MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data.

Microsatellite instability (MSI) is an indispensable biomarker in cancer immunotherapy. Currently, MSI scoring methods by high-throughput omics methods have gained popularity and demonstrated better performance than the gold standard method for MSI detection. However, the MSI detection method on expression data, especially single-cell expression data, is still lacking, limiting the scope of clinical application and prohibiting the investigation of MSI at a single-cell level. Herein, we developed MSIsensor-RNA, an accurate, robust, adaptable, and standalone software to detect MSI status based on expression values of MSI-associated genes. We demonstrated the favorable performance and promise of MSIsensor-RNA in both bulk and single-cell gene expression data in multiplatform technologies including RNA sequencing (RNA-seq), microarray, and single-cell RNA-seq. MSIsensor-RNA is a versatile, efficient, and robust method for MSI status detection from both bulk and single-cell gene expression data in clinical studies and applications. MSIsensor-RNA is available at https://github.com/xjtu-omics/msisensor-rna.

Comparison of short-term clinical efficacy between modified Kamikawa anastomosis and double tract anastomosis after laparoscopic proximal gastrectomy.

Objective: This study aimed to explore the short-term clinical efficacy of modified Kamikawa anastomosis and double tract anastomosis after laparoscopic proximal gastrectomy. Methods: A retrospective analysis was carried out by collecting the clinical and pathological data of 42 patients who underwent laparoscopic proximal gastrectomy after admission in our centre from May 2020 to October 2022. Among the 42 enrolled patients, 22 underwent modified Kamikawa anastomosis (modified Kamikawa group), and the other 20 underwent double tract anastomosis (double tract group). Outcome measures included intraoperative condition, postoperative recovery, postoperative quality of life, postoperative nutritional status and gastroesophageal reflux. The patients were followed up using outpatient examination and telephone interviews to identify their nutritional status, reflux esophagitis and anastomotic status. Results: (1) Intraoperative condition: Compared with the double tract group, the modified Kamikawa group had significantly prolonged time for operation and digestive tract reconstruction. However, no statistically significant difference in intraoperative blood loss was found between the two groups. (2) Postoperative recovery: Compared with the double tract group, the modified Kamikawa group had a significantly shorter time for the first postoperative intake of fluids, drainage tube placement and postoperative hospital stay. No statistically significant difference in the time to first postoperative anal exhaust and postoperative complications was found between the two groups. (3) Postoperative quality of life: Compared with the double tract group, the modified Kamikawa group showed better quality of life at 12 months after surgery. (4) Postoperative nutritional status and gastroesophageal reflux: No statistically significant difference in hemoglobin, total serum albumin, albumin, body mass index, MUST score, PG-SGA score, grading of reflux esophagitis using the Los Angeles classification system and GERD score was found between the two groups at 6 and 12 months after surgery. All patients did not experience anastomotic stenosis and tumour recurrence or metastasis. Conclusions: Modified Kamikawa anastomosis is a safe and feasible treatment in laparoscopic proximal gastrectomy, which can ensure good postoperative anti-reflux effect and nutritional status. It has the advantage of better postoperative recorvery and quality of life compared with double tract anastomosis.

Microchip Based Isolation and Drug Delivery of Patient-Derived Extracellular Vesicles Against Their Homologous Tumor.

Extracellular vesicles (EVs) have demonstrated significant potential in drug delivery and anti-tumor therapy. Despite this promising strategy, challenges such as specific targeting, EVs purification persist. In this study, a personalized nanodrug delivery platform using patient-derived tumor EVs (PT-EVs) based on a microchip is presented. The microchip integrates multiple functions, including capture, enrichment, drug loading, and elution of PT-EVs. The isolation and drug-carrying procedures are completed within a 12 h timeframe, achieving a recovery rate of 65%, significantly surpassing the conventional ultracentrifuge (UC) method. Furthermore, PT-EVs derived from patient tumor models are first utilized as natural drug carriers, capitalizing on their inherent homing ability to precisely target homologous tumors. Lenvatinib and doxorubicin (DOX), two commonly utilized drugs in the clinical treatment of hepatocellular carcinoma (HCC), are loaded into PT-EVs and delivered to a matched in vitro tumor model that recapitulates original tumors for drug susceptibility testing. As is proven, PT-EVs exhibit robust tumor cell targeting and efficient receptor-mediated cellular uptake, and the efficacy of chemotherapeutic drugs is improved significantly. These results suggest that this platform could be a valuable tool for efficient isolation of PT-EVs and personalized drug customization, particularly when working with limited clinical samples, thus supporting personalized and precision medicine.

