Mixed Cell Populations Research Articles

Engineering synthetic agonists for targeted activation of Notch signaling.

Notch signaling regulates cell fate decisions and has context-dependent tumorigenic or tumor suppressor functions. Although there are several classes of Notch inhibitors, the mechanical force requirement for Notch receptor activation has hindered attempts to generate soluble agonists. To address this problem, we engineered synthetic Notch agonist (SNAG) proteins by tethering affinity-matured Notch ligands to antibodies or cytokines that internalize their targets. This bispecific format enables SNAGs to "pull" on mechanosensitive Notch receptors, triggering their activation in the presence of a desired biomarker. We successfully developed SNAGs targeting six independent surface markers, including the tumor antigens PDL1, CD19, and HER2, and the immunostimulatory receptor CD40. SNAGs targeting CD40 increase expansion of central memory γδ T cells from peripheral blood, highlighting their potential to improve the phenotype and yield of low-abundance T cell subsets. These insights have broad implications for the pharmacological activation of mechanoreceptors and will expand our ability to modulate Notch signaling in biotechnology.

Cell-targeted gene modification by delivery of CRISPR-Cas9 ribonucleoprotein complexes in pseudotyped lentivirus-derived nanoparticles

To fully utilize the potential of CRISPR/Cas9-mediated genome editing, time-restricted and targeted delivery is crucial. By modulating the pseudotype of engineered lentivirus-derived nanoparticles (LVNPs), we demonstrate efficient cell-targeted delivery of Cas9/single guide RNA (sgRNA) ribonucleoprotein (RNP) complexes, supporting gene modification in a defined subset of cells in mixed cell populations. LVNPs pseudotyped with SARS-CoV-2 spike protein resulted in ACE2-dependent indel formation in an ACE2+/ACE2- population of cells, whereas Nipah virus glycoprotein-pseudotyping resulted in Ephrin-B2/B3-specific gene knockout. Additionally, LVNPs pseudotyped with Edmonston strain Measles virus glycoproteins (MV-H/F) delivered Cas9/sgRNA RNPs to CD46+ cells with and without additional expression of SLAM (signaling lymphocytic activation molecule, CD150). However, an engineered SLAM-specific Measles virus pseudotype (MV-H/F-SLAM) efficiently targeted LVNPs to SLAM+ cells. Lentiviral vectors (LVs) pseudotyped with MV-H/F-SLAM efficiently transduced >80% of IL-4/IL-21-stimulated primary B cells cultured on CD40L-expressing feeder cells. Notably, LVNPs pseudotyped with MV-H/F- and MV-H/F-SLAM reached indel rates of >80% and >60% in stimulated primary B cells, respectively. Collectively, our findings demonstrate the modularity of LVNP-directed delivery of ready-to-function Cas9/sgRNA complexes. Using a panel of different pseudotypes, we provide evidence that LVNPs can be engineered to induce effective indel formation in a subpopulation of cells defined by expression of surface receptors.

Isolation and Characterization of Meniscus Progenitor Cells From Rat, Rabbit, Goat, and Human.

Meniscus progenitor cells (MPCs) have been identified as promising candidates for meniscus regeneration, and it is crucial for us to understand meniscus injury repair mechanism at the cellular level. In this study, we investigate the biological properties of MPCs isolated from different species using the differential adhesion to fibronectin (DAF) technique. We aim to characterize MPCs in different species and evaluate the feasibility of these models for future meniscal investigation. MPCs were isolated from freshly digested meniscus from rat, rabbit, goat, and human cells using DAF. Biological properties, including proliferation, colony-forming, multilineage differentiation, and migration abilities, were compared in MPCs and their corresponding mixed meniscus cell (MCs) population in each species. MPCs were successfully isolated by the DAF technique in all species. Rat MPCs appeared cobblestone-like, rabbit MPCs were more polygonal, goat MPCs had a spindle-shaped morphology, human MPCs appear more fibroblast-like. Compared with MCs, isolated MPCs showed progenitor cell characteristics, including multilineage differentiation ability and MSC (mesenchymal stem cells) markers (CD166, CD90, CD44, Stro-1) expression. They also highly expressed fibronectin receptors CD49e and CD49c. MPCs also showed greater proliferation capacity and retained colony-forming ability. Except for goat MPCs showed greater migration abilities than MCs, no significant differences were found in the migration ability between MPCs and MCs in other species. Our study shows that DAF is an effective method for isolating MPCs from rat, rabbit, goat, and human. MPCs in these species demonstrated similar characteristics, including greater proliferation ability and better chondrogenic potential.

