Our understanding of human genomes today is affected by the ability of modern computing technology to quickly and accurately determine an individual’s entire genome. Over the past decade, high throughput sequencing (HTS) technologies have opened the door to remarkable biomedical discoveries through its ability to generate hundreds of millions to billions of DNA segments per run along with a substantial reduction in time and cost. To analyze a genome, each of these segments -called reads- must be mapped to a reference genome based on the similarity between a read and “candidate” locations in that reference genome. This process is called read mapping and it is currently a major bottleneck in the entire genome analysis pipeline as the flood of sequencing data continues to overwhelm the processing capacity of existing algorithms and hardware. It gets even worse when one tries to understand a complex disease (e.g., autism and cancer) or profile a metagenomics sample, which requires analyzing hundreds of thousands of genomes. The long execution time of modern-day sequence aligners can severely hinder such studies. There is also an urgent need for rapidly incorporating clinical DNA sequencing and analysis into clinical practice for early diagnosis of genetic disorders in critically ill infants and saving their life. This makes the development of fundamentally new, fast, and efficient read mapper the utmost necessity.

This talk describes our ongoing journey in significantly improving the performance of genome read mapping. We first provide a brief background on read mappers that can comprehensively find variations in genomes and tolerate sequencing errors. Then, we describe our new algorithmic methods and hardware-based acceleration approaches. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or new execution paradigms, like processing in memory. We show that significant improvements are possible with algorithmic methods, hardware accelerators, and their combination. We conclude with a foreshadowing of future challenges and research directions triggered by the development of very low cost yet highly error prone new sequencing technologies.

Vaccines are highly effective at preventing infectious diseases. With continued development of immunological innovations, such as check point therapy for cancer, vaccines likely will become useful therapeutic tools against cancer. The various types of vaccines against infectious diseases include live attenuated vaccines, inactivated whole vaccines, and protein- or peptide-based subunit vaccines. They all have various advantages and disadvantages. For example, subunit vaccines are much safer than live attenuated vaccines and inactivated whole vaccines; however, when used alone, subunit vaccines evoke only weak adaptive immunity. Adaptive immune responses are initiated and regulated by dendritic cells, which acquire antigens and present them to B and T lymphocytes. Therefore, to enhance adaptive immune responses in subunit vaccines, delivering vaccine antigens to dendritic cells with appropriate adjuvants is an attractive approach. In addition, it is important to discover and design optimal vaccine antigens from pathogens. In this presentation, I would like to discuss my recent research for the development of subunit vaccines about 1) dendritic cell-targeting peptide as a vehicle for vaccine antigens, 2) cellular surface receptor of oligonucleotides-based adjuvants for designing novel adjuvants, 3) optimal use of adjuvants for influenza virus vaccine and 4) development of vaccine against Mycoplasma pneumoniae.

The life cycle of Plasmodium parasites is complicated; they invade into the host and mosquito cells accompanied by the morphological changes, multiply into more than thousands of daughter parasites, and fertilize after the sexual development. In each developmental stage, several hundreds of genes express specifically and are responsible for the characteristic features of parasites at each stage, such as merozoite, ookinete, sporozoite, and gametocytes, e.t.c. However, transcriptional activation factors had not been identified even after the completion of genome sequencing, and the regulation of gene expressions had thus remained to be unclear.
In 2005, S. Balaji et.al. suggested based on the computational analysis that there were the protein family, which consists of 27 members containing the plant-origin DNA binding domain, AP2 domain, in the genomes of Plasmodium spp. parasites. Following this, we provided the experimental evidences by the molecular genetic approach that these molecules acted as the transcriptional activation factors: these AP2 transcriptional factors expressed stage-specifically, recognized the unique DNA sequence motives, and the gene targeting of them decreased the expression of a number of genes in each developmental stage. These DNA sequence motives were commonly found at the upstream region of those down-regulated genes, suggesting that they would be the cis-elements. Furthermore, our ChIP-seq analysis showed that the AP2 transcription factor bound to upstream regions of approximately 500 genes, which correspond to 10% of all parasites’ genes, suggesting that single AP2 transcription factor would activated directly more than several hundreds of genes. This result suggested that Plasmodium spp. parasites express small number of AP2 transcription factors specifically in each stage and regulate probably all genes, which are required for the development in the stages, using them. By this mechanisms, although there are only 27 transcription factors, the parasites would be able to have the complicated life cycles. In this talk, I will show the function of AP2 transcription factors in several developmental stages and would like to discuss about the future study of transcriptional regulation of Plasmodium spp. parasites.

