京都大学 / 新制・課程博士 / 博士(医学) / 甲第23772号 / 医博第4818号 / 新制||医||1056(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 村川 泰裕, 教授 松田 文彦, 教授 篠原 隆司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No presente estudo investigou-se amostras de plasma com DNA livre circulante (DNA LC) por meio da técnica Varredura Z. Esta é uma técnica eficiente na determinação de parâmetros de diferentes materiais, tais como cristais líquidos, ferrofluidos e compostos biológicos. Esta experiência é realizada através da focalização de um feixe laser de perfil gaussiano numa amostra. Na medida em que a amostra se aproxima do foco da lente, a intensidade do feixe aumenta e alcança seu valor máximo no ponto focal, então diminui para pontos distantes do foco. Na região próxima ao ponto focal se amplificam os fenômenos não-lineares. Recentemente foi demonstrado que níveis elevados de DNA LC no plasma ocorrem com frequência em pacientes com vários tipos de câncer, podendo ser utilizados para discriminar pacientes com malignidade de pessoas saudáveis. As amostras de DNA LC, submetidas ao experimento Varredura Z, forneceram respostas ópticas devido ao fenômeno de lente térmica. Os resultados revelaram que a amplitude de lente térmica das amostras extraídas do plasma de pacientes com malignidade difere daquela de doadores sãos. A técnica Varredura Z se mostrou mais vantajosa em relação a outras biológicas porque revelou uma maior diferença entre os grupos estudados e tem o caráter de detectar mudanças estruturais no DNA LC. / In the present study plasma samples with cell-free DNA were investigated by means of the Z-Scan technique. This is a powerfull technique in determining parameters of different materials, such as liquid crystals, ferrofluids and biological compounds. This experiment is performed by focusing a Gaussian profile laser beam on a sample. As the sample approaches the focus of the lens, the intensity of the beam increases and reaches its maximum value at the focal point, then decreases to points distant from the focus. In the region near the focal point non-linear phenomena are amplified. It has recently been demonstrated that high levels of plasma cell-free DNA occur frequently in patients with various cancers and can be used to discriminate patients with malignancy from healthy donors. The cell-free DNA samples, submitted to the Z-Scan experiment, provided optical responses due to the thermal lens phenomenon. The results revealed that the thermal lens amplitude of samples extracted from the plasma of patients with malignancy differs from that of healthy donors. The Z-Scan technique was more advantageous than other biological ones because it revealed a greater difference between the studied groups and has the character of detecting structural changes in cell-free DNA.

Au cours de ces dernières années, l’utilisation des acides nucléiques circulants comme outils diagnostiques et/ou pronostiques en cancérologie a largement été documentée. Récemment, le développement du diagnostic prénatal non-invasif a également révélé l’intérêt grandissant de ces biomarqueurs en gynécologie-obstétrique. Les acides nucléiques circulants ou extracellulaires ont la particularité d’être facilement détectables dans les fluides biologiques de l’organisme et sont de deux types: (1) l’ADN libre, courts ou longs fragments d’ADN provenant des processus apoptotiques et/ou nécrotiques cellulaires (2) les microARNs, petites séquences d’ARN non codantes, qui régulent l’expression des gènes en interférant avec leurs ARNm cibles. Sachant qu’il a été démontré que le taux d’ADN libre circulant est anormalement élevé dans certaines conditions pathologiques et que les microARNs sont impliqués dans la régulation de nombreux processus biologiques tels que la folliculogénèse et la stéroïdogénèse, ces deux types d’acides nucléiques pourraient alors constituer des biomarqueurs d’intérêt dans le domaine de l’Assistance Médicale à la Procréation. Dans ce travail de thèse, nous avons à la fois mesuré le taux d’ADN libre et analysé les profils d’expression de plusieurs microARNs d’intérêt par PCR quantitative, dans le liquide folliculaire (LF) de patientes prises en charge en fécondation in vitro (FIV). Nous avons observé des taux d’ADN libre significativement élevés ainsi que des profils d’expression de microARNs spécifiques dans le LF de patientes présentant des anomalies de la réserve ovarienne (telles que le syndrome des ovaires micropolykystiques ou une faible réserve ovarienne). Nous avons ensuite évalué le potentiel des acides nucléiques circulants en tant biomarqueurs prédictifs des résultats en FIV. Nous avons démontré que le taux d’ADN libre intra-folliculaire et l’expression de certains microARNs