京都大学 / 新制・課程博士 / 博士(医学) / 甲第24783号 / 医博第4975号 / 新制||医||1066(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 村川 泰裕, 教授 波多野 悦朗, 教授 小川 誠司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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Gene fusion is one of the hallmarks of cancer. Recent advances in RNA-seq of cancer transcriptomes have facilitated the discovery of fusion transcripts. In this study, we report identification of a surprisingly large number of fusion transcripts, including six KANSARL (KANSL1-ARL17A) transcripts that resulted from the fusion between the KANSL1 and ARL17A genes using a RNA splicingcode model. Five of these six KANSARL fusion transcripts are novel. By systematic analysis of RNA-seq data of glioblastoma, prostate cancer, lung cancer, breast cancer, and lymphoma from different regions of the World, we have found that KANSARL fusion transcripts were rarely detected in the tumors of individuals from Asia or Africa. In contrast, they exist in 30 - 52% of the tumors from North Americans cancer patients. Analysis of CEPH/Utah Pedigree 1463 has revealed that KANSARL is a familially-inherited fusion gene. Further analysis of RNA-seq datasets of the 1000 Genome Project has indicated that KANSARL fusion gene is specific to 28.9% of the population of European ancestry origin. In summary, we demonstrated that KANSARL is the first cancer predisposition fusion gene associated with genetic backgrounds of European ancestry origin.

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Enteropathogenic bacteria, such as Shigella and Salmonella, are associated with diarrheal diseases, which remain a significant cause of infant mortality worldwide. The secretion of protein effectors by the type III secretion apparatus (T3SA) is used by these pathogens to invade human cells and modulate host cell functions. First, we used RNA-Seq to analyze the differential transcriptome of Shigella flexneri when the T3SA is active or inactive. This allowed us to identify two uncharacterized genes that were temporarily named gem1 and gem3 and whose expression was regulated by MxiE and IpgC as other late substrates of the T3SA. Finally, we pursued the characterization of gem1 and gem3 at the protein level and renamed them icaT and icaR, respectively, when we found their protein products were secreted by the T3SA. Furthermore, we find homologs of icaT and icaR with a conserved MxiE box in several E. coli phylogroups. We also demonstrated that these homologous genes could be reactivated when both MxiE and IpgC were introduced in these strains. This discovery paved a new perspective on the evolution of pathogenesis into the E. coli lineage as both commensal and pathogenic strains harbored these genes. Treating infections caused by Enterobacteriaceae is becoming more challenging due to growing antibiotic resistance and no vaccines are widely available. Accordingly, the World Health Organization (WHO) recognized that we entered the "post-antibiotic era," where new antibiotics or antivirulence drugs are urgently needed, including for Shigella. The T3SA is an attractive target for antivirulence drugs, which may become alternative to classical antibiotics. Through screening 3,000 compounds, we found two novel inhibitors of the T3SA. Our data suggested that one of these candidate inhibitors, a dipyridyl-containing compound, reduces the virulence of Shigella at the transcriptional level. Indeed, the virulence inhibition occurs via the repression of the transcriptional activator VirB by the small chromosomal RNA RyhB, which is upregulated by this compound through an unknown mechanism involving the pyridyl groups. The repression of VirB induced by this molecule reduce the expression of several genes encoding parts of the T3SA. In comparison, the second compound is a quinone that seems to affect the assembly of the T3SA.

RNA-seq transcriptome analysis of Chenopodium quinoa at different water treatment levels was conducted in a greenhouse study using four water treatments (field capacity to drought) on a valley ecotype quinoa (variety Ingapirca) and an Altiplano Salares ecotype quinoa (variety Ollague). Physiological results support the earlier findings that the Salares ecotypes display greater tolerance to drought-like stress conditions than the valley ecotypes (as determined by growth rate, photosynthetic rate, stomatal conductance, and stem water potential). cDNA libraries from root tissue sample for each treatment x variety combination were sequenced using Illumina Hi-Seq technology in an RNA-seq experiment. De novo assembly of the transcriptome generated 20,337 unique transcripts. Gene expression analysis of the RNA-seq data identified 462 putative gene products that showed differential expression based on treatment and 27 putative gene products differential expressed based on variety x treatment, including significant increasing expression in the root tissue in response to increasing water stress. BLAST searches and gene ontology analysis show an overlap with drought tolerance stress and other abiotic stress mechanisms.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21830号 / 農博第2343号 / 新制||農||1068(附属図書館) / 学位論文||H31||N5202(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 佐藤 健司, 教授 澤山 茂樹, 准教授 豊原 治彦 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Lung cancer is one of the most aggressive cancers and the leading cause of cancer mortality in the US, mainly due to the lack of early detection. Meanwhile, gene expression profiling can identify molecular responses to carcinogen exposure and tumorigenesis. We have previously identified lung cancer-associated gene expression alterations in the normal bronchial airway epithelium of ever smokers with and without lung cancer. These alterations are the basis of a diagnostic test that is useful in clinical decision-making in patients with suspect lung cancer. Despite this success, further improvements in early lung cancer diagnosis are needed, along with a better understanding of airway biology during the initiation and development of lung cancer. Towards these goals, for the first aim of my thesis, I explored whether normal-appearing bronchial airway gene expression reflects lung cancer histologic subtypes. Genes differentially expressed in the bronchial airway between patients with lung squamous cell carcinoma and lung adenocarcinoma were identified and confirmed in independent data. Using a method developed based on independent component analysis (ICA), cell type-specific gene modules were derived from airway single-cell RNA-sequencing data and shown to be altered between lung cancer subtypes. Secondly, I sought to investigate whether integrating the bronchial airway molecular biomarker with radiomic features (i.e., quantitative features derived from radiographic images) could yield a better diagnosis for lung cancer screening. Using clinical variables, molecular signatures, and radiomic imaging features, I built and tested an integrated biomarker to improve discrimination between malignant and benign Indeterminate Pulmonary Nodules (IPNs). Finally, as COVID-19 became a pandemic during my thesis work, I sought to utilize large-scale genomic data from multiple cohorts to investigate possible clinical risk factors related to SARS-CoV-2 entry and disease severity. My analysis showed that smoking affects the expression of host genes involved in SARS-CoV-2 entry differently in the nasal and bronchial airways. The work has implications about how smoking might modulate SARS-CoV-2 infection and COVID-19 disease severity. Collectively, this work leverages computational approaches to identify airway biology associated with lung cancer subtypes, improve the diagnosis of lung cancer in patients with IPNs, and reveal relationship between smoking and SARS-CoV-2 infection. / 2024-02-18T00:00:00Z