Indiana University-Purdue University Indianapolis (IUPUI) / Cardiovascular disease is the number one cause of death for Americans. New treatments are needed for serious conditions like atherosclerosis, as it can lead to stroke and heart attack. Many types of cells contribute to the progression of cardiovascular disease, including smooth muscle cells that comprise the middle layers of arteries. Inappropriate growth and migration of smooth muscle cells into the lumen of arteries has been implicated in vascular diseases. Death associated protein kinase (DAPK) is a protein that has been found to regulate the survival and migration of cancer cells, but has not been well characterized in vascular cells. The objective of this work was to determine the signaling pathways that DAPK regulates in smooth muscle cells. These studies have focused on smooth muscle cells isolated from human coronary arteries (HCASM cells). We have determined that HCASM cells depleted of DAPK exhibit more rapid migration, showing that DAPK negatively regulates migration of vascular cells. Results from a focused RT-PCR array identified matrix metalloproteinase 9 (MMP9) as a gene that is increased in cells depleted of DAPK. MMP9 is an important enzyme that degrades collagen, a component of the extracellular matrix through which smooth muscle cells migrate during atherosclerosis. We found that DAPK regulates phosphorylation of the NF-kappa B transcription factor p65 at serine 536, a modification previously found to correlate with increased nuclear levels and activity of p65. In DAPK-depleted HCASM cells, there was more phosphorylation of p65, which causes increased MMP9 promoter activity. Additional experiments were conducted using transgenic mice in which the DAPK gene has been deleted. By studying these mice, we have determined that under some circumstances DAPK augments maximal MMP9 levels in mouse carotid arteries which have been injured by ligation surgery via other signaling pathways. MMP9 has been previously implicated as a protein that promotes vascular diseases such as atherosclerosis. Our research in identifying DAPK as a regulator of MMP9 expression identifies a new target for treatment of vascular diseases like atherosclerosis.

The Dps (DNA-Binding Protein from Starved Cells) proteins are a class of stress-specific proteins with a major role in protecting DNA during the stationary phase of bacterial growth, through direct physical binding as well as ferroxidation. These proteins are characteristically dodecameric in nature. Mycobacterium smegmatis, which is the model organism used in this study has two Dps homologues- MsDps1 and MsDps2. MsDps1, that has previously been studied, is exceptional in having trimeric as well as dodecameric states in vitro. This work focuses on the functional domains of MsDps1, with respect to its oligomerisation and DNA binding property, the identification of a new Dps homologue MsDps2, the in vitro characterization of MsDps2 and elucidation of a possible function of the protein in the physiology of Mycobacterium smegmatis. The Thesis is organized as shown below: Chapter 1: The literature on the bacterial stationary phase physiology and the role of Dps has been reviewed in this chapter. It gives a brief introduction of the background of the present study including the stationary phase response of bacteria and the significance of studying bacteria under stress as apart from ideal conditions of growth, which has been the conventional approach until recently. The advantages of using Mycobacterium smegmatis as a model system, and its starvation-induced stationary phase are also discussed. An introduction to the Dps proteins as a family of proteins branched off from ferritins and nucleoid proteins is explained. A brief summary of the ferritin and nucleoid proteins is given. Similarities connecting Dps to both these protein families is described. The review of earlier work done in our laboratory on the mycobacterial MsDps1 protein is also presented. Chapter 2: involves the study of the solution properties of the protein including its ability to oligomerize in vitro. The MsDps1 protein exists in two forms, a trimer and a dodecamer. The trimer form is a unique feature of the M.smegmatis homologue. Dps proteins from other sources are characteristically dodecameric. Earlier studies have shown that the trimeric form of the protein can perform ferroxidation while the dodecamer can bind to DNA. The dodecamer can also perform ferroxidation and accumulate the oxidized iron in its negatively charged core. In this chapter, we show that the trimeric form is extremely stable, under various conditions of pHs. The protein, when