étaient significativement associés à la qualité des embryons obtenus in vitro ainsi qu’à la survenue d’une grossesse clinique. Les acides nucléiques circulants offrent donc de nouvelles perspectives à la fois d’un point de vue diagnostique et pronostique dans la prise en charge de l’infertilité humaine. / During the last years, the use of circulating nucleic acids as diagnostic and/or prognostic tools in cancerology was widely documented. The recent development of non-invasive prenatal testing also reveals the growing interest of these biomarkers in obstetrics and gynecology. The circulating or extracellular nucleic acids have for particularity to be easily detectable in the biological fluids of the body and there are two types: (1) Cell-free DNA (cfDNA), short or long DNA fragments resulting from cellular apoptosis and/or necrosis (2) microRNAs (miRNAs), small non-coding RNA sequences, which regulate gene expression by interfering with their mRNA targets. Since it was demonstrated that cfDNA level is abnormally increased in some pathological conditions and miRNAs are involved in the regulation of several biological processes such as folliculogenesis and steroidogenesis, these two types of nucleic acids could constitute new biomarkers of interest in Assisted Reproductive Technology. In this thesis work, we quantified the cfDNA level and analysed the expression profiles of some miRNAs by quantitative PCR, in follicular fluid (FF) samples from women undergoing in vitro fertilization (IVF) procedure. We observed significant high cfDNA levels as well as specific miRNA expression profiles in FF from women with ovarian disorders (such as polycystic ovary syndrome or low ovarian reserve). Next, we investigated the potential of circulating nucleic acids as predictive biomarkers of IVF outcomes. We demonstrated that the intra-follicular cfDNA level and some miRNA expressions were significantly associated with in vitro embryo quality and the clinical pregnancy outcome. Therefore, the circulating nucleic acids offer new diagnostic and prognostic perspectives in human infertility management.

No presente estudo investigou-se amostras de plasma com DNA livre circulante (DNA LC) por meio da técnica Varredura Z. Esta é uma técnica eficiente na determinação de parâmetros de diferentes materiais, tais como cristais líquidos, ferrofluidos e compostos biológicos. Esta experiência é realizada através da focalização de um feixe laser de perfil gaussiano numa amostra. Na medida em que a amostra se aproxima do foco da lente, a intensidade do feixe aumenta e alcança seu valor máximo no ponto focal, então diminui para pontos distantes do foco. Na região próxima ao ponto focal se amplificam os fenômenos não-lineares. Recentemente foi demonstrado que níveis elevados de DNA LC no plasma ocorrem com frequência em pacientes com vários tipos de câncer, podendo ser utilizados para discriminar pacientes com malignidade de pessoas saudáveis. As amostras de DNA LC, submetidas ao experimento Varredura Z, forneceram respostas ópticas devido ao fenômeno de lente térmica. Os resultados revelaram que a amplitude de lente térmica das amostras extraídas do plasma de pacientes com malignidade difere daquela de doadores sãos. A técnica Varredura Z se mostrou mais vantajosa em relação a outras biológicas porque revelou uma maior diferença entre os grupos estudados e tem o caráter de detectar mudanças estruturais no DNA LC. / In the present study plasma samples with cell-free DNA were investigated by means of the Z-Scan technique. This is a powerfull technique in determining parameters of different materials, such as liquid crystals, ferrofluids and biological compounds. This experiment is performed by focusing a Gaussian profile laser beam on a sample. As the sample approaches the focus of the lens, the intensity of the beam increases and reaches its maximum value at the focal point, then decreases to points distant from the focus. In the region near the focal point non-linear phenomena are amplified. It has recently been demonstrated that high levels of plasma cell-free DNA occur frequently in patients with various cancers and can be used to discriminate patients with malignancy from healthy donors. The cell-free DNA samples, submitted to the Z-Scan experiment, provided optical responses due to the thermal lens phenomenon. The results revealed that the thermal lens amplitude of samples extracted from the plasma of patients with malignancy differs from that of healthy donors. The Z-Scan technique was more advantageous than other biological ones because it revealed a greater difference between the studied groups and has the character of detecting structural changes in cell-free DNA.

