Olfactory Transduction Pathway Research Articles

Joint exome and metabolome analysis in individuals with dyslexia: Evidence for associated dysregulations of olfactory perception and autoimmune functions.

Dyslexia is a learning disability that negatively affects reading, writing, and spelling development at the word level in 5%-9% of children. The phenotype is variable and complex, involving several potential cognitive and physical concomitants such as sensory dysregulation and immunodeficiencies. The biological pathogenesis is not well-understood. Toward a better understanding of the biological drivers of dyslexia, we conducted the first joint exome and metabolome investigation in a pilot sample of 30 participants with dyslexia and 13 controls. In this analysis, eight metabolites of interest emerged (pyridoxine, kynurenic acid, citraconic acid, phosphocreatine, hippuric acid, xylitol, 2-deoxyuridine, and acetylcysteine). A metabolite-metabolite interaction analysis identified Krebs cycle intermediates that may be implicated in the development of dyslexia. Gene ontology analysis based on exome variants resulted in several pathways of interest, including the sensory perception of smell (olfactory) and immune system-related responses. In the joint exome and metabolite analysis, the olfactory transduction pathway emerged as the primary pathway of interest. Although the olfactory transduction and Krebs cycle pathways have not previously been described in dyslexia literature, these pathways have been implicated in other neurodevelopmental disorders including autism spectrum disorder and obsessive-compulsive disorder, suggesting the possibility of these pathways playing a role in dyslexia as well. Immune system response pathways, on the other hand, have been implicated in both dyslexia and other neurodevelopmental disorders.

CCL7 and olfactory transduction pathway activation play an important role in the formation of CaOx and CaP kidney stones.

Background: The deposition of calcium oxalate (CaOx) and calcium phosphate (CaP) is the most common cause of kidney stone disease (KSD). Whether KSDs caused by CaOx and CaP have common genetic targets or signaling pathways remained unclear. Methods: The present study utilized public data GSE73680 to analyze differentially expressed genes between CaOx or CaP tissues and normal tissues, respectively. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of co-DEGs were performed. The protein-protein interaction (PPI) network was constructed to identify hub genes, and the top hub gene was selected for gene set enrichment analysis (GSEA). Finally, real-time PCR of patients' urine was performed to validate the bioinformatic results. Results: In total, 155 significantly co-upregulated DEGs and 64 co-downregulated DEGs were obtained from the datasets. The Gene Ontology analysis showed that DEGs were significantly enriched in chemical stimulus in sensory perception, detection of chemical stimulus in sensory perception of smell, and olfactory receptor activity. The KEGG analysis showed that the olfactory transduction pathway was significantly enriched. According to protein-protein interaction, 10 genes were identified as the hub genes, and CCL7 was the top hub gene. The olfactory transduction, maturity-onset diabetes of the young, linoleic acid metabolism, and fat digestion and absorption were significantly enriched in the high-CCL7 subgroup by GSEA. In total, 9 patients who had primarily CaOx mixed with some CaP stones and 9 healthy subjects were enrolled. The RT-PCR results showed that CCL7 level in the stone group was significantly higher than that in the control group (p < 0.05). For the olfactory transduction pathway, the expression of OR10A5, OR9A2, and OR1L3 was significantly upregulated in the stone group compared with the control group (p < 0.05). Conclusion: CCL7 may play a key role in the development of both CaOx and CaP, and this process may depend on olfactory transduction pathway activation.

Identifying candidate genes underlying isolated congenital anosmia.

An estimated 1 in 10 000 people are born without the ability to smell, a condition known as congenital anosmia, and about one third of those people have non-syndromic, or isolated congenital anosmia (ICA). Despite the significant impact of olfaction for our quality of life, the underlying causes of ICA remain largely unknown. Using whole exome sequencing (WES) in 10 families and 141 individuals with ICA, we identified a candidate list of 162 rare, segregating, deleterious variants in 158 genes. We confirmed the involvement of CNGA2, a previously implicated ICA gene that is an essential component of the olfactory transduction pathway. Furthermore, we found a loss-of-function variant in SREK1IP1 from the family gene candidate list, which was also observed in 5% of individuals in an additional non-family cohort with ICA. Although SREK1IP1 has not been previously associated with olfaction, its role in zinc ion binding suggests a potential influence on olfactory signaling. This study provides a more comprehensive understanding of the spectrum of genetic alterations and their etiology in ICA patients, which may improve the diagnosis, prognosis, and treatment of this disorder and lead to better understanding of the mechanisms governing basic olfactory function.

