Biophys Rep. 2023 Apr 30;9(2):57-66. doi: 10.52601/bpr.2023.230005.

ABSTRACT

Identifying cancer-related differentially expressed genes provides significant information for diagnosing tumors, predicting prognoses, and effective treatments. Recently, deep learning methods have been used to perform gene differential expression analysis using microarray-based high-throughput gene profiling and have achieved good results. In this study, we proposed a new robust multiple-datasets-based semi-supervised learning model, MSSL, to perform tumor type classification and candidate cancer-specific biomarkers discovery across multiple tumor types and multiple datasets, which addressed the following long-lasting obstacles: (1) the data volume of the existing single dataset is not enough to fully exert the advantages of deep learning; (2) a large number of datasets from different research institutions cannot be effectively used due to inconsistent internal variances and low quality; (3) relatively uncommon cancers have limited effects on deep learning methods. In our article, we applied MSSL to The Cancer Genome Atlas (TCGA) and the Gene Expression Comprehensive Database (GEO) pan-cancer normalized-level3 RNA-seq data and got 97.6% final classification accuracy, which had a significant performance leap compared with previous approaches. Finally, we got the ranking of the importance of the corresponding genes for each cancer type based on classification results and validated that the top genes selected in this way were biologically meaningful for corresponding tumors and some of them had been used as biomarkers, which showed the efficacy of our method.

PMID:37753058 | PMC:PMC10518520 | DOI:10.52601/bpr.2023.230005

iScience. 2023 Sep 1;26(10):107810. doi: 10.1016/j.isci.2023.107810. eCollection 2023 Oct 20.

ABSTRACT

Research shows that brain circuits controlling vital physiological processes are closely linked with endogenous time-keeping systems. In this study, we aimed to examine oscillatory gene expression patterns of well-characterized neuronal circuits by reanalyzing publicly available transcriptomic data from a spatiotemporal gene expression atlas of a non-human primate. Unexpectedly, brain structures known for regulating circadian processes (e.g., hypothalamic nuclei) did not exhibit robust cycling expression. In contrast, basal ganglia nuclei, not typically associated with circadian physiology, displayed the most dynamic cycling behavior of its genes marked by sharp temporally defined expression peaks. Intriguingly, the mammillary bodies, considered hypothalamic nuclei, exhibited gene expression patterns resembling the basal ganglia, prompting reevaluation of their classification. Our results emphasize the potential for high throughput circadian gene expression analysis to deepen our understanding of the functional synchronization across brain structures that influence physiological processes and resulting complex behaviors.

PMID:37752952 | PMC:PMC10518731 | DOI:10.1016/j.isci.2023.107810

iScience. 2023 Aug 19;26(10):107678. doi: 10.1016/j.isci.2023.107678. eCollection 2023 Oct 20.

ABSTRACT

Soft tissue sarcomas (STSs) are rare malignant tumors that are difficult to prognosticate using currently available instruments. Omics sciences could provide more accurate and individualized survival predictions for patients with metastatic STS. In this pilot, hypothesis-generating study, we integrated clinicopathological variables with proton nuclear magnetic resonance (1H NMR) plasma metabolomic and lipoproteomic profiles, capturing both tumor and host characteristics, to identify novel prognostic biomarkers of 2-year survival. Forty-five metastatic STS (mSTS) patients with prevalent leiomyosarcoma and liposarcoma histotypes receiving trabectedin treatment were enrolled. A score combining acetate, triglycerides low-density lipoprotein (LDL)-2, and red blood cell count was developed, and it predicts 2-year survival with optimal results in the present cohort (84.4% sensitivity, 84.6% specificity). This score is statistically significant and independent of other prognostic factors such as age, sex, tumor grading, tumor histotype, frailty status, and therapy administered. A nomogram based on these 3 biomarkers has been developed to inform the clinical use of the present findings.

