Expression Patterns Research Articles

Large-scale single-nuclei profiling identifies role for ATRNL1 in atrial fibrillation

Atrial fibrillation (AF) is the most common sustained arrhythmia in humans, yet the molecular basis of AF remains incompletely understood. To determine the cell type-specific transcriptional changes underlying AF, we perform single-nucleus RNA-seq (snRNA-seq) on left atrial (LA) samples from patients with AF and controls. From more than 175,000 nuclei we find that only cardiomyocytes (CMs) and macrophages (MΦs) have a significant number of differentially expressed genes in patients with AF. Attractin Like 1 (ATRNL1) was overexpressed in CMs among patients with AF and localized to the intercalated disks. Further, in both knockdown and overexpression experiments we identify a potent role for ATRNL1 in cell stress response, and in the modulation of the cardiac action potential. Finally, we detect an unexpected expression pattern for a leading AF candidate gene, KCNN3. In sum, we uncover a role for ATRNL1 which may serve as potential therapeutic target for this common arrhythmia.

Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene.

Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Despite viral genomes being smaller and more gene dense than their hosts, we generally lack a sense of scope for the features governing the transcriptional output of individual viral genes. Even having a seemingly simple expression pattern does not imply that a gene's underlying regulation is straightforward. Here, we illustrate this by combining high-density functional genomics, expression profiling, and viral-specific chromosome conformation capture to define with unprecedented detail the transcriptional regulation of a single gene from Kaposi's sarcoma-associated herpesvirus (KSHV). We used as our model KSHV ORF68 - which has simple, early expression kinetics and is essential for viral genome packaging. We first identified seven cis-regulatory regions involved in ORF68 expression by densely tiling the ~154 kb KSHV genome with dCas9 fused to a transcriptional repressor domain (CRISPRi). A parallel Cas9 nuclease screen indicated that three of these regions act as promoters of genes that regulate ORF68. RNA expression profiling demonstrated that three more of these regions act by either repressing or enhancing other distal viral genes involved in ORF68 transcriptional regulation. Finally, we tracked how the 3D structure of the viral genome changes during its lifecycle, revealing that these enhancing regulatory elements are physically closer to their targets when active, and that disrupting some elements caused large-scale changes to the 3D genome. These data enable us to construct a complete model revealing that the mechanistic diversity of this essential regulatory circuit matches that of human genes.

Exploring SLC30A6 as a potential prognostic, immunomodulatory, and therapeutic biomarker in various cancers with a focus on pancreatic cancer: a pan-cancer analysis

BackgroundOur study investigates the multifaceted role of the gene SLC30A6 across 33 distinct cancer types. Understanding the function and impact of SLC30A6 in cancer biology is crucial, as previous studies have hinted at its aberrant expression and potential involvement in tumor progression. This research aims to elucidate the expression patterns, methylation variations, mutational signatures, and survival implications of SLC30A6, along with its engagement with the immune system in various cancers and specially in pancreatic cancer.MethodsWe conducted a comprehensive analysis of SLC30A6 using data from 33 different cancer types, and all data were analyzed in silico. The study involved examining expression levels, performing correlation analyses with clinical outcomes, assessing methylation variations, and identifying mutational signatures. Functional enrichment analyses were carried out to understand the gene's involvement in biological pathways. Additionally, we evaluated the relationship between SLC30A6 expression and immune cell infiltration levels to uncover its role in the tumor microenvironment.ResultsSLC30A6 was found to be significantly up-regulated in the majority of the 33 cancer types analyzed. High expression levels of SLC30A6 were consistently correlated with poor survival outcomes, indicating its potential role in cancer prognosis. Functional enrichment analyses revealed that SLC30A6 is involved in key pathways related to tumor progression, including cell proliferation and apoptosis. Moreover, SLC30A6 showed significant associations with diverse immune pathways, suggesting its involvement in immune regulation. Notably, our analysis demonstrated a significant correlation between SLC30A6 expression and the infiltration levels of key immune cells, highlighting its dual immunosuppressive and immunostimulatory roles in a pan-cancer context. Moreover, SLC30A6 is significantly overexpression in pancreatic cancer and have shown different clinical associations as above.ConclusionOur study provides comprehensive insights into the complex interplay between SLC30A6 and cancer development. These findings position SLC30A6 as a promising prognostic biomarker and therapeutic target across diverse cancer types, highlighting its importance in future cancer research and treatment strategies.

