Dissertations / Theses on the topic 'Germline variant'

Single nucleotide polymorphisms (SNPs) have great potential to serve as important biomarkers in the clinic to identify those at increased risk for developing cancer, progressing more rapidly, and not responding to therapies. However, the clinical application of cancer-associated SNPs has proven to be more complicated than expected. One of the necessary steps will certainly be the description of the molecular and cellular mechanisms behind the observed associations. The p53 tumour suppressor pathway harbours well-described SNPs that affect p53 signalling and cancer. The aim of the work presented in this thesis was to utilise this knowledge to more efficiently characterise cancer-associated SNPs. Firstly, cancer-associated SNPs in a p53 network gene, CD44, were studied. Specifically, based on CD44’s known roles in both p53-dependent and independent signalling, it was predicted that the cancer-associated SNPs could function as biomarkers for chronic lymphocytic leukaemia progression, and for the response to anti-EGFR therapy for colorectal cancer. Indeed, supportive data is presented. Next, a methodology is presented that aims to identify cancer-associated SNPs in functional p53 binding sites using genome-wide datasets. Interestingly, a SNP is identified that dramatically influences the ability of p53 to regulate transcription of the KITLG oncogene and that associates with one of the largest risks of cancer identified to date. Intriguingly, the SNP is also shown to have undergone positive selection throughout human evolution, signifying a selective advantage, but similar SNPs are demonstrated to be rare in the genome due to negative selection, indicating that polymorphisms in p53 binding sites have been primarily detrimental to humans. Lastly, and in order to begin to explore if other polymorphic transcription factor binding motifs could be found in cancer-associated SNPs, a methodology was designed to identify SNPs in E-box transcription factor binding motifs, as they are sensitive to single base pair changes and affect cancer. Taken together, the work presented in this thesis shows how the study of how SNPs associate with, and impact upon, cancer has great potential to improve both biological knowledge and clinical outcomes.

Germline copy-number variants (CNVs), as well as somatic copy-number alterations (CNAs), play an important role in many phenotypic traits, including genetic diseases and cancer. Next Generation Sequencing (NGS) allows accurate detection of short variants, but reliable detection of large-scale CNVs in NGS data remains challenging. In this work, I address this issue and describe a novel statistical method for detection of CNVs and CNAs implemented in the tool called ClinCNV. I present analytical performance measures of “ClinCNV” in different datasets, compare it with the performance of other existing methods, and show the advantages of ClinCNV. ClinCNV is already implemented as a part of the diagnostics pipeline at the Institute of Medical Genetics and Applied Genomics (IMGAG), Tuebingen, Germany. ClinCNV has the potential to facilitate molecular diagnostic of genetic-based diseases as well as cancer through accurate detection of copy-number variants.
Las variantes en el número de copias genéticas, tanto en estado germinal (CNV) como en somático (CNA), juegan un papel muy importante en muchos rasgos fenotípicos y están frecuentemente relacionadas con una gran variedad enfermedades genéticas y cáncer. Aunque la secuenciación de próxima generación (NGS) permite detectar variantes cortas con una gran precisión, la correcta detección de CNVs a gran escala con datos de secuenciación sigue siendo un gran desafío. En esta tesis, me centro en abordar este problema y describo un nuevo método estadístico para la detección de CNV y CNA englobado en una nueva herramienta llamada ClinCNV. Para el análisis del rendimiento de ClinCNV y demostrar las ventajas de este nuevo algoritmo, comparamos nuestra herramienta con otras existentes en distintos conjuntos de datos. Por otra parte, ClinCNV ya está implementado como parte del sistema de trabajo de diagnóstico en el Instituto de Genética Médica y Genómica Aplicada (IMGAG) en Tuebingen (Alemania). En resumen, ClinCNV tiene el potencial de facilitar el diagnóstico molecular de enfermedades genéticas y cáncer mediante la precisa detección de variantes en el número de copias genéticas.

Introduction: Around 20-30% of the population are thought to have some form of inherited predisposition to colorectal cancer outside of the genetic syndromes of familial adenomatous polyposis (FAP), MYH-associated polyposis (MAP) and hereditary non-polyposis colorectal cancer (HNPCC). Inherited susceptibility should be particularly suspected when colorectal cancer is diagnosed at young age, when a patient presents with synchronous or metachronous colorectal cancers or adenomas, or where there is a strong family history of colorectal cancer. The rare variant hypothesis of inherited susceptibility proposes that a number of low frequency variants in a variety of different genes, each conferring a moderate but detectable increase in relative risk of developing disease, may be responsible for non- syndromic predisposition to colorectal cancer. Rare variants may occur in many genes involved in colorectal tumorigenesis, including those with roles in Wnt signalling, transcriptional activation, mismatch repair, cell cycle regulatory mechanisms and cellular adhesion. Methods: DNA from 124 United Kingdom patients with between 3 and 100 adenomatous polyps was screened for germline variants in genes involved in Wnt signalling (APC, AXINI and CTNNBI), mismatch repair (hMLHI and hMSH2) and cell cycling (TP53). The APC variants II307K and EJ317Q were detected using amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) and alkaline-mediated differential interaction (AMDI). For all other genes, PCR primers were designed to encompass the entire coding sequence of the gene and variant detection was carried out on the Transgenomic Wave" machine. Variants were sequenced and analysed using Sequencher" software. The findings in the sample population were compared with a population of 53 Korean patients with multiple adenomas, and with a panel of 483 healthy controls. Results: 30/124 (24.9%) of the U.K. multiple adenoma patients carried potentially pathogenic germline variants in the genes tested as compared to 55 (12%) of the controls. The overall association between the rare alleles at the loci tested and the formation of multiple adenomas, as compared to controls, was highly significant with an odds ratio of 2.2 (p = 0.0001). None of the variants identified in the U.K. patients was found in the Korean patients. Discussion: The difference in rare variants between cases and controls is highly significant, suggesting that many rare variants collectively contribute to inherited susceptibility to colorectal adenomas. Each variant would effect a subtle change in protein interaction or level of gene expression, resulting in only a marginal selective disadvantage but a clearly defined increase in relative risk. Such variants are likely to be population-specific, as in the cases of APC 1307K and E1317Q. Strategies for detection of multiple rare alleles include efficient variant detection and sequencing techniques in at-risk individuals, identification of candidate genes, large-scale population studies, careful selection of controls, and targeted statistical approaches. Each potential rare variant needs to be assessed for its functional consequences. These findings give support to the hypothesis that multiple rare alleles, predominantly missense, promoter and splice site variants, are collectively responsible for inherited susceptibility to colorectal cancer in the general population. It is probable that ultimately a large number of rare alleles will contribute more to the population burden of colorectal cancer than the classically inherited Mendelian syndromes associated with colorectal tumorigenesis.

