Characterization of RUNX1 function in hematopoiesis /

RUNX1 or runt-related transcription factor 1 is a transcription factor in the RUNX family of proteins. This family is composed of RUNX1, RUNX2, and RUNX3--all of which contain the runt homology domain, which mediates interaction with DNA and other transcriptional co-factors. RUNX1 has garnered much attention over the past decades primarily because its disruption has been associated with a variety of human diseases and malignancies. Several chromosomal translocations in leukemias involve RUNX1. The most famous one is between chromosomes 8 and 21 resulting in the RUNX1-ETO fusion and leads to acute myeloid leukemia. Since then, RUNX1 mutations have been found in acute lymphoid leukemia, myelodysplastic syndrome, myeloproliferative neoplasm, familial platelet disease, and others. Although RUNX1 has been a major focus in the field of hematology, many of the molecular and cellular mechanisms of how RUNX1 disruption leads to disease remain unknown. Uncovering these mechanisms will result in a better understanding of these diseases and may lead to meaningful therapies. As a transcription factor, RUNX1 primarily exerts its functions by regulating target genes. This dissertation explores how these target genes ultimately facilitate RUNX1 functions in hematopoiesis and in hematopoietic stem and progenitor cells (HSPCs). We first focus on Hmga2 or high mobility group AT-hook 2, which was found to be up-regulated in RUNX1 loss-of- function HSPCs. Hmga2 is an established oncogene and has roles in inducing cellular proliferation. Notably, Hmga2 was found to contribute to myeloid progenitor cell expansion, which is a main characteristic of RUNX1 loss-of -function. Next, we analyzed differential gene expression data from wildtype and RUNX1 loss-of-function HSPCs and determined that these genes are involved in pathways associated with cell-to-cell interaction and signaling. Upon further examination, we discovered that RUNX1 loss-of -function mice exhibit hypersensitivity to HSPC mobilization regimens. Finally, we focus on another RUNX1 target gene known as Gimap4 or GTPase of the immunity- associated protein 4 and confirm that up-regulation of Gimap4 contributes to HSPC expansion, a finding also found in RUNX1 loss-of-function mice. Together, these studies provide critical insight in the role of RUNX1 in hematopoiesis and blood-related diseases, and offer additional avenues for therapies for these disease

Fatigue and Peripheral Muscle Dysfunction: Studies on Vitamin D Status, Muscle Metabolism and Systemic Inflammation in Patients with COPD : Aspects of COPD severity beyond FEV1 and exacerbations

Background The severity of Chronic Obstructive Pulmonary Disease (COPD) is usually described in terms of forced expiratory volume in one second (FEV1) and number of exacerbations. However, COPD is a complex disease with different ways of expression, involving pulmonary symptoms, extra pulmonal manifestations and comorbidities, which altogether affect the patient by contributing to reduced functional capacity, increased shortness of breath, reduced health-related quality of life and increased mortality. Systemic inflammation is common in COPD and can potentially constitute a link between the lungs and other organs.   The aim of this thesis was to broaden the aspects of COPD severity beyond FEV1 and exacerbations by studying fatigue, the role of vitamin D, nutritional factors, systemic inflammation and peripheral muscle function in patients with COPD.    Methods and Results In paper I, we included 101 patients with COPD, and 34 control subjects. Assessment of experience of fatigue, functional limitation due to fatigue, and the relationships to physiological, psychological and situational variables and quality of life (QoL) were evaluated.   We found that experience of fatigue was highly prevalent (72% versus 56% in control subjects) and a troublesome symptom in COPD. Patients with COPD and fatigue had lower lung function, shorter walking distance, more dyspnoea, anxiety and depressive symptoms and poorer health status compared to patients without fatigue (all p < 0.01). Several contributing factors were identified to experience of fatigue and functional limitations of fatigue with dyspnoea, depressive symptoms and insomnia as the most prominent factors. No clear association with systemic inflammation was found.   Paper II evaluated vitamin D status in 66 patients with advanced COPD (28 with long-term oxygen therapy (LTOT)) and 47 control subjects. 25-hydroxyvitamin 25(OH)D were deter-mined in early fall in a short period of seven weeks. Questionnaires about COPD symptoms, general health, lifestyle, dietary habits and QoL were answered. Lung function tests and blood sampling including systemic inflammatory markers, carotenoids and protein carbonylation (PC) were assessed. The peak annual 25(OH)D of COPD patients was significantly lower than in the control subjects, but there was no significant difference between COPD patients with and without LTOT. Among vitamin D-deficient COPD patients, 25(OH)D correlated positively with lung function, blood oxygenation, food portion size, Mediterranean Diet Score and Ultra-violet Score and negatively with dyspnoea and DOSE-index, a composite index for COPD se-verity. Ongoing vitamin D supplementation was the single most important intervention to maintain 25(OH)D levels <50 nmol/L.   In paper III, we evaluated in the same cohort as paper II oxidative damage and levels of carotenoids. Patients with COPD (±LTOT) did not demonstrate increased oxidative damage. Com-pared with the control group, levels of several carotenoids were significantly lower in COPD, and the diet contained significantly less fruit and vegetables. Lycopene correlated positively with saturation and lutein correlated positively with some inflammatory markers but negatively with IL-6, an important marker for systemic inflammation. The study highlights the importance of dietary factors in COPD.    In paper IV, 32 patients with COPD answered questionnaires, and were subjected to lung function tests and blood analysis including systemic inflammatory markers. Magnetic resonance imaging (MRI) for analysis of whole-body and thigh muscle composition was performed. Bioenergetics in the resting thigh muscle, (PCr/Pi ratio), were analysed using 31phosphorus magnetic resonance spectroscopy (31P-MRS). We found that adverse muscle composition was common in the COPD group. Clinical characteristics reflecting COPD severity were all associated with a raise of the PCr/Pi ratio in the thigh muscle. Increased MFIa correlated positively to systemic inflammatory markers, negative to physical activity and PCr/Pi ratio. We compared the COPD group with a virtual control group from UK Biobank (n= 3200).   Conclusions Severe COPD is much more than airway obstruction and exacerbations. The presence of fatigue is associated, as well as vitamin D status and nutritional factors, with important clinical out-comes reflecting COPD severity. Adverse muscle composition is common in COPD and there seems to be a link between systemic inflammation, muscle fat infiltration and bioenergetics.