Blood microbial analyses reveal long-term effects of SARS-CoV-2 infection on patients who recovered from COVID-19

ObjectiveFew symptoms persist for a long time after patients recover from COVID-19, called “long COVID”. We explored the potential microbial risk factors for COVID-19 for a deeper understanding and assistance in the follow-up treatment of these sequelae. MethodsMicrobiome re-annotation was performed using whole blood RNA-Seq data collected from recovered COVID-19 patients and healthy controls at multiple time points. Subsequently, a series of downstream analyses were conducted to reveal the microbial characteristics of patients who recovered from SARS-CoV-2 infection. ResultsThe blood microbiome at 12 weeks post-infection was most evidently disturbed, including an increasing ratio of Bacillota/Bacteroidota and a higher microbial alpha diversity. In addition, a group of pathogenic microbes at 12 weeks post-infection were identified, including Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were positively associated with host genes involved in immune regulatory and olfactory transduction pathways. Several microbes, such as Streptococcus pneumoniae were associated with infiltrating immune cells, such as M2 macrophages. ConclusionThis study provides insights into the relationship between the blood microbiome and COVID-19 sequelae. Several pathogenic microbes were enriched in recovered COVID-19 patients and thus affected host genes participating in the immune and olfactory transduction pathways, which play critical roles in COVID-19 sequelae.

Prenatal and postnatal challenges affect the hypothalamic molecular pathways that regulate hormonal levels.

This study aimed to improve our understanding of how the hypothalamus mediates the effects of prenatal and postnatal challenges on behavior and sensitivity to stimuli. A pig model of virally initiated maternal immune activation (MIA) was used to investigate potential interactions of the prenatal challenge both with sex and with postnatal nursing withdrawal. The hypothalami of 72 females and males were profiled for the effects of MIA and nursing withdrawal using RNA-sequencing. Significant differential expression (FDR-adjusted p value < 0.05) was detected in the profile of 222 genes. Genes involved in the Gene Ontology biological process of regulation of hormone levels tended to be over-expressed in individuals exposed to both challenges relative to individuals exposed to either one challenge, and most of these genes were over-expressed in MIA females relative to males across nursing levels. Differentially expressed genes included Fshb, Ttr, Agrp, Gata3, Foxa2, Tfap2b, Gh1, En2, Cga, Msx1, and Npy. The study also found that prenatal and postnatal challenges, as well as sex, impacted the regulation of neurotransmitter activity and immune effector processes in the hypothalamus. In particular, the olfactory transduction pathway genes were over-expressed in weaned MIA males, and several transcription factors were potentially found to target the differentially expressed genes. Overall, these results highlight how multiple environmental challenges can interact and affect the molecular mechanisms of the hypothalamus, including hormonal, immune response, and neurotransmitter processes.

RAMP1 as a novel prognostic biomarker in pan-cancer and osteosarcoma.

Receptor activity modifying protein 1 (RAMP1) facilitates the localization of the calcitonin-like receptor (CLR) to the plasma membrane, but its role in osteosarcoma (OS) remains unclear. We evaluated the RAMP1 expression and prognostic value across different cancers, studying tumor immune infiltration. The prognostic value was analyzed using the GSE39058 and TARGET datasets. Differential gene expression was evaluated. a protein-protein interaction network was constructed, and gene set enrichment analysis was performed. The function of RAMP1 in the tumor microenvironment was analyzed, and its expression in OS cell lines was validated using quantitative real-time PCR. High RAMP1 expression correlated with poor prognosis relative to low RAMP1 expression (p < 0.05). Low RAMP1 expression correlated with an abundance of CD4+ memory-activated T cells. whereas a high expression level correlated with a high proportion of gamma-delta T cells (γδ T cells). Differentially expressed genes from TARGET was enriched in olfactory transduction pathways (normalized enrichment scores [NES] = 1.6998, p < 0.0001). RAMP1 expression negatively correlated with CD44 expression but positively correlated with TNFSF9 expression. The RAMP1 gene is substantially expressed in OS cells compared to the normal osteoblast cell line hFOB1.19. Thus, RAMP1 may be a prognostic biomarker and potential therapeutic target in OS.