KIF1A is a molecular motor for membrane-bound cargo important to the development and survival of sensory neurons. KIF1A dysfunction has been associated with several Mendelian disorders with a spectrum of overlapping phenotypes, ranging from spastic paraplegia to intellectual disability. We present a novel pathogenic in-frame deletion in the KIF1A molecular motor domain inherited by two affected siblings from an unaffected mother with apparent germline mosaicism. We identified eight additional cases with heterozygous, pathogenic KIF1A variants ascertained from a local data lake. Our data provide evidence for the expansion of KIF1A-associated phenotypes to include hip subluxation and dystonia as well as phenotypes observed in only a single case: gelastic cataplexy, coxa valga, and double collecting system. We review the literature and suggest that KIF1A dysfunction is better understood as a single neuromuscular disorder with variable involvement of other organ systems than a set of discrete disorders converging at a single locus.
National Institutes of Health
Revisión por pares

Abstract Childhood acute lymphoblastic leukemia (ALL) is the most common cancer in children. The overall survival rate has reached to 90%. However, ALL still presents a significant disease burden and is a major cause for deaths in children. Recently, both inherited germline variants related to ALL susceptibility and somatic genetic variants forming novel subgroups of ALL have been discovered. In this thesis two families with familial ALL were studied. Constitutional heterozygous microdeletion at chromosome 7p12.1p13, including IKZF1, was discovered in the first family with intellectual impairment, overgrowth, and susceptibility to childhood ALL. In the second family, constitutional chromosome translocation was revealed in two individuals with childhood ALL and, subsequently, in seven unaffected family members. The balanced reciprocal translocation t(12;14)(p13.2;q23.1) resulted in breakpoints on two genes; ETV6 on chromosome 12 and RTN1 on chromosome 14. Only a few familial and sporadic ALL cases with germline variants in either IKZF1 or ETV6 have been published, thus supporting the significant role of these constitutional variants in childhood ALL predisposition. Inherited bone marrow failure syndromes (IBMFS) may predispose to childhood leukemia, including ALL. Two unrelated patients were diagnosed with bone marrow failure without the symptoms of classical IBMFS. Neither patient had any signs of developmental delay or congenital anomalies. Exome sequencing revealed identical c.1457del(p.(Ile486fs)) mutation on the ERCC6L2 gene in both patients. A few patients with IBMFS and ERCC6L2 variants have been described in previous studies. Some of them also had congenital craniofacial anomalies and developmental delay that were not detected in the patients in this thesis. The ALL cohort study on genetic variation of mitochondrial DNA (mtDNA) included 36 children. Metabolic change where malignant cells uncouple energy production from oxidative phosphorylation (OXPHOS) is one of the established hallmarks of cancer. In the cohort in this study, 22% of patients harbored nonsynonymous variants on mtDNA in the protein-coding genes of OXPHOS enzyme complexes. The somatic non-neutral variants were found in patients with a poor prognosis cytogenetic marker. The results support the hypothesis that cancer cells harbor mtDNA variants that may affect the cell metabolism
Tiivistelmä Akuutti lymfoblastileukemia (ALL) on lasten yleisin syöpä. Vaikka nykyisin noin 90 prosenttia paranee, ALL aiheuttaa huomattavan paljon sairastavuutta ja on merkittävä lasten kuolinsyy. Vastikään on löydetty perinnöllisiä geneettisiä muutoksia, jotka altistavat lapsuusiän ALL:lle. Tutkimuksen kohteena oli kaksi perhettä, joissa vähintään kaksi lasta on sairastunut ALL:aan. Ensimmäisessä perheessä havaittiin lapsuusiän ALL:aan sairastuneilla kehityshäiriöisillä sisaruksilla äidiltä periytyvä heterotsygoottinen deleetio kromosomissa 7p12.1p13, jossa sijaitsee IKZF1-geeni. Toisessa perheessä perinnöllinen kahden kromosomin translokaatio todettiin kahdella lapsuusiän ALL:aan sairastuneella sekä seitsemällä perheenjäsenellä. Balansoitu translokaatio t(12;14)(p13.2;q23.1) aiheuttaa katkaisukohdan ETV6-geeniin kromosomissa 12 ja RTN1-geeniin kromosomissa 14. Tähän mennessä on julkaistu vain muutamia tutkimuksia potilaista, joilla on ollut perinnöllinen muutos joko IKZF1- tai ETV6-geenissä. Näillä geeneillä oletetaan olevan tärkeä merkitys perinnöllisessä alttiudessa sairastua lapsuusiän ALL:aan. Perinnölliset luuytimen toimintahäiriöt voivat altistaa leukemialle, kuten ALL:lle. Kahdella lapsella todettiin luuytimen toimintahäiriö, mutta ei muita oireita, jotka voisivat liittyä tyypillisiin perinnöllisiin luuytimen toimintahäiriöihin. Eksomisekvensoinnissa todettiin identtinen, homotsygoottinen mutaatio c.1457del(p.