
Dexi BiShanghai Tenth People’s Hospital, Tongji University School of Medicine · Department of Pathology
Dexi Bi
PhD
About
63
Publications
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Introduction
Additional affiliations
July 2015 - March 2016
Shanghai Pulmonary Hospital, Tongji University School of Medicine
Position
- Medical Professional
Education
May 2013 - May 2014
September 2010 - July 2015
September 2006 - July 2010
Publications
Publications (63)
Wei Wang Hua Li Yiyong Qian- [...]
Jun Zou
Purpose
This study aims to explore the regulatory role and potential mechanisms of ALKBH5-mediated N6-methyladenosine (m6A) demethylation modification in corneal neovascularization (CNV).
Methods
A mouse CNV model was established through corneal alkali burns. Total m6A levels were measured using an m6A RNA methylation quantification kit. The mRNA...
BACKGROUND & AIMS: Lactobacillus paracasei is known to confer health benefits to human and has been found depleted in gastric tumor tissues. Here, we aimed to investigate the potential role of this bacterium as a prophylactic for gastric cancer (GC).
METHODS: Isolation of L. paracasei from normal gastric tissues followed by whole genome sequencing...
Fusobacterium nucleatum (F. nucleatum) promotes intestinal tumor growth and its relative abundance varies greatly among patients with CRC, suggesting the presence of unknown, individual-specific effectors in F. nucleatum-dependent carcinogenesis. Here, we identify that F. nucleatum is enriched preferentially in KRAS p.G12D mutant CRC tumor tissues...
Background
One reason patients with cancer cannot benefit from immunotherapy is the lack of immune cell infiltration in tumor tissues. Cancer-associated fibroblasts (CAFs) are emerging as central players in immune regulation that shapes tumor microenvironment (TME). Earlier we reported that integrin α5 was enriched in CAFs in colorectal cancer (CRC...
Background
Dysregulation of RNA N6-methyladenosine (m6A) modification is indispensable in tumorigenesis. However, in muscle-invasive bladder cancer (MIBC), the key regulators and mechanisms involved in this process remain largely unknown. This study aimed to screen the key m6A regulators and explore its possible role in MIBC.
Methods
Aberrantly ex...
Background:
Poor ovarian responders (POR) are women undergoing in-vitro fertilization who respond poorly to ovarian stimulation, resulting in the retrieval of lower number of oocytes, and subsequently lower pregnancy rates. The follicular fluid (FF) provides a crucial microenvironment for the proper development of follicles and oocytes through tig...
Autism spectrum disorder (ASD) is a complex behavioral disorder diagnosed by social interaction difficulties, restricted verbal communication, and repetitive behaviors. Fecal microbiota transplantation (FMT) is a safe and efficient strategy to adjust gut microbiota dysbiosis and improve ASD-related behavioral symptoms, but its regulatory mechanism...
The ketogenic diet (KD) is a high-fat, adequate-protein, and very-low-carbohydrate diet regimen that mimics the metabolism of the fasting state to induce the production of ketone bodies. The KD has long been established as a remarkably successful dietary approach for the treatment of intractable epilepsy and has increasingly garnered research atten...
Mast cells (MCs) are abundantly distributed in the human intestinal mucosa and submucosa. However, their roles and mechanisms in the development of colorectal cancer (CRC) are still unclear. In the present research, we found that the infiltration density of MCs in CRC tissues was positively correlated with improved patients’ prognoses. Moreover, MC...
The pathogenic pVA1-type plasmids that carry pirAB toxin genes are the genetic basis for Vibrio to cause acute hepatopancreatic necrosis disease (AHPND), a lethal shrimp disease posing an urgent threat to shrimp aquaculture. Emerging evidence also demonstrate the rapid spread of pVA1-type plasmids across Vibrio species.
The bacterial genus Fusobacterium promotes colorectal cancer (CRC) development, but an understanding of its precise composition at the species level in the human gut and the relevant association with CRC is lacking. Herein, we devise a Fusobacterium rpoB amplicon sequencing (FrpoB-seq) method that enables the differentiation of Fusobacterium specie...