Network Orientation and Segmentation Refinement Using Machine Learning

Network mapping is used to extract the coordinates of a network's components in an image. Furthermore, machine learning algorithms have demonstrated their efficacy in advancing the field of network mapping across various domains, including mapping of road networks and blood vessel networks. However, accurately mapping of road networks still remains a challenge due to difficulties in identification and separation of roads in the presence of occlusion caused by trees, as well as complex environments, such as parking lots and complex intersections. Additionally, the segmentation of blood vessels networks, such as the ones in the retina, is also not trivial due to their complex shape and thin appearance. Therefore, the aim for this thesis was to investigate two deep learning approaches to improve mapping of networks, namely by refining existing road network probability maps, and by estimating road network orientations. Additionally, the thesis explores the possibility of using a machine learning model trained on road network probability maps to refine retina network segmentations. In the first approach, U-Net models with a binary output channel were implemented to refine existing probability maps of networks. In the second approach, ResNet models with a regression output were implemented to estimate the orientation of roads within a network. The models for refining road network probability maps were evaluated using F1-score and MCC-score, while the models for estimating road network orientation were evaluated based on angle loss, angle difference, F1-score, and MCC-score.  The results for refining road segmentations yielded an increase of 0.102 MCC-score compared to the baseline (0.701). However, when applying the segmentation refinement model to retina images, the output from the model achieved merely 0.226 in MCC-score. Nevertheless, the model demonstrated the capability to identify and refine the segmentation of large blood vessels. Additionally, the estimation of road network orientation achieved an average error of 10.50 degrees. It successfully distinguished roads from the background, achieving an MCC-score of 0.805. In conclusion, this thesis shows that a deep learning-based approach for road segmentation refinement is beneficial, especially in cases where occlusions are present. However, the refinement of retina image segmentations using a model trained on roads and tested on retina images produced unsatisfactory results, likely due to differences in scale between road width and vessel size. Further experiments with adjustments in image scales are likely needed to achieve better results. Moreover, the orientation model demonstrated promising results in estimating the orientation of road pixels and effectively differentiating between road and non-road pixels

