A review of disease risk prediction methods and applications in the omics era.

Risk prediction and disease prevention are the innovative care challenges of the 21st century. Apart from freeing the individual from the pain of disease, it will lead to low medical costs for society. Until very recently, risk assessments have ushered in a new era with the emergence of omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and so on, which potentially advance the ability of biomarkers to aid prediction models. While risk prediction has achieved great success, there are still some challenges and limitations. We reviewed the general process of omics-based disease risk model construction and the applications in four typical diseases. Meanwhile, we highlighted the problems in current studies and explored the potential opportunities and challenges for future clinical practice.

Effects of genetic variation on the structure of RNA and protein.

Changes in the structure of RNA and protein, have an important impact on biological functions and are even important determinants of disease pathogenesis and treatment. Some genetic variations, including copy number variation, single nucleotide variation, and so on, can lead to changes in biological function and increased susceptibility to certain diseases by changing the structure of RNA or protein. With the development of structural biology and sequencing technology, a large amount of RNA and protein structure data and genetic variation data resources has emerged to be used to explain biological processes. Here, we reviewed the effects of genetic variation on the structure of RNAs and proteins, and investigated their impact on several diseases. An online resource (http://www.onethird-lab.com/gems/) to support convenient retrieval of common tools is also built. Finally, the challenges and future development of the effects of genetic variation on RNA and protein were discussed.

Genome-wide identification of m6A-associated single nucleotide polymorphisms in complex diseases of nervous system.

N6-methyladenosine (m6A) is one of the most abundant chemical modifications on RNA and can affect the occurrence and development of diseases. Some studies have shown that the expressions of some m6A-related genes are significantly regulated by single nucleotide variants (SNV). However, the function of m6A-associated single nucleotide polymorphisms (m6A-SNP) remains unclear in multiple sclerosis (MS), Alzheimer's disease (AD) and Parkinson's disease (PD). Here, we identified the disease-associated m6A-SNPs by integrating genome-wide association study (GWAS) and m6A-SNPs from the RMVar database, and confirmed the relationship between these identified m6A-SNPs and their target genes in eQTL analysis and gene differential expression analysis. Finally, 26 genes corresponding to 20 m6A-SNPs with eQTL signals were identified and differentially expressed (P < 0.05) in MS, 15 genes corresponding to 12 m6A-SNPs (P < 1e-04) were differentially expressed in AD, and 27 PD-associated m6A-SNPs that regulated the expression of 31 genes were identified. There were 5 HLA genes with eQTL signals (HLA-DQB1, HLA-DRB1, HLA-DQA1, HLA-DQA2 and HLA-DQB1-AS1) to be detected in the three diseases. In summary, our study provided new insights into understanding the potential roles of these m6A-SNPs in disease pathogenesis as well as therapeutic target.

Flexible solar cells based on foldable silicon wafers with blunted edges.

Flexible solar cells have a lot of market potential for application in photovoltaics integrated into buildings and wearable electronics because they are lightweight, shockproof and self-powered. Silicon solar cells have been successfully used in large power plants. However, despite the efforts made for more than 50 years, there has been no notable progress in the development of flexible silicon solar cells because of their rigidity1-4. Here we provide a strategy for fabricating large-scale, foldable silicon wafers and manufacturing flexible solar cells. A textured crystalline silicon wafer always starts to crack at the sharp channels between surface pyramids in the marginal region of the wafer. This fact enabled us to improve the flexibility of silicon wafers by blunting the pyramidal structure in the marginal regions. This edge-blunting technique enables commercial production of large-scale (>240 cm2), high-efficiency (>24%) silicon solar cells that can be rolled similarly to a sheet of paper. The cells retain 100% of their power conversion efficiency after 1,000 side-to-side bending cycles. After being assembled into large (>10,000 cm2) flexible modules, these cells retain 99.62% of their power after thermal cycling between -70 °C and 85 °C for 120 h. Furthermore, they retain 96.03% of their power after 20 min of exposure to air flow when attached to a soft gasbag, which models wind blowing during a violent storm.

