TCOD: an integrated resource for tropical crops.

Tropical crops are vital for tropical agriculture, with resource scarcity, functional diversity and extensive market demand, providing considerable economic benefits for the world's tropical agriculture-producing countries. The rapid development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amount of data, which urgently needs an effective platform for data integration and sharing. However, the existing databases cannot fully satisfy researchers' requirements due to the relatively limited integration level and untimely update. Here, we present the Tropical Crop Omics Database (TCOD, https://ngdc.cncb.ac.cn/tcod), a comprehensive multi-omics data platform for tropical crops. TCOD integrates diverse omics data from 15 species, encompassing 34 chromosome-level de novo assemblies, 1 255 004 genes with functional annotations, 282 436 992 unique variants from 2048 WGS samples, 88 transcriptomic profiles from 1997 RNA-Seq samples and 13 381 germplasm items. Additionally, TCOD not only employs genes as a bridge to interconnect multi-omics data, enabling cross-species comparisons based on homology relationships, but also offers user-friendly online tools for efficient data mining and visualization. In short, TCOD integrates multi-species, multi-omics data and online tools, which will facilitate the research on genomic selective breeding and trait biology of tropical crops.

HGD: an integrated homologous gene database across multiple species.

Homology is fundamental to infer genes' evolutionary processes and relationships with shared ancestry. Existing homolog gene resources vary in terms of inferring methods, homologous relationship and identifiers, posing inevitable difficulties for choosing and mapping homology results from one to another. Here, we present HGD (Homologous Gene Database, https://ngdc.cncb.ac.cn/hgd), a comprehensive homologs resource integrating multi-species, multi-resources and multi-omics, as a complement to existing resources providing public and one-stop data service. Currently, HGD houses a total of 112 383 644 homologous pairs for 37 species, including 19 animals, 16 plants and 2 microorganisms. Meanwhile, HGD integrates various annotations from public resources, including 16 909 homologs with traits, 276 670 homologs with variants, 398 573 homologs with expression and 536 852 homologs with gene ontology (GO) annotations. HGD provides a wide range of omics gene function annotations to help users gain a deeper understanding of gene function.

Traditional Chinese medicine invigorating the spleen and kidney promotes HBsAg seroclearance in the mouse model.

Traditional Chinese medicine (TCM) is often used as an adjuvant or alternative therapy for abnormal liver biochemistry or liver fibrosis associated with chronic hepatitis B (CHB). However, the role of TCM in HBsAg seroclearance remains unclear. We aimed at exploring the role and possible mechanisms of TCM in HBsAg seroclearance. Fifteen widely used TCM granules invigorating the spleen and kidneys were screened. C57BL/6J mice were administered daily with TCM granules by gavage for 1 week. The effect of TCM on the M1 polarization of macrophages was measured using a CD86 assay. According to the principles of formulating prescriptions, three single TCM with the most noticeable effect on M1 polarization, accompanied by two other TCM granules, were used to develop a TCM formula. The hepatitis B virus-expressing mouse model was constructed by hydrodynamic injection of the pAAV/HBV1.2 plasmid. Hepatitis B virus-expressing mice were gavaged daily with phosphate-buffered saline (PBS), TCM formula, or Codonopsis Radix, for 1 week. HBsAg, HBeAg, and hepatitis B virus DNA levels were measured. In addition, gut microbiota was profiled using 16S rDNA sequencing. Several TCM granules showed significant effects on M1 polarization. The TCM formula accelerated HBsAg seroclearance compared with the Codonopsis Radix and PBS groups. Intrahepatic M1 polarization, as indicated by flow cytometry and immunohistochemistry, was induced in the TCM formula and Codonopsis Radix groups. The abundance of Alloprevotella significantly increased in the TCM formula and Codonopsis Radix groups. These results demonstrate that the TCM formula for invigorating the spleen and kidney can accelerate HBsAg seroclearance. This effect can be attributed, at least in part, to M1 polarization of intrahepatic macrophages.

Expression profiles of circular RNAs in spermatozoa from aging men.