Identification of fibrosis-associated biomarkers in heart failure and human cancers

BackgroundHeart failure (HF) and cancer share common risk factors and pathophysiological mechanisms, including fibrosis. Identifying biomarkers and therapeutic targets for both conditions is crucial.Materials and methodsRNA sequencing data from HF patients were analyzed to identify 12 genes associated with myocardial fibrosis. Validation was performed using public datasets, and functional enrichment analyses were conducted. Gene expression patterns and prognostic value in various cancers were assessed.ResultsFibromodulin (FMOD), Periostin (POSTN), Latent Transforming Growth Factor Beta Binding Protein 2 (LTBP2), Collagen Type I Alpha 1 Chain (COL1A1), Collagen Type VIII Alpha 1 Chain (COL8A1), Asporin (ASPN), and Hemoglobin Subunit Beta (HBB) showed significant dysregulation in heart failure tissues and were implicated in multiple cancer types. Pan-cancer analysis revealed associations between these genes and prognosis. Correlations with cancer-associated fibroblasts were also observed.ConclusionFMOD, POSTN, LTBP2, COL1A1, COL8A1, ASPN, and HBB are potential biomarkers for HF and cancer with fibrotic microenvironments. Targeting fibrosis may offer novel therapeutic approaches. Further validation and mechanistic studies are needed. This study contributes to understanding HF and cancer at the molecular level and suggests personalized treatment strategies.

Spatiotemporal distribution of neural crest cells in the common wall lizard Podarcis muralis.

Neural crest cells (NCCs) are migratory embryonic stem cells that give rise to a diverse set of cell types. Here we describe the dynamic distribution of NCCs in developing embryos of the common wall lizard Podarcis muralis inferred from 10 markers. Our aim is to provide insights into the NCC development of lacertid lizards and to infer evolutionary modifications by comparisons to other tetrapods. NCC migration is ongoing at oviposition, following three streams in the head and multiple in the trunk. From 21ss, we observe expression patterns indicating the beginning of differentiation toward mesenchymal and neuronal fates. By 35ss, migration is restricted to caudal levels, and fully differentiated chromaffin cells are observed. We find that some markers show patterns that differ from other tetrapods. For example, the antibody HNK-1 labels three NCC streams from the hindbrain while some comparable reptile studies describe four. However, the information emerging from all markers combined shows that the overall spatiotemporal distribution of NCCs in the common wall lizard is largely conserved with that of other tetrapods. Our study highlights the dynamic nature of seemingly canonical marker genes and provides the first description of spatiotemporal NCC dynamics in a lacertid lizard.

Rewired chromatin structure and epigenetic gene dysregulation during HTLV-1 infection to leukemogenesis.

Human T-cell leukemia virus type 1 (HTLV-1) broadly impacts host genes, affecting the infected cell population and inducing the development of a disease with a poor prognosis, adult T-cell leukemia-lymphoma (ATL). This study aimed to provide a comprehensive epigenomic characterization of the infected cell population and evaluated the transcriptome and chromatin structures of peripheral blood cells in HTLV-1-infected individuals using RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq). The infected cells showed significant changes in gene expression patterns from the polyclonal stage and before ATL onset while demonstrating similarities to tumor-forming ATL cells. These similarities were a result of large-scale open chromatin changes, supporting the independent early formation of epigenomic aberrations as an underlying mechanism for later clonal propagation. This study also demonstrated that HTLV-1 Tax directly affects the host chromatin structure, thereby developing fundamental epigenomic characteristics. Several Tax target genes, including the RASGRP3-ERK pathway, were recognized, indicating an impact on signaling pathways. This genome-wide variability in chromatin structural property is a novel feature of HTLV-1 infection and may contribute to pathogenic mechanisms. In addition, it has crucial implications for better understanding the impact of HTLV-1 on the host genome and identifying novel therapeutic targets.

