| 1. |
- Romerius, Patrik, et al.
(författare)
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High risk of azoospermia in men treated for childhood cancer.
- 2011
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Ingår i: International Journal of Andrology. - : Wiley. - 1365-2605 .- 0105-6263. ; 34, s. 69-76
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Tidskriftsartikel (refereegranskat)abstract
- Summary Childhood cancer survivors (CCS) have an increased risk of impaired spermatogenesis, but data regarding the disease- and treatment-related risk factors of azoospermia are scarce. Such information is crucial both for counselling CCS and for selecting patients for testicular tissue cryopreservation. The proportion of azoospermic men in CCS was 18% [95% confidence interval (CI): 12-26], specifically for leukaemias (19%; 95% CI: 5.5-42), Hodgkin's disease (53%; 95% CI: 29-76), non-Hodgkin's lymphoma (11%; 95% CI: 0.28-48) and testicular cancer (11%; 95% CI: 0.28-48). In CCS treated with high doses of alkylating agents, the proportion of azoospermic men was 80% (95% CI: 28-99) and if radiotherapy was used additionally, the proportion was 64% (95% CI: 35-87). In CCS with subnormal Inhibin B levels, the proportion of azoospermic men was 66% (95% CI: 47-81) and for those with elevated follicle-stimulating hormone (FSH) levels, the proportion was 50% (95% CI: 35-67). Among CCS with subnormal testicular volume (
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| 2. |
- Romerius, Patrik, et al.
(författare)
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Hypogonadism Risk in Men Treated for Childhood Cancer.
- 2009
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Ingår i: The Journal of clinical endocrinology and metabolism. - : The Endocrine Society. - 1945-7197 .- 0021-972X. ; 94, s. 4180-4186
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Tidskriftsartikel (refereegranskat)abstract
- Context: Pediatric cancer treatment may imply an increased risk of hypogonadism, leading to metabolic disorders and osteoporosis. Such complications are potentially preventable. Objective: The aim of this study was to assess diagnosis- and treatment-dependent risk of hypogonadism in male childhood cancer survivors (CCS). Design: Male CCS who were treated during the period 1970-2002 and who in 2004 were 18-45 yr of age were eligible. Setting: The study was conducted in a university hospital clinic. Patients: A consecutive group of CCS treated at Lund University Hospital was selected for the study, of whom 151 (38%) agreed to participate. Furthermore, 141 healthy fertile men served as controls. Interventions: We measured serum levels of free and total testosterone, SHBG, and LH. Main Outcome Measures: Odds ratios (OR) for biochemical hypogonadism, defined as total testosterone less than 10 nmol/liter and/or LH above 10 IU/liter, were calculated and related to type of cancer, treatment received, as well as testicular volume. Results: Hypogonadism was more commonly detected in CCS than in controls (OR, 6.7; 95% CI, 2.7, 17). The increased presence of hypogonadism was noted in the following treatment groups: brain surgery, chemotherapy (with and without radiotherapy), and testicular irradiation. Low total testicular volume (
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| 3. |
- Romerius, Patrik, et al.
(författare)
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Sperm DNA Integrity in Men Treated for Childhood Cancer.
- 2010
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Ingår i: Clinical Cancer Research. - 1078-0432. ; Jul 1, s. 3843-3850
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: It is unknown whether childhood cancer and its treatment are associated with sperm DNA damage, which subsequently affects fertility and might be transmitted to the offspring. The aim of this study was to assess DNA fragmentation index (DFI) as an indicator of sperm DNA integrity in childhood cancer survivors (CCS), treatment regimen taken into account.EXPERIMENTAL DESIGN: In 99 CCS and 193 age-matched healthy controls, the DFI was assessed by the use of Sperm Chromatin Structure Assay.RESULTS: In the whole group of CCS DFI was increased as compared to the controls with borderline statistical significance (mean difference=0.94%; 95%CI: -0.0088; 3.7%). Those treated with radiotherapy only (mean difference=6.0%; 95%CI: 1.6; 10%) or surgery only (mean difference=2.9%; 95%CI: 0.083; 3.7%) had statistically significantly higher DFI than the controls. The odds ratio (OR) for having DFI >20%, which is associated with reduced fertility, was significantly increased in CCS as compared to the control group (OR=2.2, 95%CI: 1.1; 4.4). For the radiotherapy only group the OR was even higher (OR=4.9, 95%CI 1.3; 18). The DFI was not associated to the dose of scattered testicular irradiation or the type of chemotherapy given.CONCLUSIONS: The DFI is increased in CCS, those treated with chemotherapy being the only exception. This sperm DNA impairment may be associated with the disease per se rather than due to the treatment and may have negative consequences in terms of fertility and risk of transmission to the offspring.
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| 4. |
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| 5. |
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| 6. |
- Alveteg, Mattias, et al.
(författare)
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Vad räknas som belägg för studenters måluppfyllelse?
- 2018
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Ingår i: 10:e Pedagogiska Inspirationskonferensen 2018. - 2003-3761 .- 2003-377X. ; 10
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Konferensbidrag (refereegranskat)abstract
- Universitetskanslerämbetet (UKÄ) ställer numera krav på svenska lärosäten att vi ska utvärdera oss själva. Vi på LTH bör då gemensamt försöka hitta sätt att uppfylla UKÄs krav som även ger de verktyg vi själva behöver för att förbättra våra utbildningars kvalitét.Hur tar vi reda på våra utbildningars styrkor och svagheter och vad vi kan göra för att förbättra dem ytterligare? Ett sätt är att undersöka hur väl studenterna uppfyller examensmålen. Vad som ska räknas som belägg för studenters måluppfyllelse är dock svårt, av flera olika skäl. Vår rekommendation blir att triangulera olika typer av belägg samt att tydligt involvera institutionerna i arbetet.
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| 7. |
- Araújo, Ana Catarina, et al.
