Expression Levels Of Differentially Expressed Genes Research Articles

Transcriptomic analysis of bone marrow specimens collected from Miniature Dachshunds diagnosed with non-neoplastic bone marrow disorders.

Non-neoplastic bone marrow disorders are main causes of non-regenerative anemia in dogs. Despite the high incidence of the diseases, their molecular pathophysiology has not been elucidated. We previously reported that Miniature Dachshund (MD) was a predisposed breed to be diagnosed with non-neoplastic bone marrow disorders in Japan, and immunosuppressive treatment-resistant MDs showed higher number of platelets and morphological abnormalities in peripheral blood cells. These data implied that treatment-resistant MDs might possess distinct pathophysiological features from treatment-responsive MDs. Therefore, we conducted transcriptomic analysis of bone marrow specimens to investigate the pathophysiology of treatment-resistant MDs. Transcriptomic analysis comparing treatment-resistant MDs and healthy control dogs identified 179 differentially expressed genes (DEGs). Pathway analysis using these DEGs showed that "Wnt signaling pathway" was a significantly enriched pathway. We further examined the expression levels of DEGs associated with Wnt signaling pathway and confirmed the upregulation of AXIN2 and CCND2 and the downregulation of SFRP2 in treatment-resistant MDs compared with treatment-responsive MDs and healthy control dogs. This alteration implied the activation of Wnt signaling pathway in treatment-resistant MDs. The activation of Wnt signaling pathway has been reported in human patients with myelodysplastic syndrome (MDS), which is characterized by dysplastic features of blood cells. Therefore, the results of this study implied that treatment-resistant MDs have distinct molecular pathological features from treatment-responsive MDs and the pathophysiology of treatment-resistant MDs might be similar to that of human MDS patients.

Silencing DDX3 Attenuates Interleukin-1β-Induced Intervertebral Disc Degeneration Through Inhibiting Pyroptosis.

Intervertebral disc degeneration (IVDD) is a common disorder associated with chronic inflammation and cell death. In this study, an IVDD rat model was created through Interleukin-1β (IL-1β) injection. The degeneration of intervertebral disc tissues was assessed using magnetic resonance imaging (MRI), followed by hematoxylin and eosin (H&E) and terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL) staining. RNA sequencing was performed to identify differentially expressed genes (DEGs) between the IVDD model and control rats. The expression levels of DEGs (DEAD-box polypeptide 3 (DDX3), lysine-specific demethylase 5D (KDM5D), interferon-induced gene-1 (IFIT1), ribosomal protein S10 (RPS10), tenomodulin (TNMD), and pentraxin 3 (PTX3)) were measured by real-time quantitative polymerase chain reaction (RT-qPCR). The regulatory effect of DDX3 on pyroptosis in IL-1β-treated nucleus pulpous (NP) cells was assessed after transfection with siRNA of DDX3. A total of 601 DEGs were identified from the IVDD model rat, and were abundant in extracellular matrix (ECM) organization, ECM-receptor interaction, and inflammatory pathways, including the PI3K-Akt, TNF, and AMPK signaling pathways. DDX3, KDM5D, and IFIT1 levels were notably elevated, whereas RPS10, TNMD, and PTX3 levels were decreased in the IL-1β-induced IVDD rat model. Moreover, silencing DDX3 promoted cell proliferation and abolished IL-1β-induced cell apoptosis and pyroptosis. This study revealed the role of DDX3 in IVDD pyroptosis, providing potential target for IVDD management.

Abstract 6832: Gender specific role of LMTK3 in neuronal-tumor microenvironment crosstalk in CRC