Wheat Tae-MIR1118 Constitutes a Functional Module With Calmodulin TaCaM2-1 and MYB Member TaMYB44 to Modulate Plant Low-N Stress Response.

Distinct target genes are modulated by microRNA members and affect various biological processes associated with abiotic stress responses in plants. In this study, we characterized a functional module comprising miRNA/target and a downstream MYB transcription factor partner, Tae-MIR1118/TaCaM2/TaMYB44, in Triticum aestivum to mediate the plant low-nitrogen (N) stress response. Dual luciferase (LUC) assay and expression analysis indicated that TaCaM2 is regulated by Tae-MIR1118 through a posttranscriptional cleavage mechanism. Reporter LUC activity in N. benthamiana leaves co-transformed with effector CaMV35S::Tae-MIR1118 and reporter TaCaM2::LUC was significantly reduced, and the transcripts of Tae-MIR1118 and TaCaM2 in tissues exhibited converse expression patterns under varying N levels. Specifically, the transcripts of Tae-MIR1118 decreased, whereas those of TaCaM2 increased under low-N stress in a temporal-dependent manner. Yeast two-hybrid, bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays indicated that TaCaM2 interacted with the MYB transcription factor TaMYB44. Transgene analysis revealed the negative roles of Tae-MIR1118 and the positive functions of TaCaM2 and TaMYB44 in regulating plants for low-N stress adaptation by modulating glutamine synthetase activity, N uptake capacity, and root morphology. Yeast one-hybrid, transcriptional activation, and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-PCR) assays indicated that TaMYB44 could bind to the promoters of genes TaGS2.2, TaNRT2.1, and TaPIN4 and induce transcription of these stress-defensive genes. Knockdown of these three genes reduced GS activity, N accumulation, and root growth traits in plants subjected to N starvation. The yield in the wheat variety panel was highly correlated with the transcripts of Tae-MIR1118, TaCaM2, and TaMYB44 in plants cultured under N-deprived field conditions. A major haplotype of Tae-MIR1118, TaMIR1118-Hap1, enhanced the low-N stress tolerance of plants. Our findings indicate that the Tae-MIR1118/TaCaM2/TaMYB44 pathway primarily affects the low-N response of plants by modulating associated physiological processes.

Transcriptome Responses of the Soil-Dwelling Collembolan (Entomobrya proxima Folsom) to Fertilizer Type and Concentration.

Soil collembolans have been regarded as the effective bioindicator of environmental changes. However, the physiological mechanisms through which collembolans respond to agricultural activities are largely unknown. Given the plasticity and sensitivity to environmental changes, even subtle responses can be quantified via transcriptomics. Therefore, the relevant in situ soil ecosystem and numerically dominant collembolan species Entomobrya proxima Folsom was selected to explore the dynamic responses to fertilizer type and concentration using transcriptome sequencing over three periods (6 h, 24 h and 10 d). The results showed that exposure duration caused significant alterations in gene expression profiles. At day 10 after exposure, gene expression patterns differed remarkably between the two fertilizer types and the control. Relative to organic fertilizer, the number of DEGs was increased by 114.31% under inorganic fertilizer, which declined with increasing inorganic fertilizer concentrations. Functional enrichment analysis was indicative of enhanced fatty acid and carbohydrate metabolism and reduced disease occurrence by organic fertilizer; however, an inhibited lipid synthesis process promoted susceptibility to infection, triggered oxidative stress, etc. by inorganic fertilizer. Overall, fertilizer addition changed the transcriptional pattern of the collembolan, potentially causing shifts in pathways related to metabolism, immunity, etc. In comparison to inorganic fertilizer, organic fertilizer impacted less on the gene expression patterns, implying that organic fertilizer application may be more beneficial to soil animal health.