(författare)
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Activated Paper Surfaces for the Rapid Hybridization of DNA through Capillary Transport
- 2012
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 84:7, s. 3311-3317
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Tidskriftsartikel (refereegranskat)abstract
- The development of low-cost, accurate, and equipment-free diagnostic tests is crucial to many clinical, laboratory, and field applications, including forensics and medical diagnostics. Cellulose fiber-based paper is an inexpensive, biodegradable, and renewable resource, the use of which as a biomolecule detection matrix and support confers several advantages compared to traditional materials such as glass. In this context, a new, facile method for the preparation of surface functionalized papers bearing single-stranded probe DNA (ssDNA) for rapid target hybridization via capillary transport is presented. Optimized reaction conditions were developed that allowed the direct, one-step activation of standard laboratory filters by the inexpensive and readily available bifunctional linking reagent, 1,4-phenylenediisothiocyanate. Such papers were thus amenable to subsequent coupling of amine-labeled ssDNA under standard conditions widely used for glass-based supports. The intrinsic wicking ability of the paper matrix facilitated rapid sample elution through arrays of probe DNA, leading to significant, detectable hybridization in the time required for the sample liquid to transit the vertical length of the strip (less than 2 min). The broad applicability of these paper test strips as rapid and specific diagnostics in "real-life" situations was exemplified by the discrimination of amplicons generated from canine and human mitochondrial and genomic DNA in mock forensic samples.
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| 8. |
- Asp, Michaela, et al.
(författare)
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
- 2019
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Ingår i: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 179:7, s. 1647-
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Tidskriftsartikel (refereegranskat)abstract
- The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
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| 9. |
- Asp, Michaela, et al.
(författare)
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An organ‐wide gene expression atlas of the developing human heart
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The human developing heart holds a greater proportion of stem-cell-like cells than the adult heart. However, it is not completely understood how these stem cells differentiate into various cardiac cell types. We have performed an organ-wide transcriptional landscape analysis of the developing heart to advance our understanding of cardiac morphogenesis in humans. Comprehensive spatial gene expression analyses identified distinct profiles that correspond not only to individual chamber compartments, but also distinctive regions within the outflow tract. Furthermore, the generated spatial expression reference maps facilitated the assignment of 3,787 human embryonic cardiac cells obtained from single-cell RNA-sequencing to an in situlocation. Through this approach we reveal that the outflow tract contains a wider range of cell types than the chambers, and that the epicardium expression profile can be traced to several cell types that are activated at different stages of development. We also provide a 3D spatial model of human embryonic cardiac cells to enable further studies of the developing human heart.
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| 10. |
- Asp, Michaela, et al.
(författare)
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Spatial Isoform Profiling within Individual Tissue Sections
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Spatial Transcriptomics has been shown to be a persuasive RNA sequencingtechnology for analyzing cellular heterogeneity within tissue sections. Thetechnology efficiently captures and barcodes 3’ tags of all polyadenylatedtranscripts from a tissue section, and thus provides a powerful platform whenperforming quantitative spatial gene expression studies. However, the currentprotocol does not recover the full-length information of transcripts, andconsequently lack information regarding alternative splice variants. Here, weintroduce a novel protocol for spatial isoform profiling, using SpatialTranscriptomics barcoded arrays.
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| 11. |
- Asp, Michaela
(författare)
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Spatially Resolved Gene Expression Analysis
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Spatially resolved transcriptomics has greatly expanded our knowledge of complex multicellular biological systems. To date, several technologies have been developed that combine gene expression data with information about its spatial tissue context. There is as yet no single spatial method superior to all others, and the existing methods have jointly contributed to progress in this field of technology. Some challenges presented by existing protocols include having a limited number of targets, being labor extensive, being tissue-type dependent and having low throughput or limited resolution. Within the scope of this thesis, many aspects of these challenges have been taken into consideration, resulting in a detailed evaluation of a recently developed spatial transcriptome-wide method. This method, termed Spatial Transcriptomics (ST), enables the spatial location of gene activity to be preserved and visually links it to its histological position and anatomical context. Paper I describes all the details of the experimental protocol, which starts when intact tissue sections are placed on barcoded microarrays and finishes with high throughput sequencing. Here, spatially resolved transcriptome-wide data are obtained from both mouse olfactory bulb and breast cancer samples, demonstrating the broad tissue applicability and robustness of the approach. In Paper II, the ST technology is applied to samples of human adult heart, a tissue type that contains large proportions of fibrous tissue and thus makes RNA extraction substantially more challenging. New protocol strategies are optimized in order to generate spatially resolved transcriptome data from heart failure patients. This demonstrates the advantage of using the technology for the identification of lowly expressed biomarkers that have previously been seen to correlate with disease progression in patients suffering heart failure. Paper III shows that, although the ST technology has limited resolution compared to other techniques, it can be combined with single-cell RNA-sequencing and hence allow the spatial positions of individual cells to be recovered. The combined approach is applied to developing human heart tissue and reveals cellular heterogeneity of distinct compartments within the complete organ. Since the ST technology is based on the sequencing of mRNA tags, Paper IV describes a new version of the method, in which spatially resolved analysis of full-length transcripts is being developed. Exploring the spatial distribution of full-length transcripts in tissues enables further insights into alternative splicing and fusion transcripts and possible discoveries of new genes.
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| 12. |
- Baeckdahl, Jesper, et al.
(författare)
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Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin
- 2021
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Ingår i: Cell Metabolism. - : Elsevier BV. - 1550-4131 .- 1932-7420. ; 33:9, s. 1869-
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Tidskriftsartikel (refereegranskat)abstract
- The contribution of cellular heterogeneity and architecture to white adipose tissue (WAT) function is poorly understood. Herein, we combined spatially resolved transcriptional profiling with single-cell RNA sequencing and image analyses to map human WAT composition and structure. This identified 18 cell classes with unique propensities to form spatially organized homo-and heterotypic clusters. Of these, three constituted mature adipocytes that were similar in size, but distinct in their spatial arrangements and transcriptional profiles. Based on marker genes, we termed these Adipo(LEP), Adipo(PLIN), and Adipo(SAA). We confirmed, in independent datasets, that their respective gene profiles associated differently with both adipocyte and whole-body insulin sensitivity. Corroborating our observations, insulin stimulation in vivo by hyperinsulinemic-euglycemic clamp showed that only Adipo(PLIN) displayed a transcriptional response to insulin. Altogether, by mining this multimodal resource we identify that human WAT is composed of three classes of mature adipocytes, only one of which is insulin responsive.
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| 13. |
- Berglund, Emelie, et al.
(författare)
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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.
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| 14. |
- Bhalla, Nayanika, et al.
(författare)
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Spatial transcriptomics of human placentas reveal distinct RNA patterns associated with morphology and preeclampsia
- 2023
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Ingår i: Placenta. - : Elsevier BV. - 0143-4004 .- 1532-3102. ; 139, s. 213-216
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Tidskriftsartikel (refereegranskat)abstract
- Spatial transcriptomics (ST) maps RNA level patterns within a tissue. This technology has not been previously applied to human placental tissue. We demonstrate analysis of human placental samples with ST. Unsupervised clustering revealed that distinct RNA patterns were found corresponding to different morphological structures. Additionally, when focusing upon terminal villi and hemoglobin associated structures, RNA levels differed between placentas from full term healthy pregnancies and those complicated by preeclampsia. The results from this study can provide a benchmark for future ST studies in placenta.
