Microfluidics has revolutionized how molecular biology studies are conducted. It permits profiling of genomic and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this thesis, we focus on three projects (diffusion-based PCR, MID-RRBS, and SurfaceChIP-seq), which improved the sensitivities of conventional assays by coupling with microfluidic technology. MID-RRBS and SurfaceChIP-seq projects were designed to profiling genome-wide DNA methylation and histone modifications, respectively. These assays dramatically improved the sensitivities of conventional approaches over 1000 times without compromising genomic coverages. We applied these assays to examine the neuronal/glial nuclei isolated from mouse brain tissues. We successfully identified the distinctive epigenomic signatures from neurons and glia. Another focus of this thesis is applying electrical field to investigate the intracellular contents. We report two projects, drug delivery to encapsulated bacteria and mRNA extraction under ultra-high electrical field intensity. We envision rapid growth in these directions, driven by the needs for testing scarce primary cells samples from patients in the context of precision medicine. / Ph. D. / Microfluidics is a technology that manipulates solution with extremely small volume. It is an emerging platform that has revolutionized how molecular biology studies are conducted. It permits profiling of genome wide DNA changes or DNA-related changes (e.g. epigenomics) for a wide range of applications. One of the major contribution of microfluidics is to improve the next generation sequencing (NGS) technologies with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this thesis, we focus on three projects (diffusion-based PCR, MID-RRBS, and SurfaceChIP-seq), which improved the sensitivities of conventional assays by coupling with microfluidic technology. MID-RRBS and SurfaceChIP-seq projects were designed to profiling genome-wide DNA methylation and histone modifications, respectively. DNA methylation and histone modification have been proved to affect a lot of biological processes, such as disease development. These developed technologies would benefit the development of precision medicine (a medical model that proposes the customization of healthcare) and treatment to various diseases. We applied these technologies to study the epigenomic differences between several cell types in the mouse brain.

The main focus of this research was the development of microfluidic technology for ultrasensitive and fast molecular analysis of cells. Chromatin immunoprecipitation (ChIP) assay followed by next generation sequencing serves as the primary technique to characterize the genomic locations associated with histone modifications. However, conventional ChIP-seq assay requires large numbers of cells. We demonstrate a novel microfluidics-based ChIP-seq assay which dramatically reduced the required cell number. Coupled with next generation sequencing, the assay permitted the analysis of histone modifications at the whole genome from as few as ~100 cells. Using the same device, we demonstrated that MeDIP-seq with tiny amount of DNA (<5ng) generated high quality genome-wide profiles of DNA methylation. Off-chip sonication often leads to sample loss due to multiple tube transferring. In addition, conventional sonicators are not able to manipulate samples with small volume. We developed a novel microfluidic sonicator, which is able to achieve on-chip DNA/chromatin shearing into ideal fragment size (100~600bp) for both chromatin immunoprecipitation (ChIP) and methylated DNA immunoprecipitation (MeDIP). The integrated on-chip sonication followed by immunoprecipitation (IP) reaction can significantly reduce sample loss and contamination. Simple and accessible detection methods that can rapidly screen a large cell population with single cell resolution have been seriously lacking. We demonstrate a simple protocol for detecting translocation of native proteins using a common flow cytometer which detects fluorescence intensity without imaging. Using our approach, we successfully detected the translocation of native NF-kappa B (an important transcription factor) at its native expression level and examine the temporal dynamics in the process. Droplets with encapsulated beads and cells have been increasingly used for studying molecular and cellular biology. However, a mixed population of droplets with an uneven number or type of encapsulated particles is resulted and used for screening. We developed a fluorescence-activated microfluidic droplet sorter that integrated a simple deflection mechanism. By passing droplets through a narrow interrogation channel, the encapsulated particles were detected individually. The microcontroller conducted the computation to determine the number and type of encapsulated particles in each droplet and made the sorting decision. Our results showed high efficiency and accuracy for sorting and enrichment. / Ph. D.