E3 ubiquitin ligase BTBD3 inhibits tumorigenesis of colorectal cancer by regulating the TYRO3/Wnt/ß-catenin signaling axis.

Clinical trials and studies have implicated that E3 ubiquitin ligase BTBD3 (BTB Domain Containing 3) is a cancer-associated gene. However, the role and underlying mechanism of BTBD3 in colorectal cancer (CRC) is not fully understood yet. Herein, our study demonstrated that the mRNA and protein levels of BTBD3 were decreased in CRC tissues and associated with TYPO3 and Wnt/ß-catenin pathway. Our results showed that circRAE1 knockdown and TYRO3 overexpression activated Wnt/ß-catenin signaling pathway and the EMT process-associated markers, indicating that circRAE1/miR-388-3p/TYRO3 axis exacerbated tumorigenesis of CRC by activating Wnt/ß-catenin signaling pathway. In addition, overexpression of BTBD3 reduced CRC cell migration and invasion in vitro and inhibited tumor growth in vivo. Our data demonstrated that BTBD3 suppressed CRC progression through negative regulation of the circRAE1/miR-388-3p/TYRO3 axis and the Wnt/ß-catenin pathway. Our data further confirmed that BTBD3 bound and ubiquitinated ß-catenin and led to ß-catenin degradation, therefore blocked the Wnt/ß-catenin pathway and suppressed the CRC tumorigenesis. This study explored the mechanism of BTBD3 involved in CRC tumorigenesis and provided a new theoretical basis for the prevention and treatment of CRC.

Engineered Enucleated Mesenchymal Stem Cells Regulating Immune Microenvironment and Promoting Wound Healing.

Persistent excessive inflammation caused by neutrophil and macrophage dysfunction in the wound bed leads to refractory response during wound healing. However, previous studies using cytokines or drugs often suffer from short half-lives and limited targeting, resulting in unsatisfactory therapeutic effects. Herein, the enucleated mesenchymal stem cell is engineered by aptamer bioorthogonal chemistry to modify the cell membrane and mRNA loading in the cell cytoplasm as a novel delivery vector (Cargocyte) with accurate targeting and sustained cytokine secretion. Cargocytes can successfully reduce NETosis by targeting the nuclear chromatin protein DEK protein with aptamers and sustaining interleukin (IL)-4 expression to overcome the challenges associated with the high cost and short half-life of IL-4 protein and significantly prevent the transition of macrophages into the M1 phenotype. Therapeutic effects have been demonstrated in murine and porcine wound models and have powerful potential to improve wound immune microenvironments effectively. Overall, the use of engineered enucleated mesenchymal stem cells as a delivery system may be a promising approach for wound healing.

A highly pyrrolic-N doped carbon modified SiOx anode for superior lithium storage.

The poor interfacial stability and undesirable cycling performance caused by their dramatic volume change hinder the large-scale commercial application of SiOx materials for high-energy-density lithium-ion batteries. Herein, a simple two-step carbonization process is employed to prepare highly pyrrolic-nitrogen-doped carbon modified SiOx anode materials (SiOx@NC). The designed SiOx@NC materials exhibit high electron conductivity and favorable electrochemical kinetics. As expected, the SiOx@NC electrode delivers a high specific capacity of 1003.46 mA h g-1 after 200 cycles at 500 mA g-1. The NCM622||SiOx@NC full cell also demonstrates excellent cycling stability and rate performance.

