第四届发育和疾病的表观遗传学上海国际研讨会在沪隆重开幕

2018 年 9 月 19 日，由复旦大学附属中山医院、中科大附属第一医院与生物 360 联合主办的第四届发育和疾病的表观遗传学上海国际研讨会在复旦大学附属中山医院 18 号楼 3 楼福庆厅隆重开幕，现场座无虚席。

会务组邀请到了五十多位来自全球的活跃在该领域第一线科学家与会报告。科学家和参会者进行深入广泛的学术交流。

今天上午出席演讲的嘉宾有来自中科院院士徐国良、中国科学院－马普学会计算生物学伙伴研究所 Andrew Teschendorff、（中国台湾）中央研究院分子生物研究所 James Shen、北京希望组, 武汉未来组 CEO 汪德鹏、中山大学研究员肖传乐、复旦大学徐彦辉、易毕恩基因科技 CEO 陆星宇、北京大学生命科学学院曾虎、华中农业大学生命科学技术学院李响、浙江大学钱鹏旭。

下午则由 Saha Institute of Nuclear Physics 的 Chandrima Das、日本国家癌症中心 Naoko Hattori、清华大学医学院李海涛、复旦大学蓝斐、MD Anderson 癌症中心吕志民、中科院上海生化细胞所姜海、上海交通大学杨秀岩出席演讲。

徐国良演讲精彩瞬间

徐国良院士的演讲主题是“A vitamin C-derived DNA modification”。

Andrew Teschendorff 演讲精彩瞬间

Andrew Teschendorff 的演讲主题是“Aging, epigenetic clocks and cancer risk”。报告摘要为：

It has long been observed that the DNA methylome is altered with age. More recently, DNAm alterations that occur in response to specific environmental cancer risk factors (e.g. smoking) have been characterized. Some of these alterations are thought to contribute to carcinogenesis via a hypothesized epigenetic stem cell progenitor model of oncogenesis. I will review the data from own work supporting such a model, including the detection of DNA methylation field defects in normal tissue adjacent to breast cancer. I will show how DNAm changes in normal adjacent tissue can predict breast cancer status better than corresponding copy-number alterations. Finally, I will describe our efforts to construct a mitotic-like epigenetic clock, which, unlike other existing epigenetic clocks, appears universally accelerated in preneoplastic and preinvasive cancer lesions and which may serve to predict cancer risk generally.

James Shen 演讲精彩瞬间

James Shen 的演讲主题是“Active DNA Demethylation by Vertebrate DNAMethyltransferases”。报告摘要为：

The DNA methyltransferases Dnmt 1, Dnmt 3A, and Dnmt 3B work together to shape the methylation patterns, and consequently regulate the chromatin structure and gene expression of the vertebrate genomes. Reversely, the TET enzymes play a role in the active DNA demethylation in the vertebrate cells. We have found that Dnmt 3A and Dnmt 3B also possess DNA dehydroxymethylation activity; furthermore, all 3 vertebrate Dnmt enzymes could actively demethylate DNA in an Ca-++ and redox condition-dependent manner. Data supporting the involvement in vivo of active DNA demethylation by Dnmts in the regulation of specific biological processes will be presented and discussed.

汪德鹏演讲精彩瞬间

汪德鹏的演讲主题是“The DNA modification landscape of humangenome: an experience of HuaXia1genome/Third-Generation Sequencing”。报告摘要为：

Using Nanopore sequencing data from HuaXia1 (HX1) human genome (This result was based on 10X genome-wide coverage, until now we have sequnced 80X data), we identified 822,628 6mA modification sites and 18,724,520 5mC modification sites at CpG sites, whose density (6mA/A and 5mC/CpG) was approximately 0.047% and 63.7% respectively in the human genome.

Our results showed that the 6mA/A ratio by the Nanopore sequencing technology was 0.047% in the blood genome DNA sample, consistent with the ratio resolved by PacBio SMRT sequencing (0.051%) and by the liquid chromatography tandem mass spectrometry (LC-MS/MS) assay (0.056%) on the same blood-derived DNA sample. We also applied 6mA immunoprecipitation sequencing (6mA-IP-seq) to validate the presence of 6mA modification in human genomic DNA. The 6mA-containing DNA regions identified by 6mA-IP-seq were significant overlapped with the 6mA site occupied regions identified by Nanopore and SMRT sequencing (p-value < 10^-8).