The primary purposes of this dissertation were to explore relationship between cell free DNA (cf-DNA), creatine kinase (CK), C-reactive protein (CRP), vertical jump testing delayed onset muscle soreness (DOMS) in response to a high-volume resistance training protocol, and to assess the sensitivity of cf-DNA to different resistance training volume loads. The secondary purpose was to examine the relationship between cf-DNA and relative strength. Study 1 was an exploratory attempt to discover relationships between cf-DNA, CK, CRP, delayed onset muscle soreness, and performance variables. Seventeen resistance trained males were recruited, 9 were randomly assigned to receive BCAAs while 8 received a placebo. Participants performed a high-volume resistance training session consisting of the back squat and bench press. Blood was drawn to measure serum cf-DNA, CK, and CRP levels prior to the training session, with cf-DNA collected immediately post, and CK and CRP at 24hr and 48hrs post. Self-reported DOMS on a scale of 1 to 10 was collected prior to training on day 2, day 3, and day 4. SJH, CMJH, and BOSCO were collected on day 1, day 3, and day 4. Fifty-seven correlations were run to explore the relationships between variables. Only the correlation between %Δ DOMS 48hr and %Δ CRP 48hr in the non-supplement group was significant (p = 0.02). The second study, designed to assess the sensitivity of cf-DNA to different resistance training volume loads, consisted of a high-volume resistance training protocol. Blood was drawn immediately before the resistance training session (T1), immediately after the third lifting set (T2), and immediately after the sixth lifting set (T3). cf-DNA increased significantly from T1 to T2 (p < 0.01) and T1 to T3 (p < 0.01). The linear regression model used to examine the capabilities of relative strength to predict %Δ cf-DNA from T1 to T3 was significant (p = 0.04). The results of this study demonstrate the short response time of cf-DNA in relation to variations in resistance training volume-load, suggesting it may be a valuable marker in monitoring the immune response to volume-load. Results also demonstrated the positive relationship between relative strength and %Δ cf-DNA.

No description available.

Sepsis is a clinical syndrome characterized by the systemic activation of inflammatory and coagulation pathways in response to microbial infection of normally sterile parts of the body. Despite considerable advances in our understanding of sepsis pathophysiology, sepsis remains the leading cause of death in non-coronary intensive care units (ICU) with a global disease burden between 15 and 19 million cases per year (Dellinger et al., 2008). Severe sepsis, defined as sepsis associated with organ dysfunction is associated with mortality rates of 33% to 45%. The incidence of severe sepsis continues to increase by 1.5% per annum due to the aging population, a rise in the prevalence of comorbidities, and the wider use of immunosuppressive agents and invasive procedures (Angus et al., 2001). Over the past several decades, many potential treatments for sepsis have shown early promise, yet have failed to improve survival in over 100 Phase II and Phase III clinical trials (Marshall, 2014) suggesting that some fundamental knowledge is lacking in our understanding of sepsis pathophysiology. Emerging studies on cell-free DNA (cfDNA), DNA released extracellularly into the circulation, demonstrate that cfDNA is a crucial link between inflammation and coagulation . In various conditions characterized by excessive inflammatory responses or aberrant prothrombotic responses, cfDNA has been implicated in exacerbating disease pathology (Atamaniuk, Kopecky, Skoupy, Säemann, & Weichhart, 2012; Fuchs, Brill, & Wagner, 2012; Swystun, Mukherjee, & Liaw, 2011). In clinical sepsis, levels of cfDNA upon admission into the ICU have strong prognostic value in predicting