A produção de células-tronco induzidas (iPSC) a partir de fibroblasto fetal canino abre caminhos para a obtenção de células pluripotentes e o estudo de sua aplicabilidade para terapias alternativas na medicina veterinária. Neste contexto, este trabalho investigou metodologias adequadas avaliando a eficiência destas, para a produção de células-tronco pluripotentes no modelo canino in vitro (CTE-like), uma vez que a produção de células-tronco embrionárias verdadeiras, cultivadas a partir da MCI de blastocistos, ainda não foi completamente caracterizada em animais domésticos. Os experimentos visaram o aumento do conhecimento de fatores envolvidos no processo de reprogramação em cães, bem como a produção de tais linhagens e sua completa caracterização. No primeiro experimento, foi comparada a infecção retroviral, já padronizada por diversos grupos, com a reprogramação epissomal, inédita para a espécie, na tentativa de induzir células à pluripotência sem a integração viral, e ainda, estratégias para o aumento da eficiência de reprogramação, onde o plasmídeo epissomal foi somado a fatores de transcrição. A reprogramação epissomal gerou colônias quando acrescida do fator c-MYC, que provavelmente, aumentou a proliferação destas células produzindo colônias iPS com morfologia típica e positivas para o teste da fosfatase alcalina. Tais resultados, ainda preliminares pra conclusões, são essenciais para o processo de obtenção de linhagens sem a integração viral, aumentando a aplicabilidade na terapia celular. No segundo experimento objetivou-se avaliar os fatores OCT4 e SOX2 associados a proteínas repórteres. Os fibroblastos que receberam estes fatores, foram analisados por citometria de fluxo, permitindo a avaliação da influência de cada fator no processo de reprogramação, além de permitir a separação (sorting) das células que integraram o gene, aumentando a eficiência de reprogramação e o conhecimento biológico dos mecanismos de integração rastreados por uma proteína repórter. A análise por microscopia de fluorescência revelou que a distribuição de proteínas repórteres foi semelhante entre as duas diferentes construções proteicas e que não se restringe a uma região da célula em particular. OCT4 e SOX2 mostraram uma elevada expressão exógena de cada gene alvo, bem como células dupla positivas. No entanto, nenhuma interação foi observada pelo menos 6 dias após a transdução. O último capítulo experimental descreveu o mecanismo de reprogramação por integração lentiviral para indução da pluripotência em fibroblastos fetais de cão. As linhagens obtidas e completamente caracterizadas neste estudo foram independentes de LIF ou qualquer outra suplementação com inibidores, resistentes ao repique enzimático (Tryple Express), sendo apenas bFGF dependentes. Foram obtidas 66 linhagens clonais, das quais 10 (7 h+mOSKM e 3hOSKM) se mantiveram por 15 ou mais passagens e foram utilizadas para todos os testes de caracterização in vitro, com eficiência máxima de reprogramação de 0,001%. Todas as colônias foram positivas para o teste da fosfatase alcalina, bem como formaram corpos embrióides e se diferenciaram de forma espontânea, além de expressarem altos níveis dos fatores endógenos OCT4 e SOX2. In vivo, as colônias foram capazes de desenvolver tumor 120 dias após a inoculação (confirmado por análise histopatológica) comprovando sua origem predominantemente mesodérmica. A integridade cromossomal das linhagens foi avaliada por hidridização FISH, que não evidenciou qualquer tipo de anomalia. A completa caracterização de tais linhagens, bem como os experimentos não integrativos e com fatores associados a proteínas repórteres, aumentam o conhecimento da tecnologia de reprogramação, estabelecendo novas estratégias para indução da pluripotência de forma mais eficaz e segura para seu uso em testes clínicos e terapia celular / The production of induced pluripotent stem cells (iPSC) from canine fetal fibroblast opens new ways for obtaining pluripotent cells and study its applicability for alternative therapies in veterinary medicine. In this context, this study investigated appropriate methods for producing pluripotent stem cells using a in vitro canine model (ESC-like), so far the production of true embryonic stem cells from ICM cultured blastocysts has not been fully characterized in domestic animals. The experiments aimed at increasing knowledge of the factors involved in reprogramming process in dogs, as well as the production of such strains and complete characterization. In the first experiment, a retroviral infection was compared to episomal reprogramming (never done for this specie) in an attempt to