RABC: Rheumatoid Arthritis Bioinformatics Center.

Advances in sequencing technologies have led to the rapid growth of multi-omics data on rheumatoid arthritis (RA). However, a comprehensive database that systematically collects and classifies the scattered data is still lacking. Here, we developed the Rheumatoid Arthritis Bioinformatics Center (RABC, http://www.onethird-lab.com/RABC/), the first multi-omics data resource platform (data hub) for RA. There are four categories of data in RABC: (i) 175 multi-omics sample sets covering transcriptome, epigenome, genome, and proteome; (ii) 175 209 differentially expressed genes (DEGs), 105 differentially expressed microRNAs (DEMs), 18 464 differentially DNA methylated (DNAm) genes, 1 764 KEGG pathways, 30 488 GO terms, 74 334 SNPs, 242 779 eQTLs, 105 m6A-SNPs and 18 491 669 meta-mQTLs; (iii) prior knowledge on seven types of RA molecular markers from nine public and credible databases; (iv) 127 073 literature information from PubMed (from 1972 to March 2022). RABC provides a user-friendly interface for browsing, searching and downloading these data. In addition, a visualization module also supports users to generate graphs of analysis results by inputting personalized parameters. We believe that RABC will become a valuable resource and make a significant contribution to the study of RA.

Efficient and stable perovskite-silicon tandem solar cells through contact displacement by MgFx.

The performance of perovskite solar cells with inverted polarity (p-i-n) is still limited by recombination at their electron extraction interface, which also lowers the power conversion efficiency (PCE) of p-i-n perovskite-silicon tandem solar cells. A MgFx interlayer with thickness of ~1 nanometer at the perovskite/C60 interface favorably adjusts the surface energy of the perovskite layer through thermal evaporation, which facilitates efficient electron extraction and displaces C60 from the perovskite surface to mitigate nonradiative recombination. These effects enable a champion open-circuit voltage of 1.92 volts, an improved fill factor of 80.7%, and an independently certified stabilized PCE of 29.3% for a monolithic perovskite-silicon tandem solar cell ~1 square centimeter in area. The tandem retained ~95% of its initial performance after damp-heat testing (85°C at 85% relative humidity) for >1000 hours.

Scaled Deposition of Ti3C2Tx MXene on Complex Surfaces: Application Assessment as Rear Electrodes for Silicon Heterojunction Solar Cells.

Two-dimensional transition metal carbides (MXenes) are of great interest as electrode materials for a variety of applications, including solar cells, due to their tunable optoelectronic properties, high metallic conductivity, and attractive solution processability. However, thus far, MXene electrodes have only been exploited for lab-scale device applications. Here, to demonstrate the potential of MXene electrodes at an industry-relevant level, we implemented a scalable spray coating technique to deposit highly conductive (ca. 8000 S/cm, at a ca. 55 nm thickness) Ti3C2Tx films (Tx: surface functional groups, i.e., -OH, -O, -F) via an automated spray system. We employed these Ti3C2Tx films as rear electrodes for silicon heterojunction solar cells as a proof of concept. The spray-deposited MXene flakes have formed a conformal coating on top of the indium tin oxide (ITO)-coated random pyramidal textured silicon wafers, leading to >20% power conversion efficiency (PCE) over both medium-sized (4.2 cm2) and large (243 cm2, i.e., industry-sized 6 in. pseudosquare wafers) cell areas. Notably, the Ti3C2Tx-rear-contacted devices have retained around 99% of their initial PCE for more than 600 days of ambient air storage. Their performance is comparable with state-of-the-art solar cells contacted with sputtered silver electrodes. Our findings demonstrate the high-throughput potential of spray-coated MXene-based electrodes for solar cells in addition to a wider variety of electronic device applications.

Solution-Doped Polysilicon Passivating Contacts for Silicon Solar Cells.