BACKGROUND: Advanced paternal age (APA) is associated with decreased fertility, but the mechanism underlying APA remains unknown. CircRNAs have been reported to be ideal candidate biomarkers for diagnostic and therapeutic applications in many diseases and are also involved in spermatogenesis. Hence, we aimed to assess the circRNA expression profile of spermatozoa from aging men. METHODS AND RESULTS: We recruited 6 subjects, including 3 in the younger group (men age < 40) and 3 in the APA group (men age ≥ 40). RNA sequencing was exploited to identify the expression profiles of circRNAs between the two groups. The expression levels of circRNAs were validated using real-time quantitative polymerase chain reaction (RT-qPCR). Kyoto Encyclopedia of Genes and Genomes biological pathway analysis and Gene Ontology analysis were performed to evaluate the functions of differentially expressed circRNAs (DE-circRNAs) between the two groups. In total, 18,787 circRNAs were sequenced in the spermatozoa of two groups. Our analysis revealed that there were 1056 downregulated circRNAs and 1228 upregulated circRNAs between the two groups, and KEGG analysis showed they were mainly involved in pathways including the DNA repair signaling pathway, meiotic recombination signaling pathway, and PI3K/AKT signaling pathway. CONCLUSIONS: In conclusion, our study suggested that circRNAs play a vital role in spermatozoa from aging men and provided a fresh perspective on the specific regulatory mechanism of spermatozoa from aging men.

MAFLD is associated with increased all-cause mortality in low cardiovascular-risk individuals but not in intermediate to high-risk individuals.

BACKGROUND AND AIMS: Metabolic-associated fatty liver disease (MAFLD) is increasingly recognized as a systematic disease rather than just a liver disease alone, which raises concerns about its long-term impact on different populations. This study aimed to clarify the effects of MAFLD on long-term outcomes among different cardiovascular risk-stratified populations. METHODS AND RESULTS: Eligible individuals in the Third National Health and Nutrition Examination Surveys (NHANES Ⅲ, 1988-1994) were enrolled. Participants were classified into low, intermediate, or high cardiovascular-risk populations according to the Framingham general equations. Kaplan-Meier survival analysis and Cox regression models were used to investigate the association between MAFLD and long-term outcomes in different cardiovascular-risk populations. A total of 8897 adults were enrolled in the final analysis. The median ages in the non-MAFLD and MAFLD groups were 44 and 49 years old, respectively. During a median follow-up of 22.8 years, a total of 2991 deaths were recorded, including 1694 deaths (30.3%) in non-MAFLD and 1297 deaths (39.2%) in MAFLD (P < 0.001). In the low cardiovascular-risk population, MAFLD individuals had increased all-cause mortality than non-MAFLD individuals (HR = 1.206, 95% CI:1.0338-1.400, P = 0.014). However, similar results were not observed in intermediate or high-cardiovascular-risk individuals. Further analysis of cause-specific mortality suggested that MAFLD was associated with higher cancer-related mortality in the low-risk population (HR = 1.313, 95% CI:1.000-1.725, P = 0.049). CONCLUSIONS: MAFLD was associated with increased all-cause mortality among individuals with low cardiovascular risk, rather than those with an intermediate or high cardiovascular risk.

A chromosome-level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae).

Paracymoriza distinctalis is a semiaquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea superfamily. However, the understanding of heredity, evolution, and functional genomics of P. distinctalis are limited by few genome-wide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first P. distinctalis genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of P. distinctalis and Chilo suppressalis lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of P. distinctalis, but also may promote the study of the genomes of other lepidopteran species.

Disruption of Transient SERT Expression in Thalamic Glutamatergic Neurons Alters Trajectory of Postnatal Interneuron Development in the Mouse Cortex.

In mice, terminal differentiation of subpopulations of interneurons occurs in late postnatal stages, paralleling the emergence of the adult cortical architecture. Here, we investigated the effects of altered initial cortical architecture on later interneuron development. We identified that a class of somatostatin (SOM)-expressing GABAergic interneurons undergoes terminal differentiation between 2nd and 3rd postnatal week in the mouse somatosensory barrel cortex and upregulates Reelin expression during neurite outgrowth. Our previous work demonstrated that transient expression (E15-P10) of serotonin uptake transporter (SERT) in thalamocortical projection neurons regulates barrel elaboration during cortical map establishment. We show here that in thalamic neuron SERT knockout mice, these SOM-expressing interneurons develop at the right time, reach correct positions and express correct neurochemical markers, but only 70% of the neurons remain in the adult barrel cortex. Moreover, those neurons that remain display altered dendritic patterning. Our data indicate that a precise architecture at the cortical destination is not essential for specifying late-developing interneuron identities, their cortical deposition, and spatial organization, but dictates their number and dendritic structure ultimately integrated into the cortex. Our study illuminates how disruption of temporal-specific SERT function and related key regulators during cortical map establishment can alter interneuron development trajectory that persists to adult central nervous system.