induce cells to pluripotency state without viral integration, also to observe the development of cells receiving separately the episomal plasmid plus transcription factors. The generation of colonies was possible only in the episomal plus c-MYC factor group, leading to increased cell proliferation producing iPS colonies with typical morphology and positive for the alkaline phosphatase detection. These results, so far as preliminary conclusions, are essential to obtaining strains without viral integration, increasing its applicability for clinical cell therapy. In the second experiment, we aimed to evaluate the OCT4 and SOX2 factors associated with fluorescent reporter proteins. These were analyzed by flow cytometry allowing the performance evaluation of each factor on the reprogramming process the fluorescence activated separation of cells containing the integrated gene, increasing the enriching the efficiency of reprogramming. Fluorescence microscopy analysis showed that the distribution of reporter protein was similar between the two different protein structures and not restricted to a particular cell region. OCT4 and SOX2 showed a high exogenous expression of each target gene, and double positive cells. However, no colony formation was observed at least 6 days after transduction. The last experimental chapter aimed to described the reprogramming mechanism of lentiviral integration to induce pluripotency in dog fetal fibroblasts. The lines obtained were fully characterized in this study, showing independency of LIF or any other supplemental inhibitors, resistance to enzymatic process (Tryple Express) and bFGF dependency only. A total of 66 clonal strains were obtained (hOSKM and h+mOSKM) while 10 (7 h+m and 3h) were maintained for 15 or more passages and used for in vitro characterization tests, with maximum efficiency of reprogramming 0.001% . All colonies were positive for the alkaline phosphatase detection, embryoid bodies formation, spontaneously differentiated and expressed high levels of endogenous OCT4 and SOX2. In vivo, the colonies were able to developed tumors 120 days after inoculation (confirmed via histopathology analysis), with predominantly mesodermal tissues. Chromosomal evaluations were made by FISH hybridization showing no chromosomal abnormality in iPSCs canine lines. The fully characterization of such lines as well as non-integrated experiments and factors associated via reporter proteins increases the knowledge of the iPSCs technology, establishing new strategies for more efficient and safe induction of pluripotency for potential use in cell therapy and clinical trials

Thesis advisor: Thomas N. Seyfried / Gangliosides are glycosphingolipids (GSLs) containing sialic acids that play numerous roles in neuronal maturation, apoptotic signaling, angiogenesis, and cell surface receptor activity. The GM1 and GM2 gangliosidoses are a series of autosomal recessive lysosomal storage disorders (LSDs) characterized by an inability to degrade these lipid molecules. GM1 gangliosidosis is caused by a mutation in the lysosomal hydrolase β-galactosidase, resulting in neuronal storage of ganglioside GM1 and asialo GA1. Tay-Sachs (TS) and Sandhoff Disease (SD) are GM2 gangliosidoses caused by mutations in either the α or β subunits, respectively, of the heterodimeric protein β- hexosaminidase A, resulting in the storage of ganglioside GM2 and asialo GA2. The accumulation of excess ganglioside in the central nervous system leads to abnormal intracellular vacuoles, neuronal loss, demyelination, ataxia, dementia, and premature death. In my studies, I have shown that accumulation of GM1 ganglioside may not coincide with secondary storage of cholesterol, by providing evidence that cholesterol-binding fluorescent molecule filipin reacted to GM1 ganglioside in the absence of cholesterol. In an effort to combat the early-onset gangliosidoses, I have explored the effects of combining Neural Stem Cells (NSCs) with Substrate Reduction Therapy (SRT) in juvenile Sandhoff mice. The analysis showed that SRT was more effective than NSCs in reducing stored GM2 and GA2 in young mice, and no synergy was observed. In adult GM1 gangliosidosis, Tay- Sachs, and Sandhoff mice, Adeno-Associated Viral (AAV) vector gene therapy was used to restore therapeutic levels of wild-type enzyme to the CNS. AAV therapy corrected ganglioside storage and ameliorated myelin-associated lipid loss in all tissues assayed, increasing motor performance and life in effected animals. Lastly, AAV therapy was also successful in a feline model of Sandhoff disease. These results in juvenile and adult model systems point the way towards multiple effective clinical therapies in the near future. / Thesis (PhD) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

