Yes / Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes, catalyzing 5-methylcytosine oxidation in DNA. Here, by using Keratin 14–Cre–driven ablation of Tet genes in skin epithelial cells, we demonstrate that ablation of Tet2/Tet3 results in marked alterations of hair shape and length followed by hair loss. We show that, through DNA demethylation, Tet2/Tet3 control chromatin accessibility and Dlx3 binding and promoter activity of the Krt25 and Krt28 genes regulating hair shape, as well as regulate interactions between the Krt28 gene promoter and distal enhancer. Moreover, Tet2/Tet3 also control three-dimensional chromatin topology in Keratin type I/II gene loci via DNA methylation–independent mechanisms. These data demonstrate the essential roles for Tet2/3 in establishment of lineage-specific gene expression program and control of Dlx3/Krt25/Krt28 axis in hair follicle epithelial cells and implicate modulation of DNA methylation as a novel approach for hair growth control. / This work was supported by the National Institutes of Health grant 5R01 AR075776 (V.A.B. and A.A.S.) and grant 5R01 AR071727 (V.A.B. and A.A.S.) and the National Science Foundation of China (G.-L.X.). / Research Development Fund Publication Prize Award winner, Dec 2022.

No description available.

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.

No description available.

[ES] Los síndromes mielodisplásicos (SMD) constituyen un grupo heterogéneo de enfermedades de naturaleza clonal caracterizadas por presentar una hematopoyesis ineficaz, citopenias y riesgo variable de evolución a leucemia mieloide aguda (LMA) secundaria. En la última década, las nuevas tecnologías de secuenciación masiva han revelado que más del 80 % de pacientes con SMD presenta mutaciones somáticas y que éstas pueden agruparse en diversas categorías en función de las rutas biológicas que se vean alteradas. Además, se ha visto que existen patrones de concurrencia y exclusión entre estas categorías de mutaciones. La adquisición secuencial y la concurrencia entre estas mutaciones desencadenan, en parte, el desarrollo de la enfermedad y genera la heterogeneidad clínica característica de los SMD. Las mutaciones en factores de splicing aparecen a menudo simultáneamente con mutaciones en reguladores epigenéticos como es el caso de los genes U2 Small Nuclear RNA Auxiliary Factor 1 (U2AF1) y Ten-eleven translocation 2 (TET2) que se encuentran co-mutados en un 13 % de los casos. A pesar de su prevalencia, los efectos de la concurrencia en las mutaciones en U2AF1 y TET2 no han sido estudiados. Por ello, en esta tesis nos propusimos estudiar esta cooperación cruzando, en primer lugar, dos líneas mutantes de ratón generadas mediante el sistema de edición genética CRISPR/Cas9. El efecto de estas alteraciones sobre la hematopoyesis de las tres líneas mutantes, U2af1mut/+, Tet2-/- y U2af1mut/+ Tet2-/-, fue examinado mediante el hemograma, citometría de flujo (CF), análisis morfológicos, ensayos de Unidades Formadoras de Colonias (CFU) y estudios funcionales como el trasplante hematopoyético. Para finalizar, se realizó un análisis transcriptómico mediante secuenciación de ARN (ARN-seq) para detectar los posibles cambios en el patrón de splicing entre las líneas mutantes y los controles. La línea mutante U2af1mut/+ no presentó ninguna alteración destacable de la hematopoyesis ni en ratones jóvenes (12-13 semanas) ni envejecidos (2 años). Sin embargo, sus células madre y progenitoras hematopoyéticas (HSPC) fueron incapaces de injertar en la médula ósea de ratones trasplantados. En el caso de los ratones mutantes Tet2-/-, observamos un incremento de células mieloides, esplenomegalia, aumento del compartimento LSK (HSPC con inmunofenotipo Linaje- Sca-1+ c-kit+) y, en los experimentos de trasplante, una capacidad de reconstitución hematopoyética superior a la de los controles. Por último, la cooperación de ambas alteraciones en la línea doble mutante U2af1mut/+ Tet2-/-, no mostró un efecto sinérgico entre ellas. Así pues, se detectaron variaciones en los progenitores mieloeritroides y un aumento significativo de células mieloides y LSK. No obstante, igual que ocurría con la línea U2af1mut/+, las HSPC no producían prendimiento en los ratones trasplantados. A pesar de las alteraciones observadas, ninguna de las tres líneas mutantes desarrollaba SMD ni fallecía antes que los controles. Respecto al análisis transcriptómico, el salto de exón fue el evento de splicing alternativo observado con mayor frecuencia en las líneas U2af1mut/+, Tet2-/- y U2af1mut/+ Tet2-/-. Únicamente un 6.6 % del total de genes que presentaba eventos