Origanum vulgare L. leaves extract alleviates testis and sperm damages induced by finasteride: Biochemical, Immunohistological and apoptosis genes based evidences.

The aim of the current study was to investigate antioxidant, anti-inflammatory and anti-apoptotic effects of Origanum vulgare on finasteride-induced oxidative injury in mouse testis and sperm parameters. Thirty BALB/c mice were divided into 5 groups: negative control, received 0.5 ml/day distilled water; positive control, received 25 mg/kg finasteride orally; and three groups received 100, 200 and 400 mg/kg/day O. vulgare extract plus 25 mg kg-1  day-1 finasteride for 35 days. At day 36, serum luteinising hormone, follicle-stimulating hormone and testosterone, inflammatory cytokines (IL-6, TNF-α, IL-1ß), glutathione peroxidase, superoxide dismutase and nitric oxide levels were assessed. Also, apoptotic changes investigated through genes expression and immunohistochemical staining. Finasteride in 35 days resulted in significant destructive alterations in the testis architecture, suppressed antioxidant enzymes and increased lipid peroxidation. The expression of Bcl-2 was down-regulated, whereas p53 and caspase-3 were up-regulated. Origanum vulgare improved the serum level of hormones and restored the antioxidant defence. 200 and 400 mg/kg/day of O. vulgare alleviated the testis structure and sperm parameters, up-regulated the anti-apoptotic gene Bcl-2 and down-regulated the p53, caspase-3 genes in treated groups. The findings indicate that O. vulgare extract improved function and structure of testis tissue against finasteride-induced testicular toxicity.

ß1,4-Galactosyltransferase V activates Notch1 signaling in glioma stem-like cells and promotes their transdifferentiation into endothelial cells.

Malignant glioblastoma multiforme is one of the most aggressive human cancers, with very low survival rates. Recent studies have reported that glioma stem-like cells transdifferentiate into endothelial cells, indicating a new mechanism for tumor angiogenesis and potentially providing new therapeutic options for glioblastoma treatment. Glioma malignancy is strongly associated with altered expression of N-linked oligosaccharide structures on the cell surface. We have previously reported that ß1,4-galactosyltransferase V (ß1,4GalTV), which galactosylates the GlcNAcß1-6Man arm of the branched N-glycans, is highly expressed in glioma and promotes glioma cell growth in vitro and in vivo However, the mechanism by which ß1,4GalTV stimulates glioma growth is unknown. Here we demonstrate that short hairpin RNA-mediated ß1,4GalTV knockdown inhibits the tumorigenesis of glioma stem-like cells and reduces their transdifferentiation into endothelial cells. We also found that ß1,4GalTV overexpression increased glioma stem-like cell transdifferentiation into endothelial cells and that this effect required ß1,4GalTV galactosylation activity. Moreover, ß1,4GalTV promoted ß1,4-galactosylation of Notch1 and increased Notch1 protein levels. Of note, ectopic expression of activated Notch1 rescued the inhibitory effect of ß1,4GalTV depletion on glioma stem-like cell transdifferentiation. In summary, our findings indicate that ß1,4GalTV stimulates transdifferentiation of glioma stem-like cells into endothelial cells by activating Notch1 signaling. These detailed insights shed important light on the mechanisms regulating glioma angiogenesis.

IL-17A secreted from lymphatic endothelial cells promotes tumorigenesis by upregulation of PD-L1 in hepatoma stem cells.