O meduloblastoma é o tumor maligno do sistema nervoso central mais frequente na infância e adolescência. A expressão de genes tipicamente expressos em células-tronco está correlacionada com pior prognóstico em pacientes com meduloblastoma e a expressão de POU5F1 se mostrou capaz de distinguir pacientes com desfecho clínico desfavorável e pior sobrevida. Apesar do seu valor prognóstico, não há evidências diretas da contribuição de OCT4 para a aquisição de fenótipos mais agressivos em meduloblastoma. Nesse contexto, o presente trabalho investigou o papel da isoforma OCT4A em características pró-tumorigênicas de meduloblastoma in vitro e in vivo, e também avaliou as alterações moleculares que podem ser responsáveis pela aquisição de fenótipo mais agressivo em células de meduloblastoma humano. Para tanto, foi realizada a superexpressão de OCT4A mediada por retrovírus em três linhagens celulares de meduloblastoma (Daoy, D283Med e USP-13-Med). As células de meduloblastoma com superexpressão de OCT4A exibiram maior proliferação e alterações no ciclo celular. Foram observados também aumentos na atividade clonogênica, geração de esferas tumorais e desenvolvimento tumoral em modelo subcutâneo, sendo esses efeitos dependentes dos níveis de OCT4A. A avaliação da mobilidade celular in vitro demonstrou diminuição na adesão celular e aumento da invasão celular de esferoide 3D. Em modelo ortotópico de meduloblastoma, as células com superexpressão de OCT4A geraram tumores mais desenvolvidos, com fenótipos mais agressivos, infiltrativos e metastáticos. A superexpressão de OCT4A foi associada a maior instabilidade genômica, entretanto, as aberrações em números de cópias variaram em frequência e tipo de alteração dependendo da linhagem celular, e sendo pouco associada com os genes diferencialmente expressos. De forma interessante, uma relevante expressão diferencial de RNAs não-codificadores de proteínas foi observada em células de meduloblastoma com superexpressão de OCT4A, incluindo os recém descobertos e pouco caracterizados RNAs não codificadores longos, além de múltiplos RNAs pequenos nucleolares. Assim, os resultados aqui apresentados fundamentam a relevância de fatores envolvidos em pluripotência para o agravamento de traços associados com desfecho clínico desfavorável em meduloblastoma e destacam o valor prognóstico e terapêutico de OCT4A neste tumor pediátrico do sistema nervoso central / Medulloblastoma is the most common malignant brain tumor in infants. The expression of typical pluripotency genes is correlated with poor prognosis in medulloblastoma and POU5F1 expression was shown capable of discriminating patients with poor survival outcome. Despite this prognostic value, direct evidences of OCT4 contribution to more aggressive traits in medulloblastoma are missing. In this context, we investigated the role of OCT4A isoform on pro-tumorigenic features of medulloblastoma in vitro and in vivo and evaluated molecular alterations that could be responsible for acquisition of a more aggressive phenotype in medulloblastoma cells. Retroviral-mediated overexpression of OCT4A were performed in three medulloblastoma cell lines (Daoy, D283Med and USP-13-Med). Medulloblastoma cells overexpressing OCT4A displayed enhanced cell proliferation and cell cycle alterations. Increased clonogenic activity, tumorsphere generation capability and subcutaneous tumor development were also observed, and these effects were OCT4A expression level-dependent. Evaluation of cell mobility in vitro showed loss of cell adhesion and greater 3D-spheroid invasion. In an orthotopic model of medulloblastoma, OCT4A overexpressing cells generated more developed, aggressive, infiltrative and metastatic tumors. OCT4A overexpression was associated with chromosomal instability but copy number aberrations varied in frequency and type according to the cell line, with little association with differently expressed genes. Interestingly, marked differential expression of non-coding RNAs, including newly discovered, still poorly characterized, long non-coding RNAs and multiple small nucleolar RNAs were observed in medulloblastoma cells with OCT4A overexpression. Altogether, our findings support the relevance of pluripotency-related factors in the aggravation of medulloblastoma traits classically associated with poor clinical outcome, and underscore the prognostic and therapeutic value of OCT4A in this challenging type of pediatric brain cancer

