Myelodysplastic neoplasms (MDS) are a group of heterogeneous, clonal disorders characterised by ineffective haematopoiesis and peripheral blood cytopenia. MDS is highly progressive, difficult to treat, and is one of the most common blood cancers, affecting 4-5/100.000 people below the age of 70 and many more thereafter. Single or multiple driver gene mutations and chromosomal abnormalities in the haematopoietic compartment lead to MDS. These somatic gene mutations account for the dysregulation of epigenetic, DNA repair, cohesion complex, and spliceosome pathways. The International prognostic scoring system (IPSS) that was developed in 1997, revised (IPSS-R) in 2016 and updated in 2022 (IPSS-M) classifies MDS into low risk (LR-), intermediate (Int-), and high risk (HR-) groups. The haematopoietic disorder is accompanied by changes in the bone marrow microenvironment (BMME) and especially in mesenchymal cells (MSCs). BMME provides a supportive milieu for haematopoiesis and can be targeted by clinically available drugs such as AZA. The non cellular component of the BMME, the extracellular matrix (ECM), is a framework providing structural and biochemical support via cell-ECM interactions and the maintenance of growth factor gradients. To date, studies of bone marrow interactions in homeostasis and disease have focused largely on soluble and membrane-associated factors, while the involvement of the ECM in MDS and its response to therapy is underexplored. Therefore, this study aimed to characterise the MDS MSC derived ECM of both LR- and HR-MDS in comparison to that from healthy age matched donors in terms of composition, biophysical properties and functional haematopoietic support. This study also aimed to evaluate the impact of in vivo and in vitro AZA treatment on MDS MSC derived ECM. To investigate this, in vitro ECMs were generated by culturing of MSC monolayers on chemically prepared coverslips followed by decellularization using NH4OH and DNase-1 solution. The biophysical properties of the ECM were analysed using atomic force microscopy (AFM). Using targeted approaches, a selection of biochemical ECM components including glycoprotein (fibronectin), collagens and glycosaminoglycans (GAGs) were analysed in the various ECMs generated from the different MSC samples. AFM analysis revealed that MDS MSCs producer a softer ECM than the healthy donor MSCs, and that this difference becomes more prominent as the disorder progresses from LR-to HR- MDS. An increase in overall collagen content and a specific increase in collagens I and IV was observed in the ECM deposited by both LR- and HR-MDS MSCs when compared to healthy donor MSCs. Lectin staining revealed disease stage-specific differences in GAG composition: The levels of GAGs carrying N acetyl glucosamine and those carrying N-acetyl galactosamine sugars were both increased in ECM from LR-MDS, while ECM from HR-MDS retained high levels of N acetyl glucosamine but contained only low levels of N-acetyl galactosamine GAGs. The changes in N acetyl galactosamine and N acetyl glucosamine GAGs were further confirmed by chondroitin sulphate (CS) immunostaining, and hyaluronic acid (HA) ELISA respectively. Electrophoretic analysis revealed the presence of low molecular weight (LMW)-HA in one of the LR-MDS MSC derived ECM. Furthermore, the stimulation of MNCs with LMW-HA showed an increase in gene expression of pro-inflammatory cytokines like IL6 suggesting the possible involvement of LMW-HA in the inflammatory bone marrow state of LR-MDS. ECM derived from both LR- and HR-MDS MSCs had a reduced ability to support HSPC, as revealed by a loss of both polar morphology and subsequent colony-forming potential. The decreased rigidity of the ECM produced by MSCs from MDS patients was reversed in MSCs isolated from the patients post-AZA therapy. Similarly, direct exposure of cultured MDS MSCs to AZA also resulted in a corresponding increase in the rigidity of the ECM, although this remained lower than that observed from MDS MSCs isolated post-AZA therapy. A reduction in the collagen content of the ECM was only observed when using MSC from AZA-treated patients, but not following in vitro AZA treatment of MSCs from untreated patients. This indicated that the AZA-mediated restoration of ECM rigidity is an indirect result of effects in the context of the BMME and not on the MSCs alone. Interestingly, a few ECMs derived from MDS patients after AZA therapy had an improved ability to maintain functional HSPCs, as assessed by subsequent colony formation assay. Moreover, a polarized morphology of HSPCs cultured on the ECM derived from both in vivo and in vitro AZA-treated MDS MSCs, suggests a partial restoration of the HSPC behaviour on the AZA-treated MDS ECM. In conclusion, this study has demonstrated changes in the structure, collagen content, and GAG composition of ECM derived from MSCs from MDS