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Background Hearing loss is genetically heterogeneous and is one of the most common human defects. Here we screened the underlying mutations that caused autosomal recessive non-syndromic hearing loss in a Chinese family. Case presentation The proband with profound hearing loss had received audiometric assessments. We performed target region capture and next generation sequencing of 127 known deafness-related genes because the individual tested negative for hotspot variants in the GJB2, GJB3, SLC26A4, and MTRNR1 genes. We identified a novel c.6892C > T (p.R2298*) nonsense mutation and a c.10251_10253delCTT (p.F3420del) deletion in MYO15A. Sanger sequencing confirmed that both mutations were co-segregated with hearing loss in this family and were absent in 200 ethnically matched controls. Bioinformatics analysis and protein modeling indicated the deleterious effects of both mutations. The p.R2298* mutation leads to a truncated protein and a loss of the functional domains. Conclusions Our results demonstrated that the hearing loss in this case was caused by novel, compound heterozygous mutations in MYO15A. The p.R2298* mutation in MYO15A was reported for the first time, which has implications for genetic counseling and provides insight into the functional roles of MYO15A mutations. Electronic supplementary material The online version of this article (10.1186/s12881-018-0657-y) contains supplementary material, which is available to authorized users.

We aimed to elucidate the potential mechanisms of long non-coding RNAs (lncRNAs) in the progression of non-small cell lung cancer (NSCLC). The microarray datasets of GSE37764, including 3 primary NSCLC tumors and 3 matched normal tissues isolated from 6 Korean female never-smokers, were downloaded from Gene Expression Omnibus database. The differentially expressed lncRNAs and mRNA in NSCLC samples were identified using NOISeq package. Co-expression network of differentially expressed lncRNAs and mRNA was established. Gene Ontology (GO) and pathway enrichment analysis were respectively performed. Finally, lncRNAs related to NSCLC were predicted by blasting the differentially expressed lncRNAs with all predicted lncRNAs related to NSCLC. A total of 182 and 539 differentially expressed lncRNAs and mRNA (109 up- and 73 down-regulated lncRNAs; 307 up- and 232 down-regulated mRNA) were respectively identified. Among them, 4 up-regulated lncRNAs, like lnc-geranylgeranyl diphosphate synthase 1 (GGPS1), lnc-zinc finger protein 793 (ZNF793) and lnc-serine/threonine kinase 4 (STK4), and 4 down-regulated lncRNAs including lnc-LOC284440 and lnc-peptidylprolyl isomerase E-like pseudogene (PPIEL), and lnc-zinc finger protein 461 (ZNF461) were predicted related to NSCLC. lncSSPS1, lnc-ZNF793 and lnc-STK4 were co-expressed with linker for activation of T cells (LAT) and Lck interacting transmembrane adaptor 1 (LIME1). Lnc-LOC284440, lnc-PPIEL and lnc-ZNF461 were co-expressed with Src-like-adaptor 2 (SLA2) and defensin beta 4A (DEFB4A). Our study indicates that immune response may be a crucial mechanism involved in NSCLC progression. Lnc-GGPS1, lnc-ZNF793, lnc-STK4, lnc-LOC284440, lnc-PPIEL, and lnc-ZNF461 may be involved in immune response for promoting NSCLC progression via co-expressing with LAT, LIME1, SLA2 and DEFB4A.

