hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing.

RNA splicing is pivotal in post-transcriptional gene regulation, yet the exponential expansion of intron length in humans poses a challenge for accurate splicing. Here, we identify hnRNPM as an essential RNA-binding protein that suppresses cryptic splicing through binding to deep introns, maintaining human transcriptome integrity. Long interspersed nuclear elements (LINEs) in introns harbor numerous pseudo splice sites. hnRNPM preferentially binds at intronic LINEs to repress pseudo splice site usage for cryptic splicing. Remarkably, cryptic exons can generate long dsRNAs through base-pairing of inverted ALU transposable elements interspersed among LINEs and consequently trigger an interferon response, a well-known antiviral defense mechanism. Significantly, hnRNPM-deficient tumors show upregulated interferon-associated pathways and elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity by repressing cryptic splicing and suggest that targeting hnRNPM in tumors may be used to trigger an inflammatory immune response, thereby boosting cancer surveillance.

Enhancing Thermoelectric Performance in P-Type Sb2Te3-Based Compounds Through Nb─Ag Co-Doping with Donor-Like Effect.

P-type Sb2Te3 has been recognized as a potential thermoelectric material for applications in low-medium temperature ranges. However, its inherent high carrier concentration and lattice thermal conductivity led to a relatively low ZT value, particularly around room temperature. This study addresses these limitations by leveraging high-energy ball milling and rapid hot-pressing techniques to substantially enhance the Seebeck coefficient and power factor of Sb2Te3, yielding a remarkable ZT value of 0.55 at 323 K due to the donor-like effect. Furthermore, the incorporation of Nb─Ag co-doping increases hole concentration, effectively suppressing intrinsic excitations ≈548 K while maintaining the favorable power factor. Simultaneously, the lattice thermal conductivity can be significantly reduced upon doping. As a result, the ZT values of Sb2Te3-based materials attain an impressive range of 0.5-0.6 at 323 K, representing an almost 100% improvement compared to previous research endeavors. Finally, the ZT value of Sb1.97Nb0.03Ag0.005Te3 escalates to 0.92 at 548 K with a record average ZT value (ZTavg) of 0.75 within the temperature range of 323-573 K. These achievements hold promising implications for advancing the viability of V-VI commercialized materials for low-medium temperature application.

The Remarkable Role of Indium in Synergistically Optimizing Carrier Concentration and Phase Distribution of AgCuTe-Based Materials.

Carrier regulation has proven to be an effective approach for optimizing the thermoelectric performance of materials. One common method to adjust the carrier concentration is through element doping. In the case of AgCuTe-based materials, it tends to form with cation vacancies, resulting in a high hole concentration and complex phase composition at low temperatures, which also hinders material stability. However, this also offers additional opportunities to manipulate the carrier concentration. In this study, the improved performance of AgCuTe through indium doping is reported, which leads to a reduction in hole concentration. In combination with a significant increase in the effective mass of the carriers, the enhanced Seebeck coefficient is also realized. Particularly, a notable improvement in power factor is observed in the hexagonal phase near room temperature. Furthermore, a lower electron thermal conductivity is achieved, contributing to an average figure of merit value of ≈1.21 (between 523 and 723 K). Additionally, the presence of indium inhibits the formation of the second phase and ensures a homogeneous phase distribution, which reduces the instability arising from phase transition. This work significantly enhances the potential of AgCuTe-based materials for low to medium-temperature applications.

A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear.

MOTIVATION: DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. METHODS: This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. RESULTS: A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.

A combinatorially regulated RNA splicing signature predicts breast cancer EMT states and patient survival.

During breast cancer metastasis, the developmental process epithelial-mesenchymal transition (EMT) is abnormally activated. Transcriptional regulatory networks controlling EMT are well-studied; however, alternative RNA splicing also plays a critical regulatory role during this process. A comprehensive understanding of alternative splicing (AS) and the RNA binding proteins (RBPs) that regulate it during EMT and their impact on breast cancer remains largely unknown. In this study, we annotated AS in the breast cancer TCGA data set and identified an AS signature that is capable of distinguishing epithelial and mesenchymal states of the tumors. This AS signature contains 25 AS events, among which nine showed increased exon inclusion and 16 showed exon skipping during EMT. This AS signature accurately assigns the EMT status of cells in the CCLE data set and robustly predicts patient survival. We further developed an effective computational method using bipartite networks to identify RBP-AS networks during EMT. This network analysis revealed the complexity of RBP regulation and nominated previously unknown RBPs that regulate EMT-associated AS events. This study highlights the importance of global AS regulation during EMT in cancer progression and paves the way for further investigation into RNA regulation in EMT and metastasis.

Regulation of Alternative Splicing during Epithelial-Mesenchymal Transition.

Alternative splicing is an essential mechanism of gene regulation, giving rise to remarkable protein diversity in higher eukaryotes. Epithelial-mesenchymal transition (EMT) is a developmental process that plays an essential role in metazoan embryogenesis. Recent studies have revealed that alternative splicing serves as a fundamental layer of regulation that governs cells to undergo EMT. In this review, we summarize recent findings on the functional impact of alternative splicing in EMT and EMT-associated activities. We then discuss the regulatory mechanisms that control alternative splicing changes during EMT.

Robotic-assisted total knee arthroplasty is more advantageous for knees with severe deformity: a randomized controlled trial study design.