patients compared to healthy donors. This study is one of the first to demonstrate an impact of MDS-derived ECM on both the morphology and function of HSPCs, supporting the relevance of the bone marrow ECM in haematological malignancies. The partial revision of the MDS ECM phenotype following in vivo AZA treatment suggests that the ECM itself may be a potential therapeutic target. An improved, in-depth understanding of the contribution of ECM to disease processes is therefore likely to enable us to find novel therapeutic targets to improve drug response in MDS in the future. / Myelodysplastische Neoplasien (MDS) sind eine Gruppe heterogener, klonaler Erkrankungen, die durch ineffektive Hämatopoese und Zytopenie des peripheren Blutes gekennzeichnet sind. MDS sind hochgradig progressiv, schwer zu behandeln und gehören zu den häufigsten Blutkrebserkrankungen, von denen 4-5/100.000 Menschen unter 70 Jahren betroffen sind. Die Inzidenz steigt mit zunehmendem Alter deutlich an. MDS wird durch einzelne oder mehrfache Mutationen von Treibergenen und Chromosomenanomalien im hämatopoetischen Kompartiment verursacht. Diese somatischen Genmutationen sind für die Dysregulation von epigenetischen, DNA-Reparatur-, Kohäsionskomplex- und Spleißosomen-Signalwegen verantwortlich. Das Internationale Prognosesystem (IPSS) wurde 1997 entwickelt, 2016 überarbeitet (IPSS-R) und 2022 aktualisiert (IPSS M), um MDS in Gruppen mit niedrigem Risiko (LR-), mittlerem (Int ) und hohem Risiko (HR-) einzuteilen. Die hämatopoetische Erkrankung geht mit Veränderungen in der Mikroumgebung des Knochenmarks (BMME) einher, insbesondere bei mesenchymalen Zellen (MSCs). Das BMME bietet ein unterstützendes Milieu für die Hämatopoese und kann durch klinisch verfügbare Medikamente wie AZA beeinflusst werden. Die nichtzelluläre Komponente der BMME, die extrazelluläre Matrix (ECM), ist ein Gerüst, das durch Zell-ECM-Interaktionen und die Aufrechterhaltung von Wachstumsfaktorgradienten strukturelle und biochemische Unterstützung bietet. Bislang haben sich Studien über die Interaktionen im Knochenmark bei Homöostase und Krankheit hauptsächlich auf lösliche und membranassoziierte Faktoren konzentriert, während die Beteiligung der ECM an MDS und ihre Reaktion auf die Therapie noch nicht ausreichend erforscht ist. Daher zielte diese Studie darauf ab, die aus MDS-MSCs abgeleitete ECM sowohl bei LR- als auch bei HR-MDS im Vergleich zu der von gesunden, altersgleichen Spendern zu charakterisieren, und zwar hinsichtlich der Zusammensetzung, der biophysikalischen Eigenschaften und der funktionellen hämatopoetischen Unterstützung. Ziel dieser Studie war es auch, die Auswirkungen einer in vivo und in vitro AZA-Therapie auf die aus MDS-MSCs stammende ECM zu untersuchen. Hierfür wurden in vitro ECMs durch Kultivierung von MSC-Monolayern auf chemisch-präparierten-Deckgläsern und anschließender Dezellularisierung mit NH4OH und DNase-1-Lösung erzeugt. Die biophysikalischen Eigenschaften der ECM wurden mittels Rasterkraftmikroskopie (AFM) analysiert. Mit gezielten Ansätzen wurde eine Auswahl biochemischer ECM-Komponenten, darunter Glykoproteine (Fibronektin), Kollagene und Glykosaminoglykane (GAGs), in den ECMs analysiert. Die AFM-Analyse ergab eine weichere ECM, die von MDS-MSCs im Vergleich zu gesunden Spender-MSCs gebildet wurde, was mit dem Fortschreiten der Erkrankung von LR- zu HR-MDS noch deutlicher wurde. Sowohl in LR-MDS- als auch in HR-MDS-ECMs wurde im Vergleich zu gesunden Spender-ECMs ein Anstieg des Gesamtkollagengehalts und eine spezifische Zunahme der Kollagene I und IV beobachtet. Darüber hinaus zeigte die Lektinfärbung krankheitsspezifische Unterschiede in der GAG-Zusammensetzung: Der Gehalt an N-Acetylglucosamin-tragenden GAGs und an N-Acetylgalactosamin-tragenden GAGs war in der ECM von LR-MDS erhöht, während die ECM von HR-MDS einen hohen Gehalt an N-Acetylglucosamin, aber nur einen geringen Gehalt an N-Acetylgalactosamin-GAGs aufwies. Die Veränderungen bei den N-Acetyl-Galactosamin- und N-Acetyl-Glucosamin-GAGs wurden durch Chondroitinsulfat (CS)-Immunfärbung bzw. Hyaluronsäure (HA) ELISA weiter bestätigt. Eine Elektrophoretische Analyse zeigte das Vorhandensein von niedermolekularem (LMW)-HA in einer der von LR-MDS-MSCs stammenden ECM. Darüber hinaus zeigte die Stimulierung von mononuklearen Zellen mit LMW-HA einen Anstieg der Genexpression von pro-inflammatorischen Zytokinen wie IL6, was auf eine Rolle von LMW-HA im entzündlichen Zustand des Knochenmarks von LR-MDS hindeutet. Darüber hinaus wies die ECM von LR- und von HR-MDS, eine verminderte Fähigkeit, hämatopoetische Stammvorläuferzellen (HSPCs) zu unterstützen, auf. Dies zeigte sich in einem Verlust sowohl der polaren Morphologie von HSPCs als auch des anschließenden koloniebildenden Potenzials selbiger. Darüber hinaus wurde die verringerte Steifigkeit der ECM von MDS-MSCs, die nach der AZA-Therapie aus