Borrelia burgdorferi is an elongated and helically shaped bacterium that is the causal agent of the tick-borne illness Lyme disease. The disease manifests with initial flu-like symptoms and, in many cases, the appearance of a skin rash called erythema migrans at the site of the tick bite. If left untreated the disease might cause impairment of various organs such as the skin, heart, joints and the nervous system. The bacteria have a parasitic lifestyle and are always present within a host. Hosts are usually ticks or different animals and birds that serve as reservoirs for infection. B. burgdorferi are unable to synthesize building blocks for many vital cellular processes and are therefore highly dependent on their surroundings to obtain nutrients. Because of this, porins situated in the outer membrane, involved in nutrient uptake, are believed to be very important for B. burgdorferi. Except for a role in nutrient acquisition, porins can also have a function in binding extracellular matrix proteins, such as integrins, and have also been implicated in bacterial adaptation to new environments with variations in osmotic pressure. P13 and P66 are two integral outer membrane proteins in B. burgdorferi previously shown to have porin activities. In addition to its porin function, P66 also has integrin binding activity. In this thesis, oligomeric structures formed by the P13 and P66 protein complexes were studied using the Black lipid bilayer technique in combination with nonelectrolytes. Initial attempts were also made to study the structure of P13 in Nanodiscs, whereby membrane proteins can insert into artificial lipid bilayers in their native state and the structure can be analyzed by electron microscopy. In addition, the role of P13 and P66 in B. burgdorferi osmotic stress adaptation was examined and also the importance and role of the integrin-binding activity of P66 in B. burgdorferi infections in mice. Using Black lipid bilayer studies, the pore forming activity of P13 was shown to be much smaller than previously thought, exhibiting activity at 0.6 nS. The complex formed by P13 was approximately 300 kDa and solely composed of P13 monomers. The channel size was calculated to be roughly 1.4 nm. Initial Nanodisc experiments showed a pore size of 1.3 nm, confirming the pore size determined by Black lipid bilayer experiments. P66 form pores with a single channel conductance of 11 nS and a channel size of 1.9 nm. The porin assembles in the outer membrane into a large protein complex of 420 kDa, containing exclusively P66 monomers. The integrin-binding function of P66 was found to be important for efficient bacterial dissemination in the murine host but was not essential for B. burgdorferi infectivity. Neither P13 nor P66 had an active role in osmotic stress adaptation. Instead, two p13 paralogs were up-regulated at the transcript level in B. burgdorferi cultured under glycerol-induced osmotic stress. / Borrelia burgdorferi är en bakterie med många unika egenskaper som orsakar sjukdomen Lyme borrelios. Borrelia kan idag lätt behandlas med antibiotika om sjukdomen upptäcks i ett tidigt stadium. Det är först om sjukdomen tillåts fortgå som symptom som nervsmärta och ansiktsförlamning kan uppstå och dessutom vara svåra att koppla till en Borrelia-infektion. Multiresistenta bakterier har blivit en stor del av vår vardag och även om Borrelia-bakterierna idag inte är resistenta mot flertalet antibiotika är det kanske speciellt viktigt, innan det är för sent, med forskning som kan leda till upptäckter av unika angreppsställen för nya läkemedel. Målet med denna avhandling var att studera hur två Borrelia proteiner, P13 och P66, ser ut, är uppbyggda och även vilken funktion de har. Dessa proteiner är tänkbara vaccinkandidater eftersom de sitter i yttre membranet hos bakterierna och sticker ut på ytan mot våra värdceller, vilket gör att vi reagerar mot dem vid en infektion. P13 och P66 är också viktiga kanaler för bakterierna vid upptag av näringsämnen och byggstenar från omgivningen. Ämnen som bakterierna inte kan producera själva. Pga. denna funktion är P13 och P66 tänkbara proteiner för blockering med ett läkemedel som skulle förhindra bakterien från att föröka sig i och med att de förlorar möjligheten att tillgodogöra sig näring. Detta i sin tur skulle leda till att vårt eget immunförsvar hinner rensa undan bakterierna innan infektionen blivit för stor och vi blivit sjuka. P66 har förutom porin funktionen även en adhesions funktion när proteinet kan binda integriner som sitter på olika typer av celler i vår kropp, bl. a. immunceller och epitelceller i våra blodkärl och vävnader. Den integrin bindande funktionen är viktig för bakterierna vid en infektion eftersom det gör det möjligt för bakterierna att binda till våra celler. Ett steg som är viktigt för att de senare ska kunna ta sig ut från blodkärlen till våra vävnader. P13 och P66 visade sig kunna bilda stora proteinkomplex i ytter membranet hos bakterierna med en storlek på 300 kDa respektive 420 kDa. De är inga specifika poriner som bara kan transportera en viss typ av molekyl med t.ex. en viss laddning, utan kan ombesörja upptaget av många olika typer av ämnen. Eliminering av p66 orsakade att ett annat