over expressed in M.smegmatis, also shows the presence of the trimer, thus ruling out the effect of heterologous expression of the protein in E.coli. We further report here, the ideal conditions for dodecamerisation of the protein from trimer to dodecamer, which binds to DNA. The dodecamer once formed is also highly stable and does not revert back to the trimeric form. The structural stability of the dodecamer is expected, as it is the fully functional form of the protein that physically protects the DNA from stress. However, the high stability of the trimeric form and its precise conversion into a stable dodecamer is intriguing. It is interesting to study the functional significance in vivo of the oligomerisation process in MsDps1. In addition, we looked at the effect of over expression of the protein on the overall phenotype of Mycobacterium smegmatis, as evidenced by the colony morphology and find no visible alteration, when compared with the wild type. Chapter 3: deals with a more detailed structural analysis of the MsDps1 protein. The role of N and C termini of the protein in maintaining a stable oligomeric structure is studied by making an N-terminal deletion mutant of the protein which is found to be unable to form a dodecamer in solution. On the other hand, MsDps1 with a 16 amino acid C-terminal deletion, MsDpsΔC16, is able to form stable oligomeric structures, when the N-terminal is intact. A previous deletion reported from our laboratory with 26 amino acids deleted from the C-terminal tail, called MsDpsΔC26 showed inability to form stable oligomeric structures in vitro. Putting together all the above results, a model for the interaction of the N and C-terminal tails of the protein in maintaining a stable dodecamer is presented. A demarcation of the C-terminal tail of MsDps1 into regions determining the oligomeric stability and DNA binding was also inferred. The MsDpsΔC16 protein, does not bind to DNA although it forms a stable dodecamer. A further deletion of 10 amino acids, as seen in a previously made construct, MsDpsΔC26 disrupts both the DNA binding as well as the oligomeric stability of the protein. Chapter 4: describes the discovery of a new homolog of the Dps protein in M.smegmatis. It was named as MsDps2. Bio-informatics analysis carried out on the complete genome data of Mycobacterium smegmatis yielded a second homologue of Dps in addition to the one already present and characterized. Interestingly, out of the 300 homogues of Dps found in bacteria, only 195 are present as single copies in a bacterium. The rest exist as more than one homologue in the same bacterial genome. The basic characterization of this new Dps homologue and its confirmation as a Dps family member is the focus of this chapter. Chapter 5: deals with the possible functions of the new protein MsDps2. Electron micrography shows that the purified protein forms stable nucleoprotein-like complexes. Over expression of the MsDps2 proteins presents no difference in the colony morphology when compared with the wild-type. Western analysis shows that the MsDps2 protein is not expressed under normal conditions tested for growth. MsDps1, on the other hand shows expression under conditions of starvation and osmotic stress, as has been established previously in the laboratory. Hence, it can be inferred that the new protein MsDps2 does not perform the same function as MsDps1. However, the in vivo function of this protein remains an important question to be addressed. The appearance of in vitro nucleoid structures involving this protein under the electron microscope, suggests a possible role for this protein in the formation and stabilization of the mycobacterial nucleoid. Indeed extensive evidence for the same exists for the E.coli protein. Chapter 6: describes the results obtained from the sequence comparison of MsDps2 with other Dps proteins listed in the TIGR database. ClustalW sequence analysis, followed by the construction of a phylogenetic tree using the MEGA software, suggests that the mycobacterial Dps proteins fall into two separate groups, represented by the MsDps1 and MsDps2 homologues from Mycobacterium smegmatis. Chapter 7 Summary and Conclusions: A summary of the work presented in the thesis is given followed by the appendix sections. Appendix 1 includes list and maps of plasmids used. Appendix 2 details the theoretical DNA and protein sequences of the recombinant clones generated in the study and theoretical physical and chemical properties of the proteins studied, as calculated with the Expasy Protparam software. Appendix 3 includes raw data obtained from the bio-informatic analysis of MsDps2, obtained using ClustalW analysis.