The Biological Effect of Platelet-Rich Plasma on Rotator Cuff Tears: A Prospective Randomized In Vivo Study.

The positive effect of platelet-rich plasma (PRP) on tendon metabolism has been extensively investigated and proven in vitro. Additionally, in vivo animal studies have correlated the application of PRP with the enhancement of tenocyte anabolic activity in the setting of tendon degeneration. However, less is known about its in vivo effect on human tendon biology. The purpose of the current prospective randomized comparative study was to evaluate the effect of PRP on torn human supraspinatus tendon. Twenty consecutive eligible patients with painful and magnetic resonance imaging (MRI)-confirmed degenerative supraspinatus tendon tears were randomized in a one-to-one ratio into two groups. The patients in the experimental group (n = 10) underwent an ultrasound-guided autologous PRP injection in the subacromial space 6 weeks before the scheduled operation. In the control group (n = 10), no injection was made prior to surgery. Supraspinatus tendon specimens were harvested from the lateral end of the torn tendon during shoulder arthroscopy and were evaluated under optical and electron microscopy. In the control group, a mixed cell population of oval and rounded tenocytes within disorganized collagen and sites of accumulated inflammatory cells was detected. In contrast, the experimental group yielded abundant oval-shaped cells with multiple cytoplasmic processes within mainly parallel collagen fibers and less marked inflammation, simulating the intact tendon structure. These findings indicate that PRP can induce microscopic changes in the ruptured tendon by stimulating the healing process and can facilitate a more effective recovery.

Single‐cell gene regulatory network analysis for mixed cell populations

AbstractGene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single‐cell RNA sequencing (scRNA‐seq) data. In scRNA‐seq, single cells are often profiled from mixed populations, and their cell identities are unknown. A common practice for single‐cell GRN analysis is to first cluster the cells and infer GRNs for every cluster separately. However, this two‐step procedure ignores uncertainty in the clustering step and thus could lead to inaccurate estimation of the networks. Here, we consider the mixture Poisson log‐normal model (MPLN) for network inference of count data from mixed populations. The precision matrices of the MPLN are the GRNs of different cell types. To avoid the intractable optimization of the MPLN’s log‐likelihood, we develop an algorithm called variational mixture Poisson log‐normal (VMPLN) to jointly estimate the GRNs of different cell types based on the variational inference method. We compare VMPLN with state‐of‐the‐art single‐cell regulatory network inference methods. Comprehensive simulation shows that VMPLN achieves better performance, especially in scenarios where different cell types have a high mixing degree. Benchmarking on real scRNA‐seq data also demonstrates that VMPLN can provide more accurate network estimation in most cases. Finally, we apply VMPLN to a large scRNA‐seq dataset from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and find that VMPLN identifies critical differences in regulatory networks in immune cells between patients with moderate and severe symptoms. The source codes are available on the GitHub website (github.com/XiDsLab/SCVMPLN).