Abstract Background: Lemur tail kinase 3 (LMTK3) is a serine/threonine protein kinase with roles in multiple cellular pathways, including Wnt signaling, KIT modulation, and the estrogen receptor pathway; identifying it as a potential target in various cancers. LMTK3 is highly expressed within the central nervous system (CNS) and has been demonstrated to influence neuronal signaling. This study aimed to investigate the potential connection between LMTK3 and neuronal signaling pathways in colorectal cancer (CRC). Methods: Using the Cre/loxP system, we generated a C57BL/6 mouse strain that lacks the expression of LMTK3. 1 × 106 MC38 cells were subcutaneously implanted into 8 weeks old male and female wildtype (WT) and knockout (KO) mice. Tumor growth was measured until endpoint was reached. Tumors were then processed for RNA sequencing. Differentially expressed genes (DEGs) for each comparison group: WT Female vs WT Male, WT Female vs KO Female, WT Male vs KO Male, and KO Female vs KO Male were analyzed. Ingenuity pathway analysis (IPA) was done for identification of upstream regulators involved and affected cellular pathways. Expression levels of DEGs for glutamate receptor subunits were validated using qRT-PCR. Results: Both male and female LMTK3 KO mice showed highly significant (p<0.01) reduced tumor size when compared to WT mice of the same sex. Additionally, the KO female tumors were significantly (p<0.05) smaller when compared to the KO males. RNA sequencing revealed 761 DEGs in KO and WT female and 133 DEGs in KO female and male cohort comparisons (q<0.05). IPA results showed significant (p<0.01, Z-score←2) alterations in pathways including glutaminergic receptor signaling, neurovascular coupling, CREB signaling in neurons, and synaptic long-term depression in the WT vs KO female tumor cohort comparison. Within these pathways DEGs: CACNA1E, CACNA2DA, CACNG2, GRIA1, GRIA2, GRIN1, and GRIN2B, were downregulated in KO females. Upstream regulator analysis identified transcription regulators such as OTX2 and NEUROD1 as well as beta-estradiol to be significantly inhibited (p<0.01, Z-score←2) in KO females. qRT-PCR analysis showed significant (p<0.05) decreased expression in GRIA1, GRIN1, and GRIN2B as well as GRIN2A and GRIN2C in KO females when compared to WT females or KO males, validating RNA seq results. Conclusions: These results showed the involvement of LMTK3 in the gut-brain axis and its effect on CRC tumor growth. Downregulation of multiple neuronal pathways and genes suggest that LMTK3 may influence neuron signaling and neurotransmitter release to produce stimulatory or inhibitory effects within the tumor environment. The concurrent inhibition of beta-estradiol in LMTK3 KO tumors allude to possible sex differences the kinase’s effect on the observed tumor growth. Further studies are needed to confirm the mechanism of interaction of LMTK3 within these pathways. Citation Format: Lesly Torres-Gonzalez, Shivani Soni, Yan Yang, Goar Smbatyan, Jae Ho Lo, Pooja Mittal, Francesca Battaglin, Indrakant K. Singh, Priya Jayachandran, Sandra Algaze, Alexandra Wong, Karam Ashouri, Wu Zhang, Georgios Giamas, Joshua Millstein, Heinz-Josef Lenz. Gender specific role of LMTK3 in neuronal-tumor microenvironment crosstalk in CRC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6832.

Integrated Transcriptome and Proteome Analyses of β-Conglycinin-Induced Intestinal Damage in Piglets.

β-conglycinin (β-CG) induces intestinal damage in piglets; however, its regulatory mechanisms are not fully understood. This study aimed to investigate the molecular mechanisms by which β-CG regulates intestinal injury in piglets through downstream genes and proteins. Our findings revealed that β-CG significantly reduced villus height while increasing the crypt depth. In addition, we analyzed the transcriptome and proteome of jejunum tissues after the β-CG treatment. In total, 382 differentially expressed genes (DEGs) and 292 differentially expressed proteins (DEPs) were identified between the treatment and the control groups. The expression levels of DEGs and DEPs were validated by using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blotting, respectively. The findings revealed a consistent correlation between their expression levels and transcriptomic and proteomic data. In addition, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs and DEPs revealed their enrichment in oxidation-related GOs, as well as in lysosome-related pathways. A protein-protein interaction (PPI) regulatory network was constructed based on the DEPs. The integration of transcriptomic and proteomic analyses identified six genes that were significantly different at both the transcript and the protein levels. This study provides valuable insights into the molecular mechanisms underlying β-CG-induced intestinal injury in piglets.

Mechanism of IL-17 Signaling Pathway in Spleen Inflammatory Response Induced by Altitude Hypoxia in Mice