(Ile486fs)) ERCC6L2-geenissä. Kirjallisuuslähteiden mukaan vain muutamalla potilaalla on todettu ERCC6L2-geenin muutoksesta johtuva luuytimen toimintahäiriö. Osalla heistä on ollut synnynnäisiä kallon ja kasvojen anomalioita sekä kehityshäiriö, jollaisia tähän tutkimukseen osallistuneilla potilailla ei todettu. Potilaskohorttitutkimuksessa tutkittiin mitokondriaalisen DNA:n (mtDNA) muutoksia ALL:aan sairastuneilla lapsilla. Syöpäsolut eivät hyödynnä mitokondrion elektroninsiirtoketjua energian tuotantoon, ja tämä aineenvaihdunnan muutos on tunnustettu syövän ominaisuus. Tutkimuksessa havaittiin, että 22 prosentilla potilaista ilmeni diagnoosivaiheessa poikkeavia mtDNA:n muutoksia, jotka olivat elektroninsiirtoketjun entsyymien alayksiköitä koodaavissa geeneissä. Muutoksia todettiin useimmiten potilailla, joilla oli leukemiasoluissa huonon ennusteen geneettinen tekijä. Havaitut muutokset voivat mahdollisesti vaikuttaa leukemiasolun energia-aineenvaihduntaan

Although the understanding of genetic predisposition to prostate cancer (PCa) has been improved through genome-wide association studies (GWAS), little is known about the biological implication of germline variants residing in coding or non-coding regions in cancer development and progression. Our hypothesis is that inherited variants may predispose to specific early recurrent genomic events observed in PCa adenocarcinomas, possibly in the context of variable androgen receptor (AR) signaling that changes during a man’s lifetime. Recent in silico analysis by our group on potential association between germline variants and PCa specific somatic lesions identified a non-coding polymorphic regulatory element at the 7p14.3 locus associated with DNA repair and hormone regulated transcript levels and with an early recurrent prostate cancer specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene (OR=5.54, P=1.22e-08) in human prostate tissue data. In order to functionally characterize the polymorphic 7p14.3 locus (rs1376350, single nucleotide polymorphism, G>A), we set up to establish isogenic cell lines harboring the minor allele by using the CRISPR/Cas9 system. In parallel, CRISPR/Cas9 system was used to knock out different portion of the region encompassing the 7p14.3 variant and to eliminate transcription factors (TFs) binding sites that were identified from previous in silico analysis (i.e. AR and CCAAT/Enhancer Binding Protein (C/EBP) beta (CEBPβ)). The transcriptomes of edited pools and edited single clones from macrodeletion (731 bp), microdeletion (50 bp) and alterations of TFs binding sites were analyzed and compared to the transcriptomes of isogenic cells heterozygous (A/G) and homozygous (A/A) for the minor allele A of the risk variant rs1376350 (with or without AR overexpression). These data identified a set of genes scattered throughout the genome with the same pattern of deregulation suggesting the implication of the variant on the regulation of genes residing in different chromosomes. Additionally, ChIP-qPCR experiments for histone modification supported the identification of the 7p14.3 locus with enhancer activity. Furthermore, ChIP-qPCR of histone mark associated with transcriptional activation or repression in isogenic cells harboring the minor allele A upon AR overexpression showed that the activity of the locus is higher for the minor allele A compared to G, independently from AR activation. Despite the limitations of our model and the current lack of validation in other cells, we confirmed that some of the differentially expressed genes that emerged from the comparative analysis of edited cells are deregulated in human normal and tumor prostate samples as well. This work is a proof of concept of germline predisposition to molecularly distinct cancer subclasses and has the potential to nominate new mechanisms of cancer development. Future work aims to elucidate the mechanisms implicated in the deregulation of the transcriptome by combining the information obtained until now with potential new players that we expect to identify by Mass Spectrometry experiments. To clarify the link between the 7p14.3 variant and the somatic mutations in SPOP, we plan to express mutant SPOP in isogenic cells harboring the minor allele and to asses DNA damage response upon overexpression or silencing of TFs binding at and around the rs1376350 variant. My work is an example of how the CRISPR/Cas9 system can be used to develop a technical framework with convergent approaches to functionally characterize polymorphic regulatory regions including but not limited to the establishment of isogenic cells upon single nucleotide editing.

