胰腺癌早期检测的生物标志物

胰腺癌症是最难诊断和治疗的恶性肿瘤之一,其特点是发病隐匿、进展迅速、预后差。目前,手术治疗仍然是首选治疗方法。然而由于缺乏早期症状,大约70%的患者在确诊时已经出现局部扩散或远端转移,从而无法进行手术治疗。由此看来,早期检测是提高患者治疗效果和预后的有效途径。临床上使用的成像方法(CT、MRI、EUS等)通常无法检测早期病变,并且很容易受到操作员的影响。常规临床标志物如CA19-9、CA125、CA242和CEA受到限制,其敏感性或特异性不令人满意。因此,寻找新的具有高敏感性和特异性的标志物是实现胰腺癌早期检测的关键。近年来,对生物标志物的广泛研究主要集中在遗传学、转录组学和蛋白质组学上。特别是由microRNA(miRNA)、long non-coding RNA(lncRNA)和circRNA(circRNA)组成的非蛋白质编码RNA(non-protein coding RNA,ncRNA)为胰腺癌的早期检测提出了许多新思路。然而,其中绝大多数仍处于实验室研究阶段。而一项成熟的生物标志物研究应该整合基因组学、转录组学、蛋白质组学或代谢组学的数据,并结合患者的个体特征(如体重指数、糖尿病史、吸烟、饮酒和其他危险因素)进行大规模、前瞻性和验证性研究。

Regulation of epithelium-specific Ets-like factors ESE-1 and ESE-3 in airway epithelial cells： potential roles in airway inflammation

Airway inflammation is the hallmark of many respiratory disorders, such as asthma and cystic fibrosis. Changes in airway gene expression triggered by inflammation play a key role in the pathogenesis of these diseases. Genetic linkage studies suggest that ESE-2 and ESE-3, which encode epithelium-specific Ets-domain-containing transcription factors, are candidate asthma susceptibility genes. We report here that the expression of another member of the Ets family transcription factors ESE-1, as well as ESE-3, is upregulated by the inflammatory cytokines interleukin-1β （IL-1β） and tumor necrosis factor-α （TNF-α） in bronchial epithelial cell lines. Treatment of these cells with IL-1β and TNF-α resulted in a dramatic increase in mRNA expression for both ESE-1 and ESE-3. We demonstrate that the induced expression is mediated by activation of the transcription factor NF-κB. We have characterized the ESE-1 and ESE-3 promoters and have identified the NF-κB binding sequences that are required for the cytokine-induced expression. In addition, we also demonstrate that ESE-1 upregulates ESE-3 expression and downregulates its own induction by cytokines. Finally, we have shown that in E/f3 （homologous to human ESE-1） knockout mice, the expression of the inflammatory cytokine interleukin-6 （IL-6） is downregulated. Our findings suggest that ESE-1 and ESE-3 play an important role in airway inflammation.

Key questions about the checkpoint blockade-are microRNAs an answer?

The introduction of immune-checkpoint blockade in the cancer therapy led to a paradigm change of the management of late stage cancers. There are already multiple FDA approved checkpoint inhibitors and many other agents are undergoing phase 2 and early phase 3 clinical trials. The therapeutic indication of immune checkpoint inhibitors expanded in the last years, but still remains unclear who can benefit. Micro RNAs are small RNAs with no coding potential. By complementary pairing to the 3' untranslated region of messenger RNA, microRNAs exert posttranscriptional control of protein expression. A network of microRNAs directly and indirectly controls the expression of checkpoint receptors and several microRNAs can target multiple checkpoint molecules,mimicking the therapeutic effect of a combined immune checkpoint blockade. In this review, we will describe the microRNAs that control the expression of immune checkpoints and we will present four specific issues of the immune checkpoint therapy in cancer:(1) imprecise therapeutic indication,(2) difficult response evaluation,(3) numerous immunologic adverse-events, and(4)the absence of response to immune therapy. Finally, we propose microRNAs as possible solutions for these pitfalls. We consider that in the near future microRNAs could become important therapeutic partners of the immune checkpoint therapy.