A cell, the building block of all life, stores a plethora of information in its genome, epigenome, and transcriptome which needs to be analyzed via various Omic studies. The heterogeneity in a seemingly similar group of cells is an important factor to consider and it could lead us to better understand processes such as cancer development and resistance to treatment, fetal development, and immune response. There is an ever growing demand to be able to develop more sensitive, accurate and robust ways to study Omic information and to analyze subtle biological variation between samples even with limited starting material obtained from a single cell. Microfluidics has opened up new and exciting possibilities that have revolutionized how we study and manipulate the contents of the cell like the DNA, RNA, proteins, etc. Microfluidics in conjunction with Next Gen Sequencing has provided ground-breaking capabilities for handling small sample volumes and has also provided scope for automation and multiplexing. In this thesis, we discuss a number of platforms for developing low-input or single cell Omic technologies. The first part talks about the development of a novel microfluidic platform to carry out single-cell RNA-sequencing in a one-pot method with a diffusion-based reagent swapping scheme. This platform helps to overcome the limitations of conventional microfluidic RNA seq methods reported in literature that use complicated multiple-chambered devices. It also provides good quality data that is comparable to state-of-the-art scRNA-seq methods while implementing a simpler device design that permits multiplexing. The second part talks about studying the transcriptome of innate leukocytes treated with varying levels of LPS and using RNA-seq to observe how innate immune cells undergo epigenetic reprogramming to develop phenotypes of memory cells. The third part discusses a low-cost alternative to produce tn5 enzyme which low-cost NGS studies. And finally, we discuss a microfluidic approach to carrying out low-input epigenomic studies for studying transcription factors. Today, single-cell or low-input Omic studies are rapidly moving into the clinical setting to enable studies of patient samples for personalized medicine. Our approaches and platforms will no doubt be important for transcriptomic and epigenomic studies of scarce cell samples under such settings. / Doctor of Philosophy / This is the era of personalized medicine which means that we are no longer looking at one-size-fits-all therapies. We are rather focused on finding therapies that are tailormade to every individual’s personal needs. This has become more and more essential in the context of serious diseases like cancer where therapies have a lot of side-effects. To provide tailor-made therapy to patients, it is important to know how each patient is different from another. This difference can be found from studying how the individual is unique or different at the cellular level i.e. by looking into the contents of the cell like DNA, RNA, and chromatin. In this thesis, we discussed a number of projects which we can contribute to advancement in this field of personalized medicine. Our first project, MID-RNA-seq offers a new platform for studying the information contained in the RNA of a single cell. This platform has enough potential to be scaled up and automated into an excellent platform for studying the RNA of rare or limited patient samples. The second project discussed in this thesis involves studying the RNA of innate immune cells which defend our bodies against pathogens. The RNA data that we have unearthed in this project provides an immense scope for understanding innate immunity. This data provides our biologist collaborators the scope to test various pathways in innate immune cells and their roles in innate immune modulation. Our third project discusses a method to produce an enzyme called ‘Tn5’ which is necessary for studying the sequence of DNA. This enzyme which is commercially available has a very high cost associated with it but because we produced it in the lab, we were able to greatly reduce costs. The fourth project discussed involves the study of chromatin structure in cells and enables us to understand how our lifestyle choices change the expression or repression of genes in the cell, a study called epigenetics. The findings of this study would enable us to study epigenomic profiles from limited patient samples. Overall, our projects have enabled us to understand the information from cells especially when we have limited cell numbers. Once we have all this information we can compare how each patient is different from others. The future brings us closer to putting this into clinical practice and assigning different therapies to patients based on such data.

