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| 2. |
- Arthur, Cecilia, et al.
(författare)
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Simultaneous Ultra-Sensitive Detection of Structural and Single Nucleotide Variants Using Multiplex Droplet Digital PCR in Liquid Biopsies from Children with Medulloblastoma
- 2023
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Ingår i: Cancers. - : MDPI. - 2072-6694. ; 15:7
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Tidskriftsartikel (refereegranskat)abstract
- Medulloblastoma is one of the most common types of brain tumors in children. During and after treatment with surgery, chemotherapy, and/or radiotherapy, children with this disease are monitored with imaging and cerebrospinal fluid analysis for the detection of tumor cells. These methods are not always sensitive or specific enough to confirm or rule out residual disease. Here, we develop a laboratory test based on the genetic makeup of medulloblastomas in 12 children. We analyze liquid biopsies (cerebrospinal fluid and blood plasma) for specific genetic fragments leaking from the individual tumors and find molecular traces of disease in 75% (9/12) of children overall. None of the children had malignant cells in the cerebrospinal fluid. We propose that this test could open up new technical possibilities to track measurable residual disease in children with medulloblastoma in order to further risk-adapt treatment, but first, larger studies of the approach at standardized time points are warranted.Medulloblastoma is a malignant embryonal tumor of the central nervous system (CNS) that mainly affects infants and children. Prognosis is highly variable, and molecular biomarkers for measurable residual disease (MRD) detection are lacking. Analysis of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) using broad genomic approaches, such as low-coverage whole-genome sequencing, has shown promising prognostic value. However, more sensitive methods are needed for MRD analysis. Here, we show the technical feasibility of capturing medulloblastoma-associated structural variants and point mutations simultaneously in cfDNA using multiplexed droplet digital PCR (ddPCR). Assay sensitivity was assessed with a dilution series of tumor in normal genomic DNA, and the limit of detection was below 100 pg of input DNA for all assays. False positive rates were zero for structural variant assays. Liquid biopsies (CSF and plasma, n = 47) were analyzed from 12 children with medulloblastoma, all with negative CSF cytology. MRD was detected in 75% (9/12) of patients overall. In CSF samples taken before or within 21 days of surgery, MRD was detected in 88% (7/8) of patients with localized disease and in one patient with the metastasized disease. Our results suggest that this approach could expand the utility of ddPCR and complement broader analyses of cfDNA for MRD detection.
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| 3. |
- Krynina, Olha, et al.
(författare)
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The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma
- 2024
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Ingår i: Neuro-Oncology Advances. - : Oxford University Press. - 2632-2498. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundLow-grade gliomas (LGGs) represent children’s most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples.MethodsWe examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants.ResultsOur findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9 ng).ConclusionsWhile CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.
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| 4. |
- Yamada, Takashi, et al.
(författare)
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Nitrosative modifications of the Ca2+ release complex and actin underlie arthritis-induced muscle weakness.
- 2015
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 74:10, s. 1907-1914
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Tidskriftsartikel (refereegranskat)abstract
- Skeletal muscle weakness is a prominent clinical feature in patients with rheumatoid arthritis (RA), but the underlying mechanism(s) is unknown. Here we investigate the mechanisms behind arthritis-induced skeletal muscle weakness with special focus on the role of nitrosative stress on intracellular Ca(2+) handling and specific force production.
