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Single-cell RNA sequencing (scRNA-seq) has been a powerful technique for characterizing transcriptional heterogeneity related to tumor development and disease pathogenesis. Despite the advances of technology, there is still a lack of software to systematically and easily assess the quality and different types of artifacts present in scRNA-seq data and a statistical framework for understanding heterogeneity in the gene programs of cancer cells. In this dissertation, I first introduced novel computational software to enhance and streamline the process of quality control for scRNA-seq data called SCTK-QC. SCTK-QC is a pipeline that performs comprehensive quality control (QC) of scRNA-seq data and runs a multitude of tools to assess various types of noise present in scRNA-seq data as well as quantification of general QC metrics. These metrics are displayed in a user-friendly HTML report and the pipeline has been implemented in two cloud-based platforms. Most scRNA-seq studies only profiled a small number of tumors and provided a narrow view of the transcriptome in tumor tissue. Next, I developed a novel framework to perform a large-scale meta-analysis of cancer cells from 12 studies with scRNA-seq data from patients with non-small-cell lung cancer (NSCLC). I discovered interpretable gene co-expression modules with celda and demonstrated that the activity of gene modules accounted for both inter- and intra-tumor heterogeneity of NSCLC samples. Furthermore, I used CaDRa to determine that the levels of some gene modules were significantly associated with combinations of underlying genetic alterations. I also showed that other gene modules are associated with immune cell signatures and may be important for communication with the cancer cells and the immune microenvironment. Finally, I presented a novel computational method to study the association between copy number variation (CNV) and gene expression at the single-cell level. The diversity of the CNV profile was identified in tumor subclones within each sample and I discovered cis and trans gene signatures which have expression values associated with specific somatic CNV status. This study helped us prioritize the potential cancer driver genes within each CNV region. Collectively, this work addressed the limitation in the quality control of scRNA-seq data and provided insights for understanding the heterogeneity of NSCLC samples.

Pathogenic Yersinia cause a manifold of diseases in humans ranging from mild gastroenteritis (Y. pseudotuberculosis and Y. enterocolitica) to pneumonic and bubonic plague (Y. pestis), while all three have a common virulence strategy that relies on a well-studied type III secretion system and its effector proteins to colonize the host and evade immune responses. However, the role of other protein secretion and/or translocation systems in virulence of Yersinia species is not well known. In this thesis, we sought to investigate the contribution of twin-arginine translocation (Tat) pathway and its secreted substrates to the physiology and virulence of Y. pseudotuberculosis. Tat pathway uniquely exports folded proteins including virulence factors across the cytoplasmic membranes of bacteria. The proteins exported by Tat pathway contain a highly conserved twin-arginine motif in the N-terminal signal peptide. We found that the loss of Tat pathway causes a drastic change of the transcriptome of Y. pseudotuberculosis in stationary phase at environmental temperature with differential regulation of genes involved in virulence, carbon metabolism and stress responses. Phenotypic analysis revealed novel phenotypes of the Tat-deficient strain with defects in iron acquisition, acid resistance, copper oxidation and envelope integrity, which we were partly able to associate with the related Tat substrates. Moreover, increased glucose consumption and accumulation of intracellular fumarate were observed in response to inactivation of Tat pathway implicating a generic effect in cellular physiology. We evaluated the direct role of 22 in silico predicted Tat substrate mutants in the mouse infection model and found only one strain, ΔsufI, exhibited a similar degree of attenuation as Tat-deficient strain. Comparative in vivo characterization studies demonstrated a minor defect for ΔsufI in colonization of intestinal tissues compared to the Tat-deficient strain during early infection, whereas both SufI and TatC were required for dissemination from mesenteric lymph nodes and further systemic spread during late infection. This verifies that SufI has a major role in attenuation seen for the Tat deficient strain both during late infection and initial colonization. It is possible that other Tat substrates such as those involved in iron acquisition and copper resistance also has a role in establishing infection. Further phenotypic analysis indicated that SufI function is required for cell division and stress-survival. Transcriptomic analysis revealed that the highest number of differentially regulated genes in response to loss of Tat and SufI were involved in metabolism and transport. Taken together, this thesis presents a thorough analysis of the involvement of Tat pathway in the overall physiology and virulence strategies of Y. pseudotuberculosis. Finally, we propose that strong effects in virulence render TatC and SufI as potential targets for development of novel antimicrobial compounds