A modified mycobacterial growth inhibition assay for the functional assessment of vaccine-mediated immunity

The Mycobacterial growth inhibition assay (MGIA) is an ex-vivo assay used to measure the overall functional immune response elicited by infection or vaccination. In tuberculosis (TB) vaccine development, MGIA is a potentially important tool for preclinical evaluation of early-stage vaccine candidates to complement existing assays, and to potentially reduce the need for lengthy and costly pathogenic Mycobacterium tuberculosis (Mtb) animal challenge experiments. The conventional method of MGIA in mice entails directly infecting mixed cell cultures, most commonly splenocytes, from immunised mice with mycobacteria. However, this direct infection of mixed cell populations may yield unreliable results and lacks sufficient sensitivity to discriminate well between different vaccines due to the low number of mycobacteria-permissive cells. Here, we modified the assay by inclusion of mycobacteria-infected congenic murine macrophage cell lines as the target cells, and by measuring the total number of killed cells rather than the relative reduction between different groups. Thus, using splenocytes from Mycobacterium bovis BCG immunised mice, and J774 and MH-S (BALB/c background) or BL/6-M (C57Bl/6 background) macrophage cell lines, we demonstrated that the modified assay resulted in at least 26-fold greater mycobacterial killing per set quantity of splenocytes as compared to the conventional method. This increased sensitivity of measuring mycobacterial killing was confirmed using both the standard culture forming unit (CFU) assay and luminescence readings of luciferase-tagged virulent and avirulent mycobacteria. We propose that the modified MGIA can be used as a highly calibrated tool for quantitating the killing capacity of immune cells in preclinical evaluation of vaccine candidates for TB.

An indocyanine green-based liquid biopsy test for circulating tumor cells for pediatric liver cancer.

Hepatoblastoma and HCC are the most common malignant hepatocellular tumors seen in children. The aim of this study was to develop a liquid biopsy test for circulating tumor cells (CTCs) for these tumors that would be less invasive and provide real-time information about tumor response to therapy. For this test, we utilized indocyanine green (ICG), a far-red fluorescent dye used clinically to identify malignant liver cells during surgery. We assessed ICG accumulation in cell lines using fluorescence microscopy and flow cytometry. For our CTC test, we developed a panel of liver tumor-specific markers, including ICG, Glypican-3, and DAPI, and tested it with cell lines and noncancer control blood samples. We then used this panel to analyze whole-blood samples for CTC burden with a cohort of 15 patients with hepatoblastoma and HCC and correlated with patient characteristics and outcomes. We showed that ICG accumulation is specific to liver cancer cells, compared to nonmalignant liver cells, non-liver solid tumor cells, and other nonmalignant cells, and can be used to identify liver tumor cells in a mixed population of cells. Experiments with the ICG/Glypican-3/DAPI panel showed that it specifically tagged malignant liver cells. Using patient samples, we found that CTC burden from sequential blood samples from the same patients mirrored the patients' responses to therapy. Our novel ICG-based liquid biopsy test for CTCs can be used to specifically detect and quantify CTCs in the blood of pediatric patients with liver cancer.

#1805 Renal progenitor cells isolated from urine of IgA nephropathy patients formed renal spheroids that can recapitulate the typical IgA1 deposition