In this work, we present a simple and efficient solution-doping process for preparing high-quality polycrystalline silicon (poly-Si)-based passivating contacts. Commercial phosphorus or boron-doping solutions are spin-coated on crystalline silicon (c-Si) wafers that feature SiO2/poly-Si layers; the doping process is then activated by thermal annealing at high temperatures in a nitrogen atmosphere. With optimized n- and p-type solution doping and thermal annealing, n- and p-type poly-Si passivating contacts featuring simultaneously a low contact recombination parameter (J0c) of 2.4 and 12 fA/cm2 and a low contact resistivity (ρc) of 29 and 20 mΩ·cm2 are achieved, respectively. Taking advantage of the single-sided nature of these solution-doping processes, c-Si solar cells with poly-Si passivating contacts of opposite polarity on the respective wafer surfaces are fabricated using a simple coannealing process, achieving the best power conversion efficiency (PCE) of 18.5% on a planar substrate. Overall, the solution-doping method is demonstrated to be a simple and promising alternative to gas/ion implantation doping for poly-Si passivating-contact manufacturing.

A Highly Conductive Titanium Oxynitride Electron-Selective Contact for Efficient Photovoltaic Devices.

High-quality carrier-selective contacts with suitable electronic properties are a prerequisite for photovoltaic devices with high power conversion efficiency (PCE). In this work, an efficient electron-selective contact, titanium oxynitride (TiOx Ny ), is developed for crystalline silicon (c-Si) and organic photovoltaic devices. Atomic-layer-deposited TiOx Ny is demonstrated to be highly conductive with a proper work function (4.3 eV) and a wide bandgap (3.4 eV). Thin TiOx Ny films simultaneously provide a moderate surface passivation and enable a low contact resistivity on c-Si surfaces. By implementation of an optimal TiOx Ny -based contact, a state-of-the-art PCE of 22.3% is achieved for a c-Si solar cell featuring a full-area dopant-free electron-selective contact. Simultaneously, conductive TiOx Ny is proven to be an efficient electron-transport layer for organic photovoltaic (OPV) devices. A remarkably high PCE of 17.02% is achieved for an OPV device with an electron-transport TiOx Ny layer, which is superior to conventional ZnO-based devices with a PCE of 16.10%. Atomic-layer-deposited TiOx Ny ETL on a large area with a high uniformity may help accelerate the commercialization of emerging solar technologies.

Endogenously synthesized n-3 fatty acids in fat-1 transgenic mice prevent melanoma progression by increasing E-cadherin expression and inhibiting ß-catenin signaling.

Malignant melanoma is the most lethal form of skin cancer. Although preclinical studies have shown that n-3 polyunsaturated fatty acids (PUFAs) are beneficial for prevention of melanoma, the molecular mechanisms underlying the protective effects of n­3 PUFAs on melanoma remain largely unknown. In the present study, endogenously increased levels of n-3 PUFAs in the tumor tissues of omega­3 fatty acid desaturase (fat­1) transgenic mice was associated with a reduction in the growth rate of melanoma xenografts. This reduction in tumor growth in fat­1 mice compared with wild­type controls may have been associated, in part, to the: i) Increased expression of E­cadherin and the reduced expression of its transcriptional repressors, the zinc finger E­box binding homeobox 1 and snail family transcriptional repressor 1; ii) significant repression of the epidermal growth factor receptor/Akt/ß­catenin signaling pathway; and iii) formation of significant levels of n­3 PUFA­derived lipid mediators, particularly resolvin D2 and E1, maresin 1 and 15­hydroxyeicosapentaenoic acid. In addition, vitamin E administration counteracted n­3 PUFA­induced lipid peroxidation and enhanced the antitumor effect of n­3 PUFAs, which suggests that the protective role of n­3 PUFAs against melanoma is not mediated by n­3 PUFAs­induced lipid peroxidation. These results highlight a potential role of n­3 PUFAs supplementation for the chemoprevention of melanoma in high­risk individuals, and as a putative adjuvant agent in the treatment of malignant melanoma.

Transgenic n-3 PUFAs enrichment leads to weight loss via modulating neuropeptides in hypothalamus.