To explore the mechanism of spleen tissue inflammatory response induced by altitude hypoxia in mice. C57BL/6 mice were randomly assigned to a plain, i.e., low-altitude, normoxia group and an altitude hypoxia group, with 5 mice in each group. In the plain normoxia group, the mice were kept in a normoxic environment at the altitude of 400 m above sea level (with an oxygen concentration of 19.88%). The mice in the altitude hypoxia group were kept in an environment at the altitude of 4200 m above sea level (with an oxygen concentration of 14.23%) to establish the animal model of altitude hypoxia. On day 30, spleen tissues were collected to determine the splenic index. HE staining was performed to observe the histopathological changes in the spleen tissues of the mice. Real time fluorogenic quantitative PCR (RT-qPCR) and Western blot were conducted to determine the mRNA and protein expressions of interleukin (IL)-6, IL-12, and IL-1β in the spleen tissue of the mice. High-throughput transcriptome sequencing was performed with RNA sequencing (RNA-seq). KEGG enrichment analysis was performed for the differentially expressed genes (DEGs). The DEGs in the key pathways were verified by RT-qPCR. Compared with the plain normoxia group, the mice exposed to high-altitude hypoxic environment had decreased spleen index (P<0.05) and exhibited such pathological changes as decreased white pulp, enlarged germinal center, blurred edge, and venous congestion. The mRNA and protein expression levels of IL-6, IL-12, and IL-1β in the spleen tissue of mice in the altitude hypoxia group were up-regulated (P<0.05). According to the results of transcriptome sequencing and KEGG pathway enrichment analysis, 4218 DEGs were enriched in 178 enrichment pathways (P<0.05). DEGs were significantly enriched in multiple pathways associated with immunity and inflammation, such as T cell receptor signaling pathway, TNF signaling pathway, and IL-17 signaling pathway (P<0.05) in the spleen of mice exposed to high-altitude hypoxic environment. Among them, IL-17 signaling pathway and the downstream inflammatory factors were highly up-regulated (P<0.05). Compared with the plain normoxia group, the mRNA expression levels of key genes in the IL-17 signaling pathway, including IL-17, IL-17R, and mitogen-activated protein kinase genes (MAPKs), and the downstream inflammatory factors, including matrix metallopeptidase 9 (MMP9), S100 calcium binding protein A8 gene (S100A8), S100 calcium binding protein A9 gene (S100A9), and tumor necrosis factor α (TNF-α), were up-regulated or down-regulated (P<0.05) in the altitude hypoxia group. According to the validation of RT-qPCR results, the mRNA expression levels of DEGs were consistent with the RNA-seq results. Altitude hypoxia can induce inflammatory response in the mouse spleen tissue by activating IL-17 signaling pathway and promoting the release of downstream inflammatory factors.

Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq.

Pig growth is an important economic trait that involves the co-regulation of multiple genes and related signaling pathways. High-throughput sequencing has become a powerful technology for establishing the transcriptome profiles and can be used to screen genome-wide differentially expressed genes (DEGs). In order to elucidate the molecular mechanism underlying muscle growth, this study adopted RNA sequencing (RNA-seq) to identify and compare DEGs at the genetic level in the longissimus dorsi muscle (LDM) between two indigenous Chinese pig breeds (Diannan small ears [DSE] pig and Wujin pig [WJ]) and one introduced pig breed (Landrace pig [LP]). Animals under study were from two Chinese indigenous pig breeds (DSE pig, n = 3; WJ pig, n = 3) and one introduced pig breed (LP, n = 3) were used for RNA sequencing (RNA-seq) to identify and compare the expression levels of DEGs in the LDM. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs. The results revealed that for the DSE, WJ, and LP libraries, more than 66, 65, and 71 million clean reads were generated by transcriptome sequencing, respectively. A total of 11,213 genes were identified in the LDM tissue of these pig breeds, of which 7,127 were co-expressed in the muscle tissue of the three samples. In total, 441 and 339 DEGs were identified between DSE vs. WJ and LP vs. DSE in the study, with 254, 193 up-regulated genes and 187, 193 down-regulated genes in DSE compared to WJ and LP. GO analysis and KEGG signaling pathway analysis showed that DEGs are significantly related to contractile fiber, sarcolemma, and dystrophin-associated glycoprotein complex, myofibril, sarcolemma, and myosin II complex, Glycolysis/Gluconeogenesis, Propanoate metabolism, and Pyruvate metabolism, etc. In combination with functional annotation of DEGs, key genes such as ENO3 and JUN were identified by PPI network analysis. In conclusion, the present study revealed key genes including DES, FLNC, PSMD1, PSMD6, PSME4, PSMB4, RPL11, RPL13A, ROS23, RPS29, MYH1, MYL9, MYL12B, TPM1, TPM4, ENO3, PGK1, PKM2, GPI, and the unannotated new gene ENSSSCG00000020769 and related signaling pathways that influence the difference in muscle growth and could provide a theoretical basis for improving pig muscle growth traits in the future.