Fusobacterium Nucleatum Promotes Microsatellite Instability in Colorectal Carcinoma Through Up-regulation of miRNA-155-5p-Targeted Inhibition of MSH6 via the TLR4/NF-κB Signaling Pathway.

Fusobacterium nucleatum (Fn) is significantly associated with poor prognosis in colorectal carcinoma (CRC), however, mechanisms of Fn in DNA mismatch repair (MMR) and microsatellite instability (MSI) in CRC have not been fully elucidated. Clinical samples are collected to analyze the relationship between Fn abundance and microsatellite stability. Tumor cells are treated with Fn to detect the expression of proteins related to toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (Myd88), mutS homolog 6 (MSH6), and nuclear factor-κB (NF-κB) signaling pathways, respectively. Combined with the prediction results from TargetScan, the regulatory role of microRNA upstream of MSH6 is demonstrated. The effect of this regulatory axis on CRC development is demonstrated using a nude mouse tumor model. Compared with microsatellite stability (MSS)-type CRC patients, MSI-type showed higher Fn abundance. Fn treatment of CRC cells activated TLR4/Myd88/NF-κB signaling pathway, transcriptionally activating miRNA-155-5p expression, thereby negatively regulating MSH6. Fn treatment accelerated the malignant progression of CRC in mice, and this process is inhibited by miRNA-155-5p antagomir. Fn in CRC upregulated miRNA-155-5p by activating TLR4/NF-κB signaling to inhibit MSH6, and this regulatory pathway may affect MSS of cancer cells.

Enhancing lymph node metastasis prediction in adenocarcinoma of the esophagogastric junction: A study combining radiomic with clinical features.

BACKGROUND: The incidence of adenocarcinoma of the esophagogastric junction (AEJ) is increasing, and with poor prognosis. Lymph node status (LNs) is particularly important for planning treatment and evaluating the prognosis of patients with AEJ. However, the use of radiomic based on enhanced computed tomography (CT) to predict the preoperative lymph node metastasis (PLNM) status of the AEJ has yet to be reported. PURPOSE: We sought to investigate the value of radiomic features based on enhanced CT in the accurate prediction of PLNM in patients with AEJ. METHODS: Clinical features and enhanced CT data of 235 patients with AEJ from October 2017 to May 2023 were retrospectively analyzed. The data were randomly assigned to the training cohort (n = 164) or the external testing cohort (n = 71) at a ratio of 7:3. A CT-report model, clinical model, radiomic model, and radiomic-clinical combined model were developed to predict PLNM in patients with AEJ. Univariate and multivariate logistic regression were used to screen for independent clinical risk factors. Least absolute shrinkage and selection operator (LASSO) regression was used to select the radiomic features. Finally, a nomogram for the preoperative prediction of PLNM in AEJ was constructed by combining Radiomics-score and clinical risk factors. The models were evaluated by area under the receiver operating characteristic curve (AUC-ROC), calibration curve, and decision curve analyses. RESULTS: A total of 181 patients (181/235, 77.02%) had LNM. In the testing cohort, the AUC of the radiomic-clinical model was 0.863 [95% confidence interval (CI) = 0.738-0.957], and the radiomic model (0.816; 95% CI = 0.681-0.929), clinical model (0.792; 95% CI = 0.677-0.888), and CT-report model (0.755; 95% CI = 0.647-0.840). CONCLUSION: The radiomic-clinical model is a feasible method for predicting PLNM in patients with AEJ, helping to guide clinical decision-making and personalized treatment planning.

Risk factors for the prognosis of colon cancer.

A study on clinical outcomes and prognostic factors in T4N0M0 colon cancer patients after R0 resection revealed that ileostomy, T stage, right hemicolectomy, irregular follow-up, and CA199 level were independent risk factors affecting overall survival. T4-stage cancer invades the entire thickness of the intestinal tract, increasing the difficulty of treatment and the risk of recurrence, and requires a combination of chemotherapy, immunotherapy, and targeted therapy to control the spread of cancer cells. The prognosis of right hemicolectomy is significantly worse than that of left hemicolectomy, and right hemicolectomy is an independent risk factor for a poor prognosis. Advanced age, histopathological type, and lymph node metastasis are also risk factors for colon cancer.