The shift of medical technology from a doctor's application of individualized medicine toward precision medicine has been accelerated by the advent of Next Generation Sequencing. Individualized medicine is where a doctor tries to understand the intricacies of a patient's medical state, where precision medicine uses a wealth of data to understand the individuality of a patient on a biological level to determine treatment course. Next Generation Sequencing allows for the collection of genome wide analyses such as genomic, transcriptomic, and epigenomic sequencing, which provides the backbone of the data driven precision medicine. In order to obtain and use this data, it needs to be produced from minimal amounts of patient tissue, such as the amount from a needle biopsy. In order to perform so many different assays it is paramount that we develop high sensitivity methodologies, such that we can gain an understanding of the patient's physiology without causing much discomfort in gathering large amounts of sample. In pursuit of making more tests, data, and assays available for use in precision medicine, we have developed 3 different microfluidic technologies, which automate and simplify the assays needed for the data collection at a high sensitivity, as well as a versatile platform for therapeutic production. First, we developed a epigenomic assay for chromatin immunoprecipitation, which gives us information on histone modifications across the genome. These histone modifications heavily impact gene expression and how the chromatin is organized, as well promoting or inhibiting transcription of genes. Our technology allowed us to perform multiple parallel assays from as few as 50 cells quickly and reliably using our fluidized bed technology. Next, we developed a library preparation system, which reduces the cost of library preparation by 20x and reduces operator pipetting by 100x. Our system uses a droplet based reactor to quickly and reliably prepare sequencing libraries using the lowest amount of DNA to date, 10 pg. Finally, we designed a therapeutics-on-a-chip platform which is capable of producing clinically relevant proteins on demand from temperature stable components. Using our system, we are capable of producing a number of different therapeutics on demand quickly without rearrangement of the system. / Doctor of Philosophy / Technical advances in the healthcare industry have made a range of new data available to physicians and patients. Home use DNA testing kits have made it possible to examine one’s predisposition to certain genetic diseases. Using these advanced methods, we are able to gain insights into a patient’s disease state where we were previously unable. Unfortunately, some of these new analyses currently require large amounts of patient sample, which make the examinations largely impractical to perform. In order to overcome the sample requirements, which make these analyses impractical, we develop microscale reactor systems capable of reducing the amount of material required for these new analyses. Here I demonstrate our developed technologies to automate 3 different processes aimed at enabling the study of protein-DNA interactions and produce therapeutics at the point of care. First, we developed an analytical system to study protein-DNA interactions (which are important to understanding patient responses to treatment), that allow for parallel analyses which can be done with sample from less than one needle biopsy, where existing methods would require dozens or more (50 vs 10,000,000 cells.) Next, we developed automated system for preparing DNA sequencing libraries using as little as 10 pg DNA (~2 cells of DNA). The device run multiple reactions simultaneously while reducing batch to batch variation and operator hands-on time. Finally, we developed a v Therapeutics-On-a-Chip platform that produces clinically relevant therapeutic proteins in clinically relevant dosages using a cell-free approach, while saving the trouble and cost associated with protein storage and transportation.

No / TCDD-inducible poly-ADP-ribose polymerase (TIPARP; also known as PARP7 and ARTD14) is a mono-ADP- ribosyltransferase that has emerged as an important regulator of innate immunity, stem cell pluripotency, and transcription factor regulation. Characterizing TIPARP’s catalytic activity and identifying its target proteins are critical to understanding its cellular function. Here we describe methods that we use to characterize TIPARP catalytic activity and its mono-ADP-ribosylation of its target proteins.

Background: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results: We propose a new peak-caller called \"Sierra Platinum\" that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. Conclusion: We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates.