PMID:37752948 | PMC:PMC10518687 | DOI:10.1016/j.isci.2023.107678

iScience. 2023 Sep 9;26(10):107883. doi: 10.1016/j.isci.2023.107883. eCollection 2023 Oct 20.

ABSTRACT

The colonic mucosal barrier protects against infection, inflammation, and tissue ulceration. Composed primarily of Mucin-2, proteolytic erosion of this barrier is an invariant feature of colitis; however, the molecular mechanisms are not well understood. We have applied a recurrent food poisoning model of acquired inflammatory bowel disease using Salmonella enterica Typhimurium to investigate mucosal barrier erosion. Our findings reveal an innate Toll-like receptor 4-dependent mechanism activated by previous infection that induces Neu3 neuraminidase among colonic epithelial cells concurrent with increased Cathepsin-G protease secretion by Paneth cells. These anatomically separated host responses merge with the desialylation of nascent colonic Mucin-2 by Neu3 rendering the mucosal barrier susceptible to increased proteolytic breakdown by Cathepsin-G. Depletion of Cathepsin-G or Neu3 function using pharmacological inhibitors or genetic-null alleles protected against Mucin-2 proteolysis and barrier erosion and reduced the frequency and severity of colitis, revealing approaches to preserve and potentially restore the mucosal barrier.

PMID:37752945 | PMC:PMC10518488 | DOI:10.1016/j.isci.2023.107883

Cell Rep Methods. 2023 Sep 20:100597. doi: 10.1016/j.crmeth.2023.100597. Online ahead of print.

ABSTRACT

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.

PMID:37751739 | DOI:10.1016/j.crmeth.2023.100597

Am J Hum Genet. 2023 Sep 20:S0002-9297(23)00315-4. doi: 10.1016/j.ajhg.2023.09.002. Online ahead of print.

ABSTRACT

Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense variants in plastin 3 (PLS3), a gene encoding an actin bundling protein, co-segregate with disease in all families. Loss-of-function variants in PLS3 have been previously associated with X-linked osteoporosis (MIM: 300910), so we used in silico protein modeling and a mouse model to address these seemingly disparate clinical phenotypes. The missense variants in individuals with CDH are located within the actin-binding domains of the protein but are not predicted to affect protein structure, whereas the variants in individuals with osteoporosis are predicted to result in loss of function. A mouse knockin model of a variant identified in one of the CDH-affected families, c.1497G>C (p.Trp499Cys), shows partial perinatal lethality and recapitulates the key findings of the human phenotype, including diaphragm and abdominal-wall defects. Both the mouse model and one adult human male with a CDH-associated PLS3 variant were observed to have increased rather than decreased bone mineral density. Together, these clinical and functional data in humans and mice reveal that specific missense variants affecting the actin-binding domains of PLS3 might have a gain-of-function effect and cause a Mendelian congenital disorder.

PMID:37751738 | DOI:10.1016/j.ajhg.2023.09.002

Cell Syst. 2023 Sep 22:S2405-4712(23)00244-2. doi: 10.1016/j.cels.2023.08.004. Online ahead of print.

ABSTRACT

Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.

PMID:37751736 | DOI:10.1016/j.cels.2023.08.004

Cell Rep Methods. 2023 Sep 25;3(9):100576. doi: 10.1016/j.crmeth.2023.100576. Epub 2023 Aug 29.

ABSTRACT

The mammalian gut microbiome protects the host through colonization resistance (CR) against the incursion of exogenous and often harmful microorganisms, but identifying the exact microbes responsible for the gut microbiota-mediated CR against a particular pathogen remains a challenge. To address this limitation, we developed a computational method: generalized microbe-phenotype triangulation (GMPT). We first systematically validated GMPT using a classical population dynamics model in community ecology and demonstrated its superiority over baseline methods. We then tested GMPT on simulated data generated from the ecological network inferred from a real community (GnotoComplex microflora) and real microbiome data on two mouse studies on Clostridioides difficile infection. We demonstrated GMPT's ability to streamline the discovery of microbes that are potentially responsible for microbiota-mediated CR against pathogens. GMPT holds promise to advance our understanding of CR mechanisms and facilitate the rational design of microbiome-based therapies for preventing and treating enteric infections.

