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京都大学 / 新制・課程博士 / 博士(医学) / 甲第23797号 / 医博第4843号 / 新制||医||1058(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 川口 義弥, 教授 藤田 恭之, 教授 小濱 和貴 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

The epigenome carries dynamic information that controls gene expression and maintains cell identity during both disease and normal development. The inherent plasticity of the epigenome paves new avenues for developing diagnostic and therapeutic tools for human diseases. Microfluidic technology has improved the sensitivity and resolution of epigenomic analysis due to its outstanding ability to manipulate nanoliter-scale liquid volumes. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic platforms. First, I applied Microfluidic Oscillatory Washing-based Chromatin Immunoprecipitation followed by sequencing (MOWChIP-seq) to study the effect of culture dimensionality, hypoxia stress and bacterium infection on histone modification landscapes of brain tumor cells. I identified differentially marked regions between different culture conditions. Second, I adapted indexed ChIPmentation and introduced mu-CM, a low-input microfluidic device capable of performing 8 assays in parallel on different histone marks using as few as 20 cells in less than 7 hours. Last, I investigated the spatially resolved epigenome and transcriptome of neuronal and glial cells from coronal sections of adult mouse neocortex. I applied unsupervised clustering to identify distinct spatial patterns in neocortex epigenome and transcriptome that were associated with central nervous system development. I demonstrated that our method is well suited for scarce samples, such as biopsy samples from patients in the context of precision medicine. / Doctor of Philosophy / Epigenetic is the study of alternations in organisms not caused by alternation of the genetic codes. Epigenetic information plays pivotal role during growth, aging and disease. Epigenetic information is dynamic and modifiable, and thus serves as an ideal target for various diagnostic and therapeutic strategies of human diseases. Microfluidics is a technology that manipulates liquids with extremely small volumes in miniaturized devices. Microfluidics has improved the sensitivity and resolution of epigenetic analysis. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic platforms. Histone modification is one type of epigenetic information and regulates gene expression. First, we studied the influence of culture condition and bacterium infection on histone modification profile of brain tumor cells. Second, we introduced mu-CM, combining a low-input microfluidic device with indexed ChIPmentation and is capable of performing 8 assays in parallel using as few as 20 cells. Last, we investigated spatial variations in the epigenome and transcriptome across adult mouse neocortex, the outer layer of brain involving in higher-order function, such as cognition. I identified distinct spatial patterns responsible for central nervous system development using machine learning algorithm. Our method is well suited for studying scarce samples, such as cells populations isolated from patients in the context of precision medicine.

The sperm chromatin structure assay (SCSA), as developed by Evenson et al.(1980), utilizes flow cytometry to quantify the susceptibility of sperm chromatin to in situ acid denaturation via the metachromatic properties of acridine orange. SCSA is repeatable and has been used to distinguish between fertile and subfertile males in different species; however, it does not permit morphological evaluation of cells. In the present study, the SCSA was modified for the fluorescence/differential interference contrast (DIC) microscope to examine morphology and chromatin stability on the same cell. Semen from six Holstein bulls was collected twice weekly for six weeks. Semen was cryopreserved after collection. A 48-hr scrotal insulation was applied after the first three collections to exert a mild thermal insult to the testes; this induces specific spermatozoal morphological abnormalities to appear in a predictable chronological order, as determined by Vogler et al. (1993). Using DIC optics, sperm head morphology was classified as normal, slightly misshapen, pyriform, severely misshapen, or tailless. Vacuolization in the head region was scored separately as apical, diadem, or random. SCSA and modified-SCSA for fluorescence microscopy were used to assess chromatin instability in the samples. The SCSA parameter of 'cells outside the main population of alpha t' (%COMP alpha t) and the modified-SCSA parameter of '% cells shifted from green' were positively correlated (r=0.84; P<0.01). Both variables were positively correlated with the appearance of tailless, pyriform, severely misshapen, and randomly vacuolated cells (P< 0.01), but not with the appearance of diadems or apical vacuoles. Also, the fluorescence microscope detected a significant shift from green in normally shaped cells appearing in morphologically abnormal ejaculates (P<0.01). These results demonstrate that scrotal insulation-induced morphological abnormalities in spermatozoa signify a perturbation in chromatin structure, and that the chromatin perturbation extends into normally shaped cells in the same ejaculate. / Master of Science