Search

Gengyan Xiong,1,* Lin Yao,1,* Peng Hong,1,* Li Yang,2 Weimin Ci,3 Libo Liu,1 Qun He,1 Kan Gong,1 Xuesong Li,1 Liqun Zhou1 1Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China; 2Department of Nephrology, Peking University First Hospital, Beijing, China; 3Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China *These authors contributed equally to this work Background: In China, upper tract urothelial carcinoma (UTUC) is less prevalent but more malignant in males. This study investigates the prognostic factors and causes of gender-based differences in Chinese populations. Methods: Between 1999 and 2011, 687 UTUC patients who underwent surgery were utilized for this study. We evaluated the differences in oncological characteristics, epigenetic biomarkers, cancer-specific survival (CSS), bladder recurrence (BR) rate, and contralateral upper tract recurrence (CUTR) rate. Smoking history, benzene exposure history, and the history of using aristolochic acid (AA) containing herbs were analyzed in detail. Results: Compared with male patients, female patients showed poorer renal function, lower proportions of tumor stage III/IV, and smaller tumor diameters. The CSS in male patients was lower than that in female patients. Significant gender-related differences were observed concerning various prognostic factors. In female patients, poorer survival rates were attributed to the primary tumor location in the ureter, large diameter primary tumors, severe chronic kidney disease, papillary tumor architecture, high tumor stages, positive N status, and methylated ABCC6 promoters. In male patients, older age, ipsilateral hydronephrosis, large tumor diameters, sessile tumor architecture, high tumor stages, and methylated TMEFF2 promoters were associated with higher cancer-specific mortality. AA might be the main cause of these gender-based differences. The AA-induced UTUC patients presented smaller tumor diameters, lower tumor stages, fewer positive N statuses, more multifocal tumors, lower methylation indices, and poorer renal function. Although AA-induced UTUC patients exhibited better survival rates, BR and CUTR rates were significantly worse. Conclusion: In China, there exist significant AA-induced differences between male and female UTUC patients. The bladders and contralateral upper urinary tracts of AA-induced UTUC patients should be carefully monitored after surgery. Keywords: upper tract urothelial carcinoma, aristolochic acid, gender difference, oncological outcomes, China

Praeruptorin A (PA) is a pyranocoumarin compound isolated from the dried root of Peucedanum praeruptorum Dunn (Umbelliferae). However, the antiinflammatory effect of PA has not been reported. The present study investigated the antiinflammatory effect of PA in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage cells. PA significantly inhibited the LPS-induced production of nitric oxide (NO), interleukin-1[beta] (IL-1[beta]) and tumor necrosis factor-[alpha] (TNF-[alpha]). The mRNA and protein expressions of inducible nitric oxide synthase (iNOS), IL-1[beta] and TNF-[alpha] were also suppressed by this compound. Further study showed that PA decreased the cytoplasmic loss of inhibitor [kappa]B-[alpha] (I[kappa]B-[alpha]) protein and inhibited the translocation of NF-[kappa]B from cytoplasm to nucleus. Taken together, the results suggest that PA may exert antiinflammatory effects in vitro in LPS-stimulated RAW 264.7 macrophages through inhibition of NF-[kappa]B signal pathway activation. Copyright © 2010 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Objective: Exploring the effect of Optimized New Shengmai powder (, ONSMP) on myocardial fibrosis in heart failure (HF) based on rat sarcoma (RAS)/rapidly accelerated fibrosarcoma (RAF)/mitogen-activated protein kinase kinase (MEK)/extracellular regulated protein kinases (ERK) signaling pathway., Methods: Randomized 70 Sprague-Dawley rats into sham ( n = 10) and operation ( n = 60) groups, then established the HF rat by ligating the left anterior descending branch of the coronary artery. We randomly divided the operation group rats into the model, ONSMP [including low (L), medium (M), and high (H) dose], and enalapril groups. After the 4-week drug intervention, echocardiography examines the cardiac function and calculates the ratios of the whole/left heart to the rat's body weight. Finally, we observed the degree of myocardial fibrosis by pathological sections, determined myocardium collagen (COL) I and COL Ⅲ content by enzyme-linked immunosorbent assay, detected the mRNA levels of COL I, COL Ⅲ, α-smooth muscle actin (α-SMA), and c-Fos proto-oncogene (c-Fos) by universal real-time, and detected the protein expression of p-RAS, p-RAF, p-MEK1/2, p-ERK1/2, p-ETS-like-1 transcription factor (p-ELK1), p-c-Fos, α-SMA, COL I, and COL Ⅲ by Western blot., Results: ONSMP can effectively improve HF rat's cardiac function, decrease cardiac organ coefficient, COL volume fraction, and COL I/Ⅲ content, down-regulate the mRNA of COL I/Ⅲ, α-SMA and c-Fos, and the protein of p-RAS, p-RAF, p-MEK1/ 2, p-ERK1/2, p-ELK1, c-Fos, COL Ⅰ/Ⅲ, and α-SMA., Conclusions: ONSMP can effectively reduce myocardial fibrosis in HF rats, and the mechanism may be related to the inhibition of the RAS/RAF/MEK/ERK signaling pathway.

