Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis.

Chronic epididymitis (CE) refers to a long-lasting inflammatory condition of the epididymis, which is considered the most common site of intrascrotal inflammation and an important aetiological factor of male infertility. Recent studies demonstrate that small RNAs secreted from epididymal epithelium modulate embryo development and offspring phenotypes via sperm transmission, and the resulting modifications may lead to transgenerational inheritance. However, to date, the genome-wide analysis of small RNA together with the transcriptomic expression profiles of human epididymis and CE is still lacking. In this study, we facilitated next-generation sequencing and bioinformatics to comprehensively analyze the small RNA and mRNA in an integrative way and identified signatures associated with CE. Both of the small RNA and mRNA expression data demonstrated relatively larger molecular differences among the segmental region of the epididymides, including caput, corpus, and cauda, than that of the inflammatory conditions. By comparing the inflamed caputs to the controls, a total of 1727 genes (1220 upregulated and 507 downregulated; 42 most significant genes, adjusted P <0.05) and 34 miRNAs (23 upregulated and 11 downregulated) were identified as differentially expressed. In silico functional enrichment analysis showed their roles in regulating different biological activities, including leukocyte chemotaxis, extracellular milieu reconstruction, ion channel and transporter-related processes, and nervous system development. Integrative analysis of miRNA and mRNA identified a regulatory network consisting of 22 miRNAs and 31 genes (miRNA-mRNA) which are strong candidates for CE. In addition, analysis about other species of small RNA, including (miRNA), piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), Y RNA, and rsRNA identified the distinct expression pattern of tsRNA in CE. In summary, our study performed small RNA and miRNA profiling and integrative analysis in human CE. The findings will help to understand the role of miRNA-mRNA in the pathogenesis of CE and provide molecular candidates for the development of potential biomarkers for human CE.

Deep tillage reduces the dependence of tobacco (Nicotiana tabacum L.) on arbuscular mycorrhizal fungi and promotes the growth of tobacco in dryland farming.

The traditional shallow tillage method reduces soil quality and affects the efficiency of agricultural production. Using conventional rotary tillage (12 cm) as the control, Yunyan 87 as the test variety, and paddy soil as the test site, we studied the effects of deep tillage (subsoiling 30 cm) on soil nutrients, arbuscular mycorrhizal fungi (AMF), and tobacco (Nicotiana tabacum L.) growth. The results showed that deep tillage increased the content of organic carbon, available phosphorus (AP), and available potassium (AK) in the 20-40 cm soil layer. The AMF community was also affected by deep tillage. Glomus, the dominant genus in both groups, increased significantly in soil after deep tillage. The AMF colonization rate was lower than that of conventional rotary tillage. Deep tillage was beneficial for tobacco growth in the middle and late stages. The root growth and nutrient content of the tobacco plants increased. Deep tillage significantly improved the output value of tobacco plants. Deep tillage is conducive to improving soil fertility, promoting the vigorous growth of roots, reducing the dependence of tobacco on AMF, and promoting the high quality and yield of tobacco in the drylands of Hunan.

Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data.

Transcriptomic analysis plays a key role in biomedical research. Linear dimensionality reduction methods, especially principal-component analysis (PCA), are widely used in detecting sample-to-sample heterogeneity, while recently developed non-linear methods, such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP), can efficiently cluster heterogeneous samples in single-cell RNA sequencing analysis. Yet, the application of t-SNE and UMAP in bulk transcriptomic analysis and comparison with conventional methods have not been achieved. We compare four major dimensionality reduction methods (PCA, multidimensional scaling [MDS], t-SNE, and UMAP) in analyzing 71 large bulk transcriptomic datasets. UMAP is superior to PCA and MDS but shows some advantages over t-SNE in differentiating batch effects, identifying pre-defined biological groups, and revealing in-depth clusters in two-dimensional space. Importantly, UMAP generates sample clusters uncovering biological features and clinical meaning. We recommend deploying UMAP in visualizing and analyzing sizable bulk transcriptomic datasets to reinforce sample heterogeneity analysis.

T Lymphocytes and Testicular Immunity: A New Insight into Immune Regulation in Testes.

