Determination of protein localization and RNA kinetics in human cells

In dieser Dissertation haben wir das Verhalten menschlicher Zellen in Raum und Zeit untersucht. Hochwertige Datensätze subzellulärer Regionen in HEK293-Zellen wurden mit Hilfe der BirA* Proximity-Labelling-Aktivität erstellt, wobei die Lokalisierung auf zelluläre Regionen beschränkt wurde, die mit herkömmlichen Methoden nur schwer zu reinigen sind (d. h. die dem Zytosol zugewandten Seiten des ER, Mitochondrien und Plasma-membranen). Wir entwickelten daraufhin einen Ansatz zur Kartierung der Verteilung von Proteinen, die aktiv an RNA binden, und nannten ihn f-XRNAX. Wir stellten hintergrundkorrigierte Proteome für Zellkerne, Zytoplasma und Membranen von HEK293-Zellen her. Überraschenderweise wurden viele nicht-kanonische RBPs in der Membranfraktion identifiziert, und ihre Peptidprofile waren in Regionen mit hoher Dichte an intrinsisch ungeordneten Regionen angereichert, was auf eine möglicherweise schwache, durch diese nicht-strukturellen Motive vermittelte Interaktion mit RNA hinweist. Schließlich konnten wir die unterschiedliche Bindung desselben Proteins an RNA in verschiedenen HEK293-Kompartimenten nachweisen. Im zweiten Teil dieser Arbeit konzentrierten wir uns auf die Bestimmung und Quantifizierung von neu transkribierten RNAs auf Einzelzellebene. Die Kinetik der RNA-Transkription und -Degradation war bis vor kurzem auf Einzelzellebene nicht messbar. Daher haben wir einen neuen Ansatz (SLAM-Drop-seq genannt) entwickelt, indem wir die veröffentlichte SLAM-seq-Methode an Einzelzellen angepasst haben. Wir haben SLAM-Drop-seq verwendet, um die zeitabhängigen RNA-Kinetikraten der Transkription und des Umsatzes für Hunderte von oszillierenden Transkripten während des Zellzyklus von HEK293-Zellen zu schätzen. Wir fanden heraus, dass Gene ihre Expression mit unterschiedlichen Strategien regulieren und spezifische Modi zur Feinabstimmung ihrer kinetischen Raten entlang des Zellzyklus haben.In this PhD dissertation we investigated the behaviour of human cells through space and time. High quality datasets of subcellular regions in HEK293 cells were generated using BirA* proximity labelling activity and restricting its localization at cellular regions difficult to purified with traditional methods (i.e., the cytosol-facing sides of the endoplasmic reticulum, mitochondria, and plasma membranes). We then developed an approach to map the distribution of proteins actively binding to RNA, and named it f-XRNAX. We recovered background-corrected proteomes for nuclei, cytoplasm and membranes of HEK293 cells. Surprisingly, many non-canonical RBPs were identified in the membrane fraction, and their peptide profiles were enriched in regions with high density of intrinsically disordered regions, indicating a possibly weak interaction with RNA mediated by these non-structural motives. Lastly, we provided evidence of the differential binding to RNA of the same protein in different HEK293 compartments. In the second part of this thesis, we focused on the determination and quantification of newly transcribed RNAs at the single-cell level. The kinetics of RNA transcription, processing and degradation were until recently not measurable at the single-cell level. Thus, we have developed a novel approach (called SLAM-Drop-seq ) by adapting the published SLAM-seq method to single cells. We used SLAM Drop-seq to estimate time-dependent RNA kinetics rates of transcription and turnover for hundreds of oscillating transcripts during the cell cycle of HEK293 cells. We found that genes regulate their expression with different strategies and have specific modes to fine-tune their kinetic rates along the cell cycle