Abstract Frontotemporal lobar degeneration (FTLD) is the second most common neurodegenerative disease leading to early-onset dementia (< 65 years), next to Alzheimer’s disease. FTLD is substantially a genetic disorder with up to 50% of cases having a positive family history. Mutations in the genes microtubule-associated protein tau (MAPT) and progranulin (PGRN) account for about 10–20% of all cases of FTLD. Hexanucleotide repeat expansion mutation within the gene C9ORF72 has recently been identified as the major cause of FTLD, FTLD with amyotrophic lateral sclerosis (ALS) and pure ALS. During this study, hexanucleotide repeat expansion within the C9ORF72 gene was shown to explain nearly 50% of familial and 30% of all FTLD cases in the Finnish population. Otherwise, the genetic background of Finnish FTLD is largely unknown. The object of the present work was to disentangle the genetic aetiology of FTLD in the Finnish population. We studied a cohort of patients with a clinical diagnosis of FTLD from the province of Northern Ostrobothnia, Finland. Sequencing analysis of the genes MAPT, charged multi-vesicular body protein 2B (CHMP2B) and TAR DNA binding protein (TARDBP) were performed and the MAPT haplotypes were analysed. Correlations between genotype and phenotype were studied in patients with C9ORF72 repeat expansion mutation. C9ORF72 expansion mutation explained nearly 30% of cases of FTLD in our cohort. Concomitant ALS and positive family history of the disease increased the possibility of carrying expanded C9ORF72. The clinical phenotype of C9ORF72 expansion carriers varied at presentation: both behavioural and language variants were detected with or without ALS. The behavioural presentations included prominent psychotic features, although psychiatric presentations were not overrepresented in expansion carriers. No pathogenic mutations were identified in the MAPT, CHMP2B and TARDBP genes in our series of FTLD patients. The H2 MAPT haplotype was associated with FTLD in the series. Our findings emphasise the importance of C9ORF72 expansion mutation in FTLD. While mutations in MAPT and PGRN cause a significant proportion of cases of FTLD worldwide, they seem to be rare causes of FTLD in the Finnish population. Besides being infrequent in other populations, mutations in CHMP2B and TARDBP are rare causes of FTLD in the Finnish population as well. Our findings have clinical implications for recognising phenotypic features characteristic of expanded C9ORF72 as well as for genetic counselling of Finnish patients with FTLD. Even though a considerable proportion of our cases of familial FTLD is caused by the C9ORF72 expansion, over 50 % of our familial cases are without a molecular genetic diagnosis, suggesting that there are other unidentified causal genes to be found. / Tiivistelmä Otsa-ohimolohkorappeumat on toiseksi yleisin työikäisten dementiaa aiheuttava etenevä aivojen rappeumasairaus. Toisinaan otsa-ohimolohkorappeumat esiintyvät yhdessä liikehermorappeuman, amyotrofisen lateraaliskleroosin (ALS), kanssa. Perinnöllisillä tekijöillä on todennäköisesti keskeinen merkitys taudin taustalla. Mutaatiot microtubule-associated protein tau (MAPT)- ja progranulin (PGRN) geeneissä aiheuttavat yhteensä 10–20 % otsa-ohimolohkorappeumista maailmalla. C9ORF72-geenissä sijaitsevan toistojaksomonistuman on vastikään todettu olevan yleisin otsa-ohimolohkorappeumia ja ALS:a aiheuttava mutaatio. Mutaatio on erityisen yleinen suomalaisessa väestössä selittäen lähes 50 % suvuittaisista ja 30 % kaikista otsa-ohimolohkorappeumista. Oireyhtymän perinnöllisyys on muutoin huonosti tunnettu suomalaisessa väestössä. Tutkimuksen tavoitteena oli selvittää otsa-ohimolohkorappeumien geneettisiä syitä aineistossa, joka koostui vuosina 1999–2010 Oulun yliopistollisessa sairaalassa tutkituista potilaista. Tutkimuksessa selvitettiin MAPT-, charged multi-vesicular body protein 2B (CHMP2B)- ja TAR DNA-binding protein (TARDBP) geenien mutaatioiden esiintyvyyttä ja määritettiin MAPT-geenin haplotyypit. Lisäksi tutkittiin taudin kliinisiä erityispiirteitä C9ORF72-mutaation kantajilla. C9ORF72-mutaatio selitti lähes 30 % otsa-ohimolohkorappeumista aineistossamme. Tutkimuksessa havaittiin, että suvuittain esiintyvä tautimuoto ja ALS yhdistyneenä otsa-ohimolohkorappeumaan liittyivät merkittävästi C9ORF72-mutaatioon. Monistuman kantajien fenotyyppi oli moninainen – ensioireina oli sekä käytösongelmia että kielellisiä vaikeuksia. Vaikka C9ORF72-mutaation kantajilla on kuvattu runsaasti psykoottisia oireita, psykoottiset oireet eivät olleet selvästi yliedustettuna mutaation kantajilla aineistossamme. Tutkimuksessa ei löydetty tautia aiheuttavia mutaatioita MAPT-, CHMP2B- tai TARDBP-geeneistä. Havaitsimme kuitenkin tilastollisesti merkittävän yhteyden MAPT-geenin H2-haplotyypin ja otsa-ohimolohkorappeumien välillä. Tuloksemme antavat uutta tietoa C9ORF72-mutaation kantajien kliinisistä erityispiirteistä. MAPT-geenin mutaatioiden merkitys otsa-ohimolohkorappeumien synnyssä ei näyttäisi olevan suomalaisessa väestössä niin merkittävä kuin muissa väestöissä. CHMP2B- ja TARDBP-mutaatiot ovat harvinainen oireyhtymän syy myös suomalaisessa väestössä. Tuloksiamme voidaan hyödyntää suomalaisten otsa-ohimolohkorappeumapotilaiden perinnöllisessä neuvonnassa. Huomattavista edistysaskelista huolimatta yli puolet suvuittain esiintyvistä tautitapauksistamme on vailla geneettistä diagnoosia, mikä antaa aihetta jatkotutkimuksille.