DNA cytosine methylation (5-methylcytosine, 5mC) is a predominant epigenetic modification that plays a critical role in a variety of biological and pathological processes in mammals. In active DNA demethylation, the 10-11 translocation (TET) dioxygenases can sequentially oxidize 5mC to generate three modified forms of cytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Beyond being a demethylation intermediate, recent studies have shown that 5fC has regulatory functions in gene expression and chromatin organization. While some methods have been developed to detect 5fC, genome-wide mapping of 5fC at base resolution is still highly desirable. Herein, we propose a chemical labeling enrichment and deamination sequencing (CLED-seq) method for detecting 5fC in genomic DNA at single-base resolution. The CLED-seq method utilizes selective labeling and enrichment of 5fC-containing DNA fragments, followed by deamination mediated by apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (APOBEC3A or A3A) and sequencing. In the CLED-seq process, while all C, 5mC, and 5hmC are interpreted as T during sequencing, 5fC is still read as C, enabling the precise detection of 5fC in DNA. Using the proposed CLED-seq method, we accomplished genome-wide mapping of 5fC in mouse embryonic stem cells. The mapping study revealed that promoter regions enriched with 5fC overlapped with H3K4me1, H3K4me3, and H3K27ac marks. These findings suggest a correlation between 5fC marks and active gene expression in mESCs. In conclusion, CLED-seq is a straightforward, bisulfite-free method that offers a valuable tool for detecting 5fC in genomes at a single-base resolution.

The development and application of artificial intelligence have led to the exploitation of low-power and compact intelligent information-processing systems integrated with sensing, memory, and neuromorphic computing functions. The 2D van der Waals (vdW) materials with abundant reservoirs for arbitrary stacking based on functions and enabling continued device downscaling offer an attractive alternative for continuously promoting artificial intelligence. In this study, full 2D SnS 2 /h-BN/CuInP 2 S 6 (CIPS)-based ferroelectric field-effect transistors (Fe-FETs) and utilized light-induced ferroelectric polarization reversal to achieve excellent memory properties and multi-functional sensing-memory-computing vision simulations are designed. The device exhibits a high on/off current ratio of over 10 5 , long retention time (>10 4  s), stable cyclic endurance (>350 cycles), and 128 multilevel current states (7-bit). In addition, fundamental synaptic plasticity characteristics are emulated including paired-pulse facilitation (PPF), short-term plasticity (STP), long-term plasticity (LTP), long-term potentiation, and long-term depression. A ferroelectric optoelectronic reservoir computing system for the Modified National Institute of Standards and Technology (MNIST) handwritten digital recognition achieved a high accuracy of 93.62%. Furthermore, retina-like light adaptation and Pavlovian conditioning are successfully mimicked. These results provide a strategy for developing a multilevel memory and novel neuromorphic vision systems with integrated sensing-memory-processing., (© 2023 The Authors. Advanced Science published by Wiley-VCH GmbH.)

The epigenetic modification 5-hydroxymethylcytosine (5hmC) plays a crucial role in the regulation of gene expression. Although some methods have been developed to detect 5hmC, direct genome-wide mapping of 5hmC at base resolution is still highly desirable. Herein, we proposed a single-step deamination sequencing (SSD-seq) method, designed to precisely map 5hmC across the genome at single-base resolution. SSD-seq takes advantage of a screened engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein, known as eA3A-v10, to selectively deaminate cytosine (C) and 5-methylcytosine (5mC) but not 5hmC. During sequencing, the deaminated C and 5mC are converted to uracil (U) and thymine (T), read as T in the sequencing data. However, 5hmC remains unaffected by eA3A-v10 and is read as C during sequencing. Consequently, the presence of C in the sequence reads indicates the original 5hmC. We applied SSD-seq to generate a base-resolution map of 5hmC in human lung tissue. Our findings revealed that 5hmC was predominantly localized to CpG dinucleotides. Furthermore, the base-resolution map of 5hmC generated by SSD-seq demonstrated a strong correlation with prior ACE-seq results. The advantages of SSD-seq are its single-step process, absence of bisulfite treatment or DNA glycosylation, cost effectiveness, and ability to detect and quantify 5hmC directly at single-base resolution., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Background: Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary tumor syndrome with an incidence of approximately 1/36,000. VHL disease-associated clear cell renal cell carcinoma (ccRCC) is the most common congenital RCC. Although recent advances in treating RCC have improved the long-term prognosis of patients with VHL disease, kidney cancer is still the leading cause of death in these patients. Therefore, finding new targets for diagnosing and treating VHL disease-associated ccRCC is still essential., Methods: In this study, we collected matched tumor tissues and normal samples from 25 patients with VHL disease-associated ccRCC, diagnosed and surgically treated in the Department of Urology, Peking University First Hospital. After screening, we performed whole genome bisulfite sequencing (WGBS) on 23 pairs of tissues and RNA-seq on 6 pairs of tissues. And we also compared the VHL disease-associated ccRCC transcriptome data with the sporadic ccRCC transcriptome data from the The Cancer Genome Atlas (TCGA) public database RESULTS: We found that the methylation level of VHL disease-associated ccRCC tumor tissues was significantly lower than that of normal tissues. The tumor tissues showed a difference in the copy number of 3p loss and 5q and 7q gain compared with normal tissues. We integrated RNA-seq and WGBS data to reveal methylation candidate genes associated with VHL disease-associated ccRCC; our results showed 124 hypermethylated and downregulated genes, and 245 hypomethylated and upregulated genes. By comparing the VHL disease-associated ccRCC transcriptome data with the sporadic ccRCC transcriptome data from the TCGA public database, we found that the major pathways of differential gene enrichment differed between them., Conclusions: Our study mapped the multiomics of copy number variation, methylation and mRNA level changes in tumor and normal tissues of clear cell renal cell carcinoma with VHL syndrome, which provides a solid foundation for the mechanistic study, biomarker screening, and therapeutic target discovery of clear cell renal cell carcinoma., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