Network Orientation and Segmentation Refinement Using Machine Learning

Network mapping is used to extract the coordinates of a network's components in an image. Furthermore, machine learning algorithms have demonstrated their efficacy in advancing the field of network mapping across various domains, including mapping of road networks and blood vessel networks. However, accurately mapping of road networks still remains a challenge due to difficulties in identification and separation of roads in the presence of occlusion caused by trees, as well as complex environments, such as parking lots and complex intersections. Additionally, the segmentation of blood vessels networks, such as the ones in the retina, is also not trivial due to their complex shape and thin appearance. Therefore, the aim for this thesis was to investigate two deep learning approaches to improve mapping of networks, namely by refining existing road network probability maps, and by estimating road network orientations. Additionally, the thesis explores the possibility of using a machine learning model trained on road network probability maps to refine retina network segmentations. In the first approach, U-Net models with a binary output channel were implemented to refine existing probability maps of networks. In the second approach, ResNet models with a regression output were implemented to estimate the orientation of roads within a network. The models for refining road network probability maps were evaluated using F1-score and MCC-score, while the models for estimating road network orientation were evaluated based on angle loss, angle difference, F1-score, and MCC-score.  The results for refining road segmentations yielded an increase of 0.102 MCC-score compared to the baseline (0.701). However, when applying the segmentation refinement model to retina images, the output from the model achieved merely 0.226 in MCC-score. Nevertheless, the model demonstrated the capability to identify and refine the segmentation of large blood vessels. Additionally, the estimation of road network orientation achieved an average error of 10.50 degrees. It successfully distinguished roads from the background, achieving an MCC-score of 0.805. In conclusion, this thesis shows that a deep learning-based approach for road segmentation refinement is beneficial, especially in cases where occlusions are present. However, the refinement of retina image segmentations using a model trained on roads and tested on retina images produced unsatisfactory results, likely due to differences in scale between road width and vessel size. Further experiments with adjustments in image scales are likely needed to achieve better results. Moreover, the orientation model demonstrated promising results in estimating the orientation of road pixels and effectively differentiating between road and non-road pixels

ERADicating stem cells from their niche.

Protein homeostasis preserves stem cell function, but underlying mechanisms are largely unknown. A study reveals that protein quality control mediated by the endoplasmic reticulum-associated degradation pathway ensures proper expression of MPL, a key cell surface receptor that promotes haematopoietic stem cell function through niche interaction

Oxidant status, iron homeostasis, and carotenoid levels of COPD patients with advanced disease and LTOT

Background: The pathogenesis of chronic obstructive pulmonary disease (COPD) is associated with oxidative stress. Both iron (Fe) and oxygen are involved in the chemical reactions that lead to increased formation of reactive oxygen species. Oxidative reactions are prevented by antioxidants such as carotenoids. Objective: To study the differences in Fe status, carotenoid levels, healthy eating habits, and markers of inflammation and oxidative damage on proteins in subjects with severe COPD ± long-term oxygen therapy (LTOT) and lung-healthy control subjects. Methods: Sixty-six Caucasians with advanced COPD (28 with LTOT) and 47 control subjects were included. Questionnaires about general health, lifestyle, and dietary habits were answered. Lung function tests and blood sampling were performed. Results: COPD subjects (±LTOT) did not demonstrate increased oxidative damage, assessed by protein carbonylation (PC), while levels of soluble transferrin receptors (sTfRs) were slightly elevated. Soluble TfRs, which is inversely related to Fe status, was negatively associated with PC. Levels of carotenoids, total and ß-cryptoxanthin, a- and ß-carotenes, were significantly lower in COPD subjects, and their diet contained significantly less fruits and vegetables. Lutein correlated inversely with IL-6, lycopene correlated inversely with SAT, while ß-carotene was positively associated with a Mediterranean-like diet. Conclusions: Fe could favor oxidative stress in COPD patients, suggesting a cautious use of Fe prescription to these patients. COPD subjects ate a less healthy diet than control subjects did and would, therefore, benefit by dietary counseling. COPD patients with hypoxemia are probably in particular need of a lycopene-enriched diet

The influence of disease severity and lifestyle factors on the peak annual 25(OH)D value of COPD patients