Background and objectiveDietary intake of fruits and vegetables has been suggested to have a role in promoting bone health. More specifically, the polyphenols they contain have been linked to physiological effects related to bone mineral density and bone metabolism. In this research, we use standard microarray analyses of peripheral whole blood from post-menopausal women treated with two fixed combinations of plant extracts standardized to polyphenol content to identify differentially expressed genes relevant to bone health.MethodsIn this 28-day open-label study, healthy post-menopausal women were randomized into three groups, each receiving one of three investigational fixed combinations of plant extracts: an anti-resorptive (AR) combination of pomegranate fruit (Punica granatum L.) and grape seed (Vitis vinifera L.) extracts; a bone formation (BF) combination of quercetin (Dimorphandra mollis Benth) and licorice (Glycyrrhiza glabra L.) extracts; and a fixed combination of all four plant extracts (AR plus BF). Standard microarray analysis was performed on peripheral whole blood samples taken before and after each treatment. Annotated genes were analyzed for their association to bone health by comparison to a gene library.ResultsThe AR combination down-regulated a number of genes involved in reduction of bone resorption including cathepsin G (CTSG) and tachykinin receptor 1 (TACR1). The AR combination also up-regulated genes associated with formation of extracellular matrix including heparan sulfate proteoglycan 2 (HSPG2) and hyaluronoglucosaminidase 1 (HYAL1). In contrast, treatment with the BF combination resulted in up-regulation of bone morphogenetic protein 2 (BMP-2) and COL1A1 (collagen type I α1) genes which are linked to bone and collagen formation while down-regulating genes linked to osteoclastogenesis. Treatment with a combination of all four plant extracts had a distinctly different effect on gene expression than the results of the AR and BF combinations individually. These results could be due to multiple feedback systems balancing activities of osteoblasts and osteoclasts.ConclusionIn summary, this ex-vivo microarray study indicated that the pomegranate, grape seed, quercetin and licorice combinations of plant extracts modulated gene expression for both osteoclastic and osteogenic processes.

Rice (Oryza) is a staple food in China, and rice yield is inherently sensitive to climate change. It is of great regional and global importance to understand how and to what degree climate change will impact rice yields and to determine the adaptation options effectiveness for mitigating possible adverse impacts or for taking advantage of beneficial changes. The objectives of this study are to assess the climate change impact, the carbon dioxide (CO2) fertilization effect, and the adaptation strategy effectiveness on rice yields during future periods (2011–2099) under the newly released Representative Concentration Pathway (RCP) 4.5 scenario in the Sichuan Basin, one of the most important rice production areas of China. For this purpose, the Crop Estimation through Resource and Environment Synthesis (CERES)-Rice model was applied to conduct simulation, based on high-quality meteorological, soil and agricultural experimental data. The modeling results indicated a continuing rice reduction in the future periods. Compared to that without incorporating of increased CO2 concentration, a CO2 fertilization effect could mitigate but still not totally offset the negative climate change impacts on rice yields. Three adaptive measures, including advancing planting dates, switching to current high temperature tolerant varieties, and breeding new varieties, could effectively offset the negative climate change impacts with various degrees. Our results will not only contribute to inform regional future agricultural adaptation decisions in the Sichuan Basin but also gain insight into the mechanism of regional rice yield response to global climate change and the effectiveness of widely practiced global thereby assisting with appropriate adaptive strategies.

Accumulating evidence has demonstrated that aberrant miRNAs were involved in carcinogenesis and tumor progression by regulating oncogenes or tumor suppressor expression. Dysregulation of miR-381 has been reported in different tumors. However, the clinical roles and underlying mechanism in non-small cell lung cancer (NSCLC) remains to be elucidated. We found the expression of miR-381 was significantly downregulated in both NSCLC tissues and cell lines. Clinical analysis revealed the reduced miR-381 was obviously associated with advanced TNM stage and lymph node metastasis. Moreover, we disclosed that miR-381 was a novel independent prognostic marker for predicting 5-year survival of NSCLC patients. The ectopic overexpression of miR-381 inhibited cell migration and invasion in vitro and in vivo. Notably, miR-381 could modulate LRH-1 by directly binding to its 3'-UTR. In clinical samples of NSCLC, miR-381 inversely correlated with LRH-1 expression, which performed positive roles in NSCLC migration and invasion. Alteration of LRH-1 expression at least partially abolished the migration and invasion of miR-381 on NSCLC cells. Here, we identified LRH-1 as a functional target of miR-381 in NSCLC. In conclusion, our data indicated that miR-381 inhibited migration and invasion of NSCLC by targeting LRH-1, and may represent a novel potential therapeutic target and prognostic marker for NSCLC.