Dual Hole Transport Layers Heterojunction and Band Alignment Engineered Mo:BiVO4 Photoanodes for Efficient Water Splitting.

BiVO4-based photoanode is one of the most promising photoanodes for photoelectrocatalytic water splitting. However, the serious problem of interface charge recombination limits its further development. Here, a Mo:BiVO4/NiOx/CPF-TCzB/NiCoBi photoanode is constructed with double hole transport layer and an energy level gradient to achieve an effective photo-generated holes extraction and accumulation at the surface electrocatalyst. The conjugated polycarbazole framework CPF-TCzB is used as hole transport layer to eliminate the charge recombination center between Mo:BiVO4 and NiCoBi electrocatalyst and realize the extraction and storage of photo-generated hole; NiOx nanoparticles are further inserted between Mo:BiVO4 and CPF-TCzB to form a gradient energy level, eliminating the energy level barrier and optimizing band alignment. As a result, Mo:BiVO4/NiOx/CPF-TCzB/NiCoBi achieves a much higher photocurrent densities of 3.14 mA cm-2 than that of Mo:BiVO4 (0.42 mA cm-2) at 0.6 V versus RHE. This work provides an specific way to adjust the band structure of BiVO4-based photoanodes and realize efficient hole extraction and storage for PEC water splitting.

The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.

Understanding the roles played by centromeres in chromosome evolution and speciation is complicated by the fact that centromeres comprise large arrays of tandemly repeated satellite DNA, which hinders high-quality assembly. Here, we used long-read sequencing to generate nearly complete genome assemblies for four karyotypically diverse Papaver species, P. setigerum (2n = 44), P. somniferum (2n = 22), P. rhoeas (2n = 14), and P. bracteatum (2n = 14), collectively representing 45 gapless centromeres. We identified four centromere satellite (cenSat) families and experimentally validated two representatives. For the two allopolyploid genomes (P. somniferum and P. setigerum), we characterized the subgenomic distribution of each satellite and identified a "homogenizing" phase of centromere evolution in the aftermath of hybridization. An interspecies comparison of the peri-centromeric regions further revealed extensive centromere-mediated chromosome rearrangements. Taking these results together, we propose a model for studying cenSat competition after hybridization and shed further light on the complex role of the centromere in speciation.

Preliminary study of indocyanine green-guided laparoscopic lateral lymph node dissection for rectal cancer.

BACKGROUND: LLNM can occur in mid-low rectal cancer, but LLND in patients with rectal cancer presents certain challenges. Recent years have seen the progressive application of ICG fluorescence imaging technology in colorectal surgery. This study aimed to explore the effectiveness of ICG-guided laparoscopic LLND for rectal cancer. METHODS: We applied ICG-guided laparoscopic lateral lymph node dissection in 11 patients diagnosed as rectal cancer with lateral lymph node metastasis. RESULTS: All 11 patients in this group successfully completed ICG-guided laparoscopic LLND for rectal cancer with good lateral lymph node imaging. CONCLUSIONS: ICG-guided laparoscopic LLND for rectal cancer is safe and represents a feasible solution, thereby providing valuable guidance for intraoperative lymph node dissection.

Comparison of clinical efficacy between modified Kamikawa anastomosis in laparoscopic proximal gastrectomy and Roux-en-Y anastomosis in laparoscopic total gastrectomy.