N 6 -Methyladenine (6mA) is a naturally occurring DNA modification in both prokaryotes and eukaryotes. Herein, we developed a deaminase-mediated sequencing (DM-seq) method for genome-wide mapping of 6mA at single-nucleotide resolution. The method capitalizes on the selective deamination of adenine, but not 6mA, in DNA mediated by an evolved adenine deaminase, ABE8e. By employing this method, we achieved genome-wide mapping of 6mA in Escherichia coli and in mammalian mitochondrial DNA (mtDNA) at single-nucleotide resolution. We found that the 6mA sites are mainly located in the GATC motif in the E. coli genome. We also identified 17 6mA sites in mtDNA of HepG2 cells, where all of the 6mA sites are distributed in the heavy strand of mtDNA. We envision that DM-seq will be a valuable tool for uncovering new functions of 6mA in DNA and for exploring its potential roles in mitochondria-related human diseases., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

N 6 -methyladenosine (m 6 A), the most prevalent mRNA modification in eukaryotic cells, is known to play regulatory roles in a wide array of biological processes, including aging and cellular senescence. To investigate such roles, the m 6 A modification can be identified across the entire transcriptome by immunoprecipitation of methylated RNA with an anti-m 6 A antibody, followed by high-throughput sequencing (meRIP-seq or m 6 A-seq). Presented here is a protocol for employing meRIP-seq to profile the RNA m 6 A landscape in senescent human cells. We described, in detail, sample preparation, mRNA isolation, immunoprecipitation, library preparation, sequencing, bioinformatic analysis and validation. We also provided tips and considerations for the optimization and interpretation of the results. Our protocol serves as a methodological resource for investigating transcriptomic m 6 A alterations in cellular senescence as well as a valuable paradigm for the validation of genes of interest., (© 2013-2023 The Journal of Biological Methods, All rights reserved.)

We investigated the effects of dietary supplementation with Lactobacillus acidophilus and Bacillus subtilis on the intestinal immune response, intestinal barrier function, cecal microbiota profile, and metabolite profile in late-phase laying hens. Hens were divided into three groups and fed with the basal diet (NC group), basal diet supplementation with 250 mg/kg B. subtilis and L. acidophilus mixture powder (LD group), and basal diet supplementation with 500 mg/kg B. subtilis and L. acidophilus mixture powder (HD group), respectively. The results indicated that the dietary supplementation with L. acidophilus and B. subtilis increased the integrity of the intestinal barrier as evidenced by the significant increase in the number of ileal goblet cells and improve the expression of occludin, claudin-1, and ZO-1 genes in the HD group. Moreover, the levels of IL-6, TNF-α, and IFN-γ were significantly decreased in the LD and HD groups. The levels of immunoglobulin G (IgG) increased in the LD and HD group, and the levels of secretory immunoglobulin A (sIgA) increased with the HD treatment. Furthermore, 16 s rRNA sequencing revealed L. acidophilus in combination with B. subtilis increased the diversity of gut microbiota. The metabolomic analysis revealed beneficial changes in the amino acid metabolism and lipid metabolism (decrease in LysoPC and LysoPE levels). In conclusion, dietary supplementation with L. acidophilus and B. subtilis could improve intestinal barrier function and maintain immune homeostasis. These beneficial effects may be associated with the modulation of the intestinal microbiome and metabolites., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The implication of the monocyte-to-high-density lipoprotein ratio (MHR) in Takayasu arteritis (TAK) remains unclear., Objective: We aimed to assess the predictive value of the MHR to identify coronary involvement with TAK and determine the patient prognosis., Methods: In this retrospective study, 1,184 consecutive patients with TAK were collected and assessed, and those who were initially treated and with coronary angiography were enrolled and classified according to coronary involvement or no involvement. Binary logistic analysis was performed to assess coronary involvement risk factors. Receiver-operating characteristic analysis was used to determine the MHR value to predict coronary involvement in TAK. Major adverse cardiovascular events (MACEs) were recorded in patients with TAK and coronary involvement within a 1-year follow-up, and Kaplan-Meier survival curve analysis was conducted to compare MACEs between them stratified by the MHR., Results: A total of 115 patients with TAK were included in this study, and 41 of them had coronary involvement. A higher MHR was found for TAK with coronary involvement than for TAK without coronary involvement ( P = 0.014). Multivariate analysis showed that the MHR is an independent risk factor for coronary involvement in TAK (odds ratio: 92.718, 95% confidence interval ( CI ): 2.813-3056.291, P = 0.011). With the best cut-off value of 0.35, the MHR identified coronary involvement with 53.7% sensitivity and 68.9% specificity [area under the curve (AUC): 0.639, 95% CI : 0.544-0.726, P= 0.010] and identified left main disease and/or three-vessel disease (LMD/3VD) with 70.6% sensitivity and 66.3% specificity (AUC: 0.704, 95% CI : 0.612-0.786, P = 0.003) in TAK. Combined with other variables, the MHR identified coronary involvement with 63.4% sensitivity and 90.5% specificity (AUC: 0.852, 95% CI : 0.773-0.911, P < 0.001), and identified LMD/3VD with 82.4% sensitivity and 78.6% specificity (AUC: 0.827, 95% CI : 0.720-0.934, P < 0.001) in TAK. A total of 39 patients with TAK and coronary involvement were followed up for 1 year, and 5 patients suffered a MACE. Those with an MHR >0.35 had a higher MACE incidence than their counterparts with an MHR ≤0.35 (χ 2  =   4.757, P = 0.029)., Conclusions: The MHR could be a simple, practical biomarker for identifying coronary involvement and LMD/3VD in TAK and predicting a long-term prognosis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Ci, Wan, Han, Zou, Ge, Pan and Jin.)

