Thesis (Ph. D.)--Ohio State University, 2007. / Full text release at OhioLINK's ETD Center delayed at author's request

Diss. (sammanfattning) Linköping : Linköpings universitet, 2007. / Härtill 4 uppsatser.

O carcinoma diferenciado de tireóide (CDT) abrange 95% de todas as doenças malignas da tireóide. Nos EUA, aumentou em 2,4 vezes nos últimos anos (1973-2002). O seu tratamento inclui tireoidectomia total, seguido por terapia com radioiodo e supressão do TSH com L-tiroxina. A doença pode recidivar em ~20% dos casos, sendo necessária avaliação periódica através de exames de imagens e dosagem de tireoglobulina sérica (TGs). Os Anticorpos (Acs) anti-TG podem ser detectados em 15 a 25% dos pacientes, comprometendo, parcialmente, o uso da TGs como marcador de recidiva do câncer. Um método alternativo proposto para monitorar os pacientes é a detecção de células tireoidianas em sangue periférico, através da mensuração do RNA mensageiro de TG (RNAm-TG) pela técnica de RTPCR em tempo real. Esta nova metodologia aumenta a sensibilidade da detecção desta molécula. O objetivo deste estudo é verificar a significância da quantificação do RNAm-TG, como método diagnóstico complementar no acompanhamento a longo prazo de pacientes com CDT. Amostras de sangue de 45 pacientes (25 sem metástase, 14 com metástase ganglionar e 6 com metástase à distância) foram coletadas nos tempos: antes e 24, 48, 72 horas, 7 dias, 1, 3, 6, 9 meses, 1, 2, 4, 5, 6 e 7 anos após a dose ablativa de radioiodo. Foi realizada extensiva padronização da técnica com a finalidade de excluir interferências metodológicas, empregando dois genes controles interno (GAPDH e HPRT1) para o cálculo da concentração do RNAm-TG. Concomitantemente foi realizada a mensuração de TGs, perfil hormonal e de anticorpos anti-TG. A pesquisa de corpo inteiro, realizada 7 dias após a dose terapêutica, estabeleceu o estadio clínico inicial dos pacientes. Não foi possível estabelecer um valor de corte para o RNAm-TG. O RNAm-TG não diferenciou os estadios clínicos da doença ao longo do tempo, independente do gene controle interno utilizado, e tampouco quando analisaram-se os dados na presença de Acs anti-TG e TSH30ng/mL. A TGs diferenciou os estadios clínicos ao longo do tempo. Concluiu-se que, o RNAm-TG não é um bom marcador de recidiva do CDT, mesmo quando considerou-se critérios de padronização da técnica, avaliação em longo prazo e presença de Acs anti-TG, sendo assim não poderia ser utilizado como método diagnóstico complementar no acompanhamento de pacientes com CDT. Este estudo demonstra que a técnica de RT-PCR em tempo real é muito sensível perdendo especificidade, inviabilizando sua utilização no acompanhamento dos pacientes com CDT / The differentiated thyroid carcinoma (DTC) encloses 95% of all thyroid malignant disease. In USA, it increased 2,4 times in recent years (1973- 2002). The treatment includes total thyroidectomy, ablation with radioiodine (RAI) followed by TSH suppression with L-Thyroxine. The cancer recurrence occurs in 20% of the cases. Periodic evaluation through imaging examinations and serum thyroglobulin (TG) measurements by imunoassays method is recommended for careful follow-up of these patients. The anti-TG antibodies prevalence is 15-25% and would impair, partially, the serum TG use as a tumor marker. An alternative method to identify the recurrence of the tumor is the thyroid cells detection in peripheral blood, through the TG messenger RNA quantification (mRNA-TG) by real time RT-PCR. This new methodology increases the sensitivity detection for this molecule. The objective of this study was to verify the mRNA-TG peripheral blood quantification significance, as a complementary diagnostic method in the long term follow up of patients with DTC. Fourty five blood samples from patients with DTC have been collected before and 24, 48, 72 hours, 7 days, 1, 3, 6, 9 months, 1, 2, 4, 5, 6 and 7 years after the ablation therapy. Extensive technique standardization for mRNA-TG measurements was carried out to exclude methodological interventions and two housekeeping genes (GAPDH and HPRT1) were used to calculate the mRNA-TG concentrations. Concomitantly, serum TG measurements, hormonal profile and antibodies anti-TG assays were performed. The whole body scan was performed 7 days after RAI ablation to determine the stage of the disease. It was not possible to establish a cut-point value for mRNA-TG. The mRNA-TG did not differentiated the clinical stage of the disease in the long term follow-up and neither in the presence of anti-TG antibodies and TSH30ng/mL. Serum TG was able to differentiate the clinical stage of the patients during the follow-up. In conclusion mRNA-TG is not a good marker for the DCT recurrence, even when technical standardization, long term evaluation and the presence of antibodies anti-TG were considered. Thus it could not be used as a complementary diagnostic method in the DTC patients follow-up. This study confirmed the high sensivity of the real time RT-PCR whereas with very low specificity, consequently is unviable to be used in the DTC patients follow-up