Si le syndrome de prédisposition héréditaire au cancer du sein et de l’ovaire constitue uneentité reconnue et supportée par l’identification de variations délétères sur les gènes BRCA1,BRCA2, PALB2, RAD51C et RAD51D, et si le cancer du sein de la femme jeune (avant 31 ans) estintégré dans le spectre du syndrome de Li-Fraumeni lié aux altérations de TP53, une large fractiondes patientes adressées en consultation d’oncogénétique pour ce motif demeure orpheline dediagnostic moléculaire. La connaissance du génome humain et l’avènement du séquençage denouvelle génération ont permis des avancées considérables, notamment dans l’observation de latrès grande variabilité du génome et de la survenue de variations de novo.Nous avons ainsi appliqué ces outils et ces concepts au cancer du sein de la femmejeune, afin de tenter d’identifier de nouveaux déterminants moléculaires constitutionnels. Dansune première approche basée sur la réalisation d’exomes soustractifs pour des trios parents- enfant, nous avons recherché des variants de novo délétères et effectivement identifié un variantrare de novo et délétère sur le gène INHBA dans le contexte d’un cancer de l’ovaire chez unejeune femme. Cette approche n’a cependant pu être reproduite dans le contexte d’un cancer dusein précoce. Nous avons également tenté une approche par exomes comparatifs dans unefamille remarquable avec survenue de cancers du sein précoces sur trois générations, sansvariation délétère identifiée commune à ces individus. Dans une seconde approche basée surun panel de 201 gènes impliqués dans la cancérogenèse, nous avons tenté d’identifier desvariants délétères ou des enrichissements en variants rares dans une cohorte de cancers du seinprécoces. Nous avons identifié une variation en mosaïque de TP53, sans autre détection devariations formellement délétères parmi 30 patientes atteintes de cancers du sein avant 31 ans.Un enrichissement non significatif en variants rares affectant les voies de la réparation de l’ADN aété néanmoins mis en évidence, suggérant des études plus larges ciblant ces voies. Enfin, nousavons recherché spécifiquement des variants de novo en mosaïque de TP53 dans lecontexte du cancer du sein de la femme jeune ou de cancers pédiatriques, et démontré ainsi laprévalence relativement importante de ces évènements. Ces observations supportent la nécessitéd’user d’un séquençage de forte profondeur et de ne pas restreindre les indications d’analyses deTP53 aux seules situations familiales évocatrices
Despite previous identifications of deleterious variants on BRCA1, BRCA2, PALB2,RAD51C and RAD51D supporting the hereditary breast and ovarian cancer syndrom, and thecontribution of TP53 mutations in very early-onset breast carcinomas, a large fraction of patientssuggestive of Medelian disease remains without molecular diagnosis. In the past years,sequencing of the Human genome and next-generation sequencing offered major advances, inparticular in the field of genome variability and de novo variants.We applied these new tools and concepts in the context of very early-onset breastcarcinomas, in order to identify new molecular germline determinants. First, we dealt withsoustractive exomes, in parents - child trios, and succeed in the identification of a deleterious denovo variant in the INHBA gene, in the context of very early-onset of ovarian cancer. However, wehave failed with this approach in a second trio with an index affected by early-onset breastcarcinoma. We also tried a comparative exome sequencing approach in a remarkable pedigreewith multiple probands affected by early-onset breast carcinomas, without identification of ashared deleterious variant. Secondly, we used a home-made 201 genes panel assuming thatgenes somatically affected in cancers might be altered in inherited conditions. We analyzed acohort of very early-onset breast carcinomas, and identified a mosaic TP53 variation. Moreover,we identified some interesting candidate variants and observed a non-significant trend of rarevariants enrichment in the DNA repair pathway. Finally, we designed a specific TP53 gene capturein order to detect mosaic variants in pediatric cancers and very early-onset breast carcinomas.We confirmed the clinically significant prevalence of these alterations, which support TP53analysis in these conditions even in sporadic presentations

Les cancers de l'ovaire et du sein sont définis par les principales voies impliquées dans la tumorigénèse. Dans les cancers héréditaires du sein/ovaire (HBOC), les tumeurs présentant des variants pathogènes (PV) de BRCA1/2 présentent une altération de la réparation de l'ADN par recombinaison homologue (RH). Des années après la découverte des gènes BRCA1/2, les PV ont été uniquement recherchés sur l'ADN constitutionnel. Aujourd’hui, cette information est également recherchée au niveau tumoral car en plus de leur utilité pour améliorer le conseil génétique, elle est aussi impliquée dans le choix thérapeutique. Cependant, les données recueillies indiquent que les PV inactivant la protéine ne seraient pas l’unique mécanisme d’inactivation de la voie de réparation de l’ADN par RH. Dans ce contexte, l'objectif principal de cette thèse est d'identifier des mécanismes alternatifs d'inactivation de la voie HR pour améliorer à la fois: le conseil génétique et la prise en charge thérapeutique. À cette