How N 6 -methyladenosine (m 6 A), the most abundant mRNA modification, contributes to primate tissue homeostasis and physiological aging remains elusive. Here, we characterize the m 6 A epitranscriptome across the liver, heart and skeletal muscle in young and old nonhuman primates. Our data reveal a positive correlation between m 6 A modifications and gene expression homeostasis across tissues as well as tissue-type-specific aging-associated m 6 A dynamics. Among these tissues, skeletal muscle is the most susceptible to m 6 A loss in aging and shows a reduction in the m 6 A methyltransferase METTL3. We further show that METTL3 deficiency in human pluripotent stem cell-derived myotubes leads to senescence and apoptosis, and identify NPNT as a key element downstream of METTL3 involved in myotube homeostasis, whose expression and m 6 A levels are both decreased in senescent myotubes. Our study provides a resource for elucidating m 6 A-mediated mechanisms of tissue aging and reveals a METTL3-m 6 A-NPNT axis counteracting aging-associated skeletal muscle degeneration., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant., (© 2023. Science China Press.)

Objectives: Disorders of humoral immunity in Takayasu's arteritis (TAK) have not been well explored. This study describes the characteristics of B cells and immunoglobulin (Ig) profile in patients with TAK., Methods: Peripheral B cell populations assessed using flow cytometry and serum Ig levels assessed using a biochemical analyser in 98 newly diagnosed patients with TAK were analysed and compared with those of 31 patients with systemic lupus erythematosus (SLE) and 60 healthy controls (HCs). CD19+ B cell and IgG infiltration to the aortic tissue was evaluated by immunohistochemical staining., Results: The proportion of peripheral CD3-CD19+ B cells and levels of serum IgG in TAK were lower than those in SLE, but higher than those in HCs. CD3-CD19+ B cell counts were higher in TAK than in HCs. Serum IgG and IgG1 levels were higher in active TAK than in non-active TAK. In TAK, positive correlations of serum IgG levels with erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) level, Kerr score, and Indian Takayasu Clinical Activity Score (ITAS2010, ITAS-A) were observed before immunotherapy. After 6 months of immunotherapy, serum Ig levels significantly decreased. Positive correlations between the changes in IgG levels and values of ESR, CRP, Kerr score, and ITAS-A were detected. Immunohistochemical staining confirmed CD19+ B cell and IgG infiltration to the aortic wall in patients with TAK., Conclusions: Enhanced B cells might contribute to the pathogenesis of TAK, and serum IgG levels could serve as a simple, useful biomarker to assess disease activity and monitor treatment response in TAK.

This article is concerned with the robust model predictive control (RMPC) problem for polytopic uncertain systems under the round-robin (RR) scheduling in the high-rate communication channel. From a set of sensors to the controller, several sensors transmit the data to the remote controller via a shared high-rate communication network, data collision might happen if these sensors start transmissions at the same time. For the sake of preventing data collision in the high-rate communication channel, a communication scheduling known as RR is used to arrange the data transmission order, where only one node with token is allowed to send data at each transmission instant. In accordance with the token-dependent Lyapunov-like approach, the aim of the problem addressed is to design a set of controllers in the framework of RMPC such that the asymptotical stability of the closed-loop system is guaranteed. By taking the effect of the underlying RR scheduling in the high-rate communication channel into consideration, sufficient conditions are obtained by solving a terminal constraint set of an auxiliary optimization problem. In addition, an algorithm including both off-line and online parts is provided to find a sub-optimal solution. Finally, two simulation examples are used to demonstrate the usefulness and effectiveness of the proposed RMPC strategy., Competing Interests: The authors declare that they have no competing interests., (© 2023 Wang et al.)

Background: Current methods for the detection and surveillance of urothelial carcinomas (UCs) are often invasive, costly, and not effective for low-grade, early-stage, and minimal residual disease (MRD) tumors. We aimed to develop and validate a model from urine sediments to predict different grade and stage UCs with low cost and high accuracy., Methods: We collected 167 samples, including 90 tumors and 77 individuals without tumors, as a discovery cohort. We assessed copy number variations and methylation values for them and constructed a diagnostic classifier to detect UC, UCseek, by using an individual read-based method and support vector machine. The performance of UCseek was validated in an independent cohort derived from three hospitals (n = 206) and a relapse cohort (n = 42) for monitoring recurrence., Findings: We constructed UCseek, which could predict UCs with high sensitivity (92.7%), high specificity (90.7%), and high accuracy (91.7%) in the independent validation set. The accuracy of UCseek in low-grade and early-stage patients reached 91.8% and 94.3%, respectively. Notably, UCseek retained great performance at ultralow sequencing depths (0.3X-0.5X). It also demonstrated a powerful ability to monitor recurrence in a surveillance cohort compared with cystoscopy (90.91% vs. 59.09%)., Interpretation: We optimized an improved approach named UCseek for the noninvasive diagnosis and monitoring of UCs in both low- and high-grade tumors and in early- and advanced-stage tumors, even at ultralow sequencing depths, which may reduce the burden of cystoscopy and blind second surgery., Funding: A full list of funding bodies that contributed to this study can be found in the Acknowledgments section., Competing Interests: Declaration of interests The authors declare no potential conflicts of interest., (Copyright © 2023. Published by Elsevier B.V.)