BACKGROUND & AIMS: The microenvironment regulates hepatoma stem cell behavior. However, the contributions of lymphatic endothelial cells to the hepatoma stem cell niche remain largely unknown; we aimed to analyze this contribution and elucidate the mechanisms behind it. METHODS: Associations between lymphatic endothelial cells and CD133+ hepatoma stem cells were analyzed by immunofluorescence and adhesion assays; with the effects of their association on IL-17A expression examined using western blot, quantitative reverse transcription PCR and luciferase reporter assay. The effects of IL-17A on the self-renewal and tumorigenesis of hepatoma stem cells were examined using sphere and tumor formation assays. The role of IL-17A in immune escape by hepatoma stem cells was examined using flow cytometry. The expression of IL-17A in hepatoma tissues was examined using immunohistochemistry. RESULTS: CD133+ hepatoma stem cells preferentially interact with lymphatic endothelial cells. The interaction between the mannose receptor and high-mannose type N-glycans mediates the interaction between CD133+ hepatoma stem cells and lymphatic endothelial cells. This interaction activates cytokine IL-17A expression in lymphatic endothelial cells. IL-17A promotes the self-renewal of hepatoma stem cells. It also promotes their immune escape, partly through upregulation of PD-L1. CONCLUSION: Interactions between lymphatic endothelial cells and hepatoma stem cells promote the self-renewal and immune escape of hepatoma stem cells, by activating IL-17A signaling. Thus, inhibiting IL-17A signaling may be a promising approach for hepatoma treatment. LAY SUMMARY: The microenvironment is crucial for the self-renewal and development of hepatoma stem cells, which lead to the development of liver cancer. Lymphatic endothelial cells are an important component of this niche microenvironment, helping hepatoma stem cells to self-renew and escape immune attack, by upregulating IL-17A signaling. Thus, targeting IL-17A signaling is a potential strategy for the treatment of hepatoma.

T-cell infiltration and expressions of T lymphocyte co-inhibitory B7-H1 and B7-H4 molecules among colorectal cancer patients in northeast China's Heilongjiang province.

Colorectal cancer has an extremely poor prognosis due to its high rate of recurrence and metastasis. The present study aimed to investigate the correlations between the B7-H1 and B7-H4 expressions as well as the clinicopathological characteristics and the prognosis of patients with colorectal cancer. We further inferred from these findings whether T lymphocyte co-inhibitory molecules (B7-H1 and B7-H4) led to a poor prognosis in Heilongjiang patients with colorectal cancer. Survival analysis revealed that the poor prognosis of these patients was unrelated to patient age, tumor size or histological grade, or lymph node metastasis, but was associated with TNM stage, high B7-H1 and B7-H4 expression levels. High B7-H1 and B7-H4 expressions were closely correlated with poor prognosis in patients with colorectal cancer. We speculate that the joint detection of these molecules may clinically apply for diagnosing and predicting poor prognosis of patients with colorectal cancer in northeast China's Heilongjiang province. In addition, intervention of B7-H1 and B7-H4 may be beneficial for enhancement of immunity in these patients.

Constructing immune and prognostic features associated with ADCP in hepatocellular carcinoma and pan-cancer based on scRNA-seq and bulk RNA-seq.

Aim: Despite the significant therapeutic outcomes achieved in systemic treatments for liver hepatocellular carcinoma (LIHC), it is an objective reality that only a low proportion of patients exhibit an improved objective response rate (ORR) to current immunotherapies. Antibody-dependent cellular phagocytosis (ADCP) immunotherapy is considered the new engine for precision immunotherapy. Based on this, we aim to develop an ADCP-based LIHC risk stratification system and screen for relevant targets. Method: Utilizing a combination of single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data, we screened for ADCP modulating factors in LIHC and identified differentially expressed genes along with their involved functional pathways. A risk scoring model was established by identifying ADCP-related genes with prognostic value through LASSO Cox regression analysis. The risk scoring model was then subjected to evaluations of immune infiltration and immunotherapy relevance, with pan-cancer analysis and in vitro experimental studies conducted on key targets. Results: Building on the research by Kamber RA et al., we identified GYPA, CLDN18, and IRX5 as potential key target genes regulating ADCP in LIHC. These genes demonstrated significant correlations with immune infiltration cells, such as M1-type macrophages, and the effectiveness of immunotherapy in LIHC, as well as a close association with clinical pathological staging and patient prognosis. Pan-cancer analysis revealed that CLDN18 was prognostically and immunologically relevant across multiple types of cancer. Validation through tissue and cell samples confirmed that GYPA and CLDN18 were upregulated in liver cancer tissues and cells. Furthermore, in vitro knockdown of CLDN18 inhibited the malignancy capabilities of liver cancer cells. Conclusion: We have identified an ADCP signature in LIHC comprising three genes. Analysis based on a risk scoring model derived from these three genes, coupled with subsequent experimental validation, confirmed the pivotal role of M1-type macrophages in ADCP within LIHC, establishing CLDN18 as a critical ADCP regulatory target in LIHC.