6 Abstract Transcription factors play a key role in the management of cell growth and differ- entiation and their deregulation is associated with many cancers. TEAD proteins utilise highly conserved DNA binding domain to recognise specific DNA sequences. This domain could facilitate new drug design and development. The goal of this master thesis includes recombinant preparation of DNA binding domain of transcriptional factor TEAD4 extended by a part of an unstruc- tured variable sequence, which connects this domain with transactivation domain. Purification steps include affinity chromatography followed by size exclusion chro- matography. The characterization of produced protein was performed by mass spectrometry and finally, native gel electrophoresis was used to prove the ability of the produced protein to bind DNA. During purification steps, a fragmentation from C-terminus was observed. Based on analysis of the mass spectra, three most represented forms of produced protein were described all of which were fragmented. The most abundant form (55%) consisted of amino acids 30-131 from TEAD4 protein. Second most abun- dant form (18%) consisted of amino acids 30-144 and the third form consisted of amino acids 30-81. Native gel electrophoresis verified the ability to bind DNA, the efficiency was however lower...

Colorectal cancer (CRC) is the third leading cause of cancer related deaths in the United States. The nuclear factor κB (NF-κB) is an important family of transcription factors whose aberrant activation has been found in many types of cancer, including CRC. Therefore, understanding the regulation of NF-κB is of ultimate importance for cancer therapy. Using a novel validation-based insertional mutagenesis (VBIM) strategy, our lab has identified the novel adenomatous polyposis coli (APC) like protein (ALP) gene as a negative regulator of NF-κB. Preliminary studies from our lab demonstrated that overexpression of ALP led to decreased NF-κB activity by κB reporter assay and electrophoresis mobility gel shift assay (EMSA). The current project aims to further evaluate the role of ALP in the regulation of NF-κB signaling in CRC cells. We found that overexpression of ALP in human CRC HT29 cells greatly reduced both the number and the size of colonies that were formed in a soft agar assay. ALP overexpression also decreased the cell growth rate and cell migration ability, while shRNA mediated knockdown of ALP showed opposite effects, confirming that ALP is a tumor suppressor in CRC HT29 cells. Overexpression of ALP led to decreased NF-κB activity by κB reporter assay and condition media assay in CRC HT29 cells. Furthermore, immunohistochemical analysis with human colon vii tissues revealed that there is a gradual loss of ALP protein with tumor progression. We also found that ALP predominantly localizes in the cytoplasm, and binds to the p65 subunit of NF-κB, and might be functioning downstream of IκB kinase (IKK). In summary, in this study, we provide evidence regarding the tumor suppressor role of ALP in CRC by functioning as novel negative regulator of NF-κB. This discovery could lead to the establishment of ALP as a potential biomarker and therapeutic target in CRC.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19174号 / 医博第4016号 / 新制||医||1010(附属図書館) / 32166 / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙橋 淳, 教授 村井 俊哉, 教授 渡邉 大 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Inflammation and an influx of macrophages are common elements in many diseases. Among pro-inflammatory cytokines, tumor necrosis factor (TNF) plays a central role by amplifying the cytokine network. Progranulin (PGRN) is a growth factor that binds to TNF receptors and interferes with TNF-mediated signaling. Extracellular PGRN is processed into granulins by proteases released from immune cells. PGRN exerts anti-inflammatory effects, whereas granulins are pro-inflammatory. The factors coordinating these ambivalent functions remain unclear. In our study, we identify Y-box binding protein-1 (YB-1) as a candidate for this immune-modulating activity. Using a yeast-2-hybrid assay with YB-1 protein as bait, clones encoding for progranulin were selected using stringent criteria for strong interaction. We demonstrate that at physiological concentrations, YB-1 interferes with the binding of TNF to its receptors in a dose-dependent manner using a flow cytometry-based binding assay. We show that YB-1 in combination with progranulin interferes with TNF-mediated signaling, supporting the functionality with an NF-B luciferase reporter assay. Together, we show that YB-1 displays immunomodulating functions by affecting the binding of TNF to its receptors and influencing TNF-mediated signaling via its interaction with progranulin.