To investigate the short-term clinical efficacy of laparoscopic proximal gastrectomy with modified Kamikawa anastomosis and laparoscopic total gastrectomy with Roux-en-Y anastomosis. Retrospective cohort study was conducted. The clinicopathological data of 268 patients who underwent laparoscopic proximal gastrectomy for adenocarcinoma of esophagogastric junction and upper gastric adenocarcinoma from January 2016 to October 2022 were collected. Among 268 patients, 26 underwent laparoscopic proximal gastrectomy with modified Kamikawa anastomosis were assigned to Kamikawa group and 242 underwent laparoscopic total gastrectomy with Roux-en-Y anastomosis were assigned to Roux-en-Y group. The sex, age, BMI, preoperative albumin, maximum tumor diameter, histological grade, and pathological stage of patients in the Kamikawa group and the Roux-en-Y group were subjected to 1:1 propensity score matching. After matching, 16 patients in Kamikawa group and Roux-en-Y group were respectively included in this study. Outcome measures: (1) Intraoperative condition. (2) Postoperative recovery. (3) Follow-up information. The patients' nutritional status, reflux esophagitis and anastomotic stoma were investigated by outpatient and telephone follow-up. Nutritional status assessment comprising body mass index and Nutritional Risk Screening 2002 score. (1) Intraoperative condition. All patients successfully underwent laparoscopic proximal gastrectomy and total gastrectomy. Compared with Roux-en-Y group, the digestive tract reconstruction time in Kamikawa group was longer 93.0(74.0-111.0)min vs. 39.7(35.1-46.2)min, t = -2.001, P = 0.055., and the difference was statistically significant (P < 0.05). There was no statistically significant difference in total operation time and intraoperative blood loss (P > 0.05). (2) Postoperative recovery. There was no statistically significant difference between Kamikawa group and Roux-en-Y group in first anal exhaust time, first postoperative liquid intake time, postoperative hospitalization time, and postoperative complications (P > 0.05). (3) Follow-up information. All patients were followed up. BMI and NRS 2002 scores in Kamikawa group were better than those in Roux-en-Y group at 6 and 12 months after surgery 22.9 ± 3.0 kg/m2 vs. 20.8 ± 2.2 kg/m2, t = 2.165, P = 0.038; 23.1 ± 3.0 kg/m2 vs. 20.3 ± 2.2 kg/m2, t = 3.022, P = 0.005 and 2 (1-2) vs. 2 (1-3), Z = -2.585, P = 0.010; 2 (1-2) vs. 2 (1-3), Z = -2.273, P = 0.023., the difference was statistically significant (P < 0.05). There was no significant difference in GERD scale score and occurrence of ≥ Grade B reflux esophagitis at 6 and 12 months after surgery between Kamikawa group and Roux-en-Y group (P > 0.05). Anastomotic stenosis was not found in all patients by postoperative upper gastrointestinal angiography. Laparoscopic proximal gastrectomy with modified Kamikawa anastomosis is safe and feasible for the treatment of esophagogastric junction and upper gastric adenocarcinoma, and can achieve good anti-reflux effect. Besides, compared with traditional laparoscopic total gastrectomy, its postoperative nutritional status is better.

Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach.

Tandem duplication (TD) is a major type of structural variations (SVs) that plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational signals. Herein, we developed a TD detection module for the Pindel tool, referred to as Pindel-TD, based on a TD-specific pattern growth approach. Pindel-TD is capable of detecting TDs with a wide size range at single nucleotide resolution. Using simulated and real read data from HG002, we demonstrated that Pindel-TD outperforms other leading methods in terms of precision, recall, F1-score, and robustness. Furthermore, by applying Pindel-TD to data generated from the K562 cancer cell line, we identified a TD located at the seventh exon of SAGE1, providing an explanation for its high expression. Pindel-TD is available for non-commercial use at https://github.com/xjtu-omics/pindel.

Analysis of the safety and efficacy of the self-pulling and latter transected technique in modified overlap anastomosis in total laparoscopic total gastrectomy.