The effect of exosomes in transferring TET signaling alterations

Ten eleven translocation(TET)enzymes are composed of three representatives:TET1/2/3 which are involved in the hydroxymethylation of methylated cytosines.Because of the wide array of processes that are governed by these epigenetic marks,there have been a wide range of clinical effects associated with TET alterations.Even though many research groups have focused on analyzing the effect of TET alterations within certain cells,few have taken into consideration the effect of TET in the context of intercellular communication.One important entity through which intercellular communication occurs is represented by exosomes.Thus,in the current viewpoint we discussed the direct transfer of TET by exosomes,its alterations in the cell targeted by exosomes and the effect of TET alterations on exosome secretion.

Phenylacetylglutaminate and Phenylacetate in Combination Upregulate VDUP1, Cause Cell Cycle Blockade and Apoptosis in U87 Glioblastoma Cells

Phenylacetylglutaminate (PG) and Phenylacetate (PN) are metabolites of Phenylbutyrate (PB) and are constituents of antineoplaston AS2-1. These are sodium salts of amino acid derivative and carboxylic acid that inhibit the growth of neoplastic cells without growth inhibitory effect in normal cells. The aim of this study was to identify molecular pathways involved in the anti-proliferative effect of antineoplastons. Using a total human genome microarray we have found that 1) Vitamin D3 upregulated protein (VDUP1) is significantly upregulated in response to PG and PN in the U87 glioblastoma cells;2) Isobologram analysis shows that PG and PN act in an additive or synergistic manner to effectively suppress proliferation of U87 cells;3) PG and PN cause cell cycle arrest, changes in expression of several cell cycle genes and suppress expression and activity of the G2/M checkpoint kinase, CHK1. The multiple cellular targets possibly make these compounds effective anti-proliferative agents. We propose that PG and PN in combination target important cellular pathways and upregulate VDUP1 leading to detachment-induced apoptosis in cancer cells.

Evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China

On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese mainland.As the number of infected people increased,the mutation probability of SARS-CoV-2 is also raised.Therefore,it is of great importance to monitor SARS-CoV-2 variants and its mutations in China.In this current study,665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants;to determine the composition of variants in China across different provinces;and analyze specific mutation frequency,focusing on 12 immune escape residues.The results showed that no new mutations were generated on the 12 immune escape residues.The evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites,officially named BF.7.14 by PANGO.This variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in China.The evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants,named BA.5.2.48 and BA.5.2.49 by PANGO,respectively.This variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic transmission.Finally,this study showed that current epidemic variants in China were already circulating in other countries,and there were no additional mutations on immune escape residues that could pose a threat to other countries.

The Non-Coding RNA Llme23 Drives the Malignant Property of Human Melanoma Cells

Several lines of evidence support the notion that increased RNA-binding ability of polypyrimidine tract-binding（PTB） proteinassociated splicing factor（PSF） and aberrant expression of long non-coding RNAs（IncRNAs） are associated with mouse and human tumors.To identify the PSF-binding IncRNA involved in human oncogenesis,we screened a nuclear RNA repertoire of human melanoma cell line,YUSAC,through RNA-SELEX affinity chromatography.A previously unreported IncRNA,termed as Llme23,was found to bind immobilized PSF resin.The specific binding of Llme23 to both recombinant and native PSF protein was confirmed in vitro and in vivo. The expression of PSF-binding Llme23 is exclusively detected in human melanoma lines.Knocking down Llme23 remarkably suppressed the malignant property of YUSAC cells,accompanied by the repressed expression of proto-oncogene Rab23.These results may indicate that Llme23 can function as an oncogenic RNA and directly associate the PSF-binding IncRNA with human melanoma.

Non-coding Transcripts from Enhancers:New Insights into Enhancer Activity and Gene Expression Regulation

Long non-coding RNAs （lncRNAs） have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological pro- cesses. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs （eRNAs）. The eRNAs are not merely the by-product of the enhancer transcription. In fact, many of them directly exert or regulate enhancer activity in gene activation through diverse mechanisms. Here, we provide an overview of enhancer activity, transcription of enhancer itself, characteristics of eRNAs, as well as their roles in regulating enhancer activity and gene expression.