O saco vitelino é uma das membranas extra-embrionárias que desempenha um papel importante para a sobrevivência inicial do embrião, atua como fonte de nutrição durante o período em que a placenta verdadeira ainda não está completamente formada. É uma provável fonte de células tronco, o qual abriga as primeiras células do sangue durante o desenvolvimento em mamíferos, os eritrócitos, os quais expressam fatores de transcrição que especificam estas células a seu destino hematopoiético. O objetivo deste trabalho foi caracterizar as células tronco hematopoéticas provenientes do saco vitelino de embriões bovinos, em diferentes fases gestacionais, sendo estes coletados em abatedouro local. Para descrição da análise macroscópica e cultivo celular das células do saco vitelino, os embriões bovinos foram divididos em grupos de idade gestacional: Grupo I (25 a 29 dias), Grupo II (30 a 34 dias), Grupo III (35 a 39 dias), Grupo IV (40 a 44 dias) e Grupo V (45 a 50 dias) em que permaneceram mais tempo em cultura e apresentaram a formação de aglomerados celulares, diferente dos grupos IV e V (40 a 45 dias) em que permaneceram poucos dias em cultura e não apresentaram aglomerados celulares. Esta divergência relaciona-se à idade gestacional (45 a 50 dias), período em que se inicia a regressão do saco vitelino. Em citometria de fluxo os grupos I, II e III (25 a 39 dias) obtiveram características semelhantes, alta expressão de marcadores hematopoéticos (CD34, CD90 e CD117). Para os grupos IV e V (40 a 50 dias) observa-se um declínio da expressão de CD34 e CD117 (marcadores hematopoéticos) e no grupo V houve um acréscimo da expressão de CD45 (marcador para leucócito) confirmando que estas células não estão mantendo-se indiferenciadas As células demonstraram ser resistentes a criopreservação, capazes de formar colônias em matriz de Metilcelulose, mostraram a formação de colônias após 14 dias em cultivo e a morfologia para células sanguíneas (linfócitos e monócitos) foi confirmada na citologia celular. Na expressão gênica obteve-se baixa expressão do gene GATA3, níveis diferentes de expressão entre os grupos para o marcador RUNX1 e ANXA5. Dessa forma, nossos achados mais significativos comprovaram o isolamento de células hematopoéticas a partir do saco vitelino de embriões bovinos, sugerindo que este é uma fonte laboriosa, porém viável e eficaz para a obtenção de células tronco para futuras aplicações na terapia celular e gênica. / The yolk sac is one of the extra-embryonic membranes which plays an important role in early embryonic survival and serves as source of nutrition during the period where in the placenta is not completely true formed. The yolk sac is a likely source of stem cells, which have first blood cells during development in mammals, the red blood cells, which express transcription factors that specify these hematopoietic cells to their destination. This study aimed to identify and characterize hematopoietic stem cells from the yolk sac of bovine embryos at different stages of pregnancy, which are collected at a local slaughterhouse. For a description of the macroscopic and cellular culture of yolk sac cells, are as follows bovine embryos were divided into groups of gestational age: Group I (25 to 29 days), Group II (30 to 34 days), Group III (35 to 39 days ), Group IV (40 to 44 days) and Group V (45 to 50 days) which stayed longer in culture and showed the formation of cell clusters, different from groups IV and V (40-45 days) in few that remained days in culture and showed no cell clumps. This divergence is related to gestational age (45 to 50 days), during which begins regression of the yolk sac. In flow cytometry groups I, II and III (25 to 39 days) had similar characteristics, high expression of hematopoietic markers (CD34, CD90 and CD117). For the groups IV and V (40 to 50 days) it is observed a decrease in expression of CD117 and CD34 (hematopoietic markers) and in group V were increased expression of CD45 (leukocyte marker), confirming that these cells are not keeping Undifferentiated cells are shown to be resistant to cryopreservation, capable of forming colonies in methylcellulose matrix showed the formation of colonies after 14 days in culture morphology and to blood cells (lymphocytes and monocytes) was confirmed by cytology cell. In gene expression was low GATA3 gene expression, different levels of expression between the groups for the marker and RUNX1 ANXA5. Our most significant findings confirmed the isolation and identification of hematopoietic cells from the bovine embryo yolk sac, therefore, it is feasible and an effective way of obtaining stem cells for future applications in cell therapy and gene.

