{"entity": "researcher", "timestamp": "2026-08-15T06:57:41.525Z", "family": "Rendo", "given": "Veronica", "initials": "V", "orcid": "0000-0002-2983-4020", "affiliations": ["Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden.", "Dana-Farber Cancer Institute, 450 Brookline Ave, 02115, Boston, MA, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7"}}, "publications": [{"entity": "publication", "iuid": "48838c48da18481db8283614f606bee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48838c48da18481db8283614f606bee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48838c48da18481db8283614f606bee7"}}, "title": "Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening.", "authors": [{"family": "Gezelius", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6242-6344", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad329767af94f9f9ad2c96771ff01d9.json"}}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP", "orcid": "0000-0001-6505-4198", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51093d7e7b14d5d859502c535117aad.json"}}, {"family": "Lundmark", "given": "Anders", "initials": "A", "orcid": "0000-0003-2611-1772", "researcher": {"href": "https://publications.scilifelab.se/researcher/52d2e64456104adcba388414d4197a35.json"}}, {"family": "\u00c5berg", "given": "Martin", "initials": "M"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Rudfeldt", "given": "Jakob", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Harila", "given": "Arja", "initials": "A", "orcid": "0000-0003-2767-5828", "researcher": {"href": "https://publications.scilifelab.se/researcher/440e4d697787402283eded5995b706b7.json"}}, {"family": "Rendo", "given": "Ver\u00f3nica", "initials": "V", "orcid": "0000-0002-2983-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0003-0071-6802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f47bcb3a6ec94202afc945a9f02984da.json"}}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "NAR Genom Bioinform", "issn": "2631-9268", "issn-l": null, "volume": "6", "issue": "1", "pages": "lqae001"}, "abstract": "Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.", "doi": "10.1093/nargab/lqae001", "pmid": "38288374", "labels": {"NGI Short read": "Technology development", "NGI Single cell": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10823582"}, {"db": "pii", "key": "lqae001"}], "notes": [], "created": "2024-02-27T08:22:26.710Z", "modified": "2024-11-25T10:25:20.383Z"}, {"entity": "publication", "iuid": "d18a2001ca2a484ea1267aaed4906d19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d18a2001ca2a484ea1267aaed4906d19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d18a2001ca2a484ea1267aaed4906d19"}}, "title": "Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy.", "authors": [{"family": "Rendo", "given": "Veronica", "initials": "V", "orcid": "0000-0002-2983-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/d79942eca68f4b2d8c2e72cf258f1213.json"}}, {"family": "Sj\u00f6berg", "given": "Elin", "initials": "E"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Ng", "given": "Adrian", "initials": "A"}, {"family": "O\u02bcBrien", "given": "Casey", "initials": "C", "orcid": "0000-0002-6572-4881", "researcher": {"href": "https://publications.scilifelab.se/researcher/5782c9d8ce674fe8ad55eba0d514da54.json"}}, {"family": "Giannakis", "given": "Marios", "initials": "M"}, {"family": "Artursson", "given": "Per", "initials": "P", "orcid": "0000-0002-3708-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/31575936c2714e1eb2f35c12df9a65a8.json"}}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Cheong", "given": "Ian", "initials": "I"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}], "type": "journal article", "published": "2020-03-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "1308"}, "abstract": "Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. To find exploitable targets, we map prevalent genetic polymorphisms to protein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalytic sites of 17 enzymes frequently lost in cancer. For proof of concept, we select the gastrointestinal drug metabolic enzyme NAT2 at 8p22, which is frequently lost in colorectal cancers and has a common variant with 10-fold reduced activity. Small molecule screening results in a cytotoxic kinase inhibitor that impairs growth of cells with slow NAT2 and decreases the growth of tumors with slow NAT2 by half as compared to those with wild-type NAT2. Most of the patient-derived CRC cells expressing slow NAT2 also show sensitivity to 6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes.", "doi": "10.1038/s41467-020-15111-4", "pmid": "32161261", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15111-4"}, {"db": "pmc", "key": "PMC7066191"}], "notes": [], "created": "2020-03-17T11:11:47.766Z", "modified": "2025-10-17T13:05:08.058Z"}]}