Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma.

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that 'polyvalent' vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole exome sequencing (WES) and RNA sequencing (RNA-Seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-Seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by alignment of B-cell receptor (BCR) CDR3 regions from RNA-Seq data, grouping at the protein level, and comparison to the BCR repertoire from healthy individuals using RNA-Seq data. An average of 52 somatic mutations per patient (range: 2-172) were identified, and two or more (median: 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide (SLP) vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all four patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field.

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.

Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients.

Follicular lymphoma (FL) is a generally incurable malignancy that evolves from developmentally blocked germinal center (GC) B cells. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Dynamic interactions between tumor B cells and the tumor microenvironment (TME) are hypothesized to contribute to the broad spectrum of clinical behaviors observed among FL patients. Despite the urgent need, existing clinical tools do not reliably predict disease behavior. Using a multi-modal strategy, we examined cell-intrinsic and -extrinsic factors governing progression and therapeutic outcomes in FL patients enrolled onto a prospective clinical trial. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk FL patients. These features include stromal desmoplasia and changes to the follicular growth pattern present 20 months before first progression and first relapse.

Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma.

BACKGROUND & AIMS: The complex tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) has hindered the development of reliable predictive biomarkers for targeted therapy and immunomodulatory strategies. A comprehensive characterization of the TME is necessary to advance precision therapeutics in PDAC. METHODS: A transcriptomic profiling platform for TME classification based on functional gene signatures was applied to 14 publicly available PDAC datasets (n = 1657) and validated in a clinically annotated independent cohort of patients with PDAC (n = 79). Four distinct subtypes were identified using unsupervised clustering and assessed to evaluate predictive and prognostic utility. RESULTS: TME classification using transcriptomic profiling identified 4 biologically distinct subtypes based on their TME immune composition: immune enriched (IE); immune enriched, fibrotic (IE/F); fibrotic (F); and immune depleted (D). The IE and IE/F subtypes demonstrated a more favorable prognosis and potential for response to immunotherapy compared with the F and D subtypes. Most lung metastases and liver metastases were subtypes IE and D, respectively, indicating the role of clonal phenotype and immune milieu in developing personalized therapeutic strategies. In addition, distinct TMEs with potential therapeutic implications were identified in treatment-naive primary tumors compared with tumors that underwent neoadjuvant therapy. CONCLUSIONS: This novel approach defines a distinct subgroup of PADC patients that may benefit from immunotherapeutic strategies based on their TME subtype and provides a framework to select patients for prospective clinical trials investigating precision immunotherapy in PDAC. Further, the predictive utility and real-world clinical applicability espoused by this transcriptomic-based TME classification approach will accelerate the advancement of precision medicine in PDAC.

Mathematical Model of Propagation of an Aerosol Created by an Impulse Method in Space.

When developing neutralization systems for harmful agents, it is necessary to understand the mechanisms of the formation and evolution of an aerosol cloud in a closed or open space. Effective decontamination with aerosol clouds is provided by a rather high particle concentration and dispersion in an open space or on contaminated surfaces. This paper considers neutralization systems based on pulsed powder aerosol generators. It is shown that an aerosol cloud consisting of micron- and submicron-sized particles appears for several seconds after spraying. A further evolution of the aerosol cloud in a room is associated with the gravitational settling, diffusion, and coagulation of particles and their settling on the walls and ceiling. In the case of an open space or a ventilation system in a room, the evolution of the aerosol cloud is affected by the airflow. The main purpose of this paper is to determine the most important parameters and critical conditions of pulsed aerosol generation. A mathematical model is, thus, proposed for pulsed aerosol generation, and its parametric study is conducted in the most typical conditions. The purpose performance predicted by the model is the mass concentration of aerosol particles in the air and on surfaces, depending on the time of particle spraying and dispersion.

Dataset on the proteomic response during ferroptosis induction via tamoxifen induced GPX4 KO in mouse embryonic fibroblasts.

Ferroptosis is a type of programmed cell death distinct from apoptosis and necroptosis that plays an essential role in pathophysiological conditions such as neurodegenerative diseases and tumorigenesis. Massive lipid oxidation in an iron-dependent manner is a hallmark of ferroptosis.This modality of cell death is also characterized by perturbation of several metabolic pathways, predominantly fatty acid metabolism, thiol metabolism, iron homeostasis and the mevalonate pathway. We aimed to acquire data from different timepoints of ferroptotic death in order to get information about the primary and delayed phases of the ferroptotic response. For this purpose, we used model Pfa1 cells, which are 4-OH-TAM-inducible Gpx4-/- mouse immortalized fibroblasts [1]. GPX4 is one of the main intracellular ferroptosis regulators and inhibiting it is a classic approach to induce ferroptosis. Measuring protein fold changes at different ferroptotic stages and in nontreated Pfa1 cells could give useful information on the activation of genes involved in ferroptosis and non-genomic protein regulation during ferroptotic progression. Bottom-up proteomic data were acquired from samples obtained 24 and 48 hours after genetic induction of ferroptosis. Chromato-mass spectra were registered in DDA mode and are suitable for further label-free quantification. These data might be a valuable proteome basis for further investigation of ferroptosis and complement other available omics.