Long non-coding RNA-guided regulation in organisms

It is clear that RNA is more than just a messenger between gene and protein.The mammalian genome is pervasively transcribed,giving rise to tens of thousands of non-coding transcripts.Whether all of these transcripts are functional remains to be elucidated,but it is evident that there are many functional long non-coding RNAs(lncRNAs).Recent studies have set out to decode the regulatory role and functional diversity of lncRNAs.Here we organize these studies to highlight the significant involvements of lncRNAs in regulation of gene expression and human physiological and pathological processes,which are achieved by their interaction with DNA,RNA or protein.

Comparative Analysis of Protein-Protein Interactions in Cancer-Associated Genes

Protein-protein interactions （PPIs） have been widely studied to understand the biological processes or molecular functions associated with different disease systems like cancer. While focused studies on individual cancers have generated valuable information, global and comparative analysis of datasets from different cancer types has not been done. In this work, we carried out bioinformatic analysis of PPIs corresponding to differentially expressed genes from microarrays of various tumor tissues （belonging to bladder, colon, kidney and thyroid cancers） and compared their associated biological processes and molecular functions （based on Gene Ontology terms）. We identified a set of processes or functions that are common to all these cancers, as well as those that are specific to only one or partial cancer types. Similarly, protein interaction networks in nucleic acid metabolism were compared to identify the common/specific clusters of proteins across different cancer types. Our results provide a basis for further experimental investigations to study protein interaction networks associated with cancer. The methodology developed in this work can also be applied to study similar disease systems.

The role of exosomal long non-coding RNAs in cancer drug resistance

One of the major challenges in oncology is drug resistance,which triggers relapse and shortens patients’survival.In order to promote drug desensitization,cancer cells require the establishment of an ideal tumor microenvironment that accomplishes specific conditions.To achieve this objective,cellular communication is a key factor.Classically,cells were believed to restrictively communicate by ligand-receptor binding,physical cell-to-cell interactions and synapses.Nevertheless,the crosstalk between tumor cells and stroma cells has also been recently reported to be mediated through exosomes,the smallest extracellular vesicles,which transport a plethora of functionally active molecules,such as:proteins,lipids,messenger RNA,DNA,microRNA or long non-coding RNA(lncRNAs).LncRNAs are RNA molecules greater than 200 base pairs that are deregulated in cancer and other diseases.Exosomal lncRNAs are highly stable and can be found in several body fluids,being considered potential biomarkers for tumor liquid biopsy.Exosomal lncRNAs promote angiogenesis,cell proliferation and drug resistance.The role of exosomal lncRNAs in drug resistance affects the main treatment strategies in oncology:chemotherapy,targeted therapy,hormone therapy and immunotherapy.Overall,knowing the molecular mechanisms by which exosomal lncRNA induce pharmacologic resistance could improve further drug development and identify drug resistance biomarkers.

MakeHub:Fully Automated Generation of UCSC Genome Browser Assembly Hubs

Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics.This audience requires tools that are easy to use.Such need has been addressed by several genome annotation tools and pipelines.Visualizing resulting annotation is a crucial step of quality control.The UCSC Genome Browser is a powerful and popular genome visualization tool.Assembly Hubs,which can be hosted on any publicly available web server,allow browsing genomes via UCSC Genome Browser servers.The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available.However,the number of steps for creating a novel Assembly Hub is large.In some cases,the format of input files needs to be adapted,which is a difficult task for scientists without programming background.Here,we describe Make Hub,a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion.The pipeline also allows extending previously created Hubs by additional tracks.Make Hub is freely available for downloading at https://github.com/Gaius-Augustus/Make Hub.

Aptamer blocking S-TLR4 interaction selectively inhibits SARS-CoV-2 induced inflammation

Excessive inflammatory responses lead to increased mortality from the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Nearly all deceased patients infected with SARS-CoV-2 are found to have cytokine storm syndrome and viral sepsis.They are prone to superinfections exacerbating the course of disease.1 Therefore,preventing hyperinflammation is critical for avoiding this cytokine storm syndrome.Currently,specific immunomodulators are under clinical research or application,including targeting inflammatory cytokines(sarilumab,anakinra,tocilizumab,infliximab,adalimumab)and inflammatory pathway(baricitinib,ruxolitinib).