Physiological, transcriptome and metabolome analyses provide molecular insights to seasonal development in Ginkgo biloba xylem

Ginkgo biloba’s wood has high economic value; however, little is known about the molecular response of its xylem seasonal development. Based on physiological change in secondary cell wall (SCW) components, non-structural carbohydrates (NC), and endogenous phytohormones (EP) concentrations during development seasons, we performed transcriptome and metabolome sequencing on current- and second-year xylem to explore the molecular physiological responses of Ginkgo developing xylem induced by seasonal effects. Results revealed that SCW component, NC, and EP showed distinct seasonal patterns in concentration change. The expression profiles of corresponding differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) in phenylpropanoid (monolignol) biosynthesis (14 DEGs), plant hormone biosynthesis (10 DAMs), signaling (37 DEGs) and carbohydrate metabolism (37 DEGs and 8 DAMs) were revealed. Most of these DEGs were up-regulated in spring (May) to summer (July), while down-regulated in winter (December). Trend cluster showed that 15 DEGs in brassinolide (BR) biosynthesis and signaling, jasmonic acid (JA), and auxin (IAA) signaling were clustered into top 2 profiles with most DEGs in lignin biosynthesis. Correlation analysis indicated that BR concentration was negatively related with lignin content, while positively associated with 8 DEGs in lignin biosynthesis, suggesting that BR had a potential to coordinate lignin deposition. Additionally, the expression levels of DEGs in (abscisic acid) ABA signaling had positive association with those of DEGs related starch and sucrose biosynthesis, while had inverse correlation with DEGs related glucose and galactose biosynthesis. Also, ABA concentration was positively correlated with NC content, implying the dominant role of ABA in seasonal carbohydrate metabolism, conjoint analysis of DEGs and DAMs also supported this finding. Our study provided a new foundation for endogenous hormone-mediated seasonal development of xylem.

Transcriptomics reveals a core transcriptional network of K-type cytoplasmic male sterility microspore abortion in wheat (Triticum aestivum L.)

BackgroundCytoplasmic male sterility (CMS) plays a crucial role in hybrid production. K-type CMS, a cytoplasmic male sterile line of wheat with the cytoplasms of Aegilops kotschyi, is widely used due to its excellent characteristics of agronomic performance, easy maintenance and easy restoration. However, the mechanism of its pollen abortion is not yet clear.ResultsIn this study, wheat K-type CMS MS(KOTS)-90-110 (MS line) and it’s fertile near-isogenic line MR (KOTS)-90-110 (MR line) were investigated. Cytological analysis indicated that the anthers of MS line microspore nucleus failed to divide normally into two sperm nucleus and lacked starch in mature pollen grains, and the key abortive period was the uninucleate stage to dinuclear stage. Then, we compared the transcriptome of MS line and MR line anthers at these two stages. 11,360 and 5182 differentially expressed genes (DEGs) were identified between the MS and MR lines in the early uninucleate and binucleate stages, respectively. Based on GO enrichment and KEGG pathways analysis, it was evident that significant transcriptomic differences were “plant hormone signal transduction”, “MAPK signaling pathway” and “spliceosome”. We identified 17 and 10 DEGs associated with the IAA and ABA signal transduction pathways, respectively. DEGs related to IAA signal transduction pathway were downregulated in the early uninucleate stage of MS line. The expression level of DEGs related to ABA pathway was significantly upregulated in MS line at the binucleate stage compared to MR line. The determination of plant hormone content and qRT-PCR further confirmed that hormone imbalance in MS lines. Meanwhile, 1 and 2 DEGs involved in ABA and Ethylene metabolism were also identified in the MAPK cascade pathway, respectively; the significant up regulation of spliceosome related genes in MS line may be another important factor leading to pollen abortion.ConclusionsWe proposed a transcriptome-mediated pollen abortion network for K-type CMS in wheat. The main idea is hormone imbalance may be the primary factor, MAPK cascade pathway and alternative splicing (AS) may also play important regulatory roles in this process. These findings provided intriguing insights for the molecular mechanism of microspore abortion in K-type CMS, and also give useful clues to identify the crucial genes of CMS in wheat.

Insights into the mechanism of different withering methods on flavor formation of black tea based on target metabolomics and transcriptomics

Withering leads to the formation of high-quality flavor in black tea. This study investigated the effects of natural withering (NW), sun withering (SW), and warm-air withering (WW) on the flavor compounds of withered leaves by using target metabolomic and transcriptomic approaches. The results revealed that 4282, 4770, and 1246 differentially expressed genes (DEGs) were identified in the NW, SW, and WW samples, respectively. The expression of DEGs involved in volatile compound and flavonoid biosynthesis was the highest in the WW sample, which may be the main reason for the significant increase in volatile compound and catechin contents in the WW sample. The withering methods mainly affected the contents of non-proteinaceous amino acids, such as theanine. Withering methods significantly affect the expression levels of DEGs involved in metabolic pathways; this provides a systematic explanation for flavor formation in black tea.