de splicing alternativo fueron coincidentes en las tres líneas mutantes. A pesar de que en el análisis bioinformático se detectaron alteraciones en las rutas biológicas relacionadas con el ciclo celular, en los ratones U2af1mut/+, y el daño al ADN, en las líneas U2af1mut/+ y U2af1mut/+ Tet2-/-, en la validación mediante CF no se encontraron variaciones respecto a los controles. Para concluir, nuestros datos sugieren que, a pesar de producirse alteraciones en la hematopoyesis, la cooperación entre la mutación en U2af1 y la pérdida de Tet2 es insuficiente para iniciar SMD en ratón. / [CA] Les síndromes mielodisplàstiques (SMD) constituïxen un grup heterogeni de malalties de naturalesa clonal caracteritzades per presentar una hematopoesi ineficaç, citopènies i risc variable d'evolució a leucèmia mieloide aguda (LMA) secundària. En l'última dècada, les noves tecnologies de seqüenciació massiva han revelat que més del 80 % de pacients amb SMD presenta mutacions somàtiques i que aquestes poden agrupar-se en diverses categories en funció de les rutes biològiques que es vegen alterades. A més, s'ha vist que hi ha patrons de concurrència i exclusió entre aquestes categories de mutacions. L'adquisició seqüencial i la concurrència entre aquestes mutacions desencadenen, en part, el desenvolupament de la malaltia i genera l'heterogeneïtat clínica característica de les SMD. Les mutacions en factors de splicing apareixen sovint simultàniament amb mutacions en reguladors epigenètics com és el cas dels gens U2 Small Nuclear RNA Auxiliary Factor 1 (U2AF1) i Ten-eleven translocation 2 (TET2) que es troben co-mutats en un 13 % dels casos. A pesar de la seua prevalença, els efectes de la concurrència en les mutacions en U2AF1 i TET2 no han sigut estudiats. Per això, en aquesta tesi ens vam proposar estudiar aquesta cooperació creuant, en primer lloc, dos línies mutants de ratolí generades per mitjà del sistema d'edició genètica CRISPR/Cas9. L'efecte d'aquestes alteracions sobre l'hematopoesi de les tres línies mutants, U2af1mut/+, Tet2-/- i U2af1mut/+ Tet2-/-, va ser examinat per mitjà de l'hemograma, citometría de flux (CF), anàlisis morfològiques, assajos d'Unitats Formadores de Colònies (CFU) i estudis funcionals com el trasplantament hematopoètic. Per últim, es va realitzar l'anàlisi transcriptòmic per mitjà de seqüenciació d'ARN (ARN-seq) per a detectar els possibles canvis en el patró de splicing entre les línies mutants i els controls. La línia mutant U2af1mut/+ no va presentar cap alteració destacable de l'hematopoesi ni en ratolins jóvens (12-13 setmanes) ni envellits (2 anys). No obstant això, les seues cèl·lules mare i progenitores hematopoetiques (HSPC) van ser incapaços d'empeltar en la medul·la òssia de ratolins trasplantats. En el cas dels ratolins mutants Tet2-/-, observarem un increment de cèl·lules mieloides, esplenomegàlia, augment del compartiment LSK (cèl·lules mare amb inmunofenotip Llinatge- Sca-1+ c-kit+) i, en els experiments de trasplantament, una capacitat de reconstitució hematopoética superior a la dels controls. Finalment, la cooperació d'ambdues alteracions en la línia doble mutant U2af1mut/+ Tet2-/-, no va mostrar un efecte sinèrgic entre elles. Així, doncs, es van detectar variacions en els progenitors mieloeritroids i un augment significatiu de cèl·lules mieloides i LSK. No obstant això, igual que ocorria amb la línia U2af1mut/+, les HSPC no produïen empelt en els ratolins trasplantats. A pesar de les alteracions observades, cap de les tres línies mutants desenvolupava SMD ni moria abans que els controls. Respecte a l'anàlisi transcriptòmic, el salt d'exó va ser l'esdeveniment de splicing alternatiu observat amb major freqüència en les línies U2af1mut/+, Tet2-/- i U2af1mut/+ Tet2-/-. Únicament un 6.6 % del total de gens que presentava esdeveniments de splicing alternatiu van ser coincidents en les tres línies mutants. Encara que en l'anàlisi bioinformàtica es van detectar alteracions en les rutes biològiques relacionades amb el cicle cel·lular, en els ratolins U2af1mut/+, i el dany a l'ADN, en les línies U2af1mut/+ i U2af1mut/+ Tet2-/-, en la validació per mitjà de CF no es van trobar variacions respecte als controls. Per a concloure, les nostres dades suggerixen que, a pesar de produir-se alteracions en l'hematopoesi, la cooperació entre la mutació en U2af1 i la pèrdua de Tet2 és insuficient per a iniciar SMD en ratolí. / [EN] Myelodysplastic syndromes (MDS) comprise a heterogeneous group of clonal malignancies characterized by ineffective hematopoiesis, cytopenia and a variable risk of progression to secondary acute myeloid leukemia (AML). In the last decade, next-generation sequencing technologies have deciphered that more than 80 % of MDS patients have somatic mutations and that those can be grouped into several categories depending on which biological routes have been altered. Furthermore, it has been observed that there are concurrency and exclusion patterns among these mutation categories. The sequential acquisition and the concurrency between these driver mutations trigger, in part, the development of the disease and generate the clinical heterogeneity characteristic of MDS. The splicing factor mutations often occur simultaneously with mutations in epigenetic regulators such as the U2 Small Nuclear RNA Auxiliary Factor 1 (U2AF1) and Ten-eleven translocation 2 (TET2) genes, which are found co-mutated in 13 % of cases. Despite their prevalence, the effects of concurrence in mutations in U2AF1 and TET2 have not been studied. Consequently, in this thesis we aim to study this cooperation. Firstly, we crossed two mutant mouse lines that were previously generated using the CRISPR/Cas9 gene editing system. The effects of these alterations on hematopoiesis in the three mutant lines, U2af1mut/+, Tet2-/- y U2af1mut/+ Tet2-/-, was examinated by the blood counts, flow cytometry (FC), morphological analysis, Colony Forming Units assays (CFU) and functional studies such as the hematopoietic transplantation. Finally, transcriptomic analysis was peformed by RNA sequencing (RNA-seq) to detect possible splicing pattern changes between mutant lines and control samples. U2af1mut/+ mutant line did not present any remarkable alteration of hematopoiesis in either in young (12-13 weeks) or aged (2 years) mice. However, their hematopoietic stem and progenitor cells (HSPC) were unable to engraft into the bone marrow of transplanted mice. In the case of Tet2-/- mutant mice, we observed an increase of myeloid cells, splenomegaly, an increased LSK compartment (HSPC: Lineage- Sca-1+ c-kit+) and an enhanced ability, relative to wild-type, to reconstitute hematopoiesis in transplantation assays. Finally, the cooperation of both alterations in U2af1mut/+ Tet2-/- double mutant line did not show a synergistic effect between them. Nonetheless, the myeloerythroid progenitors were altered and also myeloid and LSK cells were increased. However, as in the U2af1mut/+ line, HSPC did not produce any engraftment in transplanted mice. Despite the observed alterations, none of the three mutant lines developed MDS or die earlier than control mice. Regarding the transcriptomic analysis, exon skipping was the most frequently observed alternative splicing event in the U2af1mut/+, Tet2-/- y U2af1mut/+ Tet2-/- lines. Only 6.6 % of the total number of genes showing alternative splicing events were coincident in the three mutant lines. Although the bioinformatic analysis revealed alterations in biological pathways related to the cell cycle in the U2af1mut/+ mice and DNA damage in the U2af1mut/+ and U2af1mut/+ Tet2-/- lines, the validation by CF found no variations with respect to the controls. In conclusion, our data suggest that, despite alterations in hematopoiesis, the cooperation between U2af1 mutation and Tet2 loss is insufficient to initiate MDS in mice. / Martínez Valiente, C. (2022). Desarrollo y caracterización de un modelo de ratón doble mutante en U2af1 y Tet2 para el estudio de los Síndromes Mielodisplásicos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/187749

Increasing evidence implicates the presence of bacteria in intrauterine tissues as an important risk factor for spontaneous preterm labor. Epigenetic alterations of innate immunity genes may increase the mother’s sensitivity to subclinical levels of bacteria. This study examined the presence of TET2, TLR-2, and TLR-9 in intrauterine tissue, and evaluated whether epigenetic alterations of these genes, as well as IL-8, changed their expression in human decidual tissue and a macrophage cell culture. Immunohistochemicalstaining was used to detect the presence of these proteins in intrauterine tissue. Gene expression changes were evaluated in stimulated monocytes and macrophages. Fluorescence immunohistochemistry was used to track translocation of TET2 in stimulated monocytes and macrophages. Secreted IL-8 concentration was detected with ELISA. Decidual expression of TET2, TLR-2, and TLR-9 increased in the order TNL < TL < sPTL < iPTL. This study found that TET2, TLR-2, TLR-9, and IL-8 are regulated by epigenetic mechanisms. This study was the first to report activation of TET2 involves its translocation from the cytosol to the nucleus in macrophages.