The Interaction between Collagen 1 and High Mannose Type CD133 Up-Regulates Glutamine Transporter SLC1A5 to Promote the Tumorigenesis of Glioblastoma Stem Cells.

Targeting the niche components surrounding glioblastoma stem cells (GSCs) helps to develop more effective glioblastoma treatments. However, the mechanisms underlying the crosstalk between GSCs and microenvironment remain largely unknown. Clarifying the extracellular molecules binding to GSCs marker CD133 helps to elucidate the mechanism of the communication between GSCs and the microenvironment. Here, it is found that the extracellular domain of high mannose type CD133 physically interacts with Collagen 1 (COL1) in GSCs. COL1, mainly secreted by cancer-associated fibroblasts, is a niche component for GSCs. COL1 enhances the interaction between CD133 and p85 and activates Akt phosphorylation. Activation of Akt pathway increases transcription factor ATF4 protein level, subsequently enhances SLC1A5-dependent glutamine uptake and glutathione synthesis. The inhibition of CD133-COL1 interaction or down-regulation of SLC1A5 reduces COL1-accelerated GSCs self-renewal and tumorigenesis. Analysis of glioma samples reveals that the level of COL1 is correlated with histopathological grade of glioma and the expression of SLC1A5. Collectively, COL1, a niche component for GSCs, enhances the tumorigenesis of GSCs partially through CD133-Akt-SLC1A5 signaling axis, providing a new mechanism underlying the cross-talk between GSCs and extracellular matrix (ECM) microenvironment.

Exploring potential pharmacological mechanisms of Yiqi Tuomin Decoction in the treatment of allergic rhinitis utilizing network pharmacology prediction and molecular docking-based strategies: experimental research.

Yiqi Tuomin Decoction (YTD), which originated from the theory of lung deficiency and cold in Chinese medicine, is a common Chinese herbal formula used against allergic rhinitis (AR). In our otolaryngology department, this prescription has been used to treat so many AR patients with lung-deficiency-related colds for nearly 30 years. However, the mechanism of its ingredient-target is still unclear. Based on our early experiments and clinical case studies, in this paper, we explore the mechanism of YTD systematically against AR using bioinformatic methods of network pharmacology and molecular docking. Methods: The Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was used to screen the active ingredients and targets of YTD. The AR-related targets were retrieved from OMIM, GeneCards, TTD, DisGeNET, DrugBank databases, and PharmGKB. The Venn database was used to screen the potential core targets. After that, the STRING database was used to construct the protein-protein interaction (PPI) of the core targets and then visualize it by Cytoscape. The Gene Ontology (GO)-enriched processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the core targets were analyzed by the KOBAS-I database and Sangerbox. Molecular docking was used to assess interactions between potential targets and active ingredients. Results: A total of 169 active ingredients and 238 targets of YTD were predicted. YTD shared 115 common targets with AR from the Venn database. The GO-enriched processes and KEGG pathways indicate that genes involved in inflammation and oxidative stress, accompanying the MAPK signaling pathway, Th17 cell differentiation, IL-17 signaling pathway, and Th1 and Th2 cell differentiation, may play a mediated effect in YTD. The docking results showed good binding ability between the active ingredients and the selected targets. Conclusions: Our study systematically indicated the underlying mechanism of YTD against AR from the perspective of bioinformatics. By studying the active ingredients of YTD, we obtained molecular mechanisms and established a reliable method and molecular theoretical basis for the sensible development of Chinese medicine in the treatment of AR.

Identification of PANoptosis-relevant subgroups to evaluate the prognosis and immune landscape of patients with liver hepatocellular carcinoma.

