Pharmacogenomic modeling of bortezomib resistance in B cell malignancies

University of Minnesota Ph.D. dissertation. April 2013. Major: Molecular, Cellular, Developmental Biology and Genetics. Advisor: Brian G. Van Ness. 1 computer file (PDF); xii, 219 pages.Proteasome inhibitors are a class of drugs that have been largely successful in the treatment of cancer patients, particularly those with the plasma cell malignancy, multiple myeloma. The most successful of these drugs, bortezomib (Bz), has paved the way for the development of next-generation proteasome inhibitors. Although Bz has significantly contributed to improved outcomes in myeloma patients, acquired resistance to Bz is imminent. Furthermore, a portion of patients never initially respond to the drug. Therefore, the goal of these studies was to further characterize Bz resistance with the aim to better predict secondary therapies that may be used successfully with Bz to recapture drug sensitivity.In the first study, we describe the creation of an in vitro malignant mouse plasma cell system from which we create isogenic pairs of Bz-sensitive and -resistant cell lines. We further characterize the transcriptional responses of these cell line pairs to identify both conserved and unique expression signatures. Using the expression signatures that are unique to each pair of cell lines, we identify secondary therapies that may be useful for treatment of the Bz-refractory cell line using an in silico database called Connectivity Map (CMAP). This analysis predicted a unique response to histone deacetylase inhibitors, a class of drugs that are currently being tested for efficacy in myeloma, in only one mouse cell line pair. Indeed, we find that the predicted Bz-resistant cell line has increased sensitivity to this class of drugs (including the drug panobinostat). When these cells were transferred back into syngeneic recipient mice, panobinostat treatment could successfully extend the life of Bz-resistant animals suggesting that the Bz-resistant phenotype may select also for increased sensitivity to other drugs that may be identified through in silico approaches. In the second study, we follow up these observations by investigating other CMAP prediction patterns, such as those that are conserved across all cell line pairs. A second prediction of one class of these CMAP-predicted drugs using high-throughput drug screening of the cell lines revealed that a combination of these approaches may be highly successful for accurate prediction of secondary therapies. Based on these predictions, we further investigate the efficacy of topoisomerase inhibitors in combination with Bz for the treatment of Bz-resistant cell lines.In the third study, we provide further immunophenotypic characterization of the Bz-sensitive and -resistant mouse cell lines revealing not only cell surface markers that are associated with "acquired" and "innate" Bz resistance but perhaps a mechanism of resistance. Although Bz-sensitive mouse cells display a classic myeloma phenotype, homing to the bone marrow in vivo and expressing classic plasma cell markers, Bz-resistant mouse cells present as extramedullary disease and express a more B cell-like immunophenotype. We identify that differences in migration may be linked to the differential expression of the bone marrow homing protein, CXCR4. Lower expression of this gene in a Bz human clinical trial was also associated with inferior survival. Immunophenotypic characterization of these cell populations further revealed that forced differentiation of the Bz-resistant population could restore Bz-sensitivity.The final study investigates the acquisition of Bz-resistance in a B cell malignancy, Burkitt lymphoma, that is currently undergoing Bz clinical trials. In this particular malignancy, a DNA mutator, AID, is known to be expressed that may contribute to other types of drug resistance. Here, we identify that this is unlikely a mechanism for developing resistance to Bz. Furthermore, we provide evidence that AID activity is reduced in Bz-resistant clones and, in fact, that high AID expression may be selectively eliminated during Bz selection

Design of a framework to promote physical activity for the elderly

Physical inactivity is estimated to be one of the leading risk factors for global mortality and it is associated with several illnesses, such as type 2 diabetes, cardiovascular diseases and various types of cancers. To tackle this issue and promote physical activity amongst the elderly, a system that computes automatically, in real-time, the score of a Boccia game was developed. The objective of this paper is to infer the best design possible for the User Interface (UI) that displays this information. To achieve this, two surveys were conducted involving 45 participants. In the first survey, the participants were asked what features they would like to see in the UI. Based on these remarks, the authors designed an UI, along with several variations. The preferences between these variations were afterwards evaluated in the second survey. Thus, the final design of the UI was validated before being shown to the elders.This article is a result of the project Deus ex Machina: NORTE – 01 – 0145 – FEDER - 000026, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)

Physical activity in older men: longitudinal associations with inflammatory and hemostatic biomarkers, N-terminal pro-brain natriuretic peptide, and onset of coronary heart disease and mortality.

