Multicellular Research Articles

Multimodal fall detection for solitary individuals based on audio-video decision fusion processing

Falls often pose significant safety risks to solitary individuals, especially the elderly. Implementing a fast and efficient fall detection system is an effective strategy to address this hidden danger. We propose a multimodal method based on audio and video. On the basis of using non-intrusive equipment, it reduces to a certain extent the false negative situation that the most commonly used video-based methods may face due to insufficient lighting conditions, exceeding the monitoring range, etc. Therefore, in the foreseeable future, methods based on audio and video fusion are expected to become the best solution for fall detection. Specifically, this article outlines the following methodology: the video-based model utilizes YOLOv7-Pose to extract key skeleton joints, which are then fed into a two stream Spatial Temporal Graph Convolutional Network (ST-GCN) for classification. Meanwhile, the audio-based model employs log-scaled mel spectrograms to capture different features, which are processed through the MobileNetV2 architecture for detection. The final decision fusion of the two results is achieved through linear weighting and Dempster-Shafer (D-S) theory. After evaluation, our multimodal fall detection method significantly outperforms the single modality method, especially the evaluation metric sensitivity increased from 81.67% in single video modality to 96.67% (linear weighting) and 97.50% (D-S theory), which emphasizing the effectiveness of integrating video and audio data to achieve more powerful and reliable fall detection in complex and diverse daily life environments.

Macrophages play a nutritive role in post-metamorphic maturation in Drosophila.

In the body of multicellular organisms, macrophages play an indispensable role in maintaining tissue homeostasis by removing old, apoptotic and damaged cells. In addition, macrophages allow significant remodeling of body plans during embryonic morphogenesis, regeneration and metamorphosis. Although the huge amount of organic matter that must be removed during these processes represents a potential source of nutrients, their further use by the organism has not yet been addressed. Here, we document that, during metamorphosis, Drosophila larval adipose tissue is infiltrated by macrophages, which remove dying adipocytes by efferocytosis and engulf leaking RNA-protein granules and lipids. Consequently, the infiltrating macrophages transiently adopt the adipocyte-like metabolic profile to convert remnants of dying adipocytes to lipoproteins and storage peptides that nutritionally support post-metamorphic development. This process is fundamental for the full maturation of ovaries and the achievement of early fecundity of individuals. Whether macrophages play an analogous role in other situations of apoptotic cell removal remains to be elucidated.

Evolution of cancer resistance in the animal kingdom

Cancer is an inevitable collateral problem inherent in the evolution of multicellular organisms, which appeared at the end of the Precambrian. Faced to this constraint, a range of diverse anticancer defenses has evolved across the animal kingdom. Today, investigating how animal organisms, especially those of large size and long lifespan, manage cancer-related issues has both fundamental and applied outcomes, as it could inspire strategies for preventing or treating human cancers. In this article, we begin by presenting the conceptual framework for understanding evolutionary theories regarding the development of anti-cancer defenses. We then present a number of examples that have been extensively studied in recent years, including naked mole rats, elephants, whales, placozoa, xenarthras (such as sloths, armadillos and anteaters) and bats. The contributions of comparative genomics to understanding evolutionary convergences are also discussed. Finally, we emphasize that natural selection has also favored anti-cancer adaptations aimed at avoiding mutagenic environments, for example by maximizing immediate reproductive efforts in the event of cancer. Exploring these adaptive solutions holds promise for identifying novel approaches to improve human health.

Comparative analysis of metacyclogenesis and infection curves in different discrete typing units of Trypanosoma cruzi

Chagas disease (CD), caused by the complex life cycle parasite Trypanosoma cruzi, is a global health concern and impacts millions globally. T. cruzi’s genetic variability is categorized into discrete typing units (DTUs). Despite their widespread presence in the Americas, a comprehensive understanding of their impact on CD is lacking. This study aims to analyze life cycle traits across life cycle stages, unraveling DTU dynamics. Metacyclogenesis curves were generated, inducing nutritional stress in epimastigotes of five DTUs (TcI (MG), TcI (DA), TcII(Y), TcIII, TcIV, and TcVI), resulting in metacyclic trypomastigotes. Infection dynamics in Vero cells from various DTUs were evaluated, exploring factors like amastigotes per cell, cell-derived trypomastigotes, and infection percentage. Statistical analyses, including ANOVA tests, identified significant differences. Varying onset times for metacyclogenesis converged on the 7th day. TcI (MG) exhibited the highest metacyclogenesis potential. TcI (DA) stood out, infecting 80% of cells within 24 h. TcI demonstrated the highest potential in both metacyclogenesis and infection among the strains assessed. Intra-DTU diversity was evident among TcI strains, contributing to a comprehensive understanding of Trypanosoma cruzi dynamics and genetic diversity.

