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Nilsson, Mats
Alternative names
Publications (10 of 100) Show all publications
Schuette, M., Risch, T., Abdavi-Azar, N., Boehnke, K., Schumacher, D., Keil, M., . . . Yaspo, M.-L. (2017). Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors. Nature Communications, 8, Article ID 14262.
Open this publication in new window or tab >>Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors
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2017 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 14262Article in journal (Refereed) Published
Abstract [en]

Colorectal carcinoma represents a heterogeneous entity, with only a fraction of the tumours responding to available therapies, requiring a better molecular understanding of the disease in precision oncology. To address this challenge, the OncoTrack consortium recruited 106 CRC patients (stages I-IV) and developed a pre-clinical platform generating a compendium of drug sensitivity data totalling 44,000 assays testing 16 clinical drugs on patient-derived in vivo and in vitro models. This large biobank of 106 tumours, 35 organoids and 59 xenografts, with extensive omics data comparing donor tumours and derived models provides a resource for advancing our understanding of CRC. Models recapitulate many of the genetic and transcriptomic features of the donors, but defined less complex molecular sub-groups because of the loss of human stroma. Linking molecular profiles with drug sensitivity patterns identifies novel biomarkers, including a signature outperforming RAS/RAF mutations in predicting sensitivity to the EGFR inhibitor cetuximab.

National Category
Cancer and Oncology Genetics
Identifiers
urn:nbn:se:uu:diva-316929 (URN)10.1038/ncomms14262 (DOI)000393656400001 ()28186126 (PubMedID)
Funder
Swedish Research CouncilVINNOVAEU, European Research Council
Available from: 2017-03-09 Created: 2017-03-09 Last updated: 2017-11-29Bibliographically approved
Kühnemund, M., Hernandez-Neuta, I., Sharif, M. I., Cornaglia, M., Gijs, M. A. M. & Nilsson, M. (2017). Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules. Nucleic Acids Research, 45(8), Article ID e59.
Open this publication in new window or tab >>Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules
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2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 8, article id e59Article in journal (Refereed) Published
Abstract [en]

Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1.2 aM to 190 fM. We prove the broad applicability of our analysis platform by demonstrating 5-plex detection of as little as similar to 1 pg (similar to 300 genome copies) of pathogenic DNA with simultaneous antibiotic resistance marker detection, and the analysis of rare oncogene mutations. Our method is simpler, more cost-effective and faster than other digital analysis techniques and provides the means to implement digital analysis in any laboratory equipped with a standard fluorescent microscope.

National Category
Biochemistry and Molecular Biology Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-322522 (URN)10.1093/nar/gkw1324 (DOI)000400578600004 ()28077562 (PubMedID)
Funder
EU, FP7, Seventh Framework Programme, 264737Swedish Foundation for Strategic Research , SBE13-0125Swedish Research CouncilSwedish Research Council Formas, 221-2011-1692EU, Horizon 2020, 115843
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2017-05-23 Created: 2017-05-23 Last updated: 2018-01-13Bibliographically approved
Kühnemund, M., Wei, Q., Darai, E., Wang, Y., Hernandez-Neuta, I., Yang, Z., . . . Nilsson, M. (2017). Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy. Nature Communications, 8, Article ID 13913.
Open this publication in new window or tab >>Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy
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2017 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 13913Article in journal (Refereed) Published
Abstract [en]

Molecular diagnostics is typically outsourced to well-equipped centralized laboratories, often far from the patient. We developed molecular assays and portable optical imaging designs that permit on-site diagnostics with a cost-effective mobile-phone-based multimodal microscope. We demonstrate that targeted next-generation DNA sequencing reactions and in situ point mutation detection assays in preserved tumour samples can be imaged and analysed using mobile phone microscopy, achieving a new milestone for tele-medicine technologies.

National Category
Biomedical Laboratory Science/Technology
Identifiers
urn:nbn:se:uu:diva-315810 (URN)10.1038/ncomms13913 (DOI)000391931300001 ()28094784 (PubMedID)
Funder
Swedish Research CouncilSwedish Cancer Society, 2015/838 2015/629Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-11-29Bibliographically approved
Carinelli, S., Kühnemund, M., Nilsson, M. & Pividori, M. I. (2017). Yoctomole electrochemical genosensing of Ebola virus cDNA by rolling circle and circle to circle amplification. Paper presented at 26th Anniversary World Congress on Biosensors (Biosensors), MAY 24-28, 2016, Gothenburg, SWEDEN. Biosensors & bioelectronics, 93, 65-71
Open this publication in new window or tab >>Yoctomole electrochemical genosensing of Ebola virus cDNA by rolling circle and circle to circle amplification
2017 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 93, p. 65-71Article in journal (Refereed) Published
Abstract [en]