A vast amount of gene expression data is available to biological researchers. As of October 2010, the GEO database has 45,777 chips of publicly available gene expression pro ling data from the Affymetrix (HGU133v2) GeneChip platform, representing 2.5 billion numerical measurements. Given this wealth of data, `meta-analysis' methods allowing inferences to be made from combinations of samples from different experiments are critically important. This thesis explores the application of localized pattern-mining approaches, as exemplified by biclustering, for large-scale gene expression analysis. Biclustering methods are particularly attractive for the analysis of large compendia of gene expression data as they allow the extraction of relationships that occur only across subsets of genes and samples. Standard correlation methods, however, assume a single correlation relationship between two genes occurs across all samples in the data. There are a number of existing biclustering methods, but as these did not prove suitable for large scale analysis, a novel method named `IslandCluster' was developed. This method provided a framework for investigating the results of different approaches to biclustering meta-analysis. The biclustering methods used in this work involve preprocessing of gene expression data into a unified scale in order to assess the significance of expression patterns. A novel discretisation approach is shown to identify distinct classes of genes' expression values more appropriately than approaches reported in the literature. A Gene Expression State Transformation (`GESTr') introduced as the first reported modelling of the biological state of expression on a unified scale and is shown to facilitate effective meta-analysis. Localised co-dependency analysis is introduced, a paradigm for identifying transcriptional relationships from gene expression data. Tools implementing this analysis were developed and used to analyse specificity of transcriptional relationships, to distinguish related subsets within a set of transcription factor (TF) targets and to tease apart combinatorial regulation of a set of targets by multiple TFs. The state of pluripotency, from which a mammalian cell has the potential to differentiate into any cell from any of the three adult germ layers, is maintained by forced expression of Nanog and may be induced from a non-pluripotent state by the expression of Oct4, Sox2, Klf4 and cMyc. Analysis of cMyc regulatory targets shed light on a recent proposition that cMyc induces an `embryonic stem cell like' transcriptional signature outside embryonic stem (ES) cells, revealing a cMyc-responsive subset of the signature and identifying ES cell expressed targets with evidence of broad cMyc-induction. Regulatory targets through which cMyc, Oct4, Sox2 and Nanog may maintain or induce pluripotency were identified, offering insight into transcriptional mechanisms involved in the control of pluripotency and demonstrating the utility of the novel analysis approaches presented in this work.

Prostate cancer is a leading cause of cancer-related death in men, and while many men diagnosed with the disease will have an indolent clinical course, 20-25% of men will experience disease recurrence which is invariably lethal. There is an urgent need for prognostic biomarkers that will predict disease recurrence and risk-stratify patients upon diagnosis, allowing for personalised therapies. This thesis attempts to identify new prognostic biomarkers for prostate cancer and investigates their patterns of protein expression in human primary prostate tumour tissue. Cancer stem cells are cancer cells thought to be uniquely capable of self-renewal and tumorigenicity, and may have a role in tumour recurrence. Using a literature searching approach, potential biomarkers related to stem cells, cancer stem cells or recurrence in prostate cancer were identified, and ALDH7A1, BMI1, SDC1, MUC1-C, Nestin and ZSCAN4 were chosen for investigation. An in silico approach was also used for biomarker identification, with RS1 and SLC31A1 selected as their mRNA was found to be upregulated in recurrent tumours. The expression patterns of all 7 potential biomarkers were examined by immunohistochemistry on prostate tumour tissue and benign tissue from prostate biopsies and prostatectomies. BMI1, ALDH7A1, MUC1-C and Nestin showed no relationship to recurrence or other clinical features. RS1 protein levels increased in patients with recurrence within 5 years, negatively correlated with AR expression, and a meta-analysis showed that the RS1 gene was amplified in up to 32% of castration-resistant prostate tumours. ZSCAN4 was heterogeneously expressed in a subset of 26% of prostate tumours with unclear characteristics and was not expressed in benign tissue, but was not associated with recurrence. Finally, SDC1 expression was lost in tumour epithelium, but a population of unidentified SDC1-expressing cells were found in the stroma of a third of tumours, and an increased burden of these cells was associated with primary Gleason pattern 5 tumours. These cells do not overlap with common epithelial, mesenchymal or stromal lineages, but may be migratory. In summary, the data presented in this thesis identifies 3 potential new biomarkers for prostate cancer, and provides the basis for future characterisation of their wider roles in the disease.

