{"entity": "researcher", "timestamp": "2026-08-11T14:12:00.953Z", "family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "affiliations": ["3P-Medicine Laboratory, Medical University of Gda\u0144sk, D\u0119binki 7, 80-211, Gda\u0144sk, Poland."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca"}}, "publications": [{"entity": "publication", "iuid": "7de26605147e4edb8845e6c78bddd3aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de26605147e4edb8845e6c78bddd3aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de26605147e4edb8845e6c78bddd3aa"}}, "title": "DNA methylation patterns contribute to changes of cellular differentiation pathways in leukocytes with LOY from patients with Alzheimer\u00b4s disease.", "authors": [{"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B", "orcid": "0000-0003-2141-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa96509bbe94834858aee3c16d41b97.json"}}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Siedlar", "given": "Maciej", "initials": "M"}, {"family": "Baran", "given": "Jaros\u0142aw", "initials": "J"}, {"family": "W\u0119glarczyk", "given": "Kazimierz", "initials": "K"}, {"family": "Jaszczynski", "given": "Janusz", "initials": "J"}, {"family": "Ry\u015b", "given": "Janusz", "initials": "J"}, {"family": "Gedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Filipowicz", "given": "Natalia", "initials": "N"}, {"family": "Klich-R\u0105czka", "given": "Alicja", "initials": "A"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Cell. Mol. Life Sci.", "issn": "1420-9071", "volume": "82", "issue": "1", "pages": "93", "issn-l": "1420-682X"}, "abstract": "Alzheimer's disease (AD) is a common and increasing societal problem due to the extending human lifespan. In males, loss of chromosome Y (LOY) in leukocytes is strongly associated with AD. We studied here DNA methylation and RNA expression in sorted monocytes and granulocytes with and without LOY from male AD patients. Through multi-omic analysis, we identified new candidate genes along with those previously associated with AD. Global analyses of DNA methylation in samples with LOY vs. normal state showed that hypomethylation dominated both in granulocytes and monocytes. Our findings highlight LOY-related differences in DNA methylation that occur in gene regulatory regions. Specifically, we observed alterations in key genes involved in leukocyte differentiation: FLI1, involved in early hematopoiesis; RUNX1, essential for blood cell development; RARA, regulating gene expression in response to retinoic acid; CANX, crucial for protein folding; CEBPB, a transcription factor important for immune responses; and MYADM, implicated in cell adhesion and migration. Moreover, protein-protein interaction analysis in granulocytes identified that products of two of these genes, CANX and CEBPB, are key hub proteins. This research underscores the potential of multi-omic approach in pure hematopoietic cell populations to uncover the molecular underpinnings of AD. Finally, our results link previous analysis showing impact of LOY on leukocyte differentiation, LOY-associated transcriptional dysregulation and GWAS studies of LOY.", "doi": "10.1007/s00018-025-05618-8", "pmid": "39998604", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11861481"}, {"db": "pii", "key": "10.1007/s00018-025-05618-8"}], "notes": [], "created": "2025-09-08T06:57:22.526Z", "modified": "2025-09-08T07:12:23.743Z"}, {"entity": "publication", "iuid": "d7727b44644f4a45bf2e7b3843b07b3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7727b44644f4a45bf2e7b3843b07b3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7727b44644f4a45bf2e7b3843b07b3d"}}, "title": "Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium.", "authors": [{"family": "Sta\u0144kowska", "given": "Wiktoria", "initials": "W"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B"}, {"family": "Duzowska", "given": "Katarzyna", "initials": "K"}, {"family": "Bie\u0144kowski", "given": "Micha\u0142", "initials": "M", "orcid": "0000-0002-9291-3928", "researcher": {"href": "https://publications.scilifelab.se/researcher/8227f94ec50e481fa45e9bec035b6708.json"}}, {"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "W\u00f3jcik-Zalewska", "given": "Magdalena", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Dr\u0119\u017cek-Chy\u0142a", "given": "Kinga", "initials": "K", "orcid": "0009-0007-1008-7145", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dbc662c14754a468de99e24a60cedf2.json"}}, {"family": "P\u0119ksa", "given": "Rafa\u0142", "initials": "R", "orcid": "0000-0002-4904-7059", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dd33f6e4a9a49d6af2265bc91b77d4e.json"}}, {"family": "Harazin-Lechowska", "given": "Agnieszka", "initials": "A"}, {"family": "Ambicka", "given": "Aleksandra", "initials": "A"}, {"family": "Przewo\u017anik", "given": "Marcin", "initials": "M"}, {"family": "Adamczyk", "given": "Agnieszka", "initials": "A"}, {"family": "Sasim", "given": "Karol", "initials": "K"}, {"family": "Makarewicz", "given": "Wojciech", "initials": "W"}, {"family": "Matuszewski", "given": "Marcin", "initials": "M"}, {"family": "Biernat", "given": "Wojciech", "initials": "W"}, {"family": "J\u00e4rhult", "given": "Josef D", "initials": "JD", "orcid": "0000-0002-7075-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/2598129f86ee47ebafc696148f9da01f.json"}}, {"family": "Lipcsey", "given": "Mikl\u00f3s", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Jaszczy\u0144ski", "given": "Janusz", "initials": "J"}, {"family": "Ry\u015b", "given": "Janusz", "initials": "J"}, {"family": "Genovese", "given": "Giulio", "initials": "G"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}, {"family": "Filipowicz", "given": "Natalia", "initials": "N", "orcid": "0000-0002-9673-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/153a4d73f8cb4ec68cedfd85556e383e.json"}}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "16", "issue": "5", "issn-l": "2072-6694"}, "abstract": "Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.", "doi": "10.3390/cancers16050961", "pmid": "38473323", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10930680"}, {"db": "pii", "key": "cancers16050961"}], "notes": [], "created": "2024-03-21T08:55:56.265Z", "modified": "2024-03-21T08:55:57.016Z"}, {"entity": "publication", "iuid": "be695a433fa7423e9418d12e55b4d672", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be695a433fa7423e9418d12e55b4d672.