den Patienten isoliert wurden, umgekehrt. In ähnlicher Weise führte die direkte Exposition von kultivierten MDS-MSCs mit AZA zu einer entsprechenden Erhöhung der Steifigkeit der ECM. Diese war jedoch geringer als bei den nach der AZA-Therapie isolierten MDS-MSCs. Die Verringerung des Kollagengehalts der ECM wurde nur in der in vivo mit AZA behandelten MSC-ECM beobachtet, nicht aber in den in vitro mit AZA behandelten Proben. Dies deutet darauf hin, dass die AZA-vermittelte Wiederherstellung der ECM-Steifigkeit ein Ergebnis der indirekten Wirkung von AZA im Knochenmark ist und eventuell vom MDS-Klon ausgeht. Interessanterweise wurde bei einigen ECMs von MDS-Patienten nach der AZA-Therapie eine Verbesserung der Koloniebildung hierauf- kultivierter HSPCs beobachtet. Darüber hinaus deutet eine polarisierte Morphologie von HSPCs, die auf der ECM von in vivo und in vitro AZA-behandelten MDS-MSCs vorkultiviert wurden, auf eine teilweise Wiederherstellung des Verhaltens von HSPCs auf der AZA-behandelten MDS-ECM hin. Zusammenfassend lässt sich sagen, dass diese Studie Veränderungen in der Struktur, im Kollagengehalt und in der GAG-Zusammensetzung zwischen der ECM von MDS-MSCs und der ECM von gesunden MSCs nachgewiesen hat. Dies ist auch eine der ersten Studien, die einen Einfluss der aus MDS-MSCs stammenden ECM auf die Morphologie und Funktion von HSPCs zeigt. Dies weist auf die Rolle der ECM bei der Entstehung hämatologischer Malignome hin. Darüber hinaus deutet die teilweise Korrektur des MDS-ECM-Phänotyps nach einer in vivo AZA-Behandlung darauf hin, dass die ECM selbst ein potenzielles therapeutisches Ziel sein könnte. Ein besseres und tieferes Verständnis des Beitrags der ECM zu MDS-Krankheitsprozessen wird es uns daher ermöglichen, neue therapeutische Ziele zu finden, um das Ansprechen auf Medikamente verbessern zu können

Pulmonary arterial hypertension (PAH) is a devastating lung disease characterized by arterial pruning, occlusive vascular remodeling, and inflammation contributing to increased pulmonary vascular resistance with resultant right heart failure. Endothelial cell (EC) injury and apoptosis are commonly considered triggers for PAH, the mechanisms leading from injury to complex arterial remodeling are incompletely understood. While current therapies can improving symptoms, with the exception of parenteral prostacyclin, they do not significantly prolong transplant free survival. As well, there are no therapies that can regenerate the damaged lung short of transplantation. In this project, I sought to both advance the understanding of disease pathogenesis and explore regenerative therapeutic options for PAH. To this end, I first employed single cell RNA sequencing (scRNA-seq) at multiple time points during the Sugen 5416 (SU) – chronic hypoxia (CH) model of PAH, to provide new insights into PAH pathogenesis both during onset and progression of disease. We also employed microCT analysis to visualize and quantify the arterial pruning associated with PH and found significant loss up to 65% of the healthy arteriolar volume in this model. Through scRNA-seq analysis performed at four timepoints spanning the onset and progression of disease, two disease-specific EC cell types emerged as key drivers of PAH pathogenesis. The first was the emergence of capillary ECs with a de-differentiated gene expression profile, which we termed dedifferentiated capillary (dCap) ECs, with enrichment for the Cd74 gene. Interestingly, RNA velocity analysis suggested that these cells may be undergoing endothelial to mesenchymal transition during PAH development. At later times, a second arterial EC population became apparent, which we termed activated arterial ECs (aAECs), since it uniquely exhibited persistently elevated levels of differential gene expression consistent with a migratory, invasive and proliferative state. Interestingly, the aAECs together with the smooth muscle (SM)-like pericytes, a population which was also greatly expanded in PAH, expressed Tm4sf1, a gene previously associated with a number of cancers and abnormal cell growth. Furthermore, by immunostaining, TM4SF1 was found to be spatially localized to sites of complex and occlusive arterial remodeling, associated with both endothelial cells and pericytes in these lesions, suggesting an important role for the aAECs and SM-like pericytes in arterial remodeling and PH progression. Together, these findings suggest that aAECs, dCap ECs, and SM-like pericytes are emerging cell populations responsible for lung arterial remodeling in PAH, which drives disease progression, and that TM4SF1 may be a novel therapeutic target for this disease. As a first step in trying to develop approaches to regenerate lung arterial bed that is lost in PAH, we investigated the potential role of endothelial colony forming cells (ECFCs) and mesenchymal stromal cell (MSC) derived extracellular