Background: Poor ovarian responders (POR) are women undergoing in-vitro fertilization who respond poorly to ovarian stimulation, resulting in the retrieval of lower number of oocytes, and subsequently lower pregnancy rates. The follicular fluid (FF) provides a crucial microenvironment for the proper development of follicles and oocytes through tigh...
Given that only a subset of patients with colorectal cancer (CRC) benefit from immune checkpoint therapy, efforts are ongoing to identify markers that predict immunotherapeutic response. Increasing evidence suggests that microbes influence the efficacy of cancer therapies. Fusobacterium nucleatum induces different immune responses in CRC with diffe...
Super‐enhancers (SEs) play essential roles in colorectal cancer (CRC) progression. However, how the SE landscape is orchestrated by transcriptional regulators and evolves is not clear. Using de novo motif analysis, we show that the hepatocyte nuclear factor 1 (HNF1)‐binding motif is enriched in SEs in cell lines derived from liver metastases, but n...
Fusobacterium nucleatum, which has four subspecies (nucleatum, animalis, vincentii and polymorphum), plays an important role in promoting colorectal cancer (CRC). However, as there is no efficient method of differentiating these subspecies in the context of a rich gut microbiota, the compositions in CRC remain largely unknown. In this study, a PCR‐...
Despite numerous advances in in vitro fertilization (IVF) techniques since its first success in 1978, almost half of the patients treated remain childless. The multifactorial nature of IVF treatment means that success is dependent on variables, including the quality of oocytes. Therefore, new technologies are needed to objectively and quantitativel...
Poor ovarian responders (POR) are women undergoing in-vitro fertilization who respond poorly to ovarian stimulation, resulting in the retrieval of lower number of oocytes, and subsequently lower pregnancy rates. The follicular fluid (FF) provides a crucial microenvironment for the proper development of follicles and oocytes. Conversely, dysregulate...
Background
Centrosome aberrations have long been linked to tumorigenesis. Centrosome protein 78 (CEP78) is a centrosome component that is required to regulate the cell cycle, but its role in bladder cancer has not been elucidated.
Material/Methods
Real-time quantitative polymerase chain reaction and immunohistochemistry were used to examine the ex...
Background
Growth arrest-specific 6 (GAS6) is a secreted vitamin K-dependent protein abnormally expressed in various human tumor tissues and can activate the receptor Tyro3, Axl, and Mer to promote cancer cell proliferation and invasion. Until now, the role of GAS6 has been poorly understood in bladder cancer (BCa).
Materials and Methods
Using bio...
AbaR-type genomic islands (AbaRs) are well-known elements that can cause antimicrobial resistance in Acinetobacter baumannii . These elements contain diverse and complex genetic configurations involving different but related backbones with acquisition of diverse mobile genetic elements and antimicrobial resistance genes. Understanding their structu...
The tumorigenesis of colorectal cancer (CRC) is a complicated process, involving interactions between cancer cells and the microenvironment. The role of α5 integrin subunit in CRC remains controversial, and previous studies mainly focused on cancer cells. Herein, we report an important role of α5 in stroma fibroblasts in the tumorigenesis of CRC. T...
The cover image is based on the Original Research Toward automatic prediction of EGFR mutation status in pulmonary adenocarcinoma with 3D deep learning by Wei Zhao et al., DOI: 10.1002/cam4.2233. Design Credit: Ming Li, Wei Zhao, Jiancheng Yang and Ye Ge.
Renal cell carcinoma (RCC) is the most common malignant disease of the kidneys in adults. Patients with metastatic RCC have an unusually poor prognosis and exhibit resistance to all current therapies. Therefore, it is necessary to explore novel molecules involved in the progression of RCC and to identify effective therapeutic targets. Hepatocyte nu...
