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Characterization of RNA modifications has identified their distribution features and molecular functions. Dynamic changes in RNA modification on various forms of RNA are essential for the development and function of the immune system. In this review, we discuss the value of innovative RNA modification profiling technologies to uncover the function of these diverse, dynamic RNA modifications in various immune cells within healthy and diseased contexts. Further, we explore our current understanding of the mechanisms whereby aberrant RNA modifications modulate the immune milieu of the tumor microenvironment and point out outstanding research questions.

Background: Anti-PD-1 antibody combined with antiangiogenic drugs have demonstrated antitumor activity in advanced triple negative breast cancer (TNBC). Anlotinib, an oral multi-targeted tyrosine kinase inhibitor (TKI), has synergistic effect with anti-PD-1 antibody. Preclinical studies showed that metronomic chemotherapy inhibited angiogenesis and enhanced immunotherapy efficacy in TNBC via modulation of tumor immune microenvironment. We hereby conducted a single-arm, multicenter, phase II trial to investigate the efficacy and safety of sintilimab (anti-PD-1 antibody) in combination with anlotinib plus metronomic chemotherapy as a potential novel therapeutic strategy in advanced TNBC and explore potential biomarkers. Methods: Forty-three cases were planning to be included in this trial. The eligible patients who had received no more than two lines of chemotherapy for metastatic disease were enrolled and received sintilimab (200 mg iv q3w) in combination with anlotinib (12 mg po d1-14 q3w) plus capecitabine (500 mg po, tid) or vinorelbine (40 mg po, tiw) until disease progression or intolerable toxicity. The primary endpoint is objective response rate (ORR) and secondary endpoints are disease control rate (DCR), progression free survival (PFS), and overall survival (OS). The safety profile has also been assessed. Blood samples collected at different time points of the baseline, first and second cycle post-treatment, and disease progression were used for next-generation sequencing of ctDNA containing 654 tumor-related genes. Results: As of July 2022, a total of 32 patients were enrolled, and 29 patients were evaluable for efficacy. 2 patients (6.9%) achieved complete response (CR). 6 patients (20.7%) achieved partial response (PR). The ORR is 27.6% (8/29) and DCR is 79.3% (23/29). The median PFS was not reached. The most common grade 1 or 2 adverse events (AEs) include elevated thyroid stimulating hormone (37.0%, 10/27), hand-foot syndrome (18.5%, 5/27), elevated aspartate aminotransferase (14.8%, 4/27), elevated bilirubin (11.1%, 3/27) and hypertension (11.1%, 3/27). Grade 3 AEs include elevated bilirubin (3.7%, 1/27) and hypertension (3.7%, 1/27). No grade 4 or 5 AEs occurred. By analyzing ctDNA mutations of blood samples in 10 patients at baseline, we found that genes with high mutation frequency were HLA-DRB5 (8/10, 80%), TP53 (7/10, 70%), HLA-DRB1 (5/10, 50%) and PIK3CA (4/10, 40%). Among these 10 patients, 2, 3 and 5 patients achieved PR, SD and PD, respectively. The number of gene mutations in patients with PD was higher than that in patients with PR or SD at baseline. This indicate that mutations in ctDNA may be associated with poor efficacy in advanced TNBC. But this still needs further verification. Dynamic analysis of gene mutations at different time points showed that the amplification of HLA-DRB5 or the elimination of KMT2D, RELN and TP53 occurred in patients with PR and SD, but not in patients with PD. Conclusions: Sintilimab in combination with anlotinib plus metronomic chemotherapy has shown favorable efficacy and acceptable safety profile in patients with advanced TNBC. The clinical significance of ctDNA dynamic monitoring needs further validation. Clinical trial information: ChiCTR2100044725 Citation Format: Huihui Li, Qiaorui Tan, Shujuan Sun, Dongdong Zhou, Bo Yu, Mu Su, Baojiang Li, Shu Fang, Ling Qiang, Guohua Ren, Bing Bu, Sha Yin, Xiaochu Man, Pengfei Qiu, Xinzhao Wang, Chao Li, Fangli Cao, Qian Shao, Dali Han, Lihua Song, Bingjie Fan, Baoxuan Zhang, Liang Xu, Xianguang Zhao, Yuqian Liao, Xuemei Xie, Lanping Liu. Efficacy and safety of sintilimab in combination with anlotinib plus metronomic chemotherapy in advanced triple negative breast cancer (SPACE): preliminary results of a single-arm, multicenter phase II trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT1-05-02.

