El limfoma de cèl•lules del mantell (LCM) és una neoplàsia heterogènia en relació a les característiques clíniques, biològiques i moleculars que presenten els pacients. La morfologia, l’immunofenotip i el genotip no són suficients per explicar aquesta gran diversitat. Encara que es considera una neoplàsia agressiva alguns pacients segueixen un curs clínic indolent sense la necessitat de tractament en el moment del diagnòstic i presenten una supervivència llarga. Els resultats d’aquesta tesi demostren que els LCM amb elevada càrrega mutacional en els gens de les immunoglobulines (IGHV)(<97% d’identitat amb la línia germinal) utilitzen preferencialment certes famílies de gens IGHV, suggerint la presència de processos de selecció antigènica com a mecanisme de patogènesi d’aquesta neoplàsia i donant importància a la caracterització del receptor de les cèl•lules B (BCR). Els LCM amb gens IGHV mutats (M-LCM) presenten una menor complexitat genòmica, són preferencialment negatius per a l’expressió del factor de transcripció SOX11 i presenten afectació ganglionar amb més freqüència que els casos sense mutacions (U-LCM). Per altra banda, el perfil d’expressió gènica entre casos amb i sense mutacions en els gens IGHV, també mostra expressió diferencial de programes cel•lulars relacionats amb poblacions de cèl•lules B normals incidint amb la ontogènia d’ambdós grups. El perfil d’expressió de microRNAs també permet diferenciar entre dos grups de pacients amb diferent supervivència, reforçant la idea de la presència de dos subgrups que pertanyen a una mateixa entitat. La identificació i la correcte identificació d’aquests pacients de limfoma de cèl•lules del mantell són rellevants per al posterior maneig i tractament dels mateixos. / Mantle cell lymphoma is a malignant and heterogeneous disease regarding the clinical, biological and molecular characteristics presented by patients, all of them with the translocation t(11;14) and CCND1 overexpression. Although is considered an aggressive neoplasm some patients follow and indolent clinical course without treatment at the time of diagnosis and long survival. The results of this studies demonstrate that LCM with high mutational load in the immunoglobulins genes (IGHV) (<97% of identity with the germ line) use preferentially specific IGHV gene families, suggesting the presence of antigenic selection process as a mechanism of pathogenesis of this neoplasm and giving importance to the characterization of the B cell receptor. The LCM cases with IGHV mutated genes (M-LCM) present less genomic complexity are preferentially negative for the expression of the transcriptor factor SOX11 and also present lymphadenopathies more frequently compared with the IGHV unmutated cases (U-LCM). Furthermore, the gene expression profile between cases with and without IGHV mutations also shows differential expression of cellular programs related to normal B cell populations maybe related with the ontogeny for both groups. The expression profile of microRNAs also differentiates between two groups of patients with different survival and other molecular characteristics, reinforcing the idea of the presence of two subgroups that belong to the same entity. The correct identification and classification of these patients are relevant for subsequent handling and treatment of the patients.

Los resultados de esta tesis doctoral han permitido profundizar en el reconocimiento y clasificación del linfoma de células del manto (MCL), basándonos en dos subtipos poco habituales. Por un lado, hemos estudiado las muestras de los pacientes de MCL que no presentan la traslocación principal t(11;14), característica que ha sido objeto de discusión al pensar que el diagnóstico de MCL podía no ser el correcto. Por otro lado, hemos estudiado los MCL con presentación clínica indolente, larga supervivencia, y que no requieren tratamiento durante largos períodos de tiempo, particularidad llamativa en los pacientes de MCL. En las dos primeras publicaciones de esta tesis hemos profundizado en el estudio de los MCL ciclina D1 negativos. Hemos demostrado que el factor de transcripción SOX11, además de sobreexpresarse en MCL ciclina D1 positivos, es un biomarcador útil para identificar los MCL ciclina D1 negativos. Además, caracterizamos genéticamente estos casos y mostramos que el 55% presenta traslocaciones de la CCND2 predominantemente con cadenas ligeras de los genes de las inmunoglobulinas. El perfil de alteraciones genómicas estudiado con arrays de alta densidad ha demostrado que las alteraciones genéticas secundarias entre los MCL ciclina D1 negativos y positivos son muy similares. Los casos de MCL ciclina D1 negativos tienen características clínicas y patológicas similares a los ciclina D1 positivos. Las translocaciones de CCND2 junto con la expresión de SOX11 son herramientas de diagnóstico muy útiles en la identificación de los MCL ciclina D1 negativos para que éstos puedan beneficiarse de los mismos protocolos terapéuticos usados en los MCL convencionales. En el tercer trabajo de esta tesis, nos hemos centrado en el reconocimiento del grupo de pacientes de MCL que no necesita tratamiento durante largos periodos de tiempo, idea que está modificando la manera de entender el MCL, ya que en general está considerado un linfoma agresivo que requiere un tratamiento inmediato. En este trabajo nos basamos en el estudio de Fernandez et al.1 en que se comparó un grupo de pacientes de MCL con comportamiento clínico indolente con un grupo de pacientes con MCL convencional (agresivo). Ambos grupos de muestras tenían un perfil de expresión global similar, sugiriendo que pertenecen a la misma enfermedad, pero también diferían en la expresión de una pequeña firma de 