Molecular cloning, expression analysis, and functional characterization of an interleukin-15 like gene in common carp (Cyprinus carpio L.).

Interleukin-15 (IL-15) is a crucial cytokine involved in immune system regulation, which is produced by various cell types, including dendritic cells, monocytes, and macrophages. IL-15 plays a key role in the proliferation and activation of natural killer (NK) cells, CD8+ T cells, and memory CD8+ T cells, supporting their survival and enhancing their effector functions. Although IL-15 homologues in fish have been identified, their functions remain poorly understood. In this study, we cloned and investigated the bioactivities of an IL-15 homologue, referred to as IL-15 like (CcIL-15L), in common carp (Cyprinus carpio L.). An expression pattern analysis revealed that CcIL-15L was constitutively expressed in all examined tissues of healthy common carp, with the highest expression level observed in the intestine. Additionally, CcIL-15L expression was significantly up-regulated in the head kidney, spleen, gills, and intestine following Aeromonas hydrophila infection. In vitro, the recombinant protein CcIL-15L can significantly up-regulated the gene expression levels of pro-inflammatory cytokines (IL-1β, IL-6, IFN-γ, and TNF-α) and NK cell activation (perforin and Eomesa). We constructed a 3×FLAG eukaryotic expression vector and successfully expressed it in common carp by intramuscular injection. Additionally, the heterologous CcIL-15L protein was successfully overexpressed in vivo, and immune-related genes including CD4-1, CD8β2, TNF-α, and IgM showed significant induction in the head kidney and spleen. Furthermore, CcIL-15L overexpression reduced the bacterial loads after 24 h post-A. hydrophila infection in the liver, spleen, and kidney. Phagocytic and chemotaxis assays showed that rCcIL-15L could promoted the phagocytosis and chemotactic abilities of common carp HKLs. Our study provides a new perspective on the role for CcIL-15L in immunological functions in common carp.

Metabolic pathways and gene expression changes in Amblyseius orientalis Ehara (Acari: Phytoseiidae): The role of host plant nutrients in predator-pest dynamics

Amblyseius orientalis Ehara (Acari: Phytoseiidae) is one local predatory mite in China that has high potential for controlling Polyphagotarsonemus latus, a globally important pest to many vegetables and crops. To further evaluate the control potential of A. orientalis on different host plants against P. latus, we selected bean, cucumber, and pepper as host plants to feed P. latus, and then to feed A. orientalis. It was found when the prey P. latus fed on cucumber leaves, development of A. orientalis was the slowest, with the lowest egg production and overall poor biological performance. When A. orientalis was fed with prey hosted on cucumber and the other two plants, there were 119 differentially expressed organic compounds. The differentially metabolites were significantly enriched in the pentose phosphate pathway and carbon metabolism pathway. Further transcriptomic analysis of A. orientalis revealed 36 differentially expressed genes. Among these genes, 20 were annotated in 17 pathways in KEGG, with significant enrichment in hippo signaling pathway-fly and polysaccharide degradation pathways detected. These results indicate that the development and reproduction of A. orientalis are significantly poorer when feeding on P. latus, leading to a marked decline in amino acids, sugars, lipids, and organic compounds in A. orientalis. Additionally, there are 36 genes with consistently different expression patterns in A. orientalis when comparing cucumbers to the other two host plants. This study is an initial attempt to unravel the biological mechanisms of how nutritional substances might affect biology of natural enemies through the food chain.

ClearLLab 10C reagents panel can be applied to analyze paucicellular samples by flow cytometry.