The effect of TAGLN2 in clear cell renal cell carcinoma (ccRCC) is till unknown. This paper explored its potential role and mechanism in ccRCC. The expression of TAGLN2 in Pan-cancers was analyzed through the Genotype-Tissue Expression (GTEx) database and The Cancer Genome Atlas (TCGA) database. TCGA-KIRC database were used to analyze the subsequent prognostic survival, pathway enrichment and immune infiltration. Relevant experimental methods could explain the effect of TAGLN2 expression on tumor cell proliferation, migration, invasion and apoptosis. Apoptosis, proliferation, EMT and PI3K/AKT signaling pathway related proteins expression can be realized through Western Blot. In TCGA + GTEx database, mRNA-TAGLN2 expression was obviously increased in pan-cancer tissues, and the same result was found in ccRCC patients, based on KIRC analysis results. In addition, TAGLN2 was related to poor clinical stage, pathological grade and survival prognosis. In vitro, TAGLN2 can be highly expressed in ccRCC tissues and cells. TAGLN2 silencing could inhibit the proliferation, migration and invasion and EMT in ccRCC cancer cells. Furthermore, TAGLN2 related differential genes enriched in PI3K/AKT signaling pathway were negatively regulated after TAGLN2 silencing. Moreover, TAGLN2 may promote tumor immune escape and increase the risk of distant metastasis in immune infiltration-related analysis. TAGLN2 can be used as a single indicator to explain the survival probability of ccRCC patients. In vitro, TAGLN2 silencing inhibited malignant biological properties of ccRCC by blocking PI3K/AKT signaling pathway. In addition, TAGLN2 contributes to the development of tumor immune escape and may become the potential therapeutic target of ccRCC.

The effect of Transgelin 2 (TAGLN2) on clear cell renal cell carcinoma (ccRCC) is unknown. This study explored the potential role and mechanism of ccRCC. The expression of TAGLN2 in Pan-cancers was analyzed using the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases. TCGA-KIRC database was used to analyze subsequent prognostic survival, pathway enrichment, and immune infiltration. Relevant experimental methods could explain the effect of TAGLN2 expression on tumor cell proliferation, migration, invasion, and apoptosis. Apoptosis, proliferation, Epithelial-to-Mesenchymal Transition (EMT), and PI3K/AKT signaling pathway-related protein expression were determined through western blotting. In the TCGA + GTEx database, mRNA-TAGLN2 expression was clearly increased in pan-cancer tissues, and the same result was found in ccRCC patients based on KIRC analysis results. In addition, TAGLN2 was associated with poor clinical stage, pathological grade, and survival prognosis. TAGLN2 is highly expressed in ccRCC tissues and in vitro TAGLN2 silencing of cells inhibits the proliferation, migration, invasion, and EMT of ccRCC cancer cells. Furthermore, TAGLN2-related differential genes enriched in the PI3K/AKT signaling pathway were negatively regulated after TAGLN2 silencing. Moreover, TAGLN2 may promote tumor immune escape and increase the risk of distant metastasis in immune infiltration-related analyses. TAGLN2 can be used as a single indicator to explain the survival probability of patients with ccRCC. In vitro TAGLN2 silencing inhibited the malignant properties of ccRCC by blocking the PI3K/AKT signaling pathway. In addition, TAGLN2 contributes to tumor immune escape and may be a potential therapeutic target for ccRCC.

The emergence of immunotherapy has provided an option of treatment methods for bladder cancer (BC). However, the beneficiaries of immunotherapy are still limited to small‐scale patients, and immunotherapy‐related adverse events often occur. It is a major challenge for clinical work to study the immune subtypes of BC and the molecular mechanism of immune escape, and identify the immune responders accurately. Here, we explore the immune molecular subtypes of bladder cancer and potential escape mechanisms. First, we screened the expression profiles of 303 differentially expressed immune‐related genes in BC patients from the Cancer Genome Atlas (TCGA) database, and successfully identified 4 molecular subtypes of BC. By comparing the clinical characteristics, immune cells infiltration, the expression of checkpoint genes, human leukocyte antigen (HLA) genes, and gene mutation status of different subtypes, we identified different clinical and immunological characteristics of 4 subtypes. Among 4 subtypes, Cluster 2 met the general characteristics of immunotherapy responders and responded well to immunotherapy, while Cluster 4 had the highest expression of immune characteristics, and is similar to the immune environment of normal bladder tissue. Then, the weighted gene co‐expression network analysis (WGCNA) of immune‐related genes revealed that brown module was positively correlated with subtypes. Pathway enrichment analysis explored the major pathways associated with subtypes, which are also associated with immune escape mechanisms. Moreover, the decision tree model, which was constructed by the principle of random forest screening factors, was also validated in internal validation set and external validation set from the Gene Expression Omnibus (GEO) cohort (GSE133624), and could achieve accurate subtypes prediction for BC patients with high‐throughput sequencing. Taken together, we explored the immune molecular subtypes and their mechanisms of BC, and these results may provide guidance for the development of new BC immunotherapy strategies., We successfully identified 4 molecular subtypes of BC via TCGA database. Moreover, the establishment of decision tree model, by the principle of random forest screening factors, can achieve accurate subtype prediction for clinical BC patients with high‐throughput sequencing.

