MiR-1254 and MEGF6 regulates oxaliplatin resistance in human colorectal cancer cells

Colorectal cancer (CRC) remains one of the deadliest diseases in the whole world. Cancer recurrence and chemotherapeutic drug resistance limit the overall survival rate of patients with CRC. This study aimed to discover the latent miRNAs and genes associated with oxaliplatin resistance in CRC cells. The study found that miR-1254 is upregulated in oxaliplatin-resistant CRC cell line HCT116-R compared with its parental cell line HCT116 by transcriptome sequencing and small RNA sequencing. Meanwhile, MEGF6 (multiple EGF-like domains 6) was downregulated in HCT116-R cells. Transient transfection of miR-1254 mimics significantly reduced cell apoptosis, increased HCT116 tolerance to oxaliplatin, and enhanced MEGF6 expression. Furthermore, transfection of miR-1254 inhibitor increased apoptosis, decreased HCT116-R tolerance to oxaliplatin, and reduced MEGF6 expression. In addition, transient transfection of SiMEGF6 enhanced HCT116 cell resistance to oxaliplatin and reduced cell apoptosis. In summary, MEGF6 is a latent functional target of miR-1254 in regulating oxaliplatin resistance and apoptosis in human CRC cells, suggesting a potential therapeutic target for CRC.

[Confirmation and analysis of 2 398 positive results of cell-free fetal DNA]

Objective: To explore the clinical application value and accuracy of cell-free fetal DNA (cff-DNA) technique in prenatal screening. Methods: The results of quantitative fluorescent PCR (QF-PCR) and karyotype of amniotic fluid cells were analyzed retrospectively in 2 398 monocyesis pregnant women who had been amniocentesis at the First Affiliated Hospital of Zhengzhou University from May 2013 to December 2019, and the results of 359 cases who had been examined by single-nucleotide polymorphism array (SNP array). Results: Cff-DNA test of 2, 398 cases indicated 987 cases of trisomy 21, 351 cases of trisomy 18, 135 cases of trisomy 13, 566 cases of sex chromosome abnormality, and 359 cases of other chromosome abnormality. Chromosome karyotype analysis detected 826 cases of trisomy 21, 213 cases of trisomy 18, 17 cases of trisomy 13, 221 cases of sex chromosome abnormality, and 26 cases of other chromosome abnormality. The detection rate were 83.69% (826/987), 60.68% (213/351), 12.59% (17/135), 39.04% (221/566) and 7.24% (26/359), respectively. QF-PCR detected 1 046 cases of trisomy and 188 cases of sex chromosomes abnormality, and the detection rate was 99.05% (1 046/1 056) and 85.07% (188/221), respectively. Compared with the abnormal number detected by chromosome karyotype analysis, 10 cases of trisomeric chimerism and 24 cases of sex chromosome were missed by QF-PCR. Among the 359 other chromosomal abnormalities detected by SNP array, 64 cases were consistent with the results of cff-DNA, and the detection rate was 17.83% (64/359), which was 10.59% higher than the karyotype result. Conclusions: Karyotype analysis is the gold standard for diagnosing chromosomal abnormalities. QF-PCR could diagnose common chromosome aneuploidy rapidly and accurately, and it could be used as an auxiliary detection technique for karyotype analysis. The incidence of sex chromosome chimerism is high, so missed diagnosis should be warned. SNP array could be given priority to verify chromosome microdeletion or microduplication detected by cff-DNA.