adhesionsprotein, uppreglerades. En omplacering av ett normalt cytoplasmatiskt lokaliserat chaperon-protein till ytter-membranet hos bakterierna kunde också ses i frånvaro av P66. Chaperonet GroEL har i andra bakterier, bl. a. Helicobacter pylori, bakterien som orsakar magsår, beskrivits som ett protein som kan förflytta sig till ytan av bakterierna och där ha en liknande funktion som P66, dvs. att binda extracellulära matrisprotein. Förändringen i uttryck av adhesionsproteinet och förflyttningen av chaperonet till membranet var en följd av p66-eliminering och mest troligt ett sätt för bakterierna att komplettera den förlorade integrinbindande funktionen av P66. Det har tidigare visats att poriner är involverade i skyddet mot osmotisk stress i andra bakterier. Denna funktion hos P13 och P66 i Borrelia kunde inte ses när bakterier utsattes för osmotisk stress med glycerol, som orsakar en form av membranstress. Däremot kunde vi med hjälp av transkriptomanalys se att Borrelia-bakterier uppreglerade transkriptionen av två paraloger till P13 vid hyper-osmotisk stress. Borrelia bakteriens användning av dessa paraloga proteiner har tidigare trotts ske enbart i frånvaro av ett funktionellt P13 protein. Nu visade det sig att P13-paraloger har en egen funktion även i närvaro av P13, nämligen att vara involverade i regleringen av hyperosmotisk stress och därmed skydda bakterierna i denna stressituation. Andra gener som påverkades av osmotisk stress med glycerol var gener för stressfaktorer och pumpar i inre membranet hos bakterien.

Les leucémies chroniques à éosinophiles sans autre spécification (CEL,NOS) sont des néoplasmes myéloprolifératifs rares caractérisés par une hyperéosinophilie (HE) clonale. Avec 12 cas décrits, la translocation t(5;12)(q31;p13), différente de la translocation t(5;12)(q32;p13) ETV6-PDGFRB classique, semble être récurrente de cette entité. Peu étudiée, sa leucémogenèse reste non élucidée.L’objectif de ce travail était la caractérisation génomique et transcriptomique de ce remaniement afin d’en comprendre la physiopathologie.L’étude FISH sur cellules triées réalisée confirmait l’HE clonale, et indiquait un avantage sélectif semblant limité aux polynucléaires éosinophiles (PNE), puisque d’autres cellules, également porteuses de la translocation, ne proliféraient pas.Un transcrit de fusion ETV6-FNIP1, jamais décrit, différent des transcrits ETV6-ACSL6 habituellement observés, a été retrouvé dans le cas d’étude. La non récurrence d’un transcrit fonctionnel commun entre les cas était en défaveur de leur implication dans la leucémogenèse par l’apport d’une nouvelle fonction.ETV6 et ACSL6 étaient constamment impactés par le réarrangement, soit par formation d’un transcrit, soit par délétion comme dans le cas d’étude. Leur diminution d’expression, en l’absence de second événement, témoignait de l’haploinsuffisance de ces gènes suppresseurs de tumeurs.Par l’étude d’une cohorte de 39 patients avec HE, nous avons montré une dérégulation spécifique d’IL-3 dans la translocation t(5;12)(q31;p13), sans atteinte d’IL-5 ni de CSF2 (GM-CSF), cytokines impliquées dans l’éosinopoïèse. Des séquences conservées situées dans l’intron 2 d’ETV6 et en aval de l’exon 11 d’ACSL6 pourraient être responsables de cette dérégulation.Sans autre anomalie spécifique retrouvée, la translocation t(5;12)(q31;p13) constitue l’évènement oncogénique principal de ces cas. Parmi les mécanismes étudiés, plusieurs, sinon tous, pourraient être nécessaires au développement de la maladie. / Chronic eosinophilic leukemias not otherwise specified (CEL, NOS) is a rare myeloproliferative neoplasm characterized by clonal eosinopoiesis. In this setting, we studied a patient with a t(5;12)(q31;p13) which differs from the usual t(5;12)(q32;p13) ETV6-PDGFRB translocation. In this rare translocation (11 similar examples so far described in the litterature), mechanisms driving leukemogenesis still need to be investigated.The aim of this study was the genomic and transcriptomic characterization of this translocation in order to understand its pathophysiology.Triaged FISH study confirmed clonal HE, and suggested a specific advantage limited to eosinophils, since other nonproliferative cells also carried the translocation.A novel ETV6-FNIP1 fusion transcript hitherto never described was found. This transcript was different from the usual out-of-frame ETV6-ACSL6 transcripts, and no common functional transcript was observed among the published cases. The implication of these transcripts seems unlikely.ETV6 and ACSL6 are constantly impacted by rearrangement, either by a fusion transcript or by deletion as in the case study. Their underexpression, in the absence of a second hit, support the haploinsufficiency of these tumor suppressor genes.By studying a cohort of 39 patients with HE, we show a deregulation of IL-3 in the t(5;12)(q31;p13) translocation, without deregulation of IL-5 or CSF2 (GM-CSF), cytokines involved in eosinopoiesis. Conserved sequences in ETV6 intron 2 and downstream of ACSL6 exon 11 may be responsible for this deregulation.The t(5;12)(q31;p13) constitues the main oncogenic driver. From the mechanisms studied, many, if not all, may be associated for the development of the disease.