Muscle‐invasive bladder cancer (MIBC) is one of the common malignant tumors. Patients with MIBC still have high tumor recurrence and progression rates after surgery. Bioinformatics analysis of stromal infiltration‐related genes in the tumor microenvironment (TME) of MIBC patients was performed in this study to determine the major stromal cells types and biomarkers for their progression and poor prognosis. The ESTIMATE algorithm was applied to evaluate the stromal score and immune score of samples from MIBC patients in The Cancer Genome Atlas (TCGA) and found that stromal score was closely related to the clinical characteristics of the patients. The Gene Set Enrichment Analysis (GSEA) further revealed that stromal cells were involved in biological processes such as activation of leukocytes and positive regulation of cell migration during MIBC progression, as well as PI3K‐Akt, MAPK, and Rap1 signaling pathways. Five hub genes related to prognosis, including ACTA2, COL5A1, DCN, LUM, and PRRX1 were identified by the Weighted Gene Co‐Expression Network Analysis (WGCNA), Protein‐Protein Interaction (PPI), survival analysis, and Oncomine, Gene Expression Omnibus (GEO) database validation. Besides, we identified five stromal cell types associated with overall survival time, among which chondrocytes and fibroblasts were identified as the major stromal cell types through correlation analysis. Finally, the Receiver Operating Characteristic (ROC) curve and immunohistochemistry were used to verify the diagnostic value and expression of hub genes in different invasive tumors. In summary, we investigated the biological behavior of stromal cells in the TME of MIBC to promote tumor progression obtained hub genes associated with progression and poor prognosis and identified the main stromal cells types in the TME., Through our analysis, we found that stromal cells are closely related to the clinical prognosis of patients. Stromal cells are mainly involved in cell migration, leukocyte activation, and PI3K/AKT, MAPK, and Rap1 signaling pathways in tumor progression. In addition, we identified the hub genes of stromal cells promoting tumor progression based on bioinformatics analysis, and further identified chondrocytes and fibroblasts as the main types of 13 stromal cells.

In the era of precision medicine, establishing a patient-derived cell model is crucial, whether in vitro or in vivo. Compared to the traditional cell lines, patient-derived primary cells represent precise genetic features from specific patients, but poor proliferative activity of human primary cells restricts their popular application. Conditional reprogramming (CR) is a new cell culture technique to achieve rapid growth of patient-derived cells in vitro, making it possible to identify the individual difference and screen drugs sensitivity. In this review, we will summarize the application and limitation of CR in tumor and inflammatory-related diseases, indicating the prospect of this technique for preclinical research.

The aim of the present study was to analyze the microarray data of human colorectal cancer (CRC) tissues and identify novel therapeutic targets for CRC. Microarray analysis from the GSE73360 and GSE84984 datasets was performed to identify novel long non-coding RNAs (lncRNAs) that were differentially expressed in human CRC tissues. Additionally, small interfering RNAs were used to deplete the expression of the indicated lncRNAs in cells. Colony-formation, wound-closure, and transwell assays were performed on CRC cells to assess their proliferation and migration capacities. Through microarray analysis, SCARNA9L, SLMO2-ATP5E and LOC100132062 were identified as differentially expressed lncRNAs in CRC tissues. The present study demonstrated that the ablation of SCARNA9L inhibited cell proliferation and arrested the cell cycle of SW480 and SW620 CRC cells. Additionally, depletion of SCARNA9L restrained the migration of CRC cells in vitro. Overall, the present study investigated the potential involvement of SCARNA9L in CRC and suggests SCARNA9L as a potential biomarker.

Background To analyze perioperative conditions and long-term efficacy of open modified ureterosigmoidostomy urinary diversion (OMUUD) in patients with bladder cancer who underwent open radical cystectomy (ORC) or laparoscopic radical cystectomy (LRC). Methods In this retrospective study, the clinical data of patients who underwent open and laparoscopic radical cystectomy plus open modified ureterosigmoidostomy urinary diversion in our hospital were collected from January 2011 to December 2019. In addition, perioperative data of 56 patients who underwent ORC and OMUUD were compared with those of 118 patients who underwent laparoscopic radical cystectomy (LRC) plus OMUUD. A long-term follow-up was performed to compare the overall survival (OS) and progression-free survival (PFS) rate between the two groups. Results Results showed that the mean operation time in the open group was shorter than that in the laparoscopic group (P