P17.08.A CLINICAL AND MOLECULAR CHARACTERIZATION OF EXTRACRANIAL METASTASES IN GLIOBLASTOMAS

Abstract BACKGROUND Glioblastoma (GBM) is the most common and malignant primary brain tumor in adults, but in contrast to many other malignancies they rarely metastasize. Metastasizing GBMs cause both diagnostic and therapeutic challenges and are generally poorly investigated. Therefore, our aim was to characterize these tumors clinically and molecularly. MATERIAL AND METHODS We collected and examined the largest cohort to date of tissue from 16 glioma patients (14 GBMs and 2 lower-grade gliomas) with extracranial metastases, including metastases to scalp (7) lymph nodes (5), bone (2), liver (1), and upper neck (1). After histopathological re-evaluation of the tumors, we assessed the associated magnetic resonance imaging (MRI) scans. Paired samples from the primary tumors, recurrences and metastases were investigated by next-generation sequencing (NGS) analysis with the TSO500 panel, genome-wide 850 K methylation profiling and immunohistochemistry followed by artificial intelligence-based quantification of markers of stemness and immune cells in the tumor microenvironment (TME). RESULTS Clinically, the patients were comparable to other GBM patients (gender, age, treatment, and survival). 12/16 patients developed one or more intracranial recurrence(s). MRI scans revealed proximity of the brain tumors to dura, large vessels, and ventricles in a high proportion of the patients. Moreover, we found that (6/7) scalp lesions were in fact extracranial extensions of the brain tumors. NGS data showed that the metastases were clonally derived from the primary tumors and not from the brain recurrences. Methylation- and copy number analysis overall confirmed the initial diagnoses and revealed a patient-specific signature across paired samples in a majority of the patients. Additionally, we observed methylation subclass switch during tumor progression and identified differentially methylated regions enriched in the olfactory transduction pathway when comparing metastases to primary tumors. Levels of tumor stemness were generally preserved according to methylation-based stemness index and OLIG2 and SOX2 protein expression. Similarly, the composition of immune cells in the TME did not change significantly, as shown by cell-type deconvolution and immune cell quantification. CONCLUSION Extracranial metastases occurred as early events and overall preserved the tumor- and TME characteristics of the primary brain tumors. Factor such as brain tumor location, neurosurgery and epigenetic regulation of genes associated with olfactory transduction could be involved in glioblastoma metastasis.

The Expression of Trace Amine-Associated Receptors (TAARs) in Breast Cancer Is Coincident with the Expression of Neuroactive Ligand-Receptor Systems and Depends on Tumor Intrinsic Subtype.

Currently, the contribution of trace amine-associated receptors (TAARs) to breast cancer (BC) is recognized, but their associations with various pathological characteristics are not yet understood. There is accumulated transcriptomic data for BC tumors, which are represented in publicly accessible databases. We estimated TAARs' (including TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, and TAAR9) associations with BC stage, grade, and molecular subtypes in these data and identified that the expression of all TAARs was associated with more unfavorable cancer subtypes, including basal-like and HER2-positive tumors. Also, the significant upregulation of all TAARs was demonstrated in circulating tumor cells compared to the metastatic lesions. Considering that co-expressed genes are more likely to be involved in the same biologic processes, we analyzed genes that are co-expressed with TAARs in BC. These gene sets were enriched with the genes of the olfactory transduction pathway and neuroactive ligand-receptor interaction participants. TAARs are co-expressed with G-protein-coupled receptors of monoamine neurotransmitters including dopamine, norepinephrine, and serotonin as well as with other neuroactive ligand-specific receptors. Since TAAR1 is able to modulate the activity of monoamine receptors that are involved in the regulation of BC growth, TAAR1 and potentially other TAARs may be regarded as prospective therapeutic targets for breast cancer.

TRAF4-mediated nonproteolytic ubiquitination of androgen receptor promotes castration-resistant prostate cancer

Castration-resistant prostate cancer (CRPC) poses a major clinical challenge with the androgen receptor (AR) remaining to be a critical oncogenic player. Several lines of evidence indicate that AR induces a distinct transcriptional program after androgen deprivation in CRPCs. However, the mechanism triggering AR binding to a distinct set of genomic loci in CRPC and how it promotes CRPC development remain unclear. We demonstrate here that atypical ubiquitination of AR mediated by an E3 ubiquitin ligase TRAF4 plays an important role in this process. TRAF4 is highly expressed in CRPCs and promotes CRPC development. It mediates K27-linked ubiquitination at the C-terminal tail of AR and increases its association with the pioneer factor FOXA1. Consequently, AR binds to a distinct set of genomic loci enriched with FOXA1- and HOXB13-binding motifs to drive different transcriptional programs including an olfactory transduction pathway. Through the surprising upregulation of olfactory receptor gene transcription, TRAF4 increases intracellular cAMP levels and boosts E2F transcription factor activity to promote cell proliferation under androgen deprivation conditions. Altogether, these findings reveal a posttranslational mechanism driving AR-regulated transcriptional reprogramming to provide survival advantages for prostate cancer cells under castration conditions.