The FDA-approved ClearLLab 10C Reagents Panel (Beckman Coulter) simplified the diagnosis of leukemias and lymphomas by flow cytometry. However, the requirement of using 3 × 106 cells/mL cannot be met for paucicellular samples. Therefore, we tested whether this 10-color panel can be reliably employed to analyze specimens with low cell concentrations. Serial dilutions of 16 samples (5 normal, 11 abnormal), yielding concentrations ranging from 3.0 × 106 to 0.0469 × 106 cells/mL (64-fold difference), were stained using the B-cell and T-cell panels of the ClearLLab 10C system, and mean fluorescence intensity (MFI) was measured for each antibody. For each cell dilution, the deviation from the value obtained with the FDA-approved concentration of 3.0 × 106 cells/mL was calculated. The agreement between the highest and lowest cell concentration data was evaluated by the Bland and Altman method, Pearson's and Spearman's correlation analyses, and linear regression. In all patients, the antigen expression pattern was similar at all cell concentrations tested, and the mean deviation of the MFI from the value obtained using 3.0 × 106 cells/mL never exceeded 10% for any of the antibodies. The Bland-Altman method demonstrated the similarity between results obtained with the FDA-approved cell concentration and a 64-fold diluted cell suspension, and a high positive correlation was found between MFI acquired under these two conditions. The tests utilizing the lowest density of cells yielded the same patterns of antigen expression in all patients as those performed with the FDA-approved concentration, documenting a 100% concordance between these two protocols. The ClearLLab 10C panel can reliably determine the expression of markers of leukemias and lymphomas in paucicellular samples containing as little as 0.0469 × 106 cells/mL (64-fold lower than the FDA-approved concentration). This finding markedly expands the applicability of the ClearLLab 10C platform in a clinical setting.

Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans.

Organismal aging is marked by decline in cellular function and anatomy, ultimately resulting in death. To inform our understanding of the mechanisms underlying this degeneration, we performed standard RNA sequencing (RNA-seq) and Oxford Nanopore Technologies direct RNA-seq over an adult time course in Caenorhabditis elegans. Long reads allowed for identification of hundreds of novel isoforms and age-associated differential isoform accumulation, resulting from alternative splicing and terminal exon choice. Genome-wide analysis reveals a decline in RNA processing fidelity. Finally, we identify thousands of inosine and hundreds of pseudouridine edits genome-wide. In this first map of pseudouridine modifications for C. elegans, we find that they largely reside in coding sequences and that the number of genes with this modification increases with age. Collectively, this analysis discovers transcriptomic signatures associated with age and is a valuable resource to understand the many processes that dictate altered gene expression patterns and post-transcriptional regulation in aging.

Molecular characteristics and expression pattern of the FAR1 gene during spike sprouting in quinoa

FAR-RED IMPAIRED RESPONSE 1 (FAR1) is a class of transposase-derived transcription factors that play a very important role in the initiation of the photosensitive pigment A (phyA) signaling pathway. Despite their importance, the understanding of the function of FAR1 genes in quinoa is still limited, especially regarding how they affect the spike sprouting response. Quinoa has gained global attention in recent years for its health benefits and potential for sustainable agriculture. In our study, the CqFAR1 gene set in quinoa was characterized using HMMER (PF03101) and BLAST analyses, and 87 genes were identified. The 87 CqFAR1 genes were systematically classified into five groups that showed a high degree of conservation in gene structure and motif composition. Tissue expression profiles of the CqFAR1 gene indicated that the CqFAR1 gene plays a key role throughout the growth and development of quinoa, especially at mid (leaf) and end (spike) stages. By RT-qPCR analysis, we observed significant differences in the expression of the CqFAR1 gene at different developmental stages. Notably, the CqFAR1 gene showed significant expression enhancement at the early stage of quinoa spike sprouting. The results are useful for understanding the role of the CqFAR1 gene in quinoa growth and development and provide theoretical support for quinoa breeding.