Cancer stem cells (CSCs) have an key role in the beginning, progression and treatment of bladder cancer. In the current study, our target was to identify CSCS-related genes in bladder cancer.Bladder cancer (BLCA) transcriptome data were acquired from The Cancer Genome Atlas (TCGA) database. WGCNA was used to screen genes connected with the mRNA expression-based stemness index (mRNAsi).Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to analyze the biological function of mRNAsi-related genes. Univariate Cox regression and LASSO Cox regression algorithms were applied to build a risk score model. Additionally, a ceRNA regulatory netwok based on key mRNAsi-related genes was established via TargetScan, miRDB, miRTarBas and miRcode database,and lncRNA SNHG12 was selected for further in vitro and invivo functional assays.Between BLCA and normal samples were identified 1560 differentially expressed genes (DEGs).845 DEGs were most significantly associated with mRNAsi according to WGCNA analysis, which were mainly enriched in GO terms and KEGG pathways related to cell proliferation. Univariate Cox regression and LASSO Cox regression algorithms screened 25 mRNAsi-related genes to construct the risk score model with the significant ability to estimate prognosis of BLCA patients. A ceRNA network, including 8 lncRNA, 11 miRNA and 9 mRNAsi-related mRNA, was constructed.We found that lncRNAs ADAMTS9-AS1 and SNHG12 were observably related to the survival of BLCA patients. To verify this finding, we selected SNHG12 for further study. RT-PCR experiments revealed that SNHG12 was high expression in both bladder cancer tissues and cells.SNHG12 promoted proliferation, invasion, migration, apoptosis and stemness of bladder cancer cells in vitro and tumour proliferation in vivo.Our study identified 25 biomarkers associated with stemness indices in BLCA and established a ceRNA network based on key mRNAsi-related genes.SNHG12 promoted BLCA proliferation, invasion, migration, apoptosis and stemness in vitro. It was also showed that SNHG12 promoted tumour growth.

A new layer of transcriptional control N 6 -methyladenosine (m 6 A) is the most abundant messenger RNA modification in almost all eukaryotes. Liu et al. now show that m 6 A is also cotranscriptionally added onto various chromosome-associated regulatory RNAs (carRNAs) in mammalian cells. Disruption of m 6 A modification of these RNAs increases their abundance and promotes gene transcription by increasing the chromatin accessibility. Thus, m 6 A serves as a switch to regulate carRNA levels by tuning nearby chromatin state and downstream transcription. Science , this issue p. 580

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer featured with high intra-tumoral heterogeneity and poor prognosis. To comprehensively delineate the PDAC intra-tumoral heterogeneity and the underlying mechanism for PDAC progression, we employed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomic atlas of 57,530 individual pancreatic cells from primary PDAC tumors and control pancreases, and identified diverse malignant and stromal cell types, including two ductal subtypes with abnormal and malignant gene expression profiles respectively, in PDAC. We found that the heterogenous malignant subtype was composed of several subpopulations with differential proliferative and migratory potentials. Cell trajectory analysis revealed that components of multiple tumor-related pathways and transcription factors (TFs) were differentially expressed along PDAC progression. Furthermore, we found a subset of ductal cells with unique proliferative features were associated with an inactivation state in tumor-infiltrating T cells, providing novel markers for the prediction of antitumor immune response. Together, our findings provide a valuable resource for deciphering the intra-tumoral heterogeneity in PDAC and uncover a connection between tumor intrinsic transcriptional state and T cell activation, suggesting potential biomarkers for anticancer treatment such as targeted therapy and immunotherapy.

Background: To analyze perioperative conditions and long-term efficacy of open modified ureterosigmoidostomy urinary diversion (OMUUD) in patients with bladder cancer who underwent open radical cystectomy (ORC) and laparoscopic radical cystectomy (LRC).Methods: In this retrospective study, the clinical data of patients who underwent open and laparoscopic radical cystectomy plus open modified ureterosigmoidostomy urinary diversion in our hospital were collected from January 2011 to December 2019. In addition, perioperative data of 56 patients who underwent ORC and OMUUD were compared with those of 118 patients who underwent laparoscopic radical cystectomy (LRC) plus OMUUD. A long-term follow-up was performed to compare the overall survival (OS) and progression-free survival (PFS) rate between the two groups.Results: Results showed that there was no significant difference between ORC+OMUUD group and LRC+OMUUD group in terms of gender, age, body index, pre-operative ASA grade, history of transurethral resection of bladder tumor (TURBT) before surgery, tumor T stage, lymph node dissection range, pathological grade, and positive postoperative surgical margin. The mean operation time in the open group was shorter than that in the laparoscopic group （PConclusion: This study shows that the LRC group has long operation time, but less estimated intraoperative blood loss, short postoperative hospital stay, small trauma, and fast postoperative recovery compared to open surgery. Moreover, the incidence of complications at 30 - and 90-days postoperation, as well as the OS and PFS is not different between laparoscopy and open surgery.