Genetic toolbox for Photorhabdus and Xenorhabdus: pSEVA based heterologous expression systems and CRISPR/Cpf1 based genome editing for rapid natural product profiling

BackgroundBacteria of the genus Photorhabdus and Xenorhabdus are motile, Gram-negative bacteria that live in symbiosis with entomopathogenic nematodes. Due to their complex life cycle, they produce a large number of specialized metabolites (natural products) encoded in biosynthetic gene clusters (BGC). Genetic tools for Photorhabdus and Xenorhabdus have been rare and applicable to only a few strains. In the past, several tools have been developed for the activation of BGCs and the deletion of individual genes. However, these often have limited efficiency or are time consuming. Among the limitations, it is essential to have versatile expression systems and genome editing tools that could facilitate the practical work.ResultsIn the present study, we developed several expression vectors and a CRISPR-Cpf1 genome editing vector for genetic manipulations in Photorhabdus and Xenorhabdus using SEVA plasmids. The SEVA collection is based on modular vectors that allow exchangeability of different elements (e.g. origin of replication and antibiotic selection markers with the ability to insert desired sequences for different end applications). Initially, we tested different SEVA vectors containing the broad host range origins and three different resistance genes for kanamycin, gentamycin and chloramphenicol, respectively. We demonstrated that these vectors are replicative not only in well-known representatives, e.g. Photorhabdus laumondii TTO1, but also in other rarely described strains like Xenorhabdus sp. TS4. For our CRISPR/Cpf1-based system, we used the pSEVA231 backbone to delete not only small genes but also large parts of BGCs. Furthermore, we were able to activate and refactor BGCs to obtain high production titers of high value compounds such as safracin B, a semisynthetic precursor for the anti-cancer drug ET-743.ConclusionsThe results of this study provide new inducible expression vectors and a CRISPR/CPf1 encoding vector all based on the SEVA (Standard European Vector Architecture) collection, which can improve genetic manipulation and genome editing processes in Photorhabdus and Xenorhabdus.

Analysis of Reliability and Cost of Complex Systems with Metaheuristic Algorithms

Introduction. The assessment of the reliability and cost of complex systems, such as Complex Bridge Systems (CBS) and Life Support Systems in Space Capsules (LSSSC), is fascinating. To achieve the ideal system design through diverse constraints and increase overall system reliability, researchers have extensively explored system reliability and cost optimization problems. Hence, the significant advancement in metaheuristic methods is the primary source of further system reliability and cost optimization process refinement.
 Aim and tasks. This research attempts to enhance the reliability and cost of complex systems named CBC and LSSSC has been presented. 
 Results. The structure is based on few recent metaheuristic techniques, such as Moth Flame Optimization (MFO), Whale Optimization Algorithm (WOA), Gazelle Optimization Algorithm (GOA), Dragonfly Algorithm (DA), and Coati Optimization Algorithm (COA). Comparing the acquired findings to those found in other proposed techniques demonstrates the usefulness of a methodology based on COA. The proposed COA algorithm exhibits enhanced efficiency by offering superior solutions to reliability and cost-optimization problems. In addition, a non-parametric Friedman ranking was performed for validation. The results of this research are based on improving the reliability of the parameters and decreasing complex systems’ costs used by the five metaheuristic methods. Observing the convergence graph, Friedman ranking, statistical results test, and tables determined that COA is the most effective algorithm for a complex system’s cost and reliability parameters compared to other existing approaches, and also provided a faster solution.
 Conclusions. This study proposes unique ways to reduce costs while increasing parameter reliability in complex systems. After analysing the comparative solution, the authors found that when comparing these approaches (GOA, DA, MFO, WOA, and COA), the COA provided the best minimum solution for the cost and reliability of complex systems. Hence, the suggested COA procedure was more successful than that described in this study.