mortality (Dwivedi et al., 2012; Saukkonen et al., 2008). However, it is unclear whether these increases in cfDNA are an epiphenomenon during sepsis progression, or whether cfDNA actively plays a role in sepsis pathophysiology. In this work, in vivo studies were conducted to characterize the role of cfDNA in sepsis, the effects of DNase administration, and the potential mechanism by which cfDNA is released during experimental sepsis. In addition, mortality studies were conducted to identify surrogate markers of death to promote the design of humane and ethical animal studies in conducting sepsis research. Polymicrobial sepsis was induced via a surgical procedure whereby the cecum is exteriorized, ligated and punctured twice to introduce a continuous source of microorganisms, a model termed cecal ligation and puncture (CLP). In our CLP sepsis model, levels of cfDNA increased in a time-dependent manner. These increases accompanied an early pro-inflammatory response marked by increased pro-inflammatory IL-6, a transient increase in anti-inflammatory IL-10, and elevated lung myeloperoxidase (MPO) activity. Septic mice with elevated cfDNA levels also had high bacterial loads in the lungs, blood, and peritoneal cavity fluid. Organ damage was also observed in mice following CLP surgery versus mice subjected to the non-septic sham control surgery marked by increased levels of creatinine and alanine aminotransferase (ALT) indicative of kidney and liver injury, respectively. Histological analyses further confirmed lung and kidney damage following CLP surgery. Changes in coagulation were also observed in septic mice as mice subjected to CLP had sustained increases in thrombin-antithrombin (TAT) complexes. In addition, plasma from CLP-operated mice had increased thrombin generation (i.e. increased endogenous thromin potential, increased peak thrombin, decreased time to peak, and decreased lag time) mediated by FXIIa and enhanced by platelets. Following CLP-induced sepsis, elevations in cfDNA levels accompanied pro-inflammatory and pro-coagulant responses. The effects of in vivo DNase treatment in septic mice were time-dependent. Early DNase treatment when cfDNA levels were low resulted in an exaggerated pro-inflammatory response marked by increased plasma IL-6 levels and increased lung damage. In contrast, delayed DNase treatment at time-points when cfDNA levels were elevated suppressed inflammation characterized by an increase in anti-inflammatory IL-10 and reductions in cfDNA, IL-6, lung MPO, and ALT activity. Furthermore, delayed DNase administration resulted in decreased bacterial load in the lungs, blood, and peritoneal cavity fluid. Delayed DNase treatment also resulted in blunted pro-coagulant responses as levels of TAT complexes were suppressed and thrombin generation from septic mouse plasma was normalized. Moreover, DNase treatment when cfDNA levels were elevated increased survival in CLP-operated mice by 80% and reduced lung and liver damage. These findings suggest that administration of DNase when cfDNA levels are elevated may reduce pro-inflammatory and pro-coagulant responses and that delayed DNase treatment may infer protection in the CLP model of sepsis. One mechanism by which cfDNA is released is via the formation of neutrophil extracellular traps (NETs). Upon inflammatory stimulation, some neutrophils release chromatin material and antimicrobial proteins (i.e. neutrophil elastase, MPO, and histones) in an active process termed NETosis. Although NETs ensnare bacteria and exert antimicrobial properties, NETs may also exert harmful effects on the host by activating inflammation and coagulation. While some in vitro evidence suggest that neutrophils are the main source of cfDNA released following inflammatory stimulation, others have reported that neutrophils are not the main source of circulating cfDNA following septic challenge. To determine whether NETs contribute