The immune privilege of the testes is necessary to prevent immune attacks to gamete-specific antigens and paternal major histocompatibility complex (MHC) antigens, allowing for normal spermatogenesis. However, infection and inflammation of the male genital tract can break the immune tolerance and represent a significant cause of male infertility. Different T cell subsets have been identified in mammalian testes, which may be involved in the maintenance of immune tolerance and pathogenic immune responses in testicular infection and inflammation. We reviewed the evidence in the published literature on different T subtypes (regulatory T cells, helper T cells, cytotoxic T cells, γδ T cells, and natural killer T cells) in human and animal testes that support their regulatory roles in infertility and the orchitis pathology. While many in vitro studies have indicated the regulation potential of functional T cell subsets and their possible interaction with Sertoli cells, Leydig cells, and spermatogenesis, both under physiological and pathological processes, there have been no in situ studies to date. Nevertheless, the normal distribution and function of T cell subsets are essential for the immune privilege of the testes and intact spermatogenesis, and T cell-mediated immune response drives testicular inflammation. The distinct function of different T cell subsets in testicular homeostasis and the orchitis pathology suggests a considerable potential of targeting specific T cell subsets for therapies targeting chronic orchitis and immune infertility.

Natural killer and NKT cells in the male reproductive tract.

Natural killer (NK) cells are important effector lymphocytes that play a pivotal role in the innate and adaptive immune responses to tumors and viral infection. NKT cells are a heterogeneous group of T cells that share properties with both T cells and NK cells. They display immunoregulatory properties as they facilitate the cell-mediated immune response to tumors and infectious diseases, and inhibit cell-mediated immunity associated with autoimmune diseases and allograft rejection. However, the roles of NK and NKT cells in the male reproductive tract remain largely unexplored, in particular, NKT cells, tissue distribution, and state of health or disease. Infection and inflammation of the male genital tract are thought to be the primary etiological factors of male infertility. In this review, we considered this complex and rapidly growing field. We summarize the recent findings and the characterization and roles of NK and NKT cells in the male reproductive tract, including the testis, epididymis, prostate, seminal vesicle, and semen, to enhance our understanding of the immunological mechanisms of male infertility and for the design effective vaccines for male reproductive health in the future.

An identification of stem cell-resembling gene expression profiles in high-grade astrocytomas.

High-grade astrocytomas are among the most intractable types of cancers and are often fatal. Previous studies have suggested that high-grade astrocytomas may adopt the self-renewal and migration properties of neural stem cells (NSCs) to proliferate and spread by expressing the stem cell-specific genes. However, despite a few common molecules being documented, the molecular basis underlying these similarities remains largely unknown. To have a better understanding of the stem cell characteristics of high-grade astrocytomas, we performed the study to identify the stem cell-resembling gene expression profile in high-grade astrocytomas. cDNA microarray analysis was used to detect the differentially expressed genes of isolated human high-grade astrocytomas versus their peritumoral tissue counterparts, and the identification of stem cell-resembling genes was approached by comparing the high-grade astrocytomas-specific gene expression profile with that of NSCs identified by our previous study and other groups. We identified more than 200 high-grade astrocytomas-specific genes in this study, and near 10% genes or gene families of them exhibited similar up or down expression patterns as in NSCs. Further analysis indicated that these genes were actively involved in cell proliferation, adhesion, migration, and metastasis. This study revealed a list of stem cell-specific genes in high-grade astrocytomas, which was likely to have critical roles in determining the "stem" characteristics of high-grade astrocytomas.

C/EBPalphap30 plays transcriptional regulatory roles distinct from C/EBPalphap42.

CCAAT/enhancer binding protein alpha (C/EBPalpha) is a transcriptional regulatory factor that inhibits cell proliferation, and alternative translational initiation produces two polypeptides, C/EBPalphap30 and C/EBPalphap42. By expression profiling, it was revealed that C/EBPalphap30 specifically inhibited a unique set of genes, including MPP11, p84N5 and SMYD2, which were not affected by C/EBPalphap42 in both QSG-7701 hepatocyte cell line and QGY-7703 hepatoma cells. Semi-quantitative RT-PCR analysis independently confirmed these results. Chromatin immunoprecipitation assay showed that C/EBPalphap30 bound to the promoters of these genes more strongly than C/EBPalphap42. In clinical hepatoma samples in which C/EBPalpha was downregulated, all three genes specifically inhibited by C/EBPalphap30 were upregulated. However, repression of MPP11, p84N5 and SMYD2 genes might not be directly involved in C/EBPalphap30-mediated growth inhibition. Our data suggest that C/EBPalphap30 regulates a unique set of target genes and is more than a dominant-negative regulator of C/EBPalphap42.

A novel gene mutation (1292 deletion) in a Chinese family with cerebral cavernous malformations.