Abstract Background and Aims Recent developments in stem cell biology have made it possible to create spheroids and kidney organoids from human and mouse pluripotent stem cells and renal stem cells. Spheroids are a suitable in vitro model for studies of drug studies and can transform into organoids whose rapidly developing field has proven useful in simulating nephrotoxicity, kidney disorders, and kidney development. However, to date in all studies the generation of organoids and tubuloids required the use of sophisticated and complex differentiation protocols involving external administration of several growth factors and needs compliance with a precise and specific timescale. Here we showed for the first time that human adult renal progenitor cells (ARPCs) can be isolated from urines of healthy subjects (HS) or IgA Nephropathy (IgAN) patients and can form spheroids generating very long tubule-like structures naturally, without the external use of chemokines or growth factors to artificially induce the process and recapitulating the IgA1 deposition that is the typical characteristic of the disease. Method Spheroids and tubule-like structures were characterized by whole-mounting and frozen section immunofluorescence (IF) assays and by Flow Cytometry Analysis using CD133, NanoG, Oct3/4, GATA-3, SSEA4, CD249, Aminopepidase N, ZO-1, Uromodulin, and Lotus Tetragonolobus Lectin (LTL) antibodies. ELISA was used to determine the renin secretion and CAM assays to determine ARPCs and ARPC-derived Spheroids angiogenic properties. PKH-26 labeling was used for their in vitro and in vivo tracking. Serum of HS and IgAN patients in culture with spheroids was used to recapitulate the disease and IgA1 deposits were measured by IF. Results ARPC-derived spheroids reflected the renal progenitor properties and recapitulated organoids generating very long tubule-like structures that expressed structural and functional renal tubule markers such as CD249, Aminopepidase N, ZO-1, Uromodulin, and LTL and in some cases shared many structural similarities with some regions of nephrons, such as the distal convoluted tubule, the loop of Henle and proximal convoluted tubules. Moreover, ARPC-derived spheroids secreted elevated levels of renin and, as the cellular counterpart, showed angiogenic properties. To study the proof of concept that ARPC-derived spheroids can be used to establish in vitro models recapitulating renal diseases, we generated IgAN patient-specific renal spheroids using the ARPC mixed cell population method. ARPC-derived spheroids of IgAN patients showed deposits of IgA1 already after four days of culture with patient serum (p = 0.004) and, with a different pattern, after 8 and 15 days (p = 0.0029 and p = 0.0012, respectively). The IgA1 deposition resembled that in the glomeruli of patients diagnosticated with IgAN. In contrast, no positive signal was detected in either IgAN spheroids in culture with FBS, or with inactivated IgAN serum, as well as in spheroids derived from urine of HS in culture with IgAN serum. Conclusion The ability of ARPCs to form spheroids and differentiate into tubular-like structures without the need for external chemokines or growth factors is a significant advancement in the field, even more considering that these cells can be isolated from the urine of patients. These findings open up new possibilities for the regenerative medicine in studying kidney development, disease mechanisms, and regenerative therapy development for renal disorders.

Exploring aptamers for targeted enrichment of X sperm in bovine: unraveling selective potential

Nucleic acid aptamers have been used in the past for the development of diagnostic methods against a number of targets such as bacteria, pesticides, cancer cells etc. In the present study, six rounds of Cell-SELEX were performed on a ssDNA aptamer library against X-enriched sperm cells from Sahiwal breed cattle. Sequencing was used to examine the aptamer sequences that shown affinity for sperm carrying the X chromosome in order to find any possible X-sperm-specific sequences. Out of 35 identified sequences, 14 were selected based on bioinformatics analysis like G-Score and Mfold structures. Further validation of their specificity was done via fluorescence microscopy. The interaction of biotinylated-aptamer with sperm was also determined by visualizing the binding of streptavidin coated magnetic beads on the head region of the sperm under bright field microscopy. Finally, a real-time experiment was designed for the validation of X-sperm enrichment by synthesized aptamer sequences. Among the studied sequences, aptamer 29a exhibited a higher affinity for X sperm compared to Y sperm in a mixed population of sperm cells. By using aptamer sequence 29a, we obtained an enrichment of 70% for X chromosome bearing sperm cells.

Transcript Deconvolution Reveals Heterogeneous Cell Populations in Microdissected Nephron Segments of the Rat Kidney