to cfDNA released during CLP sepsis, genetically modified mice that are incapable of forming NETs, PAD4-/- mice, were used. Levels of cfDNA in PAD-/- mice were significantly lower than cfDNA levels in C57Bl/6 mice following CLP surgery, suggesting that NETs were a source of cfDNA in our model. Levels of IL-6, MPO, and bacterial load in the lungs, blood, and peritoneal cavity were significantly reduced, indicating that NETs exert pro-inflammatory effects in CLP sepsis. Thrombin generation was also suppressed in PAD4-/- mice which suggests that NETs contribute to thrombin generation following CLP sepsis. NETs contribute to increases in circulating cfDNA and may exacerbate pathology by driving pro-inflammatory and pro-coagulant responses in CLP-induced sepsis. Appreciating the implications of conducting research using animals, it is pertinent that researchers ensure the highest ethical standards and design animal studies in the most humane, yet scientifically rigorous manner. Using mortality studies, we validated the utility of physiological and phenotypic markers to assess disease severity and predict death in murine sepsis. Temperature via a rectal probe monitor and sepsis scoring systems which assess components such as orbital tightening, level of consciousness, and activity were effective surrogate markers of death. These tools offer a non-invasive assessment of disease progression which do not artificially exacerbate sepsis pathology and immediate information regarding any changes in the health status. Surrogate markers of death also provide reliable monitoring to meet increasing standards of ethical, humane animal research and a feasible and cost-efficient means to obtain vital signs in small rodents. We have proposed a scoring system which can be used for assessing disease severity, endpoint monitoring, and predicting death to obviate inhumane methods of using death as an endpoint in sepsis studies. In summary, cfDNA levels are elevated in CLP-induced sepsis and these elevations accompany pro-inflammatory and pro-coagulant responses. NETosis may be a mechanism by which cfDNA is released and NETs may drive inflammation and coagulation in CLP sepsis. Delayed DNase administration may suppress inflammation and coagulation and may be protective in polymicrobial sepsis. In future animal sepsis studies, surrogate markers of death and a sepsis scoring system can be used in place of death as an endpoint to raise the standards in conducting ethical, humane sepsis research. / Thesis / Doctor of Philosophy (PhD)

In breast cancer, the genetic profiling of circulating cell-free DNA (cfDNA) from blood plasma was shown to have good potential for clinical use. In contrast, only a few studies were performed investigating urinary cfDNA. In this pilot study, we analyzed plasma-derived and matching urinary cfDNA samples obtained from 15 presurgical triple-negative breast cancer patients. We used a targeted next-generation sequencing approach to identify and compare genetic alterations in both body fluids. The cfDNA concentration was higher in urine compared to plasma, but there was no significant correlation between matched samples. Bioinformatical analysis revealed a total of 3339 somatic breast-cancer-related variants (VAF ≥ 3%), whereof 1222 vs. 2117 variants were found in plasma-derived vs. urinary cfDNA, respectively. Further, 431 shared variants were found in both body fluids. Throughout the cohort, the recovery rate of plasma-derived mutations in matching urinary cfDNA was 47% and even 63% for pathogenic variants only. The most frequently occurring pathogenic and likely pathogenic mutated genes were NF1, CHEK2, KMT2C and PTEN in both body fluids. Notably, a pathogenic CHEK2 (T519M) variant was found in all 30 samples. Taken together, our results indicated that body fluids appear to be valuable sources bearing complementary information regarding the genetic tumor profile.