Лингвофилософская концепция В.И. Абаева и осетино-кабардино-балкарские идеосеманти-ческие параллели

The article is devoted to the linguophilosophical concept of the outstanding Russian theorist, his-torian and philosopher of language, the largest Iranian scholar Vasily Ivanovich Abaev. The as-pects of the author’s linguophilosophical concept are presented based on two works by V.I. Abaev: “Reflection of the work of consciousness in the lexico-semantic system of language” (1970) and “Language as ideology and language as technique” (1934). In these works, he pays special atten-tion to the problem of the origin of human language. The theory of the origin of language itself, in his opinion, should be based on an optimal scientific theory that proceeds from the correct theo-retical premises and is consistent with the available empirical data. To explain the origin of a lan-guage, it is not the grammar of the language that is important, but the subject–significant vocabu-lary, as he believes that the origin of vocabulary is a single and integral problem, and the origin of grammar is inevitably divided into several particular issues. Language, according to V.I.Abaev, arose not from biological, but from the social needs of a person, from the need to relate things to their collective, to impose their own “brand” on them. Special attention is paid to the concept of ideosemantics, firstly introduced by V.I. Abaev in-to scientific circulation. He distinguishes two types of semantics: small semantics (or signal, technical), which includes a mandatory minimum of semantic functions that determine the mod-ern communicative use of the word, and large semantics, which is the sum of those concomitant cognitive and emotional representations that reflect the complex inner life of the word in its past and present. He defined this broader understanding of semantics by the term “ideosemantics”. Id-eosemantics, according to V. Abaev, is the most important criterion for the historical characteriza-tion of linguistic phenomena. V. Abaev sees the value of language at an early stage of its for-mation in its “ethnodemarkation function”. In conclusion, the article presents ideosemantic parallels in three genetically and structurally diverse languages: Ossetian, Kabardino-Circassian and Karachay-Balkar.

Post-cellular biotic evolution in a nutshell

AbstractThe minimum requirements for post-cellular evolution from prokaryotes towards multicellular eukaryotes are outlined. The main steps are: formation of a true nucleus harboring linear chromosomes with centromeres and telomeres, establishing of mitosis and of sex via meiosis and fertilization, endosymbiotic gain of mitochondria and plastids, and epigenetic differentiation of non-separated cells into tissues of multicellular organisms. Erroneous DNA double-strand break repair and cell fusion are postulated as main drivers of eukaryotic evolution. Advantages versus disadvantages of eukaryotes compared to prokaryotes are discussed.

Cell-in-cell phenomena across the tree of life

Cells in obligately multicellular organisms by definition have aligned fitness interests, minimum conflict, and cannot reproduce independently. However, some cells eat other cells within the same body, sometimes called cell cannibalism. Such cell-in-cell events have not been thoroughly discussed in the framework of major transitions to multicellularity. We performed a systematic screening of 508 articles, from which we chose 115 relevant articles in a search for cell-in-cell events across the tree of life, the age of cell-in-cell-related genes, and whether cell-in-cell events are associated with normal multicellular development or cancer. Cell-in-cell events are found across the tree of life, from some unicellular to many multicellular organisms, including non-neoplastic and neoplastic tissue. Additionally, out of the 38 cell-in-cell-related genes found in the literature, 14 genes were over 2.2 billion years old, i.e., older than the common ancestor of some facultatively multicellular taxa. All of this suggests that cell-in-cell events may have originated before the origins of obligate multicellularity. Thus, our results show that cell-in-cell events exist in obligate multicellular organisms, but are not a defining feature of them. The idea of eradicating cell-in-cell events from obligate multicellular organisms as a way of treating cancer, without considering that cell-in-cell events are also part of normal development, should be abandoned.

Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota.

The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.