Rationale: Immune checkpoint inhibitors (ICIs) have revolutionized the management of locally advanced or metastatic urothelial carcinoma. Strikingly, compared to urothelial carcinoma of the bladder (UCB), upper tract urothelial carcinoma (UTUC) has a higher response rate to ICIs. The stratification of patients most likely to benefit from ICI therapy remains a major clinical challenge. Methods: In this study, we performed the first single-cell RNA sequencing (scRNA-seq) study of 13 surgical tissue specimens from 12 patients with UTUC. The key results were validated by the analysis of two independent cohorts with bulk RNA-seq data for UCB (n = 404) and UTUC (n = 158) and one cohort of patients with metastatic urothelial carcinoma (mUC) who were treated with atezolizumab (n = 348). Results: Using scRNA-seq, we observed a higher proportion of tumor-infiltrating immune cells in locally advanced UTUC. Similar prognostically relevant intrinsic basal and luminal-like epithelial subtypes were found in both UTUC and UCB, although UTUC is predominantly of the luminal subtype. We also discovered that immunosuppressive macrophages and exhausted T-cell subpopulations were enriched in the basal subtype and showed enhanced interactions. Furthermore, we developed a gene expression signature (Macro-C3 score) capturing the immunosuppressive macrophages that better predicts outcomes than the currently established subtypes. We also developed a computational method to model immune evasion, and the Macro-C3 score predicted therapeutic response of mUC treated with first-line anti-PD-L1 inhibitors in patients with lower basal scores. Conclusions: Overall, the distinct microenvironment and Macro-C3 score provide an explanation for ICI efficacy in urothelial carcinoma and reveal new candidate regulators of immune evasion, suggesting potential therapeutic targets for improving antitumor immunity in the basal subtype., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Aim: Systemic lupus erythematosus (SLE) with severe coronary artery disease (CAD) is associated with increased mortality. This study aimed to assess the characteristics and risk factors of severe CAD in SLE., Method: This multicenter, cross-sectional study enrolled consecutive patients with SLE included in the Chinese Rheumatism Date Center registry. Patients with severe CAD including angiography-confirmed stenosis ≥50% in the left main, ≥70% in other major coronary arteries, or myocardial infarction were classified into the CAD group. Patients without CAD were classified into the control group. Subgroups were stratified according to age (set as above and below 45 and 50 for men and women, respectively) and gender. Binary logistic regression analysis was performed to determine independent risk factors of severe CAD in SLE., Results: Forty-three patients had severe CAD from a total of 3744 patients with SLE, 30 of whom were female; 35 belonged to the older age group and 8 belonged to the younger age group. In older patients, independent risk factors included age, 5 major CAD risk factors, SLE Disease Activity Index 2000 (SLEDAI-2K), hyperuricemia, and corticosteroid exposure. In younger patients, the risk factors were 5 major CAD risk factors and positive antiphospholipid antibody (APL). Male risk factors were age and 5 major CAD risk factors, whereas female risk factors were age, 5 major CAD risk factors, SLEDAI-2K, and positive APL. Three-vessel disease was most prevalent in patients with severe CAD., Conclusion: We recommend screening for severe CAD in patients with SLE with age- and gender-stratified risk factors., (© 2022 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.)

Background: DNA 5-hydroxymethylcytosine (5hmC) is produced by dynamic 5mC oxidation process contributing to tissue specification, and loss of 5hmC has been reported in multiple cancers including genitourinary cancers. However, 5hmC is also cell-type specific, and its variability may exist between differentiated tumor cells and cancer stem cells. Thus, cancer-associated changes in 5hmC may be contributed by distinct sets of tumor cells within the tumor tissues., Results: Here, we applied a sensitive immunoprecipitation-based method (hMeDIP-seq) to analyze 5hmC changes during genitourinary carcinogenesis (including prostate, urothelial and kidney). We confirmed the tissue-specific distribution of 5hmC in genitourinary tissues and identified regional gain and global loss of 5hmC coexisting in genitourinary cancers. The genes with gain of 5hmC during tumorigenesis were functionally enriched in regulating stemness and hypoxia, whereas were associated with poor clinical prognosis irrespective of their differences in tumor type. We identified that gain of 5hmC occurred in soft fibrin gel-induced 3D tumor spheres with a tumor-repopulating phenotype in two prostate cancer cell lines, 22RV1 and PC3, compared with conventional two-dimensional (2D) rigid dishes. Then, we defined a malignant signature derived from the differentially hydroxymethylated regions affected genes of cancer stem-like cells, which could predict a worse clinical outcome and identified phenotypically malignant populations of cells from prostate cancer tumors. Notably, an oxidation-resistant vitamin C derivative, ascorbyl phosphate magnesium, restored 5hmC and killed the cancer stem cell-like cells leading to apoptosis in prostate cancer cell lines., Conclusions: Collectively, our study dissects the regional gain of 5hmC in maintaining cancer stem-like cells and related to poor prognosis, which provides proof of concept for an epigenetic differentiation therapy with vitamin C by 5hmC reprogramming., (© 2022. The Author(s).)

N 4 -methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. In the 4mC-AMD-seq method, cytosine and 5-methylcytosine (5mC) are deaminated by APOBEC3A (A3A) protein to generate uracil and thymine, both of which are read as thymine in sequencing, while 4mC is resistant to deamination and therefore read as cytosine. Thus, the readouts of cytosines from sequencing could manifest the original 4mC sites in genomes. With the 4mC-AMD-seq method, we achieved the genome-wide mapping of 4mC in Deinococcus radiodurans ( D. radiodurans ). In addition, we confirmed that 4mC, but not 5mC, was the major modification in the D. radiodurans genome. We identified 1586 4mC sites in the genome of D. radiodurans , among which 564 sites were located in the CCGCGG motif. The average methylation levels in the CCGCGG motif and non-CCGCGG sequence were 70.0% and 22.8%, respectively. We envision that the 4mC-AMD-seq method will facilitate the investigation of 4mC functions, including the 4mC-involved R-M systems, in uncharacterized but potentially useful strains., Competing Interests: The authors declare no competing financial interest., (This journal is © The Royal Society of Chemistry.)