This dissertation details the use of computational methods to understand the effect that cancer-related mutations have on proteins that complex with nucleic acids. Firstly, we perform molecular dynamics (MD) simulations of various mutations in DNA polymerase κ (pol κ). Through an experimental collaboration, we classify the mutations as more or less active than the wild type complex, depending upon the incoming nucleotide triphosphate. From these classifications we use quantum mechanics/molecular mechanics (QM/MM) to explore the reaction mechanism. Preliminary analysis points to a novel method for nucleotide addition in pol κ. Secondly, we study the ten-eleven translocation 2 (TET2) enzyme in various contexts. We find that the identities of both the substrate and complementary strands (or lack thereof) are crucial for maintaining the complex structure. Separately, we find that point mutations within the protein can affect structural features throughout the complex, only at distal sites, or only within the active site. The mutation's position within the complex alone is not indicative of its impact. Thirdly, we share a new method that combines direct coupling analysis and MD to predict potential rescue mutations using poly(ADP-ribose) polymerase 1 as a model enzyme. Fourthly, we perform MD simulations of mutations in the protection of telomeres 1 (POT1) enzyme. The investigated variants modify the POT1-ssDNA complex dynamics and protein—DNA interactions. Fifthly, we investigate the incorporation of remdesivir and other nucleotide analogue prodrugs into the protein-RNA complex of severe acute respiratory syndrome-coronavirus 2 RNA-dependent RNA polymerase. We find evidence for destabilization throughout the complex and differences in inter-subunit communication for most of the incorporation patterns studied. Finally, we share a method for determining a minimum active region for QM/MM simulations. The method is validated using 4-oxalocrotonate, TET2, and DNA polymerase λ as test cases.

Les cellules souches hématopoïétiques (CSH) assurent une production constante des cellules sanguines tout au long de la vie, mais sont vulnérables à l’acquisition de mutations pouvant mener à une transformation maligne. Les mutations qui confèrent un avantage de croissance entraîneront une prolifération clonale. L’étude de la clonalité est centrale à la compréhension de ces phénomènes. Historiquement, l’analyse de la clonalité a été possible grâce au principe de l’inactivation du chromosome X (ICX) chez les femmes qui entraîne la création de deux populations cellulaires, celle avec le X-paternel actif et celle avec le X-maternel actif. Une déviation (biais) de la proportion théorique de 1 :1 entre ces deux populations peut supposer une dominance clonale. Nous avons démontré un biais significatif de l’ICX chez les femmes avec l’âge. Ce phénomène peut être expliqué par plusieurs causes dont la sélection hémizygote (un des deux X possède des allèles plus forts que l’autre) et l’acquisition de mutations dans une CSH. Nous posons l’hypothèse que ces deux phénomènes coexistent et peuvent être distingués par une approche génomique. Nous avons recruté une cohorte de 2996 femmes canadiennes-françaises âgées entre 37 et 101 ans composée de 2172 individus issus de 321 familles et de 824 individus non apparentés. Deux tissus biologiques ont été recueillis : le sang périphérique (PMN, monocytes, lymphocytes T, lymphocytes B) et des cellules buccales. Le ratio de l’ICX a été déterminé par la méthode HUMARA, l’analyse de gènes associés à l’hématopoïèse clonale (19 gènes) a été faite par la méthode de séquençage NGS, et la cohorte a été génotypée à 700 625 loci polymorphiques de l’ADN (SNP). Des analyses bioinformatiques ont été - iv - appliquées pour étudier la contribution génétique au biais de l’ICX. Nous démontrons que : (i) le biais de l’ICX est plus prévalent dans les cellules sanguines par rapport aux cellules épithéliales et maximal dans les cellules myéloïdes; (ii) le biais augmente avec l’âge seulement dans les cellules sanguines et que cette influence est plus marquée pour les neutrophiles; (iii) la concordance du biais est très importante pour les différents types cellulaires sanguins, suggérant un