Genome-Wide Identification and Characterization of bHLH Gene Family in Hevea brasiliensis

The basic helix-loop-helix (bHLH) transcription factors play crucial roles in plant growth, development, and stress responses. However, their identification and insights into the understanding of their role in rubber trees remain largely uncovered. In this study, the bHLH gene family was explored and characterized in rubber trees using systematic bioinformatics approaches. In total, 180 bHLH genes were identified in the rubber tree genome, distributed unevenly across 18 chromosomes, and phylogenetic analysis classified these genes into 23 distinct subfamilies. Promoter regions revealed a high density of cis-elements responsive to light and hormones. Enrichment analysis indicated involvement in numerous biological processes, including growth, development, hormone responses, abiotic stress resistance, and secondary metabolite biosynthesis. Protein interaction network analysis identified extensive interactions between HbbHLH genes and other functional genes, forming key clusters related to iron homeostasis, plant growth, and stomatal development. Expression profiling of HbbHLH genes have demonstrated varied responses to endogenous and environmental changes. RT-qPCR of eleven HbbHLH genes in different tissues and under ethylene, jasmonic acid, and cold treatments revealed tissue-specific expression patterns and significant responses to these stimuli, highlighting the roles of these genes in hormone and cold stress responses. These findings establish a framework for exploring the molecular functions of bHLH transcription factors in rubber trees.

Identification of the NAC Family and a Functional Analysis of NoNAC36a Under Flooding Stress in Watercress (Nasturtium officinale R.Br.)

Watercress (Nasturtium officinale R.Br.) is a cruciferous aquatic vegetable that possesses significant nutritional value. The NAC family is a transcription factor family specific to plants that play an important role in regulating plant responses to abiotic stress. In order to investigate the response of NAC genes to flooding stress in watercress, we conducted a study on the NoNAC family. In this study, a total of 119 NoNAC genes were obtained through genome-wide identification. Phylogenetic analysis indicated that the NoNAC family members can be categorized into ten subgroups. The results of gene structure analysis revealed that each branch within the subgroups exhibited similar motif composition and gene structure. The heatmap analysis showed that several NoNAC genes demonstrated tissue-specific expression patterns, suggesting their potential as regulators of associated tissue development. As an aquatic plant, watercress serves as a valuable material for investigating plant resistance to flooding stress. This study found that flooding can significantly increase the watercress plant height, which is a typical escape strategy under flooding. The analysis of the expression of NoNAC genes in the stem transcriptome after flooding indicated that only NoNAC36a consistently exhibited significant differential changes and down-regulated expression at the three time points of flooding treatment. This suggests that NoNAC36a may be involved in regulating watercress plant height increases under flooding stress. The utilization of a virus-induced gene silencing assay to investigate the biological function of NoNAC36a revealed that NoNAC36a silencing caused cell elongation and expansion, thus increasing watercress plant height. The yeast one-hybrid and dual luciferase assays demonstrated that NoNAC36a binds the promoter of NoXTH33 and inhibits its expression. Subsequently, the results of yeast two-hybrid, luciferase complementary, and pull-down assays revealed the interaction between NoMOB1A and NoNAC36a in vivo and in vitro. Sequence alignment indicated that NoMOB1A and AtMOB1A share an identical amino acid sequence. RT-qPCR analysis indicated that flooding prompted the expression of NoMOB1A in stems. Thus, it is speculated that NoMOB1A may exhibit functions similar to AtMOB1A and that the up-regulation of NoMOB1A expression in stems may facilitate an increase in plant height under flooding. In summary, the NoNAC family was analyzed, and revealed a regulatory network centered on NoNAC36a that facilitates watercress resistance to flooding stress. This study enhanced the understanding of the NoNAC genes and established a theoretical foundation for investigating plant flooding tolerance.

SIFa and its receptors play a possibly stimulatory role during ovarian development of the mud crab Scylla paramamosain