Introduction: The kidney tubule comprises distinct segments with specialized epithelium, including proximal tubules (PT) subsegments S1, S2, and S3, descending (DTL) and ascending (ATL) thin limbs, thick ascending limb (TAL) medullary (MTAL) and cortical (CTAL) subsegments, distal convoluted tubule (DCT), connecting tubule (CNT), and collecting ducts (CD) containing principal (PC) and intercalated (IC) cells. Single-cell RNA sequencing (scRNAseq) is a crucial tool in kidney research. However, it assigns cells to nephron segments based on transcriptome similarity, disregarding anatomical context and spatial information, critical for kidney function. Hypothesis: We hypothesized that cellular deconvolution of microdissected tubule segment transcriptomes would identify mixed cell populations coexisting on different parts of the nephron. Methods: We employed CibersortX to estimate cell proportions in microdissected rat nephron segment transcriptomes (GSE56743), using rat kidney epithelial cell transcriptomes from a scRNAseq dataset (GSE137869) as reference. Raw sequencing files from the Sequence Read Archive (SRA) were downloaded and reprocessed. The number of detected genes was 34,322 for bulk RNAseq and 15,282 for scRNAseq, with a shared gene space of 13,373 used for deconvolution. Results: We discovered that PT.S1 segments primarily consist of S1 cells (81%) and some S2 cells (12%). Microdissected PT.S2 segments contain a mix of S1 (18%), S2 (58%), and S3 (19%) cells. PT.S3 segments were primarily composed of S3 cells (75%). DTL and ATL segments displayed a high percentage of the corresponding cell type. Microdissected MTAL segments were a mix of MTAL (25%) and CTAL (69%) cells, while microdissected CTAL segments were almost exclusively composed of MTAL cells (95%). DCT segments exhibited 80% DCT cells with some principal (2%) and intercalated (1%) cells. In CNT, CCD, and OMCD, we observed a continuous increase in PC abundance (58%, 72%, and 78%, respectively) along with a decrease in IC (32%, 23%, and 11%, respectively). Microdissected IMCD contained PC (58%), IC (4%), and 18% of a distinct cell type with IC characteristics not found in other segments. Conclusions: Our analysis supports the well-established cell heterogeneity in connecting tubules and the collecting duct system, including the existence of a specialized IMCD cell. Additionally, we identified mixed cell populations in the S2 segment of the proximal tubule and the medullary thick ascending limb. In the case of S2, the high proportion of cells from adjacent S1 and S3 segments suggests a differentiation continuum from S1 to S3 with diffused anatomical boundaries. We identified two different TAL cell types, the MTAL phenotype restricted to the MTAL and the CTAL phenotype present in higher abundance in both subsegments. These cell types may correspond to the medullary "rough surface" and cortical "smooth surface" cells described in rat TAL. In summary, the terminology used in scRNAseq cluster assignment referring to specific nephron segments is misleading, as it encompasses anatomical regions with multiple coexisting cell types. This highlights the need for caution when interpreting such data. This work was supported in part by CWRU BGT670107 and NIH-NIDDK DK128304 grants to AGV. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Water‐Soluble Fluorescent Polymer Dyes with Tunable Emission Spectra for Flow Cytometry Applications

AbstractThe application of spectrally unique, bright, and water‐soluble fluorescent dyes is indispensable for the analysis of biological systems. Multiparameter flow cytometry is a powerful tool for characterization of mixed cell populations. To discriminate the different cell populations, they are typically stained by a set of fluorescent reagents, e.g., antibody‐fluorophore conjugates. The number of parameters which can be studied simultaneously strongly depends on the availability of reagents which can be differentiated by their spectral properties. In this study a series of fluorescent polymer dyes was developed, that can be excited with a single violet laser (405 nm) but distinguished by their unique emission spectra. The polyfluorene‐based polymers can be used on their own, or in combination with covalently bound small‐molecule dyes to generate energy transfer constructs to red‐shift the emission wavelength based on Förster resonance energy transfer (FRET). The polymer dyes were utilized in a biological flow cytometry assay by conjugating several of them to antibodies, demonstrating their effectiveness as reagents. This report represents the first systematic investigation of structure–property relationships for this type of fluorescent dyes.

Water-Soluble Fluorescent Polymer Dyes with Tunable Emission Spectra for Flow Cytometry Applications.

The application of spectrally unique, bright, and water-soluble fluorescent dyes is indispensable for the analysis of biological systems. Multiparameter flow cytometry is a powerful tool for characterization of mixed cell populations. To discriminate the different cell populations, they are typically stained by a set of fluorescent reagents, e.g., antibody-fluorophore conjugates. The number of parameters which can be studied simultaneously strongly depends on the availability of reagents which can be differentiated by their spectral properties. In this study a series of fluorescent polymer dyes was developed, that can be excited with a single violet laser (405 nm) but distinguished by their unique emission spectra. The polyfluorene-based polymers can be used on their own, or in combination with covalently bound small-molecule dyes to generate energy transfer constructs to red-shift the emission wavelength based on Förster resonance energy transfer (FRET). The polymer dyes were utilized in a biological flow cytometry assay by conjugating several of them to antibodies, demonstrating their effectiveness as reagents. This report represents the first systematic investigation of structure-property relationships for this type of fluorescent dyes.

