Expression Patterns Research Articles

Mechanistic exploration of royal jelly production in caged honey bees (Apis mellifera)

This study investigates the impact of bee pollen nutrition on the royal jelly production of honey bees (Apis mellifera). Results demonstrate that pollen diet significantly impacts hypopharyngeal gland (HPG) development and the expression of genes associated with royal jelly biosynthesis. Bees fed Brassica napus pollen exhibited superior HPG development, and increased mrjp1 expression (encoding a key royal jelly protein). While the cyp450 6AS8 gene expression (encoding a key enzyme in 10-HDA biosynthesis) was increased by pollen consumption, no distinct expression patterns were observed among the different pollen types tested. An in vitro bee cage platform for royal jelly production has been established to further understand the mechanisms behind royal jelly production in bees. The experiment demonstrated a positive correlation between the number of worker bees and the total yield of royal jelly per cage. However, when the number of worker bees is low, the amount of royal jelly each individual worker bee needs to produce increases. In conclusion, these findings enhance our understanding of the role of bee pollen nutrition in royal jelly production. Furthermore, the results from this in vitro bee cage platform suggest that the number of worker bees is a critical factor in royal jelly production, and that bees may possess a controllable mechanism for regulating royal jelly secretion.

Mayfly developmental atlas: developmental temporal expression atlas of the mayfly, Ephemera vulgata, reveals short germ-specific hox gene activation

BackgroundOver the course of evolution, insects have seen drastic changes in their mode of development. While insects with derived modes of development have been studied extensively, information on ancestral modes of development is lacking. To address this, we selected a member of one of the earliest lineages of extant flying insects, serving as an outgroup to the modern winged insects, the short germ, non-model mayfly Ephemera vulgata Linnaeus (Insecta: Ephemeroptera, Ephemeridae). We document the embryonic morphology throughout its development and establish a global temporal expression atlas.ResultsDAPI staining was used to visualise developmental morphology to provide a frame of reference for the sequenced timepoints. A transcriptome was assembled from 3.2 billion Illumina RNAseq reads divided in 12 timepoints with 3 replicates per timepoint consisting of 35,091 putative genes. We identified 6,091 significantly differentially expressed genes (DEGs) and analysed them for broad expression patterns via gene ontology (GO) as well as for specific genes of interest. This revealed a U-shaped relationship between the sum of DEGs and developmental timepoints, over time, with the lowest number of DEGs at 72 hours after egg laying (hAEL). Based on a principal component analysis of sequenced timepoints, overall development could be divided into four stages, with a transcriptional turning point around katatrepsis. Expression patterns of zld and smg showed a persistent negative correlation and revealed the maternal-to-zygotic transition (MZT), occurring 24 hAEL. The onset of development of some major anatomical structures, including the head, body, respiratory system, limb, muscle, and eye, are reported. Finally, we show that the ancestral short germ sequential mode of segmentation translates to a sequential Hox gene activation and find diverging expression patterns for lab and pb. We incorporate these patterns and morphological observations to an overview of the developmental timeline.ConclusionsWith our comprehensive differential expression study, we demonstrate the versatility of our global temporal expression atlas. It has the capacity to contribute significantly to phylogenetic insights in early-diverging insect developmental biology and can be deployed in both molecular and genomic applications for future research.

Stimulation of locus coeruleus inputs to the prelimbic cortex in mice induces cell type-specific expression of the Apoe gene.

The medial frontal cortex (mFC) and locus coeruleus (LC) are two brain areas that have been implicated in a range of cognitive phenomena, such as attention, memory, and decision making. Regulators of these brain regions at the molecular level are not well understood, but might help to elucidate underlying mechanisms of disorders that present with deficits in these cognitive domains. To probe this, we used chemogenetic stimulation of neurons in the LC with axonal projections to the prelimbic subregion (PrL) of the mFC, and subsequent bulk RNA-sequencing from the mouse PrL. We found that stimulation of this circuit caused an increase in transcription of a host of genes, including the Apoe gene. To investigate cell type-specific expression of Apoe in the PrL, we used a dual-virus approach to express either the excitatory DREADD receptor hM3Dq in LC neurons with projections to the PrL, or a control virus, and found that increases in Apoe expression in the PrL following depolarization of LC inputs is enriched in GABAergic neurons in a sex-dependent manner. The results of these experiments yield insights into how Apoe expression affects function in a cortical microcircuit that is important for attention, memory, and decision making, and point to interneuron-specific expression of Apoe as a potential biomarker for circuit function in disorders such as attention-deficit hyperactivity disorder (ADHD), schizophrenia, and Alzheimer's disease (AD).Significance Statement Identifying patterns of gene expression in specific brain circuits is an important first step toward developing treatments for cognitive and behavioral symptoms that rely on those circuits. In this paper, we describe a transcriptome-scale motif in one such circuit - neurons in the LC that project to the PrL. This circuit has been implicated in attention, memory, and decision making, and deficits in these cognitive domains are common across many neuropsychiatric disorders. We further explored one of the top differentially expressed genes, Apoe, to identify how it is expressed in distinct cell types following stimulation of this circuit, paving the way for spatially- and genetically-specific targeting of this gene in disorders that feature dysfunction in this circuit.

