Jian Ren

Sun Yat-Sen University | SYSU · School of Life Sciences

High-quality schematic illustrations are fundamental to the publication of scientific achievements in biomedical research, which are crucial for effectively conveying complex biomedical concepts. However, creating such illustrations remains challenging for many researchers due to the need to devote a significant amount of time and effort to accompl...

Liquid–liquid phase separation (LLPS) is a crucial process for the formation of biomolecular condensates such as coacervate droplets, P-bodies and stress granules, which play critical roles in many physiological and pathological processes. Increasing studies have shown that not only proteins but also RNAs play a critical role in LLPS. To host LLPS-...

Evaluating the impact of genetic variants on RNA modifications (RMs) is crucial for identifying disease-associated variants and understanding the pathogenic mechanisms underlying human diseases. Previously, we developed a database called RMVar to catalog variants linked to RNA modifications in humans and mice. Here, we present an updated version RM...

N 6 -methyladenosine (m 6 A) is the most prevalent modification of mRNA which controls diverse physiological processes. Although m 6 A modification is reported to regulate type I interferon (IFN) responses by targeting the mRNA of IFN-β and the interferon stimulated genes (ISGs), the detailed mechanism of how m 6 A methyltransferase complex (MTC) r...

N 6 -methyladenosine (m 6 A) is the most prevalent modification of mRNA which controls diverse physiological processes. Although m 6 A modification is reported to regulate type I interferon (IFN) responses by targeting the mRNA of IFN-β and the interferon stimulated genes (ISGs), the detailed mechanism of how m 6 A methyltransferase complex (MTC) r...

Although significant progress of clinical strategy has been made in gene editing and cell engineering in immunotherapy, it is now apparent that design and modification in terms of complex signaling pathways and motifs on medical synthetic biology are still full of challenges. Innate immunity, the first line of host defense against pathogens, is cri...

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis assignments. Therefore, to aid scientists in making informed choices, a community-based platform that indexes and rates bioinformatics tools is urgently needed. In this study, we introduce Bio...

Screening biomolecular markers from high-dimensional biological data is one of the long-standing tasks for biomedical translational research. With its advantages in both feature shrinkage and biological interpretability, Least Absolute Shrinkage and Selection Operator (LASSO) algorithm is one of the most popular methods for the scenarios of clinica...

RNA modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Abnormal changes of WERs will disrupt the RNA modification homeostasis of their target genes, leading to the dysregulation of RNA metabolisms such as RNA stability and translation, and consequently to diseases such as cancer. A public...

Immunotherapy is a promising cancer treatment method; however, only a few patients benefit from it. The development of new immunotherapy strategies and effective biomarkers of response and resistance are urgently needed. Recently, high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources. However,...

The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field of molecular and cellular biology. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. Here...

Immune checkpoint blockade (ICB) therapy has been successfully applied to clinically therapeutics in multiple cancers, but its efficacy varies greatly among different patients and cancer types. Therefore, the construction of gene signatures to identify patients who could benefit from ICB therapy is particularly important for precision cancer treatm...

Immunotherapy is a promising cancer treatment method, but only a few patients benefit from it. Developing new immunotherapy strategies and effective biomarkers of response and resistance is urgent. Recent high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources in these regards. However, these re...

Liquid–liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a...

As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describe here a database called SPENCER (http://spencer.r...

Background: Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings: Here, we present MesKit, an R/...

2′-O-methylations (2′-O-Me or Nm) are one of the most important layers of regulatory control over gene expression. With increasing attentions focused on the characteristics, mechanisms and influences of 2′-O-Me, a revolutionary technique termed Nm-seq were established, allowing the identification of precise 2′-O-Me sites in RNA sequences with high...

High-throughput sequencing technologies have identified millions of genetic mutations in multiple human diseases. However, the interpretation of the pathogenesis of these mutations and the discovery of driver genes that dominate disease progression is still a major challenge. Combining functional features such as protein post-translational modifica...

Cancer staging provides a common language that is used to describe the severity of an individual's cancer, which plays a critical role in optimizing cancer treatment. Recursive partitioning analysis (RPA) is the most widely accepted method for cancer staging. Despite its widespread use, to date, only limited tools have been developed to implement t...

Distinguishing the few disease-related variants from a massive number of passenger variants is a major challenge. Variants affecting RNA modifications that play critical roles in many aspects of RNA metabolism have recently been linked to many human diseases, such as cancers. Evaluating the effect of genetic variants on RNA modifications will provi...

Herpes simplex keratitis (HSK) is the most common cause of corneal blindness in developed nations, caused by primary or recurrent herpes simplex virus 1 (HSV-1) infection of the cornea. Latent infection of HSV-1, especially in the trigeminal ganglion (TG), causes recurrence of HSV-1 infection. As antiviral treatment is not effective on latent HSV-1...

: Unsupervised clustering of high-throughput gene expression data is widely adopted for cancer subtyping. However, cancer subtypes derived from a single dataset are usually not applicable across multiple datasets from different platforms. Merging different datasets is necessary to determine accurate and applicable cancer subtypes but is still emba...

The early detection of cancer holds the key to combat and control the increasing global burden of cancer morbidity and mortality. Blood-based screenings using circulating DNAs (ctDNAs), circulating RNA (ctRNAs), circulating tumor cells (CTCs) and extracellular vesicles (EVs) have shown promising prospects in the early detection of cancer. Recent hi...

Seeing is believing. The direct observation of GFP-Atg8 vacuolar delivery under confocal microscopy is one of the most useful end-point measurements for monitoring yeast macroautophagy/autophagy. However, manually labelling individual cells from large-scale sets of images is time-consuming and labor-intensive, which has greatly hampered its extensi...