Current treatment options are limited for patients with myocardial infarction or heart failure. Cellular cardiomyoplasty is a promising therapeutic strategy being investigated as a potential treatment, which aims to deliver exogenous cells to the infarcted heart, for the purpose of restoring healthy myocardial mass and mechanical cardiac function. While several cell types have been studied for this application, only bone marrow cells and human mesenchymal stem cells (hMSCs) have been shown to be safe and effective for improving cardiac function in clinical trials. In both human and animal studies, the delivery of hMSCs to infarcted myocardium decreased inflammatory response, promoted cardiomyocyte survival, and improved cardiac functional indices. While the benefits of using hMSCs as a cell therapy for cardiac repair are encouraging, the desired expectation of cardiomyoplasty is to increase cardiomyocyte content that will contribute to active cardiac mechanical function. Delivered cells may increase myocyte content by several different mechanisms such as differentiating to a cardiomyocyte lineage, secreting paracrine factors that increase native stem cell differentiation, or secreting factors that increase native myocyte proliferation. Considerable work suggests that hMSCs can differentiate towards a cardiomyocyte lineage based on measured milestones such as cardiac-specific marker expression, sarcomere formation, ion current propagation, and gap junction formation. However, current methods for cardiac differentiation of hMSCs have significant limitations. Current differentiation techniques are complicated and tedious, signaling pathways and mechanisms are largely unknown, and only a small percentage of hMSCs appear to exhibit cardiogenic traits. In this body of work, we developed a simple strategy to initiate cardiac differentiation of hMSCs in vitro. Incorporating environmental cues typically found in a myocardial infarct (e.g. decreased oxygen tension and increased concentrations of cell-signaling factors), our novel in vitro conditioning regimen combines reduced-O2 culture and hepatocyte growth factor (HGF) treatment. Reduced-O2 culturing of hMSCs has shown to enhance differentiation, tissue formation, and the release of cardioprotective signaling factors. HGF is a pleiotropic cytokine involved in several biological processes including developmental cardiomyogenesis, through its interaction with the tyrosine kinase receptor c-Met. We hypothesize that applying a combined conditioning treatment of reduced-O2 and HGF to hMSCs in vitro will enhance cardiac-specific gene and protein expression. Additionally, the transplantation of conditioned hMSCs into an in vivo infarct model will result in differentiation of delivered hMSCs and improved cardiac mechanical function. In testing our hypothesis, we show that reduced-O2 culturing can enhance hMSC growth kinetics and total c-Met expression. Combining reduced-O2 culturing with HGF treatment, hMSCs can be conditioned to express cardiac-specific genes and proteins in vitro. Using small-molecule inhibitors to target specific effector proteins in a proposed HGF/c-Met signaling pathway, treated reduced-O2/HGF hMSCs show a decrease in cardiac gene expression. When implanted into rat infarcts in vivo, reduced-O2/HGF conditioned hMSCs increase regional cardiac mechanics within the infarct region at 1 week and 1 month. Further analysis from the in vivo study showed a significant increase in the retention of reduced-O2/HGF conditioned hMSCs. Immunohistochemistry showed that some of the reduced-O2/HGF conditioned hMSCs express cardiac-specific proteins in vivo. These results suggest that a combined regimen of reduced-O2 and HGF conditioning increases cardiac-specific marker expression in hMSCs in vitro. In addition, the implantation of reduced-O2/HGF conditioned hMSCs into an infarct significantly improves cardiac function, with contributing factors of improved cell retention and possible increases in myocyte content. Overall, we developed a simple in vitro conditioning regimen to improve cardiac differentiation capabilities in hMSCs, in order to enhance the outcomes of using hMSCs as a cell therapy for the diseased heart.