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns.

Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014 Populus trichocarpa full genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden-grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%-38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one-third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non-spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.

Evolutionary changes leading to efficient glymphatic circulation in the mammalian brain

The functional significance of the morphological and genetic changes that occurred in the brain during evolution is not fully understood. Here we show the relationships between evolutionary changes of the brain and glymphatic circulation. We establish a mathematical model to simulate glymphatic circulation in the cerebral hemispheres, and our results show that cortical neurons accumulate in areas of the cerebral hemispheres where glymphatic circulation is highly efficient. We also find that cortical folds markedly enhance the efficiency of glymphatic circulation in the cerebral hemispheres. Furthermore, our in vivo study using ferrets reveals sulcus-dominant cerebrospinal fluid (CSF) influx, which enhances the efficiency of glymphatic circulation in the enlarged cerebral hemispheres of gyrencephalic brains. Sulcus-dominant CSF influx is mediated by preferential expression of aquaporin-4 in sulcal regions, and similar expression patterns of aquaporin-4 are also found in human cerebral hemispheres. These results indicate that evolutionary changes in the cerebral hemispheres are related to improved efficiency of glymphatic circulation. It seems plausible that the efficiency of glymphatic circulation is an important factor determining the evolutionary trajectory of the cerebral hemispheres.

Hypothyroidism promotes microglia M1 polarization by inhibiting BDNF-promoted PI3K-Akt signaling pathway.

Methimazole-induced mice was used to construct hypothyroidism model and explore the polarization of microglia. Lipopolysaccharide (LPS)-treated BV2 cells were used to investigate the effecting factors on microglia M1 polarization. Finally, global transcriptome sequencing (RNA-seq) was utilized to identify the underlying regulatory mechanisms. The biomarkers of microglia M1 polarization and pro-inflammatory cytokines were significantly increased in hypothyroidism mice brain; hypothyroidism could also repress the expression of BDNF and TrkB, and the anti-inflammatory cytokine such as IL-10. In BV2 cells, LPS treatment decreased expression of BDNF, IL-10, and Arg1, while BDNF overexpression (BDNF-OE) significantly reversed the inflammation-induced by LPS by repressing iNOS and TNF-α, while increasing IL-10 and Arg1. RNA-seq analysis demonstrated that in LPS-treated BV2 cells, BDNF-OE significantly altered expression pattern of genes involved in PI3K-Akt signaling pathway, including the upregulated Thbs3, Myc, Gdnf, Thbs1, and Ccnd1, and the downregulated Gnb4, Fgf22, Pik3r3, Pgf, Cdkn1a, and Pdgfra. Myc, Gdnf, Thbs1, and Ccnd1 showed much higher expression levels than other genes in PI3K-Akt signaling pathway. Our study demonstrated a sound conclusion that hypothyroidism promotes microglia M1 polarization by inhibiting BDNF-activated PI3K-Akt signaling pathway in brain, which could serve as a promising therapeutic target for microglia-induced neurodegenerative or emotional disorders in future.