Acute hepatopancreatic necrosis disease (AHPND) has caused sharp declines in aquaculture industries of whiteleg shrimp Penaeus vannamei in Asia and the Americas since 2010. Vibrio parahaemolyticus, V. campbellii, V. owensii, and V. punensis have been proved to cause AHPND. However, the mechanisms underlying the burgeoning number of Vibrio species t...
To develop a deep learning system based on 3D convolutional neural networks (CNNs), and to automatically predict EGFR‐mutant pulmonary adenocarcinoma in CT images. A dataset of 579 nodules with EGFR mutation status labels of mutant (Mut) or wild‐type (WT) was retrospectively analyzed. A deep learning system, namely 3D DenseNets, was developed to pr...
Abstract
Rationale: Colorectal cancer (CRC) is a malignant tumor with the third highest morbidity rate among all cancers. Driven by the host’s genetic makeup and environmental exposures, the gut microbiome and its metabolites have been implicated as the causes and regulators of CRC pathogenesis. We assessed human fecal samples as noninvasive and u...
AbaR-type genomic islands (AbaRs) are important elements responsible for antimicrobial resistance in Acinetobacter baumannii . This study performed a large-scale identification of AbaRs to understand their distribution and compositions of antimicrobial resistance genes. We identified 2.89-kb left-end and 1.87-kb right-end conserved sequences (CSs)...
Objective
To evaluate the diagnostic performance of Xpert MTB/RIF Ultra for EPTB (Extrapulmonary Tuberculosis) patients on different types of extrapulmonary specimens from different anatomic sites.
Methods
Patients with suspected EPTB were prospectively included, extrapulmonary specimens were collected and subjected to culture, Xpert and Xpert Ult...
ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, includi...
IncFII K plasmids are associated with the acquisition and dissemination of multiple antimicrobial resistance in Klebsiella pneumoniae and often encountered in clinical isolates of this species. Since the phylogeny and evolution of IncFII K plasmids remain unclear, herein we performed large-scale in silico typing and comparative analysis of these pl...
Background: This study aimed to identify the influence of peripheral lymphocytes on prognosis and find prognostic markers for breast cancer patients. Methods: This study enrolled invasive breast cancer patients and they were followed-up for median 4-years over telephone. Distributions of disease-free survival (DFS) and overall survival (OS) between...
Acute hepatopancreatic necrosis disease (AHPND) is a severe shrimp disease originally shown to be caused by virulent strains of Vibrio parahaemolyticus (VPAHPND). Rare cases of AHPND caused by Vibrio species other than V. parahaemolyticus were reported. We compared an AHPND-causing V. campbellii (VCAHPND) and a VPAHPND isolate from the same AHPND-a...
Plasmids play critical roles in bacterial fitness and evolution of Pseudomonas aeruginosa. Here two plasmids found in a drug-resistant P. aeruginosa clinical isolate HS87 were completely sequenced. The pHS87b plasmid (11.2 kb) carries phage-related genes and function-unknown genes. Notably, pHS87b encodes an integrase and has an adjacent tRNAThr-as...
Coverage of the pHS87b sequence by different resources.
Coverage of a position means the times the nucleotide acid at this position was aligned. HMP, Human Microbiome Project; nr, NCBI non-redundant database; Pa plasmid, completely sequenced P. aeruginosa plasmids.
(TIF)
Southern blotting to verify that pHS87b integrates into chromosome.
The pchG gene on chromosome and the integrase gene orf2 on pHS87b were used as the probes. Lane M: 1kb plus DNA ladder. A: 1% agarose gel electrophoresis of P. aeruginosa HS87 genomic DNA. B: Sothern blotting with pHS87b-specific probe. C: Sothern blotting with chromosome-specific...
Phylogenetic tree of RepA proteins of pHS87a and pPT23A-family plasmids.
Plasmid names, host, the accession numbers of RepA proteins are given. Plasmids of pPT23A family were from Zhao et al [31].
(TIF)
Coverage of the pHS87a sequence by different resources.
Coverage of a position means the times the nucleotide acid at this position was aligned. HMP, Human Microbiome Project; nr, NCBI non-redundant database; Pa plasmid, completely sequenced P. aeruginosa plasmids.
