Biologic drug discovery pipelines are designed to deliver protein therapeutics that have exquisite functional potency and selectivity while also manifesting biophysical characteristics suitable for ...manufacturing, storage, and convenient administration to patients. The ability to use computational methods to predict biophysical properties from protein sequence, potentially in combination with high throughput assays, could decrease timelines and increase the success rates for therapeutic developability engineering by eliminating lengthy and expensive cycles of recombinant protein production and testing. To support development of high-quality predictive models for antibody developability, we designed a sequence-diverse panel of 83 effector functionless IgG1 antibodies displaying a range of biophysical properties, produced and formulated each protein under standard platform conditions, and collected a comprehensive package of analytical data, including in vitro assays and in vivo mouse pharmacokinetics. We used this robust training data set to build machine learning classifier models that can predict complex protein behavior from these data and features derived from predicted and/or experimental structures. Our models predict with 87% accuracy whether viscosity at 150 mg/mL is above or below a threshold of 15 centipoise (cP) and with 75% accuracy whether the area under the plasma drug concentration-time curve (AUC0-672 h) in normal mouse is above or below a threshold of 3.9 × 106 h x ng/mL.
Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA) on genome-wide mRNA and microRNA (miRNA) expression ...in Nucleus Accumbens (NAc) of subjects with alcohol dependence (AD; N = 18) and of matched controls (N = 18), six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05). Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. Gene set enrichment analysis demonstrated that neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling. Glial-specific modules were predominantly enriched for genes involved in processes related to immune functions, i.e. cytokine signaling (all adj. p≤ 0.05). In mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected biological functions of miRNAs, correlation analyses between mRNA and miRNA hub genes revealed a higher number of positive than negative correlations (χ2 test p≤ 0.0001). Integration of hub gene expression with genome-wide genotypic data resulted in 591 mRNA cis-eQTLs and 62 miRNA cis-eQTLs. mRNA cis-eQTLs were significantly enriched for AD diagnosis and AD symptom counts (adj. p = 0.014 and p = 0.024, respectively) in AD GWAS signals in a large, independent genetic sample from the Collaborative Study on Genetics of Alcohol (COGA). In conclusion, our study identified putative gene network hubs coordinating mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
Background Depression is a heritable trait that exists on a continuum of varying severity and duration. Yet, the search for genetic variants associated with depression has had few successes. We ...exploit the entire continuum of depression to find common variants for depressive symptoms. Methods In this genome-wide association study, we combined the results of 17 population-based studies assessing depressive symptoms with the Center for Epidemiological Studies Depression Scale. Replication of the independent top hits ( p <1×10−5 ) was performed in five studies assessing depressive symptoms with other instruments. In addition, we performed a combined meta-analysis of all 22 discovery and replication studies. Results The discovery sample comprised 34,549 individuals (mean age of 66.5) and no loci reached genome-wide significance (lowest p = 1.05×10−7 ). Seven independent single nucleotide polymorphisms were considered for replication. In the replication set ( n = 16,709), we found suggestive association of one single nucleotide polymorphism with depressive symptoms (rs161645, 5q21, p = 9.19×10−3 ). This 5q21 region reached genome-wide significance ( p = 4.78×10−8 ) in the overall meta-analysis combining discovery and replication studies ( n = 51,258). Conclusions The results suggest that only a large sample comprising more than 50,000 subjects may be sufficiently powered to detect genes for depressive symptoms.
Background
Testing for direct gene or single nucleotide polymorphism replication of association across studies may not capture the true importance of a candidate locus; rather, we suggest that ...relevant replication across studies may be found at the level of a biological process. We previously observed that variation in 2 members of the switching defective/sucrose nonfermenting (SWI/SNF) chromatin remodeling complex is associated with alcohol dependence (AD) in the Irish Affected Sib Pair Study for Alcohol Dependence. Here, we tested for association with alcohol‐related outcomes using a set of genes functioning in the SWI/SNF complex in 2 independent samples.
Methods
We used a set‐based analysis to examine the 29 genes of the SWI/SNF complex for evidence of association with (i) AD in the adult Collaborative Study on the Genetics of Alcoholism (COGA) case‐control sample and (ii) antisocial behavior, hypothesized to be a genetically related developmental precursor, in a younger population sample (Spit for Science S4S).