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| 15. |
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| 16. |
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| 17. |
- Broström, Tor, et al.
(författare)
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A method to assess the potential for and consequences of energy retrofits in Swedish historic buildings
- 2014
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Ingår i: The Historic Environment. - : Maney Publishing. - 1756-7505 .- 1756-7513. ; 5:2, s. 150-166
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Tidskriftsartikel (refereegranskat)abstract
- Tor Broström is a Professor in Conservation at Uppsala University, Campus Gotland, Sweden. With a background in engineering, his research focuses on indoor climate and energy conservation in historic buildings. He is coordinator of the Swedish national research programme on energy efficiency in historic buildings. Petra Eriksson, is a lecturer and PhD candidate in conservation at Uppsala University, Campus Gotland, Sweden. Petra has a background in the applied field of conservation and her research is in the field of heritage conservation in relation to energy efficiency. Linn Liu is a PhD candidate in the Division of Energy Systems, Department of Management and Engineering at Linköping University, Sweden. Her research area is within energy efficiency and cost efficiency of multifamily buildings and historic buildings. Patrik Rohdin is Associate Professor in the Division of Energy Systems, Department of Management and Engineering at Linköping University, Sweden. Patrik is conducting research related to energy efficiency in the built environment and building simulation and is active within the national interdisciplinary research programme, program energy systems. Bahram Moshfegh is a Professor and Head of the Division of Energy Systems, Department of Management and Engineering at Linköping University, Sweden. Professor Moshfegh has been active in the following research areas: mathematical modelling and measuring techniques for air and energy flow in buildings, energy-efficient HVAC systems and local and regional energy systems. Fredrik Ståhl is Senior Researcher in the Department of Energy Technology at SP Swedish Technical Research Institute. Currently, his research is focused on energy efficiency in historic buildings. The Swedish research project 'Potential and Policies for Energy Efficiency in Swedish Historic Buildings' aims to investigate the interdependency between political energy targets and effects on the built heritage. The fi rst part of this paper presents an iterative and interactive method to assess the potential for and consequences of improving the energy performance in a stock of historic buildings. Key elements in the method are: categorisation of the building stock, identifying targets, assessment of measures, and life-cycle cost optimisation. In the second part of the paper, the method is applied to a typical Swedish building. The selected case study shows how the method allows for an interaction between the quantitative assessment of the technoeconomic optimisation and the qualitative assessment of vulnerability and other risks. Through a multidisciplinary dialogue and iteration it is possible to arrive at a solution that best balances energy conservation and building conservation in a given decision context.
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| 18. |
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| 19. |
- Cano, F., et al.
(författare)
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Partial protection to respiratory syncytial virus (RSV) elicited in mice by intranasal immunization using live staphylococci with surface-displayed RSV-peptides
- 2000
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Ingår i: Vaccine. - 0264-410X .- 1873-2518. ; 18:24, s. 2743-2752
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Tidskriftsartikel (refereegranskat)abstract
- A live bacterial vaccine-delivery system based on the food-grade bacterium Staphylococcus carnosus was used for delivery of peptides from the G glycoprotein of human respiratory syncytial virus, subtype A (RSV-A). Three peptides, corresponding to the G protein amino acids, 144-159 (denoted G5), 190-203 (G9) and 171-188 (G4 S), the latter with four cysteine residues substituted for serines, were expressed by recombinant means as surface-exposed on three different bacteria, and their surface accessibility on the bacteria was verified by fluorescence-activated cell sorting (FACS). Intranasal immunization of mice with the live recombinant staphylococci elicited significant anti-peptide as well as anti-virus serum IgG responses of balanced IgG1/IgG2a isotype profiles, and upon viral challenge with 10(5) tissue culture infectious doses(50) (TCID50), lung protection was demonstrated for approximately half of the mice in the G9 and G4 S immunization groups. To our knowledge, this is the first study in which protective immunity to a viral pathogen has been evoked using food-grade bacteria as vaccine-delivery vehicles.
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| 20. |
- Carlberg, Konstantin, et al.
(författare)
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Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
- 2019
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Lately it has become possible to analyze transcriptomic profiles in tissue sections with retained cellular context. We aimed to explore synovial biopsies from rheumatoid arthritis (RA) and spondyloarthritis (SpA) patients, using Spatial Transcriptomics (ST) as a proof of principle approach for unbiased mRNA studies at the site of inflammation in these chronic inflammatory diseases. Synovial tissue biopsies from affected joints were studied with ST. The transcriptome data was subjected to differential gene expression analysis (DEA), pathway analysis, immune cell type identification using Xcell analysis and validation with immunohistochemistry (IHC). The ST technology allows selective analyses on areas of interest, thus we analyzed morphologically distinct areas of mononuclear cell infiltrates. The top differentially expressed genes revealed an adaptive immune response profile and T-B cell interactions in RA, while in SpA, the profiles implicate functions associated with tissue repair. With spatially resolved gene expression data, overlaid on high-resolution histological images, we digitally portrayed pre-selected cell types in silico. The RA displayed an overrepresentation of central memory T cells, while in SpA effector memory T cells were most prominent. Consequently, ST allows for deeper understanding of cellular mechanisms and diversity in tissues from chronic inflammatory diseases.
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| 21. |
- Carlberg, Konstantin, et al.
(författare)
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Integrated Single Cell and Spatial Transcriptomics Reveal Autoreactive Differentiated B Cells in Joints of Early Rheumatoid Arthritis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Rheumatoid Arthritis (RA) is a prevalent autoimmune disease characterized by inflammation of peripheral joints. Patients can be subdivided by the presence or absence of Rheumatoid Factor and anti-citrullinated protein antibodies (ACPA) in their circulation. Inflammation of the joint tissue is associated with infiltration of leukocytes from the blood, which can result in generation of lymphoid structures composed of B and T cells. Previous studies have shown that both memory B cells and antibody-secreting plasma cells populate the rheumatic joint tissue when captured from established and often long-standing disease. However, it has remained unclear, whether these cells are autoreactive and whether the associated lymphoid structures are present at the site of inflammation already at the time of diagnosis. Here, we used an integrated single cell and spatial transcriptomic approach to study B and plasma cells in synovial tissue of ACPA- and ACPA+ RA patients at this early time point. We found evidence for T cell help to B cells and presence of memory B and plasma cell pools in ACPA- as well as in ACPA+ RA. Our results demonstrated common supportive microenvironments in both patient subgroups, clonal relationships between the memory B and plasma cell pools and autoreactivity within the plasma cell compartment. These findings challenge our understanding of the dynamics of local adaptive immune responses in the RA joint of ACPA- and ACPA+ patients at the time of diagnosis, with direct implications for B and T cell targeting therapies for both patient subgroups.
