MET fusions and splicing variants is a strong adverse prognostic factor in astrocytoma, isocitrate dehydrogenase mutant

Liu et al. describe the adverse prognostic role of MET fusions and splicing variants in astrocytoma, isocitrate dehydrogenase mutant. On this basis, MET fusions and splicing variants was suggested to be a biomarker for the diagnosis of high-grade astrocytoma, isocitrate dehydrogenase mutant.

Efficacy of far infrared functional glasses in the treatment of meibomian gland dysfunction-related dry eye

Meibomian gland dysfunction (MGD)-related dry eye disease (DED) is a significant subtype of DED. In this research, we investigate the effectiveness of far infrared (FIR) functional glasses in the treatment of MGD-related DED. According to the TFO DEWS II diagnostic criteria, 61 eyes with MGD-related DED were included. All participants wore functional FIR glasses throughout the day for a period of 4 weeks and were followed up three times during the treatment. All subjects were followed up thoroughly in accordance with the DED clinical examination procedure. Ultimately, the treatment's impact was assessed. We found the Visual Analogue Scale and Ocular Surface Disease Index scores after FIR treatment were significantly lower than the baseline values (p < 0.05). Compared with the baseline, fluorescein tear breakup time and corneal fluorescein staining score after FIR treatment were significantly improved (p < 0.05). The eyelid margin signs, meibum quality, and meibomian gland expressibility after the 4-week treatment were significantly better than those at baseline (p < 0.05). We can see that wearing the FIR functional glasses significantly relieves the symptoms and signs of patients. We believe FIR therapy could be considered as a new method of MGD-related DED.

Multiparametric hippocampal signatures for early diagnosis of Alzheimer's disease using 18F-FDG PET/MRI Radiomics

PURPOSE

This study aimed to explore the utility of hippocampal radiomics using multiparametric simultaneous positron emission tomography (PET)/magnetic resonance imaging (MRI) for early diagnosis of Alzheimer's disease (AD).

METHODS

A total of 53 healthy control (HC) participants, 55 patients with amnestic mild cognitive impairment (aMCI), and 51 patients with AD were included in this study. All participants accepted simultaneous PET/MRI scans, including 18F-fluorodeoxyglucose (18F-FDG) PET, 3D arterial spin labeling (ASL), and high-resolution T1-weighted imaging (3D T1WI). Radiomics features were extracted from the hippocampus region on those three modal images. Logistic regression models were trained to classify AD and HC, AD and aMCI, aMCI and HC respectively. The diagnostic performance and radiomics score (Rad-Score) of logistic regression models were evaluated from 5-fold cross-validation.

RESULTS

The hippocampal radiomics features demonstrated favorable diagnostic performance, with the multimodal classifier outperforming the single-modal classifier in the binary classification of HC, aMCI, and AD. Using the multimodal classifier, we achieved an area under the receiver operating characteristic curve (AUC) of 0.98 and accuracy of 96.7% for classifying AD from HC, and an AUC of 0.86 and accuracy of 80.6% for classifying aMCI from HC. The value of Rad-Score differed significantly between the AD and HC (p < 0.001), aMCI and HC (p < 0.001) groups. Decision curve analysis showed superior clinical benefits of multimodal classifiers compared to neuropsychological tests.

CONCLUSION

Multiparametric hippocampal radiomics using PET/MRI aids in the identification of early AD, and may provide a potential biomarker for clinical applications.

Opportunistic lung cancer screening with low-dose computed tomography in National Cancer Center of China: The first 14 years' experience

BACKGROUND

In China, over 50% of lung cancer cases occur in nonsmokers. Thus, identifying high-risk individuals for targeted lung cancer screening is crucial. Beyond age and smoking, determining other risk factors for lung cancer in the Asian population has become a focal point of research. Using 30,000 participants in the prospectively enrolled cohort at China's National Cancer Center (NCC) over the past 14 years, we categorized participants by risk, with an emphasis on nonsmoking females.

MATERIALS AND METHODS

Between November 2005 and December 2019, 31,431 individuals voluntarily underwent low-dose computed tomography (LDCT) scans for lung cancer screening at the NCC. We recorded details like smoking history, exposure to hazards, and family history of malignant tumors. Using the 2019 NCCN criteria, participants were categorized into high-, moderate-, and low-risk groups. Additionally, we separated non-high-risk groups into female never smokers (aged over 40) exposed to second-hand smoke (SHS) and others. Any positive results from initial scans were monitored per the I-ELCAP protocol (2006), and suspected malignancies were addressed through collaborative decisions between patients and physicians. We analyzed and compared the detection rates of positive results, confirmed lung cancers, and cancer stages across risk, age, and gender groups.

RESULTS

Out of 31,431 participants (55.9% male, 44.1% female), 3695 (11.8%) showed positive baseline LDCT scans with 197 (0.6%; 106 females, 91 males) confirmed as lung cancer cases pathologically. Malignancy rate by age was 0.1% among those aged under 40 years, 0.4% among those aged 40-49 years, 0.8% among those aged 50-59 years, and 1.2% among those aged 60 years and older. From the 25,763 participants (56.9% male, 43.1% female) who completed questionnaires, 1877 (7.3%) were categorized as high risk, 6500 (25.2%) as moderate risk, and 17,386 (67.5%) as low risk. Of the 23,886 in the non-high-risk category, 8041 (33.7%) were females over 40 years old exposed to SHS. The high-risk group showed the highest lung cancer detection rate at 1.4%. However, females exposed to SHS had a notably higher detection rate than the rest of the non-high-risk group (1.1% vs. 0.5%; p < 0.0001). In this cohort, 84.8% of the detected lung cancers were at an early stage.

CONCLUSIONS

In our study, using LDCT for lung cancer screening proved significant for high-risk individuals. For non-high-risk populations, LDCT screening could be considered for nonsmoking women with exposure to SHS.

Adenine base editor-based correction of the cardiac pathogenic Lmna c.1621C > T mutation in murine hearts

Base editors are emerging as powerful tools to correct single-nucleotide variants and treat genetic diseases. In particular, the adenine base editors (ABEs) exhibit robust and accurate adenine-to-guanidine editing capacity and have entered the clinical stage for cardiovascular therapy. Despite the tremendous progress using ABEs to treat heart diseases, a standard technical route toward successful ABE-based therapy remains to be fully established. In this study, we harnessed adeno-associated virus (AAV) and a mouse model carrying the cardiomyopathy-causing Lmna c.1621C > T mutation to demonstrate key steps and concerns in designing a cardiac ABE experiment in vivo. We found DeepABE as a reliable deep-learning-based model to predict ABE editing outcomes in the heart. Screening of sgRNAs for a Cas9 mutant with relieved protospacer adjacent motif (PAM) allowed the reduction of bystander editing. The ABE editing efficiency can be significantly enhanced by modifying the TadA and Cas9 variants, which are core components of ABEs. The ABE systems can be delivered into the heart via either dual AAV or all-in-one AAV vectors. Together, this study showcased crucial technical considerations in designing an ABE system for the heart and pointed out major challenges in further improvement of this new technology for gene therapy.

Is it necessary to perform measurement-based patient-specific quality assurance for online adaptive radiotherapy with Elekta Unity MR-Linac?

This study aimed to investigate the necessity of measurement-based patient-specific quality assurance (PSQA) for online adaptive radiotherapy by analyzing measurement-based PSQA results and calculation-based 3D independent dose verification results with Elekta Unity MR-Linac. There are two workflows for Elekta Unity enabled in the treatment planning system: adapt to position (ATP) and adapt to shape (ATS). ATP plans are those which have relatively slighter shifts from reference plans by adjusting beam shapes or weights, whereas ATS plans are the new plans optimized from the beginning with probable re-contouring targets and organs-at-risk. PSQA gamma passing rates were measured using an MR-compatible ArcCHECK diode array for 78 reference plans and corresponding 208 adaptive plans (129 ATP plans and 79 ATS plans) of Elekta Unity. Subsequently, the relationships between ATP, or ATS plans and reference plans were evaluated separately. The Pearson's r correlation coefficients between ATP or ATS adaptive plans and corresponding reference plans were also characterized using regression analysis. Moreover, the Bland-Altman plot method was used to describe the agreement of PSQA results between ATP or ATS adaptive plans and reference plans. Additionally, Monte Carlo-based independent dose verification software ArcherQA was used to perform secondary dose check for adaptive plans. For ArcCHECK measurements, the average gamma passing rates (ArcCHECK vs. TPS) of PSQA (3%/2 mm criterion) were 99.51% ± 0.88% and 99.43% ± 0.54% for ATP and ATS plans, respectively, which were higher than the corresponding reference plans 99.34% ± 1.04% (p < 0.05) and 99.20% ± 0.71% (p < 0.05), respectively. The Pearson's r correlation coefficients were 0.720 between ATP and reference plans and 0.300 between ATS and reference plans with ArcCHECK, respectively. Furthermore, >95% of data points of differences between both ATP and ATS plans and reference plans were within ±2σ (standard deviation) of the mean difference between adaptive and reference plans with ArcCHECK measurements. With ArcherQA calculation, the average gamma passing rates (ArcherQA vs. TPS) were 98.23% ± 1.64% and 98.15% ± 1.07% for ATP and ATS adaptive plans, separately. It might be unnecessary to perform measurement-based PSQA for both ATP and ATS adaptive plans for Unity if the gamma passing rates of both measurements of corresponding reference plans and independent dose verification of adaptive plans have high gamma passing rates. Periodic machine QA and verification of adaptive plans were recommended to ensure treatment safety.