Transcriptome analysis of meiotic and post-meiotic spermatogenic cells reveals the potential hub genes of aging on the decline of male fertility

Genetic and epigenetic changes in sperm caused by male aging may be essential factors affecting semen parameters, but the effects and specific molecular mechanisms of aging on male reproduction have not been fully clarified. In this study, to explore the effect of aging on male fertility and seek the potential molecular etiology, we performed high-throughput RNA-sequencing in isolated spermatogenic cells, including pachytene spermatocytes (marked by the completion of chromosome synapsis) and round spermatids (produced by the separation of sister chromatids) from the elderly and the young men. Functional enrichment analysis of differentially expressed genes (DEGs) in round spermatids between the elderly and young showed that they were significantly enriched in gamete generation, spindle assembly, and cilium movement involved in cell motility. In addition, the expression levels of DEGs in round spermatids (post-meiotic cells) were found to be more susceptible to age. Furthermore, ten genes (AURKA, CCNB1, CDC20, CCNB2, KIF2C, KIAA0101, NR5A1, PLK1, PTTG1, RAD51AP1) were identified to be the hub genes involved in the regulation of sperm quality in the elderly through Protein-Protein Interaction (PPI) network construction and measuring semantic among GO terms and gene products. Our data provide aging-related molecular alterations in meiotic and post-meiotic spermatogenic cells, and the information gained from this study may explain the abnormal aging-related male fertility decline.

Natural Coumarin Shows Toxicity to Spodoptera litura by Inhibiting Detoxification Enzymes and Glycometabolism.

Coumarin and its derivatives are plant-derived compounds that exhibit potent insecticidal properties. In this study, we found that natural coumarin significantly inhibited the growth and development of Spodoptera litura larvae through toxicological assay. By transcriptomic sequencing, 80 and 45 differentially expressed genes (DEGs) related to detoxification were identified from 0 to 24 h and 24 to 48 h in S. litura after coumarin treatment, respectively. Enzyme activity analysis showed that CYP450 and acetylcholinesterase (AChE) activities significantly decreased at 48 h after coumarin treatment, while glutathione S-transferases (GST) activity increased at 24 h. Silencing of SlCYP324A16 gene by RNA interference significantly increased S. litura larval mortality and decreased individual weight after treatment with coumarin. Additionally, the expression levels of DEGs involved in glycolysis and tricarboxylic acid (TCA) cycle were inhibited at 24 h after coumarin treatment, while their expression levels were upregulated at 48 h. Furthermore, metabonomics analysis identified 391 differential metabolites involved in purine metabolism, amino acid metabolism, and TCA cycle from 0 to 24 h after treated with coumarin and 352 differential metabolites associated with ATP-binding cassette (ABC) transporters and amino acid metabolism. These results provide an in-depth understanding of the toxicological mechanism of coumarin on S. litura.

Integrated analysis of high‑throughput sequencing reveals the regulatory potential of hsa_circ_0035431 in HNSCC.

Circular RNAs (circRNAs) are molecular sponges that are involved in regulation of multiple types of cancer. The present study aimed to screen and explore the key circRNA/microRNA (miRNA or miR)/mRNA interactions in head and neck squamous cell carcinoma (HNSCC) using bioinformatics. A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome-wide transcriptional sequencing was performed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). Moreover, expression levels of DEGs were verified in HNSCC cells and tissues using reverse transcription-quantitative (RT-q)PCR. A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa-miR-940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa-miR-940/cingulin-like 1 (CGNL1). FUT6 and CGNL1 were downregulated in HNSCC compared with adjacent healthy tissue and the expression levels of these genes were associated with tumor stage. Low FUT6 and CGNL1 expression levels were associated with lower overall survival rate and progression-free intervals in HNSCC. RT-qPCR demonstrated that hsa_circ_0035431, FUT6 and CGNL1 were downregulated in HNSCC cells and tissue and hsa-miR-940 was upregulated. Notably, these results were consistent with those obtained using high-throughput sequencing. In conclusion, hsa_circ_0035431 may participate in regulation of FUT6 and CGNL1 expression by sponging hsa-miR-940, thus, impacting the occurrence, development and prognosis of HNSCC.

Comparative transcriptome analysis to identify putative genes involved in carvacrol biosynthesis pathway in two species of Satureja, endemic medicinal herbs of Iran.

