Computational methodologies for DNA-encoded libraries

Die Entdeckung von Arzneimitteln ist ein langwieriger und sehr kosten- und ressourcenintensiver Prozess. Daher wurden Screening-Technologien (physisch und virtuell) eingesetzt, um solche Prozesse zu optimieren und zu beschleunigen. DNA-kodierte Bibliotheken (DELs) haben sich in den letzten 30 Jahren als Alternative zum Hochdurchsatz-Screening herauskristallisiert, da sie zahlreiche Vorteile bieten. Die DEL-Technologie birgt jedoch drei große Herausforderungen: der Erhalt des DNA-Barcodes, die Abdeckung des chemischen Raums und die Identifizierung der Hits. Diese Faktoren werden durch die Größe der DNA-kodierten Bibliotheken und die daraus resultierende Menge der erzeugten Daten noch erschwert. Daher wurden chemoinformatische Ansätze verwendet, wie die KNIME-Analytics Platfrom. Im ersten Kapitel dieser Arbeit (Chemistry selection) wird ein Algorithmus vorgestellt, der den Raum der chemischen Reaktionen kartiert und sortiert, um Reaktionen auszuwählen, die potenziell für die DELSynthese verwendet werden können. Solche Reaktionen müssen Anforderungen erfüllen, welche die Integrität des DNA-Barcodes gewährleisten. Darüber hinaus beschreibt der Algorithmus die Reaktionen anhand spezieller molekularer Deskriptoren, die den Kern der Reaktion, d. h. den Teil der Reaktanten, der in Produkte umgewandelt wird, berücksichtigen. Auf der Grundlage solcher Deskriptoren wurden die Reaktionen geclustert, um den chemischen Reaktionsraum abzubilden. Aus den Clustern konnten Reaktionen erfolgreich auf DNA-kodierte Substrate angewendet werden. Im zweiten Kapitel (Building blocks selection) wurde die KNIME Analytics Platform eingesetzt, um die Bausteine (BBs) für die Bibliothekssynthese auszuwählen, mit dem Ziel, die strukturelle Vielfalt zu erhöhen. Virtuelle Bibliotheken konnten entsprechend der ausgewählten BBs und der etablierten DNA-kompatiblen Chemien aufgelistet werden. Die Reaktionen wurden mit Datenbanken arzneimittelähnlicher Verbindungen verglichen. Im dritten Kapitel (DNA-encoded library validation by molecular docking) wurden die Hit-Moleküle mit molekularer Docking-Software validiert. Drei Proteine wurden detailliert beschrieben und ihre jeweiligen Hits wurden als Liganden im Docking-Verfahren verwendet. Die Anwendung des Dockings als Validierungsmethode erwies sich als nützlich für die Bestätigung von Treffern, für di

Armida disvelata. L’immagine del velo nella "Gerusalemme liberata"

The essay takes into account the different occurrences of the term ‘veil’ in the Gerusalemme liberata. After an analysis of the metaphorical meanings of the term, the focus moves towards the veils that hide or embellish some of the female characters, in particular Sofronia, Erminia and Armida, bringing to light the different functions – even symbolic – that appear to be connected to this garment.The essay takes into account the different occurrences of the term ‘veil’ in the Gerusalemme liberata. After an analysis of the metaphorical meanings of the term, the focus moves towards the veils that hide or embellish some of the female characters, in particular Sofronia, Erminia and Armida, bringing to light the different functions – even symbolic – that appear to be connected to this garment

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

A genome-wide association search for type 2 diabetes genes in African Americans.

African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

At the crossroads of apoptosis and autophagy: multiple roles of the co-chaperone BAG3 in stress and therapy resistance of cancer

BAG3, a multifunctional HSP70 co-chaperone and anti-apoptotic protein that interacts with the ATPase domain of HSP70 through its C-terminal BAG domain plays a key physiological role in cellular proteostasis. The HSP70/BAG3 complex determines the levels of a large number of selective client proteins by regulating their turnover via the two major protein degradation pathways, i.e. proteasomal degradation and macroautophagy. On the one hand, BAG3 competes with BAG1 for binding to HSP70, thereby preventing the proteasomal degradation of its client proteins. By functionally interacting with HSP70 and LC3, BAG3 also delivers polyubiquitinated proteins to the autophagy pathway. BAG3 exerts a number of key physiological functions, including an involvement in cellular stress responses, proteostasis, cell death regulation, development, and cytoskeletal dynamics. Conversely, aberrant BAG3 function/expression has pathophysiological relevance correlated to cardiomyopathies, neurodegeneration, and cancer. Evidence obtained in recent years underscores the fact that BAG3 drives several key hallmarks of cancer, including cell adhesion, metastasis, angiogenesis, enhanced autophagic activity, and apoptosis inhibition. This review provides a state-of-the-art overview on the role of BAG3 in stress and therapy resistance of cancer, with a particular focus on BAG3-dependent modulation of apoptotic signaling and autophagic/lysosomal activity

DNA- Di nulla Academia

«DNA – Di Nulla Academia. Rivista di studi camporesiani»Interdisciplinare, interuniversitaria e internazionale, «DNA – Di Nulla Academia. Rivista di studi camporesiani» nasce con il duplice intento di mantenere viva la metodologia di studi iniziata da Piero Camporesi e di attualizzarne la ricchezza interpretativa. Proponiamo una rivisitazione degli studi di italianistica che muove dalla biblioteca ai molteplici ambienti del bios: il corpo, la cucina, la piazza, il carnevale, il paese della fame e quello di cuccagna

Common variants in the GDF5-UQCC region are associated with variation in human height

Identifying genetic variants that influence human height will advance our understanding of skeletal growth and development. Several rare genetic variants have been convincingly and reproducibly associated with height in mendelian syndromes, and common variants in the transcription factor gene HMGA2 are associated with variation in height in the general population. Here we report genome-wide association analyses, using genotyped and imputed markers, of 6,669 individuals from Finland and Sardinia, and follow-up analyses in an additional 28,801 individuals. We show that common variants in the osteoarthritis-associated locus GDF5-UQCC contribute to variation in height with an estimated additive effect of 0.44 cm (overall P < 10(-15)). Our results indicate that there may be a link between the genetic basis of height and osteoarthritis, potentially mediated through alterations in bone growth and development