Borrelia burgdorferi is a pathogenic spirochete which cycles between its arthropod vector and vertebrate host. If transmitted to humans, B. burgdorferi causes Lyme disease, an infection which can impair different organs, such as the skin, joints, nervous system and heart. Alterations in protein expression due to the different environments Borrelia encounters during its complicated life cycle require advanced adaptation mechanisms. The outer surface-exposed proteins play a critical role in survival and pathogenesis of Borrelia in different hosts and tissues, being involved in avoiding the host immune response, adhesion to different tissues and nutrient acquisition. This thesis aimed to characterize integral outer membrane proteins which play a role in solute and nutrient uptake, and provides support for their role in the environmental adaptation of Borrelia. In this thesis, three B. burgdorferi proteins, P13, BBA01 and P66, were shown to be porins, and characterized structurally and functionally using a combination of biochemical, biophysical and genetic methods. The channel-forming function of the 13 kDa protein, P13, was elucidated by a lipid bilayer assay. Post-translational processing of P13 occurred at the C-terminus by C-terminal processing protease (CtpA)-dependent cleavage. The membrane-spanning architecture of P13 was determined by epitope mapping and computer-based structural predictions which revealed that P13 is an unusual porin, not possessing the structural properties of conventional porins: rather than forming β-barrels, it is predicted to span the membrane with hydrophobic α-helices. p13 belongs to a paralogous gene family. The transcription of p13 and other gene family members during in vitro growth and in a mouse infection model was therefore investigated. The paralog BBA01, which has the highest sequence homology to P13, is expressed during in vitro growth in all three Lyme disease causing species, although at very low levels. Like P13, BBA01 is also processed by CtpA and exhibits very similar channel-forming activity. Furthermore, in the absence of P13, a proportion of total BBA01 protein is relocated to the bacterial surface with strong indications that BBA01 and P13 are functionally interchangeable. P66, an integrin binding protein, was also determined to be a porin. The oligomeric state of native P66, elucidated by chemical cross-linking, indicated that P66 forms trimers, as do the majority of conventional porins. Electron crystallography and a projection map of P66 crystals at 2.2 nm resolution revealed tetragonal unit cell symmetry with the area intercalated between the assembled protein structures consistent with the approximate expected size of the channel formed by P66. Finally, the biological relevance of two porins, P13 and P66, was demonstrated in a double mutant displaying a stress response as revealed by increased sensitivity to high osmolarity and elevated expression of the B. burgdorferi heat-shock protein HtrA homolog.

Rheumatoid arthritis (RA) is a chronic joint disease which mechanism of action is unknown. The immune mechanism initiates an inflammatory process that mainly affects the joints, which can lead to cartilage and bone damage but also to some generalized symptoms such as fatigue and inflammatory anemia. At present, RA is primarily treated with methotrexate (MTX) as monotherapy. Studies in the field indicate that MTX in combination with infliximab, a monoclonal antibody, is more effective in treating RA than MTX treatment alone. Most likely, infliximab is not used as first-hand therapy since the reference product Remicade® is very expensive. In 2015 the patent for Remicade® expired and there are now cheaper biosimilars available that have been approved for the same indication as Remicade®. The aim of this study was to investigate whether MTX in combination with infliximab is more effective than MTX alone in the treatment of active RA and evaluating whether there is equivalence between the reference product Remicade® and the CT-P13 biosimilar. The medical and bioscience database PubMed was used to obtain the scientific articles analyzed in this literature study. From PubMed 5 articles were selected for further analysis. The delimitation of the search was: indication RA, MTX, infliximab and biosimilar (CT-P13). Articles 1-3, based on the outcome variables of the studies indicated that infliximab in combination with MTX is more effective than MTX treatment alone in the treatment of active RA. Articles 4-5 examined equivalence between the reference product for infliximab (RP) and the biosimilar CT-P13 in the treatment of active RA. The analysis and results of articles 4-5 showed that there was a similarity between RP and CT-P13 in treatment of active RA. Based on this small-scale literature study, treatment with MTX in combination with infliximab seems more beneficial for disease control in active RA than MTX treatment alone. In addition, the biosimilar CT-P13 appears to be equivalent to the reference product Remicade® in the treatment of active RA. Replacement of Remicade® to CT-P13 can mean major savings in healthcare and the therapeutic recommendation for active RA may need to be reviewed as there are now effective, cheaper alternatives.