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be695a433fa7423e9418d12e55b4d672"}}, "title": "Loss of Y in leukocytes as a risk factor for critical COVID-19 in men", "authors": [{"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B", "orcid": "0000-0003-2141-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa96509bbe94834858aee3c16d41b97.json"}}, {"family": "Davies", "given": "Hanna", "initials": "H", "orcid": "0000-0002-6289-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d800ab99360483d8bd12ba4b386a4a4.json"}}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D", "orcid": "0000-0002-2451-4386", "researcher": {"href": "https://publications.scilifelab.se/researcher/44fdd52fbf5d420396c87a31addea920.json"}}, {"family": "Juhas", "given": "Ulana", "initials": "U", "orcid": "0000-0001-8393-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c9b9c7ba943d6836633f8bd5003bd.json"}}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E", "orcid": "0000-0001-8050-2489", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b253253073749839c443de3003ecb89.json"}}, {"family": "W\u00f3jcik", "given": "Magdalena", "initials": "M", "orcid": "0000-0001-5475-8448", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbf367a185b347c6a9bf6b6f2adfe6e5.json"}}, {"family": "Horbacz", "given": "Monika", "initials": "M", "orcid": "0000-0003-1644-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c7f6d571214ca9a6940293c3dbc6c1.json"}}, {"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P", "orcid": "0000-0002-2788-5254", "researcher": {"href": "https://publications.scilifelab.se/researcher/214b8864edb24164a1c9af68396603b9.json"}}, {"family": "Westholm", "given": "Jakub O", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Wierzba", "given": "Karol", "initials": "K", "orcid": "0000-0003-1257-4047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddedb819ee5d4e33b0382e87e7369dec.json"}}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Jern", "given": "Niklas", "initials": "N"}, {"family": "Andersson", "given": "Lars Magnus", "initials": "LM", "orcid": "0000-0002-9203-5969", "researcher": {"href": "https://publications.scilifelab.se/researcher/da6e24cc65a14537ad30353de972cd5f.json"}}, {"family": "J\u00e4rhult", "given": "Josef D", "initials": "JD", "orcid": "0000-0002-7075-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/2598129f86ee47ebafc696148f9da01f.json"}}, {"family": "Filipowicz", "given": "Natalia", "initials": "N", "orcid": "0000-0002-9673-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/153a4d73f8cb4ec68cedfd85556e383e.json"}}, {"family": "Tiensuu Janson", "given": "Eva", "initials": "E", "orcid": "0000-0002-1649-4880", "researcher": {"href": "https://publications.scilifelab.se/researcher/3838152188ee4e2580d139757ecd8df8.json"}}, {"family": "Rubertsson", "given": "Sten", "initials": "S"}, {"family": "Lipcsey", "given": "Mikl\u00f3s", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-2357-1020", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b50df8c8ecc45b89574dc76e244b07e.json"}}, {"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}], "type": "journal-article", "published": "2022-12-14", "journal": {"title": "Genome Med", "issn": "1756-994X", "issn-l": "1756-994X", "volume": "14", "issue": "1", "pages": "139"}, "abstract": "The COVID-19 pandemic, which has a prominent social and economic impact worldwide, shows a largely unexplained male bias for the severity and mortality of the disease. Loss of chromosome Y (LOY) is a risk factor candidate in COVID-19 due to its prior association with many chronic age-related diseases, and its impact on immune gene transcription.\n\nPublicly available scRNA-seq data of PBMC samples derived from male patients critically ill with COVID-19 were reanalyzed, and LOY status was added to the annotated cells. We further studied LOY in whole blood for 211 COVID-19 patients treated at intensive care units (ICU) from the first and second waves of the pandemic. Of these, 139 patients were subject to cell sorting for LOY analysis in granulocytes, low-density neutrophils (LDNs), monocytes, and PBMCs.\n\nReanalysis of available scRNA-seq data revealed LDNs and monocytes as the cell types most affected by LOY. Subsequently, DNA analysis indicated that 46%, 32%, and 29% of critically ill patients showed LOY above 5% cut-off in LDNs, granulocytes, and monocytes, respectively. Hence, the myeloid lineage that is crucial for the development of severe COVID-19 phenotype is affected by LOY. Moreover, LOY correlated with increasing WHO score (median difference 1.59%, 95% HDI 0.46% to 2.71%, p=0.025), death during ICU treatment (median difference 1.46%, 95% HDI 0.47% to 2.43%, p=0.0036), and history of vessel disease (median difference 2.16%, 95% HDI 0.74% to 3.7%, p=0.004), among other variables. In 16 recovered patients, sampled during ICU stay and 93-143 days later, LOY decreased significantly in whole blood and PBMCs. Furthermore, the number of LDNs at the recovery stage decreased dramatically (median difference 76.4 per 10,000 cell sorting events, 95% HDI 55.5 to 104, p=6e-11).\n\nWe present a link between LOY and an acute, life-threatening infectious disease. Furthermore, this study highlights LOY as the most prominent clonal mutation affecting the myeloid cell lineage during emergency myelopoiesis. The correlation between LOY level and COVID-19 severity might suggest that this mutation affects the functions of monocytes and neutrophils, which could have consequences for male innate immunity.", "doi": "10.1186/s13073-022-01144-5", "pmid": "36514076", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9747543"}, {"db": "pii", "key": "10.1186/s13073-022-01144-5"}], "notes": [], "created": "2022-12-20T08:30:45.356Z", "modified": "2023-06-19T09:07:39.861Z"}]}