A síndrome aurículo-condilar (ACS) apresenta um modelo de herança autossômica dominante e é principalmente caracterizada por malformações auriculares, articulação temporomandibular anormal e hipoplasia do côndilo e da mandíbula. Devido às estruturas acometidas, é considerada uma patologia de primeiro e segundo arcos faríngeos. Com somente alguns casos clínicos descritos na literatura, o gene causador da ACS não é conhecido. Estudos recentes de nosso grupo mapearam o primeiro lócus associado à síndrome, 1p21.1-q23.3 (família ACS1), enquanto que na segunda família estudada por nós (ACS2), não houve evidência de ligação com os marcadores desta região, sugerindo heterogeneidade genética a esta doença. Nossos principais objetivos no presente trabalho foram: identificar o gene responsável por ACS1 e mapear o lócus associado à ACS2. Para o estudo de ACS1, dada a grande extensão da região candidata, com aproximadamente 1004 genes, utilizamos uma abordagem alternativa: análise de transcriptoma durante a diferenciação condrogênica a partir de células-tronco mesenquimais para seleção e subseqüente seqüenciamento de genes candidatos. Através do estudo de expressão gênica entre controle e paciente ACS1, selecionamos e realizamos o seqüenciamento de dois genes. Não detectamos nenhuma alteração patogênica nestes genes e, portanto, é pouco provável que um destes seja responsável pela ACS1. Já na família com ACS2, através de estudo de ligação com uso de microarrays de SNP e marcadores microssatélites, mapeamos o segundo lócus associado à ACS. Estudos complementares estão sendo realizados para a identificação dos alelos causadores de ACS1 e ACS2. Estes resultados, além de sua importância para o aconselhamento genético, poderão contribuir para a compreensão do desenvolvimento embrionário das estruturas acometidas nessa síndrome. / The auriculo-condylar syndrome is an autosomal dominant disease characterized by malformed ears, abnormal temporomandibular joint and condyle and mandible hypoplasia. It is considered a syndrome of the first and second pharyngeal arches. With only a few clinical cases reported in the literature, the gene that causes ACS is not known. Recent studies from our group mapped the first locus associated to the syndrome, 1p21.1-q23.3 (ACS1 family), while in the second family studied by us (ACS2), there was no evidence of linkage with this region, suggesting genetic heterogeneity of this disease. Our main objective in this study was to identify the gene responsible for ACS1 and map the locus associated to ACS2. In the study of ACS1, given the large extent of the candidate region, with approximately 1004 genes, we used an alternative approach: transcriptome analysis during chondrogenic differentiation of stem cells of a patient and a control for screening and subsequent sequencing of candidate genes. The two genes selected through this strategy were sequenced in ACS1 patients, however, not pathogenic mutation was identified. Therefore, it is very unlikely that mutations in these genes are causative of ACS1. In the family with ACS2, through linkage study using SNP microarray and microsatellite markers, we mapped the second locus associated to ACS. Additional studies are being conducted in order to identify the alleles causing ACS1 and ACS2. These results will not only contribute to a better genetic counseling for families with ACS but they will also contribute to the understanding of the embryonic development of the structures affected in this syndrome.

Shortcomings of current methods of prostate cancer detection draw attention to a need for improved biomarkers. The TMPRSS2:ERG gene fusion leads to the overexpression of ERG, an ETS family transcription factor, and is the most prevalent genetic lesion in prostate cancer, but its clinical utility remains to be defined. Two radical prostatectomy samples were analysed by next-generation whole transcriptome sequencing. The chosen samples differed in fusion gene status, as previously determined by RT-PCR. The involvement of novel and previously reported prostate cancer-related transcripts, Wnt signalling, p53 effector loss and several ETS-regulated pathways was identified in the prostate cancer cases examined. ERG was found to directly transactivate RhoGDIB, a gene associated with fusion-positive prostate cancer. Overexpression of RhoGDIB elicited spindle-shaped morphology, faster cell migration and increased cell proliferation, phenotypic changes suggestive of cancer progression. The present findings confirm the value of comprehensive sequencing for biomarker development and indicate avenues of future study.

Shortcomings of current methods of prostate cancer detection draw attention to a need for improved biomarkers. The TMPRSS2:ERG gene fusion leads to the overexpression of ERG, an ETS family transcription factor, and is the most prevalent genetic lesion in prostate cancer, but its clinical utility remains to be defined. Two radical prostatectomy samples were analysed by next-generation whole transcriptome sequencing. The chosen samples differed in fusion gene status, as previously determined by RT-PCR. The involvement of novel and previously reported prostate cancer-related transcripts, Wnt signalling, p53 effector loss and several ETS-regulated pathways was identified in the prostate cancer cases examined. ERG was found to directly transactivate RhoGDIB, a gene associated with fusion-positive prostate cancer. Overexpression of RhoGDIB elicited spindle-shaped morphology, faster cell migration and increased cell proliferation, phenotypic changes suggestive of cancer progression. The present findings confirm the value of comprehensive sequencing for biomarker development and indicate avenues of future study.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21812号 / 農博第2325号 / 新制||農||1066(附属図書館) / 学位論文||H31||N5184(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 左子 芳彦, 教授 澤山 茂樹, 准教授 吉田 天士 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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