MicroRNAs involved in the aggressiveness of malignant melanoma

Malignant melanoma is the most severe form of skin cancer being refractory to current therapies at advanced stages (stage III and IV). The survival of individual patients can vary from months to years, but the molecular mechanism behind this broad survival time range is unknown so far. Many signaling pathways have been found to be important in melanoma and recently microRNAs (miRNAs) have emerged to be essential regulators in these pathways. This study aimed at the identification of miRNAs accounting for the aggressiveness of melanoma. Using bead-based microarray analyses, we performed miRNA expression profiling on a panel of melanoma cell lines derived from metastatic melanoma patients with either long or short survival times. Upon comparison of these two patient groups a number of differentially expressed miRNAs could be identified. However, subsequent real-time quantitative PCR (qPCR) revealed that only one candidate miRNA (miR-101) was confirmed to be down-regulated in cell lines from short term survivors, compared to long term survivors. We found that miR-101 could directly target microphthalmia-associated transcription factor (MITF) in melanoma cells, leading to a decrease in intracellular MITF protein expression. One of the predicted target sites for miR-101 in the 3’ UTR of MITF was confirmed by luciferase reporter assay. Furthermore, we show that the expression of “enhancer of zeste homolog 2” (EZH2), previously reported as miR-101 target in other types of cancer, was down-regulated by miR-101 also in melanoma. Overexpression of miR-101 inhibited proliferation, invasion and migration of melanoma cells, which could be phenocopied by siRNA-mediated knockdown of MITF or EZH2 using specific siRNA. miR-137 was reported to act as a tumor suppressor in different cancer entities including melanoma. In this study, we showed that low miR-137 expression correlated with poor survival of stage IV melanoma patients. We identified three novel targets (proto-oncogene c-Met, Y box binding protein 1 [YB1] and the ATP-binding cassette, sub-family B, member 5 [ABCB5]) and confirmed two previously reported targets (MITF and EZH2) for miR-137. Overexpression of miR-137 suppressed invasion of melanoma cells, which could be phenocopied by siRNA-mediated knockdown of the miR-137 targets c-Met, YB1, MITF and EZH2. Furthermore, miR-137 inhibited melanoma cell migration and proliferation likely through the down-regulation of certain proteins (e.g. YB1 and EZH2) whose individual impact on these processes varied among the two cell lines tested. Finally, miR-137 induced apoptosis in melanoma cell lines and decreased B-cell lymphoma 2 (BCL2) protein expression levels. In conclusion, our study suggests that miR-101 and miR-137 can function as tumor suppressors in melanoma. We show that overexpression of these miRNAs could lower the aggressiveness of melanoma cells by regulation of multiple signaling pathways, offering new options for targeted therapy against melanoma

Software-Hardware Co-design for Fast and Scalable Training of Deep Learning Recommendation Models

Deep learning recommendation models (DLRMs) are used across many business-critical services at Facebook and are the single largest AI application in terms of infrastructure demand in its data-centers. In this paper we discuss the SW/HW co-designed solution for high-performance distributed training of large-scale DLRMs. We introduce a high-performance scalable software stack based on PyTorch and pair it with the new evolution of Zion platform, namely ZionEX. We demonstrate the capability to train very large DLRMs with up to 12 Trillion parameters and show that we can attain 40X speedup in terms of time to solution over previous systems. We achieve this by (i) designing the ZionEX platform with dedicated scale-out network, provisioned with high bandwidth, optimal topology and efficient transport (ii) implementing an optimized PyTorch-based training stack supporting both model and data parallelism (iii) developing sharding algorithms capable of hierarchical partitioning of the embedding tables along row, column dimensions and load balancing them across multiple workers; (iv) adding high-performance core operators while retaining flexibility to support optimizers with fully deterministic updates (v) leveraging reduced precision communications, multi-level memory hierarchy (HBM+DDR+SSD) and pipelining. Furthermore, we develop and briefly comment on distributed data ingestion and other supporting services that are required for the robust and efficient end-to-end training in production environments