No-reflow after stroke reperfusion therapy: An emerging phenomenon to be explored

In the field of stroke thrombectomy, ineffective clinical and angiographic reperfusion after successful recanalization has drawn attention. Partial or complete microcirculatory reperfusion failure after the achievement of full patency of a former obstructed large vessel, known as the "no-reflow phenomenon" or "microvascular obstruction," was first reported in the 1960s and was later detected in both experimental models and patients with stroke. The no-reflow phenomenon (NRP) was reported to result from intraluminal occlusions formed by blood components and extraluminal constriction exerted by the surrounding structures of the vessel wall. More recently, an emerging number of clinical studies have estimated the prevalence of the NRP in stroke patients following reperfusion therapy, ranging from 3.3% to 63% depending on its evaluation methods or study population. Studies also demonstrated its detrimental effects on infarction progress and neurological outcomes. In this review, we discuss the research advances, underlying pathogenesis, diagnostic techniques, and management approaches concerning the no-reflow phenomenon in the stroke population to provide a comprehensive understanding of this phenomenon and offer references for future investigations.

Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma

BACKGROUND

Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and lethal hepatobiliary tumor with few therapeutic strategies. The metabolic reprogramming of tumor cells plays an essential role in the development of tumors, while the metabolic molecular classification of iCCA is largely unknown. Here, we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients, hoping to provide a novel perspective to understand and treat iCCA.

METHODS

We performed integrated multiomics analysis in 116 iCCA samples, including whole-exome sequencing, bulk RNA-sequencing and proteome analysis. Based on the non-negative matrix factorization method and the protein abundance of metabolic genes in human genome-scale metabolic models, the metabolic subtype of iCCA was determined. Survival and prognostic gene analyses were used to compare overall survival (OS) differences between metabolic subtypes. Cell proliferation analysis, 5-ethynyl-2'-deoxyuridine (EdU) assay, colony formation assay, RNA-sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinase α (DGKA) in iCCA cells.

RESULTS

Three metabolic subtypes (S1-S3) with subtype-specific biomarkers of iCCA were identified. These metabolic subtypes presented with distinct prognoses, metabolic features, immune microenvironments, and genetic alterations. The S2 subtype with the worst survival showed the activation of some special metabolic processes, immune-suppressed microenvironment and Kirsten rat sarcoma viral oncogene homolog (KRAS)/AT-rich interactive domain 1A (ARID1A) mutations. Among the S2 subtype-specific upregulated proteins, DGKA was further identified as a potential drug target for iCCA, which promoted cell proliferation by enhancing phosphatidic acid (PA) metabolism and activating mitogen-activated protein kinase (MAPK) signaling.

CONCLUSION

Via multiomics analyses, we identified three metabolic subtypes of iCCA, revealing that the S2 subtype exhibited the poorest survival outcomes. We further identified DGKA as a potential target for the S2 subtype.

Whole genome sequencing and annotation of Daedaleopsis sinensis, a wood-decaying fungus significantly degrading lignocellulose

Daedaleopsis sinensis is a fungus that grows on wood and secretes a series of enzymes to degrade cellulose, hemicellulose, and lignin and cause wood rot decay. Wood-decaying fungi have ecological, economic, edible, and medicinal functions. Furthermore, the use of microorganisms to biodegrade lignocellulose has high application value. Genome sequencing has allowed microorganisms to be analyzed from the aspects of genome characteristics, genome function annotation, metabolic pathways, and comparative genomics. Subsequently, the relevant information regarding lignocellulosic degradation has been mined by bioinformatics. Here, we sequenced and analyzed the genome of D. sinensis for the first time. A 51.67-Mb genome sequence was assembled to 24 contigs, which led to the prediction of 12,153 protein-coding genes. Kyoto Encyclopedia of Genes and Genomes database analysis of the D. sinensis data revealed that 3,831 genes are involved in almost 120 metabolic pathways. According to the Carbohydrate-Active Enzyme database, 481 enzymes are found in D. sinensis, of which glycoside hydrolases are the most abundant. The genome sequence of D. sinensis provides insights into its lignocellulosic degradation and subsequent applications.

First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution

Sanghuangporus, also known as "Sanghuang" in China, is a well-known genus of traditional Chinese medicinal macrofungi. To make more effective use of Sanghuangporus resources, we completed the first genome assembly and annotation of a monokaryon strain of S. weigelae in the present study. A 33.96-Mb genome sequence was assembled as 13 contigs, leading to prediction of 9377 protein-coding genes. Phylogenetic and average nucleotide identity analyses indicated that the S. weigelae genome is closely related to those of other Sanghuangporus species in evolutionary tree, which clustered in one clade. Collinearity analysis revealed a high level of collinearity of S. weigelae with S. baumii, S. vaninii, and S. sanghuang. Biosynthesis pathways potentially involved in medicinal properties, including terpenoid and polysaccharide synthesis, were identified in S. weigelae, while polysaccharides were identified as the main medicinal metabolites in S. weigelae, with flavonoids more important in Sanghuangporus than other medicinal mushroom groups. Genes encoding 332 carbohydrate-active enzymes were identified in the S. weigelae genome, including major glycoside hydrolases and glycosyltransferases predicted, revealing the robust lignocellulose degradation capacity of S. weigelae. Further, 130 genes, clustered in seven classes were annotated to encode cytochromes P450 in the S. weigelae genome. Overall, our results reveal the remarkably medicinal capacity of S. weigelae and provide new insights that will inform the study of evolution and medicinal application of S. weigelae. The data are a reference resource for the formulation of scientific and rational ecological protection policies for Sanghuangporus species.

PVT1 promotes proliferation and macrophage immunosuppressive polarization through STAT1 and CX3CL1 regulation in glioblastoma multiforme

AIMS

This study aimed to investigate the role of plasmacytoma variant translocation 1 (PVT1), a long non-coding RNA, in glioblastoma multiforme (GBM) and its impact on the tumor microenvironment (TME).

METHODS

We assessed aberrant PVT1 expression in glioma tissues and its impact on GBM cell growth in vitro and in vivo. Additionally, we investigated PVT1's role in influencing glioma-associated macrophages. To understand PVT1's role in cell growth and the immunosuppressive TME, we performed a series of comprehensive experiments.

RESULTS

PVT1 was overexpressed in GBM due to copy number amplification, correlating with poor prognosis. Elevated PVT1 promoted GBM cell proliferation, while its downregulation inhibited growth in vitro and in vivo. PVT1 inhibited type I interferon-stimulated genes (ISGs), with STAT1 as the central hub. PVT1 correlated with macrophage enrichment and regulated CX3CL1 expression, promoting recruitment and M2 phenotype polarization of macrophages. PVT1 localized to the cell nucleus and bound to DHX9, enriching at the promoter regions of STAT1 and CX3CL1, modulating ISGs and CX3CL1 expression.

CONCLUSION

PVT1 plays a significant role in GBM, correlating with poor prognosis, promoting cell growth, and shaping an immunosuppressive TME via STAT1 and CX3CL1 regulation. Targeting PVT1 may hold therapeutic promise for GBM patients.

Abnormal white matter structural network topological property in patients with temporal lobe epilepsy

BACKGROUND

Diffusion tensor imaging (DTI) studies have demonstrated white matter (WM) abnormalities in patients with temporal lobe epilepsy (TLE). However, alterations in the topological properties of the WM structural network in patients with TLE remain unclear. Graph theoretical analysis provides a new perspective for evaluating the connectivity of WM structural networks.

METHODS

DTI was used to map the structural networks of 18 patients with TLE (10 males and 8 females) and 29 (17 males and 12 females) age- and gender-matched normal controls (NC). Graph theory was used to analyze the whole-brain networks and their topological properties between the two groups. Finally, partial correlation analyses were performed on the weighted network properties and clinical characteristics, namely, duration of epilepsy, verbal intelligence quotient (IQ), and performance IQ.

RESULTS

Patients with TLE exhibited reduced global efficiency and increased characteristic path length. A total of 31 regions with nodal efficiency alterations were detected in the fractional anisotropy_ weighted network of the patients. Communication hubs, such as the middle temporal gyrus, right inferior temporal gyrus, left calcarine, and right superior parietal gyrus, were also differently distributed in the patients compared with the NC. Several node regions showed close relationships with duration of epilepsy, verbal IQ, and performance IQ.

CONCLUSIONS

Our results demonstrate the disruption of the WM structural network in TLE patients. This study may contribute to the further understanding of the pathological mechanism of TLE.