Analysis of gene expression level dominance and homoeologous expression bias in different tissues of a new synthetic amphidiploid, Raphanobrassica (Brassica rapa × Raphanus sativus)

Polyploidization is an evolutionarily and mechanistically intriguing process, that requires harmonization of genomic and regulatory interactions among divergent genome groups. Here, we examined gene expression pattern changes in the leaves and petals of Raphanobrassica, a new synthetic amphidiploid generated by a distant cross between radish (RR, 2n = 18) and purple cabbage (AA, 2n = 20). The degree and direction of expression level dominance (ELD), defined as the total expression level of two homoeologous genes, was assessed, and homoeologous expression bias (HEB) analyzed, to assess the relative contributions of homoeologous genes to the transcriptome. Comparative analysis between Raphanobrassica and its parental species revealed that most differentially expressed genes were additive (leaves, 81.63 %; flowers, 82.71 %). ELD favors the R genome in both Raphanobrassica tissues, primarily driven by up- or down-regulation of non-dominant parent genes, with radish (RR) as the dominant parent in ELD-R and cabbage (AA) in ELD-A HEB indicated a preference for the A genome in both tissues (leaves, 26.03 %; flowers, 32.74 %). To further elucidate the ELD phenomenon, we compared expression levels of individual homoeologous genes with those in the diploid parents. ELD toward genes expressed at higher levels in parents was mediated either by down-regulation of genes from the dominant parent or up-regulation of those from the non-dominant parent, whereas ELD toward genes expressed at lower levels in parents was attributable solely to down-regulation of non-dominant parent homoeologous genes. Our findings provide novel insights into gene expression changes in heterodiploids generated by hybridization prior to polyploidization, laying a foundation for understanding genome-wide expression pattern alterations during polyploid formation.

Establishing a comprehensive web-based analysis platform for Nicotiana benthamiana genome and transcriptome.

Nicotiana benthamiana has long served as a crucial plant material extensively used in plant physiology research, particularly in the field of plant pathology, because of its high susceptibility to plant viruses. Additionally, it serves as a production platform to test vaccines and other valuable substances. Among its approximately 3.1 Gb genome, 57 583 genes have been annotated within a 61 Mb region. We created a comprehensive and easy-to-use platform to use transcriptomes for modern annotation. These tools allow to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads. To demonstrate their utility, we analyzed the gene expression profiles of enzymes within the nicotine biosynthesis pathway, a secondary metabolic pathway characteristic of the Nicotiana genus. Using the developed tool, expression profiles of the nicotine biosynthesis pathway genes were generated. The expression patterns of eight gene groups in the pathway were strongly expressed in the roots and weakly expressed in leaves and flowers of N. benthamiana. The results were consistent with the established gene expression profiles in Nicotiana tabacum and provided insights into gene family composition and expression trends. The compilation of this database tool can facilitate genetic analysis of N. benthamiana in the future.

GH3 Gene Family Identification in Chinese White Pear (Pyrus bretschneideri) and the Functional Analysis of PbrGH3.5 in Fe Deficiency Responses in Tomato

Iron (Fe) deficiency poses a major threat to pear (Pyrus spp.) fruit yield and quality. The Gretchen Hagen 3 (GH3) plays a vital part in plant stress responses. However, the GH3 gene family is yet to be characterized, and little focus has been given to the function of the GH3 gene in Fe deficiency responses. Here, we identified 15 GH3 proteins from the proteome of Chinese white pear (Pyrus bretschneideri) and analyzed their features using bioinformatics approaches. Structure domain and motif analyses showed that these PbrGH3s were relatively conserved, and phylogenetic investigation displayed that they were clustered into two groups (GH3 I and GH3 II). Meanwhile, cis-acting regulatory element searches of the corresponding promoters revealed that these PbrGH3s might be involved in ABA- and drought-mediated responses. Moreover, the analysis of gene expression patterns exhibited that most of the PbrGH3s were highly expressed in the calyxes, ovaries, and stems of pear plants, and some genes were significantly differentially expressed in normal and Fe-deficient pear leaves, especially for PbrGH3.5. Subsequently, the sequence of PbrGH3.5 was isolated from the pear, and the transgenic tomato plants with PbrGH3.5 overexpression (OE) were generated to investigate its role in Fe deficiency responses. It was found that the OE plants were more sensitive to Fe deficiency stress. Compared with wild-type (WT) plants, the rhizosphere acidification and ferric reductase activities were markedly weakened, and the capacity to scavenge reactive oxygen species was prominently impaired in OE plants under Fe starvation conditions. Moreover, the expressions of Fe-acquisition-associated genes, such as SlAHA4, SlFRO1, SlIRT1, and SlFER, were all greatly repressed in OE leaves under Fe depravation stress, and the free IAA level was dramatically reduced, while the conjugated IAA contents were notably escalated. Combined, our findings suggest that pear PbrGH3.5 negatively regulates Fe deficiency responses in tomato plants, and might help enrich the molecular basis of Fe deficiency responses in woody plants.