Cytokine Profiling in Influenza A Virus and Staphylococcal(Co-)Infections

Influenza A virus and Staphylococcus aureus are common causative agents of pneumonia.Co-infections with these two pathogens frequently occur and are characterized,among others,by higher morbidity and mortality due to hyper-inflammation of the lungs.Here,we aimed to profile systemic and local cytokine composition at early acute stages of pneumonia in amurinemodel.Allmice recovered from single influenza A virus and/or staphylococcal infections.In contrast,co-infections led to a severe clinical outcome.While distinct cytokine patterns were detected in lungs of single-pathogen-infected animals,co-infections combined both virus-and bacteria-driven responses.However,analyses of infected human primarymonocytic cells as well as bronchial epithelial cells did not reflectmurine profiles.Based on infectious dose,mainly bacteria-driven responses were noted.The impact of single cells to cytokine composition of the lungs and translation of murine studies to humans remains uncertain and warrants further studies.

“Mutation blacklist”and “mutation whitelist”of SARS-CoV-2

Over the past two years,scientists throughout the world have completed more than 6 million SARS-CoV-2 genome sequences.Today,the number of SARS-CoV-2 genomes exceeds the total number of all other viral genomes.These genomes are a record of the evolution of SARS-CoV-2 in the human host,and provide information on the emergence of mutations.In this study,analysis of these sequenced genomes identified 296,728 de novo mutations(DNMs),and found that six types of base substitutions reached saturation in the sequenced genome population.Based on this analysis,a“mutation blacklist”of SARS-CoV-2 was compiled.The loci on the“mutation blacklist”are highly conserved,and these mutations likely have detrimental effects on virus survival,replication,and transmission.This information is valuable for SARS-CoV-2 research on gene function,vaccine design,and drug development.Through association analysis of DNMs and viral transmission rates,we identified 185 DNMs that positively correlated with the SARS-CoV-2 transmission rate,and these DNMs where classified as the“mutation whitelist”of SARS-CoV-2.The mutations on the“mutation whitelist”are beneficial for SARS-CoV-2 transmission and could therefore be used to evaluate the transmissibility of new variants.The occurrence of mutations and the evolution of viruses are dynamic processes.To more effectively monitor the mutations and variants of SARS-CoV-2,we built a SARS-CoV-2 mutation and variant monitoring and pre-warning system(MVMPS),which can monitor the occurrence and development of mutations and variants of SARSCoV-2,as well as provide pre-warning for the prevention and control of SARS-CoV-2(https://www.omicx.cn/).Additionally,this system could be used in real-time to update the“mutation whitelist”and“mutation blacklist”of SARS-CoV-2.

Disease X Testing:The results of an international external quality assessment exercise

The United Nations Secretary-General Mechanism(UNSGM)for investigation of the alleged use of chemical and biological weapons is the only established international mechanism of this type under the UN.The UNGSM may launch an international investigation,relying on a roster of expert consultants,qualified experts,and analytical laboratories nominated by the member states.Under the framework of the UNSGM,we organized an external quality assurance exercise for nominated laboratories,named the Disease X Test,to improve the ability to discover and identify new pathogens that may cause possible epidemics and to determine their animal origin.The“what-if”scenario was to identify the etiological agent responsible for an outbreak that has tested negative for many known pathogens,including viruses and bacteria.Three microbes were added to the samples,Dabie bandavirus,Mammarenavirus,and Gemella spp.,of which the last two have not been taxonomically named or published.The animal samples were from Rattus norvegicus,Marmota himalayana,New Zealand white rabbit,and the tick Haemaphysalis longicornis.Of the 11 international laboratories that participated in this activity,six accurately identified pathogen X as a new Mammarenavirus,and five correctly identified the animal origin as R.norvegicus.These results showed that many laboratories under the UNSGM have the capacity and ability to identify a new virus during a possible international investigation of a suspected biological event.The technical details are discussed in this report.