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| 22. |
- Carlberg, Konstantin
(författare)
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Spatial Tissue Mapping on Joint Biopsies from Arthritis Patients
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease that mainly affects joints, causing discomfort and pain that severely reduces the life quality of affected individuals. Its etiology is largely unknown, but some pathophysiological mechanisms have been identified. These include formation of anti-citrullinated protein antibodies (ACPAs) and rheumatic factors (RFs), local proliferation of mesenchymal cells, and recruitment of T- and B cells to the affected synovium. Lymphocyte infiltration results in elevated levels of cytokines such as Tumor Necrosis Factor alpha (TNF-α) and interleukin signaling, which in turn triggers protease activation that gradually degrades the synovium and underlying bone. In many cases RA can be effectively managed by early diagnosis followed by treatment with disease-modifying anti-rheumatic drugs (DMARDs). However, this is not true for all patients and there is currently no cure for RA. Synovial lesions in RA patients exhibit complex histopathological manifestations involving the formation of lymphoid follicles with highly organized Ectopic Lymphoid Structures (ELS). These have been extensively studied using immunostaining and other cytological methods, either by targeting a few specific molecular markers in tissue sections or by examining homogenized suspensions of complex samples, which causes a loss of local and spatial tissue information. This thesis reports the use of Spatial Transcriptomics (ST) to study gene expression in tissue samples from RA patients while preserving spatial information. The method was applied to RA biopsies from early onset and untreated RA to late-stage established disease with edema, providing comprehensive coverage of the spatio-temporal dynamics of the inflamed joints. Paper I introduces sRIN, a novel method of assessing the quality of RNA in tissue sections that is similar to RNA Integrity Number (RIN) analysis for bulk RNA but with single-cell resolution. The aim was to find ways of analyzing clinically rare samples for further processing with ST. Paper II uses ST to study tissue samples from RA joints with long-standing disease, using Spondyloarthritis (SpA) as a disease control. The resulting comprehensive transcriptomic data were used to perform in silico immune cell prediction and revealed how immune cell infiltration in RA differs from that in SpA in more detail than was previously possible using traditional pathological methods. As a follow up, Paper III investigates inflamed RA joints in even greater detail by using several adjacent tissue sections to build a three-dimensional atlas of assumed ELS areas. Finally, Paper IV uses four distinct technologies to study untreated early onset RA patients. Spatial tissue analysis with ST was combined with single cell RNA sequencing (scRNA-Seq) of fluorescence-activated cell sorted (FACS) B cells. These two methods were complemented with immunohistochemistry (IHC) for validation and sRIN to assess the quality of the clinical samples. B cells are known to play a key role in RA by producing self-reactive antibodies. This work showed that B cell maturation and ELS formation are detectable even in early onset RA, and revealed mechanisms supporting survival niches in hyperplastic joints. Overall, these studies shed new light on the complex nature of Rheumatoid arthritis, characterize the site of infection with greater granularity than was previously possible, and reveal novel disease patterns with clinical implications that warrant further study.
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| 23. |
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| 24. |
- Danielsson, Marcus, 1985-
(författare)
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Mosaic loss of chromosome Y : methods for detection and consequences for affected leukocytes and men
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- It has been known for centuries that men live shorter lives than women, but until recently, the biological mechanisms driving this sex bias has been poorly understood. Mosaic loss of chromosome Y (mLOY) refers to chromosome Y aneuploidy, a male specific and the most common somatic mutation in human blood cells. Known risk factors include age, smoking and genetic predisposition. Men with mLOY carry a fraction of blood cells without the Y chromosome, due to its loss from hematopoietic progenitor cells during life. Hence, in a single cell LOY is a binary event causing the absence of almost 2% of the male haploid nuclear genome. When measured in bulk samples, it is present as a continuous mosaicism affecting a fraction of cells. A paper published in 1963 demonstrated that mLOY is frequent in cells of the hematopoietic system in aging men, but it was long viewed as a neutral event. In contrast, recent discoveries demonstrate that mLOY in blood is associated with various forms of cancer, autoimmune conditions, Alzheimer’s disease, cardiovascular events, diabetes as well as age-related macular degeneration. Studies support the hypothesis that mLOY in leukocytes may exacerbate disease processes in other organs. Thus, given the associations with several common diseases, mLOY in blood cells could help explain reduced male longevity.A main aim and a long term goal of the work presented in this thesis is the development of novel methods for improved mLOY detection. Focus here is exploration of analytes such as DNA, RNA and proteins, including studies of bulk samples as well as single cell approaches. Among the evaluated methods are SNP-arrays, ddPCR, WGS, RNA-seq and CITE-seq. Furthermore, a novel method called SPARC was developed for co-detection of the transcriptome and a panel of 92 proteins in single cells. Future methods with clinical utility for mLOY should, in addition to robust detection, be able to simultaneously discriminate mLOY in different types of immune cells. The latter builds on recent results showing cell type specificity with regard to disease associations. To meet these needs, single cell analyses using mLOY associated cell surface proteins have been pursued and proof-of-concept established. Implementation of mLOY screening in general populations has the potential to identify men with increased risk for various disease. It could be envisioned that further medical examination of men affected with mLOY would enable earlier diagnoses of ongoing disease processes as well as serving to guide targeted interventions.
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| 25. |
- Ekedahl, Henrik, et al.