Results
We found evidence for association of the SWI/SNF complex with AD in COGA (p = 0.0435) and more general antisocial behavior in S4S (p = 0.00026). The genes that contributed most strongly to the signal in COGA were SS18L1, SMARCD1, BRD7, BCL7B, SMARCB1, and BCL11A. In the S4S sample, ACTB, ARID2, BCL11A, BCL11B, BCL7B, BCL7C, DPF2, and DPF3 all contributed strongly to the signal.
Conclusions
We detected associations between the SWI/SNF complex and AD in an adult population selected from treatment‐seeking probands and antisocial behavior in an adolescent population sample. This provides strong support for a role for SWI/SNF in the development of alcohol‐related problems.
Replication of genetic association at the level of the biological process, rather than the gene, may reveal important mechanisms underlying alcohol dependence (AD). We used a set of all genes encoding members of the SWI/SNF chromatin remodeling complex to test for association with AD in COGA and antisocial behavior in Spit for Science (S4S) and found association with AD (yellow), antisocial behavior (blue), and both (green). These associations suggest a role for the regulation of chromatin structure in alcohol‐related outcomes.
The absence of expanded numbers of hepatitis C virus (HCV)-reactive CD8+ T lymphocytes (CTLs) in patients chronically infected with HCV has led to the investigation of dendritic cell (DC) function in ...this population as a potential cause for this defect. Several studies have shown evidence for impaired monocyte-derived DCs in chronically infected patients. As it is difficult to reconcile these data with the fact that patients with chronic HCV are immune competent, we re-evaluated this finding, carefully assessing phenotypic markers and functional activity of patient DCs as compared with noninfected controls. In contrast to these prior studies, DCs from 13 of 13 chronic HCV patients expressed typical maturation markers. These mature DCs were capable of priming allogeneic T lymphocytes, as well as stimulating influenza-specific memory T cells. This finding is consistent with clinical and immunologic data that the deficit in the patient’s immune repertoire is HCV-specific and suggests that refined models are required for understanding the role of DCs in HCV pathogenesis. (Blood. 2004;103:1026-1029)
Background: Given the presence of neural progenitor cells (NPC) in the retina of other species capable of differentiating into multiple neural components, the authors report the presence of NPC in ...the adult human retina. A resident population of NPC suggests that the retina may constitutively replace neurons, photoreceptors, and glia. Methods: Adult human postmortem retinal explants and cell suspensions were used to generate cells in tissue culture that display the features of NPC. The phenotype of cells and differentiation into neurons was determined by immunocytochemistry. Dividing cells were labelled with 5-bromo-2-deoxyuridine (BrdU) and neurospheres were generated and passaged. Results: Cells labelled with nestin, neurofilament M (NFM), rhodopsin, or glial fibrillary acidic protein (GFAP) grew out from explant cultures. BrdU labelling of these cells occurred only with basic fibroblast growth factor (FGF-2). Dissociated retina and pars plana generated primary neurospheres. From primary neurospheres, NPC were passaged to generate secondary neurospheres, neurons, photoreceptors, and glia. BrdU labelling identified dividing cells from neurospheres that differentiated to express NFM and rhodopsin. Conclusion: The adult human retina contains NPC and may have the potential to replace neurons and photoreceptors. This has implications for the pathogenesis and treatment of retinal disorders and degenerations, including glaucoma, and those disorders associated with retinal scarring.
BACKGROUND
Preoperative ordering of blood products has been an area of optimization due to considerable variability among physicians; overpreparation can lead to extra costs and underpreparation of ...blood can potentially compromise patient safety.
STUDY DESIGN AND METHODS
We examined the potential cost savings of extending the storage interval of a presurgical type‐and‐screen sample from 7 to 14 days, thereby reducing the need for a new specimen on the day of surgery.
RESULTS
Sensitivity analysis showed annual cost savings for our institution to be an estimated $38,770 ($22,420‐$73,120).
CONCLUSION
These results are even more robust when incorporating the additional potential savings from improved operating room efficiency.
