Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in patients with cancer.

The lack of comprehensive diagnostics and consensus analytical models for evaluating the status of a patient's immune system has hindered a wider adoption of immunoprofiling for treatment monitoring and response prediction in cancer patients. To address this unmet need, we developed an immunoprofiling platform that uses multiparameter flow cytometry to characterize immune cell heterogeneity in the peripheral blood of healthy donors and patients with advanced cancers. Using unsupervised clustering, we identified five immunotypes with unique distributions of different cell types and gene expression profiles. An independent analysis of 17,800 open-source transcriptomes with the same approach corroborated these findings. Continuous immunotype-based signature scores were developed to correlate systemic immunity with patient responses to different cancer treatments, including immunotherapy, prognostically and predictively. Our approach and findings illustrate the potential utility of a simple blood test as a flexible tool for stratifying cancer patients into therapy response groups based on systemic immunoprofiling.

Theory of tip structure-dependent microtubule catastrophes and damage-induced microtubule rescues.

Microtubules are essential cytoskeletal polymers that exhibit stochastic switches between tubulin assembly and disassembly. Here, we examine possible mechanisms for these switches, called catastrophes and rescues. We formulate a four-state Monte Carlo model, explicitly considering two biochemical and two conformational states of tubulin, based on a recently conceived view of microtubule assembly with flared ends. The model predicts that high activation energy barriers for lateral tubulin interactions can cause lagging of curled protofilaments, leading to a ragged appearance of the growing tip. Changes in the extent of tip raggedness explain some important but poorly understood features of microtubule catastrophe: weak dependence on tubulin concentration and an increase in its probability over time, known as aging. The model predicts a vanishingly rare frequency of spontaneous rescue unless patches of guanosine triphosphate tubulin are artificially embedded into microtubule lattice. To test our model, we used in vitro reconstitution, designed to minimize artifacts induced by microtubule interaction with nearby surfaces. Microtubules were assembled from seeds overhanging from microfabricated pedestals and thus well separated from the coverslip. This geometry reduced the rescue frequency and the incorporation of tubulins into the microtubule shaft compared with the conventional assay, producing data consistent with the model. Moreover, the rescue positions of microtubules nucleated from coverslip-immobilized seeds displayed a nonexponential distribution, confirming that coverslips can affect microtubule dynamics. Overall, our study establishes a unified theory accounting for microtubule assembly with flared ends, a tip structure-dependent catastrophe frequency, and a microtubule rescue frequency dependent on lattice damage and repair.

Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes.

Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. We present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of >9,400 tissue and blood sorted cell RNA profiles incorporated into millions of artificial transcriptomes to accurately reconstruct the tumor microenvironment (TME). Bioinformatics correction for technical and biological variability, aberrant cancer cell expression inclusion, and accurate quantification and normalization of transcript expression increased Kassandra stability and robustness. Performance was validated on 4,000 H&E slides and 1,000 tissues by comparison with cytometric, immunohistochemical, or single-cell RNA-seq measurements. Kassandra accurately deconvolved TME elements, showing the role of these populations in tumor pathogenesis and other biological processes. Digital TME reconstruction revealed that the presence of PD-1-positive CD8+ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.

The total content of toxic elements in horsehair given the level of essential elements.

Elemental status of 214 mares aged 3-7 years from 11 breeds was studied: Arabian purebred (n = 20), Bashkir (n = 20), Kabarda (n = 20), Vyatka (n = 20), Tuva (n = 19), Yakutsk (n = 30), Mezenskaya (n = 20), Thoroughbred (n = 20), Akhal-Teke (n = 20), Russian trotter (n = 15), Soviet Heavy Draft (n = 10) bred in 13 regions of Russia. The research objective is to study the content of chemical elements in hair from the horse's mane, depending on the sum of toxic elements in animal hair expressed in moles. The elemental composition of the hair was defined by atomic emission and mass spectrometry (AES and MS). Elemental composition of biosubstrates was studied by 25 indicators (Al, As, B, Ca, Cd, Co, Cr, Cu, Fe, I, K, Li, Mg, Mn, Na, Ni, P, Pb, Se, Si, Sn, Hg, Sr, V, Zn). In the studies, an estimate of the total toxic load of the horse's body (∑tox) was given as the sum of mmoles of Al, Cd, Pb, Sn, Hg, and Sr in horsehair. Based on ∑tox percentile calculations, animals were divided into three groups up to 25 percentile (n = 54) with concentrations up to 1.09 mmol/kg, within the 25 and 75 percentile limits (n = 105) and over 75 percentile (n = 55) with a concentration above 6.08 mmol/kg. As follows from the obtained results, the ∑tox indicator in the mane's hair is closely connected with the total hair mineralization. For the studied range of ∑tox values, the relationship of this indicator with 13 essential and conditionally essential chemical elements is described. Moreover, as ∑tox increases, it indicates an increase in the concentration of eleven (Ca, P, Co, Cr, Fe, I, Mn, Li, Ni, V, As) and a decrease of two elements in hair (B, Si); for six elements (K, Mg, Na, Cu, Zn, Sn), such a connection was not revealed. At ∑tox values higher than 75 percentile, a critical increase in the exchange pools of two or more toxic elements in the body was observed in 85% of cases. Intensive exchange of selenium and iodine is observed; it is expressed by an increase in the number of animals with the content of these elements in hair beyond the "physiological standard," estimated as the range of 25-75 percentile.

Rat liver folate metabolism can provide an independent functioning of associated metabolic pathways.

Folate metabolism in mammalian cells is essential for multiple vital processes, including purine and pyrimidine synthesis, histidine catabolism, methionine recycling, and utilization of formic acid. It remains unknown, however, whether these processes affect each other via folate metabolism or can function independently based on cellular needs. We addressed this question using a quantitative mathematical model of folate metabolism in rat liver cytoplasm. Variation in the rates of metabolic processes associated with folate metabolism (i.e., purine and pyrimidine synthesis, histidine catabolism, and influxes of formate and methionine) in the model revealed that folate metabolism is organized in a striking manner that enables activation or inhibition of each individual process independently of the metabolic fluxes in others. In mechanistic terms, this independence is based on the high activities of a group of enzymes involved in folate metabolism, which efficiently maintain close-to-equilibrium ratios between substrates and products of enzymatic reactions.