CRISPR/Cas9-based genome editing of 14 lipid metabolic genes reveals a sporopollenin metabolon ZmPKSB-ZmTKPR1-1/-2 required for pollen exine formation in maize

Lipid biosynthesis and transport are essential for plant male reproduction. Compared with Arabidopsis and rice, relatively fewer maize lipid metabolic genic male-sterility (GMS) genes have been identified, and the sporopollenin metabolon in maize anther remains unknown. Here, we identified two maize GMS genes, ZmTKPR1-1 and ZmTKPR1-2, by CRISPR/Cas9 mutagenesis of 14 lipid metabolic genes with anther stage-specific expression patterns. Among them, tkpr1-1/-2 double mutants displayed complete male sterility with delayed tapetum degradation and abortive pollen. ZmTKPR1-1 and ZmTKPR1-2 encode tetraketide α-pyrone reductases and have catalytic activities in reducing tetraketide α-pyrone produced by ZmPKSB (polyketide synthase B). Several conserved catalytic sites (S128/130, Y164/166 and K168/170 in ZmTKPR1-1/-2) are essential for their enzymatic activities. Both ZmTKPR1-1 and ZmTKPR1-2 are directly activated by ZmMYB84, and their encoded proteins are localized in both the endoplasmic reticulum and nuclei. Based on protein structure prediction, molecular docking, site-directed mutagenesis and biochemical assays, the sporopollenin biosynthetic metabolon ZmPKSB-ZmTKPR1-1/-2 was identified to control pollen exine formation in maize anther. Although ZmTKPR1-1/-2 and ZmPKSB formed a protein complex, their mutants showed different, even opposite, defective phenotypes of anther cuticle and pollen exine. Our findings discover new maize GMS genes that can contribute to male-sterility line-assisted maize breeding and also provide new insights into the metabolon-regulated sporopollenin biosynthesis in maize anther.

Protective role of Cecropin AD against LPS-induced intestinal mucosal injury in chickens

Introduction

Cecropin AD (CAD), a renowned antimicrobial peptide, has shown promising potential in treating various bacterial infections. This study investigates the protective effects of CAD against lipopolysaccharide (LPS)-induced intestinal adversities in chickens.

Methods

Sixty SPF-grade chicks were divided into groups and exposed to different dosages of CAD, followed by LPS administration. The study assessed the impact of CAD on intestinal mucosal injury markers, oxidative stress, and inflammation.

Results

LPS significantly increased Diamine oxidase (DAO) and D-lactate (D-LA) levels, both indicators of intestinal mucosal injury. CAD treatment substantially attenuated these elevations, particularly at higher dosages. Additionally, CAD markedly reduced oxidative stress in intestinal tissues, as shown by normalized antioxidant levels and decreased reactive oxygen species. Histological analysis supported these findings, showing better-preserved villi structures in CAD-treated groups. Furthermore, CAD significantly reduced IL-6 and IL-8 expression post-LPS stimulation and effectively regulated the NLRP3 inflammasome pathway, decreasing associated factors like NLRP3, Caspase-1, IL-1b, and IL-18.

Discussion

The study demonstrates CAD's therapeutic potential in alleviating LPS-induced intestinal injuries. The protective effects are primarily attributed to its anti-inflammatory and antioxidative actions and modulation of the NLRP3 inflammasome pathway.

Biomarkers and experimental models for cancer immunology investigation

The rapid advancement of tumor immunotherapies poses challenges for the tools used in cancer immunology research, highlighting the need for highly effective biomarkers and reproducible experimental models. Current immunotherapy biomarkers encompass surface protein markers such as PD-L1, genetic features such as microsatellite instability, tumor-infiltrating lymphocytes, and biomarkers in liquid biopsy such as circulating tumor DNAs. Experimental models, ranging from 3D in vitro cultures (spheroids, submerged models, air-liquid interface models, organ-on-a-chips) to advanced 3D bioprinting techniques, have emerged as valuable platforms for cancer immunology investigations and immunotherapy biomarker research. By preserving native immune components or coculturing with exogenous immune cells, these models replicate the tumor microenvironment in vitro. Animal models like syngeneic models, genetically engineered models, and patient-derived xenografts provide opportunities to study in vivo tumor-immune interactions. Humanized animal models further enable the simulation of the human-specific tumor microenvironment. Here, we provide a comprehensive overview of the advantages, limitations, and prospects of different biomarkers and experimental models, specifically focusing on the role of biomarkers in predicting immunotherapy outcomes and the ability of experimental models to replicate the tumor microenvironment. By integrating cutting-edge biomarkers and experimental models, this review serves as a valuable resource for accessing the forefront of cancer immunology investigation.

Clinically Translatable Solid-State Dye for NIR-II Imaging of Medical Devices

Medical devices are commonly implanted underneath the skin, but how to real-time noninvasively monitor their migration, integrity, and biodegradation in human body is still a formidable challenge. Here, the study demonstrates that benzyl violet 4B (BV-4B), a main component in the FDA-approved surgical suture, is found to produce fluorescence signal in the first near-infrared window (NIR-I, 700-900 nm) in polar solutions, whereas BV-4B self-assembles into highly crystalline aggregates upon a formation of ultrasmall nanodots and can emit strong fluorescence in the second near-infrared window (NIR-II, 1000-1700 nm) with a dramatic bathochromic shift in the absorption spectrum of ≈200 nm. Intriguingly, BV-4B-involved suture knots underneath the skin can be facilely monitored during the whole degradation process in vivo, and the rupture of the customized BV-4B-coated silicone catheter is noninvasively diagnosed by NIR-II imaging. Furthermore, BV-4B suspended in embolization glue achieves hybrid fluorescence-guided surgery (hybrid FGS) for arteriovenous malformation. As a proof-of-concept study, the solid-state BV-4B is successfully used for NIR-II imaging of surgical sutures in operations of patients. Overall, as a clinically translatable solid-state dye, BV-4B can be applied for in vivo monitoring the fate of medical devices by NIR-II imaging.

Engineering high-affinity dual targeting cellular nanovesicles for optimised cancer immunotherapy

Dual targeting to immune checkpoints has achieved a better therapeutic efficacy than single targeting due to synergistic extrication of tumour immunity. However, most dual targeting strategies are usually antibody dependent which facing drawbacks of antibodies, such as poor solid tumour penetration and unsatisfied affinity. To meet the challenges, we engineered a cell membrane displaying a fusion protein composed of SIRPα and PD-1 variants, the high-affinity consensus (HAC) of wild-type molecules, and with which prepared nanovesicles (NVs). Through disabling both SIRPα/CD47 and PD-1/PD-L1 signalling, HAC NVs significantly preserved the phagocytosis and antitumour effect of macrophages and T cells, respectively. In vivo study revealed that HAC NVs had better tumour penetration than monoclonal antibodies and higher binding affinity to CD47 and PD-L1 on tumour cells compared with the NVs expressing wild-type fusion protein. Exhilaratingly, dual-blockade of CD47 and PD-L1 with HAC NVs exhibited excellent therapeutic efficacy and biosafety. This study provided a novel biomaterial against tumoural immune escape and more importantly an attractive biomimetic technology of protein delivery for multi-targeting therapies.

Manganese Mineralization of Pathogenic Viruses as a Universal Vaccine Platform

Biomimetic viral mineralization improves viral vaccine stability and immunogenicity using inorganic metals such as Ca, Al, or Fe. Mn is a metal found in high concentrations in mammalian tissues; however, under natural or laboratory conditions, Mn mineralization by medical viruses has yet to be established. Herein, a single IAV particle is successfully encapsulated with manganese phosphate (MnP) under specific conditions using the human influenza A virus (IAV). MnP-mineralized IAVs (IAV@Mn) exhibited physiochemical and in vitro properties similar to Ca-mineralized IAVs. In animal models, IAV@Mn shows limited replication in immune-competent cells and a significant attenuation compared to naïve cells. Moreover, a single-dose vaccination with IAV@Mn induced robust humoral and cellular immune responses and conferred significant protection against a wild-type IAV challenge in mice. Thus, Mn mineralization in pathogenic viruses provides a rapid and universal strategy for generating an emergency vaccine in response to emerging viruses.

How should extra-large Lugol-unstained lesions of the esophagus be treated? Results from a population-based cohort study

BACKGROUND

Current guidelines recommend only severe dysplasia and above (SDA) lesions of the esophageal squamous epithelium for clinical intervention. However, the histopathologic diagnosis derived from tissue biopsies may be subject to underestimation of severity.

METHODS

1073 participants from whom biopsies were taken at baseline chromoendoscopic examination in a population-based screening trial were enrolled in this study. The size of the Lugol-unstained lesions (LULs) was mainly analyzed. The outcome was defined as SDA lesions either identified at baseline screening, or during follow-up, collectively referred to as the cumulative risk of SDA. Multivariable logistic regression models were used to evaluate the cumulative risk of SDA.