Lung cancer including non-small cell lung cancer (NSCLC) and small cell lung cancer is one of the most aggressive tumors with high incidence and low survival rate. The typical NSCLC patients account for 80-85 % of the total lung cancer patients. To systemically explore the molecular mechanisms of NSCLC, we performed a molecular network analysis between human and mouse to identify key genes (pathways) involved in the occurrence of NSCLC. We automatically extracted the human-to-mouse orthologous interactions using the GeneWays system by natural language processing and further constructed molecular (gene and its products) networks by mapping the human-to-mouse interactions to NSCLC-related mammalian phenotypes, followed by module analysis using ClusterONE of Cytoscape and pathway enrichment analysis using the database for annotation, visualization and integrated discovery (DAVID) successively. A total of 70 genes were proven to be related to the mammalian phenotypes of NSCLC, and seven genes (ATAD5, BECN1, CDKN2A, FNTB, E2F1, KRAS and PTEN) were found to have a bearing on more than one mammalian phenotype (MP) each. Four network clusters centered by four genes thyroglobulin (TG), neurofibromatosis type-1 (NF1 ), neurofibromatosis type 2 (NF2 ) and E2F transcription factor 1 (E2F1) were generated. Genes in the four network modules were enriched in eight KEGG pathways (p value < 0.05), including pathways in cancer, small cell lung cancer, cell cycle and p53 signaling pathway. Genes p53 and E2F1 may play important roles in NSCLC occurrence, and thus can be considered as therapeutic targets for NSCLC.

VSV-G-pseudotyped lentiviral vectors expressing p16INK4a or p14ARF were used to infect at high-efficiency Philadelphia chromosome (Ph)-positive leukemia cell lines lacking endogenous transcripts. Restoration of p16INK4a accumulated cells in the G0/G1 phase of cell cycle and restoration of p14ARF induced their apoptosis, followed by significant growth inhibition. Transduction of primary blast cells from chronic myeloid leukemia in blast crisis (CML-BC) and Ph-positive acute lymphoblastic leukemia (ALL) with p16INK4a or p14ARF virus also resulted in cell growth inhibition and/or apoptosis with a patient-to-patient variation, whereas clonal growth and differentiation of cord blood progenitor cells were not affected by enforced expression of INK4a/ARF. Furthermore, upon viral transduction at low multiplicity of infection, INK4a/ARF potentiated the effect of imatinib mesylate on Ph-positive leukemia cell lines in an additive but not synergistic manner. These results suggest that INK4a/ARF protein-mimetic agents may be promising options for Ph-positive leukemias in combination with imatinib mesylate.

Among the five serine incorporator (SERINC) family members, SERINC5 (Ser5) was reported to strongly inhibit HIV-1 replication, which is counteracted by Nef. Ser5 produces 5 alternatively spliced isoforms: Ser5-001 has 10 putative transmembrane domains, whereas Ser5-004, -005, -008a, and -008b do not have the last one. Here, we confirmed the strong Ser5 anti-HIV-1 activity and investigated its isoforms' expression and antiviral activities. It was found that Ser5-001 transcripts were detected at least 10-fold more than the other isoforms by real-time quantitative PCR. When Ser5-001 and its two isoforms Ser5-005 and Ser5-008a were expressed from the same mammalian expression vector, only Ser5-001 was stably expressed, whereas the others were poorly expressed due to rapid degradation. In addition, unlike the other isoforms, which are located mainly in the cytoplasm, Ser5-001 is localized primarily to the plasma membrane. To map the critical determinant, Ser5 mutants bearing C-terminal deletions were created. It was found that the 10th transmembrane domain is required for Ser5 stable expression and plasma membrane localization. As expected, only Ser5-001 strongly inhibits HIV-1 infectivity, whereas the other Ser5 isoforms and mutants that do not have the 10th transmembrane domain show very poor activity. It was also observed that the Nef counteractive activity could be easily saturated by Ser5 overexpression. Thus, we conclude that Ser5-001 is the predominant antiviral isoform that restricts HIV-1, and the 10th transmembrane domain plays a critical role in this process by regulating its protein stability and plasma membrane targeting. IMPORTANCE Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) express a small protein, Nef, to enhance viral pathogenesis in vivo . Nef has an important in vitro function, which is to make virus particles more infectious, but the mechanism has been unclear. Recently, Nef was reported to counteract a novel anti-HIV host protein, SERINC5 (Ser5). Ser5 has five alternatively spliced isoforms, Ser5-001, -004, -005, -008a, and -008b, and only Ser5-001 has an extra C-terminal transmembrane domain. We now show that the Ser5-001 transcripts are produced at least 10-fold more than the others, and only Ser5-001 produces stable proteins that are targeted to the plasma membrane. Importantly, only Ser5-001 shows strong anti-HIV-1 activity. We further demonstrate that the extra transmembrane domain is required for Ser5 stable expression and plasma membrane localization. These results suggest that plasma membrane localization is required for Ser5 antiviral activity, and Ser5-001 is the predominant isoform that contributes to the activity.