OBJECTIVE: Hereditary cerebral cavernous malformations (CCMs) are characterized by focal abnormalities of small blood vessels in the brain and consequent hemorrhage and seizures. Previous studies of this type of CCM have mainly reported on this disorder in Hispanic and Caucasian cases. Here, we report on hereditary CCM in a Chinese family further characterized by a novel CCM1 gene mutation. METHODS: We investigated a family of 21 members, of whom 3 died and 16 of the survivors became the subjects of this study by brain magnetic resonance imaging. RESULTS: Brain magnetic resonance imaging demonstrated abnormal results in 11 members (69% penetrance), including multiple intracranial lesions in seven cases and single lesions in four cases. The clinical manifestation of CCM was found in these cases. The youngest patient was 4 years old. The remaining 5 members were normal. Nucleotide sequencing analysis of the family member representing the index case and other affected members revealed a deletion frameshift mutation of A and T at nucleotides 1292 and 1293 in exon 13 of the CCM1 gene, which resulted in truncated encoding Krev interaction trapped-1 protein. CONCLUSION: Our results indicated a novel hereditary CCM1 gene mutation of 1292delAT, a finding that may contribute to the clarification of the mechanism of the disease.

[Identification of a novel inheritable CCM1 gene mutation of 671del AT in a Chinese family with cerebral cavernous malformation].

OBJECTIVE: To investigate the hereditary characters of familial cerebral cavernous malformation (FCCM) and the novel gene mutation in a Chinese family. METHODS: Head MRI examination and clinical neurological check were performed on a Chinese family with one proband of FCCM, female, 27 years old, and 16 family members, 9 males and 12 females, and 19 controls, including patients with sporadic CCM and other diseases and healthy persons. DNA was extracted from the white blood cells of the peripheral blood of the subjects. PCR and DNA direct sequencing were used to detect the mutation in CCM1 gene. RESULTS: Head MRI found 11 FCCM patients in the 16 family members of the proband (69%), the youngest one being 4 years old, including multiple intracranial lesions in 7 patients and single lesion in 4. Relevant clinical manifestations were found in 6 out of the 11 family members. Nucleotide sequence analysis of the proband and other affected family members revealed a deletion frameshift mutation of A and T at nucleotides (nt) 671 and 672 in exon 13 of the CCM1 gene, resulting in truncated encoding KRIT1 protein. No mutation was detected in the healthy family members and the controls. CONCLUSION: A novel inheritable CCM1 gene mutation of 671del AT has been found in patients with FCCM.

[Investigation on recurrent-associated gene expression pattern of recurrent-laryngeal squamous cell carcinoma].

OBJECTIVE: To screen out recurrent-associated gene in expression pattern of laryngeal squamous cell carcinoma(LSCC). METHOD: By cDNA array chip containing 18,000 gene, the gene expression pattern of cancer and normal mucosal tissues in 2 cases of LSCC, were compared and analyzed. RESULT: 1. 218 genes expressed repeatedly and differentially in LSCC were discovery. Among these genes, up- and down-regulated were 137 and 81; 2. The genes whose expression difference was over 10 times were U02570, AW863712, AA523939 and NM_014381. CONCLUSION: The episode of recurrent LSCC was a process of disturbance of numerous gene expression. GTPase activating protein (U02570) and DNA mismatch repair gene(NM_014381) probably played a major role in the episode.

Identification of tissue-specific genes in nasopharyngeal epithelial tissue and differentially expressed genes in nasopharyngeal carcinoma by suppression subtractive hybridization and cDNA microarray.

Suppression subtractive hybridization (SSH) was performed for isolation of tissue-specific genes in nasopharyngeal epithelial tissue, by use of cDNAs from human adult nasopharyngeal epithelial tissue as tester and mixed cDNAs from esophagus, lung, liver, heart, stomach, spleen, skeletal muscle, kidney, and skin as drivers. Fourteen differentially expressed genes in nasopharyngeal epithelial tissue were obtained. Among these genes, LPLUNC1 and SPLUNC1 were confirmed to be specifically expressed in nasopharyngeal epithelial tissue and the trachea. A novel transcript of SPLUNC1, which we designate NASG, was found. We also combined SSH and cDNA microarray hybridization to identify genes whose expressions were altered in nasopharyngeal carcinoma (NPC). We used NPC cell line HNE1 and primary human embryo nasopharyngeal epithelial cells in one SSH experiment, and NPC biopsies and normal adult nasopharyngeal epithelial tissue in another. Some 1,200 SSH inserts from four subtractive cDNA libraries were arrayed onto nylon membranes by use of robotic printing. Differential gene expression was verified by hybridizing of the membranes with radioactively labeled first-strand cDNA from NPC cell line HNE1, primary human embryo nasopharyngeal epithelial cells, NPC biopsies, and normal adult nasopharyngeal epithelial tissue. Seventeen differentially expressed genes in NPC were obtained. Among these genes, we identified SPLUNC1 and LPLUNC1 to be down-expressed in NPC biopsies (34/48, 33/48).