Background: The prevalence of individuals deficient in vitamin D (defined as a serum level of the stable metabolite 25(OH)D amp;lt; 50 nmol/L) is increasing in countries with low annual ultraviolet (UV) radiation and among individuals unable to perform outdoor activities, for example, COPD patients. Objective: To assess the role of vitamin D deficiency, independently of seasonal variation, the peak annual value of 25(OH)D was measured in subjects with advanced COPD +/- long-term oxygen therapy (LTOT) and lung healthy control subjects. A method to grade the individual annual UV light exposure was designed and tested. Subjects and methods: Sixty-six Caucasians with advanced COPD (28 with LTOT) and 47 control subjects were included, and the levels of 25(OH)D were determined in late summer/ early fall when the annual peak was assumed. Questionnaires about COPD symptoms, general health, lifestyle, dietary habits and QoL were used to collect data. Lung function tests and blood sampling were performed. Results: The peak annual 25(OH)D of COPD subjects was significantly lower than in the control subjects, but there was no significant difference between COPD patients with and without LTOT. Ongoing vitamin D supplementation was the single most important intervention to maintain 25(OH)D levels amp;gt;= 50 nmol/L. Among vitamin D-deficient COPD subjects, 25(OH)D correlated positively with forced expiratory volume in 1 second as % predicted, Modified British Medical Research Council score, blood oxygenation, food portion size, Mediterranean Diet Score and Ultraviolet Score. Conclusion: Vitamin D deficiency was common among healthy individuals and COPD subjects. Peak annual 25(OH)D levels of COPD subjects correlated with clinically important outcomes. The present study emphasizes the need to routinely monitor vitamin D status among patients with advanced COPD and to consider to medicate those with vitamin D deficiency with vitamin D supplementation.Funding Agencies|County Council of Ostergotland Region Ostergotland, ALF [LIO-275901, LIO-355741, LIO-432861, LIO-534761, LIO-601911, LIO-697521]; Medical Research Council of Southeast Sweden (FORSS) [FORSS-308331, FORSS-559931, FORSS-226801]; Linkoping University Hospital Foundation for Medical Research, Sweden [LIO-475131]; Heart and Lung Foundation, Sweden [20140245, 20140330]; Swedish Society of Medicine [SLS-368431]; County Council of Ostergotland (ALF), Sweden [LIO-201751]; County Council of Jonkoping (Futurum), Sweden [FUTURUM-342821, FUTURUM-489691, FUTURUM-608651, FUTURUM-712082, FUTURUM-712181]</p

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Experience of fatigue, and its relationship t

Experience of fatigue, and its relationship to physical capacity and disease severity in men and women with COPD

Kristina T&ouml;dt,1,2 Elisabeth Skargren,3 Magnus Kentson,4 Kersti Theander,5,6 Per Jakobsson,2 Mitra Unosson1 1Department of Social and Welfare Studies, Faculty of Health Sciences, Link&ouml;ping University, Norrk&ouml;ping, Sweden; 2Department of Pulmonary Medicine, University Hospital, 3Department of Medicine and Health, Faculty of Health Sciences, Link&ouml;ping University, Link&ouml;ping, Sweden; 4Department of Pulmonary Medicine, Ryhov Hospital, J&ouml;nk&ouml;ping, Sweden; 5Department of Nursing, Faculty of Social and Life Sciences, Karlstad University, Karlstad, Sweden; 6Primary Care Research Unit, County Council of V&auml;rmland, Sweden Introduction: Several differences have been reported in the clinical characteristics of chronic obstructive pulmonary disease (COPD) between men and women. Differences have been found in the association between respiratory symptoms and lung function, and in the factors associated with dyspnea. This raises the question of whether there are differences between the sexes in the relationship between fatigue, the second most prevalent symptom, and the variables of physical capacity and disease severity. Objectives: To examine the experience of fatigue and its relationship to physical capacity and disease severity in men and women with COPD. Methods: In a cross-sectional study 121 patients with COPD (54 men and 67 women), the experience of fatigue (frequency, duration, and severity) and physical capacity (lung function, 6-minute walk distance [6MWD], grip strength, and timed-stand test) were assessed. Disease severity was graded according to the Body mass index, airway Obstruction, Dyspnoea and Exercise capacity (BODE) index. Two multiple logistic regression models were tested, both of which were performed separately in men and women, to examine the association between the experience of fatigue and variables of physical capacity and the BODE index. Results: Eighty-nine (73.6%) patients experienced fatigue, with similar proportions in men and women. The men with fatigue had worse physical capacity and more severe disease than did the men without fatigue: for men with and without fatigue, respectively, the percent of predicted forced expiratory volume in 1 second (FEV1) (mean [standard deviation]) was 47 (14) vs 64 (17); the 6MWD (mean [standard deviation]) was 398 (138) vs 539 (105) m; and the BODE index (median [quartile 1-3]) was 3 (2&ndash;5) vs 1 (0&ndash;1) (P&lt;0.01). In women, only higher leg fatigue post-6MWD was seen among those experiencing fatigue compared with women without fatigue: for women with and without fatigue, respectively, leg fatigue (median [quartile 1-3]) was 4 (3&ndash;5) vs 2 (0&ndash;3) (P&lt;0.001). The regression models showed that the 6MWD and the BODE index were associated with fatigue in both men and women, but in women, leg fatigue remained an independent associate in both models. Conclusion: Exercise capacity and disease severity were associated with fatigue in both men and women. In women, leg fatigue was strongly associated with fatigue, which warrants further investigation. Keywords: chronic obstructive pulmonary disease, disease state, functional capacity, sex differences, symptom experience, leg fatigu