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| 5. |
- Arthur, Cecilia
(författare)
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Liquid biopsies in pediatric oncology : towards clinical implementation
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- During the last few years, liquid biopsies based on cell-free DNA (cfDNA) have become approved for clinical use in several areas of adult oncology. Due to the minimally invasive nature of this procedure, liquid biopsies could serve many purposes in childhood oncology as well. For instance, the method can provide highly specific biomarkers for molecular diagnostics, enable identification therapeutic targets and, more frequently, be used to assess therapeutic response or disease recurrence. This information could aid clinical decision-making in tailoring treatment and follow-up for each individual patient. However, developing customized assays for children's cancers is demanding for several reasons. First, childhood cancer is rare compared to adult cancers, making it difficult to get the numbers needed for statistically powered studies. Second, children’s cancers generally have few and often private mutations, and display a different mutational landscape than adult counterparts, meaning that generic assays are very challenging to develop. Third, small children mean small liquid biopsy volumes and high risk for subsampling errors, demanding ultrasensitive techniques for disease detection. Due to these circumstances, liquid biopsy assays for children with cancer require some innovative strategies. In this thesis, we describe a few liquid biopsy pilot studies focusing on the two main groups of childhood cancers; acute lymphoblastic leukemia and central nervous system (CNS) tumors. In paper I, we use whole genome sequencing to identify structural variants (SVs) in leukemic cells and use the resulting unique sequences as targets for patient-specific droplet digital PCR (ddPCR) assays. Based on analysis of samples from six children, we show that it is technically feasible to use this approach to accurately quantify measurable residual disease in bone marrow as well as in cfDNA from plasma. The molecular assays also enabled detection of potential low-grade CNSinvolvement in half of patients at diagnosis. In paper II, we use a similar approach analyzing samples from 12 children with medulloblastoma, this time combining single nucleotide variants and SVs in our assays. We show that post-operatively, all tumors that grew in contact with cerebrospinal fluid (CSF) prior to resection, and where imaging supported or could not rule out residual tumor after surgery, molecular signs of the disease were seen in liquid biopsies on at least one occasion within three weeks of surgery. Furthermore, most plasma samples at diagnosis also bore molecular signs of the tumors. In paper III, we analyze cfDNA in CSF from a child with an inoperable brainstem tumor for BRAF V600E/K/R mutations. After confirmation of a BRAF mutation, molecular targeted therapy was initiated with dramatic clinical response during the first nine months of treatment. In paper IV, we used multiomics data to seek a molecular diagnosis for a child born with a large CNS tumor. The data revealed a rare type of glioma, most likely caused by a novel fusion gene; SNRNP70::ALK. Molecular targeted therapy was initiated and four months into treatment, there are clinical and radiological signs of treatment effect. Taken together, the results indicate that our approach to design molecular assays could expand the utility of ddPCR for liquid biopsy analysis. Furthermore, in clinically challenging cases, multiomics can resolve complex diagnoses and liquid biopsies can guide choice of treatment. These studies are the initial efforts of our research group to promote liquid biopsies as a powerful precision diagnostic tool in pediatric oncology. Apart from the 20 patients described in these studies, another 130 children have been included for research and a liquid biopsy biobank of >1800 samples has been established. We have also set up clinical liquid biopsy analysis for BRAF V600 and H3-3A K27M mutations during this period. This was achieved through a close collaboration between the Departments of Clinical Genetics, Pediatric Oncology, Pediatric Neurosurgery, Clinical Pathology and The Swedish Childhood Tumor Biobank.
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| 6. |
- Arthur, Cecilia, et al.
(författare)
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Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia : A Proof of Concept Study
- 2022
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Ingår i: Frontiers in Oncology. - : Frontiers Media S.A.. - 2234-943X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Risk-adapted treatment in acute lymphoblastic leukemia (ALL) relies on genetic information and measurable residual disease (MRD) monitoring. In this proof of concept study, DNA from diagnostic bone marrow (BM) of six children with ALL, without stratifying genetics or central nervous system (CNS) involvement, underwent whole-genome sequencing (WGS) to identify structural variants (SVs) in the leukemic blasts. Unique sequences generated by SVs were targeted with patient-specific droplet digital PCR (ddPCR) assays. Genomic DNA (gDNA) from BM and cell-free DNA (cfDNA) from plasma and cerebrospinal fluid (CSF) were analyzed longitudinally. WGS with 30x coverage enabled target identification in all cases. Limit of quantifiability (LoQ) and limit of detection (LoD) for the ddPCR assays (n = 15) were up to 10(-5) and 10(-6), respectively. All targets were readily detectable in a multiplexed ddPCR with minimal DNA input (1 ng of gDNA) at a 10(-1) dilution, and targets for half of the patients were also detectable at a 10(-2) dilution. The level of MRD in BM at end of induction and end of consolidation block 1 was in a comparable range between ddPCR and clinical routine methods for samples with detectable residual disease, although our approach consistently detected higher MRD values for patients with B-cell precursor ALL. Additionally, several samples with undetectable MRD by flow cytometry were MRD-positive by ddPCR. In plasma, the level of leukemic targets decreased in cfDNA over time following the MRD level detected in BM. cfDNA was successfully extracted from all diagnostic CSF samples (n = 6), and leukemic targets were detected in half of these. The results suggest that our approach to design molecular assays, together with ddPCR quantification, is a technically feasible option for accurate MRD quantification and that cfDNA may contribute valuable information regarding MRD and low-grade CNS involvement.