PMID:37751698 | DOI:10.1016/j.crmeth.2023.100576

Cell Rep Methods. 2023 Sep 25;3(9):100567. doi: 10.1016/j.crmeth.2023.100567. Epub 2023 Aug 28.

ABSTRACT

Chronological age prediction from DNA methylation sheds light on human aging, health, and lifespan. Current clocks are mostly based on linear models and rely upon hundreds of sites across the genome. Here, we present GP-age, an epigenetic non-linear cohort-based clock for blood, based upon 11,910 methylomes. Using 30 CpG sites alone, GP-age outperforms state-of-the-art models, with a median accuracy of ∼2 years on held-out blood samples, for both array and sequencing-based data. We show that aging-related changes occur at multiple neighboring CpGs, with implications for using fragment-level analysis of sequencing data in aging research. By training three independent clocks, we show enrichment of donors with consistent deviation between predicted and actual age, suggesting individual rates of biological aging. Overall, we provide a compact yet accurate alternative to array-based clocks for blood, with applications in longitudinal aging research, forensic profiling, and monitoring epigenetic processes in transplantation medicine and cancer.

PMID:37751697 | DOI:10.1016/j.crmeth.2023.100567

Cell Rep Methods. 2023 Sep 25;3(9):100577. doi: 10.1016/j.crmeth.2023.100577. Epub 2023 Aug 31.

ABSTRACT

The rapid accumulation of single-cell RNA-seq data has provided rich resources to characterize various human cell populations. However, achieving accurate cell-type annotation using public references presents challenges due to inconsistent annotations, batch effects, and rare cell types. Here, we introduce SELINA (single-cell identity navigator), an integrative and automatic cell-type annotation framework based on a pre-curated reference atlas spanning various tissues. SELINA employs a multiple-adversarial domain adaptation network to remove batch effects within the reference dataset. Additionally, it enhances the annotation of less frequent cell types by synthetic minority oversampling and fits query data with the reference data using an autoencoder. SELINA culminates in the creation of a comprehensive and uniform reference atlas, encompassing 1.7 million cells covering 230 distinct human cell types. We substantiate its robustness and superiority across a multitude of human tissues. Notably, SELINA could accurately annotate cells within diverse disease contexts. SELINA provides a complete solution for human single-cell RNA-seq data annotation with both python and R packages.

PMID:37751689 | DOI:10.1016/j.crmeth.2023.100577

Influenza Other Respir Viruses. 2023 Sep;17(9):e13185. doi: 10.1111/irv.13185.

ABSTRACT

BACKGROUND: We estimated the secondary attack rate of SARS-CoV-2 among household contacts of PCR-confirmed cases of COVID-19 in rural Kenya and analysed risk factors for transmission.

METHODS: We enrolled incident PCR-confirmed cases and their household members. At baseline, a questionnaire, a blood sample, and naso-oropharyngeal swabs were collected. Household members were followed 4, 7, 10, 14, 21 and 28 days after the date of the first PCR-positive in the household; naso-oropharyngeal swabs were collected at each visit and used to define secondary cases. Blood samples were collected every 1-2 weeks. Symptoms were collected in a daily symptom diary. We used binomial regression to estimate secondary attack rates and survival analysis to analyse risk factors for transmission.

RESULTS: A total of 119 households with at least one positive household member were enrolled between October 2020 and September 2022, comprising 503 household members; 226 remained in follow-up at day 14 (45%). A total of 43 secondary cases arose within 14 days of identification of the primary case, and 81 household members remained negative. The 7-day secondary attack rate was 4% (95% CI 1%-10%), the 14-day secondary attack rate was 28% (95% CI 17%-40%). Of 38 secondary cases with data, eight reported symptoms (21%, 95% CI 8%-34%). Antibody to SARS-CoV-2 spike protein at enrolment was not associated with risk of becoming a secondary case.