Localized folate deficiency may be a risk factor for cancer. Since, folate binding proteins (FBP) and reduced folate carrier proteins (RFC) mediate cellular transport of folate, we compared FBP concentrations in several organs from tumor-bearing transgenic (TBT) mice and tumor-free non-transgenic controls (NTC) of the same strain, age, and fed identical diets. Liver, spleen, brain, small intestine and kidney were individually homogenized in phosphate-buffered saline (PBS) and separated into membrane, cytoplasmic, mitochondrial/lysomal and nuclear fractions (confirmed with marker enzymes). Homogenates and fractions was analyzed for total protein, and FBP. We used rabbit anti-bovine milk antibody and ELISA to measure FBP. FBP concentrations in kidney, small intestine, and spleen of TBT mice were higher than those of NTC mice; the opposite was true in liver and lung. FBP seemed to be upregulated in kidneys (all fractions), small intestine (all fractions), and spleen (cytoplasmic and nuclear fractions only) of TBT mice compared to NTC mice; the opposite appeared true in liver (all fractions) and lung (all fractions). FBP concentrations in brain, heart, and muscle of TBT mice were not different from those in brain, heart and muscle of NTC mice. A longitudinal study will determine if these changes in FBP concentrations precede tumor onset.

This study was carried out to investigate the genetic polymorphism of nine short tandem repeat (STR) loci including D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364 and D22GATA198B05 in Chinese Han population of Henan province and to assess its value in forensic science. Genomic DNA was extracted by means of phenol-chloroform from 212 blood samples of unrelated healthy individuals in Henan Han population, and alleles were amplified with STRtyper-10F/G kit. The genotype distributions were in accordance with Hardy-Weinberg equilibrium (p>0.05). New core sequences were found in D2S1772, D7S3048, and D22GATA198B05 STR loci in Chinese Han population of Henan province, which were different from those of other populations. Two single-nucleotide polymorphism (SNP) sites were found at locus D18S1364 and D22GATA198B05, respectively. The heterozygosity (H), power of discrimination (PD), probability of exclusion (PE) and polymorphism information contents (PIC) ranged from 0.778 to 0.887, 0.928 to 0.967, 0.559 to 0.769 and 0.77 to 0.86, respectively. The total PD and combined PE of nine STR loci reached 0.999999999999363 and 0.999951, respectively. The nine STR loci are highly polymorphic in Chinese Han population of Henan province and they may be of great value in forensic science and human population genetics.Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics.

Lung cancer including non-small cell lung cancer (NSCLC) and small cell lung cancer is one of the most aggressive tumors with high incidence and low survival rate. The typical NSCLC patients account for 80–85 % of the total lung cancer patients. To systemically explore the molecular mechanisms of NSCLC, we performed a molecular network analysis between human and mouse to identify key genes (pathways) involved in the occurrence of NSCLC. We automatically extracted the human-to-mouse orthologous interactions using the GeneWays system by natural language processing and further constructed molecular (gene and its products) networks by mapping the human-to-mouse interactions to NSCLC-related mammalian phenotypes, followed by module analysis using ClusterONE of Cytoscape and pathway enrichment analysis using the database for annotation, visualization and integrated discovery (DAVID) successively. A total of 70 genes were proven to be related to the mammalian phenotypes of NSCLC, and seven genes (ATAD5, BECN1, CDKN2A, FNTB, E2F1, KRAS and PTEN) were found to have a bearing on more than one mammalian phenotype (MP) each. Four network clusters centered by four genes thyroglobulin (TG), neurofibromatosis type-1 (NF1 ), neurofibromatosis type 2 (NF2 ) and E2F transcription factor 1 (E2F1) were generated. Genes in the four network modules were enriched in eight KEGG pathways (p value