La période de réceptivité endométriale chez l’humain coïncide avec la différentiation des cellules stromales de l’endomètre en cellules hautement spécifiques, les cellules déciduales, durant le processus dit de décidualisation. Or, on sait qu’une transformation anormale des cellules endométriales peut être à l’origine de pertes récurrentes de grossesses. LRH-1 est un récepteur nucléaire orphelin et un facteur de transcription régulant de nombreux évènements relatif à la reproduction et comme tout récepteur, son activation promouvoit l’activité transcriptionnelle de ses gènes cibles. Nous avons déjà montré que LRH-1 et son activité sont essentiels pour la décidualisation au niveau de l’utérus chez la souris et nous savons qu’il est présent dans l’utérus chez l’humain au moment de la phase de prolifération mais aussi de sécrétion du cycle menstruel, et que son expression augmente dans des conditions de décidualisation in vitro. Notre hypothèse est alors la suivante : LRH-1 est indispensable à la décidualisation du stroma endométrial, agissant par le biais de la régulation transcriptionnelle de gènes requis pour la transformation de cellules stromales en cellules déciduales. Afin d’explorer le mécanisme moléculaire impliqué dans la régulation transcriptionnelle effectuée par l’intermédiaire de ce récepteur, nous avons mis en place un modèle de décidualisation in vitro utilisant une lignée de cellules stromales de l’endomètre, cellules humaines et immortelles (hESC). Notre modèle de surexpression développé en transfectant les dites cellules avec un plasmide exprimant LRH-1, résulte en l’augmentation, d’un facteur 5, de l’abondance du transcriptome de gènes marqueurs de la décidualisation que sont la prolactine (PRL) et l’insulin-like growth factor binding protein-1 (IGFBP-1). En outre, la sous-régulation de ce récepteur par l’intermédiaire de petits ARN interférents (shRNA) abolit la réaction déciduale, d’un point de vue morphologique mais aussi en terme d’expression des deux gènes marqueurs cités ci-dessus. Une analyse par Chromatin ImmunoPrécipitation (ou ChIP) a démontré que LRH-1 se lie à des régions génomiques se trouvant en aval de certains gènes importants pour la décidualisation comme PRL, WNT 4, WNT 5, CDKN1A ou encore IL-24, et dans chacun de ces cas cités, cette capacité de liaison augmente dans le cadre de la décidualisation in vitro. Par ailleurs, des études structurelles ont identifié les phospholipides comme des ligands potentiels pour LRH-1. Nous avons donc choisi d’orienter notre travail de façon à explorer les effets sur les ligands liés à LRH-1 de traitements impliquant des agonistes et antagonistes à notre récepteur nucléaire. Les analyses par q-PCR et Western blot ont montré que la modulation de l’activité de LRH-1 par ses ligands influait aussi sur la réaction déciduale. Enfin, des études récentes de Salker et al (Salker, Teklenburg et al. 2010) ont mis en évidence que les cellules stromales humaines décidualisées sont de véritables biocapteurs de la qualité embryonnaire et qu’elles ont la capacité de migrer en direction de l’embryon. La série d’expériences que nous avons réalisée à l’aide de cellules hESC placées en co-culture avec des embryons de souris confirme que la migration cellulaire est bien dirigée vers les embryons. Cette propriété quant à l’orientation de la migration cellulaire est notoirement diminuée dans le cas où l’expression de LRH-1 est déplétée par shRNA dans les hESC. Nos données prouvent donc que LRH-1 régule non seulement la transcription d’un ensemble de gènes impliqués dans le processus de décidualisation mais agit aussi sur la motilité directionnelle de ces cellules hESC décidualisées in vitro. / The period of endometrial receptivity in humans coincides with the differentiation of endometrial stromal cells into highly specialized decidual cells through a process known as decidualization. This transformation of endometrial cells is abnormal in recurrent pregnancy loss patients. Liver homolog receptor 1 (LHR-1, NR5A2) is an orphan nuclear receptor and a transcription factor that regulates many reproductive events. The activation of this receptor leads to transcriptional activation of its target genes. We have previously shown that it is essential for decidualization in the mouse uterus. LRH-1 is expressed in the human uterus in both proliferative and secretory phases of the menstrual cycle and its expression increases during in vitro decidualization. We hypothesize that LRH-1 is indispensable for proper decidualization of the endometrial stroma, acting through the transcriptional regulation of genes required for transformation of stromal cells into decidual cells. To explore the molecular mechanism of transcriptional regulation mediated by this receptor, we established an in vitro model of decidualization, using an immortal human endometrial stromal cell line (hESC). An overexpression model developed by transfecting the cells with a plasmid constitutively