CONCLUSION: Households in our setting experienced a lower 7-day attack rate than a recent meta-analysis indicated as the global average (23%-43% depending on variant), and infection is mostly asymptomatic in our setting.

PMID:37752066 | DOI:10.1111/irv.13185

Br J Sports Med. 2023 Sep;57(17):1098-1108. doi: 10.1136/bjsports-2023-107335.

ABSTRACT

The 2023 International Olympic Committee (IOC) consensus statement on Relative Energy Deficiency in Sport (REDs) notes that exposure to low energy availability (LEA) exists on a continuum between adaptable and problematic LEA, with a range of potential effects on both health and performance. However, there is variability in the outcomes of LEA exposure between and among individuals as well as the specific manifestations of REDs. We outline a framework for a 'systems biology' examination of the effect of LEA on individual body systems, with the eventual goal of creating an integrated map of body system interactions. We provide a template that systematically identifies characteristics of LEA exposure (eg, magnitude, duration, origin) and a variety of moderating factors (eg, medical history, diet and training characteristics) that could exacerbate or attenuate the type and severity of impairments to health and performance faced by an individual athlete. The REDs Physiological Model may assist the diagnosis of underlying causes of problems associated with LEA, with a personalised and nuanced treatment plan promoting compliance and treatment efficacy. It could also be used in the strategic prevention of REDs by drawing attention to scenarios of LEA in which impairments of health and performance are most likely, based on knowledge of the characteristics of the LEA exposure or moderating factors that may increase the risk of harmful outcomes. We challenge researchers and practitioners to create a unifying and dynamic physiological model for each body system that can be continuously updated and mapped as knowledge is gained.

PMID:37752007 | DOI:10.1136/bjsports-2023-107335

PLoS One. 2023 Sep 26;18(9):e0288006. doi: 10.1371/journal.pone.0288006. eCollection 2023.

ABSTRACT

Despite that more than one hundred vaccines against SARS-CoV-2 have been developed and that some of them were evaluated in clinical trials, the latest results revealed that these vaccines still face great challenges. Among the components of the virus, the N-protein constitutes an attractive target for a subunit vaccine because it is the most abundant, highly conserved and immunogenic protein. In the present work, a chimeric protein (N-CD protein) was constructed by the fusion of the N-protein to the extracellular domain of human CD154 as the molecular adjuvant. HEK-293 cells were transduced with lentiviral vector bearing the N-CD gene and polyclonal cell populations were obtained. The N-CD protein was purified from cell culture supernatant and further characterized by several techniques. Immunogenicity studies in mice and non-human primates showed the N-CD protein induced high IgG titers in both models after two doses. Moreover, overall health monitoring of non-human primates demonstrated that animals were healthy during 228 days after first immunization. Data obtained support further investigation in order to develop this chimeric protein as vaccine candidate against COVID-19 and other coronavirus diseases.

PMID:37751460 | DOI:10.1371/journal.pone.0288006

Cell Rep. 2023 Sep 25;42(10):113177. doi: 10.1016/j.celrep.2023.113177. Online ahead of print.

ABSTRACT

Embryonic stem cells (ESCs) can undergo lineage-specific differentiation, giving rise to different cell types that constitute an organism. Although roles of transcription factors and chromatin modifiers in these cells have been described, how the alternative splicing (AS) machinery regulates their expression has not been sufficiently explored. Here, we show that the long non-coding RNA (lncRNA)-associated protein TOBF1 modulates the AS of transcripts necessary for maintaining stem cell identity in mouse ESCs. Among the genes affected is serine/arginine splicing factor 1 (SRSF1), whose AS leads to global changes in splicing and expression of a large number of downstream genes involved in the maintenance of ESC pluripotency. By overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and AS upon its knockout, we describe local nuclear territories where these distinct events converge. Collectively, these contribute to the maintenance of mouse ESC identity.