Background: At present, the extent and clinical relevance of epigenetic differences between upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) remain largely unknown. Here, we conducted a study to describe the global DNA methylation landscape of UTUC and UCB and to address the prognostic value of DNA methylation subtype and responses to the DNA methyltransferase inhibitor SGI-110 in urothelial carcinoma (UC)., Methods: Using whole-genome bisulfite sequencing (n = 49 samples), we analyzed epigenomic features and profiles of UTUC (n = 36) and UCB (n = 9). Next, we characterized potential links between DNA methylation, gene expression (n = 9 samples), and clinical outcomes. Then, we integrated an independent UTUC cohort (Fujii et al., n = 86) and UCB cohort (TCGA, n = 411) to validate the prognostic significance. Furthermore, we performed an integrative analysis of genome-wide DNA methylation and gene expression in two UC cell lines following transient DNA methyltransferase inhibitor SGI-110 treatment to identify potential epigenetic driver events that contribute to drug efficacy., Results: We showed that UTUC and UCB have very similar DNA methylation profiles. Unsupervised DNA methylation classification identified two epi-clusters, Methy-High and Methy-Low, associated with distinct muscle-invasive statuses and patient outcomes. Methy-High samples were hypermethylated, immune-infiltrated, and enriched for exhausted T cells, with poor clinical outcome. SGI-110 inhibited the migration and invasion of Methy-High UC cell lines (UMUC-3 and T24) by upregulating multiple antitumor immune pathways., Conclusions: DNA methylation subtypes pave the way for predicting patient prognosis in UC. Our results provide mechanistic rationale for evaluating SGI-110 in treating UC patients in the clinic., (© 2022. The Author(s).)

In this paper, a simultaneous localization and mapping algorithm based on the weighted asynchronous fusion of laser and vision sensors is proposed for an assistant robot. When compared to the synchronous fusion algorithm, this method can effectively use the redundant data in the vision sensor and improve the tracking accuracy of the algorithm. At the same time, the attitude estimation of the visual sensor is taken as a prior of the attitude estimation of the laser sensor to reduce the number of iterations and improve the efficiency of the algorithm. Further, according to the running state of the robot, a weighting coefficient based on angle is introduced to improve the confidence of the measurement. Experimental results show that the algorithm is robust and can work in a degraded environment. When compared to the synchronous fusion method, the asynchronous fusion algorithm has a more accurate prior, faster operation speed, higher pose estimation frequency, and more accurate positioning accuracy., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xing, Zhang, Lin, Ci and Dong.)

Prostate cancer (PCa) is a complex disease. An ongoing accumulation of mutations results in increased genetic diversity, with the tumor acquiring distinct subclones. However, non-genetic intra-tumoral heterogeneity, the cellular differentiation state and the interplay between subclonal evolution and transcriptional heterogeneity are poorly understood. Here, the authors perform single-cell RNA sequencing from 14 untreated PCa patients. They create an extensive cell atlas of the PCa patients and mapped developmental states onto tumor subclonal evolution. They identify distinct subclones across PCa patients and then stratify tumor cells into four transcriptional subtypes, EMT-like (subtype 0), luminal A-like (subtype 1), luminal B/C-like (subtype 2), and basal-like (subtype 3). These subtypes are hierarchically organized into stem cell-like and differentiated status. Strikingly, multiple subclones within a single primary tumor present with distinct combinations of preferential subtypes. In addition, subclones show different communication strengths with other cell types within the tumor ecosystem, which may modulate the distinct transcriptional subtypes of the subclones. Notably, by integrating TCGA data, they discover that both tumor cell transcriptional heterogeneity and cellular ecosystem diversity correlate with features of a poor prognosis. Collectively, their study provides the analysis of subclonal and transcriptional heterogeneity and its implication for patient prognosis., (© 2022 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Pyroptosis has profound impacts on tumor cell proliferation, invasion, and metastasis and is of great clinical significance for different cancers. However, the role of pyroptosis in the progression and prognosis of muscle invasive bladder cancer (MIBC) remains poorly characterized. Here, we collected multicenter MIBC data and performed integrated analysis to dissect the role of pyroptosis in MIBC and provide an optimized treatment for this disease. Based on transcriptomic data, we developed a novel prognostic model named the pyroptosis-related gene score (PRGScore), which summarizes immunological features, genomic alterations, and clinical characteristics associated with the pyroptosis phenotype. Samples with high PRGScore showed enhancement in CD8 + T cell effector function, antigen processing machinery and immune checkpoint and better response to immunotherapy by programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors, which indicates that PRGScore is a valuable signature in the identification of populations sensitive to immune checkpoint inhibitors. Collectively, our study provides insights into further research targeting pyroptosis and its tumor immune microenvironment (TME) and offers an opportunity to optimize the treatment of MIBC., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Tan, Zhang, Shi, Qi, Zou and Ci.)