Background: Laparoscopic total gastrectomy plus lymph node dissection is an effective treatment method for patients with gastric cancer. With the development and popularization of laparoscopic techniques in recent years, surgeons have become more skilled in laparoscopic techniques. Totally laparoscopic total gastrectomy (TLTG) has been developed; however, digestive tract reconstruction remains difficult, especially with anastomosis of the esophagus and jejunum. Using the self-pulling and latter transection (SPLT) method combined with a linear stapler has effectively solved the problem of narrow space in esophagojejunostomy. Here, we examined the safety and effectiveness of the SPLT technique in TLTG compared with SPLT with traditional esophagojejunostomy overlap anastomosis. Methods: We retrospectively analyzed all patients with gastric cancer admitted to the Department of Gastrointestinal Surgery of the Second Affiliated Hospital of Fujian Medical University from September 2020 to September 2023. In total, 158 patients met the inclusion criteria and were included. Patients were grouped according to whether the lower esophagus was transected after self-pulling. Patient demographics, tumor characteristics, surgical conditions, and postoperative results between the two groups were statistically analyzed. Results: A total of 158 patients were included in the study. All patients underwent TLTG and completed intracavitary anastomosis. There were 70 cases (44%) in the SPLT-Overlap group and 88 cases (56%) in the traditional overlap group. There was no significant difference in demographic and oncological characteristics between the two groups. The operation time (P = 0.002) and esophageal jejunum anastomosis time (P<0.001) were significantly shorter in the SPLT-Overlap group compared with the traditional overlap group. The intraoperative blood loss of the SPLT-Overlap group was 80.29 ± 36.36 ml, and the intraoperative blood loss of the traditional overlap group was 101.40 ± 46.68 ml. The difference was statistically significant (P=0.003). The SPLT-Overlap group also achieved a higher upper cutting edge (P =0.03). There was no significant difference between the two groups in terms of the incision size, postoperative hospital stay, time to first flatus, time to first liquid intake, drainage tube removal time, and esophagojejunal anastomotic diameter. There were 15 and 19 cases of short-term postoperative complications in the SPLT-Overlap and traditional Overlap groups, respectively. All patients received R0 resection, and no secondary surgery or death occurred. Conclusion: We applied SPLT to overlap anastomosis. Short-term, SPLT has good safety and feasibility in TLTG. It can effectively shorten the time of digestive tract reconstruction, simplify the reconstruction procedure, and make the digestive tract reconstruction simple and fast; at the same time, a safe cutting edge can be obtained.

Oncoprotein LAMTOR5-mediated CHOP silence via DNA hypermethylation and miR-182/miR-769 in promotion of liver cancer growth.

C/EBP homologous protein (CHOP) triggers the death of multiple cancers via endoplasmic reticulum (ER) stress. However, the function and regulatory mechanism of CHOP in liver cancer remain elusive. We have reported that late endosomal/lysosomal adapter, mitogen-activated protein kinase and mTOR activator 5 (LAMTOR5) suppresses apoptosis in various cancers. Here, we show that the transcriptional and posttranscriptional inactivation of CHOP mediated by LAMTOR5 accelerates liver cancer growth. Clinical bioinformatic analysis revealed that the expression of CHOP was low in liver cancer tissues and that its increased expression predicted a good prognosis. Elevated CHOP contributed to destruction of LAMTOR5-induced apoptotic suppression and proliferation. Mechanistically, LAMTOR5-recruited DNA methyltransferase 1 (DNMT1) to the CpG3 region (-559/-429) of the CHOP promoter and potentiated its hypermethylation to block its interaction with general transcription factor IIi (TFII-I), resulting in its inactivation. Moreover, LAMTOR5-enhanced miR-182/miR-769 reduced CHOP expression by targeting its 3'UTR. Notably, lenvatinib, a first-line targeted therapy for liver cancer, could target the LAMTOR5/CHOP axis to prevent liver cancer progression. Accordingly, LAMTOR5-mediated silencing of CHOP via the regulation of ER stress-related apoptosis promotes liver cancer growth, providing a theoretical basis for the use of lenvatinib for the treatment of liver cancer.

Modulating built-in electric field via Bi-VO4-Fe interfacial bridges to enhance charge separation for efficient photoelectrochemical water splitting.