Bioprinting, defined as depositing cells, extracellular matrices and other biologically relevant materials in user-defined patterns to build tissue constructs de novo or to build upon pre-fabricated scaffolds, is among one of the most promising techniques in tissue engineering. Among the various technologies used for Bioprinting, pressure driven systems are most conducive to preserving cell viability. Herein, we explore the abilities of a novel bioprinter - Digilab, Inc.'s prototype cell printer. The prototype cell printer (Digilab Inc., Holliston, MA) is an automated liquid handling device capable of delivering cell suspension in user-defined patterns onto standard cell culture substrates or custom-designed scaffolds. In this work, the feasibility of using the cell printer to deliver cell suspensions to biological sutures was explored. Cell therapy using stem cells of various types shows promise to aid healing and regeneration in various ailments, including heart failure. Recent evidence suggests that delivering bone-marrow derived mesenchymal stem cells to the infarcted heart reduces infarct size and improves ventricular performance. Current cell delivery systems, however, have critical limitations such as inefficient cell retention, poor survival, and lack of targeted localization. Our laboratories have developed a method to produce discrete fibrin microthreads that can be bundled to form a suture and attached to a needle. These sutures can then be seeded with bone-marrow derived mesenchymal stem cells to deliver these cells to a precise location within the heart wall, both in terms of depth and surface localization. The efficiency of the process of seeding cells onto fibrin thread bundles (sutures) has previously been shown to be 11.8 ± 3.9 %, suggesting that 88% of the cells in suspension are not used. Considering that the proposed cell-therapy model for treatment of myocardial infarction contemplates use of autologous bone-marrow derived stem cells, an improvement in the efficiency of seeding cells onto the fibrin sutures is highly desirable. The feasibility of using Digilab's prototype cell printer to deliver concentrated cell suspension containing human mesenchymal stem cells (hMSCs) directly onto a fibrin thread bundle was explored in this work, in order to determine if this technology could be adapted to seed cells onto such biological sutures. First the effect of the printing process on the viability of hMSCs was assessed by comparing to cells dispensed manually using a hand-held pipette. The viability of hMSCs 24 hours post-dispensing using the cell printer was found to be 90.9 ± 4.0 % and by manual pipetting was 90.6 ± 8.2 % (p = ns). Thereafter a special bioreactor assembly composed of sterilizable Delrin plastic and stainless steel pins was designed to mount fibrin thread bundles onto the deck of the cell printer, to deliver a suspension containing hMSCs on the bundles. Highly targeted delivery of cell suspension directly onto fibrin thread bundles (average diameter 310 µm) was achieved with the bundle suspended in mid-air horizontally parallel to the printer's deck mounted on the bioreactor assembly. To compare seeding efficiency, fibrin thread bundles were simultaneously seeded with hMSCs using either the cell printer or the current method (tube-rotator method) and incubated for 24 hours. Seeded thread bundles were visualized using confocal microscopy and the number of cells per unit length of the bundle was determined for each group. The average seeding efficiency with the tube rotator method was 7.0 ± 0.03 % while the cell printer was 3.46 ± 2.24% (p = ns). In conclusion, the cell printer was found to handle cells as gently as manual pipetting, preserve their viability, with the added abilities to dispense cells in user-defined patterns in an automated manner. With further development, such as localized temperature, gas and humidity control on the cell printer's deck to aid cell survival, the seeding efficiency is likely to improve. The feasibility of using this automated liquid handling technology to deliver cells to biological scaffolds in specified patterns to develop vehicles for cell therapy was shown in this study. Seeding other cell types on other scaffolds along with selectively loading them with growth factors or multiple cell types can also be considered. In sum, the cell printer shows considerable potential to develop novel vehicles for cell therapy. It empowers researchers with a supervision-free, gentle, patterned cell dispensing technique while preserving cell viability and a sterile environment. Looking forward, de novo biofabrication of tissue replicates on a small scale using the cell printer to dispense cells, extracellular matrices, and growth factors in different combinations is a very realistic possibility.