fin, nous avons tenté de contribuer à la classification de variants non-codants et faux-sens (autre que provoquant un stop prématuré) de BRCA1/2 et également recherché de nouveaux biomarqueurs de réponse thérapeutique dans d’autres gènes de la voie de HR.Nous avons décrit des variants constitutionnels dans des régions potentiellement importantes de régulation des gènes BRCA1 et BRCA2, et démontré qu'une partie d'entre eux étaient fonctionnellement actifs à mettre en lien avec la pathogénicité. Nous avons également exploré les caractéristiques moléculaires des tumeurs du sein et de l'ovaire des porteurs des variants BRCA1 et observé une prédominance de la perte de l'allèle sauvage pour les tumeurs des porteurs de variants pathogènes. Etant donné ces résultats, nous proposons d’intégrer les informations de LOH dans le modèle multifactoriel de classification des variants BRCA1. Enfin, nous avons mis en évidence des mécanismes alternatifs d'inactivation de la voie RH, dans une cohorte de patientes avec un cancer de l'ovaire présentant une excellente réponse aux platines, y compris des mutations constitutionnelles et somatiques des gènes BRCA1/2, l'hyperméthylation du promoteur BRCA1 ainsi que des mutations dans d'autres gènes de la voie RH
Ovarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 pathogenic variants (PV) present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 PV were only searched on germline DNA. Currently, this information is also searched at tumor level to personalize treatment. Even so, the reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of HR deficient signature.Gathered evidence indicates that protein inactivating PV may not be the only mechanism of HR dysfunction. In this context, the main objective of this thesis is to identify alternative mechanisms of HR inactivation to improve both: genetic counseling and therapeutic response. For this purpose, we have attempted to contribute to non-coding and missense (other than premature stop codon) BRCA1/2 variant classification and searched for new biomarkers of therapeutic response to DNA damage agents in other HR genes.We identified germline variants in key transcriptional regulatory elements of BRCA1 and BRCA2, and demonstrated that part of them were functionally active and had additional arguments suggesting pathogenicity. We also explored molecular features of breast and ovarian tumors from BRCA1 variant carriers and observed a predominance of loss of the wild-type allele. Conforming to this evidence, we propose to incorporate LOH information, into the multifactorial model for BRCA1 variant classification. Finally, besides the enrichment of BRCA1/2 germline and somatic PV, we described alternative mechanisms of HR inactivation in a OC population presenting optimal response to platinum-based chemotherapy, including BRCA1 promoter hypermethylation and also mutations in other genes of HR pathway

In dieser Arbeit wurde die Affinitätsreifung des murinen anti-c-myc-Peptid-Antikörpers 9E10 analysiert. Hierfür wurden Fab-Fragmente mit Keimbahnrückmutationen gentechnisch hergestellt und in ihrem Bindungsverhalten zum humanen c-myc-Peptid charakterisiert. Das von 9E10 erkannte Epitop besitzt die Aminosäuresequenz EQKLISEEDLLRKR mit den darin sehr selektiv erkannten Schlüsselpositionen LISEXXL.Der 3300-fache Affinitätsgewinn während der 9E10-Reifung kommt sowohl durch eine Zunahme der Assoziations- als auch durch eine Abnahme der Dissoziationsgeschwindigkeit des Komplexes zustande. Der Affinitätsgewinn resultiert weniger aus zusätzlichen Kontakten des Antikörpers zum Peptid, sondern vor allem aus der Beeinflussung der Konformation und/oder der Flexibilität der an der Bindung beteiligten CDRs. Die außergewöhnlich lange CDR-H3 liefert einen wesentlichen Beitrag zur Affinitätsreifung. Die variable leichte Domäne dient dabei mit der langen CDR-L1 und -L3 als eine Bindungsplattform für die flexible CDR-H3. Änderungen in der Spezifität von 9E10 sind vorrangig auf die Reifung der variablen schweren Domäne zurückzuführen. Dabei ist die selektive Erkennung der Schlüsselpositionen im Peptid im Anfangsstadium der Affinitätsreifung von 9E10 stark ausgeprägt.
In this work the affinity maturation of the murine anti c-myc-peptide antibody 9E10 was analysed. Therefore Fab fragments with reversed mutations directed towards germline genes were genetically produced and characterised for their binding to the human c-myc peptide. The epitope recognized by 9E10 consists of the amino acid sequence EQKLISEEDLLRKR of which the key positions LISEXXL are very selectively recognized. The maturation of 9E10 leads to a 3300-fold higher affinity, which is achieved by a faster association as well as by a slower dissociation of the complex. For the gain in affinity formation of additional contacts to the peptide is less important than conformational and/or flexibility changes of the CDRs which are involved in binding. The exceptionally long CDR-H3 contributes essentially to the affinity maturation. The variable light domain serves thereby with its long CDR-L1 and -L3 as a binding platform for the flexible CDR-H3. Changes in specificity of 9E10 are primarily due to maturation of the variable heavy domain. Selective recognition of the key positions in the peptide is already highly pronounced in the initial stage of affinity maturation of 9E10.

