| 1. |
- Björn, Niclas, 1990-, et al.
(author)
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Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients
- 2020
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In: npj Systems Biology and Applications. - : Nature Publishing Group. - 2056-7189. ; 6:1
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Journal article (peer-reviewed)abstract
- Gemcitabine/carboplatin chemotherapy commonly induces myelosuppression, including neutropenia, leukopenia, and thrombocytopenia. Predicting patients at risk of these adverse drug reactions (ADRs) and adjusting treatments accordingly is a long-term goal of personalized medicine. This study used whole-genome sequencing (WGS) of blood samples from 96 gemcitabine/carboplatin-treated non-small cell lung cancer (NSCLC) patients and gene network modules for predicting myelosuppression. Association of genetic variants in PLINK found 4594, 5019, and 5066 autosomal SNVs/INDELs with p ≤ 1 × 10−3 for neutropenia, leukopenia, and thrombocytopenia, respectively. Based on the SNVs/INDELs we identified the toxicity module, consisting of 215 unique overlapping genes inferred from MCODE-generated gene network modules of 350, 345, and 313 genes, respectively. These module genes showed enrichment for differentially expressed genes in rat bone marrow, human bone marrow, and human cell lines exposed to carboplatin and gemcitabine (p < 0.05). Then using 80% of the patients as training data, random LASSO reduced the number of SNVs/INDELs in the toxicity module into a feasible prediction model consisting of 62 SNVs/INDELs that accurately predict both the training and the test (remaining 20%) data with high (CTCAE 3–4) and low (CTCAE 0–1) maximal myelosuppressive toxicity completely, with the receiver-operating characteristic (ROC) area under the curve (AUC) of 100%. The present study shows how WGS, gene network modules, and random LASSO can be used to develop a feasible and tested model for predicting myelosuppressive toxicity. Although the proposed model predicts myelosuppression in this study, further evaluation in other studies is required to determine its reproducibility, usability, and clinical effect.
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| 2. |
- Lindblom, Jessica, 1969-
(author)
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Minding the Body : Interacting socially through embodied action
- 2007
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Doctoral thesis (other academic/artistic)abstract
- This dissertation clarifies the role and relevance of the body in social interaction and cognition from an embodied cognitive science perspective. Theories of embodied cognition have during the past two decades offered a radical shift in explanations of the human mind, from traditional computationalism which considers cognition in terms of internal symbolic representations and computational processes, to emphasizing the way cognition is shaped by the body and its sensorimotor interaction with the surrounding social and material world. This thesis develops a framework for the embodied nature of social interaction and cognition, which is based on an interdisciplinary approach that ranges historically in time and across different disciplines. The theoretical framework presents a thorough and integrated understanding that supports and explains the embodied nature of social interaction and cognition. It is argued that embodiment is the part and parcel of social interaction and cognition in the most general and specific ways, in which dynamically embodied actions themselves have meaning and agency. The framework is illustrated by empirical work that provides some detailed observational fieldwork on embodied actions captured in three different episodes of spontaneous social interaction in situ. Besides illustrating the theoretical issues discussed in the thesis, the empirical work also reveals some novel characteristics of embodied action in social interaction and cognition. Furthermore, the ontogeny of social interaction and cognition is considered, in which social scaffolding and embodied experience play crucial roles during child development. In addition, the issue what it would take for an artificial system to be (socially) embodied is discussed from the perspectives of cognitive modeling and technology. Finally, the theoretical contributions and implications of the study of embodied actions in social interaction and cognition for cognitive science and related disciplines are summed up. The practical relevance for applications to artificial intelligence and human-computer interaction is also outlined as well as some aspects for future work.
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| 3. |
- Mak, Wing Cheung, et al.
(author)
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Controlled Delivery of Human Cells by Temperature Responsive Microcapsules
- 2015
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In: Journal of Functional Biomaterials. - : MDPI. - 2079-4983. ; 6:2, s. 439-453
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Journal article (peer-reviewed)abstract
- Cell therapy is one of the most promising areas within regenerative medicine. However, its full potential is limited by the rapid loss of introduced therapeutic cells before their full effects can be exploited, due in part to anoikis, and in part to the adverse environments often found within the pathologic tissues that the cells have been grafted into. Encapsulation of individual cells has been proposed as a means of increasing cell viability. In this study, we developed a facile, high throughput method for creating temperature responsive microcapsules comprising agarose, gelatin and fibrinogen for delivery and subsequent controlled release of cells. We verified the hypothesis that composite capsules combining agarose and gelatin, which possess different phase transition temperatures from solid to liquid, facilitated the destabilization of the capsules for cell release. Cell encapsulation and controlled release was demonstrated using human fibroblasts as model cells, as well as a therapeutically relevant cell line—human umbilical vein endothelial cells (HUVECs). While such temperature responsive cell microcapsules promise effective, controlled release of potential therapeutic cells at physiological temperatures, further work will be needed to augment the composition of the microcapsules and optimize the numbers of cells per capsule prior to clinical evaluation.
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| 4. |
- Nilsson, Emma, et al.