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| 7. |
- Avila, Harold C., et al.
(författare)
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High hole-mobility of rrP3HT in organic field-effect transistors using low-polarity polyurethane gate dielectric
- 2018
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Ingår i: Organic electronics. - : ELSEVIER SCIENCE BV. - 1566-1199 .- 1878-5530. ; 58, s. 33-37
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Tidskriftsartikel (refereegranskat)abstract
- We report unusually high charge carrier mobilities for regioregular poly(3-hexyltiophene) (rrP3HT) in organic field-effect transistors (OFETs) using polyurethane (PU) as dielectric layer. Our devices display hole mobilities up to 1.37 cm(2)/V in the saturation regime and an ON/OFF current ratio higher than 10(3), operating at voltages as low as -10 V, with a high I-DS current of 1.5 mu A. We assign the measured high mobilities mainly to the low density of randomly-oriented electric dipoles at the semiconductor/dielectric interface, which leads to a narrow energy distribution of the electronic levels available for charge transport in rrP3HT. This is confirmed by experimental and theoretical techniques: (1) temperature-dependent transport measurements for extraction of disorder-induced distribution of electronic levels; (2) density functional theory (DFT) calculations of electric dipole moments of PU; and (3) liquid contact-angle measurements for the dipolar component of dielectric surface tension.
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| 8. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 10. |
- Calissendorff, Per, 1989-, et al.
(författare)
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Updated orbital monitoring and dynamical masses for nearby M-dwarf binaries
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 666
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Tidskriftsartikel (refereegranskat)abstract
- Young M-type binaries are particularly useful for precise isochronal dating by taking advantage of their extended pre-main sequence evolution. Orbital monitoring of these low-mass objects becomes essential in constraining their fundamental properties, as dynamical masses can be extracted from their Keplerian motion. Here, we present the combined efforts of the AstraLux Large Multiplicity Survey, together with a filler sub-programme from the SpHere INfrared Exoplanet (SHINE) project and previously unpublished data from the FastCam lucky imaging camera at the Nordical Optical Telescope (NOT) and the NaCo instrument at the Very Large Telescope (VLT). Building on previous work, we use archival and new astrometric data to constrain orbital parameters for 20 M-type binaries. We identify that eight of the binaries have strong Bayesian probabilities and belong to known young moving groups (YMGs). We provide a first attempt at constraining orbital parameters for 14 of the binaries in our sample, with the remaining six having previously fitted orbits for which we provide additional astrometric data and updated Gaia parallaxes. The substantial orbital information built up here for four of the binaries allows for direct comparison between individual dynamical masses and theoretical masses from stellar evolutionary model isochrones, with an additional three binary systems with tentative individual dynamical mass estimates likely to be improved in the near future. We attained an overall agreement between the dynamical masses and the theoretical masses from the isochrones based on the assumed YMG age of the respective binary pair. The two systems with the best orbital constrains for which we obtained individual dynamical masses, J0728 and J2317, display higher dynamical masses than predicted by evolutionary models.
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