PMID:37751355 | DOI:10.1016/j.celrep.2023.113177

Eur J Immunol. 2023 Sep 26:e2350749. doi: 10.1002/eji.202350749. Online ahead of print.

NO ABSTRACT

PMID:37751329 | DOI:10.1002/eji.202350749

Lab Chip. 2023 Sep 26. doi: 10.1039/d3lc00651d. Online ahead of print.

ABSTRACT

Cell migration is a complex process that plays a crucial role in normal physiology and pathologies such as cancer, autoimmune diseases, and mental disorders. Conventional cell migration assays face limitations in tracking a large number of individual migrating cells. To address this challenge, we have developed a high-throughput microfluidic cell migration chip, which seamlessly integrates robotic liquid handling and computer vision to swiftly monitor the movement of 3200 individual cells, providing unparalleled single-cell resolution for discerning distinct behaviors of the fast-moving cell population. This study focuses on the ECM's role in regulating cellular migration, utilizing this cutting-edge microfluidic technology to investigate the impact of ten different ECMs on triple-negative breast cancer cell lines. We found that collagen IV, collagen III, and collagen I coatings were the top enhancers of cell movement. Combining these ECMs increased cell motility, but the effect was sub-additive. Furthermore, we examined 87 compounds and found that while some compounds inhibited migration on all substrates, significantly distinct effects on differently coated substrates were observed, underscoring the importance of considering ECM coating. We also utilized cells expressing a fluorescent actin reporter and observed distinct actin structures in ECM-interacting cells. ScRNA-Seq analysis revealed that ECM coatings induced EMT and enhanced cell migration. Finally, we identified genes that were particularly up-regulated by collagen IV and the selective inhibitors successfully blocked cell migration on collagen IV. Overall, the study provides insights into the impact of various ECMs on cell migration and dynamics of cell movement with implications for developing therapeutic strategies to combat diseases related to cell motility.

PMID:37750357 | DOI:10.1039/d3lc00651d

Mol Oral Microbiol. 2023 Sep 26. doi: 10.1111/omi.12433. Online ahead of print.

ABSTRACT

Porphyromonas gingivalis is a key pathobiont in periodontitis. Its long fimbriae consist of a single anchor (FimB), a varying number of stalk (FimA), and three accessory (tip-related) proteins (FimC, FimD, and FimE). Based on 133 strains/genomes available, it was our aim to investigate the diversity within FimA and FimB and explain the variety of long fimbriae (super-)structures. Combining the new forward primer fimAnewF with the established fimAunivR, we were able to amplify and sequence fimA including its leader region covering all genotypes and serotypes for phylogenetic analysis. We designed two primer pairs sensing the presence of an internal stop codon in fimB with an impact on fimbrial length. Finally, we examined fimbrial secondary structures by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). The phylogeny of fimA/FimA revealed two new subtypes (IIa and IIb) with specific changes in functional domains and thus adding to the current classification scheme (I, Ib, and II-V). Regarding evolution, we confirm that Porphyromonas gulae fimA-type A is closely related to human P. gingivalis strains of cluster Ib and might be its ancestor genotype. A fimB internal stop codon is rare and was found in ATCC 33277 only. Comparing P. gingivalis TEM/SEM pictures of type I ATCC 33277 with type V OMI622 revealed a broad spectrum of fimbrial structures including bundling, cell-cell knotting, and brick-wall formation. In conclusion, FimA forms more distinct subtypes than previously known. The bundling of long fimbriae, a mechanism known from EPEC/EHEC and Salmonella, is proposed and supported by TEM/SEM pictures for the first time here. The role and variations of terminal accessory FimC-E in superstructure formation and/or (co-) adhesion should be investigated more closely next.

PMID:37750230 | DOI:10.1111/omi.12433

Chem Biol Interact. 2023 Sep 23:110720. doi: 10.1016/j.cbi.2023.110720. Online ahead of print.