Application and Technique of Liquid Crystal-Based Biosensors

Liquid crystal biosensors are based on changes in the orientation of liquid crystal molecules induced by specific bonding events of biomolecules. These biosensors are expected to serve as a promising system to detect biomolecules, biomolecular activity, and even small chemical molecules because they are inexpensive, sensitive, simple, effective, and portable. Herein, we introduce the principle and fabrication of liquid crystal biosensors and review the research progress in signal-amplified technology for liquid crystal sensing and its application in the detection of viruses, bacteria, proteins, nucleic acids, and small chemical molecules. In addition, the current theoretical and practical issues related to liquid crystal biosensors were investigated

Rare Drosha Splice Variants Are Deficient in MicroRNA Processing but Do Not Affect General MicroRNA Expression in Cancer Cells12

Drosha is a key enzyme in microRNA biogenesis, generating the precursor miRNA (pre-miRNA) by excising the stem-loop embedded in the primary transcripts (pri-miRNA). The specificity for the pri-miRNAs and determination of the cleavage site are provided by its binding partner DGCR8, which is necessary for efficient processing. The crucial Drosha domains for pri-miRNA cleavage are the middle part, the two enzymatic RNase III domains (RIIID), and the dsRNA binding domain (dsRBD) in the C-terminus. Here, we identify alternatively spliced transcripts in human melanoma and NT2 cell lines, encoding C-terminally truncated Drosha proteins lacking part of the RIIIDb and the entire dsRBD. Proteins generated from these alternative splice variants fail to bind to DGCR8 but still interact with Ewing sarcoma protein (EWS). In vitro as well as in vivo, the Drosha splice variants are deficient in pri-miRNA processing. However, the aberrant transcripts in melanoma cells do not consistently reduce mature miRNA levels compared with melanoma cell lines lacking those splice variants, possibly owing to their limited abundance. Our findings show that alternative processing-deficient Drosha splice variants exist in melanoma cells. In elevated amounts, these alternatively spliced transcripts could provide one potential mechanism accounting for the deregulation of miRNAs in cancer cells. On the basis of our results, the search for alternative inactive splice variants might be fruitful in different tumor entities to unravel the molecular basis of the previously observed decreased microRNA processing efficiency in cancer

RANGE: Gene Transfer of Reversibly Controlled Polycistronic Genes

We developed a single vector recombinant adeno-associated viral (rAAV) expression system for spatial and reversible control of polycistronic gene expression. Our approach (i) integrates the advantages of the tetracycline (Tet)-controlled transcriptional silencer tTSKid and the self-cleaving 2A peptide bridge, (ii) combines essential regulatory components as an autoregulatory loop, (iii) simplifies the gene delivery scheme, and (iv) regulates multiple genes in a synchronized manner. Controlled by an upstream Tet-responsive element (TRE), both the ubiquitous chicken β-actin promoter (CAG) and the neuron-specific synapsin-1 promoter (Syn) could regulate expression of tTSKid together with two 2A-linked reporter genes. Transduction in vitro exhibited maximally 50-fold regulation by doxycycline (Dox). Determined by gene delivery method as well as promoter, highly specific tissues were transduced in vivo. Bioluminescence imaging (BLI) visualized reversible “ON/OFF” gene switches over repeated “Doxy-Cycling” in living mice. Thus, the reversible rAAV-mediated N-cistronic gene expression system, termed RANGE, may serve as a versatile tool to achieve reversible polycistronic gene regulation for the study of gene function as well as gene therapy

Novel Compound Heterozygous BBS2 and Homozygous MKKS Variants Detected in Chinese Families with Bardet–Biedl Syndrome

Background. Bardet–Biedl syndrome (BBS) is a rare multisystem developmental disorder. In this study, we report the genetic causes and clinical manifestations in two Chinese families with BBS. Materials and Methods. Two families were recruited in this study. Family A was a four-generation family with four affected and 15 unaffected members participating in the study, and family B was a consanguineous family with one affected and three unaffected members participating. Whole exome sequencing was performed in the two families, followed by a multistep bioinformatics analysis. Sanger sequencing was used to verify the variants and to perform a segregation analysis. Comprehensive ocular and systemic examinations were also conducted. Results. Novel compound heterozygous variants c.235T > G (p.T79P) and c.534 + 1G > T were detected in the BBS2 gene in family A, and known homozygous variant c.748G > A (p.G250R) was detected in the MKKS gene in family B. Both families presented with retinitis pigmentosa; however, except for polydactyly, all other systemic manifestations were different. All of the affected family members in family A were overweight with a high body mass index (range from 26.5 to 41.9) and high blood pressure. Family A also presented with a delay in the onset of secondary sex characteristics and genital anomalies, while other systemic abnormalities were absent in family B. Conclusions. This study presents one family with two novel BBS2 variants, expanding the variant spectrum of BBS, and one family with a known homozygous MKKS variant. The different phenotypes seen between the families with BBS2 and MKKS variants will contribute to the literature and our overall understanding of BBS