All cancers were once normal cells. They became cancerous through the chance acquisition of particular somatic mutations that gave them a selective advantage over their neighbours. Thus, the mutations that initiate cancer occur in normal cells, and the normal clonal dynamics of the tissue determine a mutant cell's ability to establish a malignant clone; yet these remain poorly understood in humans. One tissue was selected for the exploration of each of these two facets of somatic evolution: blood for clonal dynamics; colon for mutational processes. Blood presents an opportunity to study normal human clonal dynamics, as clones mix spatially and longitudinal samples can be taken. We isolated 140 single haematopoietic stem and progenitor cells from a healthy 59 year-old and grew them in vitro into colonies that were whole genome sequenced. Population genetics approaches were applied to this dataset, allowing us to elucidate for the first time the number of active haematopoietic stem cells, the rate at which clones grow and shrink, and the cellular output of stem cell clones. Colonic epithelium is organised into crypts, at the base of which sit a small number of stem cells. All cells in a crypt ultimately share an ancestor in one stem cell that existed recently, and consequently share the mutations that were present in this ancestor. We exploited this natural clonal unit, isolating single colonic crypts through laser capture microdissection. 570 colonic crypts from 42 individuals were whole genome sequenced. We describe the burden and pattern of somatic mutations in these genomes and their variability across and within different people, identifying some mutational processes that are ubiquitous and others that are sporadic. Targeted sequencing of an additional 1,500 crypts allowed us to quantify the frequency of driver mutations in normal human colon. Together, these two studies inform on the somatic evolution of normal tissues, describing new biology in human tissue homeostasis and providing a window into the processes that govern cancer incidence.

Immunomodulatory drugs (IMiDs) could enhance both direct anti-tumour and graft-versus-tumour effects after allogeneic haematopoietic stem cell transplantation (AHSCT). However, clinical experience with IMiDs after AHSCT using adult peripheral blood (APB) as a stem-cell source has been limited by graft-versus-host disease. Characterization of the mechanisms by which IMIDs modulate alloresponses of T cells and identification of differential effects on T cells from different cell sources could facilitate more effective use of these drugs in the setting of AHSCT. Using in vitro modelling, multi-parameter flow cytometry and gene expression analysis, I have determined the impact of the widely used IMiD lenalidomide on alloresponses of APB and umbilical cord blood (UCB)-derived T cells. Lenalidomide-treatment potentiates net alloproliferation of APB-derived T cells by selectively enhancing proliferation of CD8+ T cells. These CD8+ T cells have enhanced effector memory differentiation, are enriched for polyfunctional effectors, have enhanced direct-cytotoxicity against heamatopoietic target-cells and have a distinct gene expression profile with altered expression of key immunoregulatory-genes and depletion of cellular ikaros. Importantly, while effects on CD8+ T cells derived from UCB are similar, lenalidomide has contrasting effects on allospecific proliferation of APB and UCB-derived CD4+ T cells. While lenalidomide-treatment has no effect on alloproliferation of APB-derived CD4+ T cells, it reduces alloproliferation of UCB-derived CD4+ T cells. The reduction in UCB-derived CD4+ T cell alloproliferation is accompanied by selective expansion of CD4+CD25+FOXP3+ regulatory T cells (Treg), resulting in an overall reduction in UCB-derived T cell alloproliferation. These findings demonstrate that lenalidomide has a differential impact on alloresponses of T cells from different cell sources; alloresponses of APB-derived T cells are increased via selective expansion of polyfunctional CD8+ effectors, while alloresponses of UCB-derived T cells are limited by expansion of tolerogenic Treg. These findings have important implications for the future use of IMiDs in the setting of AHSCT.