OBJECTIVE: A prospective, multicenter, randomized controlled trial was conducted to explore the short-term effect of a new robotic-assisted total knee arthroplasty (TKA) system, and the clinical and radiographic effectiveness between the robotic-assisted system and conventional TKA were compared and analyzed. MATERIALS AND METHODS: Overall, 144 patients were randomly divided into two groups, wherein 72 patients underwent TKA using the robotic­assisted system and 72 underwent conventional TKA. The demographic data and radiographic parameters of the patients were collected. The factors influencing postoperative hip-knee-ankle (HKA) angle deviation were determined by multiple linear regression. Clinical outcomes including postoperative Knee Society score, 10-cm visual analog scale, and range of motion (ROM) and radiographic results including the deviation value of coronal tibial component angle, coronal femoral component angle (CFCA), sagittal tibial component angle, sagittal femoral component angle (SFCA), and HKA angle as well as the rate of outliers in each angle were observed and compared between the two groups. RESULTS: The preoperative demographic data and imaging parameters, including Knee Society score, ROM, sex, surgical side, age, BMI, preoperative HKA angle, preoperative HKA angle deviation, and visual analog scale, showed no significant differences between groups. The robotic­assisted system group (RAS group) showed a postoperative malalignment of 3.2% for a mechanical axis higher than 3° and the conventional techniques group (CON group) showed a postoperative malalignment of 41.0% for a mechanical axis higher than 3°; the difference was statistically significant ( P <0.001). According to the results of multiple linear regression analysis, when the preoperative HKA angle deviation increased by 1°, the postoperative HKA angle deviation increased by 0.134° ( ß =0.134 min; 95% CI: 0.045-0.222). Therefore, patients were divided into a slight lower extremity alignment deviation group (preoperative HKA angle deviation <6°) and severe lower extremity alignment deviation group (preoperative HKA angle deviation ≥6°). For the patients with preoperatively slight lower extremity alignment deviation, the rate of postoperative HKA angle outlier in the RAS group was better than that in the CON group, and the operation duration in the RAS group was significantly longer than that in the CON group ( P <0.05). In the patients with a preoperative HKA angle deviation ≥6°, the rate of postoperative HKA angle and CFCA outliers in the RAS group was better than that in the CON group; the operation duration in the RAS group was significantly longer than that in the CON group, and the HKA angle deviation and CFCA deviation in the RAS group were significantly lower than those in the CON group ( P <0.05). No significant difference was observed in other indexes between the two groups ( P >0.05). CONCLUSION: This new robotic-assisted TKA system is safe and effective. The authors found that preoperative HKA angle deviation affects the postoperative HKA angle deviation. The robotic-assisted system has similar results to those reported by the traditional method with regard to restoring the mechanical axis of the leg and improving prosthesis alignment and clinical outcomes in patients with slight lower extremity alignment deviations preoperatively. For patients with severe preoperative lower extremity alignment deviations, the effectiveness in terms of the improvement in mechanical axis of the leg and prosthesis alignment were better with the robotic-assisted system, whereas the effectiveness of clinical outcomes was similar. A larger sample size and longer follow-up period are needed to determine whether the improved mechanical axis of the leg and prosthesis alignment observed with the robotic-assisted system can achieve better long-term radiographic and clinical outcomes.

LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity.

RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.

Efficient recycling of silicon cutting waste by AlSi alloying with the assistance of cryolite.

Silicon cutting waste (SCW) generated during Si wafers producing process can be recycled by AlSi alloying process. However, the presence of O in SCW has a detrimental impact on recycling process. In this study, cryolite was introduced to eliminate the hindrance of O. The influences of smelting temperature and the amount of cryolite additive on the yield of the blocky AlSi alloys and the Si recovery ratio of the SCW have been investigated and the alloying conditions were optimized to a smelting temperature of 1000 °C and a cryolite/SCW mass ratio of 0.8, achieving a AlSi alloys yield of 95.99% and a Si recovery ratio of 84.77%, which were far greater than those without cryolite additive. The results showed that the addition of cryolite additive can effectively improve the smelting effect and reduce the alloying temperature. Furthermore, the action mechanism of cryolite in Al-SCW system was analyzed, and the results revealed that the molten cryolite can dissolve the generated Al2O3 existing on the surface of AlSi alloy droplets and finally contributes to the aggregation of these droplets. This method has advantages including high Si recovery ratio of SCW, low alloying temperature and simple technological process.

Methods for Characterization of Alternative RNA Splicing.

Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semiquantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We will also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

The RNA-binding protein AKAP8 suppresses tumor metastasis by antagonizing EMT-associated alternative splicing.

Alternative splicing has been shown to causally contribute to the epithelial-mesenchymal transition (EMT) and tumor metastasis. However, the scope of splicing factors that govern alternative splicing in these processes remains largely unexplored. Here we report the identification of A-Kinase Anchor Protein (AKAP8) as a splicing regulatory factor that impedes EMT and breast cancer metastasis. AKAP8 not only is capable of inhibiting splicing activity of the EMT-promoting splicing regulator hnRNPM through protein-protein interaction, it also directly binds to RNA and alters splicing outcomes. Genome-wide analysis shows that AKAP8 promotes an epithelial cell state splicing program. Experimental manipulation of an AKAP8 splicing target CLSTN1 revealed that splice isoform switching of CLSTN1 is crucial for EMT. Moreover, AKAP8 expression and the alternative splicing of CLSTN1 predict breast cancer patient survival. Together, our work demonstrates the essentiality of RNA metabolism that impinges on metastatic breast cancer.