Artificial Internalizing Receptor Affords Fast, Potent, Specific Drug Delivery to the Chemically Engineered Cells

AbstractReceptors are lipid bilayer‐resident molecules that perform a myriad of functions in a cell, from recognition to signaling and solute internalization, and are typically based on proteins. Herein, artificial receptors are engineered based on small organic molecules, toward chemical, non‐genetic engineering of cells. Specifically, artificial internalizing receptors are designed for selective targeting and cell‐specific drug delivery. The artificial receptors are shown to afford nanomolar potency of action for the cognate antibody‐drug conjugates. In the chemically engineered cells, the conjugate activity is at the same time more potent and significantly faster than that observed with the use of the pristine drug. In a mixed cell population, an antibody‐drug conjugate targeted to the artificial receptor can selectively eliminate the chemical receptor‐engineered cells. Taken together, these results illustrate that artificial receptors based on small organic molecules are simple by structure but can mediate one of the foundational cellular functions, namely endocytosis, with excellence. Most importantly, these receptors are truly bio‐orthogonal and thus afford a dedicated route of communication with the chemically engineered cells.

Applications of Flow Cytometry in Drug Discovery and Translational Research.

Flow cytometry is a mainstay technique in cell biology research, where it is used for phenotypic analysis of mixed cell populations. Quantitative approaches have unlocked a deeper value of flow cytometry in drug discovery research. As the number of drug modalities and druggable mechanisms increases, there is an increasing drive to identify meaningful biomarkers, evaluate the relationship between pharmacokinetics and pharmacodynamics (PK/PD), and translate these insights into the evaluation of patients enrolled in early clinical trials. In this review, we discuss emerging roles for flow cytometry in the translational setting that supports the transition and evaluation of novel compounds in the clinic.

Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice.

Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent HSV-1 is also present in immune cells recovered from the ganglia of experimentally infected mice. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for that conclusion. Unexpectedly, off-target priming in 3' scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were near-exclusively detected in mixed populations of cells undergoing cell death. Specific loss of HSV-1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained using compromised scRNA-Seq datasets.IMPORTANCEMost people are infected with herpes simplex virus type 1 (HSV-1) during their life. Once infected, the virus generally remains in a latent (silent) state, hiding within the neurons of peripheral ganglia. Periodic reactivation (reawakening) of the virus may cause fresh diseases such as cold sores. A recent study using single-cell RNA sequencing (scRNA-Seq) proposed that HSV-1 can also establish latency in the immune cells of mice, challenging existing dogma. We reanalyzed the data from that study and identified several flaws in the methodologies and analyses performed that invalidate the published conclusions. Specifically, we showed that the methodologies used resulted in widespread destruction of neurons which resulted in the presence of contaminants that confound the data analysis. We thus conclude that there remains little to no evidence for HSV-1 latency in immune cells.

Mechanical convergence in mixed populations of mammalian epithelial cells

Tissues consist of cells with different molecular and/or mechanical properties. Measuring the forces and stresses in mixed-cell populations is essential for understanding the mechanisms by which tissue development, homeostasis, and disease emerge from the cooperation of distinct cell types. However, many previous studies have primarily focused their mechanical measurements on dissociated cells or aggregates of a single-cell type, leaving the mechanics of mixed-cell populations largely unexplored. In the present study, we aimed to elucidate the influence of interactions between different cell types on cell mechanics by conducting in situ mechanical measurements on a monolayer of mammalian epithelial cells. Our findings revealed that while individual cell types displayed varying magnitudes of traction and intercellular stress before mixing, these mechanical values shifted in the mixed monolayer, becoming nearly indistinguishable between the cell types. Moreover, by analyzing a mixed-phase model of active tissues, we identified physical conditions under which such mechanical convergence is induced. Overall, the present study underscores the importance of in situ mechanical measurements in mixed-cell populations to deepen our understanding of the mechanics of multicellular systems.Graphical abstract

Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation.