Background: Vascular invasion with tumor thrombus frequently occurs in advanced renal cell carcinoma (RCC). Thrombectomy is one of the most challenging surgeries with high rate of perioperative morbidity and mortality. However, the mechanisms driving tumor thrombus formation are poorly understood which is required for designing effective therapy for eliminating tumor thrombus., Results: We perform single-cell RNA sequencing analysis of 19 surgical tissue specimens from 8 clear cell renal cell carcinoma (ccRCC) patients with tumor thrombus. We observe tumor thrombus has increased tissue resident CD8 + T cells with a progenitor exhausted phenotype compared with the matched primary tumors. Remarkably, macrophages, malignant cells, endothelial cells and myofibroblasts from TTs exhibit enhanced remodeling of the extracellular matrix. The macrophages and malignant cells from primary tumors represent proinflammatory states, but also increase the expression of immunosuppressive markers compared to tumor thrombus. Finally, differential gene expression and interaction analyses reveal that tumor-stroma interplay reshapes the extracellular matrix in tumor thrombus associated with poor survival., Conclusions: Our comprehensive picture of the ecosystem of ccRCC with tumor thrombus provides deeper insights into the mechanisms of tumor thrombus formation, which may aid in the design of effective neoadjuvant therapy to promote downstaging of tumor thrombus and decrease the perioperative morbidity and mortality of thrombectomy., (© 2022. The Author(s).)

Renal cell carcinoma (RCC) is one of the most common urological cancers. RCC has a poor prognosis and is considered a metabolic disease. It has been reported that many metabolic pathways are associated with the development of RCC. However, the prognostic value of metabolism-related genes in RCC is unclear. We herein aimed to establish a scoring system based on the gene expression profile of metabolic genes to evaluate the response to immunotherapy and predict the prognosis of RCC. In this study, we collected multicentre RCC data and performed integrated analysis to characterize the role of tumour metabolism in RCC and explore the relationship between metabolism and prognosis and immune therapy. Based on transcriptomic data, metabolism-related genes were used for nonnegative matrix factorization clustering. We obtained three subclasses of RCC (M1, M2, and M3), and they are associated with different prognoses and immune infiltrate levels. Then, based on the pathway activity of 113 metabolism-related gene signatures, we classified patients into three distinct metabolism-related signatures. Finally, we provide a metabolism-related pathway score (MRPScore) that is significantly associated with RCC prognosis and the response to immunotherapy. Taken together, in this study, we established an RCC classification system based on metabolic gene expression profiles that could further the understanding of the diversity of RCC. We also present the MRPScore, which may be used as an indicator to predict the response to clinical immune therapy., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Zhang, Shi, Wang, Gong, He, Li, Feng, Wang, Jiang, Ci, Li and Zhou.)

Background: Vitamin C deficiency is found in patients with variable kidney diseases. However, the role of vitamin C as an epigenetic regulator in renal homeostasis and pathogenesis remains largely unknown., Methods: We showed that vitamin C deficiency leads to acute tubular necrosis (ATN) using a vitamin C-deficient mouse model ( Gulo knock-out). DNA/RNA epigenetic modifications and injured S3 proximal tubule cells were identified in the vitamin C-deficient kidneys using whole-genome bisulfite sequencing, methylated RNA immunoprecipitation sequencing, and single-cell RNA sequencing., Results: Integrated evidence suggested that epigenetic modifications affected the proximal tubule cells and fenestrated endothelial cells, leading to tubule injury and hypoxia through transcriptional regulation. Strikingly, loss of DNA hydroxymethylation and DNA hypermethylation in vitamin C-deficient kidneys preceded the histologic sign of tubule necrosis, indicating the causality of vitamin C-induced epigenetic modification in ATN. Consistently, prophylactic supplementation of an oxidation-resistant vitamin C derivative, ascorbyl phosphate magnesium, promoted DNA demethylation and prevented the progression of cisplatin-induced ATN., Conclusions: Vitamin C played a critical role in renal homeostasis and pathogenesis in a mouse model, suggesting vitamin supplementation may be an approach to lower the risk of kidney injury., (Copyright © 2022 by the American Society of Nephrology.)

Objective: To compare the effects of cutting and retaining the pes anserinus tendon on effectiveness following tibial plateau fracture., Methods: A clinical data of 40 patients with tibial plateau fracture treated with open reduction and internal fixation with plate via posteromedial approach between January 2015 and January 2020 was retrospectively analyzed, including 18 patients retained the pes anserinus tendon (study group) and 22 patients cut the pes anserinus tendon (control group) during operation. There was no significant difference in gender, age, side of affected knee, cause of injury, Schatzker classification, time from injury to operation, and associated ligament injury between the two groups ( P >0.05). The operation time, intraoperative blood loss, hospital stay, anatomic reduction rate, incidence of complications, fracture healing time, knee flexion and extension range of motion at 2 weeks and 12 months, and knee extension range of motion at 3 months after operation were recorded and compared between the two groups. The visual analogue scale (VAS) score was used to evaluate the early postoperative pain improvement at 1, 3, and 14 days after operation and hospital for special surgery (HSS) score was used to evaluate the improvement of knee function at 3, 6, and 12 months after operation., Results: The patients in both groups were followed up 12-15 months with an average of 12.8 months. There was no significant difference in operation time, intraoperative blood loss, and fracture healing time between the two groups ( P >0.05). The hospital stay in the control group was significantly longer than that in the study group ( t =8.339, P =0.000). There was no significant difference in the anatomic reduction rate (90.9% vs. 83.3%) between the control group and the study group ( χ 2 =0.058, P =0.810). There were 1 case of proximal tibial osteomyelitis, 3 cases of skin necrosis, 3 cases of traumatic arthritis, and 2 cases of lower deep venous thrombosis after operation in the control group, and 1 case of metaphyseal nonunion, 2 cases of traumatic arthritis, and 1 case of lower deep venous thrombosis in the study group, showing no significant difference in the incidence of complications (40.9% vs. 22.2%) between the two groups ( χ 2 =1.576, P =0.209). In the study group, knee flexion and extension range of motion at 2 weeks and 12 months and knee extension range of motion at 3 months after operation were significantly better than those of the control group ( P <0.05). VAS scores and HSS scores in both groups improved with time after operation ( P <0.05), in addition, the HSS score and VAS score of the study group were significantly better than those of the control group ( P <0.05)., Conclusion: Compared with traditional pes anserinus tendon cutting group, pes anserinus tendon retaining group can significantly reduce postoperative short-term pain, improve postoperative knee range of motion and knee function within 1 year after operation.