Meine Untersuchungen zeigen, dass es sich bei der zellfreien DNA (cfDNA, engl. cell-free DNA) des Spenderorgans (GcfDNA, engl. graft-derived cell-free DNA) um einen klinisch vielversprechenden Biomarker zur direkten Ermittlung der Organschädigung im Sinne einer „flüssigen Biopsie“ handelt. Alles was dafür notwendig ist, ist eine Blutprobe des Empfängerpatienten. Im Gegensatz zu konventionellen Markern wird die Organschädigung unmittelbar, direkt und hochspezifisch angezeigt. Durch neue Entwicklungen in der Labordiagnostik lässt sich dieser Marker im routinemäßigen Einsatz mittels digital droplet PCR (ddPCR) bestimmen. Die Analyseergebnisse können bei verhältnismäßig niedrigen Kosten innerhalb eines Arbeitstages erstellt werden. Unmittelbar nach Transplantation ist bei allen Patienten eine sehr hohe Konzentration der GcfDNA messbar. Innerhalb von wenigen Tagen fallen die Werte schnell ab und erreichen die Größenordnung stabiler Transplantatempfänger, die in der Lebertransplantation unter 10% liegen. Dabei besteht keine signifikante Korrelation der initialen GcfDNA-Freisetzung mit der Ischämieschädigung des Spenderorgans, ermittelt durch die Dauer der kalten Ischämiezeit (WIZ). Bei unzureichender Immunsuppression ist eine erhöhte GcfDNA-Freisetzung zu beobachten. Mithilfe der GcfDNA als Marker der Organintegrität lässt sich auch der gemeinsame Effekt verschiedener Immunsuppressiva ermitteln. Die GcfDNA verhält sich dabei umgekehrt proportional zur immunsuppressiven Therapie. Patienten mit akuten Abstoßungen haben im Mittel GcfDNA-Werte oberhalb von 50%. Die GcfDNA-Werte sind bereits mehrere Tage vor einer klinisch manifestierten akuten Abstoßung erhöht. Auch eine virusassoziierte Transplantatschädigung durch Hepatitis C manifestiert sich in vergleichsweise höheren GcfDNA-Werten. Cholestasen gehen hingegen nicht mit erhöhten GcfDNA-Werten einher. Die immunsuppressive Therapie könnte sich durch den routinemäßigen Einsatz der GcfDNA sicherer, einfacher, zuverlässiger und individueller gestalten lassen. Unter-Immunsuppressionen und daraus resultierende Abstoßungen würden sich bereits in der subklinischen Phase erkennen lassen und die Therapie von der bloßen Reaktion auf klinische Ereignisse hin zur Prävention verschieben. Um das Ziel einer personalisierten Medizin zu erreichen, könnte die Immunsuppression für jeden Patienten auf das absolut notwendige und damit gegenüber der bisherigen Praxis optimale Maß festgelegt werden. Geringere Nebenwirkungen und eine Reduktion der Kosten für das Gesundheitswesen wären die Konsequenz. Dieser Marker könnte dazu beitragen, das finale Ziel, nämlich eine Verbesserung des Langzeiterfolges nach Organtransplantationen, zu erreichen. Multizentrische Studien zur Validierung dieses Markers vor dem routinemäßigen Einsatz laufen bereits.

The detection of plasma cell–free tumor DNA (ctDNA) is prognostic in colorectal cancer (CRC) and has potential for early prediction of disease recurrence. In clinical routine, ctDNA-based diagnostics are limited by the low concentration of ctDNA and error rates of standard next-generation sequencing (NGS) approaches. We evaluated the potential to increase the stability and yield of plasma cell–free DNA (cfDNA) for routine diagnostic purposes using different blood collection tubes and various manual or automated cfDNA extraction protocols. Sensitivity for low-level ctDNA was measured in KRAS-mutant cfDNA using an error-reduced NGS procedure. To test the applicability of rapid evaluation of ctDNA persistence in clinical routine, we prospectively analyzed postoperative samples of 67 CRC (stage II) patients. ctDNA detection was linear between 0.0045 and 45%, with high sensitivity (94%) and specificity (100%) for mutations at 0.1% VAF. The stability and yield of cfDNA were superior when using Streck BCT tubes and a protocol by Zymo Research. Sensitivity for ctDNA increased 1.5-fold by the integration of variant reads from triplicate PCRs and with PCR template concentration. In clinical samples, ctDNA persistence was found in ∼9% of samples, drawn 2 weeks after surgery. Moreover, in a retrospective analysis of 14 CRC patients with relapse during adjuvant therapy, we successfully detected ctDNA (median 0.38% VAF; range 0.18–5.04% VAF) in 92.85% of patients significantly prior (median 112 days) to imaging-based surveillance. Using optimized pre-analytical conditions, the detection of postoperative ctDNA is feasible with excellent sensitivity and allows the prediction of CRC recurrence in routine oncology testing.