vesicles (EVs) as novel therapeutics, on the premise that these stem/progenitor cells would stimulate lung regeneration by mainly paracrine mechanisms. Additionally, we used biomaterials to microencapsulate cells and EVs to improve their local delivery and retention. While ECFCs were found to be ineffective in treating the monocrotaline model on their own, they were poorly retained in the lung and microencapsulation of ECFCs led to enhanced lung delivery within the first 72 hours, with resultant hemodynamic improvements in this model of PAH. MSCs are well known to be immunomodulatory and proangiogenic, largely acting through paracrine mechanisms, including by the release of EVs. Yet, following intravenous administration, nano sized EVs are rapidly cleared from circulation, potentially limiting their therapeutic potential. I adapted our microencapsulation strategy for EVs, and demonstrated significantly greater retention of microgel-loaded EVs were within the lung, resulting in enhanced local cell uptake. Interestingly, the hydrogel used for microencapsulation induced a local immune response which made it unsuitable for testing any potential therapeutic benefits of MSC-EVs in this study. Nonetheless, this work demonstrated proof-of-principle for the utility of microencapsulation as a strategy to enhance EV lung delivery. Overall, this work has identified novel lung cell populations (aAECs, dCap ECs, SM-like pericytes) driving arterial remodeling associated with PH progression, demonstrated the potential of ECFCs as a regenerative cell for the treatment of PAH, and illustrated the utility of microencapsulation as a tool to enhance lung targeting of both cells and EVs.

ABSTRAKT:Isolering och karaktärisering av mesenkymala stamceller från periodontalligamentet hos friskatänderSYFTE: Att isolera och odla celler från periodontalligamentet samt karaktärisera dem sommesenkymala stamceller.MATERIAL OCH METOD: Friska premolarer gjordes tillgängliga vid ortodontiskaextraktioner. Den mellersta 1/3 av periodontalligamentet skrapades varpå en enzymatiskmetod användes för isolering av individuella celler. Resulterande celler odlades understandardiserade metoder. Karaktärisering av celler skedde genom flödescymetri med 2 olikapaneler av cellyta markörer; en för etablerat positiva uttryck och en för kända negativauttryck hos mesenkymala stamceller. Möjlighet av celler att differentieras in vitro tilladipocyter och osteocyter testades genom tillförsel av specifika substanser till odlingsmediet.RESULTAT: Celler från 11 av 13 tänder isolerades och odlades framgångsrikt adherenta tillodlingsytan i upp till 8 generationer. Celluttryck av de positiva markörerna CD73, CD90 samtCD44 bekräftades genom flödescymetri. Inget uttryck observerades för den negativa panelenCD45, CD34, CD11b, CD19 eller HLA class II. Uttrycket av CD105 kunde inte fastställas pgaofullständigt data. Försök till differentiering av celler till adipocyter och osteocyter visade påfenotypiska förändringar efter 21 dagar.SLUTSATS: Den här studien har bidragit till framgångsrik isolering och delvis karaktäriseringav mesenkymala stamceller från periodontalligamentet hos friska tänder. En icke-invasivmetod av detta slag, resulterande i tillgång till denna cellpopulation utgör ett lovande verktygför framtida studier med goda möjligheter till ytterligare kunskap applicerbart till kliniskasituationer inom tandvården. / ABSTRACT:Isolation and Characterization of Mesenchymal Stem Cells from the Periodontal Ligament ofHealthy TeethAIM: To isolate and culture viable cells from the periodontal ligament and confirming theiridentity as mesenchymal stem cells.METHODS AND MATERIALS: Healthy premolars were collected at the time oforthodontic extractions. The middle 1/3 of the periodontal ligament was scraped andsubsequent cell isolation was performed using an enzymatic method; yielding single cellisolates. Cells were cultured and maintained under standard culture conditions. Cellcharacterization was performed by flow cytometry using two sets of cell surface markers; oneknown to be present and one known to be absent in mesenchymal stem cells. Ability of thecells for in vitro differentiation into adipogenic and osteogenic lineages was tested usingspecifically formulated media supplements.RESULTS: Cells were successfully isolated from 11 of 13 teeth and were maintained asadherent cultures for up to 8 generations. Cellular expression of positive markers; CD73, CD90and CD44 were confirmed by flow cytometry. For the negative marker panel, expression ofCD45, CD34, CD11b, CD19 and HLA class II were not detectable. The expression of CD105was inconclusive. As determined by phenotypic changes, cells appeared to have undergoneadipogenic and osteocytic differentiation at 21 days.CONCLUSION: This study has resulted in successful isolation and partial characterization ofmesenchymal stem cells from the periodontal ligament of healthy teeth. Non-invasive accessto these cells, provides an excellent tool for future studies, potentially leading to beneficialknowledge transferable to the dental clinical situation.

