:14:24.965Z", "modified": "2024-11-25T10:17:37.116Z"}, {"entity": "publication", "iuid": "df5638c2c3d442cd861fa36a108950d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df5638c2c3d442cd861fa36a108950d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df5638c2c3d442cd861fa36a108950d6"}}, "title": "Proteomics reveal biomarkers for diagnosis, disease activity and long-term disability outcomes in multiple sclerosis.", "authors": [{"family": "\u00c5kesson", "given": "Julia", "initials": "J", "orcid": "0000-0002-9276-0546", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba1adc3a1e614b87808e3b1b5d4d9cb1.json"}}, {"family": "Hojjati", "given": "Sara", "initials": "S"}, {"family": "Hellberg", "given": "Sandra", "initials": "S"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J", "orcid": "0000-0001-8871-2560", "researcher": {"href": "https://publications.scilifelab.se/researcher/604da06820f542ef84b97cf0e4641e2c.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Rynkowski", "given": "Robert", "initials": "R"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Altafini", "given": "Claudio", "initials": "C", "orcid": "0000-0003-4142-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/397523f1994046fdb4c462d5127e4c1d.json"}}, {"family": "Lubovac-Pilav", "given": "Zelmina", "initials": "Z", "orcid": "0000-0001-6427-0315", "researcher": {"href": "https://publications.scilifelab.se/researcher/af98c65fa2964875bd6d46f9c2488e6b.json"}}, {"family": "Mellerg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-0120-3734", "researcher": {"href": "https://publications.scilifelab.se/researcher/f471bdcfc7fc4c2fb282484ac7e148bd.json"}}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC", "orcid": "0000-0002-2117-5366", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf1f485192744e0c95ccecdb5471b577.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Ernerudh", "given": "Jan", "initials": "J", "orcid": "0000-0001-9456-2044", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc016a1ad2b14e91b97b65d5aaae7f59.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}], "type": "journal article", "published": "2023-10-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6903", "issn-l": "2041-1723"}, "abstract": "Sensitive and reliable protein biomarkers are needed to predict disease trajectory and personalize treatment strategies for multiple sclerosis (MS). Here, we use the highly sensitive proximity-extension assay combined with next-generation sequencing (Olink Explore) to quantify 1463 proteins in cerebrospinal fluid (CSF) and plasma from 143 people with early-stage MS and 43 healthy controls. With longitudinally followed discovery and replication cohorts, we identify CSF proteins that consistently predicted both short- and long-term disease progression. Lower levels of neurofilament light chain (NfL) in CSF is superior in predicting the absence of disease activity two years after sampling (replication AUC = 0.77) compared to all other tested proteins. Importantly, we also identify a combination of 11 CSF proteins (CXCL13, LTA, FCN2, ICAM3, LY9, SLAMF7, TYMP, CHI3L1, FYB1, TNFRSF1B and NfL) that predict the severity of disability worsening according to the normalized age-related MS severity score (replication AUC = 0.90). The identification of these proteins may help elucidate pathogenetic processes and might aid decisions on treatment strategies for persons with MS.", "doi": "10.1038/s41467-023-42682-9", "pmid": "37903821", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10616092"}, {"db": "pii", "key": "10.1038/s41467-023-42682-9"}], "notes": [], "created": "2023-11-23T07:26:00.330Z", "modified": "2023-11-29T18:44:34.331Z"}, {"entity": "publication", "iuid": "be6dfc07d42b41648f42432ddcda8787", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be6dfc07d42b41648f42432ddcda8787.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be6dfc07d42b41648f42432ddcda8787"}}, "title": "Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.", "authors": [{"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "Badam", "given": "Tejaswi Venkata Satya", "initials": "TVS", "orcid": "0000-0002-6719-4861", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e4b28972942434fba0d715354352267.json"}}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H", "orcid": "0000-0001-5797-7873", "researcher": {"href": "https://publications.scilifelab.se/researcher/020d1b7e7693495484dc85c4ba6f2adc.json"}}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}, {"family": "Lubovac-Pilav", "given": "Zelmina", "initials": "Z", "orcid": "0000-0001-6427-0315", "researcher": {"href": "https://publications.scilifelab.se/researcher/af98c65fa2964875bd6d46f9c2488e6b.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-08-24", "journal": {"title": "npj Syst Biol Appl", "issn": "2056-7189", "volume": "6", "issue": "1", "pages": "25", "issn-l": "2056-7189"}, "abstract": "Gemcitabine/carboplatin chemotherapy commonly induces myelosuppression, including neutropenia, leukopenia, and thrombocytopenia. Predicting patients at risk of these adverse drug reactions (ADRs) and adjusting treatments accordingly is a long-term goal of personalized medicine. This study used whole-genome sequencing (WGS) of blood samples from 96 gemcitabine/carboplatin-treated non-small cell lung cancer (NSCLC) patients and gene network modules for predicting myelosuppression. Association of genetic variants in PLINK found 4594, 5019, and 5066 autosomal SNVs/INDELs with p \u2264 1 \u00d7 10-3 for neutropenia, leukopenia, and thrombocytopenia, respectively. Based on the SNVs/INDELs we identified the toxicity module, consisting of 215 unique overlapping genes inferred from MCODE-generated gene network modules of 350, 345, and 313 genes, respectively. These module genes showed enrichment for differentially expressed genes in rat bone marrow, human bone marrow, and human cell lines exposed to carboplatin and gemcitabine (p < 0.05). Then using 80% of the patients as training data, random LASSO reduced the number of SNVs/INDELs in the toxicity module into a feasible prediction model consisting of 62 SNVs/INDELs that accurately predict both the training and the test (remaining 20%) data with high (CTCAE 3-4) and low (CTCAE 0-1) maximal myelosuppressive toxicity completely, with the receiver-operating characteristic (ROC) area under the curve (AUC) of 100%. The present study shows how WGS, gene network modules, and random LASSO can be used to develop a feasible and tested model for predicting myelosuppressive toxicity. Although the proposed model predicts myelosuppression in this study, further evaluation in other studies is required to determine its reproducibility, usability, and clinical effect.", "doi": "10.1038/s41540-020-00146-6", "pmid": "32839457", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41540-020-00146-6"}, {"db": "pmc", "key": "PMC7445166"}], "notes": [], "created": "2020-12-07T16:27:04.771Z", "modified": "2024-01-16T13:48:41.889Z"}]}