RESULTS

One hundred and forty-six SDA cases were identified in the study period. Participants with large LULs had a high cumulative incidence of SDA (cumulative incidence16-20mm : 55.88%; cumulative incidence>20mm : 76.92%) in the median of 7-year duration. LULs of large size were significantly associated with a higher cumulative risk of SDA, regardless of the pathologic diagnosis (adjusted OR16-20mmvs.≤5mm  = 21.02, 95% CI: 7.56-58.47; adjusted OR>20mmvs.≤5mm  = 33.62, 95% CI: 11.79-95.87).

CONCLUSIONS

Results from this study suggest physician-patient shared decision-making regarding clinical treatment or intensive surveillance should be carried out for LULs >20 mm in the esophagus, regardless of the histologic diagnosis. For those with LULs of 16-20 mm, intensive surveillance would also best be considered.

Vacancy Augmented Piezo-Sonosensitizer for Cancer Therapy

Sonodynamic therapy (SDT) has been widely reported as a noninvasive and high-penetration therapy for cancer; however, the design of an efficient sonosensitizer remains an urgent need. To address this issue, molybdenum disulfide nanoflowers (MoS2 NF) as piezo-sonosensitizers and introduced sulfur vacancies on the MoS2 NF (Sv-MoS2 NF) to improve their piezoelectric property for cancer therapy are designed. Under ultrasonic mechanical stress, the Sv-MoS2 NF resulted in piezoelectric polarization and band tilting, which enhanced the charge carrier separation and migration. This resulted in an improved catalytic reaction for reactive oxygen species (ROS) production, ultimately enhancing the SDT performance. Thanks to the high efficiency of ROS generation, the Sv-MoS2 NF have demonstrated a good anticancer effect in vitro and in vivo. Following a systematic evaluation, Sv-MoS2 NF also demonstrated good biocompatibility. This novel piezo-sonosensitizer and vacancy engineering strategy provides a promising new approach for achieving efficient SDT.

Efficient Mining of Anticancer Peptides from Gut Metagenome

The gut microbiome plays a crucial role in modulating host health and disease. It serves as a vast reservoir of functional molecules that hold great potential for clinical applications. One specific area of interest is identifying anticancer peptides (ACPs) for innovative cancer therapies. However, ACPs discovery is hindered by a heavy reliance on experimental methodologies. To overcome this limitation, we here employed a novel approach by leveraging the overlap between ACPs and antimicrobial peptides (AMPs). By combining well-established AMP prediction methods with mining techniques in metagenomic cohorts, a total of 40 potential ACPs is identified. Out of the identified ACPs, 39 demonstrated inhibitory effects against at least one cancer cell line, exhibiting significant differences from known ACPs. Moreover, the therapeutic potential of the two most promising peptides in a mouse xenograft cancer model is evaluated. Encouragingly, the peptides exhibit effective tumor inhibition without any detectable toxic effects. Interestingly, both peptides display uncommon secondary structures, highlighting its distinctive characteristics. This findings highlight the efficacy of the multi-center mining approach, which effectively uncovers novel ACPs from the gut microbiome. This approach has significant implications for expanding treatment options not only for CRC, but also for other cancer types.

Development of effective model for non-destructive detection of defective kiwifruit based on graded lines

The accurate detection of external defects in kiwifruit is an important part of postharvest quality assessment. Previous studies have not considered the problems posed by the actual grading environment. In this study, we designed a novel approach based on improved Yolov5 to achieve real-time and efficient non-destructive detection of multiple defect categories in kiwifruit. First, a kiwifruit image acquisition device based on grading lines was developed to enhance the image acquisition. Subsequently, a kiwifruit dataset was constructed based on the external defect characteristics and a new data enhancement method was proposed to augment the kiwifruit samples. Thereafter, the SPD-Conv and DW-Conv modules were combined to improve Yolov5s, with EIOU as the loss calculation function. The results demonstrated that the improved model training loss value was 0.013 lower, the convergence was accelerated, the number of parameters was reduced, and the computational effort was increased. The detection accuracies of the samples in the test set, which included healthy, leaf-rubbing damaged, healed cuts or scarred, and sunburned samples, were 98.8%, 98.7%, 97.6%, and 95.9%, respectively, with an overall detection accuracy of 97.7%. The detection time was 8.0 ms, thereby meeting real-time sorting demands. The average detection accuracy and model size of SSD, Yolov5s, Yolov7, and Yolov5-Ours were compared. When the confidence threshold was 0.5, the detection accuracy of Yolov5-Ours was 10% and 6.4% higher than that of SSD and Yolov5s, respectively. In terms of the model size, Yolov5-Ours was approximately 6.5- and 4-fold smaller than SSD and Yolov7, respectively. Thus, Yolov5-Ours achieved the highest accuracy, adaptability, and robustness for the detection of all kiwifruit categories as well as a small volume and portability. These results can provide technical support for the non-destructive detection and grading of agricultural products in the future.

Rapid, ultrasensitive and highly specific diagnosis of Mycoplasma pneumoniae by a CRISPR-based detection platform

Mycoplasma pneumoniae (MP) is an important causative agent of morbidity and mortality among all age groups, especially among patients of extreme ages. Improved and readily available tests for accurate, sensitive and rapid diagnosis of MP infection is sorely needed. Here, we developed a CRISPR-Cas12b-based detection platform on the basis of recombinase polymerase amplification (RPA) for rapid, simple, and accurate diagnosis of MP infection, named MP-RPA-CRISPR. The RPA was employed for amplifying the community-acquired respiratory distress syndrome (CARDS) toxin gene of MP strains at the optimal reaction temperature 37°C. The resulting amplicons were decoded by the CRISPR-Cas12b-based detection platform, which was interpreted by real-time PCR system and by naked eye under blue light. The MP-RPA-CRISPR can detected down to 5 fg of genomic DNA templates of MP strains and accurately distinguish MP strains from non-MP strains without any cross-reactivity. A total of 96 bronchoalveolar lavage fluid (BALF)samples collected from patients suspected of respiratory infection were used to evaluate the clinical performance of the MP-RPA-CRISPR assay. As a result, our assay accurately diagnosed 45 MP-infected samples and 51 non-MP infected sample, and the results obtained from MP-RPA-CRISPR were consistent with microfluidic chip technology. In conclusion, our MP-RPA-CRISPR assay is a simple, rapid, portable and highly sensitive method to diagnose MP infection, which can be used as a promising tool in a variety of settings including clinical, field, and resource-limited aeras.

Anti-apoptotic protein BCL-XL as a therapeutic vulnerability in gastric cancer

BACKGROUND

New therapeutic targets are needed to improve the outcomes for gastric cancer (GC) patients with advanced disease. Evasion of programmed cell death (apoptosis) is a hallmark of cancer cells and direct induction of apoptosis by targeting the pro-survival BCL2 family proteins represents a promising therapeutic strategy for cancer treatment. Therefore, understanding the molecular mechanisms underpinning cancer cell survival could provide a molecular basis for potential therapeutic interventions.

METHOD

Here we explored the role of BCL2L1 and the encoded anti-apoptotic BCL-XL in GC. Using Droplet Digital PCR (ddPCR) technology to investigate the DNA amplification of BCL2L1 in GC samples and GC cell lines, the sensitivity of GC cell lines to selective BCL-XL inhibitors A1155463 and A1331852, pan-inhibitor ABT-263, and VHL-based PROTAC-BCL-XL was analyzed using (CellTiter-Glo) CTG assay in vitro. Western Blot (WB) was used to detect the protein expression of BCL2 family members in GC cell lines and the manner in which PROTAC-BCL-XL kills GC cells. Co-immunoprecipitation (Co-IP) was used to investigate the mechanism of A1331852 and ABT-263 kills GC cell lines. DDPCR, WB, and real-time PCR (RTPCR) were used to investigate the correlation between DNA, RNA, protein levels, and drug activity.

RESULTS

The functional assay showed that a subset of GC cell lines relies on BCL-XL for survival. In gastric cancer cell lines, BCL-XL inhibitors A1155463 and A1331852 are more sensitive than the pan BCL2 family inhibitor ABT-263, indicating that ABT-263 is not an optimal inhibitor of BCL-XL. VHL-based PROTAC-BCL-XL DT2216 appears to be active in GC cells. DT2216 induces apoptosis of gastric cancer cells in a time- and dose-dependent manner through the proteasome pathway. Statistical analysis showed that the BCL-XL protein level predicts the response of GC cells to BCL-XL targeting therapy and BCL2L1 gene CNVs do not reliably predict BCL-XL expression.

CONCLUSION

We identified BCL-XL as a promising therapeutic target in a subset of GC cases with high levels of BCL-XL protein expression. Functionally, we demonstrated that both selective BCL-XL inhibitors and VHL-based PROTAC BCL-XL can potently kill GC cells that are reliant on BCL-XL for survival. However, we found that BCL2L1 copy number variations (CNVs) cannot reliably predict BCL-XL expression, but the BCL-XL protein level serves as a useful biomarker for predicting the sensitivity of GC cells to BCL-XL-targeting compounds. Taken together, our study pinpointed BCL-XL as potential druggable target for specific subsets of GC.