expressing Lrh-1, resulted in 5 fold increases in abundance of transcripts for the decidualization marker genes prolactin (PRL) and insulin-like growth factor binding protein-1 (IGFBP-1). Furthermore, the downregulation of the receptor using short hairpin RNA (shRNA) abrogates the decidual reaction, from both a morphological point of view and in terms of expression of the two marker genes. Chromatin immunoprecipitation (ChIP) analysis showed that LRH-1 binds to genomic regions upstream of genes important for decidualization such as PRL, wingless-type MMTV integration site family, member 4 (WNT4), wingless-type MMTV integration site family, member 5 (WNT5), cyclin-dependent kinase inhibitor 1A (p21, CDKN1A) and interleukin-24(IL-24). For each of these genes, the binding increased during in vitro decidualization. Structural studies have identified phospholipids as potential LRH-1 ligands. We therefore explored the effect of ligand treatment on LRH-1 with an agonist and an inverse agonist for the nuclear receptor. Analysis by quantitative polymerase chain reaction (qPCR) and Western blot demonstrated that the modulation of LRH-1 activity by its ligands also affects the decidual reaction. Recent studies have shown that decidualized human stromal cells are biosensors of embryo quality and that they have the capacity to migrate towards the embryo. Our time-lapse evaluation of hESC cells co-cultured with mouse embryos indicates directed migration of the cells toward the embryo. This effect is markedly diminished when LRH-1 is depleted by shRNA in hESC. Our data provide evidence that LRH-1 regulates not only the transcription of a set of genes involved in decidualization but also the directional motility of these cells in vitro.

Les facteurs de transcription FLI-1 et SPI-1/PU.1 appartiennent à la famille ETS et reconnaissent le même motif sur l’ADN GGAA. Leur activation est observée de manière récurrente dans les érythroleucémies murines induites par le virus de Friend. Ces observations suggèrent un rôle crucial de ces deux facteurs dans la transformation de la lignée érythrocytaire potentiellement par la dérégulation de gènes cibles communs. Mon travail de thèse a consisté à tester la contribution de ces deux facteurs au phénotype des cellules érythroleucémiques et à rechercher les gènes cibles directs communs.Nous avons pu montrer que FLI-1 et SPI-1/PU.1 ont des contributions additives au phénotype des cellules érythroleucémiques surexprimant les deux facteurs. Par une approche transcriptomique, nous avons identifié une grande proportion de gènes cibles directs communs à FLI-1 et à SPI-1/PU.1 impliqués dans différentes étapes de la biogenèse des ribosomes. La déplétion de ces facteurs induit une réduction de la biogenèse des ribosomes qui n’induit pas de stress ribosomique stabilisant p53. Néanmoins, nous avons mis en évidence une contribution spécifique de RPL11, un médiateur essentiel du stress ribosomique, à la différenciation des cellules érythroleucémiques induites par l’absence de ces facteurs.Nous avons mené en parallèle l’inventaire par ChIP-Seq des sites de recrutement de FLI-1 et de SPI-1/PU.1 sur le génome entier de 3 lignées érythroleucémiques indépendantes. Cette stratégie nous a permis de montrer que les régions de recrutement communes sont la conséquence de la proximité de consensus spécifiques et distincts et du recrutement de FLI-1 et de SPI-1/PU.1 sur leur propre consensus. / The transcription factors FLI-1 and SPI-1/PU.1 belong to the ETS family and recognize the same DNA motif GGAA. Their activation is recurrently observed in murine erythroleukemia induced by Friend virus. These observations suggest a crucial role of these two factors in erythroid lineage transformation potentielly by deregulating common target genes. My thesis work consisted of testing both factors contribution to the phenotype of erythroleukemia cells and of searching for common direct target genes.We showed that FLI-1 and SPI-1/PU.1 have additive contributions to the phenotype of erythroleukemia cells overexpressing both factors. By a transcriptomic approach, we identified a high proportion of common direct target genes of FLI-1 and SPI-1/PU.1 involved in ribosome biogenesis at different levels. The déplétion of these factors induced a decrease of ribosome number which doesn’t induce a ribosomal stress leading to the p53 stabilization. However, we highlighted a specific contribution of RPL11, an essential ribosomal stress médiator, in erythroleukemia cell differentiation induced by depletion of both factors. In parallel, we mapped at whole génome scale by ChIP-Seq the recruitment site of FLI-1 and SPI-1/PU.1 in 3 independent erythroleukemia cell lines. This strategy allowed us to show that the common recruitment régions are the conséquence of a very close association of clearly distinct and specific consensus binding sites for FLI-1 and SPI-1/PU.1 and that each of those factor sis recruited to its own consensus.