Study on Anti-Constipation Effects of Hemerocallis citrina Baroni through a Novel Strategy of Network Pharmacology Screening.

Daylily (Hemerocallis citrina Baroni) is an edible plant widely distributed worldwide, especially in Asia. It has traditionally been considered a potential anti-constipation vegetable. This study aimed to investigate the anti-constipation effects of daylily from the perspective of gastro-intestinal transit, defecation parameters, short-chain organic acids, gut microbiome, transcriptomes and network pharmacology. The results show that dried daylily (DHC) intake accelerated the defecation frequency of mice, while it did not significantly alter the levels of short-chain organic acids in the cecum. The 16S rRNA sequencing showed that DHC elevated the abundance of Akkermansia, Bifidobacterium and Flavonifractor, while it reduced the level of pathogens (such as Helicobacter and Vibrio). Furthermore, a transcriptomics analysis revealed 736 differentially expressed genes (DEGs) after DHC treatment, which are mainly enriched in the olfactory transduction pathway. The integration of transcriptomes and network pharmacology revealed seven overlapping targets (Alb, Drd2, Igf2, Pon1, Tshr, Mc2r and Nalcn). A qPCR analysis further showed that DHC reduced the expression of Alb, Pon1 and Cnr1 in the colon of constipated mice. Our findings provide a novel insight into the anti-constipation effects of DHC.

Children with Acute Lymphoblastic Leukemia and Early Thrombosis Have Dysregulated Coagulation-Related Genes and Pathways

Introduction Thrombo-embolic events (TE) are a frequent complication of childhood acute lymphoblastic leukemia (ALL). Disease-specific mechanistic insights governing the development of TE in this disease remain unclear. Overexpression of coagulation-related genes (coagulome) and pathways have been identified in cancer-induced TE. We investigate whether coagulome dysregulation in newly-diagnosed children with ALL is associated with TE development. Methods We included patients aged 1-21 years old with newly-diagnosed ALL from September 3, 2015, to June 30, 2021, with available RNA-sequencing (RNAseq) data at diagnosis, either enrolled on the Dana-Farber Cancer Institute (DFCI) ALL Consortium Protocol 16-001 or treated following the DFCI 11-001 protocol. RNAseq was performed through an optional study performed as part of the DFCI 16-001 clinical trial for patients who consented to it, or through the research oncogenomic program of the province of Quebec. The primary outcome was the occurrence of TE during ALL therapy requiring medical intervention (grade ≥2 as per the CTCAE version 5). TE were classified as early thrombosis (ET) if they occurred within 6 weeks from treatment start. Patients' characteristics were compared using Chi-Square or Fisher's exact test. Differential gene expression (DE) was performed to compare children with and without TE, adjusted for ALL phenotype (B- or T-cell lineage). The dysregulated genes were compared to a customized panel of 174 genes known to be implicated in cancer-related TE (coagulome and podoplanin) and in coagulation pathways. A secondary analysis, determined a priori, stratified children between ET and no TE, based on the hypothesis that the leukemia environment might predominantly affect early complications. Gene set enrichment analyses (GSEA) were performed on KEGG and gene ontology (GO) databases from the molecular signatures database (MSigDB). DE was considered for absolute fold change (FC) ≥2, and benjamini-Hochberg adjusted p-values (adj p) <0.05. Results We included 274 ALL patients (median age: 6.7 years [interquartile range, IQR: 3.7-12.0 years], 54% male, 81% B-ALL) of whom 49 (17.9%) experienced a TE (including 21 ET) at a median of 76 days (IQR: 27-155 days) following ALL diagnosis. Patients with TE were more likely to be ≥10 years old (57.1% vs. 31.6%, p<0.001) compared to those without TE. Sex, immunophenotype, mediastinal mass, central nervous system disease (CNS) involvement at diagnosis and risk status were otherwise not significantly different among the two groups. Three coagulation pathway-related genes were dysregulated in children with TE compared to those without TE. Glycoprotein 9 (GP9) and platelet factor 4 (PF4), implicated in von Willebrand-dependent platelet adhesion and platelet aggregation, were upregulated (log2FC = 2.1 and 1.5, respectively). Metalloproteinase-2 (MMP2), involved in collagenolysis and thrombus degradation, was downregulated (log2FC = -1.9). The KEGG olfactory transduction pathway was downregulated in the group with TE (normalized enrichment score (NES) = 1.55, adj p<0.001). In the secondary analysis stratified by timing of TE, patients with early TE were more likely to be ≥10 years (80.9% vs. 31.6%, p<0.001), have T-ALL (38.1% vs. 16.9%, p=0.002) and be CNS-positive at diagnosis (52.4% vs. 22.7%, p=0.004). Patients with ET showed overexpression of the GP9, PF4, integrin subunit beta 3 (ITGB3) and clusterin (CLU) genes involved in platelet aggregation and adhesion (log2FC = 3.3, 3.7, 2.7 and 1.6, respectively). The following GO pathways were significantly upregulated: blood coagulation (NES=1.73, adj p<0.001), platelet activation (NES=2.21, adj p<0.01), and platelet alpha granules (NES=2.48, adj p<0.001) while the KEGG olfactory transduction pathway was downregulated (NES=-1.70, adj p<0.001). Dysregulation of the olfactory transduction pathway has previously been described in cancer-associated TE in adults. Conclusion Our study identified coagulation-related genes and pathways that might be drivers of leukemia-induced thrombosis. Early TEs in childhood ALL were associated with significant upregulation of coagulation and platelet activation pathways, suggesting a role of the leukemia microenvironment in TE development. Additional studies are required to validate these observations that could be incorporated in future algorithms to predict TE risk in children with ALL. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Anti-Depressant Fluoxetine Hampers Olfaction of Goldfish by Interfering with the Initiation, Transmission, and Processing of Olfactory Signals.