A CRISPR-Cas12a-based platform for ultrasensitive rapid highly specific detection of Mycobacterium tuberculosis in clinical application

Tuberculosis, caused by Mycobacterium tuberculosis (MTB), is the second leading cause of death after COVID-19 pandemic. Here, we coupled multiple cross displacement amplification (MCDA) technique with CRISPR-Cas12a-based biosensing system to design a novel detection platform for tuberculosis diagnosis, termed MTB-MCDA-CRISPR. MTB-MCDA-CRISPR pre-amplified the specific sdaA gene of MTB by MCDA, and the MCDA results were then decoded by CRISPR-Cas12a-based detection, resulting in simple visual fluorescent signal readouts. A set of standard MCDA primers, an engineered CP1 primer, a quenched fluorescent ssDNA reporter, and a gRNA were designed targeting the sdaA gene of MTB. The optimal temperature for MCDA pre-amplification is 67°C. The whole experiment process can be completed within one hour, including sputum rapid genomic DNA extraction (15 minutes), MCDA reaction (40 minutes), and CRISPR-Cas12a-gRNA biosensing process (5 minutes). The limit of detection (LoD) of the MTB-MCDA-CRISPR assay is 40 fg per reaction. The MTB-MCDA-CRISPR assay does not cross reaction with non-tuberculosis mycobacterium (NTM) strains and other species, validating its specificity. The clinical performance of MTB-MCDA-CRISPR assay was higher than that of the sputum smear microscopy test and comparable to that of Xpert method. In summary, the MTB-MCDA-CRISPR assay is a promising and effective tool for tuberculosis infection diagnosis, surveillance and prevention, especially for point-of-care (POC) test and field deployment in source-limited regions.

Clinical characteristics and changing trajectories of esophageal cancer and gastric cancer in China from 2010 to 2019: An analysis of a hospital-based database of 24,327 patients

Purpose

This analysis aimed to investigate the clinical characteristics and changing trajectories of gastric cancer (GC) and esophageal cancer (EC).

Methods

We collected data from a large cancer hospital in Beijing, China, from 2010 to 2019. Joinpoint regression was used to analyze the trends of histological characteristics and comorbidities.

Results

From 2010 to 2019, there were a total of 10,083 EC patients and 14,244 GC patients. Patients were mainly men and diagnosed at 55-64 years old. Metabolic comorbidity was the most common comorbidity, with hypertension being predominant. The percentages of stage I showed significant increases for EC [average annual percent change (AAPC): 10.5%] and GC (AAPC: 9.7%) patients. We also observed an increasing trend of EC and GC patients over 65 years old. For EC patients, esophageal squamous cell carcinoma (93.1%) remained as the prioritized subtype, and the middle third of the esophagus was the most common site. EC patients with three or more comorbidities increased from 0.1% to 2.2% (AAPC, 27.7%; 95% CI, 14.7% to 42.2%). For GC patients, adenocarcinoma accounts for 86.9% of the total cases, and cardia was the most common site. The ulcerative comorbidity rate decreased from 2.0% to 1.2% (AAPC, −6.1%; 95% CI, −11.6% to −0.3%).

Conclusion

ESCC remained as the prioritized histological subtype, and the middle third of the esophagus was the most common site of EC. The majority of GC patients had adenocarcinoma, and the cardia was the most common site. There was an increasing trend of patients diagnosed at stage I. These findings provide scientific evidence to guide future treatment.

Spatiotemporal dynamics of net primary productivity and its influencing factors in the middle reaches of the Yellow River from 2000 to 2020

Introduction

Net primary productivity (NPP) is an important indicator used to characterize the productivity of terrestrial ecosystems. The spatial distribution and dynamic change in NPP are closely related to regional climate, vegetation growth and human activities. Studying the spatiotemporal dynamics of NPP and its influencing factors plays a vital role in understanding ecosystem carbon sink capacity.

Methods

Based on MODIS-NPP data, meteorological data, and land use data from 2000 to 2020, we analyzed the spatiotemporal variation characteristics and influencing factors of NPP in the middle reaches of the Yellow River (MRYR) by using unary linear regression analysis, third-order partial correlation analysis, and Sen+Mann-Kendall trend analysis.

Results

The results showed that the annual average NPP of the MRYR was 319.24 gCm-2a-1 with a spatially decreasing trend from the southern part to the northern part. From 2000 to 2020, the annual average NPP experienced a fluctuating upward trend at a rate of 2.83 gCm-2a-1, and the area with a significant upward trend accounted for 87.68%. The NPP of different land use types differed greatly, in which forest had the greatest increase in NPP. Temperature had a negative correlation with NPP in most parts of the MRYR. Water vapor pressure promoted the accumulation of NPP in the northwestern MRYR. The areas with a positive correlation between NPP and water vapor pressure accounted for 87.6%, and 20.43% of the MRYR area passed the significance test of P< 0.05.

Conclusion

The results of the study highlight the impact of climate factors and land-use changes on NPP and provide theoretical guidance for high-quality sustainable development in the MRYR.

DNA damage contributes to age-associated differences in SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is known to disproportionately affect older individuals. How aging processes affect SARS-CoV-2 infection and disease progression remains largely unknown. Here, we found that DNA damage, one of the hallmarks of aging, promoted SARS-CoV-2 infection in vitro and in vivo. SARS-CoV-2 entry was facilitated by DNA damage caused by extrinsic genotoxic stress or telomere dysfunction and hampered by inhibition of the DNA damage response (DDR). Mechanistic analysis revealed that DDR increased expression of angiotensin-converting enzyme 2 (ACE2), the primary receptor of SARS-CoV-2, by activation of transcription factor c-Jun. Importantly, in vivo experiment using a mouse-adapted viral strain also verified the significant roles of DNA damage in viral entry and severity of infection. Expression of ACE2 was elevated in the older human and mice tissues and positively correlated with γH2AX, a DNA damage biomarker, and phosphorylated c-Jun (p-c-Jun). Finally, nicotinamide mononucleotide (NMN) and MDL-800, which promote DNA repair, alleviated SARS-CoV-2 infection and disease severity in vitro and in vivo. Taken together, our data provide insights into the age-associated differences in SARS-CoV-2 infection and a novel approach for antiviral intervention.

Treatment plan prescreening for patient-specific quality assurance measurements using independent Monte Carlo dose calculations

PURPOSE

This study proposes a method to identify plans that failed patient-specific quality assurance (QA) and attempts to establish a criterion to prescreen treatment plans for patient-specific QA measurements with independent Monte Carlo dose calculations.

MATERIALS AND METHODS

Patient-specific QA results measured with an ArcCHECK diode array of 207 patients (head and neck: 25; thorax: 61; abdomen: 121) were retrospectively analyzed. All patients were treated with the volumetric modulated arc therapy (VMAT) technique and plans were optimized with a Pinnacle v16.2 treatment planning system using an analytical algorithm-based dose engine. Afterwards, phantom verification plans were designed and recalculated by an independent GPU-accelerated Monte Carlo (MC) dose engine, ArcherQA. Moreover, sensitivity and specificity analyzes of gamma passing rates between measurements and MC calculations were carried out to show the ability of MC to monitor failing plans (ArcCHECK 3%/3 mm,<90%), and attempt to determine the appropriate threshold and gamma passing rate criterion utilized by ArcherQA to prescreen treatment plans for ArcCHECK measurements. The receiver operator characteristic (ROC) curve was also utilized to characterize the performance of different gamma passing rate criterion used by ArcherQA.

RESULTS

The thresholds for 100% sensitivity to detect plans that failed patient-specific QA by independent calculation were 97.0%, 95.4%, and 91.0% for criterion 3%/3 mm, 3%/2 mm, and 2%/2 mm, respectively, which corresponded to specificities of 0.720, 0.528, and 0.585, respectively. It was shown that the 3%/3 mm criterion with 97% threshold for ArcherQA demonstrated perfect sensitivity and the highest specificity compared with other criteria, which may be suitable for prescreening treatment plans treated with the investigated machine to implement measurement-based patient-specific QA of patient plans. In addition, the area under the curve (AUC) calculated from ROC analysis for criterion 3%/3 mm, 3%/2 mm, and 2%/2 mm used by ArcherQA were 0.948, 0.924, and 0.929, respectively.

CONCLUSIONS

Independent dose calculation with the MC-based program ArcherQA has potential as a prescreen treatment for measurement-based patient-specific QA. AUC values (>0.9) showed excellent classification accuracy for monitoring failing plans with independent MC calculations.