Self-made Salmonella Pullorum agglutination antigen development and its potential practical application

Pullorum disease caused by Salmonella Pullorum is one of the most important infectious diseases in the poultry industry worldwide, which leads to serious economic losses in many developing countries because of its high mortality rate in young chicks. The traditional slide agglutination test with low cost, fast reaction, and on-site detection has been widely used in the diagnosis of Pullorum disease. However, in practice, the test performance is with the disadvantages of false positive results and unstable detection results. In this paper, we developed self-made agglutination antigens prepared by local isolates in the poultry farm and compare the detection performance with commercial agglutination antigens (China Institute of Veterinary Drug Control) and Group D Salmonella ELISA kit (BioChek UK Ltd). The results of detecting 200 serum samples indicated that the consistency of commercial agglutination antigen detecting in 2 times was only 79.5%. Using the ELISA kit as the reference method, the commercial agglutination antigen detecting results of the Kappa test were only moderately consistent (0.58 ∼ 0.59). Meanwhile, positive and total coincidence rates of the self-made agglutination antigen test with more reliable repeat could reach 97.4 and 88%, respectively, and the result of Kappa test was highly consistent (0.75). The Receiver Operating Characteristic curve analysis clarified that the area under the receiver-operating-characteristic curve values of self-made and commercial agglutination antigen tests could reach 0.861 and 0.804, respectively. These results were coincident when detecting known positive serum from the infected chickens. It's worth mentioning that the visible positive reaction of self-made agglutination antigen test appeared faster and stronger than commercial antigen test. In conclusion, self-made Salmonella Pullorum agglutination antigen developed in this study was much better than commercial agglutination antigen and is expected to be a valuable tool in the diagnosis of the epidemiology of Salmonella Pullorum.

Computer-generated photorealistic hologram using ray-wavefront conversion based on the additive compressive light field approach

The conventional computer-generated hologram reconstructing photorealistic three-dimensional (3D) images based on ray-wavefront conversion has the disadvantage of spatio-angular resolution trade-off. In this Letter, we propose for the first time, to the best of our knowledge, a computer-generated photorealistic hologram without spatio-angular resolution trade-off based on the additive compressive light field (CLF) approach. The original light field is compressed into multiple layer images through numerical optimization based on the additive light field principle. Then, by independently calculating the wave propagation from each layer image to the hologram plane and adding them together, a CLF hologram is generated. Since the CLF information is presented through a holographic method, the advantage of high resolution in CLF is preserved while the limitation of the number of physically stacked layers (such as liquid crystal displays) is removed, leading to higher quality, larger depth of field, and higher brightness compared with a conventional CLF display. The proposed method is verified with a photorealistic optical experiment.

[PTPN11 and the deafness]

Summary PTPN11 gene encodes tyrosine phosphatase SHP-2 which locates on chromosome 12（12q24.1）, expresses in most embryonic and adult tissues, and plays pivotal roles in cell proliferation, differentiation, survival and cell death. SHP-2 apparently participates in signaling events downstream of RAS-MAPK and JAK/STAT. Diseases related to PTPN11 gene mutations include the Noonan syndrome（NS） and the NS with Multiple Lentigines（NSML）. Both NS and NSML contain the phenotypes of deafness, craniofacial anomalies, short stature, congenital heart defects, skin disorders, ophthalmologic abnormalities and cancer predisposition.

Diversity and frequency of resistance and virulence genes in bla KPC and bla NDM co-producing Klebsiella pneumoniae strains from China

Background

Emergence of bla_KPC and bla_NDM co-producing Klebsiella pneumoniae strains have led to the limited therapeutic options for clinical treatment. Understanding the diversity and frequency of resistance and virulence genes of these isolates is of great significance.

Purpose

The aim of this study is to research the diversity and frequency of resistance and virulence genes in the bla_KPC and bla_NDM co-producing Klebsiella pneumoniae strains.