(författare)
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Low-grade inflammation in survivors of childhood cancer and testicular cancer and its association with hypogonadism and metabolic risk factors
- 2022
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 22, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In childhood (CCS) and testicular cancer (TCS) survivors, low-grade inflammation may represent a link between testosterone deficiency (hypogonadism) and risk of metabolic syndrome. We aimed to study levels of inflammatory markers in CCS and TCS and the association with hypogonadism and future cardio-metabolic risk factors.METHODS: Serum levels of inflammatory markers and testosterone were analyzed in CCS (n = 90), and TCS (n = 64, median time from diagnosis: 20 and 2.0 years, respectively), and in controls (n = 44). Differences in levels between patients and controls were calculated using univariate analysis of variance. T-test and logistic regression were applied to compare levels of cardio-metabolic risk factors and odds ratio (OR) of hypogonadism and metabolic syndrome in low and high inflammatory marker groups after 4-12 years of follow up. Adjustment for age, smoking, and active cancer was made.RESULTS: TCS and CCS, as compared to controls, had 1.44 (95%CI 1.06-1.96) and 1.25 (95 CI 1.02-1.53) times higher levels of IL-8, respectively. High IL-6 levels were associated with hypogonadism at baseline (OR 2.83, 95%CI 1.25-6.43) and the association was stronger for high IL-6 combined with low IL-10 levels (OR 3.10, 95%CI 1.37-7.01). High IL-6 levels were also associated with higher BMI, waist circumference, insulin, and HbA1c at follow up. High TNF-α was associated with higher diastolic blood pressure. No individual inflammatory marker was significantly associated with risk of metabolic syndrome at follow up. High IL-6 combined with low IL-10 levels were associated with risk of metabolic syndrome (OR 3.83, 95%CI 1.07-13.75), however not statistically significantly after adjustment.CONCLUSION: TCS and CCS present with low-grade inflammation. High IL-6 levels were associated with hypogonadism and cardio-metabolic risk factors. Low IL-10 levels might reinforce the IL-6 mediated risk of developing metabolic syndrome.
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| 26. |
- Fernandez Navarro, Jose, et al.
(författare)
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ST viewer : a tool for analysis and visualization of spatial transcriptomics datasets
- 2019
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 35:6, s. 1058-1060
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Tidskriftsartikel (refereegranskat)abstract
- Motivation Spatial Transcriptomics (ST) is a technique that combines high-resolution imaging with spatially resolved transcriptome-wide sequencing. This novel type of data opens up many possibilities for analysis and visualization, most of which are either not available with standard tools or too complex for normal users. Results Here, we present a tool, ST Viewer, which allows real-time interaction, analysis and visualization of Spatial Transcriptomics datasets through a seamless and smooth user interface. Availability and implementation The ST Viewer is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_viewer. Supplementary information Supplementary data are available at Bioinformatics online.
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| 27. |
- Fjordén, Karin, et al.
(författare)
-
Gene expression profiling indicates that immunohistochemical expression of CD40 is a marker of an inflammatory reaction in the tumor stroma of diffuse large B-cell lymphoma
- 2012
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Ingår i: Leukemia & Lymphoma. - : Informa UK Limited. - 1042-8194 .- 1029-2403. ; 53:9, s. 1764-1768
-
Tidskriftsartikel (refereegranskat)abstract
- Immunohistochemical expression of CD40 is seen in 60-70% of diffuse large B-cell lymphoma (DLBCL) and is associated with a superior prognosis. By using gene expression profiling we aimed to further explore the underlying mechanisms for this effect. Ninety-eight immunohistochemically defined CD40 positive or negative DLBCL tumors, 63 and 35 respectively, were examined using spotted 55K oligonucleotide arrays. CD40 expressing tumors were characterized by up-regulated expression of genes encoding proteins involved in cell-matrix interactions: collagens, integrin a V, proteoglycans and proteolytic enzymes, and antigen presentation. Immunohistochemistry confirmed that CD40 positive tumors co-express the proinflammatory proteoglycan biglycan (p = 0.005), which in turn correlates with the amount of infiltrating macrophages and CD4 and CD8 positive T-cells. We postulate that immunohistochemical expression of CD40 mainly reflects the inflammatory status in tumors. A high intratumoral inflammatory reaction may correlate with an increased autologous tumor response, and thereby a better prognosis.
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| 28. |
- Franzén, Lovisa, et al.
(författare)
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Spatially resolved transcriptomics of human and mouse fibrotic lung
- 2022
-
Ingår i: European Respiratory Journal. - : European Respiratory Society (ERS). - 0903-1936 .- 1399-3003. ; 60
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by progressive and irreversible scarring of the lung tissue. Development of new efficacious and safe treatments is hampered by limited understanding of disease pathogenesis, lack of predictive preclinical models, and narrow therapeutic index of candidate drugs targeting complex biologies. Here, we tackle these aspects by generating spatially resolved transcriptomic maps of fibrotic lungs from clinical samples and a preclinical mouse model. We utilized the Visium platform to study parenchyma biopsies from four healthy lungs and regions of varying fibrotic severity from four IPF patient lungs. By mapping single cell RNA-seq data spatially, we were able to detect distinct fibroblast populations in different regions of the lesioned IPF lung, as well as the presence of various immune cell populations. To study lung fibrosis preclinically in vivo, the bleomycin mouse model is the most widely used alternative, although its translatability to human disease is disputed. Visium data from mouse lungs collected at two time points following bleomycin administration were generated, which allowed us to characterize the fibrotic lesions and inflammatory areas in their spatiotemporal context. In addition, mass spectrometry imaging was performed on adjacent tissue sections to provide paired spatial metabolomics. Herein, we have generated spatial maps of the lung fibrosis transcriptome from IPF lung biopsies and bleomycin-injured mouse lungs, providing an extensive resource to probe disease pathogenesis and animal model translatability.
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| 29. |
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| 30. |
- Giacomello, Stefania, et al.
(författare)
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Spatially resolved transcriptome profiling in model plant species
- 2017
-
Ingår i: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 3:6
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Tidskriftsartikel (refereegranskat)abstract
- Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study highresolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes highthroughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.
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| 31. |
- Hansson, M., et al.
(författare)
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General expression vectors for Staphylococcus carnosus enabled efficient production of the outer membrane protein A of Klebsiella pneumoniae
- 2002
-
Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 210:2, s. 263-270
-
Tidskriftsartikel (refereegranskat)abstract
- General expression vectors, designed for intracellular expression or secretion of recombinant proteins in the non-pathogenic Staphylococcus carnosus, were constructed. Both vector systems encode two different affinity tags, an upstream albumin binding protein and a downstream hexahistidyl peptide, and are furnished with cleavage sites for two site-specific proteases for optional affinity tag removal. To evaluate the novel vectors, the gene encoding the outer membrane protein A (OmpA) of Klebsiella pneumoniae was introduced into the vectors. Efficient production was demonstrated in both systems, although, as expected for OmpA fusions, somewhat better intracellularly, and the fusion proteins could be recovered as full-length products by affinity chromatography.