The fraction of methylated C at CpG sites over the number of all CpG sites by the Nanopore sequencing technology was 63.7% in the blood genome DNA sample, consistent with the ratio resolved by bisulfite sequencing (60.4%). And the 5mC-containing regions identified by the two methods were highly overlapped.

Collectively, our results demonstrate that nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 6mA and 5mC. We can apply Nanopore to sequence the methylome of human DNA, without requiring special steps for library preparation.

肖传乐的演讲主题是“N6-Methyladenine DNA Modification in the Human Genome”。报告摘要为：

DNA N6-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in the human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA siteswere enriched in the coding regions and mark actively transcribed genes in human cells. DNA 6mA and N6-demethyladenine modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.

徐彦辉演讲精彩瞬间

徐彦辉的演讲主题是“Structural Insight into dynamic regulation of DNA methylation”。报告摘要为：

DNA methylation is an important epigenetic modification and essential for various developmental processes through regulating gene expression, genomic imprinting, and epigenetic inheritance. Mammalian genomic DNA methylation is established during embryogenesis by de novo DNA methyltransferases, DNMT3A and DNMT3B. The pattern of DNA methylation is maintained by DNMT1 and UHRF1. Ten-Eleven Translocation (TET) proteins were found to be essential for DNA demethylation. TET1/2/3 oxidize 5mC to 5hmC, 5fC, and 5caC, which are replaced by unmethylated cytosine through active and passive mechanisms.

Our systematic studies reveal the underlying mechanisms for catalysis, substrate recognition, and regulation of enzymatic activity of these epigenetic regulators and provide structural basis for designing of specific inhibitors or activators for functional studies and potential therapeutic applications.

陆星宇演讲精彩瞬间

陆星宇的演讲主题是“DNA 5-Hydroxymethylcytosines from Cell-free Circulating DNA as Diagnostic Biomarkers for Human Cancers”。报告摘要为：

DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals[1-2]. Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology[3], we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and in genomic DNA of paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-associated 5hmC signatures in cfDNA were identified with specificity for different cancers. 5hmC-based biomarkers of circulating cfDNA demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to 5hmC biomarkers from tissue biopsies. This new strategy could lead to the development of effective blood-based, minimally-invasive cancer diagnosis and prognosis approaches.

曾虎演讲精彩瞬间

曾虎的演讲主题是“Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution.”。报告摘要为：

Emerging evidence reveals that 5-hydroxymethylcytosine (5hmC) serves as not only an active DNA demethylation intermediate, but also a stable DNA modification that plays distinct epigenetic roles and impacts a broad range of biological processes. High-resolution detection of genome-wide 5hmC sites of small-scale samples remains challenging. We developed CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the genome of human embryonic stem cells and base-resolution hydroxymethylome in human cell-free DNA.

李响演讲精彩瞬间

李响的演讲主题是“BRIF-seq: bisulfite-converted randomly integrated fragments sequencing at single cell level”。报告摘要为：

The ability to access DNA methylation in single cells is limited by genome coverage. We developed an efficient method, bisulfite-converted randomly integrated fragments sequencing (BRIF-seq), with high rates of read mapping and genome coverage. Single microspores of maize with high-repetitive haploid genome were used to perform BRIF-seq. Up to 55% of the genome was covered to allow evaluation of CG, CHG (H = A, C, or T), and CHH methylation states as well as the genetic polymorphisms. By comparing both DNA methylation levels and genotypes between each microspore with their two parents, we identified cytosine site where the coupling of DNA methylation and genotype was disrupted in microspores. These sites, termed heterogeneity independent on genetic background (HIG), suggest rapid DNA methylation reprogramming at tetrad stage. These results propose that single cell BRIF-seq (scBRIF-seq) works well for species with complex genome as well as individuals with diverse backgrounds.

钱鹏旭演讲精彩瞬间

钱鹏旭的演讲主题是“The role of differentially methylated regions in normal hematopoiesis and leukemogenesis”。报告摘要为：