Background: Artificial intelligence (AI) constructs and machine learning (ML) algorithms have demonstrated utility in predicting various clinical, surgical, and financial outcomes. In this study, we ...applied AI to shoulder hemiarthroplasty (HA) to predict various post-operative complications. Methods: The sample was queried from the American college of surgeons-national surgical quality improvement program (ACS-NSQIP) database for all shoulder HA cases from 2008-2018. Six ML algorithms-random forest classifier, gradient boosting classifier, decision tree classifier, SVM classifier-tuned model, Gaussian Naïve Bayes classifier, multi-layer perception-analyzed the sample dataset. Postoperative complications included extended length of stay, non-home discharge destination, transfusion, and any adverse event. Each ML model was compared to logistic regression (LR), and model strength was evaluated. Results: We identified a total of 1585 shoulder HA cases. Mean age, BMI, operative time, and length of stay were 66±12 years, 31±8 kg/m2, 114±61 minutes, and 2.93±6.61 days. Preop hematocrit, longer operative time, and older age were most predictive of extended length of stay. Preop hematocrit, operative time, and ASA class had the highest importance in any adverse events (AAE) prediction. ML models outperformed traditional comorbidity indices, LR, for predicting extended length of stay (79% vs. 66%), non-home discharge destination (79% vs. 65%), any adverse event (78% vs. 66%), and transfusion requirement (82% vs. 63%). Conclusions: ML algorithms predicted post-surgical outcomes of interest following shoulder HA at a higher rate to conventional LR and can assist orthopedic surgeons in decision making.
DNA Vaccines to Attack Cancer Stevenson, Freda K.; Ottensmeier, Christian H.; Johnson, Peter ...
Proceedings of the National Academy of Sciences - PNAS,
10/2004, Letnik:
101, Številka:
Suppl 2
Journal Article
Recenzirano
Odprti dostop
Delivery of antigens by injection of the encoding DNA allows access to multiple antigen-presenting pathways. Knowledge of immunological processes can therefore be used to modify construct design to ...induce selected effector functions. Expression can be directed to specific intracellular sites, and additional genes can be fused or codelivered to amplify responses. Therapeutic vaccination against cancer adds a requirement to overcome tolerance and to activate a weakened immune repertoire. Induction of CD4+ T helper cells is critical for both antibody and T cell effector responses. To activate immunity against tumor antigens, we fused the tumor-derived sequences to genes encoding microbial proteins. This strategy engages T helper cells from the large antimicrobial repertoire for linked help for inducing antibody against cell-surface tumor antigens. The principle of linked T cell help also holds for induction of epitope-specific antitumor CD8+ T cells, but the microbial sequence has to be minimized to avoid competition with tumor antigens. Epitope-specific DNA vaccination leads to powerful antitumor attack and can activate immunity from a profoundly tolerized repertoire. Vaccine designs validated in preclinical models are now in clinical trial with immune responses detected against both tumor antigens and fused microbial antigens. DNA priming is highly efficient, but boosting may benefit from increased antigen expression. Physical methods including electroporation provide increased expression without introducing additional competing antigens. A wide range of cancers can be targeted, and objective assays of response will determine efficacy.
Aims
The current WHO classification of thymic epithelial neoplasms describes type A and type AB thymomas as behaving ‘like benign neoplasms’. However, recent published data suggest that rare cases ...may show more aggressive behaviour. The aim of this study was to assess the frequency of atypical cases, and to determine whether atypia is associated with more advanced disease.
Methods and results
One hundred and twenty‐one thymomas (type A, n = 68; type AB, n = 53) were retrospectively reviewed for ‘atypical’ features (nuclear pleomorphism, mitotic activity, and necrosis). Logistic regression was used to ascertain the association with increasing Masaoka–Koga stage. Where available, follow‐up data were also reviewed. There were 72 stage I, 42 stage II, five stage III and two stage IV tumours. Only the presence of necrosis showed a significant association with increased stage in univariate and multivariate analysis. Nuclear atypia and increased mitotic activity were not associated with increasing stage of disease.
Conclusions
Our data support the concept of there being more aggressive atypical variants of both type A and type AB thymoma, and suggest that the presence of necrosis could be used to predict aggressive behaviour.
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