Evolution of <I>Yersinia pestis</I> as the Causative Agent of a Vector-Borne Disease Transmitted by Arthropods

The review summarizes the data of modern domestic and foreign studies on the mechanisms of evolutionary adaptation of the plague pathogen to transmissive spread by arthropods. The data on the molecular basis of the rapid formation of a highly pathogenic bacterium due to the acquisition of new genetic information; structural and functional changes in the genome, causing the disruption of functionality of some genes that prevent survival in the vector are presented. The stage of the complex life cycle of the pathogen associated with the peculiarities of its stay in the vector’s organism and its tactics of evasion from the action of antibacterial substances formed by the flea is considered. The importance of biofilm formation for effective transmission of the pathogen is discussed. A complex cascade of transcriptional regulators of biofilm in Yersinia pestis is considered, which includes activators and repressors of biofilm formation, as well as regulators of synthesis or modification/transport of exopolysaccharide. The hms-dependent mechanism of biofilm formation in Y. pestis is described in detail, as well as the impact on biofilm formation through the regulation of LPS-related genes and its role in the modification and transport of biofilm exopolysaccharide. The data from our own studies on the variability of genes involved in biofilm formation in the main subspecies of the plague pathogen in comparison with non-main subspecies of the plague pathogen, as well as on the ability of strains of different subspecies to form biofilm not only in the proventriculus of the flea, but also on the cuticle of soil nematodes of the Tylenchida and Rhabditida orders and the genus Panagrolaimus are presented. The latter allows us to assume the possible participation of soil and entomoparasitic nematodes in the removal of Y. pestis biofilms from the soil to the above-ground biocoenosis of the natural plague focus.

Paternalism, Supported Decision-Making and Expressive Respect

It has been argued by disability advocates that supported decision-making must replace surrogate, or substituted, decision-making for people with cognitive disabilities. From a moral perspective surrogate decision-making it is said to be an indefensible form of paternalism. At the heart of this argument against surrogate decision-making is the belief that such paternalistic action expresses something fundamentally disrespectful about those upon whom it is imposed: that they are inferior, deficient or child-like in some way. Contrary to this widespread belief, I will argue that surrogate decision-making often expresses more respect for people with life-long, ‘severe’ or ‘profound’ cognitive disabilities than does the adoption of supported decision-making. Specifically, I argue that in some cases supported decision-making can arguably express that people with cognitive disabilities lack equal moral value. I also argue that supported decision-making for people with profound intellectual disabilities can arguably express that they lack complex and rich inner lives. If our aim is to ensure our behaviour and practices express respect for people with life-long cognitive disabilities, then sometimes surrogate rather than supportive decision-making will be a better option.

CPPLS-MLP: a method for constructing cell-cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data.

In the growth and development of multicellular organisms, the immune processes of the immune system and the maintenance of the organism's internal environment, cell communication plays a crucial role. It exerts a significant influence on regulating internal cellular states such as gene expression and cell functionality. Currently, the mainstream methods for studying intercellular communication are focused on exploring the ligand-receptor-transcription factor and ligand-receptor-subunit scales. However, there is relatively limited research on the association between intercellular communication and highly variable genes (HVGs). As some HVGs are closely related to cell communication, accurately identifying these HVGs can enhance the accuracy of constructing cell communication networks. The rapid development of single-cell sequencing (scRNA-seq) and spatial transcriptomics technologies provides a data foundation for exploring the relationship between intercellular communication and HVGs. Therefore, we propose CPPLS-MLP, which can identify HVGs closely related to intercellular communication and further analyze the impact of Multiple Input Multiple Output cellular communication on the differential expression of these HVGs. By comparing with the commonly used method CCPLS for constructing intercellular communication networks, we validated the superior performance of our method in identifying cell-type-specific HVGs and effectively analyzing the influence of neighboring cell types on HVG expression regulation. Source codes for the CPPLS_MLP R, python packages and the related scripts are available at 'CPPLS_MLP Github [https://github.com/wuzhenao/CPPLS-MLP]'.

Neural Circuits Underlying Reciprocal Cardiometabolic Crosstalk: 2023 Arthur C. Corcoran Memorial Lecture.

The interplay of various body systems, encompassing those that govern cardiovascular and metabolic functions, has evolved alongside the development of multicellular organisms. This evolutionary process is essential for the coordination and maintenance of homeostasis and overall health by facilitating the adaptation of the organism to internal and external cues. Disruption of these complex interactions contributes to the development and progression of pathologies that involve multiple organs. Obesity-associated cardiovascular risks, such as hypertension, highlight the significant influence that metabolic processes exert on the cardiovascular system. This cardiometabolic communication is reciprocal, as indicated by substantial evidence pointing to the ability of the cardiovascular system to affect metabolic processes, with pathophysiological implications in disease conditions. In this review, I outline the bidirectional nature of the cardiometabolic interaction, with special emphasis on the impact that metabolic organs have on the cardiovascular system. I also discuss the contribution of the neural circuits and autonomic nervous system in mediating the crosstalk between cardiovascular and metabolic functions in health and disease, along with the molecular mechanisms involved.