SIFamide is an amidated neuropeptide with a conserved Ser-Ile-Phe structure at its C-terminal, which is crucial in insect courtship, sleep and feeding in insects. However, little information exists regarding its function in crustaceans. This study aimed to identify the cDNA of Sp-SIFa and its two putative receptors (Sp-SIFaR1 and Sp-SIFaR2) in the mud crab Scylla paramamosain. The expression profiles of Sp-SIFa and its receptors signaling were investigated to explore their potential roles. The results indicated that Sp-SIFa was expressed primarily in the nervous tissues and the midgut, and Sp-SIFaR1 was extensively expressed in the eyestalk ganglion, cerebral ganglion, hepatopancreas and the ovary whereas Sp-SIFaR2 was restricted to the eyestalk ganglion and ovary. The Sp-SIFa expression in the cerebral ganglion was significantly increased at the late vitellogenic stage during the ovarian development. The expression patterns of Sp-SIFaR1 and Sp-SIFaR2 in the ovary were similar to Sp-SIFa, indicating a potential function in regulating ovarian development. Subsequently, in vitro and in vivo experiments were performed to further support this hypothesis. The expression of Sp-Vg and Sp-VgR was significantly induced by Sp-SIFa peptide in vitro and in vivo. Moreover, prolonged injection of the Sp-SIFa peptide caused a significant increase in Sp-VgR expression, oocyte diameter and gonadal development index, demonstrating a possible stimulatory effect on ovarian development. In conclusion, our results suggest that Sp-SIFa may regulate ovarian development by promoting Vg biosynthesis and oocyte uptake in the mud crab S. paramamosain.

Cooperative participation of CagA and NFATc1 in the pathogenesis of antibiotics-responsive gastric MALT lymphoma

BackgroundThis study aimed to explore whether cytotoxin-associated gene A (CagA) can inhibit cell cycle progression by activating nuclear factor of activated T cells (NFAT) in lymphoma B cells and contribute to Helicobacter pylori eradication (HPE) responsiveness (complete remission [CR] after HPE) in gastric mucosa-associated lymphoid tissue (MALT) lymphoma.Materials and MethodsWe co-cultured three B-lymphoma cell lines (MA-1, OCI-Ly3, and OCI-Ly7) with HP strains (derived from HPE-responsive gastric MALT lymphoma) and evaluated the expression patterns of CagA, phosphorylated (p)-CagA (CagAP−Tyr), and CagA-signaling molecules, cell-cycle inhibitors, p-NFATc1 (Ser172), and NFATc1 using western blotting. Furthermore, we evaluated the association between nuclear NFATc1 expression in the tumor cells of 91 patients who received first-line HPE (59 patients with HPE responsiveness and 32 without HPE responsiveness) and HPE responsiveness and CagA expression in tumor cells.ResultsIn HP strains co-cultured with B cell lymphoma cell lines, CagA was translocated to the nucleus through tyrosine phosphorylation (CagAP−Tyr) and simultaneously dephosphorylated NFATc1, subsequently causing nuclear NFATc1 translocation and stimulating the expression of p-SHP-2/p-ERK/Bcl-xL. Activated NFATc1 causes G1 cell cycle retardation in both MA-1 and OCI-Ly3 cells by triggering p21 and p27 production. Nuclear NFATc1 localization was significantly associated with the presence of CagA in gastric MALT lymphomas (80% [41/51] vs. 33% [13/40]; p < 0.001) and with HPE responsiveness (73% [43/59] vs. 25% [8/32]; p < 0.001). Patients exhibiting both the presence of CagA and nuclear NFATc1 localization responded more rapidly to HPE than those without (median interval to CR, 4.00 vs. 6.00 months, p = 0.003).ConclusionsOur findings indicated that CagA and NFATc1 cooperatively participate in the lymphomagenesis of HPE-responsive gastric MALT lymphoma.

Transcriptomic analysis reveals pathogenicity mechanisms of Phytophthora capsici in black pepper.

