{"entity": "researcher", "timestamp": "2026-08-15T07:15:06.010Z", "family": "Frengen", "given": "Nicolai", "initials": "N", "orcid": "0000-0003-1834-7638", "affiliations": ["Karolinska Institutet, Huddinge, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623"}}, "publications": [{"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": "8e627a82e39d4c059ca3d5e9ae6a57d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e627a82e39d4c059ca3d5e9ae6a57d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e627a82e39d4c059ca3d5e9ae6a57d8"}}, "title": "Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.", "authors": [{"family": "Pe\u00f1a-P\u00e9rez", "given": "Luc\u00eda", "initials": "L", "orcid": "0000-0002-5044-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/111f8a8c4c6d4d2ea60e5fc76831b7fa.json"}}, {"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": "Gran", "given": "Charlotte", "initials": "C"}, {"family": "Gustafsson", "given": "Charlotte", "initials": "C"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F", "orcid": "0000-0001-7198-5116", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a3bc9c440024ec994e534c3a6627f55.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Wallblom", "given": "Ann", "initials": "A"}, {"family": "Krstic", "given": "Aleksandra", "initials": "A"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}], "type": "journal article", "published": "2022-09-13", "journal": {"title": "Blood Adv", "issn": "2473-9537", "issn-l": "2473-9529", "volume": "6", "issue": "17", "pages": "5009-5023"}, "abstract": "Multiple myeloma (MM) is an incurable and aggressive plasma cell malignancy characterized by a complex karyotype with multiple structural variants (SVs) and copy-number variations (CNVs). Linked-read whole-genome sequencing (lrWGS) allows for refined detection and reconstruction of SVs by providing long-range genetic information from standard short-read sequencing. This makes lrWGS an attractive solution for capturing the full genomic complexity of MM. Here we show that high-quality lrWGS data can be generated from low numbers of cells subjected to fluorescence-activated cell sorting (FACS) without DNA purification. Using this protocol, we analyzed MM cells after FACS from 37 patients with MM using lrWGS. We found high concordance between lrWGS and fluorescence in situ hybridization (FISH) for the detection of recurrent translocations and CNVs. Outside of the regions investigated by FISH, we identified >150 additional SVs and CNVs across the cohort. Analysis of the lrWGS data allowed for resolution of the structure of diverse SVs affecting the MYC and t(11;14) loci, causing the duplication of genes and gene regulatory elements. In addition, we identified private SVs causing the dysregulation of genes recurrently involved in translocations with the IGH locus and show that these can alter the molecular classification of MM. Overall, we conclude that lrWGS allows for the detection of aberrations critical for MM prognostics and provides a feasible route for providing comprehensive genetics. Implementing lrWGS could provide more accurate clinical prognostics, facilitate genomic medicine initiatives, and greatly improve the stratification of patients included in clinical trials.", "doi": "10.1182/bloodadvances.2021006720", "pmid": "35675515", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9631623"}, {"db": "pii", "key": "485485"}], "notes": [], "created": "2022-08-19T08:37:59.788Z", "modified": "2024-01-16T13:48:35.011Z"}]}