Invading new climates at what cost? Ontogenetic differences in the thermal dependence of metabolic rate in an invasive amphibian

Global warming can either promote or constrain the invasive potential of alien species. In ectotherm invaders that exhibit a complex life cycle, success is inherently dependent on the capacity of each developmental stage to cope with environmental change. This is particularly relevant for invasive anurans, which disperse on land while requiring water for reproduction. However, it remains unknown how the different life stages respond in terms of energy expenditure under different climate change scenarios. We here quantified the oxygen uptake of frogs at rest (a proxy of the standard metabolic rate) in the aquatic phase (at the tadpole and climax, i.e. during metamorphosis, stages) and in the terrestrial phase (metamorphosed stage) at three environmental temperatures. To do so, we used marsh frogs (Pelophylax ridibundus), an amphibian with the largest invasive range within the palearctic realm and for which their adaptation to global warming might be key to their invasion success. Beyond an increase of metabolic rate with temperature, our data show variation in thermal adaptation across life stages and a higher metabolic cost during metamorphosis. These results suggest that the cost to shift habitat and face changes in temperature may be a constraint on the invasive potential of species with a complex life cycle which may be particularly vulnerable during metamorphosis.

Хемилюминесцентные характеристики периферической крови при облучении in vitro в диапазоне доз 100–500 мГр

Abstract. Nowadays a lot of examinations are dedicated to determination of radiobiological effects under low doses of ionising radiation. It is known that ionising radiation in the cells of an organism increases generation of reactive oxygen species (ROS). The purpose of the work is to determine basic parameters of chemiluminescent kinetics of ROS in peripheral blood under in vitro radiation in the range of 100–500 mGy doses. The research will extend the knowledge of the impact degree of ionising radiation in low doses on organism tissue of farm animals. Scientific novelty is that the results of the research will allow to predict radiobiological effects of low doses in a multicellular organism. The research is included in practical and fundamental directions of radiobiology. Research methods. In vitro radiation of blood samples in the range of 100–500 mGy doses. The kinetics of generation of ROS is registered on 36-channel chemiluminometer 3604-PC. Results. The doses in the range of 100–300 mGy accelerated the time of the first peak of spontaneous and activated generation of radicals, under 500 mGy dose the formation of the first peak of spontaneous and activated generation of primary ROS decelerated. Under the impact of low absorbed doses maximum intensity of primary and secondary radicals generation decreased. The inhibition of primary radicals spontaneous production occurred under 100–300 mGy doses, the inhibition of antigen activated generation of primary ROS was under 400 mGy. The reduction of the amount of spontaneous secondary ROS was registered under 100 mGy dose. The decrease of antigen activated secondary radicals production occurred under 100–300 mGy doses. 500 mGy dose inhibited a reaction ability of blood cells to generate primary radicals. The external in vitro gamma radiation in the range of 100–500 mGy had a negative impact on peripheral blood cells showing an acceleration of chemiluminescent reaction as well as decrease of maximum intensity of the first peak of spontaneous and antigen activated primary and secondary radicals production. As a consequence, a decrease of the amount of primary and secondary radicals production was revealed.

Functional characterization of serine proteinase inhibitor Kazal-Type in the red claw crayfish Cherax quadricarinatus