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| 32. |
- Hansson, M., et al.
(författare)
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Surface display on gram positive bacteria
- 2001
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Ingår i: Combinatorial chemistry & high throughput screening. - : Bentham Science Publishers Ltd.. - 1386-2073 .- 1875-5402. ; 4:2, s. 171-184
-
Tidskriftsartikel (refereegranskat)abstract
- Heterologous surface display on Gram-positive bacteria was first described almost a decade ago and has since then developed into an active research area. Gram-positive bacterial surface display has today found a range of applications, in immunology, microbiology and biotechnology. Live bacterial vaccine delivery vehicles are being developed through the surface display of selected foreign antigens on the bacterial surfaces. In this field, second generation vaccine delivery vehicles are at present being generated by the addition of mucosal targeting signals through co-display of adhesins, in order to achieve targeting of the live bacteria to immunoreactive sites to thereby increase immune responses. Engineered Gram-positive bacteria are further being evaluated as novel microbial biocatalysts with heterologous enzymes immobilized as surface exposed on the bacterial cell surface. A discussion has started whether bacteria can find use as new types of whole-cell diagnostic devices since single-chain antibodies and other variants of tailor-made binding proteins can be displayed on bacteria. Bacteria with increased binding capacity for certain metal ions can be created and potential environmental or biosensor applications for such recombinant bacteria as biosorbents are being discussed. This article explains the basis of Grampositive bacterial surface display, and discusses current uses and possible future trends of this emerging technology.
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| 33. |
- Hardt, Uta, et al.
(författare)
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Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis
- 2022
-
Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- B cells play a significant role in established Rheumatoid Arthritis (RA). However, it is unclear to what extent differentiated B cells are present in joint tissue already at the onset of disease. Here, we studied synovial biopsies (n = 8) captured from untreated patients at time of diagnosis. 3414 index-sorted B cells underwent RNA sequencing and paired tissue pieces were subjected to spatial transcriptomics (n = 4). We performed extensive bioinformatics analyses to dissect the local B cell composition. Select plasma cell immunoglobulin sequences were expressed as monoclonal antibodies and tested by ELISA. Memory and plasma cells were found irrespective of autoantibody status of the patients. Double negative memory B cells were prominent, but did not display a distinct transcriptional profile. The tissue architecture implicate both local B cell maturation via T cell help and plasma cell survival niches with a strong CXCL12-CXCR4 axis. The immunoglobulin sequence analyses revealed clonality between the memory B and plasma cell pools further supporting local maturation. One of the plasma cell-derived antibodies displayed citrulline autoreactivity, demonstrating local autoreactive plasma cell differentiation in joint biopsies captured from untreated early RA. Hence, plasma cell niches are not a consequence of chronic inflammation, but are already present at the time of diagnosis.
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| 34. |
- Huttner, Hagen B, et al.
(författare)
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The age and genomic integrity of neurons after cortical stroke in humans
- 2014
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Ingår i: Nature Neuroscience. - : Springer Science and Business Media LLC. - 1097-6256 .- 1546-1726. ; 17:6, s. 801-803
-
Tidskriftsartikel (refereegranskat)abstract
- It has been unclear whether ischemic stroke induces neurogenesis or neuronal DNA rearrangements in the human neocortex. Using immunohistochemistry; transcriptome, genome and ploidy analyses; and determination of nuclear bomb test-derived (14)C concentration in neuronal DNA, we found neither to be the case. A large proportion of cortical neurons displayed DNA fragmentation and DNA repair a short time after stroke, whereas neurons at chronic stages after stroke showed DNA integrity, demonstrating the relevance of an intact genome for survival.
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| 35. |
- Jemt, Anders, 1985-, et al.
(författare)
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An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.
- 2016
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Furthermore, an increased understanding of tissue heterogeneity has lead to the development of several unique sequencing protocols that aim to retain or infer spatial context. In this study, a protocol for retaining spatial information of transcripts has been adapted to run on a robotic workstation. The method spatial transcriptomics is evaluated in terms of robustness and variability through the preparation of reference RNA, as well as through preparation and sequencing of six replicate sections of a gingival tissue biopsy from a patient with periodontitis. The results are reduced technical variability between replicates and a higher throughput, processing four times more samples with less than a third of the hands on time, compared to the standard protocol.
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| 36. |
- Kostallas, George
(författare)
-
Intracellular systems for characterization and engineering of proteases and their substrates
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Over the years, the view on proteases as relatively non-specific protein degradation enzymes, mainly involved in food digestion and intracellular protein turnover, has shifted and they are now recognized as key regulators of many biological processes that determine the fate of a cell. Besides their biological role, proteases have emerged as important tools in various biotechnical, industrial and medical applications. At present, there are worldwide efforts made that aim at deciphering the biological role of proteases and understanding their mechanism of action in greater detail. In addition, with the growing demand of novel protease variants adapted to specific applications, protease engineering is attracting a lot of attention. With the vision of contributing to the field of protein science, we have developed a platform for the identification of site-specific proteolysis, consisting of two intracellular genetic assays; one fluorescence-based (Paper I) and one antibiotic resistance-based (Paper IV). More specifically, the assays take advantage of genetically encoded short-lived reporter substrates that upon cleavage by a coexpressed protease confer either increased whole-cell fluorescence or antibiotic resistance to the cells in proportion to the efficiency with which the substrates are processed. Thus, the fluorescence-based assay is highly suitable for high-throughput analysis of substrate processing efficiency by flow cytometry analysis and cell sorting, while the antibiotic resistance assay can be used to monitor and identify proteolysis through (competitive) growth in selective media. By using the highly sequence specific tobacco etch virus protease (TEVp) as a model in our systems, we could show that both allowed for (i) discrimination among closely related substrate peptides (Paper I & IV) and (ii) enrichment and identification of the best performing substrate-protease combination from a background of suboptimal variants (Paper I & IV). In addition, the fluorescence-based assay was used successfully to determine the substrate specificity of TEVp by flow cytometric screening of large combinatorial substrate libraries (Paper II), and in a separate study also used as one of several methods for the characterization of different TEVp mutants engineered for improved solubility (Paper III). We believe that our assays present a new and promising path forward for high-throughput substrate profiling of proteases, directed evolution of proteases and identification of protease inhibitors, which all are areas of great biological, biotechnical and medical interest.
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| 37. |
- Larsson, Ludvig, et al.