Purpose To compare the efficacy and safety of induction chemotherapy followed by concurrent chemoradiotherapy(I-CCRT), induction chemotherapy followed by concurrent chemoradiotherapy and consolidation chemotherapy(I-CCRT-C), and concurrent chemoradiotherapy followed by consolidation chemotherapy(CCRT-C) for locally advanced esophageal squamous cell carcinoma(ESSC). Methods Patients with locally advanced ESCC who underwent definitive chemoradiotherapy with cisplatin plus fluorouracil or docetaxel from February 2012 to December 2018 were retrospectively reviewed. Kaplan-Meier curve was used to estimate survival. Efficacy was assessed using RECIST, version 1.0. Prognosis factors were identified with Cox regression analysis. Results Patients were treated with CCRT-C(n=59), I-CCRT(n=20), and I-CCRT-C(n=48), SCRT(n=119). The median follow-up duration was 73.9 months for the entire cohort. The ORR of the CCRT-C, I-CCRT, and I-CCRT-C, SCRT groups was 89.8%, 70.0%, and 77.1%, respectively ( P = 0.078). The median PFS in the CCRT-C, I-CCRT, and I-CCRT-C groups was 32.5, 16.1, and 27.1 months, respectively ( P = 0.464). The median OS of the CCRT-C, I-CCRT, and I-CCRT-C groups was 45.9, 35.5, and 54.0 months, respectively ( P = 0.788). Cox regression analysis indicated that I-CCRT and I-CCRT had comparable PFS and OS with CCRT-C( P > 0.05). Neutropenia grade ≥ 3 in CCRT-C, I-CCRT, I-CCRT-C, and SCRT groups was 47.5%, 15%, and 33.3% of patients, respectively( P =0.027). Conclusions I-CCRT and I-CCRT-C using cisplatin plus fluorouracil or docetaxel regimen had comparable outcomes with CCRT-C for locally advanced ESCC. I-CCRT and I-CCRT-C seem to have less severe neutropenia than CCRT-C, and potential to be a standard treatment option for locally advanced ESCC.

Tumor-associated macrophages (TAMs) can dampen the antitumor activity of T cells, yet the underlying mechanism remains incompletely understood. Here, we show that C1q

On 22 January 2020, the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), created the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access SARS-CoV-2 information resource. 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by our in-house automated pipeline. Of particular note, 2019nCoVR performs systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. It also generates visualization of the spatiotemporal change for each variant and yields historical viral haplotype network maps for the course of the outbreak from all complete and high-quality genomes. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on COVID-19 (Coronavirus Disease 2019), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB-NGDC, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with National Center for Biotechnology Information. Collectively, all SARS-CoV-2 genome sequences, variants, haplotypes and literature are updated daily to provide timely information, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

The emergence of the new coronavirus (nCoV-19) has impacted human health on a global scale, while the interaction between the virus and the host is the foundation of the disease. The viral genome codes a cluster of proteins, each with a unique function in the event of host invasion or viral development. Under the current adverse situation, we employ virtual screening tools in searching for drugs and natural products which have been already deposited in DrugBank in an attempt to accelerate the drug discovery process. This study provides an initial evaluation of current drug candidates from various reports using our systemic in silico drug screening based on structures of viral proteins and human ACE2 receptor. Additionally, we have built an interactive online platform (https://shennongproject.ai/) for browsing these results with the visual display of a small molecule docked on its potential target protein, without installing any specialized structural software. With continuous maintenance and incorporation of data from laboratory work, it may serve not only as the assessment tool for the new drug discovery but also an educational web site for the public.

Background: Cancer is often defined as a disease of aging. The majority of patients with urogenital cancers are the elderly, whose clinical characteristics are greatly affected by age and aging. Here, we aimed to explore age-related biological changes in three major urogenital cancers by integrative bioinformatics analysis.Methods: First, mRNA (count format) and clinical data for bladder cancer, prostate cancer and renal cell carcinoma were downloaded from the Cancer Genome Atlas (TCGA) portal. The expressions of 64 cells were obtained by xCell deconvolution method. EdgeR package and limma package were used to analyze differentially expressed genes and cells in the young group and the old group, respectively. ClusterProfiler R package and clueGO plugin were used for enrichment analysis, and cytohubba plugin was used for hub genes analysis. Then co-expression analysis and chromosome distribution for hub genes were analyzed and demonstrated by RIdeogram R package. The clinical correlation of hub genes and key cells was analyzed by Graphpad Prism software. Finally, the correlation between hub genes and key cells was explored by corrplot R package.Results: We screened and identified 14 hub genes and 4 key cells related to age and urogenital cancers. The age-related differentially expressed genes and co-expressed genes were mainly enriched in muscle movement (Cl-, Ca2+), inflammatory response, antibacterial humoral immune response, substance metabolism and transport, redox reaction, etc. Most of the age-related genes are on chromosome 17. Moreover, the correlation between cells and genes was analyzed. Conclusion: Our study analyzed age-related genes and cells in the tumor microenvironment of urogenital cancers, and explored the pathways involved. This could contribute to personalized therapy for patients of different ages and a new understanding of the potential relationship between the aging microenvironment and urogenital cancers.