mécanisme opérant au niveau de la CSH ; (iv) il y a une composante héréditaire liée au biais de l’ICX; (v) la présence de mutations acquises (TET2, DNMT3A, etc.) explique seulement une partie du biais ; (vi) à l’aide d’analyses par liaison génétique la présence d’une région sur le chromosome X à Xq21 (LOD score 4.9) qui est associée au biais des lymphocytes T et une autre sur le chromosome 1 à 1q21 (LOD score 6) qui est associée au biais des neutrophiles. Nous avons départagé la contribution liée à l’acquisition de mutations somatiques et identifié pour la première fois des régions liées à une prédisposition génétique. Nos travaux se poursuivront d’une part par l’analyse de gènes candidats dans les régions identifiées, et d’autre part nous tenterons d’identifier les cibles génétiques qui confèrent un potentiel de transformation maligne en utilisant une approche basée sur l’analyse du méthylome, de l’hydroxyméthylome et du transcriptome que nous venons de valider. Notre étude démontre la complexité de l’adaptation de l’hématopoïèse au vieillissement et ouvre des portes sur l’identification de facteurs prédisposant aux cancers hématologiques. / Hematopoietic stem cells (HSC) ensure a constant lifelong production of blood cells, but are vulnerable to acquisition of mutations, which may lead to malignant transformation. Mutations that confer a growth advantage will lead to clonal derivation of cells. The study of clonality is central to the understanding of hematopoiesis adaptation to aging. Historically, the first clonality assays were based on the principle of X-chromosome inactivation (XCI) in women. Women are mosaics with half the cells with the paternal X active and the other half with the maternal one. A skewing from the theoretical 1:1 ratio between these two populations of cells could infer clonal derivation of cells. More than 20 years ago, our team demonstrated, through analysis of (XCI) in women, that skewing increases with age. This intriguing phenomenon can be explained by several etiology including hemizygous selection (one of the 2 Xs has stronger alleles) or the acquisition of mutations giving a growth advantage. The first etiology is genetically predetermined and the second, acquired in somatic cells of bone marrow. We hypothesize that these two phenomena coexist and can be distinguished with a genomic approach. To test our hypothesis, we investigated skewing in a cohort of 2996 French-Canadian women aged 37 to 101 comprised of 2172 related individuals from 321 families and 824 unrelated individuals. We analyzed XCI ratios at the HUMARA locus in epithelial cells, neutrophils, T-cells, monocytes, B-lymphocytes. We genotyped the cohort for clonal hematopoiesis and looked for germline heritable components by genome wide association studies and linkage analyses. We document that skewing was more prevalent in blood cells than in epithelial cells, and maximal in myeloid cells. Skewing increases with age only in blood cells. Intra- vi - individual correlation of skewing blood cell types was strongly correlated, suggesting selection influences operating at the HSC. Sibship analyses demonstrated heritability which was strongest when parental origin of skewing was taken into account. Clonal hematopoiesis accounted only for a small proportion of the skewing trait but its importance increased in the very old. Linkage analysis identified a region at Xq21 for skewing occurring in T-cells (LOD score 4.9) suggesting a hemizygous cell selection influence. We also identified a region at 1q21 for skewing in neutrophils (LOD score 6) suggesting a gene-gene interaction with Xlinked genes. We have demonstrated that age-associated skewing is a complex trait caused in part by acquired mutations and genetic predisposition variants. We will pursue our investigation using a candidate gene approach in the two identified regions and will try to identify genetic targets of oncogenic potential by a method based on analysis of the methylome, hydroxymethylome and transcriptome that was have validated in this cohort. This thesis demonstrates the complexity of the adaptation mechanisms of hematopoiesis to aging and set the stage to identification of factors predisposing to hematological cancers.