Methods and Results

In this study, 117 K. pneumonia strains were isolated from China, and among of which, 24 were found to be bla_KPC and bla_NDM co-producing with significant resistance against almost all the commonly used antibiotics. Additionally, 4 strains were hypermucoviscous and 8 showed high serum resistance. Overall, bla_SHV, bla_CTX-M, tetA and sul1 resistance genes found in 100% of the isolates, followed by bla_TEM (95.8%), oqxA/B (91.7%), qnrB (87.5%), aac(6’)Ib-cr (83.3%), bla_DHA (79.2%), rmtB (66.7%), qnrS (54.2%), cat(54.2%), floR (50.0%), sul2 (45.8%) cmlA (20.8%)andbla_CMY (8.33%), respectively. What’ more, seven bla_CTX-M subtypes [bla_CTX-M-14 (n=18), bla_CTX-M-3(n=11), bla_CTX-M-65 (n=4), bla_CTX-M-15 (n=3), bla_CTX-M-28 (n=2), bla_CTX-M-55 (n=2), bla_CTX-M-22 (n=1)] and six bla_SHV subtypes [bla_SHV-12(n=16), bla_SHV-11 (n=4), bla_SHV-2a(n=1), bla_SHV-1(n=1), bla_SHV-38(n=1) and bla_SHV-28(n=1)] were detected. The frequency of virulence genes was as follows: 100% for entB, ybtS and irp, 95.8% for mrkD, 91.66% for fimH, 79.2% for iutA, 62.5% for iroBCDE, aerobactin and kfu, 66.7% for allS, 45.8% for wcaG, 37.5% for rmpA, 20.8% for pagO and 16.7% for magA.

Conclusion

From this study, we concluded that the bla_KPC and bla_NDM co-producing Klebsiella pneumoniae strains have a high diversity and frequency of resistance and virulence genes. This study may offer hospitals important information about the control of infections caused by bla_KPC and bla_NDM co-producing Klebsiella pneumoniae.

[Case report and diagnosis of Noonan syndrome with multiple lentigines with deafness as its main clinical feature]

Summary Noonan syndrome with multiple lentigines（NSML） is a disorder with syndromic hearing loss. Abnormalities of other systems in NSML have received increasing attention, but hearing loss is rarely concerned. And due to the incomplete phenotype, some patients with NSML maybe missed or maybe confused with other syndromic deafness such as Waardenburg syndrome. Our study will familiarize more otolaryngologists with Leopard syndrome. A 5-year-old boy with bilateral sensorineural hearing loss and numerous symmetrically distributed dark brown macules that had good effect of cochlear implantation was collected in this study. And his father had bilateral sensorineural hearing loss and numerous symmetrically distributed dark brown macules. Waardenburg syndrome was initially diagnosed by clinical phenotype and its molecular etiology was confirmed by gene diagnosis. Waardenburg syndrome-related deafness genes and 131 known deafness genes were not identified by second-generation sequencing. Whole-exon sequencing was performed for 4 individuals in the family and the results were confirmed by Sanger sequencing. This study confirmed the diagnosis by identifying a disease-causing mutation in the PTPN11 gene, which was a heterozygous missense mutation at p. Tyr279Cys（c. 836A>G）. The mutation co-segregated with hearing loss in the family. Our results demonstrated that hearing loss in this family was caused by heterozygous mutations in PTPN11. These cases will familiarize more otolaryngologists with NSML, and they emphasize the importance of considering NSML as a possible cause of hearing problems.

MiR-483-3p regulates oxaliplatin resistance by targeting FAM171B in human colorectal cancer cells

Oxaliplatin resistance limits the efficiency of treatment for colorectal cancer (CRC). Studies have shown that abnormal expression of microRNAs (miRNAs) were associated with tumorigenesis, cancer development and chemoresistance. The purpose of this study was to identify potential miRNAs related to oxaliplatin resistance in CRC cells. In this work, using small RNA sequencing (small RNA-Seq) and transcriptome sequencing (RNA-Seq), we found that down-regulated miR-483-3p was concurrent with up-regulated FAM171B in oxaliplatin-resistant colorectal cancer cell line HCT116/L as compared with its parental cell line HCT116. Transient transfection of miR-483-3p mimics markedly decreased the levels of FAM171B and restored oxaliplatin responsiveness of HCT116/L cells, and this alteration enhanced cell apoptosis and weakened cell migration. Whereas miR-483-3p inhibitor dramatically promoted the expression of FAM171B and enhanced oxaliplatin resistance of HCT116 cells by repressing cell apoptosis. Furthermore, knockdown of FAM171B in HCT116/L cells could also sensitize its reaction of the treatment with oxaliplatin, which was verified by the reduced cell migration. These findings demonstrate that FAM171B is a functional target of miR-483-3p in the regulation of oxaliplatin resistance in human CRC cells.