(författare)
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Semla : a versatile toolkit for spatially resolved transcriptomics analysis and visualization
- 2023
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 39:10
-
Tidskriftsartikel (refereegranskat)abstract
- SUMMARY: Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analyses and present analysis results in their histological context. Here, we present semla, an R package for processing, analysis, and visualization of spatially resolved transcriptomics data generated by the Visium platform, that includes interactive web applications for data exploration and tissue annotation. AVAILABILITY AND IMPLEMENTATION: The R package semla is available on GitHub (https://github.com/ludvigla/semla), under the MIT License, and deposited on Zenodo (https://doi.org/10.5281/zenodo.8321645). Documentation and tutorials with detailed descriptions of usage can be found at https://ludvigla.github.io/semla/.
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| 38. |
- Lehtio, J., et al.
(författare)
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Directed immobilization of recombinant staphylococci on cotton fibers by functional display of a fungal cellulose-binding domain
- 2001
-
Ingår i: FEMS Microbiology Letters. - 0378-1097 .- 1574-6968. ; 195:2, s. 197-204
-
Tidskriftsartikel (refereegranskat)abstract
- The immobilization of recombinant staphylococci onto cellulose fibers through surface display of a fungal cellulose-binding domain (CBD) was investigated. Chimeric proteins containing the CBD from Trichoderma reesei cellulase Cel6A were found to be correctly targeted to the cell wall of Staphylococcus carnosus cells. since full-length proteins could be extracted and affinity-purified. Furthermore. surface accessibility of the CBD was verified using a monoclonal antibody and functionality in terms of cellulose-binding was demonstrated in two different assays in which recombinant staphylococci were found to efficiently bind to cotton fibers. The implications of this strategy of directed immobilization Tor the generation of whole-cell microbial tools Fur different applications will be discussed.
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| 39. |
- Linderoth, Johan, et al.
(författare)
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Genes associated with the tumour microenvironment are differentially expressed in cured versus primary chemotherapy-refractory diffuse large B-cell lymphoma
- 2008
-
Ingår i: British Journal of Haematology. - : Wiley. - 0007-1048 .- 1365-2141. ; 141:4, s. 423-32
-
Tidskriftsartikel (refereegranskat)abstract
- In order to identify genes associated with primary chemotherapy-resistance, gene expression profiles (GEP) in tumour tissue from 37 patients with de novo diffuse large B-cell lymphoma (DLBCL), stage II-IV, either in continuous complete remission (n = 24) or with progressive disease during primary treatment (n = 13), were examined using spotted 55K oligonucleotide arrays. Immunohistochemistry was used for confirmation at the protein level. The top 86 genes that best discriminated between the two cohorts were chosen for further analysis. Only seven of 86 genes were overexpressed in the refractory cohort, e.g. RABGGTB and POLE, both potential targets for drug intervention. Seventy-nine of 86 genes were overexpressed in the cured cohort and mainly coded for proteins expressed in the tumour microenvironment, many of them involved in proteolytic activity and remodelling of extra cellular matrix. Furthermore, major histocompatibility complex class I molecules, CD3D and ICAM1 were overexpressed, indicating an enhanced immunological reaction. Immunohistochemistry confirmed the GEP results. The frequency of tumour infiltrating lymphocytes, macrophages, and reactive cells expressing ICAM-1, lysozyme, cathepsin D, urokinase plasminogen activator receptor, signal transducer and activator of transcription 1, and galectin-3 was higher in the cured cohort. These findings indicate that a reactive microenvironment has an impact on the outcome of chemotherapy in DLBCL.
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| 40. |
- Llorens-Bobadilla, Enric, et al.
(författare)
-
Solid-phase capture and profiling of open chromatin by spatial ATAC
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Current methods for epigenomic profiling are limited in the ability to obtain genome wideinformation with spatial resolution. Here we introduce spatial ATAC, a method that integratestransposase-accessible chromatin profiling in tissue sections with barcoded solid-phase captureto perform spatially resolved epigenomics. We show that spatial ATAC enables the discoveryof the regulatory programs underlying spatial gene expression during mouse organogenesis,lineage differentiation and in human pathology.
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| 41. |
- Llorens-Bobadilla, Enric, et al.
(författare)
-
Solid-phase capture and profiling of open chromatin by spatial ATAC
- 2023
-
Ingår i: Nature Biotechnology. - : Nature Research. - 1087-0156 .- 1546-1696. ; 41:8, s. 1085-1088
-
Tidskriftsartikel (refereegranskat)abstract
- Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
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| 42. |
- Marklund, Maja
(författare)
-
Spatial transcriptome and epigenome analysis with focus on prostate cancer
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Each cancer is unique, and therefore the use of general treatments are often suboptimal. If we can understand the mechanisms of cancer development, we might be able to develop effective treatments tailored to each patient. Our bodies are complex three-dimensional structures and how things are organized correlate with proper functioning. Technologies for biological research have escalated enormously in the last years. Going from bulk analysis of tissues to the advent of single cell sequencing and spatially resolved transcriptomics has initiated a new era in biological research. The technology Spatial Transcriptomics (ST) combines histology with next-generation sequencing, making it possible to map which genes that are active at thousands of sub-areas in a tissue section. In Paper I, ST was combined with an in-house developed artificial intelligence method to explore the landscape of prostate cancer tissue. We identified a gene expression-based tumor signature in healthy tissue areas not possible to recognize through visual assessment, indicating that the genotype changes before phenotype. A gradient of the tumor microenvironment was also identified. In Paper II, prostate cancer tissue from three patients were investigated before and after androgen deprivation therapy using ST. All patients treated with this therapy long enough will reach a clinically defined stage called castration-resistant prostate cancer. We could see that only a set of cancer cells across the tissue responded to the treatment, which allowed comparison of gene expression program in responding versus non-responding cells. By understanding the underlying mechanisms to resistance, it might be possible to target these cells and decrease relapse risk. In Paper III, we inferred copy number variation from ST data allowing for the generation of genome integrity maps in cancerous tissue of prostate, breast, brain, and skin, and in a lymph node. This allowed us to identify tumor clones not recognizable histologically, indicating how genomic instability can be initiated and spread before visible for the naked eye. In Paper IV, we developed a method for spatial ATAC-seq by fusing the ST-technology with ATAC-seq, enabling the analyses of accessible chromatin while preserving histological information. The Visium platform by 10x Genomics was used and we demonstrate a similar capture efficiency to single-cell ATACseq.
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| 43. |
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| 44. |
- Massier, Lucas, et al.