The ubiquitous presence of fluoxetine (FLX) in aquatic environments poses great threat to fish species. However, little is known about its deleterious impacts on fish olfaction. In this study, the olfactory toxicity of FLX at environmentally realistic levels was assessed by monitoring the behavioral and electroolfactogram (EOG) responses to olfactory stimuli with goldfish (Carassius auratus), and the toxification mechanisms underlying the observed olfaction dysfunction were also investigated. Our results showed that the behavioral and EOG responses of goldfish to olfactory stimuli were significantly weakened by FLX, indicating an evident toxicity of FLX to olfaction. Moreover, FLX exposure led to significant alterations in olfactory initiation-related genes, suppression of ion pumps (Ca2+-ATPase and Na+/K+-ATPase), tissue lesions, and fewer olfactory sensory neurons in olfactory epithelium. In addition to altering the expression of olfactory transmission-related genes, comparative metabolomic analysis found that olfaction-related neurotransmitters (i.e., l-glutamate and acetylcholine) and the olfactory transduction pathway were significantly affected by FLX. Furthermore, evident tissue lesions, aggravated lipid peroxidation and apoptosis, and less neuropeptide Y were observed in the olfactory bulbs of FLX-exposed goldfish. Our findings indicate that FLX may hamper goldfish olfaction by interfering with the initiation, transmission, and processing of olfactory signals.

Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats

BackgroundChanges in the abundance of ovarian proteins play a key role in the regulation of reproduction. However, to date, no studies have investigated such changes in pubescent goats. Herein we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography–tandem mass spectrometry to analyze the expression levels of ovarian proteins in pre-pubertal (n = 3) and pubertal (n = 3) goats.ResultsOverall, 7,550 proteins were recognized; 301 (176 up- and 125 downregulated) were identified as differentially abundant proteins (DAPs). Five DAPs were randomly selected for expression level validation by Western blotting; the results of Western blotting and iTRAQ analysis were consistent. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that DAPs were enriched in olfactory transduction, glutathione metabolism, and calcium signaling pathways. Besides, gene ontology functional enrichment analysis revealed that several DAPs enriched in biological processes were associated with cellular process, biological regulation, metabolic process, and response to stimulus. Protein–protein interaction network showed that proteins interacting with CDK1, HSPA1A, and UCK2 were the most abundant.ConclusionsWe identified 301 DAPs, which were enriched in olfactory transduction, glutathione metabolism, and calcium signaling pathways, suggesting the involvement of these processes in the onset of puberty. Further studies are warranted to more comprehensively explore the function of the identified DAPs and aforementioned signaling pathways to gain novel, deeper insights into the mechanisms underlying the onset of puberty.