Analysis of polymorphisms in genes associated with the FA/BRCA pathway in three patients with multiple primary malignant neoplasms

Cases of more than three primary cancers are very rare. This study analyzed the genetic susceptibility of gene polymorphisms in three patients with multiple primary malignant neoplasms and examined the possible pathogenesis. The clinical data and whole genome sequence of three patients (1 with 5 primary cancers, 1 with 4 primary cancers, and 1 with 3 primary cancers) were aligned with a series of databases. We found the three patients contained a total of seven types of malignant tumours (endometrial cancer, ovarian cancer, breast cancer, colon cancer, ureter cancer, bladder cancer and kidney cancer). It was found that the varied genes in Patient 1 (5 primary cancers) were BRIP1, FANCG, NBN, AXIN2, SRD5A2, and CEBPA. Patient 2 (4 primary cancers) had variations in the following genes: BMPR1A, FANCD2, MLH3, BRCA2, and FANCM. Patient 3 (3 primary cancers) had variations in the following genes: MEN1, ATM, MSH3, BRCA1, FANCL, CEBPA, and FANCA. String software was used to analyze the KEGG pathway of the variations in these three samples, which revealed that the genes are involved in the Fanconi anaemia pathway. Defects in DNA damage repair may be one of the causes of multiple primary cancers.

Screening candidate microRNA-mRNA network for predicting the response to chemoresistance in osteosarcoma by bioinformatics analysis

The search for biomarkers is important for providing more targeted treatments for osteosarcoma patients with chemoresistance. In this study, differentially expressed microRNAs (miRNAs) were identified from miRNA expression profiles. And the target messenger RNAs (mRNAs) of miRNA were obtained from two websites in public domains. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway by these miRNA targets suggests that they may have potential links to osteosarcoma chemoresistance. In the protein-protein interaction (PPI) network, we screened three subnetworks and 10 hub RNAs, and analyzed through KEGG pathway and searched the PubMed database, indicating that they were significantly associated with drug resistance. Then we found 12 key mRNAs by analyzing the mRNA expression profile. Survival analyses showed that most of the 10 hub mRNAs and 12 key mRNAs had a significant influence on the prognosis of patients with chemoresistance osteosarcoma. A miRNA-mRNA network is constructed by integrating mRNAs and miRNAs information. The network biomarkers in this study have an advantage over traditional single-molecule biomarkers in terms of predictive power. And the mRNAs in this network biomarkers are supported by survival analysis or by existing theories. These results will contribute to the choice of chemotherapy before treatment and the prediction of patient prognosis.

[Clinical diagnosis and surgical management of 110 cases of facial nerve schwannomas]