This work addresses the design of an Ebola diagnostic test involving a simple, rapid, specific and highly sensitive procedure based on isothermal amplification on magnetic particles with electrochemical readout. Ebola padlock probes were designed to detect a specific L-gene sequence present in the five most common Ebola species. Ebola cDNA was amplified by rolling circle amplification (RCA) on magnetic particles. Further re-amplification was performed by circle-to-circle amplification (C2CA) and the products were detected in a double-tagging approach using a biotinylated capture probe for immobilization on magnetic particles and a readout probe for electrochemical detection by square-wave voltammetry on commercial screen-printed electrodes. The electrochemical genosensor was able to detect as low as 200 ymol, corresponding to 120 cDNA molecules of L-gene Ebola virus with a limit of detection of 33 cDNA molecules. The isothermal double-amplification procedure by C2CA combined with the electrochemical readout and the magnetic actuation enables the high sensitivity, resulting in a rapid, inexpensive, robust and user-friendly sensing strategy that offers a promising approach for the primary care in low resource settings, especially in less developed countries.

Keyword
Ebola virus, Electrochemical genosensing, Magnetic particle, Isothermal amplification, Circle-to-circle amplification
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:uu:diva-322442 (URN)10.1016/j.bios.2016.09.099 (DOI)000399259000011 ()27838201 (PubMedID)
Conference
26th Anniversary World Congress on Biosensors (Biosensors), MAY 24-28, 2016, Gothenburg, SWEDEN
Available from: 2017-05-23 Created: 2017-05-23 Last updated: 2017-05-23Bibliographically approved
McGinn, S., Bauer, D., Brefort, T., Dong, L., El-Sagheer, A., Elsharawy, A., . . . Gut, I. G. (2016). New technologies for DNA analysis: a review of the READNA Project. New Biotechnology, 33(3), 311-330
Open this publication in new window or tab >>New technologies for DNA analysis: a review of the READNA Project
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2016 (English)In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, no 3, p. 311-330Article, review/survey (Refereed) Published
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-279724 (URN)10.1016/j.nbt.2015.10.003 (DOI)000373545600001 ()26514324 (PubMedID)
Funder
EU, European Research Council, HEALTH-F4-2008-201418
Available from: 2015-10-26 Created: 2016-03-03 Last updated: 2017-11-30Bibliographically approved
Kuhnemund, M. & Nilsson, M. (2015). Digital quantification of rolling circle amplified single DNA molecules in a resistive pulse sensing nanopore. Biosensors & bioelectronics, 67(SI), 11-17
Open this publication in new window or tab >>Digital quantification of rolling circle amplified single DNA molecules in a resistive pulse sensing nanopore
2015 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 67, no SI, p. 11-17Article in journal (Refereed) Published
Abstract [en]

Novel portable, sensitive and selective DNA sensor methods for bio-sensing applications are required that can rival conventionally used non-portable and expensive fluorescence-based sensors. In this paper, rolling circle amplification (RCA) products are detected in solution and on magnetic particles using a resistive pulse sensing (RPS) nanopore. Low amounts of DNA molecules are detected by padlock probes which are circularized in a strictly target dependent ligation reaction. The DNA-padlock probe-complex is captured on magnetic particles by sequence specific capture oligonucleotides and amplified by a short RCA. Subsequent RPS analysis is used to identify individual particles with single attached RCA products from blank particles. This proof of concept opens up for a novel non-fluorescent digital DNA quantification method that can have many applications in bio-sensing and diagnostic approaches.

Keyword
Padlock probe, RCA, Single molecule detection, Resistive pulse sensing, Nanopore
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-248795 (URN)10.1016/j.bios.2014.06.040 (DOI)000350076900003 ()25000851 (PubMedID)
Available from: 2015-04-10 Created: 2015-04-08 Last updated: 2017-12-04Bibliographically approved
Russell, C., Roy, S., Ganguly, S., Qian, X., Caruthers, M. H. & Nilsson, M. (2015). Formation of Silver Nanostructures by Rolling Circle Amplification Using Boranephosphonate-Modified Nucleotides. Analytical Chemistry, 87(13), 6660-6666
Open this publication in new window or tab >>Formation of Silver Nanostructures by Rolling Circle Amplification Using Boranephosphonate-Modified Nucleotides
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2015 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 87, no 13, p. 6660-6666Article in journal (Refereed) Published
Abstract [en]

We investigate the efficiency of incorporation of boranephosphonate-modified nucleotides by phi29 DNA poly, merase and present a simple method for forming large defined silver nanostructures by rolling circle amplification (RCA) using boranephosphonate internudeotide linkages. RCA is a linear DNA amplification technique that can use specifically circularized DNA probes for detection of target nucleic acids and proteins. The resulting product is a collapsed single-stranded DNA molecule with tandem repeats of the DNA probe. By substituting each of the natural nucleotides with the corresponding 5'-(alpha-P-borano)-deoxynudeosidetriphosphate, only a small reduction in amplification rate is observed. Also, by substituting all four natural nucleotides, it is possible to enzymatically synthesize a micrometensized, single-stranded DNA molecule with only boranephosphonate internucleotide linkages. Well-defined silver particles are then readily formed along the rolling circle product.