Satureja is rich in phenolic monoterpenoids, mainly carvacrol, that is of interest due to diverse biological activities including antifungal and antibacterial. However, limited information is available regarding the molecular mechanisms underlying carvacrol biosynthesis and its regulation for this wonderful medicinal herb. To identify the putative genes involved in carvacrol and other monoterpene biosynthesis pathway, we generated a reference transcriptome in two endemic Satureja species of Iran, containing different yields (Satureja khuzistanica and Satureja rechingeri). Cross-species differential expression analysis was conducted between two species of Satureja. 210 and 186 transcripts related to terpenoid backbone biosynthesis were identified for S. khuzistanica and S. rechingeri, respectively. 29 differentially expressed genes (DEGs) involved in terpenoid biosynthesis were identified, and these DEGs were significantly enriched in monoterpenoid biosynthesis, diterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, carotenoid biosynthesis and ubiquinone and other terpenoid-quinone biosynthesis pathways. Expression patterns of S. khuzistanica and S. rechingeri transcripts involved in the terpenoid biosynthetic pathway were evaluated. In addition, we identified 19 differentially expressed transcription factors (such as MYC4, bHLH, and ARF18) that may control terpenoid biosynthesis. We confirmed the altered expression levels of DEGs that encode carvacrol biosynthetic enzymes using quantitative real-time PCR (qRT-PCR). This study is the first report on de novo assembly and transcriptome data analysis in Satureja which could be useful for an understanding of the main constituents of Satureja essential oil and future research in this genus.

A novel disulfidptosis-associated expression pattern in breast cancer based on machine learning.

Background: Breast cancer (BC), the leading cause of cancer-related deaths among women, remains a serious threat to human health worldwide. The biological function and prognostic value of disulfidptosis as a novel strategy for BC treatment via induction of cell death remain unknown. Methods: Gene mutations and copy number variations (CNVs) in 10 disulfidptosis genes were evaluated. Differential expression, prognostic, and univariate Cox analyses were then performed for 10 genes, and BC-specific disulfidptosis-related genes (DRGs) were screened. Unsupervised consensus clustering was used to identify different expression clusters. In addition, we screened the differentially expressed genes (DEGs) among different expression clusters and identified hub genes. Moreover, the expression level of DEGs was detected by RT-qPCR in cellular level. Finally, we used the least absolute shrinkage and selection operator (LASSO) regression algorithm to establish a prognostic feature based on DEGs, and verified the accuracy and sensitivity of its prediction through prognostic analysis and subject operating characteristic curve analysis. The correlation of the signature with the tumor immune microenvironment and tumor stemness was analyzed. Results: Disulfidptosis genes showed significant CNVs. Two clusters were identified based on three DRGs (DNUFS1, LRPPRC, SLC7A11). Cluster A was found to be associated with better survival outcomes(p < 0.05) and higher levels of immune cell infiltration(p < 0.05). A prognostic signature of four disulfidptosis-related DEGs (KIF21A, APOD, ALOX15B, ELOVL2) was developed by LASSO regression analysis. The signature showed a good prediction ability. In addition, the prognostic signature in this study were strongly related to the tumor microenvironment (TME), tumor immune cell infiltration, tumor mutation burden (TMB), tumor stemness, and drug sensitivity. Conclusion: The prognostic signature we constructed based on disulfidptosis-DEGs is a good predictor of prognosis in patients with BC. This prognostic signature is closely related to TME, and its potential correlation provides clues for further studies.

Identification of risk for ovarian disease enhanced by BPB or BPAF exposure

The ban on bisphenol A (BPA) has led to a rapid increase in the use of BPA analogs, and they are increasingly being detected in the natural environment and biological organisms. Studies have pointed out that BPA analogs can lead to adverse health outcomes. However, their interference with ovarian tissue has not been fully elucidated. In this study, seven- to eight-week-old CD-1 mice were exposed to corn oil containing 300 μg/kg/day bisphenol B (BPB) or bisphenol AF (BPAF) through oral gavage, and ovarian tissues were collected at 14 and 28 days of exposure. Ovarian toxicity was evaluated by the ovarian index, ovarian area, and follicle number. mRNA-seq was used to identify differentially expressed genes (DEGs) and infer the association of DEGs with ovarian diseases. BPB or BPAF exposure induced morphological changes in ovarian tissue in CD-1 mice. In addition, Gene Ontology (GO) analysis revealed disturbances in biological processes (BP) associated with steroid biosynthetic process (GO:0006694) and cellular calcium ion homeostasis (GO:0006874). Subsequently, regulatory networks of BPA analogs (BPB or BPAF)-DEGs-ovarian diseases were constructed. Importantly, the expression levels of DEGs and transcription factors (TFs) associated with ovarian disease were altered. BPB or BPAF exposure causes damage to ovarian morphology through the synergistic effects of multiple biological processes and may be associated with altered mRNA expression profiles as a risk factor for ovarian diseases.