Use of the ML-Flow test as a tool in classifying and treating leprosy

FUNDAMENTOS: O tratamento da hanseníase é definido pela classificação de pacientes em paucibacilares (PB) e multibacilares (MB). A OMS (Organização Mundial de Saúde) classifica os doentes de acordo com o número de lesões, mas Ridley-Jopling (R&J) utiliza também exames complementares, porém é de difícil utilização fora dos serviços de referência. Em 2003 foi desenvolvido um teste denominado ML-Flow, uma alternativa à sorologia por ELISA para auxiliar na classificação de pacientes em PB e MB e auxiliar na decisão terapêutica. OBJETIVOS: Observar a concordância entre o teste de ML-Flow e baciloscopia de linfa, exame já consagrado para detecção de MB. Analisar a utilidade do teste de ML-Flow em campo. MATERIAL E MÉTODOS: Estudo retrospectivo avaliando prontuário de 55 pacientes virgens de tratamento, diagnosticados como PB ou MB por R&J. Submetidos à baciloscopia e ao teste de ML-Flow. RESULTADOS: Nos MB, a baciloscopia foi positiva em 80% dos casos, o ML-flow foi positivo em 82,5%. Entre os PB, o ML-Flow foi positivo em 37,5% e a baciloscopia do esfregaço foi negativa em 100% dos casos. A concordância entre os resultados da baciloscopia do esfregaço e ML-Flow foi de 87,5%, kappa=0,59, p<0,001. CONCLUSÃO: Nenhum teste laboratorial é 100% sensível e específico para a correta classificação de todas as formas de hanseníase. O ML-Flow é um teste rápido, de fácil manuseio em campo, menos invasivo que a baciloscopia podendo ser útil para auxiliar na decisão terapêutica em locais de difícil acesso a serviços de referência.BACKGROUND: The treatment of leprosy is defined by the classification of patients as paucibacillary (PB) or multibacillary (MB). The WHO (World Health Organization) classifies patients according to the number of lesions, but Ridley-Jopling (R & J) also uses complementary exams, which are difficult to use outside reference services. In 2003, a test called ML-Flow, an alternative to Elisa serology, was developed to help classify patients as PB or MB and decide about their treatment. OBJECTIVES: To assess the agreement between the ML-Flow test and slit skin smears, already largely used for MB detection, and to observe the efficacy of the ML-Flow test in the field. MATERIAL AND METHODS: A retrospective study evaluating the medical records of 55 patients who had not undergone previous treatment, diagnosed as PB or MB according to R & J and subjected to slit skin smears and the ML- Flow test. RESULTS: In MB patients, slit skin smears were positive in 80% of the cases, the ML-flow was positive in 82.5%. Among PB patients, the ML-Flow was positive in 37.5% and slit skin smears were negative in 100% of the cases. The agreement between skin smear and ML-Flow results was 87.5%, with a kappa value of 0.59, p <0.001. CONCLUSION: No laboratory test is 100% sensitive and specific for the correct classification of all forms of leprosy. The ML-Flow test is faster, easier to use, and less invasive than slit skin smears and therefore may be useful when making therapeutic decisions in areas of difficult access to reference services

A New Generation of Hydrogen-Fueled Hybrid Propulsion Systems for the Urban Mobility of the Future

The H2-ICE project aims at developing, through numerical simulation, a new generation of hybrid powertrains featuring a hydrogen-fueled Internal Combustion Engine (ICE) suitable for 12 m urban buses in order to provide a reliable and cost-effective solution for the abatement of both CO2 and criteria pollutant emissions. The full exploitation of the potential of such a traction system requires a substantial enhancement of the state of the art since several issues have to be addressed. In particular, the choice of a more suitable fuel injection system and the control of the combustion process are extremely challenging. Firstly, a high-fidelity 3D-CFD model will be exploited to analyze the in-cylinder H2 fuel injection through supersonic flows. Then, after the optimization of the injection and combustion process, a 1D model of the whole engine system will be built and calibrated, allowing the identification of a “sweet spot” in the ultra-lean combustion region, characterized by extremely low NOx emissions and, at the same time, high combustion efficiencies. Moreover, to further enhance the engine efficiency well above 40%, different Waste Heat Recovery (WHR) systems will be carefully scrutinized, including both Organic Rankine Cycle (ORC)-based recovery units as well as electric turbo-compounding. A Selective Catalytic Reduction (SCR) aftertreatment system will be developed to further reduce NOx emissions to near-zero levels. Finally, a dedicated torque-based control strategy for the ICE coupled with the Energy Management Systems (EMSs) of the hybrid powertrain, both optimized by exploiting Vehicle-To-Everything (V2X) connection, allows targeting H2 consumption of 0.1 kg/km. Technologies developed in the H2-ICE project will enhance the know-how necessary to design and build engines and aftertreatment systems for the efficient exploitation of H2 as a fuel, as well as for their integration into hybrid powertrains

Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer

In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define transcriptional states of colorectal cancer cells and signals controlling their development by performing single-cell transcriptome analysis of tumors and matched non-cancerous tissues of twelve colorectal cancer patients. We defined patient-overarching colorectal cancer cell clusters characterized by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories. Our results highlight directional cancer cell development as a driver of non-genetic cancer cell heterogeneity and re-routing of trajectories as a response to targeted therapy