<p> Mesenchymal stromal cells (MSC) are a multipotent stromal population of interest as cancer therapeutics for their inherent tropism towards cancer sites. This renders them a potential cellular vehicle for delivering anti-tumor therapies. A limitation to their broader use is a plasticity in their biological roles, which depending on the context, may potentiate opposite roles in tumor modulation. Therefore, strategies to “guide” these cells towards a desired functional role are of high interest in the field of cancer therapeutics. In this dissertation, the functional polarization paradigm via stimulation with toll-like receptor ligands (poly I:C or LPS), previously described in bone-marrow derived MSC (BM-MSC), was evaluated in MSC sourced from adipose tissues (ASC). ASC provide several advantages over BM-MSC, such as the relative ease of acquisition of clinically relevant cellular doses via <em>in vitro </em>expansion. Findings in our studies in prostate cancer models <em>in vitro</em> suggested that a generation of phenotypically and functionally distinct ASC populations could be achieved via differential pre-stimulation approaches on ASC. We observed significant effects on the migratory and immunomodulatory capability of ASC, demonstrated via <em>in vitro </em>assays. Upon administration of these cells <em>in vivo </em>in a mouse model of prostate cancer, poly I:C-primed (or pre-conditioned) ASC were found to accelerate tumor growth progression. While unprimed and LPS-primed ASC did not exert a significant effect on tumor growth at the macroscopic level, gene expression analyses suggested that all treatments promoted distinct modulatory effects in the tumor microenvironment, including altered modulation of angiogenesis, and immune response processes, however, only in the case of poly I:C-primed ASC these effects translated to a significant effect in the tumor growth rate in the mouse model examined.  </p>

<p>The work presented in this thesis was focused on design and construction of novel cell-loaded microcapsules by incorporation of bioactive molecules (proteins or peptides) for potential application in hemophilia B treatment. The objective of this study was to improve the viability and functionality of the encapsulated cells by creating biomimetic microenvironments for cells that more closely mimic their physiological extracellular matrix (ECM) environment.</p> <p>Three cell-adhesive molecules were used in this work: fibrinogen and fibronectin, two abundant proteins present in ECM, and arginine-glycine-aspartic acid (RGD) tri-peptide, the minimal essential cell adhesion peptide sequence and the most widely studied peptide for cell adhesion. Alginate, the most commonly used biomaterial used for cell encapsulation, was combined with either of these molecules to create biomimetic microcapsules. Non-modified alginate (control) and modified alginate matrices were used to encapsulate the factor IX (FIX) secreting cells for protein delivery. In this work, FIX-engineered cord blood-derived human mesenchymal stem cells CB MSCs were used as a cell source for FIX delivery.</p> <p>Our data suggested that fibrinogen-alginate, fibronectin-alginate and RGD-alginate microcapsules improved the viability of encapsulated MSC and are applicable in cell therapy technologies. However, fibrinogen-alginate and fibronectin-alginate microcapsules more significantly enhanced the proliferation and protein secretion from the encapsulated cells and may have potential for FIX delivery for hemophilia B and other inherited or acquired protein deficiencies. RGD-alginate microcapsules can v potentially be used for other tissue engineering applications with the aim of enhanced viability and attachment of the enclosed cells. Differentiation studies showed the osteogenic (but not chondrogenic or adipogenic) differentiation capability of FIX-engineered CB MSCs and their efficient FIX secretion while encapsulated in fibrinogen-alginate and fibronectin-alginate microcapsules.</p> / Doctor of Philosophy (PhD)