Mycobacterium tuberculosis, the causative agent of pulmonary tuberculosis, infects one-third of the world’s human population. Despite the multiplicity of antimicrobial mechanisms mounted by its host, M. tuberculosis shows a remarkable ability to survive either by evoking survival strategies or by interference with critical macrophage functions that are required to successfully respond to the infection. It has been postulated that the outcome of exposure to M. tuberculosis (in terms of disease symptoms) largely depends upon the selective gene expression of tuberculosis bacilli along with activation of specific signaling pathways in the infected host cells during different phases of infection. In this perspective, determination of the complete genome sequence of Mycobacterium tuberculosis has provided crucial information with respect to the physiology of this bacterium and the pathogenesis of tuberculosis. However, putative functional annotation to all hypothetical proteins coded by M. tuberculosis genome remains complex. One important outcome of the genome-sequencing project was the discovery of two new multigene families designated PE and PPE. About 10% of the M. tuberculosis coding capacity is devoted to the PE and PPE genes, named for the Pro-Glu (PE) and Pro-Pro-Glu (PPE) motifs near the N terminus of their gene products. In addition to these motifs, proteins of PE family share N-terminal domains of approximately 100 amino acids, whereas the PPE proteins possess an N-terminal domain of about 180 amino acids. Many PE and PPE proteins are composed only of these N-terminal homologous domains. However, other members possess an additional C-terminal segment of variable length, often composed of multiple copies of polymorphic GC rich sequences (PGRS). The uniqueness of the PE genes is further illustrated by the fact that these genes are restricted to mycobacteria. However, despite their abundance in mycobacteria, very little is known regarding the expression or the functions of PE family genes. Although the PE and PPE families of mycobacterial proteins are the focus of intense research, no precise function has so far been unraveled for any member of these families. In perspective of above-mentioned observations, we have chosen Rv0754 as a representative PE family gene. Rv0754 was shown to be upregulated in tubercle bacilli upon infection of bone marrow derived macrophages as well as in M. tuberculosis isolated from alveolar macrophages of infected mice. In the current investigation, we demonstrate that Rv0754 is hypoxia responsive gene based on promoter or transcript expression analysis. Further, extensive bioinformatics analysis predicated that Rv0754 posses possible Phosphoglycerate Mutase domain, an enzyme known for its significant role not only in the glycolytic pathway of the carbohydrate metabolism, but also for the crucial cell fate decision during conditions like oxidative stress as well as infection. Experimental data clearly suggests that hypoxic environment dependent expression of Rv0754 imparts resistance to macrophages from oxidative stress. These findings could be attributed to the presence of catalytically active Phosphoglycerate Mutase domain of Rv0754. More often, sophisticated regulation/modulation of key signaling events regulate the critical cell fate decisions during oxidative stress. In this context, TLR2 dependent triggering of PI3K-ERK1/2- NF-κB signaling axis by Rv0754 may be operative in imparting resistance to oxidative stress. Further, Rv0754 triggers COX-2 expression by activating PI3K-ERK1/2-NF-κB cascade in mouse macrophages. These observations are of relevance as Rv0754 is associated with cell wall and is exposed outside the surface of the bacterium suggesting the possible access to intracellular compartments of the infected macrophages. Additionally, Rv0754 elicited humoral antibody reactivities in a panel of human sera or in cerebrospinal fluid samples obtained from different clinical categories of tuberculosis patients. DNA immunizations experiments in mice clearly suggested that Rv0754 is an immunodominant antigen demonstrating significant T cell and humoral reactivity. These observations clearly advocate that Rv0754 protein is expressed in vivo during active infection with M. tuberculosis and that the Rv0754 is immunogenic. Taken together, our findings suggest that Rv0754 is a novel PE_PGRS protein with unique features which could generate conditions that favor survival of the mycobacteria.