INTRODUÇÃO: As proteínas desacopladoras de prótons (UCPs: uncoupling proteins) pertencem à família dos transportadores mitocondriais H+/ácidos graxos e têm distribuição diferenciada nos tecidos. Sabe-se que a UCP1 é responsável pela termogênese, mas o exato papel fisiológico da UCP2 e UCP3 ainda não está completamente estabelecido. Os hormônios tireoideanos (T3 e T4) estimulam a expressão da UCP3 em músculo cardíaco e esquelético, no entanto o mecanismo pelo qual exercem esse efeito não é conhecido. Este projeto visa avaliar se as alterações na expressão gênica da UCP3 são relacionadas a efeito primário do T3 ou são secundárias à estimulação do sistema renina-angiotensina ou do sistema ?-adrenérgico. MÉTODOS: Para a realização do estudo, criou-se um modelo animal de hipertireodismo, em ratos machos Sprague-Dawley, através da 3 administrações de 100 ?g/100 g peso corpóreo de LT3, em dias alternados, associado ou não à captopril (1 mg/100 g de peso corpóreo), ?-bloqueador propranolol (1 mg/100g de peso corpóreo) ou ?2-agonista clenbuterol (0,04 mg/100 g de peso corpóreo). A expressão do mRNA da UCP3 foi semi-quantitativamente determinada por Northern blot em amostras de músculo ventricular cardíaco e músculo esquelético (gastrocnemius e soleus). A expressão da proteína UCP3 foi avaliada por Western blot em músculo esquelético (quadríceps). Os resultados foram expressos em unidades arbitrárias de densitometria óptica. RESULTADOS: O tratamento com LT3 resultou em aumento estatisticamente significativo do conteúdo de mRNA da UCP3 em miocárdio (~3 vezes) e músculo esquelético (~8 vezes) (p<0,05) e esse efeito não foi alterado por nenhuma das medicações usadas concomitantemente. Não houve efeito sinergístico ou aditivo sobre a expressão do mRNA da UCP3 quando o LT3 foi administrado conjuntamente ao ?2-agonista. O aumento na quantidade de mRNA da UCP3, em músculo esquelético, foi associado à aumento na expressão da proteína UCP3. CONCLUSÃO: O efeito do LT3 sobre a expressão da UCP3, nos tecidos analisados, não são dependentes da angiotensina II, nem do sistema ?-adrenérgico, provavelmente refletindo uma ação direta do LT3 sobre a expressão do gene UCP3 / Thyroid hormones (T3 and T4) stimulate UCP-3 expression in skeletal muscle. Here, we examined whether thyroid hormone-induced changes in UCP-3 mRNA expression are related to directs effects of T3 or reflect secondary effects of the hormone through stimulation of renin-angiotensin or ?-adrenergic systems. Hyperthyroidism was produced by three injections of 100 ?g T3/100 g body weight on alternate days with or without concomitant treatment with either captopril (an ACE inhibitor), propranolol (a ?-blocker) or clenbuterol (a ?2-agonist). The relative abundance of UCP-3 mRNA was measured in ventricular myocardium and skeletal muscle (gastrocnemius and soleus). T3 resulted in a significant increase in the relative abundance of UCP-3 in heart and skeletal muscle (P < 0.05), and the effect was not altered by captopril or propanolol; the inhibitors alone had no effect of UCP-3 mRNA content. There was no synergistic or additive effect of T3 and clenbuterol on UCP-3 mRNA expression in skeletal muscle. Increased UCP-3 mRNA levels were associated with increased UCP-3 protein expression in skeletal muscle. We conclude that the effect of T3 on UCP-3 expression in cardiac and skeletal muscle is not dependent on either angiotensin II or the ?-adrenergic system and probably reflects a direct action of the hormone on UCP-3 gene expression