Body weight is related to fat mass, which is associated with obesity. Our study explored the effect of fat-1 gene on body weight in fat-1 transgenic mice. In present study, we observed that the weight/length ratio of fat-1 transgenic mice was lower than that of wild-type mice. The serum levels of triglycerides (TG), cholesterol (CT), high-density lipoprotein cholesterol (HDL-c), low-density lipoprotein cholesterol (LDL-c) and blood glucose (BG) in fat-1 transgenic mice were all decreased. The weights of peri-bowels fat, perirenal fat and peri-testicular fat in fat-1 transgenic mice were reduced. We hypothesized that increase of n-3 PUFAs might alter the expression of hypothalamic neuropeptide genes and lead to loss of body weight in fat-1 transgenic mice. Therefore, we measured mRNA levels of appetite neuropeptides, Neuropeptide Y (NPY), Agouti-related peptides (AgRP), Proopiomelanocortin (POMC), Cocaine and amphetamine regulated transcript (CART), ghrelin and nesfatin-1 in hypothalamus by real-time PCR. Compared with wild-type mice, the mRNA levels of CART, POMC and ghrelin were higher, while the mRNA levels of NPY, AgRP and nesfatin-1 were lower in fat-1 transgenic mice. The results indicate that fat-1 gene or n-3 PUFAs participates in regulation of body weight, and the mechanism of this phenomenon involves the expression of appetite neuropeptides and lipoproteins in fat-1 transgenic mice.

Omega-3 polyunsaturated fatty acids protect neural progenitor cells against oxidative injury.

The omega-3 polyunsaturated fatty acids (ω-3 PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), derived mainly from fish oil, play important roles in brain development and neuroplasticity. Here, we reported that application of ω-3 PUFAs significantly protected mouse neural progenitor cells (NPCs) against H2O2-induced oxidative injury. We also isolated NPCs from transgenic mice expressing the Caenorhabditis elegans fat-1 gene. The fat-1 gene, which is absent in mammals, can add a double bond into an unsaturated fatty acid hydrocarbon chain and convert ω-6 to ω-3 fatty acids. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining showed that a marked decrease in apoptotic cells was found in fat-1 NPCs after oxidative injury with H2O2 as compared with wild-type NPCs. Quantitative RT-PCR and Western blot analysis demonstrated a much higher expression of nuclear factor erythroid 2-related factor 2 (Nrf2), a master transcriptional factor for antioxidant genes, in fat-1 NPCs. The results of the study provide evidence that ω-3 PUFAs resist oxidative injury to NPCs.

Analysis of global DNA methylation by hydrophilic interaction ultra high-pressure liquid chromatography tandem mass spectrometry.

We developed and validated a rapid, sensitive, and specific liquid chromatography tandem mass spectrometry (LC-MS/MS) method for determination of global DNA methylation in tissue. DNA was extracted by phenol-chloroform, hydrolyzed using 88% formic acid at 140°C, spiked with cytosine-2,4-(13)C(15)N(2) as internal standard, evaporated under nitrogen, reconstituted in methanol, and analyzed by LC-MS/MS in multiple reaction monitoring mode to reflect the global DNA methylation of the tissue. The method was linear throughout the range of clinical interest and had good sensitivity, with a limit of quantification of 0.5pg for both cytosine (Cyt) and 5-methylcytosine (5mCyt). The linear range of calibration curve was 1-50 and 1-100ng/ml for 5mCyt and Cyt, respectively, with a correlation coefficient higher than 0.99. The relative standard deviation (RSD) was 0.70-4.09% and 0.60-4.81% for Cyt and 5mCyt, respectively. The intraday precision expressed as RSD ranged from 1.86% to 4.67%, whereas the interday values ranged from 3.72% to 4.68%. The recovery of the method varied from 86.52% to 105.14%. This yielded a simple and reliable LC-MS/MS assay for detection of Cyt and 5mCyt, thereby enabling the evaluation of global DNA methylation.