13 genes que estaba altamente expresada en los casos convencionales de MCL pero era negativa en los tumores de los pacientes con comportamiento indolente. Por lo que en el presente estudio, diseñamos y validamos un ensayo de PCR cuantitativa, seleccionando tres genes de la firma de perfil de expresión génica: SOX11, HDGFRP3 y DBN1 que permiten clasificar los casos en uno de estos dos grupos. El subgrupo con baja expresión de los tres genes incluye principalmente los pacientes con clínica indolente, afectación no-ganglionar, genes de las inmunoglobulinas hipermutados, y una supervivencia significativamente superior en comparación a los casos con expresión alta. Además, los MCL leucémicos sin afectación ganglionar y con alta expresión de los tres genes tienen una supervivencia significativamente inferior y un comportamiento clínico más agresivo que los pacientes con firma de expresión baja sin afectación ganglionar. En cuanto a las alteraciones genéticas, tanto los MCL con alta o baja expresión de los tres genes tenían una supervivencia significativamente inferior si presentan alteraciones en 17p. Por tanto, concluimos que la evaluación de la firma de los tres genes junto con el estudio de 17p/TP53 en muestras leucémicas puede ayudar a identificar un subgrupo particular de MCL y determinar la evolución clínica de estos los pacientes. Por tanto, estos estudios pueden proporcionar una evaluación más precisa del MCL y una ayuda en la decisión de tratamiento más adecuado para cada paciente. / In the first publication of this thesis we have studied the cyclin D1-negative mantle cell lymphomas (MCL). These cases are not well characterized due to the difficulties in their recognition. Overexpression of the transcription factor SOX11 has been observed in conventional MCL. In this study we demonstrated that SOX11 was highly expressed in cyclin D1-negative MCL, thus SOX11 expression is a highly specific marker for both cyclin D1-positive and negative MCL. In the second study we investigated 40 cyclin D1-negative MCL. Chromosomal rearrangements of CCND2 were detected in 55% of the cases and frequently with light chain immunoglobulin (IG) genes as partners. The genomic profile of the cyclin D1-negative cases analyzed by high resolution arrays were similar to the cyclin D1-positive MCL. This characterization of a large series of cyclin D1-negative MCL indicates that these tumors are clinically and biologically similar to the cyclin D1-positive MCL and provides a basis for the proper identification and clinical management of these patients. In the third publication, we studied the clinical and biological features of mantle cell lymphoma with a more indolent disease and long survival. The expression of 3 genes (SOX11, HDGFRP3, DBN1) selected from a gene expression signature distinguishing conventional an indolent MCL was studied in 68 leukemic MCL by quantitative PCR. An unsupervised analysis segregated two groups of MCL based on the expression levels of these genes. The tumors with low expression presented mainly with a non-nodal disease, had more frequently mutated IG, fewer genomic alterations, remained untreated more frequently and longer time, and had a better outcome than the tumors with high expression. The presence of 17p/TP53 alterations had an adverse effect on the outcome of both subgroups of MCL. The detection of the 3-gene signature may help to identify this particular subtype of MCL.

Mantle cell lymphoma (MCL) is one of several sub-types of B-cell lymphomas. The malignancy is very aggressive and average survival time is short. The hallmark of MCL is over expression of cyclin D1, however about 15% of all MCL cases do not display this over expression and are easily misdiagnosed. Recently the transcription factor Sox11 has been shown to be specifically over expressed in the nucleus of MCL-tumour cells, and polyclonal rabbit anti-Sox11 antibodies have been used to successfully identify MCL in both cyclin D1 positive and negative cases. Howev-er, human recombinant MCL-specific antibodies as have several advantages over these polyclonal rabbit antibodies; they can easily be produced in large quantities in vitro, their specificity is constant from batch to batch and they can possibly be used for therapeutic purposes. Because of this, it is desirable to produce human recombinant antibodies against proteins over expressed in MCL. In this study human recombinant IgGs have been produced towards two pro-teins over expressed in MCL, Sox11 and KIAA0882. This was done by cloning of single chain variable fragments (scFvs), previously selected from a large scFv library through phage display selection against Sox11- and KIAA0882-protein epitope signature tag (PrEST), into vectors containing human IgG constant regions followed by expression of human IgG antibodies in human embryonic kidney (HEK) 293 cells. One IgG clone for each antigen was shown to be functional and specific. Both clones were shown to have overlapping binding epitopes with their polyclonal rabbit antibody counterpart (rabbit anti-Sox11/KIAA0882) through competitive ELISA. The anti-Sox11 IgG was able to detect two bands in cell lysate in Western blot, of which one probably is Sox11 while the other band possibly could be Sox4. However, this needs to be confirmed in future experiments. The affinity of the anti-Sox11 IgG was measured in Biacore and compared to the affinity of its original scFv. This gave a rough estimation of the affinities, but the values are unreliable and the measurements need to be redone. Although more work has to be put into evaluating the potential of the produced IgGs, they compose a promising starting point to an improved understanding and improved diagnosis of MCL.