(författare)
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An integrated single cell and spatial transcriptomic map of human white adipose tissue
- 2023
-
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
-
Tidskriftsartikel (refereegranskat)abstract
- Single-cell studies of human white adipose tissue (WAT) provide insights into the specialized cell types in the tissue. Here the authors combine publicly available and newly generated high-resolution and bulk transcriptomic results from multiple human datasets to provide a comprehensive cellular map of white adipose tissue. To date, single-cell studies of human white adipose tissue (WAT) have been based on small cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a comprehensive meta-analysis of publicly available and newly generated single-cell, single-nucleus, and spatial transcriptomic results from human subcutaneous, omental, and perivascular WAT. Our high-resolution map is built on data from ten studies and allowed us to robustly identify >60 subpopulations of adipocytes, fibroblast and adipogenic progenitors, vascular, and immune cells. Using these results, we deconvolved spatial and bulk transcriptomic data from nine additional cohorts to provide spatial and clinical dimensions to the map. This identified cell-cell interactions as well as relationships between specific cell subtypes and insulin resistance, dyslipidemia, adipocyte volume, and lipolysis upon long-term weight changes. Altogether, our meta-map provides a rich resource defining the cellular and microarchitectural landscape of human WAT and describes the associations between specific cell types and metabolic states.
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| 45. |
- Moberg, Christina, et al.
(författare)
-
De unga gör helt rätt när de stämmer staten
- 2022
-
Ingår i: Aftonbladet. - 1103-9000.
-
Tidskriftsartikel (populärvet., debatt m.m.)abstract
- 1 620 forskare och lärare i forskarvärlden: Vi ställer oss bakom Auroras klimatkrav
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| 46. |
- Mold, Jeff E., et al.
(författare)
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Divergent clonal differentiation trajectories establish CD8(+) memory T cell heterogeneity during acute viral infections in humans
- 2021
-
Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 35:8
-
Tidskriftsartikel (refereegranskat)abstract
- The CD8(+) T cell response to an antigen is composed of many T cell clones with unique T cell receptors, together forming a heterogeneous repertoire of effector and memory cells. How individual T cell clones contribute to this heterogeneity throughout immune responses remains largely unknown. In this study, we longitudinally track human CD8(+) T cell clones expanding in response to yellow fever virus (YFV) vaccination at the single-cell level. We observed a drop in clonal diversity in blood from the acute to memory phase, suggesting that clonal selection shapes the circulating memory repertoire. Clones in the memory phase display biased differentiation trajectories along a gradient from stem cell to terminally differentiated effector memory fates. In secondary responses, YFV- and influenza-specific CD8(+) T cell clones are poised to recapitulate skewed differentiation trajectories. Collectively, we show that the sum of distinct clonal phenotypes results in the multifaceted human T cell response to acute viral infections.
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| 47. |
- Navarro, Jose Fernandez, et al.
(författare)
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ST Pipeline : an automated pipeline for spatial mapping of unique transcripts
- 2017
-
Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 33:16, s. 2591-2593
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: In recent years we have witnessed an increase in novel RNA-seq based techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based technique that allows spatial mapping of transcripts in tissue sections. The spatial resolution adds an extra level of complexity, which requires the development of new tools and algorithms for efficient and accurate data processing. Results: Here we present a pipeline to automatically and efficiently process RNA-seq data obtained from spatial transcriptomics experiments to generate datasets for downstream analysis.
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| 48. |
- Nguyen, N, et al.
(författare)
-
Chromosomal sequencing using a PCR-based biotin-capture method allowed isolation of the complete gene for the outer membrane protein A of Klebsiella pneumoniae
- 1998
-
Ingår i: Gene. - 0378-1119 .- 1879-0038. ; 210:1, s. 93-101
-
Tidskriftsartikel (refereegranskat)abstract
- By employing a novel biotin-and PCR-assisted capture method, which allows determination of unknown sequences on chromosomal DNA. the gene for the outer membrane protein A (OmpA) of Klebsiella pneumoniae has been isolated and sequenced to completion. The method involves linear amplification of DNA from a biotinylated primer annealing to a region with known sequence. After capture of the amplified single-stranded DNA on to paramagnetic beads, unspecifically annealing primers, i.e. arbitrary primers, were used to generate fragments with only partly determined nt sequences. The homology of the sequenced gene to ompAs of related bacteria is discussed. The ompA gene was assembled for intracellular expression in Escherichia coli, and two different fusion proteins were produced and recovered with good yields. The importance of the novel chromosomal sequencing method for gene isolation in general and the potential use of the OmpA fusion proteins are discussed. (C) 1998 Elsevier Science B.V.
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| 49. |
- Pettersson, Erik, et al.
(författare)
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A Novel Method for Rapid Hybridization of DNA to a Solid Support
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:8, s. e70504-
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Tidskriftsartikel (refereegranskat)abstract
- Here we present a novel approach entitled Magnetic Forced Hybridization (MFH) that provides the means for efficient and direct hybridization of target nucleic acids to complementary probes immobilized on a glass surface in less than 15 seconds at ambient temperature. In addition, detection is carried out instantly since the beads become visible on the surface. The concept of MFH was tested for quality control of array manufacturing, and was combined with a multiplex competitive hybridization (MUCH) approach for typing of Human Papilloma Virus (HPV). Magnetic Forced Hybridization of bead-DNA constructs to a surface achieves a significant reduction in diagnostic testing time. In addition, readout of results by visual inspection of the unassisted eye eliminates the need for additional expensive instrumentation. The method uses the same set of beads throughout the whole process of manipulating and washing DNA constructs prior to detection, as in the actual detection step itself.
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| 50. |
- Pettersson, Erik, et al.
(författare)
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Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads
- 2008
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 29:2, s. 323-329
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Tidskriftsartikel (refereegranskat)abstract
- Here we present an approach for allelotyping combining the multiplexing features of the trinucleotide threading (TnT) method with pooling of genomic DNA and massively parallel pyrosequencing, enabling reliable allele frequency estimation in large cohorts. The approach offers several benefits as compared to array-based methods and allows undertaking highly complex studies without compromising accuracy, while keeping the workload to a minimum. This proof-of-concept study involves formation of trinucleotide threads, targeting a total of 147 single-nucleotide polymorphisms (SNPs) related to obesity and cancer, for multiplex amplification and allele extraction from a pool of 462 genomes, followed by massively parallel pyrosequencing. Approximately 177k reads were approved, identified, and assigned to SNP-carrying threads rendering representative allele frequencies in the cohort.
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