As one of the major epigenetic marks, DNA methylation dictates spatial and temporal gene expression in stem cells and their progeny and plays fundamental roles in multiple biological processes, such as embryonic development, stem cell regulation, X-chromosome inactivation and genomic imprinting. Aberrant DNA methylation and mutations in DNA methyltransferase and methylcytosine dioxygenase enzymes, such as Dnmt3a and Tet2, have been frequently found in multiple types of cancer including leukemia. Although advanced technologies of genome-wide methylome sequencing have identified thousands of differentially methylated regions (DMRs) on cis-regulatory modules, much remains unknown about the physiological functions and underlying mechanisms of individual DMR in stem cell differentiation and cancer development. Our recent studies have demonstrated the critical roles of two imprinting DMRs, H19-DMR and IG-DMR, in maintaining quiescent and low metabolic states of LT-HSCs. To systematically identify DMRs during HSC differentiation, we have performed whole genome bisulfite sequencing in four adult HSC populations and found thousands of DMRs from pairwise comparison analyses. In combination with our transcriptome data, we identified a retinoid-dependent HSC-specific DMR, distal element RARE (DERARE). Deletion of the DERARE reduced Hoxb expression resulting in changes to many downstream signaling pathways (e.g. non-canonical Wnt signaling), and loss of HSC self-renewal and reconstitution capacity. DNA methyltransferases mediate DNA methylation on the DERARE, leading to reduced Hoxb cluster expression. Acute myeloid leukemia patients with DNMT3A mutations exhibit DERARE hypomethylation, elevated HOXB expression and adverse outcomes. CRISPR-Cas9-mediated specific DNA methylation at DERARE attenuated HOXB expression and alleviated leukemogenesis. Collectively, these findings demonstrate pivotal roles for retinoid signaling and the DERARE in maintaining HSCs and preventing leukemogenesis by coordinate regulation of Hoxb genes.

Chandrima Das 演讲精彩瞬间

Chandrima Das 的演讲主题是“Decoding the Epigenetic Landscape by the Histone Readers: Implications in human diseases”。报告摘要为：

The alterations in the epigenomic landscape of chromatin are causally related to normal homeostasis of the organism and so as the pathobiological state. The molecular mechanism of epigenetic modification based functions is operated through a class of proteins called chromatin readers which recognizes this modification and thereby differentially recruits several other regulatory factors. The research focus of Chromatin Dynamics laboratory is to understand some of these epigenetic readers in the context of cellular functions and their possible connection to the disease, including metabolic as well as infectious diseases. In this context, we have recently uncovered the physiological functions of chromatin reader Sp110, a Promyelocytic leukemia nuclear bodies (PML-NBs) protein. DNA/RNA viruses often hijack cellular-factors resident in PML-NBs to promote their proliferation in host cells although the molecular mechanism is not well elucidated. Hepatitis B virus (HBV), belonging to Hepadnaviridae family remains undetected in early infection as it does not induce the innate immune response and is known to be cause of several hepatic diseases leading to cirrhosis and hepatocellular-carcinoma. In our recent study, we show that PML-NB protein Speckled 110kDa (Sp110), is SUMO1-modified and undergoes a deSUMOylation driven release from the PML-NB in presence of HBV. Intriguingly, Sp110 knock-down significantly reduces the viral DNA-load in the culture supernatant by activation of type-I interferon response pathway. Further, we show that Sp110 differentially regulates several direct target genes of HBx, a viral co-factor. Subsequently, we identified Sp110, as a novel interactor of HBx and found this association to be essential for the exit of Sp110 from the PML-NB during HBV infection and HBx recruitment on the promoter of these genes. HBx, in turn, modulates the recruitment of its associated transcription cofactors p300/HDAC1 to these co-regulated genes, thereby altering the host gene expression programme in favour of viral persistence. Thus, our study reported a mechanism by which HBV can evade host immune-response by hijacking PML-NB protein Sp110 and therefore it can be a novel target for antiviral therapy for HBV.

Naoko Hattori 演讲精彩瞬间

Naoko Hattori 的演讲主题是“Epigenome Reprogramming as a Basis for Combination Therapy”。报告摘要为：

Applications of epigenetic therapies are expanding from hematological to solid tumors. However, the modes of action of epigenetic drugs are not completely understood. Here, we demonstrated that targeting the epigenome, which includes DNA methylation and histone modifications, can reprogram the cancer epigenome and normalize the response to other therapies. In colorectal cancers, three of four BRAFV600E mutant cell lines were sensitive to JQ1, a BET inhibitor, and addition of JQ1 to vemurafenib suppressed cell growth through the inhibition of feedback activation of the MAPK signaling pathway by vemurafenib. A pretreatment with decitabine could help overcome the resistance to irinotecan in gastric cancer cells in vitro and in vivo. Furthermore, decitabine enhanced the differentiation ability induced by a synthetic retinoid in neuroblasoma cells. Our data provide potential new strategies for epigenetic therapies against solid tumors.