Liver hepatocellular carcinoma (LIHC) is one of the most common malignant tumors, which is difficult to be diagnosed at an early stage due to its poor prognosis. Despite the fact that PANoptosis is important in the occurrence and development of tumors, no bioinformatic explanation related to PANoptosis in LIHC can be found. A bioinformatics analysis on the data of LIHC patients in TCGA database was carried out on the basis of previously identified PANoptosis-related genes (PRGs). LIHC patients were divided into two PRG clusters whose gene characteristics of differentially expressed genes (DEGs) were discussed. According to DEGs, the patients were further divided into two DEG clusters, and prognostic-related DEGs (PRDEGs) were applied to risk score calculation, the latter of which turned out to be practical in identifying the relationship among risk score, patient prognosis, and immune landscape. The results suggested that PRGs and relevant clusters were bound up with the survival and immunity of patients. Moreover, the prognostic value based on two PRDEGs was evaluated, the risk scoring model was constructed, and the nomogram model for predicting the survival rate of patients was further developed. Therefore, it was found that the prognosis of the high-risk subgroup was poor. Additionally, three factors, namely, the abundance of immune cells, the expression of immune checkpoints, and immunotherapy and chemotherapy were considered to be associated with the risk score. RT-qPCR results indicated higher positive expression of CD8A and CXCL6 in both LIHC tissues and most human liver cancer cell lines. In summary, the results suggested that PANoptosis was bound up with LIHC-related survival and immunity. Two PRDEGs were identified as potential markers. Thus, the understanding of PANoptosis in LIHC was enriched, with some strategies provided for the clinical therapy of LIHC.

Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).

With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.

Notch1 is involved in cell proliferation and neuronal differentiation in the HVC of zebra finch (Taeniopygia guttata).

Significant sex differences are found in songbirds' song control nuclei and their controlled song behaviors. To elucidate the underlying mechanisms, we explored the role of Notch1 during the development of the high vocal centre (HVC) and song learning in zebra finch. Our study first found that Notch1 positive cells were distributed in HVC with female-biased densities at posthatching day (PHD) 15, but male-biased at PHD 45 and adult. There were about 60 putative oestrogen-responsive elements within 2.5 kb upstream of Notch1, and Notch1 mRNA in the explants that contained the developing male HVC was significantly increased after estrogen addition into the cultured medium for 48 h. After injecting Notch1-interfering lentivirus into the male or female HVC at PHD 15, cell proliferation was significantly promoted in the ventricle zone overlying the HVC at PHD 23. In addition, neuronal differentiation towards Hu+ /BrdU+ at PHD 31, mature neurons (NeuN+/BrdU+) including those projecting to RA in HVC and the sizes of HVC and RA at adult increased significantly after Notch1-interfering lentiviruses were injected into the male HVC at PHD 15. However, the above measurements decreased, following the injection of the lentiviruses expressing Notch intracellular domain (NICD). Finally, the repeat numbers of syllables 'b' or 'c' of learned songs changed after the injection of Notch1-interfering or NICD-expressing lentiviruses into the HVC at PHD15. Our study suggests that Notch1 is related to the development of HVC and song learning in the zebra finch.

Loss of α-1,2-mannosidase MAN1C1 promotes tumorigenesis of intrahepatic cholangiocarcinoma through enhancing CD133-FIP200 interaction.

CD133 is widely used as a marker to isolate tumor-initiating cells in many types of cancers. The structure of N-glycan on CD133 is altered during the differentiation of tumor-initiating cells. However, the relationship between CD133 N-glycosylation and stem cell characteristics remains elusive. Here, we found that the level of α-1,2-mannosylated CD133 was associated with the level of stemness genes in intrahepatic cholangiocarcinoma (iCCA) tissues. α-1,2-mannosylated CD133+ cells possessed the characteristics of tumor-initiating cells. The loss of the Golgi α-mannosidase I coding gene MAN1C1 resulted in the formation of α-1,2-mannosylated CD133 in iCCA-initiating cells. Mechanistically, α-1,2-mannosylation promoted the cytoplasmic distribution of CD133 and enhanced the interaction between CD133 and the autophagy gene FIP200, subsequently promoting the tumorigenesis of α-1,2-mannosylated CD133+ cells. Analysis of iCCA samples showed that the level of cytoplasmic CD133 was associated with poor iCCA prognosis. Collectively, α-1,2-mannosylated CD133 is a functional marker of iCCA-initiating cells.