Association between olfactory pathway gene variants and obesity in Chinese Han population: A case-control study based on genetic score.

Our previous bivariate genome-wide association study in dizygotic twins suggested that the olfactory transduction pathway genes were associated with obesity in Northern Han Chinese adults. In this study, we attempted to verify the associations of the olfactory transduction pathway genes score with obesity in population with the same genetic background, and to estimate the interaction between gene variants and potential environment factors. A case-control study was conducted in Qingdao, China in 2019-2021, which enrolled 301 obesity cases and 307 controls. Based on the candidate gene selection method, 29 single nucleotide polymorphisms (SNPs) in 7 olfactory pathway genes were selected. Genomic deoxyribonucleic acid (DNA) was isolated and purified from the peripheral blood leukocytes by using DNA extraction kits and was genotyped by the MassArray system. The weighted genetic score of each gene was calculated to analyze the effect of whole gene. The effect of gene scores on obesity and the gene-environment interaction were estimated by logistic regression. After adjusting for age, sex, smoking, alcohol drinking, physical activity, we observed positive associations of OR4D1 (OR=1.531, 95% CI=1.083-2.164, P=0.016) and OR52K1 (OR=1.437, 95% CI=1.055-1.957, P=0.022) gene scores with obesity, as well as negative associations of OR2L8 (OR=0.708, 95% CI=0.504-0.995, P=0.046) and CALML3 (OR=0.601, 95% CI=0.410-0.881, P=0.009) gene scores with obesity. Significant multiplicative model interaction between OR4D1 and smoking (Pinteraction=0.041) as well as CALML3 and smoking (Pinteraction=0.026) on obesity were identified. Stratified analysis showed that in smokers, OR4D1 gene score was positively associated with obesity (OR=2.673, 95% CI=1.348-5.299, P=0.005) and CALML3 gene score was negatively correlated with obesity (OR=0.252, 95% CI=0.103-0.618, P=0.003). The relationships were not statistically significant in non-smokers (OR4D1: OR=1.216, 95% CI=0.806-1.836, P=0.351; CALML3: OR=0.764, 95% CI=0.492-1.188, P=0.232). Genetic variations in the olfactory pathway were associated with obesity in Northern Han Chinese adults. Smoking modified the effect of OR4D1 and CALML3 gene variants on obesity.

RNA sequencing analysis of hepatocellular carcinoma identified oxidative phosphorylation as a major pathologic feature.

Dysregulation of expression of functional genes and pathways plays critical roles in the etiology and progression of hepatocellular carcinoma (HCC). Next generation‐based RNA sequencing (RNA‐seq) offers unparalleled power to comprehensively characterize HCC at the whole transcriptome level. In this study, 17 fresh‐frozen HCC samples with paired non‐neoplastic liver tissue from Caucasian patients undergoing liver resection or transplantation were used for RNA‐seq analysis. Pairwise differential expression analysis of the RNA‐seq data was performed to identify genes, pathways, and functional terms differentially regulated in HCC versus normal tissues. At a false discovery rate (FDR) of 0.10, 13% (n = 4335) of transcripts were up‐regulated and 19% (n = 6454) of transcripts were down‐regulated in HCC versus non‐neoplastic tissue. Eighty‐five Kyoto Encyclopedia of Genes and Genomes pathways were differentially regulated (FDR, <0.10), with almost all pathways (n = 83) being up‐regulated in HCC versus non‐neoplastic tissue. Among the top up‐regulated pathways was oxidative phosphorylation (hsa00190; FDR, 1.12E‐15), which was confirmed by Database for Annotation, Visualization, and Integrated Discovery (DAVID) gene set enrichment analysis. Consistent with potential oxidative stress due to activated oxidative phosphorylation, DNA damage‐related signals (e.g., the up‐regulated hsa03420 nucleotide excision repair [FDR, 1.14E‐04] and hsa03410 base excision repair [FDR, 2.71E‐04] pathways) were observed. Among down‐regulated genes (FDR, <0.10), functional terms related to cellular structures (e.g., cell membrane [FDR, 3.05E‐21] and cell junction [FDR, 2.41E‐07], were highly enriched, suggesting compromised formation of cellular structure in HCC at the transcriptome level. Interestingly, the olfactory transduction (hsa04740; FDR, 1.53E‐07) pathway was observed to be down‐regulated in HCC versus non‐neoplastic tissue, suggesting impaired liver chemosensory functions in HCC. Our findings suggest oxidative phosphorylation and the associated DNA damage may be the major driving pathologic feature in HCC.