Jun Li,1,* Lintao Bi,1 Yumei Lin,1,* Zhenxia Lu,1 Gang Hou2 1Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun,Jilin, People’s Republic of China; 2Department of Respiratory Medicine, The First Hospital of China Medical University, Shenyang, People’s Republic of China *These authors contributed equally tothis work Abstract: Multiple myeloma (MM) is a clonal malignancy characterized by the proliferation of malignant plasma cells in the bone marrow and the production of monoclonal immunoglobulin. In addition to genetic changes, gene hypermethylation is an alternative mechanism of tumor suppressor gene inactivation in MM. The cyclin-dependent kinase inhibitor 1 (CDKN2B or p15INK4B) gene lies adjacent to the tumor suppressor gene, cyclin-dependent kinase inhibitor 2 (CDKN2A), and is frequently mutated and deleted in a wide variety of tumors, including MM. However, there is a lack of systematic analysis of p15 epigenetic modification such as methylation in MM from different studies that can provide more powerful estimation of an effect. In this study, we have systematically reviewed the studies of p15INK4B promoter methylation in MM and quantified the association between p15INK4B promoter methylation and MM using meta-analysis methods. We observed that the frequency of p15INK4B methylation is significantly higher in MM patients than in normal healthy controls. The pooled odds ratio (OR) from ten studies including 394 MM and 99 normal individuals is 0.08, while confidence interval (CI) is 0.03–0.21 (P

Under states of protein deficiency, the dietary limiting amino acid, rather than protein content, can act as the dietary stimulus to control diet selection. If fact, threonine-deficient rats will alter their diet selection patterns solely on the basis of very small changes (0.009 g/100 g) in the dietary threonine concentration. In these studies, we assessed whether lysine-deficient rats will also alter their diet selection patterns on the basis of small changes in dietary Lys concentration. In all experiments, growing rats were adapted to diets in which the protein fraction (purified amino acids or wheat gluten) was limiting in Lys. They were then given a choice between the adaptation diet (AD) diet and a slightly more deficient diet. Rats that were adapted to a Lys-deficient diet (0.25 g Lys/100 g) selected their AD over diets containing as little as 0.01% less Lys (P < 0.01) within 5 d. To determine how deficient rats must be before they alter their selection patterns, rats were adapted to diets containing various levels of Lys, i.e., 2 levels below the requirement for growth and 2 levels above the requirement for growth, but below the requirement for maximal nitrogen retention. Only rats adapted to diets containing Lys below their requirement for growth selected their AD over a diet containing 0.05% less Lys (P < 0.005). Finally, to determine whether rats will alter their selection to whole protein-based diets, rats were adapted to 25% wheat gluten diets supplemented with 0.03-0.21% Lys. Rats selected the AD over a diet containing as little as 0.09% less supplemental Lys by d 4 of the trial (P < 0.05). We conclude that rats are sensitive to changes as small as 0.01% in dietary Lys concentration, but that sensitivity requires prior adaptation to Lys-deficient diets.

Global temperatures are rising, and concerns about the response of agricultural production to climate change are increasing. Adaptation is a key factor that will shape the severity of impacts of future climate change on food production. Based on actual meteorological, soil and agricultural management data at site scale, the CERES-Rice model, combined with the Regional Climate Model (RCM)-PRECIS, was used to simulate both the effects of climate change on rice yields and the efficacy of adaptive options in Northeast China. The impact simulation showed that rice yield changes ranged from +0.1% to –44.9% (A2 scenario) and from –0.3% to –40.1% (B2 scenario) without considering CO2 fertilisation effects. When considering CO2 fertilisation effects, rice yield reductions induced by temperature increases were decreased at all sites. The CO2 fertilisation effects may partly offset the negative impacts of climate change on rice yields. Adaptive option results revealed that the adverse impacts of climate change on rice yields could be mitigated by advancing the planting dates, transplanting mid–late-maturing rice cultivars to replace early-maturing ones, and breeding new rice cultivars with high thermal requirements. Our findings provide insight into the possible impacts of climate change on rice production, and we suggest which adaptive strategies could be used to cope with future climate change, thus providing evidence-based suggestions for government policy on adaptive strategies.