Master’s degree in Biotechnology for Health Sciences
O cancro colorretal (CRC) representa a quarta causa de morte relacionada com o cancro no mundo. Sendo causada por diversos fatores de risco como a dieta, história familiar, doenças inflamatórias, o cancro colorretal é influenciado por alterações em genes importantes para a função celular. A linfotoxina alfa (LTA) pertence à superfamília do fator de necrose tumoral. Esta citocina é expressa pelos linfócitos T e B, células dendríticas e linfócitos NK. LTA pode ligar-se ao recetor linfotoxina-beta e aos recetores fator de necrose tumoral. Após a ligação aos seus recetores nas células no microambiente tumoral, a proteína LTA pode regular a apoptose, proliferação, sobrevivência e a diferenciação. No cancro, a sua influência ainda não está bem explicada. Foram realizados alguns estudos, contudo os resultados não são conclusivos. A LTA pode estar associada com atividade anti-tumoral tendo efeitos citotóxicos nas células de cancro pelo recrutamento de células NK para a lesão. Contudo, outros estudos têm revelado que LTA pode promover o crescimento celular e a adesão das células de cancro. Desta forma, os objetivos deste estudo foram caracterizar e analisar se os genótipos do polimorfismo funcional rs1041981 do LTA, particularmente a sobrevivência global e a sobrevivência livre de progressão em pacientes com cancro colorretal e avaliar os macrófagos e linfócitos T em tecidos CRC, por imunohistoquímica, e a sua associação com os dados dos genótipos. Para realizar o estudo, foram recolhidas amostras sanguíneas em 172 pacientes sobreviventes com CRC no departamento de Oncologia, Centro Hospitalar de Trás-os-Montes e Alto Douro (CHTMAD) pelos clínicos. As amostras foram transportadas para o departamento de Genética e Biotecnologia na UTAD, para separação em soro, plasma e buffy coat. Foi otimizado um protocolo de extração de DNA, e foi realizado PCR em tempo-real para descriminação alélica usando sondas Taqman e subsequente confirmação por sequenciação de um amplicão específico. O alelo C e o alelo A apresentaram, respetivamente, frequências alélicas de 70 % e 30 %. As frequências genotípicas do CC, CA e AA foram 49%, 42% e 9%, respetivamente. Considerando os parâmetros clinico-patológicos e a associação com os dados genéticos, foi possível colocar em evidência que as variáveis que influenciam a sobrevivência dos pacientes com CRC nesta população foram a percentagem de linfócitos no sangue, a localização e o lado do tumor, terapia adjuvante e o genótipo CA/AA pelo modelo dominante. O alelo A parece ter um efeito protetor para os pacientes com cancro colorretal nesta população para o endpoints primário e secundário, respetivamente a sobrevivência global e a sobrevivência livre de progressão. Os pacientes com a asparagina na proteína LTA parecem ter um melhor prognóstico que os pacientes com a treonina na proteína LTA na mesma posição. Os resultados para a possível associação entre TAMs e TILs no cancro colorretal e a variante LTA rs1041981 revelaram diferenças significativas no rácio TILs/TAMs entre os indivíduos CC e CA no estudo. Este gene, como demostrado neste trabalho, parece ter uma importante função no cancro colorretal. A compreensão do impacto deste polimorfismo na evolução da doença pode trazer novas informações na regulação do microambiente tumoral.
The colorectal cancer (CRC) represents the fourth cause of cancer death in the world. Being caused by several risk factors as diet, family history, inflammatory diseases, the colorectal cancer can be influenced by alterations in important genes to cell function. Lymphotoxin alpha (LTA) belongs to tumor necrosis factor superfamily. This cytokine is expressed by T and B lymphocytes, dendritic cells and NK lymphocytes. LTA can bind to lymphotoxin-beta receptor and tumor necrosis factor receptors. After binding to its receptors in tumor microenvironment cells, LTA protein can regulate apoptosis, proliferation, survival and differentiation. In cancer, its influence is not well explained. Some studies were already performed; however, the results are not conclusive. The LTA may be associated with anti-tumor activity having cytotoxic effects on cancer cells by recruitment of NK cells to lesion. However, other studies have revealed that LTA can promote the cell growth and adhesion of cancer cells. Thus, the objectives of this study were to characterize and analyze whether genotype of LTA functional polymorphism rs1041981 influences clinicopathological parameters, particularly overall and progression-free survival in colorectal cancer patients and evaluate the macrophage and T lymphocytes in the CRC tissues, by immunohistochemistry, and its association with genotype data. To perform the study, blood samples of 172 survivor patients with CRC were collected in the Department of Oncology, Centro Hospitalar de Trás-os-Montes e Alto Douro (CHTMAD) by clinical researchers. The samples were transported to the Department of Genetics and Biotechnology at UTAD, to separate in serum, plasma and buffy coat. A DNA extraction protocol was optimized, and the allele discrimination was performed by real time-PCR using Taqman probes and subsequent confirmation by sequencing of a specific LTA amplicon. The C and A alleles presented, respectively, allelic frequency of 70 % 30 %. CC, CA and AA genotypic frequencies were 49%, 42% and 9%, respectively. Considering the clinicopathological parameters and the association with the genetic data, it was possible to put in evidence that the variables that influence the survival of CRC patients under study were blood lymphocytes percentage, tumor side and localization, adjuvant chemotherapy and the genotype CA/AA, by a dominant model. The A allele appears to be a protective factor for patients with colorectal cancer in this population for primary and secondary endpoints, respectively overall survival and progression-free survival. The patients with asparagine in LTA protein appear to have a better prognosis than patients that have the threonine in the same position. The results of possible association between TAMs and TILs in colorectal tumors and rs1041981 LTA variant revealed statistical differences in TILs/TAMs ratio between CC and CA individuals under study. This gene, as evidenced in this work, appears to have an important role in colorectal cancer. The understanding of the impact of this polymorphism on the evolution of the disease can bring new information on tumor microenvironment regulation.