Sperm Transcripts Associated With Odorant Binding and Olfactory Transduction Pathways Are Altered in Breeding Bulls Producing Poor-Quality Semen.

Spermatozoa carries a reservoir of mRNAs regulating sperm functions and fertilizing potential. Although it is well recognized that a considerable proportion of high genetic merit breeding bulls produce poor-quality semen, the transcriptomic alterations in spermatozoa from such bulls are not understood. In the present study, comparative high-throughput transcriptomic profiling of spermatozoa from good and poor-quality semen-producing bulls was carried out to identify the transcripts associated with semen quality. Using next-generation sequencing (NGS), we identified 11,632 transcripts in Holstein Friesian bull spermatozoa; after total hit normalization, a total of 544 transcripts were detected, of which 185 transcripts were common to both good and poor-quality semen, while 181 sperm transcripts were unique to good quality semen, and 178 transcripts were unique to poor-quality semen. Among the co-expressed transcripts, 31 were upregulated, while 108 were downregulated, and 46 were neutrally expressed in poor-quality semen. Bioinformatics analysis revealed that the dysregulated transcripts were predominantly involved in molecular function, such as olfactory receptor activity and odor binding, and in biological process, such as detection of chemical stimulus involved in sensory perception, sensory perception of smell, signal transduction, and signal synaptic transmission. Since a majority of the dysregulated transcripts were involved in the olfactory pathway (85% of enriched dysregulated genes were involved in this pathway), the expression of selected five transcripts associated with this pathway (OR2T11, OR10S1, ORIL3, OR5M11, and PRRX1) were validated using real-time qPCR, and it was found that their transcriptional abundance followed the same trend as observed in NGS; the sperm transcriptional abundance of OR2T11 and OR10S1 differed significantly (p < 0.05) between good and poor-quality semen. It is concluded that poor-quality semen showed altered expression of transcripts associated with olfactory receptors and pathways indicating the relationship between olfactory pathway and semen quality in bulls.

Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling

BackgroundWith over 350,000 estimated deaths worldwide in 2018, prostate cancer (PCa) continues to be a major health concern and a significant cause of cancer-associated mortality among men. While cancer in general is considered a disease of the human genome, there is a growing body of evidence suggesting that changes to the healthy microbiota could play a vital role in cancer development, progression, and/or treatment outcome.MethodsUsing a metatranscriptomic approach, we annotated the microbial reads obtained from total RNA sequencing of 106 prostate tissue samples from 94 PCa patients (discovery cohort). We investigated microbial dysbiosis associated with PCa by systematically comparing the microbiomes between benign and malignant tissue samples, between less vs. more-aggressive PCa, and between patients who had biochemical recurrence as opposed to those who did not. We further performed differential gene expression and cell type enrichment analysis to explore the host transcriptomic and cellular responses to selected microbial genera. A public dataset (GSE115414) of total RNA sequencing reads from 24 prostate tissue samples (8 benign and 16 malignant) served as the validation cohort.ResultsWe observed decreased species diversity and significant under-representation of Staphylococcus saprophyticus and Vibrio parahaemolyticus, as well as significant over-abundance of Shewanella in malignant as compared to benign prostate tissue samples in both the discovery (p < 0.01) and validation (p < 0.05) cohorts. In addition, we identified Microbacterium species (p < 0.01) to be significantly over-abundant in pathologically advanced T3 tumors compared to T2 in the discovery cohort. Malignant samples having high vs. low Shewanella counts were associated with downregulated Toll-like receptor signaling pathways and decreased enrichment of dendritic cells. Malignant samples having low vs. high V. parahaemolyticus counts were enriched for olfactory transduction and drug metabolism pathways. Finally, malignant samples were enriched for M1 and M2 macrophages as compared to benign tissue samples.ConclusionsThe results from this exploratory study support the existence of an important biological link between the prostate microbiota and PCa development/progression. Our results highlight Shewanella, V. parahaemolyticus, and Microbacterium sp. as interesting candidates for further investigation of their association with PCa.