This paper proposes a novel unsupervised learning framework for depth recovery and camera ego-motion estimation from monocular video. The framework exploits the optical flow (OF) property to jointly train the depth and the ego-motion models. Unlike the existing unsupervised methods, our method extracts the features from the optical flow rather than from the raw RGB images, thereby enhancing unsupervised learning. In addition, we exploit the forward-backward consistency check of the optical flow to generate a mask of the invalid region in the image, and accordingly, eliminate the outlier regions such as occlusion regions and moving objects for the learning. Furthermore, in addition to using view synthesis as a supervised signal, we impose additional loss functions, including optical flow consistency loss and depth consistency loss, as additional supervision signals on the valid image region to further enhance the training of the models. Substantial experiments on multiple benchmark datasets demonstrate that our method outperforms other unsupervised methods.

Exploring the regulatory mechanism of PD-L1 in renal cancer is one of the key strategies to improve the response of renal cancer patients to checkpoint blockade therapy. In this study, the synergistic effect of ascorbic acid (vitamin C) supplementation and the impact of TET2 depletion on anti-PD-L1 therapy were determined in xenograft model experiments. Lymphocyte infiltration and chemokine expression were determined using flow cytometry and qRT-PCR. To determine the downstream targets of TET2, we performed hMeDip-seq and RNA-seq analyses. The molecular mechanism was further confirmed by hMeDip-qPCR, MeDip-qPCR, bisulfite sequencing, Western blotting, qRT-PCR and xenograft model experiments in vitro and in vivo . The present study demonstrated that ascorbic acid enhanced the efficacy of immunotherapy and that the loss of TET2 function enabled renal cancer cells to evade antitumor immunity. Ascorbic acid treatment significantly increased the intratumoral infiltration of T cells and the expression of cytokines and chemokines, while the loss of TET2 impaired the infiltration of T cells and the expression of cytokines and chemokines. TET2 was recruited to IRF1 by IFN-γ-STAT1 signaling, thereby maintaining IRF1 demethylation and ultimately inducing PD-L1 expression. These results suggest a new strategy of stimulating TET activity to improve immunotherapy for renal cell carcinoma., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Background: Takayasu arteritis (TAK) is a rare autoimmune vasculitis that predominantly affects the aorta and its major branches, including the coronary arteries. Information is limited regarding sex-specific differences in coronary artery involvement among TAK patients., Objective: To assess the differences in coronary angiographic findings and long-term outcomes between male and female TAK patients with coronary artery involvement., Methods: This retrospective cohort study included 87 TAK patients, grouped by sex, who underwent coronary angiography. General characteristics, clinical features, coronary angiographic findings, and therapeutic strategies were obtained from medical records. Major Adverse Cardiac Events (MACE), including death from any cause, myocardial infarction, repeated coronary artery revascularization, and rehospitalization due to unstable or progressive angina or heart failure occurring during follow-up, were also recorded., Results: A total of 207 coronary lesions with stenosis were found in 87 TAK patients. The prevalence of ostial coronary lesions was lower in men than in women (9.1 vs. 23.9%, p=0.031). We observed less moderate stenosis (6.8 vs. 22.7%, p=0.018) and more severe stenosis or occlusion (70.5 vs. 46.0%, p=0.004) in the coronary lesions of male TAK patients. During the up to 7-year follow- up, death from any cause was greater in men than in women (21.4 vs. 1.5%, p=0.003); no other significant differences in MACE occurrence were observed between sexes., Conclusion: Among TAK patients with coronary artery involvement, males tend to have more serious coronary stenosis and a higher risk for long-term mortality than females., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Renal cell carcinoma (RCC) is one of the most common urological cancers and has a poor prognosis. RCC is classified into several subtypes, among which kidney renal clear cell carcinoma (KIRC) and kidney renal papillary cell carcinoma (KIRP) are the two most common subtypes. Due to the lack of adequate screening and comparative analysis of RCC subtypes, effective diagnosis and treatment strategies have not yet been achieved., Methods: In this study, 450K methylation array data were collected from The Cancer Genome Atlas (TCGA). The 'limma moderated t-test' and LASSO were used to construct diagnostic and subtyping models, and survival analysis was conducted online by GEPIA., Results: We built a model with 15 methylation sites, which showed high diagnostic and subtyping performance in specificity and sensitivity. At the same time, for potential clinical usability, we calculated the diagnostic and subtyping scores to classify RCC from normal tissue and distinguish the different RCC subtypes. Additionally, the CpG sites were mapped to their corresponding genes, which could also be used to predict the prognosis of RCC., Conclusions: Different methylation sites can be used as diagnostic and subtyping markers that are specific to RCC and RCC subtypes (KIRC and KIRP) with high sensitivity and accuracy., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://dx.doi.org/10.21037/tau-21-674). XL serves as an unpaid editorial board member of Translational Andrology and Urology. LZ serves as an unpaid editorial board member of Translational Andrology and Urology from March 2020 to February 2022. The other authors have no conflicts of interest to declare., (2021 Translational Andrology and Urology. All rights reserved.)