Osteoblast-derived exosomal miR-140-3p targets ACER2 and increases the progression of prostate cancer via the AKT/mTOR pathway-mediated inhibition of autophagy.

Advanced prostate cancer (aPCa) often results in bone metastases (BM). However, the mechanism underlying its progression and metastasis to bones remains unclear. Therefore, we examined whether exosomal miR-140-3p affects prostate cancer (PCa) progression. We obtained from cell lines, clinical data analyses, and animal models consistently provide important evidence. Patients with PCa having BM had higher miR-140-3p expression in their serum exosomes than those without BM. Clinical investigations have manifested that the exosomal miR-140-3p overexpression connects with serum prostate-specific antigen (PSA) levels and Gleason grade in patients with PCa. Osteoblast-derived exosomal miR-140-3p targeting ACER2 activates the AKT/mTOR pathway invitro, inhibits autophagy, and promotes PCa cell proliferation, invasion, and migration. miR-140-3p significantly increased tumorigenesis and metastasis of LNCaP invitro. Bone metastatic PCa tissues exhibited elevated levels of miR-140-3p, p-GSK3, p-mTOR, p62, p-AKT (S473), and p-AKT (T308) contrasted with non-BM tissues. Moreover, their expression was intensified in the metastatic bone tissues. However, ACER2 and LC3 II showed opposite expression patterns. Based on our study outcomes, the evidence suggests that osteoblast-derived miR-140-3p inhibition of autophagy through the AKT/mTOR pathway is involved in PCa progression. Osteoblast-secreted exosomal miR-140-3p activates the AKT/mTOR pathway by targeting ACER2, inhibiting autophagy, and promoting the progression of PCa cells invitro. Moreover, miR-140-3p induces the progression and metastasis of PCa invivo.

An adult myogenic cell line of the Japanese fire-bellied newt Cynops pyrrhogaster

Adult myogenic cell lines are useful to study muscle development, repair and regeneration. In newts, which are known for their high regenerative capacity, myogenic cell lines have not been established in species other than the Eastern newt Notophthalmus viridescens. In this study, we established another myogenic cell line, named CpM01, from the skeletal muscle of the forearm of the adult Japanese fire-bellied newt Cynops pyrrhogaster. CpM01 maintained high proliferative ability even after numerous passages, and could be induced to differentiate into myotubes by changing the culture medium. CpM01 expressed myogenic regulatory factors (MRFs) such as Myf5, MRF4 and myogenin. Changes in the immunorectivities of MRFs during differentiation of CpM01 into myotubes were consistent with those during new muscle generation in limb regeneration. In newts, myogenic cells have two origins, muscle fibers or satellite cells. CpM01 expressed Pax7, suggesting the origin might be satellite cells. scRNA-seq analysis deeply characterized CpM01 and demonstrated that the expression patterns of myogenic genes (Pax3, Pax7, myocyte-specific enhancer factor 2 A, and genes encoding MRFs) in CpM01 are related to progress of the cell cycle. CpM01 can be a useful tool for future studies of limb muscle regeneration in adult newts.

ADAMDEC1 promotes cervical squamous cell carcinoma by enhancing the JAK/STAT signaling pathway through modulation of TYMP.

Cervical squamous cell carcinoma (CSCC) poses a significant health challenge, especially in developing countries. Identifying novel prognostic biomarkers and potential drug targets is crucial for improving CSCC management. We analyzed ADAMDEC1 expression patterns in CSCC using various bioinformatic datasets. Clinical samples from CSCC patients were evaluated for ADAMDEC1 and TYMP levels through Western blot and qRT-PCR. Multiple in vitro techniques, including flow cytometry, CCK-8, Transwell, Western blot, wound healing assays, and Co-IP, were employed to investigate the role and molecular pathways associated with ADAMDEC1. Our findings reveal that ADAMDEC1 is significantly overexpressed in CSCC tissues compared to adjacent healthy tissues. Functional assays demonstrated that ADAMDEC1 overexpression significantly enhances cell proliferation, migration, and invasion in vitro, while concurrently inhibiting apoptosis. Conversely, the knockdown of ADAMDEC1 reversed these effects, leading to reduced cell proliferation and increased apoptosis. Mechanistically, we identified a direct interaction between ADAMDEC1 and TYMP, which activates the JAK/STAT signaling pathway in CSCC cells. This activation was confirmed through Western blot analysis, indicating increased phosphorylation of JAK1 and STAT3 in response to ADAMDEC1 overexpression. ADAMDEC1 promotes CSCC progression by modulating the JAK/STAT pathway through regulation of TYMP. These findings suggest that ADAMDEC1 could serve as a molecular biomarker for early diagnosis and targeted therapy in CSCC.