This study presents a viable strategy using fmoc-protected peptides hydrogels, to encapsulate and stretch mesenchymal stem cells (MSC). To explore the peptide hydrogel potential, a custom mechanical stretching device with polydimethylsiloxane (PDMS) chambers were used to stretch MSCs encapsulated in Fmoc hydrogels. We investigated the impact of fmoc- FF prepared in dimethyl sulfoxide (DMSO), 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) and deionizied water in the self-assembly, and mechanical properties of the gels. The peptide hydrogel is formed through molecular self-assembly of peptide sequence into β-sheets that are connected with the π-π aromatic stacking of F-F groups. The hydrogels provided a stiff, hydrated gel with round nanofiber morphology representing an elastic modulus of 174-266 KPa. MSCs cultured on peptide hydrogels undergo viability, morphology, and alignment evaluations using MTT, live/dead, and phalloidin (F-actin) staining. The F-actins of 3D- cultured MSCs in Fmoc-FF/HFP, and Fmoc-FF/DMSO followed by mechanical stretching showed elongated morphology with defined microfilament fibers compared to the round and spherical F-actin shape of the control cells. Peptide gels with 5mM concentration preserved 100% viability of MSC. Results reveals the feasibility and conditions for successful cell encapsulation and alignment within peptide hydrogels. Encapsulation of MSC in peptide nanofiber followed by a stretching process present a promising tissue engineering platform. By enhancing our understanding of MSC-peptide hydrogel interactions, this research con- tributes to the development of biomaterials tailored for regenerative medicine.

Partial or complete tears of the anterior cruciate ligament (ACL) can greatly afflict quality of life and often require surgical reconstruction with autograft or allograft tissue to restore native knee biomechanical function. However, limitations exist with these treatments that include donor site pain and weakness found with autografts, and longer "ligamentization" and integration times due to the devitalization of allograft tissue. Alternatively, a tissue engineering approach has been proposed for the fabrication of patient-specific grafts that can more rapidly and completely heal after ACL reconstruction. Electrospun micro-fiber networks have been widely utilized as biomaterial scaffolds to support the growth and differentiation of mesenchymal stem cells toward many tissue lineages including ligament. However, these micro-fiber networks do not possess suitable sizes and shapes for a ligament application and cannot support cell infiltration. The objective of this work was to develop techniques to 1) rapidly cellularize micro-fiber networks, 2) assemble micro-fiber networks into cylindrical composites, 3) provide cues to mesenchymal stem cells (MSCs) to guide their differentiation toward a ligament phenotype. The cellularization of micro-fiber networks was performed utilizing a co-electrospinning/electrospraying technique. Cells deposited within a cell culture medium solution remained where they were deposited and did not proliferate. The inclusion of space-filling hydrogel network such as collagen was necessary to reduce the density of the micro-fiber network to facilitate spreading. However, it became apparent that the incorporation of significant collagen phase was necessary for long-term MSC survival within the micro-fiber network. Next, two approaches were developed to fabricate large cylindrical, composites. The first approach utilized a co-electrospinning/electrospraying technique to generate micro-fiber/collagen composites that were subsequently rolled into cylinders. These cylindrical composites exhibited greater diameters and water weight percentages as collagen content increased. However, the high micro-fiber content of these composites was inhibitory to cell survival. In the second approach, thin layers (~5-10 fibers) of aligned electrospun PEUR fibers were encapsulated within a collagen gel and subsequently rolled the composites into cylinders. These sparse-fiber composites were nearly 98% by weight water and confocal imaging revealed the presence of sparse fiber layers (~5 fibers thick) separated by approximately 200 μm thick collagen layers. We hypothesize that the proliferation and migration of MSCs within these micro-fiber/collagen composites may not be restricted by the presence of a dense, non-manipulatable electrospun fiber network present in traditionally rolled fiber composites. Simple model platforms were then developed to study the influence of sparse micro-fibers on MSCs differentiation within a collagen hydrogel. MSCs in the presence of the softest (5.6 MPa) micro-fibers elongated and oriented to the underlying network and exhibited greater expression of scleraxis, and α-smooth muscle actin compared to the stiffest (31 MPa) fibers. Additionally, preliminary results revealed that the incorporation of fibroblast growth factor-2 and growth and differentiation factor-5 onto micro-fibers through chemical conjugation enhanced expression of the ligamentous markers collagen I, scleraxis, and tenomodulin. In conclusion, micro-fiber/collagen composite materials must possess sufficient space to support the infiltration and differentiation of MSCs. The strategies described in this document could be combined to fabricate large, micro-fiber/collagen composites that can support cell infiltration and provide relevant cues to guide the formation of an engineered ligament tissue. / Ph. D.