Physiological and Transcriptomic Analysis Revealed the Molecular Mechanism of Pinus koraiensis Responses to Light.

Korean pine (Pinus koraiensis Sieb. et Zucc.), as the main tree species in northeast China, has important economic and ecological values. Currently, supplementary light has been widely used in plant cultivation projects. However, the studies about different supplementary light sources on the growth and development of Korean pine are few. In this study, the one with no supplementary light was used as the control, and two kinds of light sources were set up: light-emitting diode (LED) and incandescent lamp, to supplement light treatment of Korean pine. The spectrum and intensity of these two light sources were different. The results showed that the growth and physiological-biochemical indicators were significantly different under different supplementary light treatments. The biomass of supplementary light treatment was significantly lower than the control. Compared with the control, IAA and GA were lower, and JA, ABA, ZT, and ETH were higher under supplementary light conditions. Photosynthetic parameters in supplementary light conditions were significantly lower than the control. Supplemental light induces chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid accumulation. From RNA-seq data, differentially expressed genes (DEGs) were observed in all the comparison groups, and there were 487 common DEGs. The expression levels of DEGs encoding transcription factors were also changed. According to GO and KEGG analysis, the plant hormone signal transduction, circadian rhythm-plant, and flavonoid biosynthesis pathways were the most enriched. These results provided a theoretical basis for the response of Korean pine to different supplementary lights.

Exosomal miR-22-3p from Mesenchymal Stem Cells Inhibits the Epithelial-Mesenchymal Transition (EMT) of Melanoma Cells by Regulating LGALS1.

The mortality rate from melanoma has been rising and hence new therapeutic approaches for this disease have received extensive attention, especially the search for novel therapeutic targets. The aim of this study was to find new targets for the treatment of melanoma through a bioinformatics and experimental approach. First, we screened for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) between melanoma and normal tissues using the TCGA-SKCM, GTEX, and GSE24996 datasets. Next, we identified epithelial-mesenchymal transition (EMT)-related DEGs and analyzed their expression levels and association with patient survival. The expression level of DEGs was then confirmed in normal human melanocytes and melanoma cells. Bioinformatics analysis was used to identify miRNAs that targeted the most highly expressed DEG, LGALS1, and their binding confirmed using dual luciferase. Enriched pathways for the LGALS1 target miR-22-3p were also analyzed. miR-22-3p was overexpressed in cells in order to investigate changes in cell activity and in related genes and proteins. Exosomes from human bone marrow mesenchymal stem cells (MSCs) were coated with miR-22-3p to examine its effect on EMT. The expression levels of LGALS1, CPXM1, and APLNR were higher in melanoma than in normal tissues and were associated with worse patient survival. The differential expression of these genes was confirmed using normal human skin melanocytes (PIG1) and human melanoma cells (WM-266-4). LGALS1 was the most differentially expressed gene between WM-266-4 and PIG1 cells, and was also predicted to be a target for miR-22-3p. The results of dual luciferase experiments confirmed that miR-22-3p could bind to LGALS1. Following the overexpression of miR-22-3p in WM-266-4 cells, the cell viability decreased, the expression levels of LGALS1, VIM and SNAI2 decreased, the expression level of CDH1 increased, and cell apoptosis increased. Transfection of miR-22-3p using exosomes resulted in similar effects. We identified three genes (LGALS1, CPXM1, APLNR) that showed a high level of differential expression in melanoma. LGALS1 is a target for miR-22-3p binding and this can inhibit the EMT of melanoma cells, thereby preventing the development of melanoma. Moreover, exosomes secreted by MSCs can be loaded with miR-22-3p, thus regulating the EMT process in melanoma cells.

Beneficial Effect of Selenium Doped Carbon Quantum Dots Supplementation on the in vitro Development Competence of Ovine Oocytes.