Serine protease inhibitors Kazal type (SPINKs) function in physiological and immunological processes across multicellular organisms. In the present study, we identified a SPINK gene, designated as CqSPINK, in the red claw crayfish Cherax quadricarinatus, which is the ortholog of human SPINK5. The deduced CqSPINK contains two Kazal domains consisting of 45 amino acid residues with a typical signature motif C-X3-C-X5-PVCG-X5-Y-X3-C-X6-C-X12-14-C. Each Kazal domain contains six conserved cysteine residues forming three pairs of disulfide bonds, segmenting the structure into three rings. Phylogenetic analysis revealed CqSPINK as a homolog of human SPINK5. CqSPINK expression was detected exclusively in hepatopancreas and epithelium, with rapid up-regulation in hepatopancreas upon Vibrio parahaemolyticus E1 challenge. Recombinant CqSPINK protein (rCqSPINK) was heterologously expressed in Escherichia coli and purified for further study. Proteinase inhibition assays demonstrated that rCqSPINK could potently inhibit proteinase K and subtilisin A, weakly inhibit α-chymotrypsin and elastase, but extremely weak inhibit trypsin. Furthermore, CqSPINK inhibited bacterial secretory proteinase activity from Bacillus subtilis, E. coli, and Staphylococcus aureus, and inhibited B. subtilis growth. These findings suggest CqSPINK's involvement in antibacterial immunity through direct inhibition of bacterial proteases, contributing to resistance against pathogen invasion.

Mutation Rate and Effective Population Size of the Model Cooperative Bacterium Myxococcus xanthus.

Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here, we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation accumulation experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life cycle-such as group-size reduction during fruiting-body development-or its highly structured spatial distribution have significantly influenced how these parameters have evolved.

Abstract 5488: AI-enhanced spatial proteomics reveals B-cells & FoxP3+ cells interactions in HPV(+) oropharyngeal squamous cell carcinoma Progression

Abstract Background: Analyzing interactions and the microanatomical distribution of the tumor immune microenvironment (TIME) is essential for a comprehensive understanding of tumor progression. Imaging Mass Cytometry (IMC) is a high-dimensional tissue imaging system that enables the deeper and multiparametric in situ exploration of tumor microenvironments at a single-cell level. This study describes a pipeline for analyzing 39-plex IMC images of human HPV(+) oropharyngeal squamous cell carcinoma (OPSCC) tumor sections, elucidating immune cells' nature, functions, and interactions with tumor cells. The IMC data analysis provides valuable information for clinical studies that could be used for the identification of prognostic biomarkers and mechanisms of resistance to current immunotherapies. Methods: A retrospective study was conducted on (N=20) patients (10 progressors and 10 non-progressors) with HPV(+) OPSCC. The dataset comprises paired hematoxylin and eosin (H&E) images with IMC data from multiple Regions of Interest (ROIs) (N=82), enabling the in-situ profiling of 39 proteins in primary tumor tissue. Cell segmentation was followed by employing original images and their segmentation masks for cell phenotype identification using a probabilistic neural network method to spatially profile cancer cells, macrophages, NK-M cells, B-cells, and distinct T-cell populations. We identified protein expression at single-cell resolution and investigated the impact of multicellular spatial organization on the disease progression. The spatial neighborhood interaction score of tumor cells with various other cells was computed for all the ROIs across the two groups. Results: The markers showed varying expression levels of intensity distribution, likely due to differences in tissue sample composition. Specifically, CD3, CD4, CD8, CD19, CD20, and CD68 showed significantly higher intensity in non-progressors. Interestingly, FoxP3 also had a significantly higher intensity level in non-progressors. Cell phenotyping emphasized that non-progressors generally have increased levels of NK-M cell markers. Spatial analysis revealed a significant increase in interaction between CD3 cells and tumor cells in non-progressors (p-value=0.07, Mann-Whitney U test). Furthermore, a significant rise in the interaction between B-cells and FoxP3+ cells was observed in non-progressors (p-value<0.05, Mann-Whitney U test) suggesting a coordinated suppression of tumor growth. Conclusion: We developed a deep learning-based pipeline to analyze spatial relationships in the TIME of IMC data, demonstrating its clinical relevance in predicting disease progression. Our findings emphasize the importance of spatial relationships in the TME for response and suggest that proximity between either CD3+ T-cells to cancer cells or B-cells to FoxP3+ cells are candidate biomarkers. Citation Format: Sumanth Reddy Nakkireddy, Routman David, Kathleen Bartemes, Daniel Ma, Tae Hyun Hwang, Kathryn Van Abel, Chadi Nimeh Abdel-Halim. AI-enhanced spatial proteomics reveals B-cells & FoxP3+ cells interactions in HPV(+) oropharyngeal squamous cell carcinoma Progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5488.

Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2.

Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation-or lack thereof-of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with Caenorhabditis elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity and has revealed the first loss of PRC2 in a multicellular organism.