Abstract: The retina is an accessible system for identifying the molecular mechanisms that control CNS cell fate specification, and is a prime target for regenerative therapies aimed at restoring photoreceptors lost to blinding diseases. I will discuss our recent large-scale single-cell RNA-Seq analysis of multiple vertebrate species – including human, mouse and zebrafish -- that is aimed at identifying gene regulatory networks that drive the acquisition of neuronal and glial identity in the developing retina. I will discuss our identification of transcription factors that control both temporal identity and proliferative quiescence, new tools we and our collaborators have developed to identify both core evolutionarily-conserved and species-specific gene regulatory networks controlling retinal development, and mechanisms controlling injury-induced neurogenic competence in retinal glia.

CRISPR/Cas9をはじめとしたゲノム編集技術は、基礎研究分野に広く普及し、がんや遺伝病の治療に向けた臨床研究・試験が急速に進められている。また今年7月には、先天性黒内症に対してCRISPR/Cas9を利用した世界初のin vivo遺伝子治療の患者登録が始まった。しかし、ヒトゲノム上の標的以外に意図せぬ変異を導入してしまうオフターゲット作用、ゲノム編集効率、デリバリーなど、ゲノム編集の臨床応用には多くの問題が残されている。また、現在ゲノム編集治療で使われているAAVベクターはアデノウイルスベクターに比べて組み込めるサイズが小さく、オフターゲットの回避が難しい等の欠点がある。我々は、CRISPR/Cas9のガイドRNA 8個とCas9 nickaseを搭載した一体型多重ガイドRNA発現アデノベクターの開発に成功し、動物実験が可能な量まで欠失なく調製できることを見出した（日経産業新聞8月14日）。このベクターを使えば、2個のガイドRNAとCas9 nickaseによる安全なダブルニッキング切断（DN切断）により、理論上オフターゲットを生ずることなく標的を確実にノックアウト可能である。また、複数のカスケードや多数のファミリー遺伝子を最多で8遺伝子まで同時にノックアウトできるため、機能遺伝子が不明な時にその候補遺伝子をすべてノックアウトして機能消失を確認してから絞り込むトップダウン戦略などへの応用も考えられる。現在は、遺伝性疾患であるフェニルケトン尿症に対する治療法開発や、ヒトパピローマウイルスによる子宮頸がんの悪性化予防法開発や、DN切断によるマウス肝臓腫瘍に対するin vivoゲノム編集治療モデルの開発に取り組んでいる。本セミナーでは、遺伝病とがんを標的としたゲノム編集治療および基礎研究への応用にむけたアデノベクターの開発について紹介するとともに、ゲノム編集治療における高額な特許状況とそれを回避するベクターについても言及する。さらに、医科学研究所における基礎・応用研究を支援する新たな改変ベクター作製の可能性ついても議論したい。

Most survivors in malaria endemic regions are able to develop partial immunity after repeated malaria infections throughout the years. This partial immunity protects them from developing severe complications, and they can survive with chronic asymptomatic infection. It is common to find sequestration of the Plasmodium parasites and the retention of the parasite byproducts, hemozoin, in various tissues in malaria patients. This raises the concern whether single infection or chronic asymptomatic infection imposes any risks in chronic tissue damage and immune dysregulation. The Plasmodium parasites invade the bone marrow that serves as a niche for gametocyte differentiation, and they leave their byproducts in the bone marrow. We previously reported that these Plasmodium products accumulate and persist in the bone marrow for a long time even after recovery from malaria infection. These parasite products induce chronic inflammation in the bone marrow and activate osteoclast resorption to cause bone loss with only a single infection. This suggests single malaria infection is sufficient to disrupt the crosstalk between bone and immune systems. It is still unclear why malaria survivors can only develop partial immunity and the only malaria vaccine exhibits limited efficacy. It is our interest to elucidate how malaria parasites evade host immunity and the chronic impact it leaves on the host immune system. Understanding immune regulation of malaria infection will help to set strategy for better intervention of the disease.