Long noncoding RNAs (lncRNA) have emerged as promising biomarkers in cancer diagnosis, treatment, and prognosis. Recent studies suggest that a large number of coding gene expression microarray probes could be reannotated as lncRNAs. Microarray, once the most cutting-edge high-throughput gene expression technology, has been used for thousands of can...

Protein nitration and nitrosylation are essential post-translational modifications (PTMs) involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases. Therefore, the identification of substrates that undergo such...

The optimal flanking regions for each feature-encoding scheme Shown are the selected flanking regions for tyrosine nitration (A), tryptophan nitration (B), and S-nitrosylation sites prediction (C) using different feature-encoding schemes. PSSM, position specific scoring matrix; ROC, receiver operating characteristic curve.

The precision-recall curves of the DeepNitro models The precision-recall curves of tyrosine nitration (A), tryptophan nitration (B), and cysteine nitrosylation (C) by 4, 6, 8, 10-fold cross-validation.

The performance comparison between deep neural network and traditional shallow machine learning algorithm The prediction performance for tyrosine nitration (A), tryptophan nitration (B), and cysteine nitrosylation (C) using different algorithms was compared by 4-fold cross-validation. SVM, support vector machine.

The calculated amino acid preferences Amino acid preferences were calculated using a modified PSSM approach and presented in the heat maps for tyrosine nitration (A), tryptophan nitration (B), and cysteine nitrosylation (C). The calculated PSSM scores are presented in a color gradient from blue to red for values ranging from low to high.

The abstraction abilities of the tyrosine nitration and cysteine nitrosylation prediction models calculated from the independent test set The abstraction abilities quantified using AUC values were evaluated for tyrosine nitration (A) and cysteine nitrosylation (B). Also, the abstraction abilities per unit of feature were also calculated for tyrosin...

Large-scale tumor genome sequencing projects have revealed a complex landscape of genomic mutations in multiple cancer types. A major goal of these projects is to characterize somatic mutations and discover cancer drivers, thereby providing important clues to uncover diagnostic or therapeutic targets for clinical treatment. However, distinguishing...

Differential expression (DE) analysis is a fundamental task in the downstream analysis of the next-generation sequencing (NGS) data. Up to now, a number of R packages have been developed for detecting differentially expressed genes. Although R language has an interaction-oriented programming design, for many biology researchers, a lack of basic pro...

N⁶-Methyladenosine (m⁶A) is the most abundant post-transcriptional modification in mammalian RNA molecules and has a critical role in many diseases, including cancer. However, the systematic investigation of the role of m⁶A in cancer is still lacking. We conducted a systematic analysis of the m⁶A-associated somatic mutations and expression of m⁶A w...

Background Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m⁶A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have...

Yin Yang 1 (YY1) regulates early embryogenesis and adult tissue formation. However, the role of YY1 in stem cell regulation remains unclear. YY1 has a Polycomb group (PcG) protein-dependent role in mammalian cells. The PcG-independent functions of YY1 are also reported, although their underlying mechanism is still undefined. This paper reports the...

Document S1. Supplemental Experimental Procedures, Figures S1–S4, and Tables S2, S3, S5, and S6

Table S1. Genes with Significant Expression Alterations in Response to Either Yy1 or Oct4 Knockdown

Genes listed in this table include YY1-all, YY1-only and co-occupied with SMARCA4 genes, and genes with promoters enriched for SMARCA4, OCT4, H3K4me3, and H3K27me3, respectively. The table also includes a pluripotent gene module we established previously.

Table S7. The Binding Sites of the Transcriptional Factors and Histone Markers Used in the Study by ChIP-Seq Analysis This table includes the ChIP-seq analysis of YY1, SMARCA4, OCT4, MED1, H3K4me3, H3K27me3, and c-MYC.

Liver X receptorβ (LXRβ) is a promising therapeutic target for lipid disorders, atherosclerosis, chronic inflammation, autoimmunity, cancer and neurodegenerative diseases. Druggable LXRβ agonists have been explored over the past decades. However, the pocket of LXRβ ligand-binding domain (LBD) is too large to predict LXRβ agonists with novel scaffol...

Although long noncoding RNAs (lncRNAs) have been emerging as critical regulators in various tissues and biological processes, little is known about their expression and regulation during the osteogenic differentiation of periodontal ligament stem cells (PDLSCs) in inflammatory microenvironment. In this study, we have identified 63 lncRNAs that are...

Identifying disease-causing variants among a large number of single nucleotide variants (SNVs) is still a major challenge. Recently, N6-methyladenosine (m6A) has become a research hotspot because of its critical roles in many fundamental biological processes and a variety of diseases. Therefore, it is important to evaluate the effect of variants on...

Background: In approximately 15% of human cancers, telomere length is maintained independently of telomerase by the homologous recombination (HR)-mediated alternative lengthening of telomeres (ALT) pathway. Whether the ALT pathway can be exploited for therapeutic treatment remains unknown. The purpose of this study is to develop oncotherapeutic ag...

Cancer stem cells (CSCs) are believed to have a critical role in tumorigenesis, metastasis, therapeutic resistance or recurrence. Therefore, strategies designed to specifically target and eliminate CSCs have become one of the most promising and desirable ways for tumor treatment. Osteosarcoma stem cells (OSCs), the CSCs in osteosarcoma (OS), are cr...

G-quadruplexes are specialized secondary structures in nucleic acids that possess significant conformational polymorphisms. The precise G-quadruplex conformations in vivo and their relevance to biological functions remain controversial and unclear, especially for telomeric G-quadruplexes. Here, we report a novel single-chain variable fragment (scFv...