Cell phenotypic transitions, or cell fate decision making processes, are regulated by complex regulatory networks composed of genes, RNAs, proteins and metabolites. The regulation can take place at the epigenetic, transcriptional, translational, and post-translational levels to name a few. Epigenetic histone modification plays an important role in cell phenotype maintenance and transitions. However, the underlying mechanism relating dynamical histone modifications to stable epigenetic cell memory remains elusive. Incorporating key pieces of molecular level experimental information, we built a statistical mechanics model for the inheritance of epigenetic histone modifications. The model reveals that enzyme selectivity of different histone substrates and cooperativity between neighboring nucleosomes are essential to generate bistability of the epigenetic memory. We then applied the epigenetic modeling framework to the differentiation process of olfactory sensory neurons (OSNs), where the observed 'one-neuron-one-allele' phenomenon has remained as a long-standing puzzle. Our model successfully explains this singular behavior in terms of epigenetic competition and enhancer cooperativity during the differentiation process. Epigenetic level events and transcriptional level events cooperate synergistically in the OSN differentiation process. The model also makes a list of testable experimental predictions. In general, the epigenetic modeling framework can be used to study phenotypic transitions when histone modification is a major regulatory element in the system. Post-transcriptional level regulation plays important roles in cell phenotype maintenance. Our integrated experimental and computational studies revealed such a motif regulating the differentiation of definitive endoderm. We identified two RNA binding proteins, hnRNPA1 and KSRP, which repress each other through microRNAs miR-375 and miR-135a. The motif can generate switch behavior and serve as a noise filter in the stem cell differentiation process. Manipulating the motif could enhance the differentiation efficiency toward a specific lineage one desires. Last we performed mathematical modeling on an epithelial-to-mesenchymal transition (EMT) process, which could be used by tumor cells for their migration. Our model predicts that the IL-6 induced EMT is a stepwise process with multiple intermediate states. In summary, our theoretical and computational analyses about cell phenotypic transitions provide novel insights on the underlying mechanism of cell fate decision. The modeling studies revealed general physical principles underlying complex regulatory networks. / Ph. D.

Among the most common knee ligament injuries are those to the anterior cruciate ligament (ACL). Annually, approximately 350,000 people require surgical ACL reconstruction, accounting for more than $6 billion of health-care costs in the United States alone. An injured ACL loses its functions as it cannot heal with larger injuries and heals slowly with smaller ones. This may introduce complications, such as abnormal joint kinematics and deterioration, prior to complete rupture. Although the use of an autologous graft is the current gold standard for ACL reconstruction surgery, it is associated with donor site morbidity and a decrease in mechanical strength at the donor site. The use of allogenic grafts instead of autografts introduces the risk of disease transmission. Furthermore, integration of soft tissue grafts (e.g., hamstring tendon) to native bone is slow and risks graft pullout. To circumvent these limitations, tissue engineering seeks to fabricate suitable biomaterials that could replace the entire ACL, stimulate regeneration of the ligament tissue, and integrate with host bone tissue. Numerous efforts have led to the development of complex, multi-phased biomaterial scaffold designs that are intended to deliver an array of cell types and biological cues. Particularly, scaffolds that possess bone-regenerating biomaterials at the ends are envisioned to facilitate rapid integration with the femur and tibia. Electrospun fiber scaffolds continue to be regularly utilized for their high tensile strength, flexibility, and ability to bend. Nevertheless, fibrous scaffolds are inert and require the incorporation of trophic factors to guide tissue regeneration. Additionally, electrospun fibers are often densely packed, which can hinder cell infiltration and subsequent tissue formation. The objective of this work was to guide bone remodeling through the incorporation of trophic factors with 1) electrospun fiber scaffolds or 2) nanoparticles that could be combined with electrospun fiber scaffolds, and 3) to develop model three-dimensional fiber-hydrogel composites that support cell viability and proliferation. Two approaches were utilized to present the trophic factor bone morphogenic protein (BMP)-2 to stimulate bone formation. In the first approach, electrospun fibers were modified through the adsorption or covalent conjugation of BMP-2. These fibers exhibited increased BMP-2 concentrations with covalent conjugation over adsorption, and the incorporation of heparin into the fibers improved both adsorption and conjugation. Mesenchymal stem cells (MSCs) – that have the capacity to differentiate into osteoblastic cells – were able to attach and proliferate on all films yet appeared to do so to a