Study on the changes of miRNAs and their target genes in regulating anthocyanin synthesis during purple discoloration of cauliflower curd under low temperature stress

IntroductionCauliflower is widely cultivated all over the world is attributed to its palatable flavor, high levels of anti-cancer compounds, and diverse array of nutrients. Exposure to extremely cold stress during production can result in a more frequent occurrence of purple discoloration in cauliflower curds. In response to cold stress, plants naturally produce anthocyanins to eliminate reactive oxygen species (ROS) generated as a defense mechanism.MethodsThis research involved conducting mRNA sequencing analysis on cauliflower curds both before and after exposure to cold stress treatment.ResultsIt was determined that the up-regulation of anthocyanin biosynthesis-related genes CHS, CHI, DFR, ANS, UGFT, PAP1/2, and MYBL2 occurred significantly in response to cold stress, resulting in a significant increase in total anthocyanin content. Subsequently, miRNA sequencing was employed to identify miRNAs in cauliflower curds, followed by differential expression analysis. The results showed that Bna-miR289 and Ath-miR157a may play a key role in regulating the accumulation of anthocyanin in cauliflower curds. Furthermore, we utilized degradome sequencing data to predict the target genes of the identified miRNAs, resulting in the identification of BolK_3g48940.1, BolK_9g11680.1, BolK_7g41780.1, BolK_3g68050.1, and BolK_3g729700.1 as targets. Subsequently, the expression patterns of the miRNAs and their target genes were validated using qRT-PCR, the results showed that Ath-miR157a and its target genes BolK_3g68050.1 and BolK_3g72970.1 may be the key to the purple of cauliflower curds under cold stress. DiscussionOur preliminary findings identified key miRNAs and their target genes that may be involved in regulating anthocyanin synthesis, thereby enhancing the cold tolerance of cauliflower through mRNA, miRNA, and degradome sequencing. Overall, our study sheds light on the activation of anthocyanin synthesis in flower curds under cold stress conditions as a mechanism to enhance resilience to adverse environmental conditions.

Profile of miRNAs induced during sheep fat tail development and roles of four key miRNAs in proliferation and differentiation of sheep preadipocytes

BackgroundThe fat tail of sheep is an adaptive trait that facilitates their adaptation to harsh natural environments. MicroRNAs (miRNAs) have been demonstrated to play crucial roles in the regulation of tail fat deposition.MethodsIn this study, miRNA-Seq was employed to investigate the expression profiles of miRNAs during different developmental stages of sheep fat tails and elucidate the functions of differentially expressed miRNAs (DE miRNAs).ResultsA total of 350 DE miRNAs were identified, among which 191, 60, 26, and 21 were significantly upregulated in tail fat tissues of fetal, lamb, hogget Altay sheep, and adult Xinjiang fine wool (XFW) sheep but downregulated in other stages. Furthermore, we predicted a set of candidate target genes (4,476) for the top 20 DE miRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that they involve in several adipogenesis-related pathways. Subsequent investigations indicated that four DE miRNAs, miR-433-3p, miR-485-3p, miR-409-3p, and miR-495-3p, could suppress the expression of peroxisome proliferator-activated receptor gamma (PPARγ) and phosphoinositide-3-kinase regulatory subunit 3 (PIK3R3) and regulate the preadipocyte development in sheep. Meanwhile, the lipid metabolism-related genes, fatty acid-binding protein (FABP3), perilipin 1 (PLIN1), adiponectin C1Q and collagen domain containing (ADIPOQ), and lipoprotein lipase (LPL), were significantly downregulated (p < 0.01).ConclusionThe expression patterns of miRNAs exhibited significant fluctuations during different development periods of the fat tail, and some of them may participate in the regulation of tail fat deposition by modulating the proliferation and differentiation of preadipocytes.