National Category
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-260302 (URN)10.1021/acs.analchem.5b00783 (DOI)000357839700037 ()26059318 (PubMedID)
Funder
VINNOVASwedish Research Council
Available from: 2015-08-20 Created: 2015-08-18 Last updated: 2017-12-04Bibliographically approved
Mansouri, L., Sutton, L.-A., Ljungström, V., Bondza, S., Arngården, L., Bhoi, S., . . . Rosenquist Brandell, R. (2015). Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia. Journal of Experimental Medicine, 212(6), 833-843
Open this publication in new window or tab >>Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
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2015 (English)In: Journal of Experimental Medicine, ISSN 0022-1007, E-ISSN 1540-9538, Vol. 212, no 6, p. 833-843Article in journal (Refereed) Published
Abstract [en]

NF-κB is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-κB pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7%), which encodes IκBε, a negative regulator of NF-κB in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced IκBε protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that IκBε loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-κB deregulation during lymphomagenesis.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-279237 (URN)10.1084/jem.20142009 (DOI)000355569300001 ()25987724 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), b2011080Swedish Cancer SocietySwedish Research CouncilNIH (National Institute of Health), CA81554; CA081554EU, European Research Council, 259796EU, FP7, Seventh Framework Programme, 306242
Available from: 2016-02-29 Created: 2016-02-29 Last updated: 2018-01-10Bibliographically approved
Moens, L. N. J., Falk-Sörqvist, E., Ljungström, V., Mattsson, J., Sundström, M., La Fleur, L., . . . Botling, J. (2015). HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples. Journal of Molecular Diagnostics, 17(6), 729-739
Open this publication in new window or tab >>HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples
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2015 (English)In: Journal of Molecular Diagnostics, ISSN 1525-1578, E-ISSN 1943-7811, Vol. 17, no 6, p. 729-739Article in journal (Refereed) Published
Abstract [en]

In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomotecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment Length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and Lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.

National Category
Clinical Medicine Immunology in the medical area
Identifiers
urn:nbn:se:uu:diva-269252 (URN)10.1016/j.jmoldx.2015.06.009 (DOI)000363830000013 ()26354930 (PubMedID)
Available from: 2015-12-17 Created: 2015-12-15 Last updated: 2018-02-01Bibliographically approved
Lundin, K. E., Hamasy, A., Backe, P. H., Moens, L. N., Falk-Sörqvist, E., Elgstoen, K. B., . . . Smith, C. I. (2015). Susceptibility to infections, without concomitant hyper-IgE, reported in 1976, is caused by hypomorphic mutation in the phosphoglucomutase 3 (PGM3) gene. Clinical Immunology, 161(2), 366-372
Open this publication in new window or tab >>Susceptibility to infections, without concomitant hyper-IgE, reported in 1976, is caused by hypomorphic mutation in the phosphoglucomutase 3 (PGM3) gene
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2015 (English)In: Clinical Immunology, ISSN 1521-6616, E-ISSN 1521-7035, Vol. 161, no 2, p. 366-372Article in journal (Refereed) Published
Abstract [en]

Phosphoglucomutase 3 (PGM3) is an enzyme converting N-acetyl-glucosamine-6-phosphate to N-acetylglucosamine-l-phosphate, a precursor important for glycosylation. Mutations in the PGM3 gene have recently been identified as the cause of novel primary immunodeficiency with a hyper-IgE like syndrome. Here we report the occurrence of a homozygous mutation in the PGM3 gene in a family with immunodeficient children, described already in 1976. DNA from two of the immunodeficient siblings was sequenced and shown to encode the same homozygous missense mutation, causing a destabilized protein with reduced enzymatic capacity. Affected individuals were highly prone to infections, but lack the developmental defects in the nervous and skeletal systems, reported in other families. Moreover, normal IgE levels were found. Thus, belonging to the expanding group of congenital glycosylation defects, PGM3 deficiency is characterized by immunodeficiency, with or without increased IgE levels, and with variable forms of developmental defects affecting other organ systems.

Keyword
Primary immunodeficiency, N-acetylglucosamine-phosphate mutase hyper-IgE syndrome, Congenital defects of glycosylation, CDG
National Category
Immunology in the medical area
Identifiers
urn:nbn:se:uu:diva-270937 (URN)10.1016/j.clim.2015.10.002 (DOI)000365831600042 ()26482871 (PubMedID)
Funder
EU, FP7, Seventh Framework ProgrammeSwedish Research CouncilStockholm County Council
Available from: 2016-01-05 Created: 2016-01-05 Last updated: 2018-01-10Bibliographically approved
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