greater extent on surfaces with higher heparin contents. Additionally, markers of osteoblastic differentiation were significantly higher on surfaces with covalently conjugated BMP-2 than on those with adsorbed BMP-2. In the second approach, a nanoparticle system was produced to control BMP-2 delivery and release. Importantly, this flexible system can be fabricated separately, and then combined with a scaffold for tissue regeneration. In this approach, BMP-2 was combined with chitosan nanoparticles through adsorption, encapsulation, or covalent conjugation. The particular BMP-2 incorporation technique had no significant effect on BMP-2 incorporation efficiencies, but affected particle size and BMP-2 release kinetics. Specifically, covalent conjugation method caused the aggregation of particles while adsorption method allowed the most sustainable release. MSCs cultured in the presence of the different particles survived and proliferated, but only particles with adsorbed BMP-2 stimulated osteoblastic differentiation. Finally, three-dimensional fiber-hydrogel composites of various models were fabricated to mimic the complexity of full-sized scaffolds for ACL regeneration, and to study cell infiltration, differentiation, and tissue formation. A collagen hydrogel phase was introduced to electrospun fiber scaffolds using different approaches. MSCs seeded within a thin collagen layer were able to proliferate, sense underlying substrate and spread according to fiber orientation, while those within thicker layers were not. Additionally, cells initially present in only the collagen phase infiltrated to the fiber phase. These results demonstrate that minor changes in fabrication steps to combine the two phases could significantly alter cell function during the formation of three-dimensional fiber-hydrogel composites for tissue regeneration. / Doctor of Philosophy / The anterior cruciate ligament (ACL) is one of four ligaments that connect the thigh bone to the shin bone and stabilize the knee. Injuries to the ACL often occur during high impact sports, and ruptures can necessitate surgical intervention. ACL reconstruction surgery involves drilling tunnels through the ends of leg bones, deploying the tissue graft through the knee joint and bone tunnels, and anchoring it within the bone tunnels. The most common grafts are autografts that use tendons of the patient's own body or allografts that are obtained from cadavers. The complications associated with autografts include pain at the site of tissue harvest, while allografts risk disease transmission. Additionally, directly affixing a soft tissue graft (e.g., the hamstring tendon) to bone within the bone tunnel suffers from slow tissue integration and risk of pull-out. Tissue engineering is a field that seeks to develop devices to direct the regeneration of damaged tissues and organs. In the context of ACL repair, it seeks to achieve a biomaterial device with the properties of ACL, that can both guide the regeneration of ligament tissue and facilitate integration with bone tunnels, eliminating the need for autografts and allografts and their associated risks. Toward the development of an engineered ACL, this work focuses on improving graft-to-bone integration. In the first project, fibrous materials are surface-modified with bone morphogenetic protein (BMP)-2 (a bone-forming protein), and then tested for their ability to stimulate formation of a bone-like tissue in cell culture. In the second project, the deployment of BMP-2 either on the surface of or within nanoparticle delivery vehicles is evaluated as an alternative strategy to stimulate bone-like tissue formation. The third project explores the inclusion of a hydrogel phase to facilitate cell infiltration and bone-like tissue formation within fibrous materials. Together these studies provide insights into how the architecture of the engineered tissue and the deployment of bone-forming proteins can be used to enhance ACL regeneration.

No / The development of hair follicle organ culture techniques is a significant milestone in cutaneous biology research. The hair follicle, or more accurately the "pilo-sebaceous unit", encapsulates all the important physiologic processes found in the human body; controlled cell growth/death, interactions between cells of different histologic type, cell differentiation and migration, and hormone responsitivity to name a few. Thus, the value of the hair follicle as a model for biological scientific research goes way beyond its scope for cutaneous biology or dermatology alone. Indeed, the recent and dramatic upturn in interest in hair follicle biology has focused principally on the pursuit of two of biology's holy grails; post-embryonic morphogenesis and control of cyclical tissue activity. The hair follicle organ culture model, pioneered by Philpott and colleagues, ushered in an exceptionally accessible way to assess how cells of epithelial (e.g., keratinocytes), mesenchymal (e.g., fibroblasts), and neuroectodermal (e.g., melanocytes) origin interact in a three-dimensional manner. Moreover, this assay system allows us to assess how various natural and pharmacologic agents affect complex tissues for growth modulation. In this article, I focus on the culture of the human hair follicle mini-organ, discussing both the practical issues involved and some possible research applications of this assay.