Epidermal Growth Factor Receptor (EGFR) and SMAD4 negatively correlated in the progression of gallbladder cancer in Eastern Indian patients

Background and introductionTwo and half percent of the Indian population suffer from gallbladder cancer (GBC). The primary factors that lead GBC are associated with mutation of several protooncogenes such as EGFR, ERBB2, Myc, and CCND1 along with dysregulation of several tumor suppressor genes such as SMAD4 and CDKN2A. Bacterial infection caused by S.typhi and H.pylori are also hypothesized to be potential factors driving GBC.AimsThis study aims to investigate the molecular mechanisms driving the progression of gallbladder adenocarcinoma in Eastern Indian patients. We specifically focussed on analyzing the mutational status of the KRAS gene, examining the amplification of the ERBB2/Her2-neu gene, and evaluating the expression patterns of six dysregulated genes (CCND1, MYC, EGFR, ERBB2/Her2-neu, CDKN2A, SMAD4). Additionally, we assessed the expression status of TGF-beta, the association between bacterial infections (S. Typhi and H. pylori) and GBC, and the impact of single nucleotide polymorphisms in ERBB2/Her2-neu and CCND1 genes within this population.MethodsSixty-seven samples from GBC-diagnosed patients, 26 other unrelated GBC samples for validation cohort, and 68 gallstone tissue samples were collected for this study. Genomic DNA from normal as well as tumor tissues were isolated, exon 2 and exon 3 of KRAS gene were amplified along, DNA sequenced and analyzed. KRAS codon 12 mutation was detected by allele specific PCR (ASPCR) method. Amplification of UreC A (coding for urease subunit α), VacA (coding for Vacuolating cytotoxin A) and CagA genes (coding for cytotoxin-associated gene A) in H.pylori were amplified using PCR. Similarly, FlicC (coding for flagellin gene C) in S.typhi was amplified using PCR. The ERBB2/Her2-neu SNP I655V, and CCND1 SNP A870G were analyzed using PCR followed by RFLP. Expression studies of CCND1, Myc, CDKN2A, ERBB2/Her2-neu, EGFR, and SMAD4 genes were measured in GBC tumor tissues by sybr green quantitative RT PCR.ResultsThe oncogenes (EGFR and ERBB2/Her2-neu) were statistically significantly overexpressed and the tumor suppressor gene (SMAD4) downregulated in our GBC tumor patient samples. The EGFR and SMAD4 genes were negatively correlated (r = -0.01) in GBC patients and the data is statistically significant and validated through IHC technique. A significant downregulation of TGF-beta had also been observed. Lower frequency (i.e. 11.5%) of KRAS mutation in GBC tumor was observed.ConclusionsEGFR and SMAD4 expression were found to be negatively correlated in GBC tissue samples. ERBB2 overexpression/amplification was observed in 30% of the GBC samples. We also found a low percentage of GBC samples to show KRAS codon 12 mutation in Indian GBC patient population, as had been previously documented in pancreatic cancers.

The varying responses of leaves and roots and the link between sugar metabolic genes and the SWEET family in Dendrobium officinale under salt stress

BackgroundDendrobium officinale Kimura et Migo is a perennial epiphytic herb in traditional Chinese medicine, showing remarkable resistance to salt stress. Water-soluble sugars serve as important osmoprotectants and play crucial roles in plant stress responses. Previous studies have primarily focused on sugar metabolism in individual tissues under stress, resulting in a limited understanding of the regulatory differences between tissues and the relationship between sugar metabolism and transport.ResultsA variety of salt-responsive genes were identified through transcriptome analysis of D. officinale. GO and KEGG enrichment analyses revealed functional differences among the differentially expressed genes (DEGs) between leaves and roots. Expression analysis indicated that sugar metabolic genes and D. officinale Sugars Will Eventually be Exported Transporters (DoSWEETs) displayed distinct expression patterns in leaves and roots under salt stress. Most sugar metabolic genes were up-regulated in the leaves and down-regulated in the roots in response to salt, while DoSWEETs predominantly responded in the roots. Specifically, DoSWEET2a, 6a, 12a, 14, and 16 were confirmed via RT-qPCR. Additionally, positive correlations were observed between certain genes (scrK, INV, SUS) and DoSWEETs, with INV (LOC110096666) showing a strong positive correlation with all detected DoSWEETs in both leaves and roots.ConclusionsOur findings not only illustrated the distinct responses of leaves and roots to salt stress, but also highlighted the relationship between sugar metabolic genes and DoSWEETs in adapting to such stress. This enhances our understanding of the differential responses of plant tissues to salt stress and identified candidate genes for salt-resistance breeding in D. officinale.