Global and national trends in the age-specific sex ratio of esophageal cancer and gastric cancer by subtype

A male predominance was observed in esophageal and gastric cancers, though present limited data has revealed variations by age. We aim to investigate the global age-specific sex differences in esophageal squamous cell carcinoma (ESCC), esophageal adenocarcinoma (EAC), gastric cardia cancer (GCC) and gastric noncardia cancer (GNCC). Data on esophageal and gastric cancers incidence by diagnosis year, sex, histology, subsite and age group were extracted from 171 registries in 54 countries included in the last two volumes (X and XI, 2003-2012) of Cancer Incidence in Five Continents, which contributing to over 80% of the global burdens of these cancers. Age-standardized incidence rates (ASIRs) and male-to-female ASIRs ratios were estimated for esophageal and gastric cancers, by histological subtype and subsite, globally and by country. We consistently observed a male predominance in esophageal and gastric cancers across the world from 2003 to 2012, with male-to-female ASIRs ratios of 6.7:1 for EAC, 3.3:1 for ESCC, 4.0:1 for GCC and 2.1:1 for GNCC. The sex differences were consistent across time periods but varied significantly by age across the life span. Across the four cancer types, the male-to-female incidence rate ratios increased from young ages, approaching a peak at ages 60-64, but sharply declined thereafter. Similar "low-high-low" trends of age-specific sex ratio were observed in other digestive cancers including liver, pancreas, colon and rectum with peak ages ranging from 50 to 65. Age-dependent risk factors warrant further investigation to aid our understanding of the underlying etiologies of esophageal and gastric cancers by histological subtype and subsite.

Immunostimulatory activity and structure-activity relationship of epimedin B from Epimedium brevicornu Maxim

Epimedii Folium (EF, Epimedium brevicornu Maxim.), a traditional botanical drug, is famous for treating bone fractures, joint diseases, and several chronic illnesses. However, some studies indicated that EF could induce idiosyncratic drug-induced liver injury (IDILI) in the clinic. The NLRP3 inflammasome plays a crucial role in the pathogenesis of various human diseases, including IDILI. In the present study, we showed that epimedin B could specifically facilitate nigericin- or ATP-induced NLRP3 inflammasome activation under synergistic induction of mitochondrial reactive oxygen species. Moreover, epimedin B resulted in activation of Caspase-1 and IL-1β secretion in a lipopolysaccharide (LPS)-mediated susceptibility mouse model. MCC950 pretreatment completely abrogated activation of the NLRP3 inflammasome and prevented liver injury. Importantly, several studies have confirmed that some active constituents of EF could enhance activation of the NLRP3 inflammasome and may be involved in the pathogenesis of EF-IDILI. No reports are available on whether the structure-activity relationship associated with the immunostimulatory activity in EF contributes to the pathogenesis of EF-IDILI. These findings have changed our conventional understanding about the more glycogen, the more immunostimulatory activity.

Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

Background

Chordoma is a slow-growing but malignant subtype of bone sarcoma with relatively high recurrence rates and high resistance to chemotherapy. It is urgent to understand the underlying regulatory networks to determine more effective potential targets. Phosphorylative regulation is currently regarded as playing a significant role in tumorigenesis, and the use of tyrosine kinase inhibitors in clinical practice has yielded new promise for the treatment of a variety of sarcoma types.

Materials and methods

We performed comprehensive proteomic and phosphoproteomic analyses of chordoma using four-dimensional label-free liquid chromatography–tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis. The potential aberrantly expressed kinases and their functions were validated using western blotting and CCK-8 assays.

Results

Compared with paired normal muscle tissues, 1,139 differentially expressed proteins (DEPs) and 776 differentially phosphorylated proteins (DPPs) were identified in chordoma tumor tissues. The developmentally significant Wnt-signaling pathway and oxidative phosphorylation were aberrant in chordoma. Moreover, we predicted three kinases (AURA, CDK9, and MOK) with elevated activity by kinase-pathway network analysis (KiPNA) and verified their increased expression levels. The knockdown of these kinases markedly suppressed chordoma cell growth, and this was also the case for cells treated with the CDK9 inhibitor AZD4573. We additionally examined 208 proteins whose expression and phosphorylation levels were synergetically altered.

Conclusions

We herein depicted the collective protein profiles of chordomas, providing insight into chordomagenesis and the potential development of new therapeutic targets.

Transplant or dialysis: What’s the better choice for RCC-induced ESRD patients? A 20-year analysis of OPTN/UNOS data

Purpose

The incidence of end-stage renal disease (ESRD) caused by renal cell carcinoma (RCC) is increasing with the high prevalence of RCC as well as those with treatment-related renal function impairment. Worries about tumor recurrence after transplant-related immunosuppression hinder the recommendation of kidney transplantation for RCC-induced ESRD patients. However, no direct analysis has been performed to identify whether kidney transplantation can offer better survival than maintaining dialysis.

Materials and methods

This retrospective population-based cohort study was based on Organ Procurement and Transplantation Network data released in March 2021. Characteristics and outcomes were compared, including the patient and graft survival of candidates and recipients with RCC-induced ESRD etiology as well as other primary diseases.

Results

Patients with RCC-induced ESRD were older; more likely to be male, White, and obese; and more likely to have a history of diabetes and dialysis. They also had higher creatinine levels, more delayed graft function, more primary non-function, and higher Kidney Donor Profile Index score donors, compared with the glomerulonephritis (GN) group. While waiting, RCC candidates suffered the worst outcomes of all groups, a 44% (adjusted hazard ratio [aHR], 1.44 [1.27–1.62]) higher risk of removal than GN patients. After transplantation, RCC recipients demonstrated comparable patient survival and better graft survival (p=0.21 and p=0.13, respectively). Compared with still-waiting RCC patients, the RCC recipients who received kidney transplants had significantly better outcomes (13.6 [9.3–17.8] vs. 61 [52–68.4] %), decreasing the death or deteriorating risk by 84% (aHR, 0.16 [0.13–0.20]).

Conclusions

Patients with RCC-induced ESRD can dramatically benefit from kidney transplantation. Hence, these patients should not be limited to transplantation by strict strategies or a delayed waiting time out of their malignancy history.

Multi-omics approaches for deciphering the complexity of traditional Chinese medicine syndromes in stroke: A systematic review

Background: Deciphering the biological basis of traditional Chinese medicine (TCM) syndromes in complex diseases is challenging. Rapid advances in multi-omics approaches provide new opportunities to unveil the biological basis of TCM syndromes. We intend to summarize the latest significant progress and highlight the crucial value of applying multi-omics approaches to reveal TCM syndromes of stroke in a new horizon.

Methods: We systematically searched PubMed, EMBASE, Web of Science Core Collection (WOSCC), Cochrane Library, China National Knowledge Infrastructure (CNKI), Chinese Science and Technology Periodical Database (VIP), Wanfang database and China Biology Medicine Database (SinoMed) for relevant studies from their inception to 31 March 2022, and conducted a comprehensive systematic review (PROSPERO registration number: CRD42021285922).

Results: A total of 43 relevant studies were included in the final systematic review, genomics, transcriptomics, proteomics, and metabolomics were all involved. Some gene polymorphisms, differential lncRNAs, mRNAs, miRNAs, proteins, and metabolites may be associated with TCM syndromes of stroke. In addition, some studies conducted a preliminary exploration on the different diseases with the same TCM syndrome. The results showed that thioredoxin-dependent peroxidase reductase may be the specific marker protein of Liver-yang transforming into wind syndrome, and the network formed by mir-146b-5p, -199a-5p, and 23 targeted mRNAs may be the biomarker of Blood-stasis syndrome.

Conclusion: Multi-omics technologies have served as powerful tools to investigate the complexity of TCM syndromes and may hold the promise of promoting the modernization of TCM as well as personalized medicine of TCM in stroke.

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients

Objective

To explore the composition of the intestinal microbiota in ulcerative colitis (UC) patients and to identify differences in the microbiota between patients with active disease and those in remission.

Methods

Between September 2020 and June 2021, we enrolled into our study, and collected stool samples from, patients with active UC or in remission and healthy control subjects. The diagnosis of UC was based on clinical, endoscopic, radiological, and histological findings. The composition of the intestinal microbiota was determined by sequencing of the 16S rRNA V3–V4 region and by bioinformatic methods. The functional composition of the intestinal microbiota was predicted using PICRUSt 2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software.

Results

We found that the intestinal flora was significantly less rich and diverse in UC patients than in healthy control subjects. Beta diversity analysis revealed notable differences in the intestinal flora compositions among the three groups, but there was no statistical difference in alpha diversity between UC patients with active disease and those in remission. At the phylum level, the relative abundances of Proteobacteria and Patescibacteria were significantly higher, and the relative abundances of Desulfobacterota and Verrucomicrobiota were lower, in UC patients with active disease than in the healthy control group. Higher levels of potential pathogens and lower levels of butyrate-producing bacteria were also detected in UC patients with active disease. Linear discriminant analysis Effect Size (LefSe) revealed that 71 bacterial taxa could serve as biomarkers, with 26 biomarkers at the genus level. In addition, network analysis showed that there was a positive correlation between Roseburia and Lachnospira. Functional predictions indicated that gene functions involving the metabolism of some substances, such as methane, lipopolysaccharide, geraniol, and ansamycins, were significantly different among the three groups.