Prof. Pascale Cossart is an outstanding cellular microbiologist who made breakthrough discoveries on our understanding of how bacteria Listeria monocytogenes infect and survive in host cells. She is one of the pioneers showing how bacteria can invade host cells and evade immune system by using host’s own mechanism. Her works’ new insights into the pathophysiology of infectious diseases have crossed the borders of bacteriology and reached to the new concepts in molecular biology, cell biology and immunology. She won numerous awards in her scientific career from various societies and countries including Koch Prize.

The mammalian gastrointestinal tract, the site of digestion and nutrient absorption, is home to a microbial ecosystem that enhances resistance to infection, inflammation, allergy, and metabolic diseases. Commensal bacteria are key participants in the digestion of food, and are responsible for the extraction and synthesis of nutrients and other metabolites that are essential for the maintenance of mammalian health. Over the past decade, the connection between various disorders and gut microbiota has become a major focus of biomedical research. Because of the complexity of the microbiota community, however, the underlying molecular mechanisms by which the gut microbiota is associated with diseases remain poorly understood. In this talk, I summarize recent studies that investigate the role of the microbiota in animal models of disease and discuss relevant therapeutic targets for future research.

ウイルスは宿主細胞内で複製・蓄積する。ウイルスの遺伝子産物は多くの場合、各細胞内のウイルス集団によって共有利用されるが、これはウイルスにとって潜在的な問題となる。すなわち、自らは遺伝子産物を生産せず他のウイルスゲノム由来の遺伝子産物を利用して増殖するフリーライダーが出現する問題や、適応的な変異をもつウイルスゲノムがその利益を享受できない問題が生じうる。ウイルスはこの問題を様々な方法で解決しているが、その方法には宿主組織の構造に依存して異なる制約が存在し、これが現存の菌類・植物・動物ウイルスのゲノムの在り方（ゲノム核酸の種類、分節数）を規定してきたものと演者は考えている。これについて、演者らが植物ウイルスを使って行った実験の結果と、数理モデルを作成して得たシミュレーションの結果を基に議論したい。
また、今年9月に新学術領域「ネオウイルス学」トレーニングコースとして「ゼロから始める実験屋のためのシミュレーションモデリング」を開催した。この際に演習として行ったインフルエンザ流行のシミュレーションモデル化について紹介し、議論したい。

Kawasaki Disease (KD), a systemic vasculitis of unknown etiology is the leading cause of acquired heart disease among children in the US. Subsets of KD children display gastrointestinal abnormalities during the acute phase of the disease and may have increased serum levels of secretory IgA (SIgA), suggestive of a “leaky gut” phenotype. Additionally, KD patients have higher frequencies of IgA producing B cells in the inflamed coronary artery and in the respiratory and gastrointestinal tracts. How intestinal permeability participates in cardiovascular lesions of KD remains unknown. We observed increased intestinal permeability and elevated circulating sIgA in KD patients as well as elevated sIgA and IgA deposition in vascular tissues in the Lactobacillus casei-cell wall extract murine model of KD vasculitis. Pharmacological blocking of intestinal permeability prevented gut permeability, vascular tissues IgA deposition, and ameliorated cardiovascular pathology. By using genetic and pharmacologic inhibition of IL-1β signaling, we demonstrated that IL-1β lies upstream of disrupted intestinal barrier function, subsequent IgA vasculitis development, and cardiac inflammation. Thus, targeting mucosal barrier dysfunction and the IL-1β pathway may be applicable to other IgA-related diseases including IgA vasculitis and IgA nephropathy. These observations enhance our current understanding of KD pathogenesis and may provide new diagnostic and therapeutic strategies for affected patients.