Cancer often develops from specific DNA alterations, and these cancer-associated mutations influence precision cancer treatment. These alterations can be specific to the tumor DNA (somatic mutations) or they can be heritable and present in normal and tumor DNA (germline mutations). Germline variants can affect how patients respond to therapy and can influence clinical surveillance of patients and their families. While identifying cancer-associated germline variants traditionally required studying families with inherited cancer predispositions, large-scale cancer sequencing cohorts enable alternative analysis of germline variants. In this dissertation, we develop and apply multiple strategies for analyzing germline DNA from cancer sequencing cohorts. First, we develop the Tumor-Only Boosting Identification framework (TOBI) to learn biological features of true somatic mutations and generate a classification model that identifies DNA variants with somatic characteristics. TOBI has high sensitivity in identifying true somatic variants across several cancer types, particularly in known driver genes. After predicting somatic variants with TOBI, we assess the identified somatic-like germline variants for known oncogenic germline variants and enrichment in biological pathways. We find germline and somatic variants inactivating the Fanconi anemia pathway in 11% of patients with bladder cancer. Finally, we investigate germline, diagnosis, and relapse variants in a large cohort of patients with pediatric acute lymphoblastic leukemia (ALL). Our somatic analysis captures known ALL driver genes, and we describe the sequential order of diagnosis and relapse mutations, including late events in NT5C2. We apply both the TOBI framework and guidelines American College of Medical Genetics and Genomics to identify potentially cancer-associated germline variants, and nominate nonsynonymous variants in TERT and ATM.

Familial colorectal cancer type X (FCCTX) defines families that fulfill the Amsterdam criteria without evidence of defects in the DNA mismatch repair (MMR) genes and whose tumors do not present microsatellite instability. However, its genetic etiology remains unknown, therefore this study aimed to identify and evaluate novel variants and candidate genes that may play a role in FCCTX susceptibility. Based on a previous whole exome sequencing (WES) study in a FCCTX family, a bioinformatic analysis and a subsequent in silico and segregation studies were conducted to identify candidate genes and/or specific variants that may predispose for this syndrome. Since this analysis was already started, variants in 6 genes have already been identified to segregate with the disease. Therefore, the aim of this project was to continue this work by completing the selection of candidate variants and to characterize and try to clarify the role of these variants for FCCTX susceptibility. In order to elucidate the possible contribution of the corresponding genes for FCCTX, a mutational analysis was performed to search for germline mutations in index patients from FCCTX and FCCTX-like families. In addition, using the WES data, a copy number variation (CNV) analysis was also performed for the family subjected to WES, followed by a bioinformatic and in silico analysis to reveal amplicon deletions that may segregate with disease. It was also evaluated the involvement of the TPP2 gene, previously identified as a possible candidate gene for FCCTX in another family, in healthy and affected FCCTX patients, by mutational/splicing analysis, relative quantification by quantitative PCR and protein truncation test to assess resulting truncating proteins. The bioinformatic followed by in silico and segregation analysis of the variants obtained from WES, revealed 1 variant in the CACNA1S gene that segregated with the disease. Adding this variant to the already obtained, a total of 7 variants in different genes were found as possible contributors to FCCTX in this family. The segregation analysis also revealed the segregation of the previously identified MTMR3 and TAS1R1 variants in a patient from an older generation of the family. The CNV analysis revealed, after selective criteria, 22 amplicons of interest with a deletion scenario, for further segregation studies. The germline mutational analysis in a set of FCCTX and FCCTX-like families uncovered 2 and 3 potentially pathogenic variants for the MTMR3 and TAS1R1 genes, respectively. One of the variants found in MTMR3 was the same found in the WES analysis. Thus far no relevant variants were observed for LGR6 and DUSP12, however this analysis is not completed. The TPP2 study revealed the presence of non-described splicing isoforms. One of these isoforms exhibited a differential expression between healthy and affected individuals and the protein truncation test revealed that this alternative transcript gives rise to a truncated protein. In conclusion, the identification of more than one genetic variant appears to agree with the suggestion that FCCTX is a heterogeneous entity and the discovery of potentially pathogenic variants in MTMR3 and TAS1R1 reinforce their possible involvement in FCCTX. The alternative TPP2 transcript appears to be involved in the earlier stages of colorectal carcinogenesis