Objective: To elucidate the clinical behavior, causes of misdiagnosis, surgical management, and outcomes of facial nerve schwannomas (FNS). Methods: A retrospective review in Chinese People's Liberation Army General Hospital from January 1, 2002 to December 31, 2015 was carried out and evaluated 110 patients with FNS, including 50 males and 60 females, aged 16-67 years old. The appropriate surgical strategy was selected based on each patient's clinical manifestations, facial nerve function, and imaging characteristics. After surgery, patients received follow-up visits to assess their facial nerve functions, with the effect of treatment compared to the reality before surgery. The Kruskal-Wallis H test was used to distinguish between the pre- and post-operation facial nerve functions in patients who had different facial nerve functions before the operations. Results: 110 cases of FNS mainly presented with facial paralysis, hearing loss, tinnitus, otalgia, dizziness, and facial spasm. 20 of the cases were misdiagnosed as Bell's Palsy, 6 were mistaken for chronic otitis media/cholesteatoma with radical mastoidectomy, 3 were mistaken for Meniere's disease, 1 was misdiagnosed as petrous bone cholesteatoma, and 4 were mistaken for acoustic neuroma. 81.8 % (90/110) of the patients had multiple segments of the facial nerve, including the vertical segment of the facial nerve, accounting for 65.5% (72/110), followed by the labyrinthine/geniculate segment, for 61.8% (68/110), and the horizontal segment, for 55.5% (61/110). The appropriate surgical approaches were chosed based on the sizes and scopes of the tumors evaluated by imaging: transmastoid approach in 73 cases, translabyrinthe approach in 14 cases, middle cranial fossa approach in 13 cases, retrosigmoid approach in 3 cases, transmastoid-middle cranial fossa approach in 3 cases, and transmastoid-neck approach in 4 cases, with all the patients undergoing a total/subtotal resection of the tumor. Eighty-seven patients had their facial nerves reconstructed. Among them, 6 received facial nerve end-to-end anastomosis, 55 received great auricular nerve graft, and 26 were subjected to facial nerve-hypoglossal nerve anastomosis. Because of long histories, facial muscle atrophies, or other reasons, the remaining patients were not received facial nerve reconstruction. The House-Brackmann(H-B) grading scale was used to evaluate the facial nerve function pre- and post-operation. Patients with better facial nerve functions and shorter history of facial paralysis before operation would get relatively better facial nerve function. The before and after operation comparisons revealed that the recovery of the facial nerve functions in patients with H-B Ⅰ-Ⅲ was better than the improvement in patients with H-B Ⅳ-Ⅴ. The difference was statistically significant (Kruskal-Wallis H test, H=8.508, P<0.05). Conclusions: The diagnosis of patients with unknown facial paralysis, hearing loss, and tinnitus should take into account the possibility of FNS. CT and other imaging examinations of the temporal bone can avoid misdiagnosis and determine the tumor size and extent of lesions, as well as provide the basis for the choice of the surgical approach. After tumors have been completely resected, facial nerve reconstruction can be performed simultaneously, according to the defect of the nerve.

A Comparative Study of Cluster Detection Algorithms in Protein-Protein Interaction for Drug Target Discovery and Drug Repurposing

The interactions between drugs and their target proteins induce altered expression of genes involved in complex intracellular networks. The properties of these functional network modules are critical for the identification of drug targets, for drug repurposing, and for understanding the underlying mode of action of the drug. The topological modules generated by a computational approach are defined as functional clusters. However, the functions inferred for these topological modules extracted from a large-scale molecular interaction network, such as a protein–protein interaction (PPI) network, could differ depending on different cluster detection algorithms. Moreover, the dynamic gene expression profiles among tissues or cell types causes differential functional interaction patterns between the molecular components. Thus, the connections in the PPI network should be modified by the transcriptomic landscape of specific cell lines before producing topological clusters. Here, we systematically investigated the clusters of a cell-based PPI network by using four cluster detection algorithms. We subsequently compared the performance of these algorithms for target gene prediction, which integrates gene perturbation data with the cell-based PPI network using two drug target prioritization methods, shortest path and diffusion correlation. In addition, we validated the proportion of perturbed genes in clusters by finding candidate anti-breast cancer drugs and confirming our predictions using literature evidence and cases in the ClinicalTrials.gov. Our results indicate that the Walktrap (CW) clustering algorithm achieved the best performance overall in our comparative study.