The devastating disease "quick wilt" or "foot rot" is caused by the oomycete Phytophthora capsici Leonian and is affecting the economically significant spice crop black pepper (Piper nigrum L.). The details on the mechanism of interaction of P. capsici with its host black pepper remain poorly understood, hindering efforts to enhance disease resistance. To address this knowledge gap, we conducted an RNA-seq analysis to investigate the gene expression profile of P. capsici infecting black pepper. Comparative transcriptome analysis between axenic culture, and early and late infection stages of P. capsici revealed a substantial number of differentially expressed genes. Our findings demonstrate the induction of metabolic pathways, signaling cascades, and crucial pathogenicity-related processes during infection of black pepper by P. capsici. Specifically, we observed orchestrated expression of cell wall-degrading enzymes, effectors, and, detoxifying transporters at different infection time points, implicating their roles in pathogenicity. The expression patterns of key pathogenicity-associated genes, including effectors, were validated using reverse transcription quantitative real-time PCR. The effectiveness of agroinfiltration-mediated transient expression in black pepper for functional studies of effectors is also demonstrated in this study. Overall, this study establishes a strong foundation for further studies elucidating the pathogenic mechanisms employed by P. capsici infecting black pepper and for developing effective disease management strategies. Future investigations building upon these findings are essential for advancing our understanding of this pathosystem and for implementing targeted approaches to mitigate black pepper foot rot.

A Single‐Cell Atlas of Crab Ovary Provides New Insights Into Oogenesis in Crustaceans

AbstractOogenesis is crucial for sexual reproduction and provides the material basis for population continuation. Nonetheless, the identity of the cells involved, the nature of transformation, and underlying regulators of oogenesis in crustaceans remain elusive. Here, an atlas of the ovary is plotted via single‐nuclei RNA sequencing (snRNA‐seq) in the mud crab Scylla paramamosain, resulting in five cell types, including germ cells, somatic cells, and three follicle cell types identified, which in turn provides abundant candidate markers for them. Moreover, profiles of ligand‐receptor in different cells of the crab ovary indicate the roles of cell communication in oogenesis. Dozens of transcription factors in the trajectory from oogonia to oocytes as well as the key molecules/pathways in somatic cells and follicle cells relevant to oogenesis are screened, which is evolutionarily conserved and its underlying regulatory mechanism is subject to some modification across various phyla. The spatiotemporal expression patterns of seven markers are further verified and the RNAi confirms the essential roles of piwi and VgR in oogenesis. These data help to elucidate the mechanism underlying gametogenesis and the evolution of reproductive strategy in invertebrates.

Isolation and identification of patient-derived liver cancer stem cells and development of personalized treatment strategies

BackgroundLiver cancer stem cells (LCSCs) are thought to drive the metastasis and recurrence, however, the heterogeneity of molecular markers of LCSCs has hindered the development of effective methods to isolate them.MethodsThis study introduced an effective approach to isolate and culture LCSCs from human primary liver cancer (HPLC), leveraging mouse embryonic fibroblasts (MEFs) as feeder cells in conjunction with using defined medium. Isolated LCSCs were further characterized by multiple approaches. Transcriptome sequencing data analysis was conducted to identify highly expressed genes in LCSCs and classify different subtypes of liver cancers.ResultsTotal sixteen cell strains were directly isolated from 24 tissues of three types of HPLC without sorting, seven of which could be maintained long-term culture as colony growth on MEFs, which is unique characteristics of stem cells. Even 10 of cloned cells formed the tumors in immunodeficient mice, indicating that those cloned cells were tumorgenic. The histologies and gene expression pattern of human xenografts were very similar to those of HPLC where these cloned cells were isolated. Moreover, putative markers of LCSCs were further verified to all express in cloned cells, confirming that these cells were LCSCs. These cloned LCSCs could be cryopreserved, and still maintained the feature of colony growth on MEFs after the recovery. Compared to suspension culture as conventional approach to culture LCSCs, our approach much better maintained stemness of LCSCs for a long time. To date, these cloned cells could be cultured on MEFs over 12 passages. Moreover, bioinformatics analysis of sequencing data revealed the gene expression profiles in LCSCs, and liver cancers were classified into two subtypes C1 and C2 based on genes associated with the prognosis of LCSCs. Patients of the C2 subtype, which is closely related to the extracellular matrix, were found to be sensitive to treatments such as Cisplatin, Axitinib, JAK1 inhibitors, WNT-c59, Sorafenib, and RO-3306.ConclusionIn summary, this effective approach offers new insights into the molecular landscape of human liver cancers, and the identification of the C2 subtype and its unique response to the treatment pave the way for the creation of more effective, personalized therapeutic strategies.