(TIF)
Abundance of the empty tRNAThr site and the circular and integrated forms of pHS87b.
The attB, attP and attR indicates the empty integration site, circular and integrated forms of pHS87b, respectively. The gyrB gene is used as endogenous reference. The fold change was calculated by 2-ΔΔCT, as the amplification efficiencies of different primers were...
Digestion profile of the GI occupying the tRNAThr gene site is consistent with the predicted profile of the integrated form of pHS87b.
The amplicon (*) was purified. Sequence analysis of the integrated form of pHS87b was based on the sequence of the pHS87b and sequenced junctions. The size number in the table is placed in accord with the maker. Gre...
Klebsiella pneumoniae is an increasingly important bacterial pathogen to human. This Gram-negative bacterium species has become a serious concern due to its dramatic increase in the levels of multiple antibiotic resistances, particularly to carbapenems. The toxin-antitoxin (TA) system has recently been reported to be involved in the formation of dr...
This study aims to investigate the landscape of the mobile genome, with a focus on antibiotic resistance-associated factors in carbapenem-resistant Klebsiella pneumoniae.
The mobile genome of the completely sequenced K. pneumoniae HS11286 strain (an ST11, carbapenem-resistant, near-pan-resistant, clinical isolate) was annotated in fine detail. The...
In order to understand the genetic background and dissemination mechanism of carbapenem resistance and fosfomycin resistance
in Enterobacteriaceae isolates, we studied a clinical Escherichia coli strain HS102707 isolate and an Enterobacter aerogenes strain HS112625 isolate, both of which were resistant to carbapenem and fosfomycin and positive for...
The web-based database TADB offers a comprehensive compilation of both predicted and experimentally supported type II toxin-antitoxin (TA) locus data and genetic features. Here, we examine the distribution and diversity of TADB-recorded TA loci throughout bacterial and archaeal genomes; in particular, those carried by the chromosomal mobile element...
SecReT4 (http://db-mml.sjtu.edu.cn/SecReT4/) is an integrated database providing comprehensive information of type IV secretion systems (T4SSs) in bacteria. T4SSs are versatile assemblages that promote genetic exchange and/or effector translocation with consequent impacts on pathogenesis and genome plasticity. T4SSs have been implicated in conjugat...
Thiopeptides are a growing class of sulfur-rich, highly modified heterocyclic peptides that are mainly active against Gram-positive bacteria including various drug-resistant pathogens. Recent studies also reveal that many thiopeptides inhibit the proliferation of human cancer cells, further expanding their application potentials for clinical use. T...
Organized catalogues on the ‘Browse’ page of ThioBase. (A) List of the known thiopeptides. (B) Detailed information of thiopeptides, regarding the chemical structure, analogue, biological activity, producing strain, biosynthetic gene cluster, structure peptide sequence and reference, as exemplified by that for nosiheptide. Hyperlinks to NCBI PubChe...
The list of the thiopeptide gene clusters identified by ThioFinder.
(DOC)
Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic infections. Here we report the genome sequence of a strain,
HS11286, isolated from human sputum in 2011 in Shanghai, China. It contains one chromosome (5.3 Mb), three multidrug resistance
plasmids (∼110 kb), including a carbapenemase producer, and three small plas...
ICEberg (http://db-mml.sjtu.edu.cn/ICEberg/) is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excisio...
TADB (http://bioinfo-mml.sjtu.edu.cn/TADB/) is an integrated database that provides comprehensive information about Type 2 toxin–antitoxin (TA) loci, genetic features
that are richly distributed throughout bacterial and archaeal genomes. Two-gene and much less frequently three-gene Type 2
TA loci code for cognate partners that have been hypothesize...
Dry distiller's grain and solubles (DDGS) is a major by-product of corn-based ethanol production and is usually used as animal feed. Here, it was added to the simultaneous saccharification and ethanol fermentation (SSF) carried out at high solids loading of steam explosion pretreated corn stover using a mutant strain Saccharomyces cerevisiae DQ1. T...