<p>Mantle cell lymphoma (MCL) is one of several sub-types of B-cell lymphomas. The malignancy is very aggressive and average survival time is short. The hallmark of MCL is over expression of cyclin D1, however about 15% of all MCL cases do not display this over expression and are easily misdiagnosed. Recently the transcription factor Sox11 has been shown to be specifically over expressed in the nucleus of MCL-tumour cells, and polyclonal rabbit anti-Sox11 antibodies have been used to successfully identify MCL in both cyclin D1 positive and negative cases. Howev-er, human recombinant MCL-specific antibodies as have several advantages over these polyclonal rabbit antibodies; they can easily be produced in large quantities in vitro, their specificity is constant from batch to batch and they can possibly be used for therapeutic purposes. Because of this, it is desirable to produce human recombinant antibodies against proteins over expressed in MCL. In this study human recombinant IgGs have been produced towards two pro-teins over expressed in MCL, Sox11 and KIAA0882. This was done by cloning of single chain variable fragments (scFvs), previously selected from a large scFv library through phage display selection against Sox11- and KIAA0882-protein epitope signature tag (PrEST), into vectors containing human IgG constant regions followed by expression of human IgG antibodies in human embryonic kidney (HEK) 293 cells. One IgG clone for each antigen was shown to be functional and specific. Both clones were shown to have overlapping binding epitopes with their polyclonal rabbit antibody counterpart (rabbit anti-Sox11/KIAA0882) through competitive ELISA. The anti-Sox11 IgG was able to detect two bands in cell lysate in Western blot, of which one probably is Sox11 while the other band possibly could be Sox4. However, this needs to be confirmed in future experiments. The affinity of the anti-Sox11 IgG was measured in Biacore and compared to the affinity of its original scFv. This gave a rough estimation of the affinities, but the values are unreliable and the measurements need to be redone. Although more work has to be put into evaluating the potential of the produced IgGs, they compose a promising starting point to an improved understanding and improved diagnosis of MCL.</p>

Microphthalmia, anophthalmia, and coloboma (MAC) are distinct abnormalities demonstrating a continuum of developmental eye defects that contribute to 15-20% of blindness and severe vision deficiencies in children worldwide. The genetic etiology of MAC is large, complex and encompasses the whole developmental biology of the eye. Understanding how the eye develops will aid in identifying genes and developmental pathways involved in MAC. Although investigation of the genetic architecture of congenital anomalies is growing exponentially, much work remains to be accomplished to understand the complex, genetically heterogeneous congenital anomalies, which significantly impact childhood vision. With an interest in elucidating the mechanisms that are involved in eye morphogenesis, I have characterized a SRY-Box transcription factor, Sox11, during zebrafish ocular development. The SRY (sex determining region Y)-box 11 (sox11) gene, codes for a transcription factor which functions as a regulator of cell fate, survival, and differentiation in the embryonic and adult nervous system. By titrating the levels of sox11 gene function in developing zebrafish embryos I have investigated the role of Sox11 during ocular morphogenesis and retinal neurogenesis. Chapter 1 of this dissertation provides a review of vertebrate eye development with a focus on emerging roles of SoxC proteins during vertebrate ocular morphogenesis. Chapter 2 presents data demonstrating that knockdown of both paralogs of sox11 in zebrafish results in microphthalmia, coloboma, as well as a specific deficit in mature rod photoreceptors. Additionally, we demonstrate for the first time that Sox11 regulates early ocular and photoreceptor development in part by maintaining proper levels of Hedgehog (Hh) signaling. Deficiency of Sox11 results in elevated Sonic Hedgehog a (Shha) transcript levels, which in turn leads to improper patterning of the optic vesicle into the proxio-distal territories. Furthermore, the data indicate that alterations in SOX11 gene dosage or mutation within the SOX11 coding region are potentially disease causing and contribute to human ocular defects like MAC and rod dysfunction. Chapter 3 presents data indicating that sox11 gene function is required during the critical period of neurulation (4-10 hours post fertilization) to guide choroid fissure closure and proper ocular morphogenesis to occur in the developing zebrafish. Chapter 4 is a technical report on the progress towards generating stable sox11a/b knockout zebrafish lines using the CRISPR/Cas9 genome editing approach. Transient F0 injected embryos and F0 adults carry mutations in the sox11a/b target site in addition to displaying ocular abnormalities similar to those previously reported in sox11 morphants. F1 juveniles are ready to be screened for establishment of mutagenesis efficiency and germ line transmission. Finally, in Chapter 5 I discuss how the results of each chapter demonstrate the functional requirement of Sox11 for ocular development. Furthermore, I discuss the implications of this work in the field of developmental biology and how the current data will shape future investigations. My dissertation incorporates human genetics, biochemical analyses, and zebrafish reverse genetic analyses, and will help in better understanding the exact role of Sox11 during eye development at the cellular and molecular level. Moreover, by identifying Sox11 targets belonging to the Hh pathway, as well as novel targets of Sox11 regulation, these studies may also contribute to our understanding of the function of Sox11in development and disease pathogenesis.