Mutation Spectrum and De Novo Mutation Analysis in Stickler Syndrome Patients with High Myopia or Retinal Detachment

Stickler syndrome is a connective tissue disorder that affects multiple systems, including the visual system. Seven genes were reported to cause Stickler syndrome in patients with different phenotypes. In this study, we aimed to evaluate the mutation features of the phenotypes of high myopia and retinal detachment. Forty-two probands diagnosed with Stickler syndrome were included. Comprehensive ocular examinations were performed. A targeted gene panel test or whole exome sequencing was used to detect the mutations, and Sanger sequencing was conducted for verification and segregation analysis. Among the 42 probands, 32 (76%) presented with high myopia and 29 (69%), with retinal detachment. Pathogenic mutations were detected in 35 (83%) probands: 27 (64%) probands had COL2A1 mutations, and eight (19%) probands had COL11A1 mutations. Truncational mutations in COL2A1 were present in 21 (78%) probands. Missense mutations in COL2A1 were present in six probands, five of which presented with retinal detachment. De novo COL2A1 mutations were detected in 10 (37%) probands, with a mean paternal childbearing age of 29.64 ± 4.97 years old. The mutation features of probands with high myopia or retinal detachment showed that the probands had a high prevalence of COL2A1 mutations, truncational mutations, and de novo mutations

Clinical manifestation and genetic analysis in Chinese early onset X‐linked retinoschisis

Abstract Background X‐linked retinoschisis (XLRS) is one type of retinal dystrophy leading to the schisis of the neural retina and causing reduced visual acuity. The study aimed to investigate the clinical manifestations and retinoschisin 1 (RS1) mutations in Chinese patients with early onset XLRS. Methods Thirty‐eight probands with early onset XLRS were recruited, comprehensive ophthalmic examination was performed. A targeted gene panel was used to test the RS1 mutations. Results All probands had RS1 hemizygous mutations including 16 known and 14 novel mutations. The median onset age was 2 years old (range 0.1–6 years). Probands with onset age ≤1 years. had more complications (retinal detachment and vitreous hemorrhage, p 1 years. Macular and peripheral involvement was present in 77.27% of probands, and inner and outer nuclear layer splitting were present in 53.57% of probands. Electroretinography showed an electronegative waveform. The relatively rare phenotypes of lamellar macular hole and macular hole were present in a unilateral eye in three probands. Conclusion In conclusion, the early onset XLRS developed more severe complications which need close monitoring and clinical manifestations illustrated here may facilitate the early diagnosis of retinoschisis

Anomaly Negative Resistance Phenomena in Highly Epitaxial PrBa_0.7Ca_0.3Co₂O₅₊_δ Thin Films Induced from Superfast Redox Reactions

Thin films of Ca-doped double perovskite, PrBa0.7Ca0.3Co2O5+δ (PBCC), were epitaxially grown on (001) SrTiO3, and their redox reactions under a switching flow of H2 and O2 gases were examined at various temperatures by measuring the resistance R(t) of the films as a function of the gas flow time t. In the temperature range between 350 and 725 °C, these thin films are reduced and oxidized in an ultrafast manner under the flow of H2 and O2 gases, respectively, suggesting that PBCC thin films are promising candidates for developing ultra-sensitive oxygen sensors or SOFC cathodes at intermediate or high temperatures. When the gas flow is switched to O2, the reduced PBCC thin films exhibit a negative resistance at temperatures above 600 °C but a positive resistance at temperatures below 600 °C. The probable cause for these anomalous transport properties is the diffusion of the H atoms from the cathode to the anode in the PBCC film, which provides a current opposite to that resulting from the external voltage