Conclusion

The richness and diversity of the intestinal microbiota differed significantly among the three groups. Richness describes the state of being rich in number of intestinal bacteria, whereas diversity is the number of different species of intestinal bacteria. Different bacterial taxa could be used as biomarkers, expanding our understanding of the relationship between the intestinal microbiota microenvironment and UC in the future.

A more effective CT synthesizer using transformers for cone-beam CT-guided adaptive radiotherapy

Purpose

The challenge of cone-beam computed tomography (CBCT) is its low image quality, which limits its application for adaptive radiotherapy (ART). Despite recent substantial improvement in CBCT imaging using the deep learning method, the image quality still needs to be improved for effective ART application. Spurred by the advantages of transformers, which employs multi-head attention mechanisms to capture long-range contextual relations between image pixels, we proposed a novel transformer-based network (called TransCBCT) to generate synthetic CT (sCT) from CBCT. This study aimed to further improve the accuracy and efficiency of ART.

Materials and methods

In this study, 91 patients diagnosed with prostate cancer were enrolled. We constructed a transformer-based hierarchical encoder–decoder structure with skip connection, called TransCBCT. The network also employed several convolutional layers to capture local context. The proposed TransCBCT was trained and validated on 6,144 paired CBCT/deformed CT images from 76 patients and tested on 1,026 paired images from 15 patients. The performance of the proposed TransCBCT was compared with a widely recognized style transferring deep learning method, the cycle-consistent adversarial network (CycleGAN). We evaluated the image quality and clinical value (application in auto-segmentation and dose calculation) for ART need.

Results

TransCBCT had superior performance in generating sCT from CBCT. The mean absolute error of TransCBCT was 28.8 ± 16.7 HU, compared to 66.5 ± 13.2 for raw CBCT, and 34.3 ± 17.3 for CycleGAN. It can preserve the structure of raw CBCT and reduce artifacts. When applied in auto-segmentation, the Dice similarity coefficients of bladder and rectum between auto-segmentation and oncologist manual contours were 0.92 and 0.84 for TransCBCT, respectively, compared to 0.90 and 0.83 for CycleGAN. When applied in dose calculation, the gamma passing rate (1%/1 mm criterion) was 97.5% ± 1.1% for TransCBCT, compared to 96.9% ± 1.8% for CycleGAN.

Conclusions

The proposed TransCBCT can effectively generate sCT for CBCT. It has the potential to improve radiotherapy accuracy.

FAM135B sustains the reservoir of Tip60-ATM assembly to promote DNA damage response

BACKGROUND

Recently, the mechanism by which cells adapt to intrinsic and extrinsic stresses has received considerable attention. Tat-interactive protein 60-kDa/ataxia-telangiectasia-mutated (TIP60/ATM) axis-mediated DNA damage response (DDR) is vital for maintaining genomic integrity.

METHODS

Protein levels were detected by western blot, protein colocalisation was examined by immunofluorescence (IF) and protein interactions were measured by co-immunoprecipitation, proximity ligation assay and GST pull-down assays. Flow cytometry, comet assay and IF assays were used to explore the biological functions of sequence similarity 135 family member B (FAM135B) in DDR. Xenograft tumour, FAM135B transgenic mouse models and immunohistochemistry were utilised to confirm in vitro observations.

RESULTS

We identified a novel DDR regulator FAM135B which could protect cancer cells from genotoxic stress in vitro and in vivo. The overexpression of FAM135B promoted the removal of γH2AX and 53BP1 foci, whereas the elimination of FAM135B attenuated these effects. Consistently, our findings revealed that FAM135B could promote homologous recombination and non-homologous end-joining repairs. Further study demonstrated that FAM135B physically bound to the chromodomain of TIP60 and improved its histone acetyltransferase activity. Moreover, FAM135B enhanced the interactions between TIP60 and ATM under resting conditions. Intriguingly, the protein levels of FAM135B dramatically decreased following DNA damage stress but gradually increased during the DNA repair period. Thus, we proposed a potential DDR mechanism where FAM135B sustains a reservoir of pre-existing TIP60-ATM assemblies under resting conditions. Once cancer cells suffer DNA damage, FAM135B is released from TIP60, and the functioning pre-assembled TIP60-ATM complex participates in DDR.

CONCLUSIONS

We characterised FAM135B as a novel DDR regulator and further elucidated the role of the TIP60-ATM axis in response to DNA damage, which suggests that targeting FAM135B in combination with radiation therapy or chemotherapy could be a potentially effective approach for cancer treatment.

Differences of Corneal Biomechanics Among Thin Normal Cornea, Forme-Fruste Keratoconus, and Cornea After SMILE

Background: To compare the corneal biomechanics of thin normal cornea (TNC) with thinnest corneal thickness (TCT) (≤500 µm), forme-fruste keratoconus (FFKC) and cornea after small incision lenticule extraction (Post-SMILE) had their central corneal thickness (CCT) matched by Corneal Visualization Scheimpflug Technology (Corvis ST).

Methods: CCT were matched in 23 eyes with FFKC, 23 eyes by SMILE in 3 months post-operatively, and 23 TNC eyes. The differences in corneal biomechanics by Corvis ST among the three groups were compared.

Results: There was no significant difference in CCT among the three groups, and the biomechanically corrected intraocular pressure (bIOP) did not differ significantly among the three groups (all p &gt; 0.05). There were significant differences in most DCR parameters between pre- and post-operatively (all p &lt; 0.05). Compared with TNC, the values of corneal deflection amplitude during the first applanation (A1DA), length at the first applanation (A1L), corneal deflection amplitude during the second applanation (A2DA), and maximum deformation amplitude (DA) decreased in 3 months after SMILE (all p &lt; 0.05), these values increased in the FFKC (all p &lt; 0.05).

Conclusion: The majority of the DCR parameters were different among the three groups. The parameters A1DA, A1L, A2DA, and DA may be different between TNC and Post-SMILE, TNC and FFKC, and Post-SMILE and FFKC.

RNA Sequencing of Tumor-Educated Platelets Reveals a Three-Gene Diagnostic Signature in Esophageal Squamous Cell Carcinoma

There is no cost-effective, accurate, and non-invasive method for the detection of esophageal squamous cell carcinoma (ESCC) in clinical practice. We aimed to investigate the diagnostic potential of tumor-educated platelets in ESCC. In this study, seventy-one ESCC patients and eighty healthy individuals were enrolled and divided into a training cohort (23 patients and 27 healthy individuals) and a validation cohort (48 patients and 53 healthy individuals). Next-generation RNA sequencing was performed on platelets isolated from peripheral blood of all participants, and a support vector machine/leave-one-out cross validation (SVM/LOOCV) approach was used for binary classification. A diagnostic signature composed of ARID1A, GTF2H2, and PRKRIR discriminated ESCC patients from healthy individuals with 91.3% sensitivity and 85.2% specificity in the training cohort and 87.5% sensitivity and 81.1% specificity in the validation cohort. The AUC was 0.924 (95% CI, 0.845–0.956) and 0.893 (95% CI, 0.821–0.966), respectively, in the training cohort and validation cohort. This 3-gene platelet RNA signature could effectively discriminate ESCC from healthy control. Our data highlighted the potential of tumor-educated platelets for the noninvasive diagnosis of ESCC. Moreover, we found that keratin and collagen protein families and ECM-related pathways might be involved in tumor progression and metastasis of ESCC, which might provide insights to understand ESCC pathobiology and advance novel therapeutics.

Microsimulation Model for Prevention and Intervention of Coloretal Cancer in China (MIMIC-CRC): Development, Calibration, Validation, and Application

Introduction

A microsimulation model provides important references for decision-making regarding colorectal cancer (CRC) prevention strategies, yet such a well-validated model is scarce in China.

Methods

We comprehensively introduce the development of MIcrosimulation Model for the prevention and Intervention of Colorectal Cancer in China (MIMIC-CRC). The MIMIC-CRC was first constructed to simulate the natural history of CRC based on the adenoma-carcinoma pathway. The parameters were calibrated and validated using data from population-based cancer registry data and CRC screening programs. Furthermore, to assess the model’s external validity, we compared the model-derived results to outcome patterns of a sigmoidoscopy screening trial in the UK [UK Flexible Sigmoidoscopy Screening (UKFSS) trial]. Finally, we evaluated the application potential of the MIMIC-CRC model in CRC screening by comparing the 8 different strategies.

Results

We found that most of the model-predicted colorectal lesion prevalence was within the 95% CIs of observed prevalence in a large population-based CRC screening program in China. In addition, model-predicted sex- and age-specific CRC incidence and mortality were equivalent to the registry-based data. The hazard ratios of model-estimated CRC-related incidence and mortality for sigmoidoscopy screening compared to no screening were 0.60 and 0.51, respectively, which were comparable to the reported results of the UKFSS trial. Moreover, we found that all 8 strategies could reduce CRC incidence and mortality compared to no screening.

Conclusions

The well-calibrated and validated MIMIC-CRC model may represent a valid tool to assess the comparative effectiveness of CRC screening strategies and will be useful for further decision-making to CRC prevention.