Background Bladder cancer is the most common malignancy in urinary system, but the therapeutic targets remain elusive. This study aims to reveal the relationship between AMIGO2 and proliferation, migration, drug-resistance and tumorigenicity of bladder cancer, and explore the potential molecular mechanisms. Methods The expression of AMIGO2 in human bladder cancer tissues is measured by qRT-PCR and immunohistochemistry (IHC). Stable AMIGO2 knockdown cell lines T24 and 5637 were established by lentivirus transfection. Cell viability assay (CCK-8 assay) was used to determine cell proliferation, flow cytometry analysis was utilized to detect cell cycle, and wound healing assay was proceeded to test migration ability of bladder cancer cells. Chemosensitivity to cisplatin was measured by CCK-8 assay. Xenograft mouse model was established for investigating the effect of AMIGO2 on tumor formation in vivo. The RNA Sequencing technology was used to explore differentially expressed genes (DEGs) between knockdown group and negative control group of T24. Bioinformatics analysis upon the results of RNA-Seq was proceeded to understand underlying mechanisms. Results AMIGO2 was upregulated in bladder cancer cells and tissues. Inhibited expression of AMIGO2 suppresses cell proliferation and migration, which might be mediated by cell cycle arrest in G1 phase. AMIGO2 could reduce chemoresistance to cisplatin in bladder cancer cells. Low AMIGO2 expression inhibited tumorigenicity of T24 in nude mice. 917 DEGs were identified by RNA-Sequencing technology and bioinformatics analysis. The DEGs were mainly enriched in cell-cell adhesion, ATP-binding cassette transporters (ABC transporters), PPAR signaling pathway and some other pathways. Among ten hub genes, four of them might be associated with the prognosis of bladder cancer patients. Conclusion AMIGO2 is overexpressed in bladder cancer cells and tissues and serves as an oncogene in bladder cancer. It also reduces chemoresistance to cisplatin. The process might be regulated by particular pathways including ABC transporters and PPAR signaling pathway. Four hub genes might be associated with prognosis of bladder cancer patients.

There is growing evidence that tumour neoantigens have important roles in generating spontaneous antitumour immune responses and predicting clinical responses to immunotherapies1,2. Despite the presence of numerous neoantigens in patients, complete tumour elimination is rare, owing to failures in mounting a sufficient and lasting antitumour immune response3,4. Here we show that durable neoantigen-specific immunity is regulated by mRNA N6-methyadenosine (m6A) methylation through the m6A-binding protein YTHDF15. In contrast to wild-type mice, Ythdf1-deficient mice show an elevated antigen-specific CD8+ T cell antitumour response. Loss of YTHDF1 in classical dendritic cells enhanced the cross-presentation of tumour antigens and the cross-priming of CD8+ T cells in vivo. Mechanistically, transcripts encoding lysosomal proteases are marked by m6A and recognized by YTHDF1. Binding of YTHDF1 to these transcripts increases the translation of lysosomal cathepsins in dendritic cells, and inhibition of cathepsins markedly enhances cross-presentation of wild-type dendritic cells. Furthermore, the therapeutic efficacy of PD-L1 checkpoint blockade is enhanced in Ythdf1-/- mice, implicating YTHDF1 as a potential therapeutic target in anticancer immunotherapy.

The emergence of the new coronavirus (nCoV-19) has brought global impact on human health, whilst the interaction between the virus and the host is the foundation of the disease. The viral genome codes a cluster of proteins, each with a unique function in the event of host invasion or viral development. Under current adverse situation, we employ virtual screening tools in searching for drugs and nature products which have been already deposited in the DrugBank in attempt to accelerate the drug discovery process. This study provides an initial evaluation of current drug candidates from various reports using our systemic in silico drug screening based on structures of viral proteins and human ACE2 receptor. Besides, we built an interactive online platform (https://shennongproject.com:11443/#/home) for browsing these results with the visual display of small molecule docked on its potential target protein, without installing any specialized structural software. With continuous maintenance and incorporation of data from laboratory works, it may serve not only as the assessment tool for the new drug discovery but also an educational website to meet general interest from the public.