OBJECTIVES: To examine associations between habitual physical activity (PA) and changes in PA and onset of coronary heart disease (CHD) and the pathways linking PA to CHD. DESIGN: British Regional Heart Study population-based cohort; men completed questionnaires in 1996 and 1998 to 2000, attended rescreen in 1998 to 2000, and were followed up to June 2010. SETTING: Community. PARTICIPANTS: Of 4,252 men recruited from primary care centers (77% of those invited and eligible) who were rescreened in 1998 to 2000, 3,320 were ambulatory and free from CHD, stroke, and heart failure and participated in the current study. MEASUREMENTS: Usual PA (regular walking and cycling, recreational activity and sport). Outcome was first fatal or nonfatal myocardial infarction. RESULTS: In 3,320 ambulatory men, 303 first and 184 fatal CHD events occurred during a median of 11 years of follow-up; 9% reported no usual PA, 23% occasional PA, and 68% light or more-intense PA. PA was inversely associated with novel risk markers C-reactive protein, D-dimer, von Willebrand Factor and N-terminal pro-brain natriuretic peptide (NT-proBNP). Compared with no usual PA, hazard ratios (HRs) for CHD events, adjusted for age and region, were 0.52 (95% confidence interval (CI) = 0.34-0.79) for occasional PA, 0.47 (95% CI = 0.30-0.74) for light PA, 0.51 (95% CI = 0.32-0.82) for moderate PA, and 0.44 (95% CI = 0.29-0.65) for moderately vigorous or vigorous PA (P for linear trend =.004). Adjustment for established and novel risk markers somewhat attenuated HRs and abolished linear trends. Compared with men who remained inactive, men who maintained at least light PA had an HR for CHD events of 0.73 (95% CI = 0.53-1.02) and men whose PA level increased had an HR of 0.86 (95% CI = 0.55-1.35). CONCLUSION: Even light PA was associated with significantly lower risk of CHD events in healthy older men, partly through inflammatory and hemostatic mechanisms and cardiac function (NT-proBNP)

Boccia court analysis for promoting elderly physical activity

Physical inactivity is one of the leading risk factors for global mortality. Older adults, in particular, are more probable to suffer the consequences of physical inactivity, since it is one of the most sedentary age groups. On the other hand, engaging physical activity can have various benefits for the prevention of several diseases and functional loss prevention, therefore, it is critical to encourage its regular practice amongst the elderly. Boccia is a simple precision ball sport that is easily adaptable for individuals with physical limitations, which makes it a perfectly good game for this circumstance. The present paper proposes a ball-detection based system for monitoring the Boccia court, compute the current game score and display it on a user interface. The future goal of such system will be to motivate the elders to participate more frequently in the Boccia game and make the overall game experience more enjoyable. The proposed system was tested with twenty video recordings of different simulated game situations. Overall, the obtained results were encouraging, having only one incorrect game score being computed by the developed algorithm.This article is a result of the project Deus ex Machina: NORTE01-0145-FEDER-000026, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)

High-throughput fluorescence-activated cell sorting for lipid hyperaccumulating Chlamydomonas reinhardtii mutants

The genetically tractable microalga Chlamydomonas reinhardtii has many advantages as a model for renewable bioproducts and/or biofuels production. However, one limitation of C. reinhardtii is its relatively low-lipid content compared with some other algal species. To overcome this limitation, we combined ethane methyl sulfonate mutagenesis with fluorescence-activated cell sorting (FACS) of cells stained with the lipophilic stain Nile Red to isolate lipid hyperaccumulating mutants of C. reinhardtii. By manipulating the FACS gates, we sorted mutagenized cells with extremely high Nile Red fluorescence signals that were rarely detected in nonmutagenized populations. This strategy successfully isolated several putative lipid hyperaccumulating mutants exhibiting 23% to 58% (dry weight basis) higher fatty acid contents than their progenitor strains. Significantly, for most mutants, nitrogen starvation was not required to attain high-lipid content nor was there a requirement for a deficiency in starch accumulation. Microscopy of Nile Red stained cells revealed that some mutants exhibit an increase in the number of lipid bodies, which correlated with TLC analysis of triacyglycerol content. Increased lipid content could also arise through increased biomass production. Collectively, our findings highlight the ability to enhance intracellular lipid accumulation in algae using random mutagenesis in conjunction with a robust FACS and lipid yield verification regime. Our lipid hyperaccumulating mutants could serve as a genetic resource for stacking additional desirable traits to further increase lipid production and for identifying genes contributing to lipid hyperaccumulation, without lengthy lipid-induction periods

In Vitro Data Suggest a Role for PMS2 Kozak Sequence Mutations in Lynch Syndrome Risk

This study investigates the role of 5′ UTR PMS2 Kozak sequence genetic variation in cancer risk. It accomplishes this through the development of a mid-throughput reporter assay where variants can be tested for protein translation efficiency. The results highlight the importance of continued study of the Kozak sequence related to human disease

The relationship between back pain and mortality in older adults varies with disability and gender: results from the Cambridge City over-75s Cohort (CC75C) study.