Many fish face low oxygen concentrations (hypoxia) in their natural environments, and they respond to hypoxia through a variety of behavioral, physiological, and cellular mechanisms. Some of these responses involve changes in gene expression. In mammals, the hypoxia inducible factor (HIF) family of transcription factors are the “master regulators” of gene expression during hypoxia, but the study of HIF in fish has been hampered by the lack of reagents to detect this protein in non-mammalian vertebrates. The goals of this thesis are to affinity purify antibodies against HIF from the killifish Fundulus heteroclitus and use them to recover and quantify HIF from killifish cells and tissues. The purified, validated antibodies represent a critical reagent for future studies of the role of HIF in the molecular response of this and other fish to fluctuations in oxygen in their natural environments.

In eukaryotic cells, the genome is packed into chromatin, a hierarchically organized complex composed of DNA and histone and nonhistone proteins. In this thesis we have addressed the role of chromatin in cellular response to DNA damage (DDR) using various methodologies encompassing functional genomics and proteomics. First, we analyzed histone post-translational modifications (PTM) in the context of specific kind of DNA lesions (ICL-Interstrand Crosslinks) in Fanconi anemia using quantitative proteomics methodology, SILAC (Stable Isotope Labeling of Amino acids during Cell Culture). Using mass spectrometry (MS), we have successfully identified and quantified a number of histone PTM marks in histone H3 and H4, mainly acetylations and methylations,which have shown dependence upon functional FA-pathway. As a next step, we applied a functional genomics approach to study DDR in FA cells. In this analysis we first monitored the expression profile of histone modifying enzymes related to histone acetylations and methylations. Our results suggest some correlations between histone PTMs and gene expression of histone modifying enzymes, although conclusive evidence warrants further investigations. Next, we analyzed the total transcriptome after DNA damage induction in FA mutant and wild type cells. We also included in this analysis IR irradiation, in an attempt to dissociate more generic DDR from more specific changes that are associated with the role of FA pathway to the DNA ICLs. By performing a factorial interaction analysis, we were able to isolate the part of transcriptional response to DNA damage that was requiring functional FA pathway, as well as the genes that were sensitized to DNA damage by the inactivation of FA pathway. In the final part of the thesis, we attempted to solve one of the limitations that we encountered in the histone PTM analysis. The current approaches used to study histone PTMs from particular loci involves classical chromatin immunoprecipitation, which due to involvement of formaldehyde crosslinking render the protein part mostly unavailable for MS-based proteomics. We have proposed a novel methodology, which is based upon the biotin tagging of histones proximal to a protein of interest and subsequent purification of nucleosomes carrying the tagged histone. This methodology does not involve any crosslinking, enabling us to purify histones from specific loci, and subject them to large scale MS-based histone PTM analysis. A time dimension can also be added to our approach, as we can follow the modification status of particular fraction of histones once they get biotinylated. Another advantage is the use of alternate variant histones, which allows us to study the PTM profile of different functional states of chromatin. This methodology certainly has an edge on current techniques to study histone PTMs pattern associated with a particular protein of interest or with particular chromatin state.