The emergence of the new coronavirus (nCoV-19) has brought global impact on human health, whilst the interaction between the virus and the host is the foundation of the disease. The viral genome codes a cluster of proteins, each with a unique function in the event of host invasion or viral development. Under current adverse situation, we employ virtual screening tools in searching for drugs and nature products which have been already deposited in the DrugBank in attempt to accelerate the drug discovery process. This study provides an initial evaluation of current drug candidates from various reports using our systemic in silico drug screening based on structures of viral proteins and human ACE2 receptor. Besides, we built an interactive online platform (https://shennongproject.com:11443/#/home) for browsing these results with the visual display of small molecule docked on its potential target protein, without installing any specialized structural software. With continuous maintenance and incorporation of data from laboratory works, it may serve not only as the assessment tool for the new drug discovery but also an educational website to meet general interest from the public.

Introduction Acute myeloid leukemia (AML) is an aggressive disease with genetic and phenotypic heterogeneity that results in a highly variable response to standard chemotherapy. Azacitidine (AZA) is a hypomethylating agent (HMA) and has been investigated in combination with intensive chemotherapy as an epigenetic primer to sensitize leukemic cells to treatment. In a phase 1 trial, this regimen was safe and well-tolerated with overall response rate (CR+CRi) of 61% and complete remission rate of 41% (Cahill et al, Blood Adv 2020). Predictive biomarkers for response to this treatment strategy have not yet been identified. Since 5-hydroxymethylcytosine (5hmC) is an epigenetic biomarker in cancer, we hypothesized that Nano-5hmC-Seal sequencing technology may serve as a novel approach to identifying 5hmC profiles predictive of treatment response to epigenetic priming. Methods We performed RNA-seq gene expression and Nano-5hmC-Seal DNA profiling from peripheral blood/bone marrow samples of patients with high-risk AML to identify potential 5hmC profile biomarkers and gene expression changes (Figure 1A). Patients (n=46) were treated in a 3+3 dose-escalation scheme of AZA (37.5 mg/m 2, 50 mg/m 2, or 75 mg/m 2) on days 1-5 followed by high-dose cytarabine (3000 mg/m 2) and mitoxantrone (30 mg/m 2) (AZA-HiDAC-Mito) on day 6 and day 10 in a phase 1 trial previously reported (Cahill et al, Blood Adv 2020). We compared pre-treatment RNA-seq gene expression and 5hmC DNA profiles between responders (CR+CRi) and non-responders, as well as between pre-treatment and after 5 days of AZA for individual patients. We used an XGBoost machine learning model in Python based on a training set of patients to develop a 5hmC gene signature to predict response to AZA-HiDAC-Mito in an independent test set of patients. We compared continuous variables with two-tailed Student's t-test and used the Kaplan-Meier method with log-rank test for survival analysis. Results Thirty-three patients (72%) had adequate RNA samples for RNA-seq gene expression analysis. Eighteen responded to treatment (CR +CRi) and were enriched with gene expression patterns involved in cell-cell interaction and activation of cell cycle, while non-responders (n=15) had a higher expression of leukemic stem cell (LSC) signatures. There was no difference in gene expression profile when comparing pre-treatment samples to day 5 samples after AZA exposure. From the 5hmC profiling [n=40 (87%) patients with adequate samples], increased 5hmC in LSC genes was associated with treatment resistance to AZA-HiDAC-Mito (p=0.044). The number of differentially hydroxy-methylated genes (DhMGs) increased with higher doses of AZA exposure suggesting a dose-dependent epigenetic effect from AZA. Patients with a greater number of DhMGs following 5 days of AZA treatment had improved survival (p=0.015) (Figure 1B). Using the 5hmC-based XGBoost machine learning model comparing 5hmC profiles between responders to non-responders from a training set of patients (n=22), we developed an 11-gene 5hmC pre-treatment signature (including SKP1, WNT8A, CYP2E1, and NBPF9) to predict treatment response. The model was highly effective in predicting response to therapy, with an area under the curve (AUC) of 0.86 in an independent test set of patients (n=18) treated with AZA-HiDAC-Mito (Figure 1C). Conclusion In patients with AML treated with AZA-HiDAC-Mito, a pre-treatment LSC gene expression signature enriched with 5hmC was associated with treatment resistance. More DhMGs at day 5 appear to be a dose-dependent epigenetic effect that is induced by AZA and is associated with longer survival despite the absence of an immediate change in gene expression levels. An 11-gene 5hmC pre-treatment signature may be a predictive biomarker for AZA-HiDAC-Mito therapy and other HMA-based approaches. These findings warrant validation in a larger prospective trial. Figure 1 Figure 1. Disclosures Zhang: Bristol-Myers Squibb: Current Employment. Stock: Pfizer: Consultancy, Honoraria, Research Funding; amgen: Honoraria; agios: Honoraria; jazz: Honoraria; kura: Honoraria; kite: Honoraria; morphosys: Honoraria; servier: Honoraria; syndax: Consultancy, Honoraria; Pluristeem: Consultancy, Honoraria. Odenike: Celgene, Incyte, AstraZeneca, Astex, NS Pharma, AbbVie, Gilead, Janssen, Oncotherapy, Agios, CTI/Baxalta, Aprea: Research Funding; AbbVie, Celgene, Impact Biomedicines, Novartis, Taiho Oncology, Takeda: Consultancy. He: Epican Genetech: Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company.