Genome-wide analysis and expression profiling of the polyamine oxidase gene family in Solanum tuberosum L.

BackgroundPolyamine oxidase (PAO) is a crucial enzyme involved in the breakdown of polyamines (PAs) in plants. It not only regulates the levels of PAs, but also plays a role in the oxidative decomposition of PAs and the release of stress-related signals, contributing to the plant’s response and resistance to various adversities. While there have been numerous studies on the response of PAO to stress in other crops, there is a lack of research on this topic in potatoes, a major food crop.ResultsIn this study, we aimed to explore the biological function of the StPAO gene in potato growth and development, as well as its expression patterns under stress. Using bioinformatics methods, we identified 14 StPAO genes in the potato genome. Protein sequence comparisons revealed a high similarity between the PAO proteins of potato and Arabidopsis. Chromosomal mapping and gene structure analysis showed that the StPAO genes were not evenly distributed on the chromosome and all contained an amino-oxidase domain. Furthermore, analysis of the promoters of these genes revealed the presence of abiotic and stress-related cis-acting elements, indicating their potential role in responding to different stresses. To investigate the expression patterns of these genes under stress, we used qRT-PCR to study their response to high temperature, drought, and ABA stress. Our results showed that StPAO6 and StPAO10 were significantly up-regulated under high temperature stress, indicating that they were involved in the process of potato resistance to high temperatures. Similarly, StPAO1, StPAO3, and StPAO4 were significantly up-regulated under drought stress, indicating their potential role in potatoes’ responses to drought. After ABA treatment, the expression levels of StPAO4, StPAO5, StPAO7, and StPAO14 were significantly up-regulated, suggesting their involvement in chemical defense mechanisms. Interestingly, the expression of StPAO11–13 was inhibited by all three stresses.ConclusionsIn conclusion, our study highlights the multifunctional nature of the StPAO gene family in potatoes, which plays a crucial role in coping with various stresses. This research deepens our understanding of the potato StPAO gene family and provides a reference for future studies on its function. It also serves as a theoretical basis for breeding stress-resistant potato varieties in the future.

Ubiquitin Ligase U-Box51 Positively Regulates Drought Stress in Potato (Solanum tuberosum L.)

The ubiquitin-proteasome system (UPS) is a key protein degradation pathway in eukaryotes, in which E3 ubiquitin ligases mediate protein ubiquitination, directly or indirectly targeting substrate proteins to regulate various biological processes, including plant growth, hormone signaling, immune responses, and adaptation to abiotic stress. In this study, we identified plant U-box protein 51 in Solanum tuberosum (StPUB51) as an E3 ubiquitin ligase through transcriptomic analysis, and used it as a candidate gene for gene-function analysis. Quantitative real-time PCR (qRT-PCR) was used to examine StPUB51 expression across different tissues, and its expression patterns under simulated drought stress induced by polyethylene glycol (PEG 6000) were assessed. Transgenic plants overexpressing StPUB51 and plants with down-regulated StPUB51 expression were generated to evaluate drought tolerance. The activities of key antioxidant enzymes-superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) as well as malondialdehyde (MDA) content in transgenic plants’ leaves were measured under drought conditions. Protein–protein interactions involving StPUB51 were explored via yeast two-hybrid (Y2H) screening, with interaction verification by bimolecular fluorescence complementation (BiFC). StPUB51 was predominantly expressed in stems, with lower expression observed in tubers, and its expression was significantly upregulated in response to 20% PEG-6000 simulated drought. Subcellular localization assays revealed nuclear localization of the StPUB51 protein. Under drought stress, StPUB51-overexpressing plants exhibited enhanced SOD, POD, and CAT activities and reduced MDA levels, in contrast to plants with suppressed StPUB51 expression. Y2H and BiFC analyses identified two interacting proteins, StSKP2A and StGATA1, which may be functionally linked to StPUB51. Collectively, these findings suggest that StPUB51 plays a positive regulatory role in drought tolerance, enhancing resilience in potato growth and stress adaptation.