(author)
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Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome
- 2018
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In: Journal of Clinical Endocrinology & Metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 103:12, s. 4465-4477
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Journal article (peer-reviewed)abstract
- Context: Insulin resistance in skeletal muscle is a major risk factor for the development of type 2 diabetes in women with polycystic ovary syndrome (PCOS). Despite this, the mechanisms underlying insulin resistance in PCOS are largely unknown. Objective: To investigate the genome-wide DNA methylation and gene expression patterns in skeletal muscle from women with PCOS and controls and relate them to phenotypic variations. Design/Participants: In a case-control study, skeletal muscle biopsies from women with PCOS (n = 17) and age-, weight-, and body mass index. matched controls (n = 14) were analyzed by array-based DNA methylation and mRNA expression profiling. Results: Eighty-five unique transcripts were differentially expressed in muscle from women with PCOS vs controls, including DYRK1A, SYNPO2, SCP2, and NAMPT. Furthermore, women with PCOS had reduced expression of genes involved in immune system pathways. Two CpG sites showed differential DNA methylation after correction for multiple testing. However, an mRNA expression of similar to 30% of the differentially expressed genes correlated with DNA methylation levels of CpG sites in or near the gene. Functional follow-up studies demonstrated that KLF10 is under transcriptional control of insulin, where insulin promotes glycogen accumulation in myotubes of human muscle cells. Testosterone downregulates the expression levels of COL1A1 and MAP2K6. Conclusion: PCOS is associated with aberrant skeletal muscle gene expression with dysregulated pathways. Furthermore, we identified specific changes in muscle DNA methylation that may affect gene expression. This study showed that women with PCOS have epigenetic and transcriptional changes in skeletal muscle that, in part, can explain the metabolic abnormalities seen in these women.
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| 5. |
- Ohlsson, Monica, et al.
(author)
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Hereditary myopathy with early respiratory failure associated with a mutation in A-band titin
- 2012
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In: Brain. - : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 135:6, s. 1682-1694
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Journal article (peer-reviewed)abstract
- Hereditary myopathy with early respiratory failure and extensive myofibrillar lesions has been described in sporadic and familial cases and linked to various chromosomal regions. The mutated gene is unknown in most cases. We studied eight individuals, from three apparently unrelated families, with clinical and pathological features of hereditary myopathy with early respiratory failure. The investigations included clinical examination, muscle histopathology and genetic analysis by whole exome sequencing and single nucleotide polymorphism arrays. All patients had adult onset muscle weakness in the pelvic girdle, neck flexors, respiratory and trunk muscles, and the majority had prominent calf hypertrophy. Examination of pulmonary function showed decreased vital capacity. No signs of cardiac muscle involvement were found. Muscle histopathological features included marked muscle fibre size variation, fibre splitting, numerous internal nuclei and fatty infiltration. Frequent groups of fibres showed eosinophilic inclusions and deposits. At the ultrastructural level, there were extensive myofibrillar lesions with marked Z-disc alterations. Whole exome sequencing in four individuals from one family revealed a missense mutation, g.274375T > C; p.Cys30071Arg, in the titin gene (TTN). The mutation, which changes a highly conserved residue in the myosin binding A-band titin, was demonstrated to segregate with the disease in all three families. High density single nucleotide polymorphism arrays covering the entire genome demonstrated sharing of a 6.99 Mb haplotype, located in chromosome region 2q31 including TTN, indicating common ancestry. Our results demonstrate a novel and the first disease-causing mutation in A-band titin associated with hereditary myopathy with early respiratory failure. The typical histopathological features with prominent myofibrillar lesions and inclusions in muscle and respiratory failure early in the clinical course should be incentives for analysis of TTN mutations.
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| 6. |
- Olesen, Kim, et al.
(author)
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Spatiotemporal extracellular matrix modeling for in situ cell niche studies
- 2021
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In: Stem Cells. - : John Wiley & Sons. - 1066-5099 .- 1549-4918. ; 39:12, s. 1751-1765
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Journal article (peer-reviewed)abstract
- Extracellular matrix (ECM) components govern a range of cell functions such as migration, proliferation, maintenance of stemness and differentiation. Cell niches that harbor stem-/progenitor cells, with matching ECM, have been shown in a range of organs, although their presence in the heart is still under debate. Determining niches depends on a range of in vitro and in vivo models and techniques, where animal models are powerful tools for studying cell-ECM dynamics, however, they are costly and time-consuming to use. In vitro models based on recombinant ECM proteins lack the complexity of the in vivo ECM. To address these issues, we present the Spatiotemporal Extracellular Matrix Model (StEMM) for studies of cell-ECM dynamics, such as cell niches. This model combines gentle decellularization and sectioning of cardiac tissue, allowing retention of a complex ECM, with recellularization and subsequent image processing using image stitching, segmentation, automatic binning and generation of cluster maps. We have thereby developed an in situ representation of the cardiac ECM that is useful for assessment of repopulation dynamics and to study the effect of local ECM composition on phenotype preservation of reseeded mesenchymal progenitor cells. This model provides a platform for studies of organ-specific cell-ECM dynamics and identification of potential cell niches. © AlphaMed Press 2021 SIGNIFICANCE STATEMENT: Stem cells reside in adult organs within specific microenvironments called cell niches. The heart is a complex organ and so far, the presence and localization of stem-/progenitor cell niches are subject to constant debate. To address these issues, the authors have developed the Spatiotemporal Extracellular Matrix Model (StEMM), which combines a modified protocol for decellularization, with cryo-sectioning, recellularization, and subsequent image processing including automatic binning and generation of cluster maps. StEMM was developed within a cardiac context and validated using syngeneic mesenchymal progenitor cells. However, this model is not restricted with regard to species or organs.
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