O cancro do cólon e reto familiar do tipo X (FCCTX) define as famílias que preenchem os critérios de Amesterdão nas quais não é identificada mutação germinal nos genes de reparação de erros de DNA do tipo mismatch (MMR) e cujos tumores não apresentam instabilidade de microssatélites. Sendo a sua causa molecular desconhecida. Assim, o presente estudo teve como objetivo identificar e avaliar novas variantes e genes candidatos que possam estar envolvidos na suscetibilidade para o FCCTX. Com base num estudo prévio de whole exome sequencing (WES), realizado numa família FCCTX, foi efetuada uma análise bioinformática e in silico e um subsequente estudo de segregação, de modo a identificar genes candidatos e/ou variantes específicas que possam predispor para esta condição hereditária. Uma vez que esta análise já tinha sido iniciada, 6 variantes em diferentes genes, que segregaram com a doença, já tinham sido identificadas. Assim, o objetivo deste trabalho consistiu na continuação deste estudo, completando a seleção das variantes candidatas, e na caracterização e clarificação destas variantes para a suscetibilidade para o FCCTX. De modo a elucidar a possível contribuição destes genes para o FCCTX, foi realizada uma análise mutacional em indivíduos index de famílias FCCTX e potenciais famílias FCCTX. Adicionalmente, utilizando os resultados da WES, foi também realizada uma análise de copy number variantion (CNV) para a família integrada na análise de WES, seguida de uma análise bioinformática e estudos in silico de modo a avaliar a presença de deleções de amplicons que pudessem segregar com a doença. O envolvimento de transcritos alternativos do gene TPP2, previamente identificado como um possível gene candidato para o FCCTX noutra família, foi também avaliado em indivíduos saudáveis e afetados por análise mutacional/splicing, quantificação relativa por PCR quantitativo e teste da proteína truncada, para avaliar a existência de proteínas truncantes. A análise bioinformática seguida pela análise in silico e segregação das variantes obtidas por WES revelou a segregação com a doença de uma variante no gene CACNA1S. Tendo em conta as variantes já obtidas, foram identificadas 7 variantes em diferentes genes como possíveis intervenientes na suscetibilidade para o FCCTX nesta família. A análise de segregação revelou ainda a segregação das variantes dos genes MTMR3 e TAS1R1 num individuo proveniente de uma geração anterior. A análise de CNV revelou, após a introdução de critérios seletivos, 22 amplicons de interesse com um cenário de deleção, para estudos de segregação adicionais. A análise de mutações germinais num conjunto de famílias FCCTX e potenciais famílias FCCTX revelou 2 e 3 variantes potencialmente patogênicas para os genes MTMR3 e TAS1R1, respetivamente. Uma das variantes encontradas no gene MTMR3 correspondeu à variante encontrada no estudo de WES. Não foram observadas até ao momento variantes relevantes para os genes LGR6 e DUSP12, porém esta análise não está completa. O estudo do gene TPP2 revelou a presença de isoformas não descritas. Uma destas isoformas apresentou uma expressão diferencial entre o transcrito normal e o alternativo em indivíduos saudáveis e afetados e, o teste da proteína truncada revelou que este transcrito alternativo dá origem a uma proteína truncada. Em conclusão, a identificação de mais de uma variante genética parece concordar com a sugestão de que o FCCTX é uma entidade heterogénea, e a descoberta de variantes potencialmente patogénicas nos genes MTMR3 e TAS1R1 reforçam seu possível envolvimento no FCCTX. O transcrito alternativo do gene TPP2 parece estar envolvido numa fase inicial da carcinogénese colorretal.

VASA ist ein DEAD-Box-Protein, das in der Keimbahn vorkommt und dem eine essentielle Rolle in der Entstehung und Erhaltung von Keimzellen zugeschrieben wird (Yajima und Wessel 2011a). VASA wurde in jedem bisher untersuchten Organismus in der Keimbahn gefunden (Raz 2000) und ist, da es in Säugetieren als keimzellspezifisch gilt (Castrillon et al. 2000), einer der derzeit meist genutzten Keimzellmarker. Allerdings zeigen neuere Daten aus unkonventionellen Modellorganismen sowie aus Drosophila, dass VASA in diesen Organismen, zusätzlich zu seinen Funktionen in der Keimbahn, noch weitere Funktionen außerhalb der Keimbahn übernimmt. Bisher existieren allerdings keine vergleichbaren Daten, die die Keimzellspezifität von VASA in Säugetieren widerlegen, weshalb VASA hier weiter-hin als spezifischer Keimzellmarker gilt (Alié et al. 2011). Vorarbeiten von Selma Drallé, die in der Arbeitsgruppe von Prof. Dr. rer. nat. R. Behr durchgeführt wurden, ergaben jedoch Hinweise auf eine VASA-Expression in somatischen Zellen des Weißbüschelaffen. In Weiterführung dieser Untersuchungen wurde in der vorliegenden Arbeit eine systematische Expressionsanalyse von VASA in unterschiedlichen Organen des adulten und neugeborenen Weißbüschelaffen durchgeführt. Die Arbeitshypothese hierbei war, dass VASA im Weischbüschelaffen nicht keimzellspezifisch exprimiert wird. Die Untersuchungen erfolgten mittels immunhistochemischer Färbungen, Western Blotting sowie PCR, wobei aufgrund präliminarer Hinweise jeweils Niere, Magen, Leber, Haut und Pankreas des neugeborenen und des adulten Weißbüschelaffen detailliert auf eine VASA-Expression untersucht wurden. Ovar und Hoden adulter Weißbüschelaffen dienten als Positivkontrollen. Die Ergebnisse dieser Arbeit deuten stark auf eine Expression von VASA in der Haut des neugeborenen Weißbüschelaffen hin. Dieser Befund legt nahe, das VASA im neugeborenen Weißbüschel-affen nicht keimzellspezifisch ist und über seine Funktionen in der Keimbahn hinaus noch weitere extragonadale Funktionen innehaben könnte. In den weiteren untersuchten Organen wurde keine VASA-Expression festgestellt; einzelne Befunde, die auf eine VASA-Expression hinwiesen, erwiesen sich als falsch-positiv. In dieser Arbeit wurde zudem eine für C. jacchus noch nicht in der Literatur beschriebene Splice-Variante von VASA im Ovar und im Hoden vom adulten Weißbüschelaffen gefunden, der das Exon 7 fehlt und die zudem modifizierte N- und/oder C-Termini aufweisen könnte. Die vorliegenden Ergebnisse weisen darauf hin, dass VASA im Weißbüschelaffen auch außerhalb der Keimbahn exprimiert wird und somit in dieser Spezies kein spezifischer Keim-zellmarker ist. Um diese Frage jedoch abschließend zu klären, sollten sich weitere Untersuchungen anschließen, um die in dieser Arbeit gezeigten Befunde zu untermauern.