Determine Corneal Biomechanical Parameters by Finite Element Simulation and Parametric Analysis Based on ORA Measurements

Purpose: The Ocular Response Analyzer (ORA) is one of the most commonly used devices to measure corneal biomechanics in vivo. Until now, the relationship between the output parameters and corneal typical biomechanical parameters was not clear. Hence, we defined the output parameters of ORA as ORA output parameters. This study aims to propose a method to determine corneal biomechanical parameters based on ORA measurements by finite element simulation and parametric analysis.

Methods: Finite element analysis was used to simulate the mechanics process of ORA measurements with different intraocular pressure (IOP), corneal geometrical parameters and corneal biomechanical parameters. A simplified geometrical optics model was built to simulate the optical process of the measurements to extract ORA output parameters. After that, 70% of the simulated data was used to establish the quantitative relationship between corneal biomechanical parameters and ORA output parameters by parametric analysis and 30% of the simulated data was used to validate the established model. Besides, ten normal subjects were included to evaluate the normal range of corneal biomechanical parameters calculated from ORA.

Results: The quantitative relationship between corneal biomechanical parameters and ORA output parameters is established by combining parametric analysis with finite element simulation. The elastic modulus (E) and relaxation limit (G_∞) of the ten normal subjects were 0.65 ± 0.07 MPa and 0.26 ± 0.15, respectively.

Conclusions: A method was proposed to determine corneal biomechanical parameters based on the results of ORA measurements. The magnitude of the corneal biomechanical parameters calculated according to our method was reasonable.

Cas9/AAV9-Mediated Somatic Mutagenesis Uncovered the Cell-Autonomous Role of Sarcoplasmic/Endoplasmic Reticulum Calcium ATPase 2 in Murine Cardiomyocyte Maturation

Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) is a key player in cardiomyocyte calcium handling and also a classic target in the gene therapy for heart failure. SERCA2 expression dramatically increases during cardiomyocyte maturation in the postnatal phase of heart development, which is essential for the heart to acquire its full function in adults. However, whether and how SERCA2 regulates cardiomyocyte maturation remains unclear. Here, we performed Cas9/AAV9-mediated somatic mutagenesis (CASAAV) in mice and achieved cardiomyocyte-specific knockout of Atp2a2, the gene coding SERCA2. Through a cardiac genetic mosaic analysis, we demonstrated the cell-autonomous role of SERCA2 in building key ultrastructures of mature ventricular cardiomyocytes, including transverse-tubules and sarcomeres. SERCA2 also exerts a profound impact on oxidative respiration gene expression and sarcomere isoform switching from Myh7/Tnni1 to Myh6/Tnni3, which are transcriptional hallmarks of cardiomyocyte maturation. Together, this study uncovered a pivotal role of SERCA2 in heart development and provided new insights about SERCA2-based cardiac gene therapy.

lncRNA Mirt1: A Critical Regulatory Factor in Chronic Intermittent Hypoxia Exaggerated Post-MI Cardiac Remodeling

Chronic intermittent hypoxia (CIH) is the main feature of obstructive sleep apnea (OSA) and is known to exaggerate cardiac remodeling after myocardial infarction (MI). However, the specific contribution of CIH to overall OSA-induced pathological complications and the transcriptomic mechanisms underlying CIH-exaggerated post-MI remodeling remains unclear. In this study, we used RNA-sequencing to construct the expression profiles of cardiac mRNAs, microRNAs, and long non-coding RNAs (lncRNA) in four groups of C57BL/6J mice (Sham, CIH, MI, MI + CIH) to evaluate how CIH regulates cardiac remodeling after MI. Compared with the other three groups, the MI + CIH group exhibited 345 lncRNAs, 35 microRNAs, and 5,220 differentially expressed mRNAs. Further analysis showed that CIH led to significant changes in Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the differentially expressed mRNAs. Co-expression network analysis identified two core lncRNAs (Mirt1 and AC125351.1) and two core microRNAs (miR-466i-5p and miR-574-5p) during the development of CIH-exaggerated post-MI remodeling, and they were verified by quantitative real-time PCR (qRT-PCR). LncRNA-mRNA correlation analysis further showed that lncRNA Mirt1 was positively correlated with Apbb1ip and Lcp2. In addition, microRNA-mRNA correlation analysis showed that microRNA miR-466i-5p was positively correlated with Snai2, Cdc27, and Ngfr. Furthermore, combining with lncRNA-mRNA and miRNA-mRNA networks, 44 RNAs were identified in the competitive endogenous RNA (ceRNA) network. Mirt1 acts as a ceRNA to bind to miR-466i-5p to further regulate the expression levels of the target gene, thereby aggravating cardiac remodeling after MI. In conclusion, our study provides a systematic perspective on the potential functions of mRNAs, microRNAs, and lncRNAs in CIH-exaggerated post-MI cardiac remodeling. Our data suggest that lncRNA Mirt1 may be the most critical regulator of MI aggravated by CIH.

A Dansyl Amide N-Oxide Fluorogenic Probe Based on a Bioorthogonal Decaging Reaction

A smart fluorescence "turn-on" probe which contained a dansyl amide fluorophore and an N-oxide group was designed based on the bioorthogonal decaging reaction between N-oxide and the boron reagent. The reaction proceeds in a rapid kinetics (k2 =57.1±2.5 m-1  s-1 ), and the resulting reduction product showcases prominent fluorescence enhancement (up to 72-fold). Time dependent density functional theoretical (TD-DFT) calculation revealed that the process of photoinduced electron transfer (PET) from the N-oxide moiety to the dansyl amide fluorophore accounts for the quenching mechanism of N-oxide. This probe also showed high selectivity over various nucleophilic amino acids and good biocompatibility in physiological conditions. The successful application of the probe in HaloTag protein labeling and HepG2 live-cell imaging proves it a valuable tool for visualization of biomolecules.

Endophytes isolated from Panax notoginseng converted ginsenosides

Endophytes may participate in the conversion of metabolites within medicinal plants, influencing the efficacy of host. However, the distribution of endophytes within medicinal plants P. notoginseng and how it contributes to the conversion of saponins are not well understood. Here, we determined the distribution of saponins and endophytes within P. notoginseng compartments and further confirm the saponin conversion by endophytes. We found metabolites showed compartment specificity within P. notoginseng. Potential saponin biomarkers, such as Rb1, Rg1, Re, Rc and Rd, were obtained. Endophytic diversity, composition and co-occurrence networks also showed compartment specificity, and bacterial alpha diversity values were highest in root compartment, consistently decreased in the stem and leaf compartments, whereas those of fungi showed the opposite trend. Potential bacterial biomarkers, such as Rhizobium, Bacillus, Pseudomonas, Enterobacter, Klebsiella, Pantoea and fungal biomarkers Phoma, Epicoccum, Xylariales, were also obtained. Endophytes related to saponin contents were found by Spearman correlation analysis, and further verification experiments showed that Enterobacter chengduensis could convert ginsenoside Rg1 to F1 at a rate of 13.24%; Trichoderma koningii could convert ginsenoside Rb1 to Rd at a rate of 40.00% and to Rg3 at a rate of 32.31%; Penicillium chermesinum could convert ginsenoside Rb1 to Rd at a rate of 74.24%.

Do East Asians With Normal Glucose Tolerance Have Worse β-Cell Function? A Meta-Analysis of Epidemiological Studies

BACKGROUND

The difference in the relationship between β-cell function and insulin resistance among Africans, Caucasians and East Asians with normal glucose tolerance (NGT) was not well investigated.

METHODS

We searched PubMed and Web of Science with keywords and identified studies that used the homeostasis model assessment (HOMA) model to evaluate β-cell function (HOMA-B) and insulin sensitivity/resistance (HOMA-S/HOMA-IR) in certain ethnic groups. We used random-effect model to pool data of HOMAs and compared the combined data among the three ethnic groups using subgroup analysis. Linear regression analysis was used to estimate the coefficient of HOMA-S on HOMA-B in these ethnic groups.

RESULTS

We evaluated pooled data of HOMAs in eight African, 26 Caucasian, and 84 East Asian cohorts with NGT, and also 2,392, 6,645 and 67,317 individuals, respectively. The three ethnic groups had distinct HOMA-B but similar HOMA-IR. The regression coefficient of lnHOMA-B on lnHOMA-S was different between Africans and Caucasians (-1.126 vs -0.401, P = 0.0006) or East Asian (-1.126 vs -0.586, P = 0.0087), but similar between Caucasians and East Asians (-0.401 vs -0.586, P = 0.1282). The coefficient in all ethnic groups was similar when age, BMI, and gender were adjusted (African vs Caucasian P = 0.0885, African vs East Asian P = 0.1092, and Caucasian vs East Asian P = 0.6298).

CONCLUSIONS

In subjects with NGT, East Asians had lower HOMA-B but similar β-cell response relative to insulin resistance with Caucasians and Africans when age, BMI, and gender were controlled. This result may challenge the allegation that there was an Asian-specific diabetes phenotype with worse β-cell function.