Photoelectrochemical (PEC) water splitting on semiconductor electrodes is considered to be one of the important ways to produce clean and sustainable hydrogen fuel, which is a great help in solving energy and environmental problems. Bismuth vanadate (BiVO4) as a promising photoanode for photoelectrochemical water splitting still suffers from poor charge separation efficiency and photo-induced self-corrosion. Herein, we develop heterojunction-rich photoanodes composed of BiVO4 and iron vanadate (FeVO4), coated with nickel iron oxide (NiFeOx/FeVO4/BiVO4). The formation of the interface between BiVO4 and FeVO4 (Bi-VO4-Fe bridges) enhances the interfacial interaction, resulting in improved performance. Meanwhile, high-conductivity FeVO4 and NiFeOx oxygen evolution co-catalysts effectively enhance bulk electron/hole separation, interface water's kinetics and photostability. Concurrently, the optimized NiFeOx/FeVO4/BiVO4 possesses a remarkable photocurrent density of 5.59 mA/cm2 at 1.23 V versus reversible hydrogen electrode (vs RHE) under AM 1.5G (Air Mass 1.5 Global) simulated sunlight, accompanied by superior stability without any decreased of its photocurrent density after 14 h. This work not only reveals the crucial role of built-in electric field in BiVO4-based photoanode during PEC water splitting, but also provides a new guide to the design of efficient photoanode for PEC.

NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads.

The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here, we describe an upgraded genome polishing tool - NextPolish2, which can fix base errors remaining in those "highly accurate" genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors. We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere (T2T) genomes. NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.

Dual-Recognition-Mediated Autocatalytic Amplification Assay for the Subpopulations of PD-L1 Positive Extracellular Vesicle.

The PD-L1 protein on extracellular vesicles (EVs) is a promising biomarker for tumor immunotherapy. However, PD-L1+ EVs have various cell origins, so further analysis of the subpopulations is essential to help understand better their relationship with tumor immunotherapy. Different from the previous work which focus on the level of total PD-L1+ EVs expression, we, herein, report a dual-recognition mediated autocatalytic amplification (DRMAA) assay to detect the PD-L1 derived from tumors (EpCAM+), immune T cells (CD3+), and total (Lipids) EVs, respectively. The DRMAA assay employed proximity hybridization to construct a complete trigger sequence and then catalyzed the cross-hybridization of three hairpin probes, producing a three-way DNA junction (3-WJ) structure carrying the newly exposed trigger sequence. The 3-WJ complex subsequently initiated an autocatalytic amplification reaction and higher sensitivity than the traditional catalytic hairpin assembly assay was obtained. It was found that the EpCAM+ and PD-L1+ EVs were more effective than others in distinguishing lung cancer patients from healthy people. Surprisingly, the CD3+ and PD-L1+ EVs in lung cancer patients were also upregulated, indicating that immune cell-derived PD-L1+ EVs are also non-negligible marker in a tumor microenvironment. Our results suggested that the DRMAA assay would improve the study of subpopulations of PD-L1+ EVs to provide new insights for cancer immunotherapies.

Scalable Synthesis of SiOx-TiON Composite As an Ultrastable Anode for Li-Ion Half/Full Batteries.

Among various anode materials, SiOx is regarded as the next generation of promising anode due to its advantages of high theoretical capacity with 2680 mA h g-1, low lithium voltage platform, and rich natural resources. However, the pure SiOx-based materials have slow lithium storage kinetics attributed to their low electron/ion conductive properties and the large volume change during lithiation/delithiation, restricting their practical application. Optimizing the SiOx material structures and the fabricating methods to mitigate these fatal defects and adapt to the market demand for energy density is critical. Hence, SiOx material with TiO1-xNx phase modification has been prepared by simple, low-cost, and scalable ball milling and then combined with nitridation. Consequently, based on the TiO1-xNx modified layer, which boosts high ionic/electronic conductivity, chemical stability, and excellent mechanical properties, the SiOx@TON-10 electrode shows highly stable lithium-ion storage performance for lithium-ion half/full batteries due to a stable solid-electrolyte interface layer, fast Li+ transport channel, and alleviative volumetric expansion, further verifying its practical feasibility and universal applicability.