Deep learning have made great successes in traditional fields like computer vision (CV), natural language processing (NLP) and speech processing. Those achievements greatly inspire researchers in genomic study and make deep learning in genomics a very hot topic. Convolutional neural network (CNN) and recurrent neural network (RNN) are frequently used for genomic sequence prediction problems; multiple layer perception (MLP) and auto-encoders (AE) are frequently used for genomic profiling data like RNA expression data and gene mutation data. Here, we introduce a new neural network architecture, named residual fully-connected neural network (RFCN) and demonstrate its advantage for modeling genomic profiling data. We further incorporate AutoML algorithms and implement AutoGenome, an end-to-end automated genomic deep learning framework. By utilizing the proposed RFCN architectures, automatic hyper-parameter search and neural architecture search algorithms, AutoGenome can train high-performance deep learning models for various kinds of genomic profiling data automatically. To make researchers better understand the trained models, AutoGenome can assess the feature importance and export the most important features for supervised learning tasks, and the representative latent vectors for unsupervised learning tasks. We envision AutoGenome to become a popular tool in genomic studies.

Tumour-associated macrophages (TAMs) are associated with both the progression and poor prognosis of a variety of solid tumours. This study aimed to investigate and clarify the tumour-promoting role of CXCL8 secreted by TAMs in the urothelial carcinoma microenvironment of the bladder. Immunohistochemistry (n = 55) was used to detect Chemokine (C-X-C motif) ligand 8 (CXCL8), CD163 (a TAM marker), Matrixmetalloproteinase-9 (MMP-9), vascular endothelial growth factor (VEGF), and E-cadherin in cancerous and adjacent tissues of bladder cancer patients. TAMs-like PBM (peripheral blood mononuclear)-derived macrophages were developed using in vitro experiments. T24, 5637, and UM-UC-3 were treated with conditioned medium (CM) for the experimental intervention group, without CM for the blank control group, and with CM and an anti-CXCL8 neutralizing antibody for the experimental control group, respectively. The immunohistochemical study showed that the expression of CXCL8 was significantly upregulated as the number of infiltrating TAMs increased in the tumour tissues. A high expression of CXCL8 significantly correlated with an increase in the expression of MMP-9 and VEGF and a decrease in expression of E-cadherin in the microenvironment. This revealed that TAM-derived CXCL8 is highly associated with bladder cancer migration, invasion, and angiogenesis. The concentration of CXCL8 was significantly higher in CM collected from TAM-like PBM-derived macrophages than that from THP-1 cells. In subsequent in vitro experiments, we found that CM derived from TAM-like PBM-derived macrophages can also increase the migration rate, invasiveness, and pro-angiogenic properties of tumour cells. Additionally, the effect of CXCL8 was significantly diminished by the addition of an anti-CXCL8 neutralizing antibody to CM. The infiltration of TAMs in the tumour microenvironment leads to the elevation of CXCL8, which in turn promotes the secretion of MMP-9, VEGF, and E-cadherin by bladder cancer cells. This alters the migration, invasion, and pro-angiogenic capacity of bladder cancer cells and accelerates cancer progression.

Summary Tumor-associated macrophages (TAMs) can dampen the antitumor activity of T cells, yet the underlying mechanism remains incompletely understood. Here, we show that C1q+ TAMs are regulated by an RNA N6-methyladenosine (m6A) program and modulate tumor-infiltrating CD8+ T cells by expressing multiple immunomodulatory ligands. Macrophage-specific knockout of an m6A methyltransferase Mettl14 drives CD8+ T cell differentiation along a dysfunctional trajectory, impairing CD8+ T cells to eliminate tumors. Mettl14-deficient C1q+ TAMs show a decreased m6A abundance on and a higher level of transcripts of Ebi3, a cytokine subunit. In addition, neutralization of EBI3 leads to reinvigoration of dysfunctional CD8+ T cells and overcomes immunosuppressive impact in mice. We show that the METTL14-m6A levels are negatively correlated with dysfunctional T cell levels in patients with colorectal cancer, supporting the clinical relevance of this regulatory pathway. Thus, our study demonstrates how an m6A methyltransferase in TAMs promotes CD8+ T cell dysfunction and tumor progression.