ABSTRACT

Breast cancer (BC) is one of the most frequent type of cancer in women worldwide. Current therapeutic strategies for BC are not always effective. In this study, we investigated the anticancer activity of an epigenetic compound UNC0642 and its mechanism of action in suppressing BC cell growth and survival. UNC0642 was developed as a selective inhibitor of G9a that is responsible for histone H3K9 methylation. After screening different BC cell lines, we found UNC0642 had the lowest IC-50 against MDA-MB-231 cells, a triple-negative BC cell line. To identify additional UNC0642 targets, we performed RNA-seq analyses in BC cells following UNC0642 treatment. UNC0642 significantly upregulated mRNA expression of thioredoxin-interacting protein (TXNIP), which was also validated by western blotting. We further showed that TXNIP upregulation was associated with dose-dependent elevation of reactive oxygen species, concurrent with loss of mitochondrial membrane potential and activation of caspase-3-dependent apoptosis. Finally, we demonstrated that UNC0642 treatment induced BC cell apoptosis in vitro and suppression of tumor growth in xenograft mouse models that was coupled with TXNIP activation. Taken together, our results show that UNC0642 exerts its antitumor function via upregulating TXNIP expression and oxidative stress to impair mitochondrial function and induce caspase-dependent cell death. This observation could inform future breast cancer therapies by targeting TXNIP-dependent ROS signaling.

PMID:37748637 | DOI:10.1016/j.cbi.2023.110720

Semin Thromb Hemost. 2023 Sep 25. doi: 10.1055/s-0043-1774796. Online ahead of print.

ABSTRACT

Microscopy imaging has enabled us to establish the presence of fibrin(ogen) amyloid (fibrinaloid) microclots in a range of chronic, inflammatory diseases. Microclots may also be induced by a variety of purified substances, often at very low concentrations. These molecules include bacterial inflammagens, serum amyloid A, and the S1 spike protein of severe acute respiratory syndrome coronavirus 2. Here, we explore which of the properties of these microclots might be used to contribute to differential clinical diagnoses and prognoses of the various diseases with which they may be associated. Such properties include distributions in their size and number before and after the addition of exogenous thrombin, their spectral properties, the diameter of the fibers of which they are made, their resistance to proteolysis by various proteases, their cross-seeding ability, and the concentration dependence of their ability to bind small molecules including fluorogenic amyloid stains. Measuring these microclot parameters, together with microscopy imaging itself, along with methodologies like proteomics and imaging flow cytometry, as well as more conventional assays such as those for cytokines, might open up the possibility of a much finer use of these microclot properties in generative methods for a future where personalized medicine will be standard procedures in all clotting pathology disease diagnoses.

PMID:37748515 | DOI:10.1055/s-0043-1774796

Nat Cell Biol. 2023 Sep 25. doi: 10.1038/s41556-023-01225-6. Online ahead of print.

ABSTRACT

All eukaryotic cells require a minimal iron threshold to sustain anabolic metabolism. However, the mechanisms by which cells sense iron to regulate anabolic processes are unclear. Here we report a previously undescribed eukaryotic pathway for iron sensing in which molecular iron is required to sustain active histone demethylation and maintain the expression of critical components of the pro-anabolic mTORC1 pathway. Specifically, we identify the iron-binding histone-demethylase KDM3B as an intrinsic iron sensor that regulates mTORC1 activity by demethylating H3K9me2 at enhancers of a high-affinity leucine transporter, LAT3, and RPTOR. By directly suppressing leucine availability and RAPTOR levels, iron deficiency supersedes other nutrient inputs into mTORC1. This process occurs in vivo and is not an indirect effect by canonical iron-utilizing pathways. Because ancestral eukaryotes share homologues of KDMs and mTORC1 core components, this pathway probably pre-dated the emergence of the other kingdom-specific nutrient sensors for mTORC1.

PMID:37749225 | DOI:10.1038/s41556-023-01225-6