O transplante cardíaco é a última opção terapêutica para pacientes portadores de insuficiência cardíaca grave. Apesar dos avanços na terapia imunossupressora, a rejeição continua sendo o principal obstáculo para o sucesso do transplante. No presente estudo, propõe-se avaliar o perfil de expressão gênica no tecido cardíaco. Com isso, espera-se contribuir para o melhor entendimento do processo de rejeição a nível molecular. Foram analisadas as amostras sequenciais (1, 3 e 6 meses, 1 e 2 anos pós-transplante) de biópsias endomiocárdicas em parafina de 63 indivíduos transplantados cardíacos. O diagnóstico de rejeição humoral foi realizado pela detecção de C3d e C4d do complemento na reação de imuno-histoquímica, e as expressões dos genes protetores (ADIPOR1, ADIPOR2, HMOXO-1, BCL2L1 e VEGF) e genes associados à inflamação (IL-6, TNF?, IFN?, TGF-?, AIF-1, NOS2, ICAM, VCAM e MCP-1); foram avaliadas pela reação em cadeia da polimerase quantitativa em tempo real (qPCR). As frequências de indivíduos positivos para C4d (28,6%) e vasculite (20,0%) foram significantemente maiores em relação ao teste de reatividade de anticorpos realizado nos receptores antes do transplante (6,3%). Houve mudança no perfil de expressão gênica no tecido cardíaco após o transplante, com aumento da expressão dos genes inflamatórios (AIF-1, TNF?, IL-6, NOS2 e VCAM) e diminuição da expressão dos genes protetores (ADIPOR1, ADIPOR2, BCL2L1 e VEGF). Além disso, as expressões dos genes ADIPOR1 e ADIPOR2 foram significantemente menores nos indivíduos positivos para C4d (p<0,001) e gene VEGF (p<0,001) no grupo com vasculite. Houve também uma correlação positiva entre a expressão do gene VEGF e ADIPOR1 (r=0,5688) e ADIPOR2 (r=0,5191). Por outro lado, a expressão aumentada do gene VCAM (p<0,001) foi detectada em todos os tipos de rejeição. Conclui-se que, depois do transplante, o sistema imune do receptor passou a reconhecer os antígenos do órgão transplantado. Com isso, ocorreu uma mudança no perfil de expressão gênica no enxerto cardíaco, caracterizada pela expressão aumentada dos genes inflamatórios e diminuição dos genes protetores. A expressão aumentada do gene VCAM associada à baixa expressão dos genes protetores: ADIPOR1, ADIPOR2, BCL2L1 e VEGF resultaram em maior gravidade da rejeição celular, humoral e vasculopatia do aloenxerto cardíaco. / Heart transplantation is the ultimate treatment for patients with severe heart failure. Despite advances in immunosuppressive therapy, rejection still remains the main obstacle to successful transplant. The purpose of this study is to evaluate the gene expression profile in cardiac tissue. With this we hope to contribute to a better understanding of the rejection process at the molecular level. Sequential samples (1, 3, and 6 months, 1 to 2 years post-transplant) endomyocardial biopsies paraffin of 63 heart transplant subjects were analyzed. The diagnosis of humoral rejection was performed by detection of C3d and C4d complement in immunohistochemistry and the expression of protective genes (ADIPOR1, ADIPOR2, HMOXO-1, and VEGF BCL2L1) and genes associated with inflammation (IL-6,TNF?, IFN?, TGF-?, AIF-1, NOS2, ICAM, VCAM and MCP-1); were evaluated by quantitative real-time polymerase chain reaction (qPCR). The frequency of individuals positive for C4d (28.6%) and vasculitis (20.0%) were significantly higher compared to antibodies reactivity test conducted in the recipients before transplantation (6.3%). There was a change in the gene expression profile in cardiac tissue after transplantation, with increased expression of inflammatory genes (AIF-1,TNF?, IL-6, NOS2, and VCAM) and a decreased expression of protective genes (ADIPOR1, ADIPOR2, BCL2L1, and VEGF). Furthermore, the expressions of ADIPOR1 and ADIPOR2 genes were significantly lower in C4d positive individuals (p<0,001), and VEGF (p<0,001) in the group with vasculitis. There was also a positive correlation between VEGF expression and ADIPOR1 (r=0.5688) and DIPOR2 (r=0.5191). Moreover, increased expression of VCAM (p<0,001) was detected in all types of rejection. We conclude that, after transplantation, the recipient\'s immune system began to recognize the antigens of the transplanted organ. Thus, a change in gene expression profile in cardiac graft is characterized by increased inflammatory genes and decreased expression of protective genes. Increased VCAM gene associated with lower expression of protective genes expression: ADIPOR1, ADIPOR2, BCL2L1 and VEGF resulted in increased severity of cellular and humoral rejection and cardiac allograft vasculopathy.

