Expression-based subtypes define pathologic response to neoadjuvant immune-checkpoint inhibitors in muscle-invasive bladder cancer

Checkpoint immunotherapy (CPI) has increased survival for some patients with advanced-stage bladder cancer (BCa). However, most patients do not respond. Here, we characterized the tumor and immune microenvironment in pre- and post-treatment tumors from the PURE01 neoadjuvant pembrolizumab immunotherapy trial, using a consolidative approach that combined transcriptional and genetic profiling with digital spatial profiling. We identify five distinctive genetic and transcriptomic programs and validate these in an independent neoadjuvant CPI trial to identify the features of response or resistance to CPI. By modeling the regulatory network, we identify the histone demethylase KDM5B as a repressor of tumor immune signaling pathways in one resistant subtype (S1, Luminal-excluded) and demonstrate that inhibition of KDM5B enhances immunogenicity in FGFR3-mutated BCa cells. Our study identifies signatures associated with response to CPI that can be used to molecularly stratify patients and suggests therapeutic alternatives for subtypes with poor response to neoadjuvant immunotherapy.

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

The diversity of T-cell receptors recognizing foreign pathogens is generated through a highly stochastic recombination process, making the independent production of the same sequence rare. Yet unrelated individuals do share receptors, which together constitute a "public" repertoire of abundant clonotypes. The TCR repertoire is initially formed prenatally, when the enzyme inserting random nucleotides is downregulated, producing a limited diversity subset. By statistically analyzing deep sequencing T-cell repertoire data from twins, unrelated individuals of various ages, and cord blood, we show that T-cell clones generated before birth persist and maintain high abundances in adult organisms for decades, slowly decaying with age. Our results suggest that large, low-diversity public clones are created during pre-natal life, and survive over long periods, providing the basis of the public repertoire.

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

tcR: an R package for T cell receptor repertoire advanced data analysis

Background

The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing.

Results

Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies.

Conclusions

tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples.

[The alcoholism as a medical social problem]

The anti alcoholic policy in the Russian Federation has to be developed against a background of the enhancement of quality of statistics of mortality and actual losses due to alcoholisation. Also, the monitoring of epidemic aftermaths of the new framework of alcohol consumption among the youth and the results of target research studies of alcoholism situation in various social groups of Russia has to be considered.

[The interrelationship of alcoholic psychoses and lethal alcohol intoxications with population cash income]

The analysis of dependence of alcoholic psychoses and lethal alcohol intoxications from the portion of poor population all over 87 regions of the Russian Federation revealed the decrease in alcoholism morbidity up to 70.7%. Thereby, the poorer is the territory the higher is the indexes of morbidity and mortality because of alcoholism.

Application of neutron generators for high explosives, toxic agents and fissile material detection

The portable pulsed neutron generators developed and designed by VNIIA are presented. The neutron methods are good tools for non-destructive assay of dangerous materials. The samples of various systems for the detection of high explosives in luggage, identification of toxic agents in chemical munitions, and also for the prevention of illicit trafficking of fissile elements in passengers' luggage are discussed.

[Not Available]

The ideas of such prominent geneticists as Vries, Cuenot, Guyenot, Johannsen, Tchetverykov, Philiptchenko are considered. The conjectures on the specific mechanisms of evolution above the species level may be found in many of them. The very terms of micro- and macroevolution have been proposed by Philiptchenko in 1927. But he denied any role of genetics in puzzling of the higher taxa origin, the letter being connected him with sexual sells plasma. The actual significance of Goldschmidt's conception about systemic mutations is mentioned.

[The protective action of arbidol during a rise in respiratory diseases in 1990]

Prophylactic properties of a new chemical drug, arbidol, against acute respiratory diseases (ARD) were studied. Arbidol given daily in a dose of 0.2 g for 19 days reduced the morbidity rate 2.3-fold in adults during an outbreak of ARD. Geometric mean titres of antibodies to respiratory viruses among healthy persons did not change after treatment with arbidol indicating the lack of immunosuppressive properties in the drug. The prophylactic effect of arbidol may be due to both specific effect of the drug on influenza and parainfluenza viruses, and its interferon-inducing and immunity-stimulating properties.