Plusieurs indices suggèrent que le repliement du chromosome et la régulation de l’expression génétique sont étroitement liés. Par exemple, la co-expression d’un grand nombre de gènes est favorisée par leur rapprochement dans l’espace cellulaire. En outre, le repliement du chromosome permet de faire émerger des structures fonctionnelles. Celles-ci peuvent être des amas condensés et fibrillaires, interdisant l’accès à l’ADN, ou au contraire des configurations plus ouvertes de l’ADN avec quelques amas globulaires, comme c’est le cas avec les usines de transcription. Bien que dissemblables au premier abord, de telles structures sont rendues possibles par l’existence de protéines bivalentes, capable d’apparier des régions parfois très éloignées sur la séquence d’ADN. Le système physique ainsi constitué du chromosome et de protéines bivalentes peut être très complexe. C’est pourquoi les mécanismes régissant le repliement du chromosome sont restés majoritairement incompris.Nous avons étudié des modèles d’architecture du chromosome en utilisant le formalisme de la physique statistique. Notre point de départ est la représentation du chromosome sous la forme d’un polymère rigide, pouvant interagir avec une solution de protéines liantes. Les structures résultant de ces interactions ont été caractérisées à l’équilibre thermodynamique. De plus, nous avons utilisé des simulations de dynamique Brownienne en complément des méthodes théoriques, car elles permettent de prendre en considération une plus grande complexité dans les phénomènes biologiques étudiés.Les principaux aboutissements de cette thèse ont été : (i) de fournir un modèle pour l’existence des usines de transcriptions caractérisées in vivo à l’aide de microscopie par fluorescence ; (ii) de proposer une explication physique pour une conjecture portant sur un mécanisme de régulation de la transcription impliquant la formation de boucles d’ADN en tête d’épingle sous l’effet de la protéine H-NS, qui a été émise suite à l’observation de ces boucles au microscope à force atomique ; (iii) de proposer un modèle du chromosome qui reproduise les contacts mesurés à l’aide des techniques Hi-C. Les conséquences de ces mécanismes sur la régulation de la transcription ont été systématiquement discutées. / Increasing evidences suggest that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. These can be rather compact bundle-like aggregates that prevent the access to DNA, or in contrast, open coil configurations with several (presumably) globular clusters like transcription factories. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanisms responsible for chromosome folding and for the formation of functional structures have remained elusive.Using methods from statistical physics, we investigated models of chromosome architecture. A common denominator of our approach has been to represent the chromosome as a polymer with bending rigidity and consider its interaction with a solution of DNA-binding proteins. Structures entailed by the binding of such proteins were then characterized at the thermodynamical equilibrium. Furthermore, we complemented theoretical results with Brownian dynamics simulations, allowing to reproduce more of the biological complexity.The main contributions of this thesis have been: (i) to provide a model for the existence of transcrip- tion factories characterized in vivo with fluorescence microscopy; (ii) to propose a physical basis for a conjectured regulatory mechanism of the transcription involving the formation of DNA hairpin loops by the H-NS protein as characterized with atomic-force microscopy experiments; (iii) to propose a physical model of the chromosome that reproduces contacts measured in chromosome conformation capture (CCC) experiments. Consequences on the regulation of transcription are discussed in each of these studies.