During each life cycle, gametes must preserve and pass on both genetic and epigenetic information, making the germline both immortal and totipotent. In the male germline the dramatic morphological transformation of a germ cell through meiosis, into a sperm competent for fertilization, while retaining this information is an incredible example of cellular differentiation. This process of spermatogenesis is inherently thermosensitive in numerous metazoa ranging from worms to man. Here, I describe the role of two redundant AGO-class paralogs, ALG-3/4, and their small RNA cofactors, in promoting thermotolerant male fertility in Caenorhabditis elegans. alg-3/4 double mutants exhibit temperature dependent sterility resulting from defective spermiogenesis, the postmeiotic differentiation of haploid spermatids into spermatozoa competent for fertilization. The essential Argonaute CSR-1 functions with ALG-3/4 to positively regulate target genes required for spermiogenesis by promoting transcription via a small RNA positive feedback loop. Our findings suggest that ALG-3/4 functions during spermatogenesis to amplify a small-RNA signal loaded into CSR-1 to maintain transcriptionally active chromatin at genes required for spermiogenesis and to provide an epigenetic memory of male-specific gene expression. CSR-1, which is abundant in mature sperm, appears to transmit this memory to offspring. Surprisingly, in addition to small RNAs targeting male-specific genes, we show that males also harbor an extensive repertoire of CSR-1 small RNAs targeting oogenesis-specific mRNAs. The ALG-3/4 small RNA pathway also initiates silencing small RNA signals loaded into WAGO vii Argonautes, which function to posttranscripitonally silence their target mRNAs. Silencing WAGO/small RNA-complexes are present in sperm and presumably transmitted to offspring upon fertilization. Together these findings suggest that C. elegans sperm transmit not only the genome but also epigenetic activating and silencing signals in the form of Argonaute/small-RNA complexes, constituting a memory of gene expression in preceding generations.

Nonsense-mediated mRNA decay (NMD) specifically targets mRNAs with premature translation termination codons for rapid degradation. NMD is a highly conserved translation-dependent mRNA decay pathway, and its core Upf factors are thought to be recruited to prematurely terminating mRNP complexes, possibly through the release factors that orchestrate translation termination. Upf1 is the central regulator of NMD and recent studies have challenged the notion that this protein is specifically targeted to aberrant, nonsense-containing mRNAs. Rather, it has been proposed that Upf1 binds to most mRNAs in a translation-independent manner. In this thesis, I investigated the nature of Upf1 association with its substrates in the yeast Saccharomyces cerevisiae. Using biochemical and genetic approaches, the basis for Upf1 interaction with ribosomes was evaluated to determine the specificity of Upf1 association with ribosomes, and the extent to which such binding is dependent on prior association of Upf1’s interacting partners. I discovered that Upf1 is specifically associated with Rps26 of the 40S ribosomal subunit, and that this association requires the N-terminal Upf1 CH domain. In addition, using selective ribosome profiling, I investigated when during translation Upf1 associates with ribosomes and showed that Upf1 binding was not limited to polyribosomes that were engaged in translating NMD substrate mRNAs. Rather, Upf1 associated with translating ribosomes on most mRNAs, binding preferentially as ribosomes approached the 3’ ends of open reading frames. Collectively, these studies provide new mechanistic insights into NMD and the dynamics of Upf1 during translation.

Eukaryotic genomes can produce two types of transcripts: protein-coding and non-coding RNAs (ncRNAs). Cryptic ncRNA transcripts are bona fide RNA Pol II products that originate from bidirectional promoters, yet they are degraded by the RNA exosome. Such pervasive transcription is prevalent across eukaryotes, yet its regulation and function is poorly understood. We hypothesized that chromatin architecture at cryptic promoters may regulate ncRNA transcription. Nucleosomes that flank promoters are highly enriched in two histone marks: H3-K56Ac and the variant H2A.Z, which make nucleosomes highly dynamic. These histone modifications are present at a majority of promoters and their stereotypic pattern is conserved from yeast to mammals, suggesting their evolutionary importance. Although required for inducing a handful of genes, their contribution to steady-state transcription has remained elusive. In this work, we set out to understand if dynamic nucleosomes regulate cryptic transcription and how this is coordinated with the RNA exosome. Remarkably, we find that H3-K56Ac promotes RNA polymerase II occupancy at a large number of protein coding and noncoding loci, yet neither histone mark has a significant impact on steady state mRNA levels in budding yeast. Instead, broad effects of H3-K56Ac or H2A.Z on levels of both coding and ncRNAs are only revealed in the absence of the nuclear RNA exosome. We show that H2A.Z functions with H3-K56Ac in chromosome folding, facilitating formation of Chromosomal Interaction Domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA levels, perhaps in part by regulating higher order chromatin structures. Together, these chromatin factors achieve a balance of RNA exosome activity (yin; negative) and Pol II (yang; positive) to maintain transcriptional homeostasis.