Network-based approach to identify principal isoforms among four cancer types

Protein isoforms are structurally similar proteins produced by alternative splicing of a single gene or genes from the same family. Isoforms of a protein can perform the same, similar, or even opposite biological functions. A previous study identified principal isoforms of proteins based on the extent of interactions per isoform in a functional relationship network, focusing on data from normal tissues. Additionally, the expression levels of specific isoforms of various genes associated with tumorigenesis and prognosis are frequently altered in tumors compared with those in normal tissues. In this study, we aimed to identify higher degree isoforms (HDIs) of multi-isoform genes (MIGs) in cancer by applying a meta-analytical framework to calculate co-expression between each pair of isoforms in two large datasets of RNA-seq profiles from breast cancer, lung cancer, leukemia, and colon cancer cell lines. Then, we compared HDIs with isoforms identified by proteomic data and prognostic and predictive evidence in various cancers. In addition, we separately analyzed the associations between HDIs and non-HDIs (nHDIs) of the same genes according to transcript expression and drug responses in various cancer type cell lines. Collectively, these results indicated the complex properties of HDIs per gene identified by cancer type-based isoform-isoform co-expression networks and showed the potential of HDIs as novel therapeutic targets for cancer treatment.

Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations

We investigated the allele frequencies of drug absorption, distribution, metabolism and elimination (ADME)-related drug-metabolizing enzymes and transporters (DMET) genes in the Northwestern Han, Tibetan and Uyghur populations and compared the related genes in these three populations with those in eleven 1000 Genome populations. We examined 1936 single nucleotide polymorphisms of 225 DMET genes involved in ADME processes and found 732, 679 and 804 sites were polymorphic in Han, Tibetan and Uyghur. Tibetan differed from Han in only four sites (p < .05), whereas Uyghur differed from Han and Tibetan in 24 and 21 sites, respectively (p < .05). The distributions of 1058 genotyping data of 245 individuals from Han, Tibetan and Uyghur were compared with 1207 other individuals from the eleven 1000 Genomes populations. The top four populations in Han that exhibited the smallest pairwise Fst values were CHB, Tibetan, CHD and JPT; those in Tibetan were Han, CHB, Uyghur and CHD; and those in Uyghur were Han, Tibetan, GIH and CEU. MEGA results revealed that CHB, CHD, JPT, Han, Tibetan and Uyghur were grouped in cluster 1. GIH, MEX, CEU and TSI were grouped in cluster 2. MKK, ASW, LWK and YRI were grouped in cluster 3.

Transcriptome profiling identified differentially expressed genes and pathways associated with tamoxifen resistance in human breast cancer

Tamoxifen (TAM) resistance is an important clinical problem in the treatment of breast cancer. In order to identify the mechanism of TAM resistance for estrogen receptor (ER)-positive breast cancer, we screened the transcriptome using RNA-seq and compared the gene expression profiles between the MCF-7 mamma carcinoma cell line and the TAM-resistant cell line TAMR/MCF-7, 52 significant differential expression genes (DEGs) were identified including SLIT2, ROBO, LHX, KLF, VEGFC, BAMBI, LAMA1, FLT4, PNMT, DHRS2, MAOA and ALDH. The DEGs were annotated in the GO, COG and KEGG databases. Annotation of the function of the DEGs in the KEGG database revealed the top three pathways enriched with the most DEGs, including pathways in cancer, the PI3K-AKT pathway, and focal adhesion. Then we compared the gene expression profiles between the Clinical progressive disease (PD) and the complete response (CR) from the cancer genome altas (TCGA). 10 common DEGs were identified through combining the clinical and cellular analysis results. Protein-protein interaction network was applied to analyze the association of ER signal pathway with the 10 DEGs. 3 significant genes (GFRA3, NPY1R and PTPRN2) were closely related to ER related pathway. These significant DEGs regulated many biological activities such as cell proliferation and survival, motility and migration, and tumor cell invasion. The interactions between these DEGs and drug resistance phenomenon need to be further elucidated at a functional level in further studies. Based on our findings, we believed that these DEGs could be therapeutic targets, which can be explored to develop new treatment options.