李海涛演讲精彩瞬间

李海涛的演讲主题是“Structure and Function of YEATS Domain in Health and Disease”。报告摘要为：

Histone post-translational modifications (PTMs) carry critical epigenetic information that governs the decoding of the genetic message at the chromosomal level. Growing evidence shows that epigenetic regulations play key roles in many biological processes, and it has become clear that their dysregulation can give rise to diverse diseases, notably cancer. To enable the delicate regulation of gene transcription, diverse reader modules have evolved to recognize these marks in type- and site-specific manner. Here I report on the structural and functional characterization of the YEATS domain – a novel family of histone acylation reader that participates in transcriptional regulation in health and disease. The molecular recognition events discussed here illustrate how the cell makes use of the reader modules for transcription control under physiological and pathological conditions.

蓝斐演讲精彩瞬间

蓝斐的演讲主题是“The Dynamic Regulation of Histone Methylation”。报告摘要为：

Epigenetics misregulation is extensively involved in many steps of tumorigenesis. My laboratory is focused on the deciphering of the mis-regulated epigenetics information, especially the histone methylations, in various cancers. Along this line, we have recently discovered previously underappreciated functions of two “reader” proteins in interpreting histone methylations. These two proteins are ZMYND8 and ZMYND11, both of which are frequently mutated in many cancers. Although sharing significant homology, ZMYND8 and ZMYND11 recognize distinct histone methylation types that occur at enhancers and gene bodies. Detailed epigenomics analyses revealed novel functions of these two factors in regulating enhancer activation and RNA splicing, respectively.

吕志民演讲精彩瞬间

吕志民的演讲主题是“Metabolic regulation of gene expression”。报告摘要为：

Metabolism plays an instrumental role in the regulation of gene expression via metabolic enzymes and metabolites. Metabolic enzymes and intermediates or products of metabolism, either alone or by coupling with histone modifiers, regulate transcription factor activity and histone posttranscriptional modification. Metabolic enzyme-and metabolite-mediated modulation of chromatin or activity of transcription factors regulates gene expression and thereby instrumental cellular activities.

姜海的演讲主题是“UTX functions as an escape from X-inactivation tumor-suppressor in B cell lymphoma”。报告摘要为：

Comparing to females, males are more prone to develop cancer. To explain such difference, several candidates for ‘escape from X-inactivation tumor-suppressor’ (EXITS) were recently proposed. It is proposed that certain tumor suppressors on X chromsome escape from X-inactivation. Therefore females exhibit two functional copies of such tumor suppressor, and are therefore better protected against cancer than males. One of such EXITS candidate is UTX, which is an epigenetic regulator commonly mutated or deleted in human cancers. Combining tissue-specific UTX knockout mice and mouse models of lymphoma, we interrogated the role of UTX as a potential EXITS. Our results show that UTX copy number clearly impacted tumor development, which strongly supports the EXITS theory. Importantly, UTX deletion not only accelerates lymphomagenesis, it also strongly promotes tumor progression. UTX deficient tumor displayed significantly enhanced brain dissemination and blood vessel formation. We also studied the potential weakness associated with UTX deficiency and showed that UTX deficiency renders lymphoma sensitive to cytarabine treatment. Taken together, these data highlight UTX loss’s profound impacts on tumor initiation, progression and drug response.

杨秀岩的演讲主题是“Discovery and Functional Insight of a SIRT6 Allosteric Activator”。报告摘要为：

SIRT6, a member of deacetylase Sirtuins family, regulates diverse physiological processes, including genome stability, metabolism, and aging through deacetylation reactions of histone H3 Nε-acetyllysines 9 (H3K9Ac) and 56 (H3K56Ac). SIRT6. Especially, as a tumor suppressor, SIRT6, is frequently reduced for its expressions in various cancers. Here, we reported the identification of MDL-800, a selective SIRT6 activator that promoted the deacetylase activity of SIRT6 by binding to an uncharacterized allosteric site, leading to a global decrease in H3K9Ac and H3K56Ac of human hepatocellular carcinoma (HCC) cells. Consequently, MDL-800 inhibited the proliferation of HCC cells in a manner of SIRT6-driven cell-cycle arrest and was effective in tumor xenograft model. Together, these data demonstrate that pharmacological activation of SIRT6 is a valid therapeutic approach for the treatment of cancer. MDL-800 represents a first-in-class cellular small-molecule SIRT6 activator that can be used to investigate the roles of SIRT6 deacetylation physiologically and pathologically.

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