As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.

Bioinformatics identification of characteristic genes of cervical cancer via an artificial neural network.

Artificial neural networks (ANNs) have been extensively used in the field of medicine. The present hypothesis-free study sought to use an ANN to identify the characteristic genes of cervical cancer (CC). RNA sequencing profiles were obtained from the GSE7410, GSE9750, GSE63514, and GSE52903 datasets. The differentially expressed genes (DEGs) were identified and compared between the normal and CC tissues. An ANN analysis was conducted to obtain the random-forest tree and to examine differences in gene filtering. A neural network model was established using the characteristic genes of CC, while the verification accuracy of the model was examined by Cox regression. The differences in the immune infiltrating cells between the normal cervical and CC tissues were compared by CIBERSORT (an analytical tool can provide an estimation of the abundances of member cell types in a mixed cell population). Nine genes' characteristics for CC were identified: cyclin-dependent kinase inhibitor 2A (CDKN2A), chromosome 1 open reading frame 112 (C1orf112), helicase, lymphoid-specific (HELLS), mini-chromosome maintenance protein 5 (MCM5), mini-chromosome maintenance protein 2 (MCM2), kinetochore associated 1 (KNTC1), cysteine-rich secretory protein 3 (CRISP3), phytanoyl-CoA 2-hydroxylase interacting protein (PHYHIP), and cornulin (CRNN). ANN is a robust neural network model that can be used to potentially predict CC based on the gene score. It can provide novel insights into the pathogenesis and molecular mechanisms of CC.

Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma

BackgroundOmics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method to enrich specific regions from bulk tissue and then perform proteogenomic analyses.MethodsWe used the Biopsy Trifecta Extraction (BioTExt) technique to isolate cores of epithelial-enriched and stroma-enriched tissue from pancreatic tumor and adjacent tissue blocks. Histology was assessed at multiple depths throughout each core. DNA sequencing, RNA sequencing, and proteomics were performed on the cored and bulk tissue samples. Supervised and unsupervised analyses were performed based on integrated molecular and histology data.ResultsTissue cores had mixed cell composition at varying depths throughout. Average cell type percentages assessed by histology throughout the core were better associated with KRAS variant allele frequencies than standard histology assessment of the cut surface. Clustering based on serial histology data separated the cores into three groups with enrichment of neoplastic epithelium, stroma, and acinar cells, respectively. Using this classification, tumor overexpressed proteins identified in bulk tissue analysis were assigned into epithelial- or stroma-specific categories, which revealed novel epithelial-specific tumor overexpressed proteins.ConclusionsOur study demonstrates the feasibility of multi-omics data generation from tissue cores, the necessity of interval H&E stains in serial histology sections, and the utility of coring to improve analysis over bulk tissue data.

Monoamine oxidase B activatable red fluorescence probe for bioimaging in cells and zebrafish

A real-time and specific for the detection of Monoamine Oxidase B (MAO-B) to investigate the MAO-B-relevant disease development and treatment process is urgently desirable. Here, we utilized MAO-B to catalyze the conversion of propylamino groups to aldehyde groups, which was then quickly followed by a β-elimination process to produce fluorescent probes (FNJP) that may be used to detect MAO-B in vitro and in vivo. The FNJP probe possesses unique properties, including favorable reactivity (Km = 10.8 μM), high cell permeability, and NIR characteristics (λem = 610 nm). Moreover, the FNJP probe showed high selectivity for MAO-B and was able to detect endogenous MAO-B levels from a mixed population of NIH-3 T3 and HepG2 cells. MAO-B expression was found to be increased in cells under lipopolysaccharide-stimulated cellular oxidative stress in neuronal-like SH-SY5Y cells. In addition, the visualization of FNJP for MAO-B activity in zebrafish can be an effective tool for exploring the biofunctions of MAO-B. Considering these excellent properties, the FNJP probe may be a powerful tool for detecting MAO-B levels in living organisms and can be used for accurate clinical diagnoses of related diseases.