BACKGROUND: This study aims to determine whether older adults reporting back pain (BP) are at increased risk of premature mortality, specifically, to examine the association with disabling/non-disabling pain separately. METHODS: Participants aged ≥75 years were recruited to the Cambridge City over-75s Cohort (CC75C) study. Participants answered interviewer-administered questions on BP and were followed up until death. The relationship between BP and mortality was examined using Cox regression, adjusted for potential confounding factors. Separate models were computed for men and women. RESULTS: From 1174 individuals with BP data, the date of death was known for 1158 (99%). A significant association was found between disabling BP and mortality (hazard ratio: 1.4; 95% confidence interval: 1.1-1.8) and this remained, albeit of borderline significance, following adjustment for socio-demographic variables and potential disease markers (1.3; 0.99-1.7). Further, this association was found to vary with sex: women experienced a 40% increase in the risk of mortality associated with disabling BP (1.4; 1.1-1.9), whereas no such increase was observed for men (1.0; 0.5-1.9). Participants with non-disabling BP were not at increased risk of mortality. CONCLUSIONS: This study confirmed previous findings regarding the relationship between pain and excess mortality. Further, we have shown that, among older adults, this association is specific to disabling pain and to women. Clinicians should be aware not only of the short-term implications of disabling BP but also the longer-term effects. Future research should attempt to understand the mechanisms underpinning this relationship to avoid excess mortality and should aim to determine why the relationship differs in men and women

Photosynthetic Adaptation to Length of Day Is Dependent on S-Sulfocysteine Synthase Activity in the Thylakoid Lumen

Abstract Arabidopsis (Arabidopsis thaliana) chloroplasts contain two O-acetyl-serine(thiol)lyase (OASTL) homologs, OAS-B, which is an authentic OASTL, and CS26, which has S-sulfocysteine synthase activity. In contrast with OAS-B, the loss of CS26 function resulted in dramatic phenotypic changes, which were dependent on the light treatment. We have performed a detailed characterization of the photosynthetic and chlorophyll fluorescence parameters in cs26 plants compared with those of wild-type plants under short-day growth conditions (SD) and long-day growth conditions (LD). Under LD, the photosynthetic characterization, which was based on substomatal CO2 concentrations and CO2 concentration in the chloroplast curves, revealed significant reductions in most of the photosynthetic parameters for cs26, which were unchanged under SD. These parameters included net CO2 assimilation rate, mesophyll conductance, and mitochondrial respiration at darkness. The analysis also showed that cs26 under LD required more absorbed quanta per driven electron flux and fixed CO2. The nonphotochemical quenching values suggested that in cs26 plants, the excess electrons that are not used in photochemical reactions may form reactive oxygen species. A photoinhibitory effect was confirmed by the background fluorescence signal values under LD and SD, which were higher in young leaves compared with mature ones under SD. To hypothesize the role of CS26 in relation to the photosynthetic machinery, we addressed its location inside of the chloroplast. The activity determination and localization analyses that were performed using immunoblotting indicated the presence of an active CS26 enzyme exclusively in the thylakoid lumen. This finding was reinforced by the observation of marked alterations in many lumenal proteins in the cs26 mutant compared with the wild type.</jats:p

Diminishing benefits of urban living for children and adolescents’ growth and development

Optimal growth and development in childhood and adolescence is crucial for lifelong health and well-being1,2,3,4,5,6. Here we used data from 2,325 population-based studies, with measurements of height and weight from 71 million participants, to report the height and body-mass index (BMI) of children and adolescents aged 5–19 years on the basis of rural and urban place of residence in 200 countries and territories from 1990 to 2020. In 1990, children and adolescents residing in cities were taller than their rural counterparts in all but a few high-income countries. By 2020, the urban height advantage became smaller in most countries, and in many high-income western countries it reversed into a small urban-based disadvantage. The exception was for boys in most countries in sub-Saharan Africa and in some countries in Oceania, south Asia and the region of central Asia, Middle East and north Africa. In these countries, successive cohorts of boys from rural places either did not gain height or possibly became shorter, and hence fell further behind their urban peers. The difference between the age-standardized mean BMI of children in urban and rural areas wa