Comprehensive Analysis Revealed that CDKN2A is a Biomarker for Immune Infiltrates in Multiple Cancers.

The CDKN2A (cyclin dependent kinase inhibitor 2A/multiple tumor suppressor 1) gene, also known as the P16 gene, encodes multiple tumor suppressor 1 (MTS1), which belongs to the INK4 family. In tumor tissue, CDKN2A has a high expression level compared with normal tissue and reflects prognosis in tumor patients. Our research targeted the analysis of CDKN2A expression in 33 tumors and clinical parameters, patient prognosis and tumor immunity roles. The CDKN2A expression level was significantly correlated with the tumor mutation burden (TMB) in 10 tumors, and the expression of CDKN2A was also correlated with MSI (microsatellite instability) in 10 tumors. CDKN2A expression was associated with infiltrating lymphocyte (TIL) levels in 22 pancancers, thus suggesting that CDKN2A expression is associated with tumor immunity. Enrichment analysis indicated that CDKN2A expression was involved in natural killer cell-mediated cytotoxicity pathways, antigen processing and presentation, olfactory transduction pathways, and regulation of the autophagy pathway in multiple cancers. CDKN2A was significantly associated with several immune cell infiltrates in pantumors. CDKN2A may serve as a promising prognostic biomarker and is associated with immune infiltrates across cancers.

Comparative Analysis of piRNA Profiles Helps to Elucidate Cryoinjury Between Giant Panda and Boar Sperm During Cryopreservation.

Cryopreservation induces sperm cryoinjuries, including physiological and functional changes. However, the molecular mechanisms of sperm cryoinjury and cryoresistance are still unknown. Cryoresistance or the freeze tolerance of sperm varies across species, and boar sperm is more susceptible to cold stress. Contrary to boar sperm, giant panda sperm appears to be strongly freeze-tolerant and is capable of surviving repeated cycles of freeze-thawing. In this study, differentially expressed (DE) PIWI-interacting RNAs (piRNAs) of fresh and frozen-thawed sperm with different freeze tolerance capacity from giant panda and boar were evaluated. The results showed that 1,160 (22 downregulated and 1,138 upregulated) and 384 (110 upregulated and 274 downregulated) DE piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE messenger RNAs (mRNAs) of DE piRNAs were mainly enriched in biological regulation, cellular, and metabolic processes in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed in DNA replication and the cyclic adenosine monophosphate (cAMP) signaling pathway in giant panda, but the cAMP, cyclic guanosine monophosphate (cGMP), and mitogen-activated protein kinase (MAPK) signaling pathways in boar sperm were considered as part of the olfactory transduction pathway. In conclusion, we speculated that the difference in the piRNA profiles and the DE piRNAs involved in the cAMP signaling pathway in boar and giant panda may have contributed to the different freeze tolerance capacities between giant panda and boar sperm, which helps to elucidate the molecular mechanism behind sperm cryoinjury and cryoresistance.

Diagnostic and therapeutic values of PMEPA1 and its correlation with tumor immunity in pan-cancer

AimsThe prostate transmembrane protein, androgen induced 1 (PMEPA1) is differentially expressed in pan-cancer. However, PMEPA1 specific role in cancers has not been fully clarified. This study aims to explore the potential role of Pmepa1 in pan-cancer and specific cancer, with a view to deepening the research on the pathological mechanism of cancer. Main methodsThe Perl language and R language were used to identify the correlation between PMEPA1 expression level and clinical indicators, prognosis values, tumor microenvironment, immune cells' infiltration, immune checkpoint genes, TMB and MSI. The Therapeutic Target Database was used for identifying potential therapeutic drugs that target the pathways that are significantly affected by PMEPA1 expression. Key findingsPMEPA1 differential expression significantly correlated with patients' age, race, tumors' stage and status. PMEPA1 high expression was closely correlated with poor prognosis in many cancer types, excluding prostate adenocarcinoma. PMEPA1 expression was closely related to tumor cells and the immune microenvironment in stromal and immune cells' level, immune cells' infiltration, immune checkpoint genes, tumor mutational burden and microsatellite instability. We also found that the activity of the olfactory transduction pathway was closely related to PMEPA1 expression. In pan-cancer, Trifluoperazine and Halofantrine have the potential to reduce PMEPA1 expression. SignificanceThis study integrated existing data to explore PMEPA1 potential function in cancers, provided insights for the future cancer-related studies.