BackgroundAfter the synthesis of selenium doped carbon quantum dots (Se/CDs) via a step-by-step hydrothermal synthesis method with diphenyl diselenide (DPDSe) as precursor, the beneficial effects of Se/CDs’ supplementation on the in vitro development competence of ovine oocytes were firstly investigated in this study by the assay of maturation rate, cortical granules’ (CGs) dynamics, mitochondrial activity, reactive oxygen species (ROS) production, epigenetic modification, transcript profile, and embryonic development competence.ResultsThe results showed that the Se/CDs’ supplementation during the in vitro maturation (IVM) process not only enhanced the maturation rate, CGs’ dynamics, mitochondrial activity and embryonic developmental competence of ovine oocytes, but remarkably decreased the ROS production level of ovine oocytes. In addition, the expression levels of H3K9me3 and H3K27me3 in the ovine oocytes were significantly up-regulated after the Se/CDs’ supplementation, in consistent with the expression levels of 5mC and 5hmC. Moreover, 2994 up-regulated differentially expressed genes (DEGs) and 846 repressed DEGs were found in the oocytes after the Se/CDs’ supplementation. According to the analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), these DEGs induced by the Se/CDs’ supplementation were positively related to the progesterone mediated oocyte maturation and mitochondrial functions. And these remarkably up-regulated expression levels of DEGs related to oocyte maturation, mitochondrial function, and epigenetic modification induced by the Se/CDs’ supplementation further confirmed the beneficial effect of Se/CDs’ supplementation on the in vitro development competence of ovine oocytes.ConclusionThe Se/CDs prepared in our study significantly promoted the in vitro development competence of ovine oocytes, benefiting the extended research about the potential applications of Se/CDs in mammalian breeding technologies.

Effects of postharvest treatment with pullulan, calcium chloride, and chitosan on quality and sugar metabolism of Annona squamosa during storage

In this study, the effects of postharvest treatment with 1% pullulan, 2% calcium chloride, and 1% chitosan on the physiological and biochemical properties, enzymatic activities and the differentially expressed genes (DEGs) with sucrose metabolism of Annona squamosa L. fruits stored at 15 ± 1°C for 12 days were investigated. Exogenous substances treatment retained a higher level of firmness, surface color, total soluble solids, organic acids, and tvolatile flavor substances compared to the control fruit. Exogenous substances treatments, particularly calcium chloride, enhanced sucrose phosphate synthase activity, whereas it inhibited acid invertase (AI) and neutral invertase (NI) activities. These changes in enzyme activities together resulted in a significantly higher sucrose content and lower glucose and fructose contents. The number (1550 genes), proportion (6.46%), and expression levels of DEGs in the calcium chloride-treated fruit, which was enriched in the starch and sucrose metabolism pathways, were all significantly higher than in chitosan treatment. The findings indicated that exogenous calcium chloride might alter sucrose metabolism during fruit ripening by regulating the enzymatic activities and metabolism pathway. This will provide a theoretical basis for further research on the regulation of sugar metabolism by exogenous substances treatment to solve the problem of quality degradation in the storage of A. squamosa. Novelty impact statement This study indicated that the application of chitosan, pullulan, or calcium chloride, especially calcium chloride treatment, can effectively maintain the quality of Annona squamosa fruit during storage. It was found that exogenous calcium chloride might alter sucrose metabolism during fruit ripening by regulating the enzymatic activities and metabolism pathway. The results provided a theoretical basis for exploring the mechanism of exogenous substances for maintaining the postharvest quality and enhancing the shelf life of A. squamosa fruit in further research.

Decoding the Mechanism behind the Pathogenesis of the Focal Segmental Glomerulosclerosis.

Focal segmental glomerulosclerosis (FSGS) is a chronic glomerular disease associated with podocyte injury which is named after the pathologic features of the kidney. The aim of this study is to decode the key changes in gene expression and regulatory network involved in the formation of FSGS. Integrated network analysis included Gene Expression Omnibus (GEO) datasets to identify differentially expressed genes (DEGs) between FSGS patients and healthy donors. Bioinformatics analysis was used to identify the roles of the DEGs and included the development of protein-protein interaction (PPI) networks, Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and the key modules were assured. The expression levels of DEGs were validated using the additional dataset. Eventually, transcription factors and ceRNA networks were established to illuminate the regulatory relationships in the formation of FSGS. 1130 DEGs including 475 upregulated genes and 655 downregulated genes with functional enrichment analysis were determined. Further analysis uncovered that the validated hub genes were defined as candidate genes, including Complement C3a Receptor 1 (C3AR1), C-C Motif Chemokine Receptor 1(CCR1), C-X3-C Motif Chemokine Ligand 1 (CX3CL1), Melatonin Receptor 1A (MTNR1A), and Purinergic Receptor P2Y13 (P2RY13). More importantly, we identified transcription factors and mRNA-miRNA-lncRNA regulatory networks associated with the candidate genes. The candidate genes and regulatory networks discovered in this study can help to comprehend the molecular mechanism of FSGS and supply potential targets for the diagnosis and therapy of FSGS.