Genome-Wide Identification of the GbUBC Gene Family in Sea-Island Cotton (Gossypium barbadense) and the Active Regulation of Drought Resistance in Cotton by GbUBC23

Cotton is an economically critical crop worldwide, and drought stress strongly affects its growth and development. Ubiquitination modifies protein activity and is crucial in numerous biological processes. Ubiquitin-conjugating enzymes serve as intermediaries in the protein ubiquitination process and play important roles in plant responses to abiotic stress. However, the impact of ubiquitination on the response of cotton to abiotic stress is not fully understood. Bioinformatic methods were employed in this study to analyze the physiochemical characteristics, gene structure, collinearity, expression patterns, and evolutionary relationships of GbUBC gene family members in sea-island cotton. In sea-island cotton, a minimum of 125 GbUBC genes are irregularly distributed across the 26 chromosomes, with multiple instances of gene duplication observed among the members. Phylogenetic analysis categorized the GbUBC gene family into 15 ubiquitin-conjugating enzyme (E2) subgroups, one ubiquitin E2 enzyme variant (UEV) subgroup, and one COP10 subgroup. GbUBC gene expression pattern analyses revealed that most GbUBC genes responded differently to cold, heat, NaCl, and polyethylene glycol (PEG) treatments, with certain GbUBC genes exhibiting high expression levels in specific fiber development period and organs. Furthermore, molecular biology methods were employed to elucidate the biological functions of GbUBC23. The GbUBC23 gene was highly expressed in the cotyledons of sea-island cotton and was activated by PEG treatment. GbUBC23 is localized to the nucleus and cytomembrane. The silencing of the GbUBC23 gene under drought conditions led to decreased drought tolerance and survival rates in sea-island cotton. Compared with those in the control plants, the activity of proline and superoxide dismutase and the expression levels of the drought-induced genes GbNCED3, GbRD22, GbRD26 were significantly lower, but the levels of malondialdehyde and hydrogen peroxide were significantly higher. Our findings revealed 125 members of the GbUBC gene family in sea-island cotton, with the GbUBC23 gene critically contributing to the abiotic stress response. These findings indicate that the GbUBC gene family may play a crucial role in the drought stress response in sea-island cotton.

Prognostic Value of PD-L1, BAP-1 and ILK in Pleural Mesothelioma

Background: Pleural mesothelioma (PM) is a rare type of cancer with poor prognosis. Prognostic and predictive biomarkers could improve treatment strategies in these patients. Programmed death ligand 1 (PD-L1), integrin-linked kinase (ILK) and breast cancer gene 1-associated protein (BAP-1) have been proposed to predict outcomes in PM, but existing data are limited and controversial. Design and Methods: This single-center, retrospective study analyzed data on expression patterns and the prognostic role of PD-L1, ILK and BAP-1 in consecutive patients diagnosed with PM. Results: Of all patients (n = 52) included, more than half showed a positive PD-L1 expression (52% TPS ≥ 1%, 65% CPS ≥ 1), 69% showed a BAP-1 loss and 80% an ILK ≥ 50%. Positive PD-L1 expression was more frequent in the non-epithelioid subtype (p = 0.045). ILK intensity (p = 0.032) and positive PD-L1 (p = 0.034) were associated with more advanced tumor stages. The median overall survival (OS) was 16.9 (95% CI 13.1–25.2) months. Multimodality therapy (MMT) including surgery and early stage were independent prognostic factors for longer OS (MMT: HR 0.347, 95% CI 0.13–0.90, p = 0.029; advanced stage: HR 4.989; 95% CI 1.64–15.13, p = 0.005). Patients with an expression of PD-L1 TPS ≥ 1% or BAP-1 positivity showed numerically worse survival with a median OS of 15.3 (11.5; 24.4) vs. 20.0 (11.2; 34.9) and 11.3 (5.6; 31.0) vs. 20.0 (15.2; 28.1) months, respectively. Furthermore, PD-L1 was associated with worse survival in patients receiving MMT (PD-L1 TPS ≥ 1%: 15.8 (12.1–25.4) vs. 31.3 (17.4–95.4) p = 0.053). ILK expression ≥50% did not influence survival. The combinations of CPS ≥ 1% with BAP-1 positivity or ILK expression ≥50% were associated with worse survival (p = 0.045, p = 0.019). Conclusions: In this real-world analysis, expressions of PD-L1 and BAP-1 were associated with worse survival in patients with PM. ILK showed no prognostic value. Further studies with larger cohorts are needed to identify prognostic and predictive biomarkers facilitating optimized individual treatment decision in this rare type of cancer.