Preclinical models for prediction of immunotherapy outcomes and immune evasion mechanisms in genetically heterogeneous multiple myeloma.

The historical lack of preclinical models reflecting the genetic heterogeneity of multiple myeloma (MM) hampers the advance of therapeutic discoveries. To circumvent this limitation, we screened mice engineered to carry eight MM lesions (NF-κB, KRAS, MYC, TP53, BCL2, cyclin D1, MMSET/NSD2 and c-MAF) combinatorially activated in B lymphocytes following T cell-driven immunization. Fifteen genetically diverse models developed bone marrow (BM) tumors fulfilling MM pathogenesis. Integrative analyses of ∼500 mice and ∼1,000 patients revealed a common MAPK-MYC genetic pathway that accelerated time to progression from precursor states across genetically heterogeneous MM. MYC-dependent time to progression conditioned immune evasion mechanisms that remodeled the BM microenvironment differently. Rapid MYC-driven progressors exhibited a high number of activated/exhausted CD8+ T cells with reduced immunosuppressive regulatory T (Treg) cells, while late MYC acquisition in slow progressors was associated with lower CD8+ T cell infiltration and more abundant Treg cells. Single-cell transcriptomics and functional assays defined a high ratio of CD8+ T cells versus Treg cells as a predictor of response to immune checkpoint blockade (ICB). In clinical series, high CD8+ T/Treg cell ratios underlie early progression in untreated smoldering MM, and correlated with early relapse in newly diagnosed patients with MM under Len/Dex therapy. In ICB-refractory MM models, increasing CD8+ T cell cytotoxicity or depleting Treg cells reversed immunotherapy resistance and yielded prolonged MM control. Our experimental models enable the correlation of MM genetic and immunological traits with preclinical therapy responses, which may inform the next-generation immunotherapy trials.

Mathematical modeling of high-energy materials rheological behavior in 3D printing technology.

In this paper, a mathematical model of the extrusion process in 3D printing of high-energy composites is studied. These composites are formed from polymer binder and powder with bimodal particles obtained by electric explosion technique. The main difficulty of extrusion 3D printing method is primarily linked to the high viscosity of utilized material, especially one with high concentration of particles. In this case, the viscosity of the initial mixture depends on the pressure, temperature and concentration of the filler, as well as on the particle dispersion. Under certain conditions the ignition of high-energy material in the nozzle is possible, thus the search for optimal printing parameters based on the mathematical modeling and the following experimental verification are the main purposes of the current work.

Mathematical Model of the Pulse Generation of Decontaminating Aerosols.

A mathematical model of the pulse generation of decontaminating aerosols utilizing the energy of high-energy materials (HEM) is proposed with account for the physical and chemical properties of the atomized substance, HEM characteristics, and gas generator parameters. Such a model is needed to counter the environmental hazards, process emissions, and terrorist attacks with hazardous and dangerous aerosols. Another aspect of the problem is the danger of biological aerosols carrying viral or microbial particles that are spread naturally or induced using biological weapons. In many cases, the mission is not only to neutralize aerosol particles in indoor air and on surfaces but also to do it quickly. In this regard, an attractive option is the pulse method for generating special aerosols aimed at quickly, within a few seconds, creating a cloud of particles that will interact with hazardous aerosol particles and decontaminate them. HEM energy is proposed to be used for the pulse generation of such aerosols. It is important not only to atomize the decontaminating aerosol quickly and evenly in space but also to preserve the useful physical and chemical properties of the particles. To test the regimes and methods of pulse generation, an adequate mathematical model of the process is required, which is proposed in this manuscript.

A Mathematical Model for Sublimation of a Thin Film in Trace Explosive Detection Problem.

Here, we introduce an advanced mathematical model for the sublimation of thin films of explosives. The model relies on the Hertz-Knudsen-Langmuir (HKL) equation that describes the vaporization rate of an explosive and controls the mass exchange between the surface and the ambient air. The latest experimental data on sublimation and diffusion of 2,4,6-trinitrotoluene (TNT) monocrystals were factored in, as well as the data on the sublimation rate of hexogen (RDX), octogen (HMX), and picramide (TNA) traces. To advance the mathematical model we suggested previously, we took into account the structure of a substrate on which a thin explosive layer was deposited. The measurement problem of the sublimation rate and limits of an explosive arises from developing and advancing remote detection methods for explosives traces. Using mathematical modelling, we can identify a detectable quantity of a specific explosive under given conditions. We calculated the mass of the explosive in the air upon sublimation of thin explosive films from the surfaces over a wide range of the parameters in question and made conclusions regarding the application limits of the devised standoff trace explosive detection techniques.

Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression.

Follicular lymphoma (FL) is a B-cell malignancy with a complex tumor microenvironment that is rich in nonmalignant immune cells. We applied single-cell RNA sequencing to characterize the diverse tumor and immune cell populations of FL and identified major phenotypic subsets of FL T cells, including a cytotoxic CD4 T-cell population. We characterized four major FL subtypes with differential representation or relative depletion of distinct T-cell subsets. By integrating exome sequencing, we observed that somatic mutations are associated with, but not definitive for, reduced MHC expression on FL cells. In turn, expression of MHCII genes by FL cells was associated with significant differences in the proportions and targetable immunophenotypic characteristics of T cells. This provides a classification framework of the FL microenvironment in association with FL genotypes and MHC expression, and informs different potential immunotherapeutic strategies based upon tumor cell MHCII expression. SIGNIFICANCE: We have characterized the FL-infiltrating T cells, identified cytotoxic CD4 T cells as an important component that is associated with tumor cell-intrinsic characteristics, and identified sets of targetable immune checkpoints on T cells that differed from FLs with normal versus low MHC expression. See related commentary by Melnick, p. 374. This article is highlighted in the In This Issue feature, p. 369.

Review of the Problems of Additive Manufacturing of Nanostructured High-Energy Materials.

This article dwells upon the additive manufacturing of high-energy materials (HEM) with regards to the problems of this technology's development. This work is aimed at identifying and describing the main problems currently arising in the use of AM for nanostructured high-energy materials and gives an idea of the valuable opportunities that it provides in the hope of promoting further development in this area. Original approaches are proposed for solving one of the main problems in the production of nanostructured HEM-safety and viscosity reduction of the polymer-nanopowder system. Studies have shown an almost complete degree of deagglomeration of microencapsulated aluminum powders. Such powders have the potential to create new systems for safe 3D printing using high-energy materials.

Propagation of viral bioaerosols indoors.

Here we look into the spread of aerosols indoors that may potentially carry viruses. Many viruses, including the novel SARS-CoV-2, are known to spread via airborne and air-dust pathways. From the literature data and our research on the propagation of fine aerosols, we simulate herein the carryover of viral aerosols in indoor air. We demonstrate that a lot of fine droplets released from an infected person's coughing, sneezing, or talking propagate very fast and for large distances indoors, as well as bend around obstacles, lift up and down over staircases, and so on. This study suggests equations to evaluate the concentration of those droplets, depending on time and distance from the source of infection. Estimates are given for the safe distance to the source of infection, and available methods for neutralizing viral aerosols indoors are considered.

Spores of puffball fungus Lycoperdon pyriforme as a reference standard of stable monodisperse aerosol for calibration of optical instruments.

Advanced air quality control requires real-time monitoring of particulate matter size and concentration, which can only be done using optical instruments. However, such techniques need regular calibration with reference samples. In this study, we suggest that puffball fungus (Lycoperdon pyriforme) spores can be utilized as a reference standard having a monodisperse size distribution. We compare the Lycoperdon pyriforme spores with the other commonly used reference samples, such as Al2O3 powder and polystyrene latex (PSL) microspheres. Here we demonstrate that the puffball spores do not coagulate and, thus, maintain the same particle size in the aerosol state for at least 15 minutes, which is enough for instrument calibration. Moreover, the puffball mushrooms can be stored for several years and no agglomeration of the spores occurs. They are also much cheaper than other calibration samples and no additional devices are needed for aerosol generation since the fungal fruiting body acts as an atomizer itself. The aforementioned features make the fungal spores a highly promising substance for calibration and validation of particle size analyzers, which outperforms the existing, artificially produced particles for aerosol sampling. Furthermore, the L. pyriforme spores are convenient for basic research and development of new optical measurement techniques, taking into account their uniform particle size and absent coagulation in the aerosol.

Adaptive response of blood lymphocytes as a marker of hemopoiesis status in exposed persons.

After the onset of a long-term low dose rate radiation exposure (55-60 y later) of the Techa riverside residents within a range of individual red bone marrow (RBM) doses from 0.01 to 1.79 Gy, it was established that there was an obvious association between the type of reaction manifested by peripheral blood lymphocytes to small dose irradiation in vitro (adaptive potential) and the RBM cell composition (during the period of the major exposure), as well as the peripheral blood cell composition (at a late time period coincident with the studies of induced radioresistance). The nature of these dependencies observed in chronically exposed individuals differs from that revealed in the controls. Based on the results of the study, it can be suggested that the capacity for adaptive response shown by peripheral blood lymphocytes donated by exposed persons at late time after exposure can be regarded as a biological marker of the functional state of the hemopoietic stem cell pool.