Small RNAs are single-stranded, 18–36 nucleotide RNAs that can be categorized as miRNA, siRNA, and piRNA. miRNA are expressed ubiquitously in tissues and at particular developmental stages. They fine-tune gene expression by regulating the stability and translation of mRNAs. piRNAs are mainly expressed in the animal gonads and their major function is repressing transposable elements to ensure the faithful transfer of genetic information from generation to generation. My thesis research focused on the biogenesis of miRNAs and piRNAs using both experimental and computational strategies. The biogenesis of miRNAs involves sequential processing of their precursors by the RNase III enzymes Drosha and Dicer to generate miRNA/miRNA* duplexes, which are subsequently loaded into Argonaute proteins to form the RNA-induced silencing complex (RISC). We discovered that, after assembled into Ago1, more than a quarter of Drosophila miRNAs undergo 3′ end trimming by the 3′-to-5′ exoribonuclease Nibbler. Such trimming occurs after removal of the miRNA* strand from pre-RISC and may be the final step in RISC assembly, ultimately enhancing target messenger RNA repression. Moreover, by developing a specialized Burrow-Wheeler Transform based short reads aligner, we discovered that in the absence of Nibbler a subgroup of miRNAs undergoes increased tailing—non-templated nucleotide addition to their 3′ ends, which are usually associated with miRNA degradation. Therefore, the 3′ trimming by Nibbler might increase miRNA stability by protecting them from degradation. In Drosophila germ line, piRNAs associate with three PIWI-clade Argonaute proteins, Piwi, Aub, and Ago3. piRNAs bound by Aub and Ago3 are generated by reciprocal cleavages of sense and antisense transposon transcripts (a.k.a., the “Ping-Pong” cycle), which amplifies piRNA abundance and degrades transposon transcripts in the cytoplasm. On the other hand, Piwi and its associated piRNA repress the transcription of transposons in the nucleus. We discovered that Aub- and Ago3-mediated transposon RNA cleavage not only generates piRNAs bound to each other, but also produces substrates for the endonuclease Zucchini, which processively cleaves those substrates in a periodicity of ~26 nt and generates piRNAs that predominantly load into Piwi. Without Aub or Ago3, the abundance of Piwi-bound piRNAs drops and transcriptional silencing is compromised. Our discovery revises the current model of piRNA biogenesis.

Chemerin is a chemoattractant adipokine that regulates adipogenesis and may induce insulin resistance. Chemerin serum concentrations are elevated in obese, insulin-resistant, and inflammatory states in vivo. Here we investigate the role of omental (OM) and subcutaneous (SC) adipose tissue chemerin and CMKLR1 messenger RNA (mRNA) expression in human obesity. In addition, we test the hypothesis that changes in chemerin serum concentrations are primarily associated with reduced body fat mass in the context of 3 weight loss intervention studies. Chemerin serum concentration was measured in 740 individuals in a cross-sectional (n = 629) study including a subgroup (n = 161) for which OM and SC chemerin mRNA expression has been analyzed as well as in 3 interventions including 12 weeks of exercise (n = 60), 6 months of calorie-restricted diet (n = 19) studies, and 12 months after bariatric surgery (n = 32). Chemerin mRNA is significantly higher expressed in adipose tissue of patients with type 2 diabetes mellitus and correlates with circulating chemerin, body mass index (BMI), percentage body fat, C-reactive protein, homeostasis model assessment of insulin resistance, and glucose infusion rate in euglycemic-hyperinsulinemic clamps. CMKLR1 mRNA expression was not significantly different between the 2 fat depots. Obesity surgery–induced weight loss causes a significant reduction on both OM and SC chemerin expression. All interventions led to significantly reduced chemerin serum concentrations. Decreased chemerin serum concentrations significantly correlate with improved glucose infusion rate and reduced C-reactive protein levels independently of changes in BMI. Insulin resistance and inflammation are BMI-independent predictors of elevated chemerin serum concentrations. Reduced chemerin expression and serum concentration may contribute to improved insulin sensitivity and subclinical inflammation beyond significant weight loss.