The Mechanobiology of Disease group currently offers several topics focused on mechanosensing in cardiomyocytes and alternative mRNA splicing at Faculty of Sciences and Faculty of Medicine at Masaryk University:
PhD topics:
- Dissection of YAP1 activity on sarcomere maturation and force generation in human cardiomyocytes
- The effect of mechanical stimuli on the RNA splicing
MSc topics:
- Effects of chromatin modifications on proliferation, cardiomyocyte maturation and structure of sarcomere in vitro.
- The effect of mechanical stimuli on the splicing regulation in human stem cells (Vliv mechanického signálování na regulaci sestřihu RNA v lidských kmenových buňkách)
BSc topic: Splicing regulation via mechanical signalling (Regulace sestřihu RNA pomocí mechanického signálování)
To read more about the topics scroll below and use the links/contacts to get in touch with supervisors.
PhD topics
1. Dissection of YAP1 activity on sarcomere maturation and force generation in human cardiomyocytes
Reactivation of developmental pathways is an emerging avenue in efforts to regenerate adult failing heart. Hippo pathway effector YAP1, key player during development, which is deactivated in an adult heart, is one of such targets. While the Hippo mediated (pro-proliferative) effects of YAP1 activity have been thoroughly explored, the effects of Hippo independent activation of YAP1 on sarcomere structure, maturation, and force development are just starting to be explored.
The student will work with in vitro model of pluripotent stem cell derived cardiomyocytes. Initially the student will prepare inducible human pluripotent stem cell lines to 1. silence endogenous YAP1 2. induce expression of mutated variants of YAP1. Next, impact of temporally restricted expression of YAP1 variants on cardiomyocyte mechanosensing, maturation, and force production using super-resolution microscopy, traction force microscopy in single cell cultivation model will be assessed. Finally, mechanistic understanding of the process will be facilitated by identification of interactors and transcription factors mediating differential outcomes of different mutant forms of YAP1.
contact: [email protected]
link to apply
2. The effect of mechanical stimuli on the RNA splicing
Several studies published in recent years brought evidence that RNA-splicing is altered when mechanical stimuli are applied. This is catalysed through RNA-binding proteins (mainly heterogenous nuclear ribonucleoproteins, hnRNPs, and serine/arginine-rich proteins, SR) that play a major role in splicing regulation. The process is closely related to three-dimensional spatial re-organization of splicing regulators. Recent data also associate the abnormal regulation of alternative splicing to the occurrence and development of tumors and therapeutic approaches based on targeting the splicing machinery emerge. Tumors display altered mechanical properties compared to healthy tissues that reflect into changes in proliferation, apoptosis, invasion, metastasis, angiogenesis, and metabolism of the tumor cells.
The overall aim of the doctoral thesis is to elucidate the relationship between mechanical signalling and splicing regulation. This topic is novel and ambitious with possible outcomes ranging from describing mechanisms fundamental for cellular biology in the early stages of development to the new insights into the regulation in cancer cells.
contact: [email protected]
link to apply
MSc topics
1. Effects of chromatin modifications on proliferation, cardiomyocyte maturation and structure of sarcomere in vitro.
Annotation
The student will focus on effects of histone modifiers on DNA replication and sarcomere structure to get insight into regenerative potential of human cardiomyocytes. Cardiomyocytes of human foetal heart progress from proliferating cells to post-mitotic cells of the adult heart characterized by well established, force producing sarcomere. The process of maturation is accompanied by restrictive changes of histone modifications locking in the adult transcriptional landscape. During injury and regeneration of adult heart, these modifications are partially reversed resulting re-expression of foetal genes. While this transcriptional shift leads to changes in sarcomere structure and increased DNA synthesis, it is not sufficient to promote proliferation required for tissue replacement. Human cardiomyocytes derived from pluripotent stem cells in vitro are useful tool to study cardiomyocyte development, sarcomere maturation, and regeneration. The student will learn and apply methods of cardiomyocyte differentiation to established model of single cell cardiomyocytes in vitro. Next he/she will screen a library of histone modifiers using confocal microscopy followed by image analysis to identify the most pronounced effects on cardiomyocyte proliferation, sarcomere structure, and cardiomyocyte maturation to assess the potential of histone modifiers on regeneration.
Supervisor: MSc. Vladimir Vinarsky, Ph.D.
UČO MUNI: 106932
contact: [email protected]
link to full annotation at Masaryk University
2. The effect of mechanical stimuli on the splicing regulation in human stem cells (Vliv mechanického signálování na regulaci sestřihu RNA v lidských kmenových buňkách)
Annotation
Heterogenous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins whose main function is to regulate alternative splicing. Several studies published in recent years brought evidence that RNA-splicing is altered when mechanical stimuli are applied. Some data imply that this process might be closely related to three-dimensional (3D) spatial re-organization of splicing regulators, including hnRNPs. This mechanism might turn out to be fundamental for cellular biology, especially in the early stages of development.
The aim of this diploma thesis is to expand our understanding of hnRNPs mechanosensitivity and connect it to the positional identity in human induced pluripotent stem cell (hiPSC) colonies. The main tasks will include culturing and treating hiPSCs on micropatterned surfaces, immunocytochemistry analysis, siRNA cell transfection to silence selected genes, Western blotting and gene expression analysis by RT-qPCR. The overall goal of the proposed diploma thesis is to disclose the effect of mechanical stimuli on the hiPSC splicing regulation and their positional identity.
Anotace
Heterogenní nukleární ribonukleoproteiny (hnRNPs) jsou RNA-vazebné proteiny, jejichž hlavní funkcí je regulace alternativního sestřihu. Řada současných studií prokázala změny v sestřihu RNA v důsledku mechanické stimulace. Některá data naznačují, že tento proces úzce souvisí s 3D uspořádáním sestřihových regulátorů v jádře, včetně proteinů z rodiny hnRNP. Tento jev by mohl být zásadní pro celkovou regulaci buněčných procesů, zejména v raných fázích vývoje.
Cílem diplomové práce (DP) je rozšířit naše znalosti o mechanosensitivitě hnRNP proteinů a jejich roli v poziční identitě v kolonii lidských indukovaných kmenových buněk (hiPSC). K tomu student(ka) využije celou řadu molekulárně biologických laboratorních metod, zejména kultivaci a treatment hiPSCs na mikropatternovaných površích, imunocytochemickou analýzu, transfekci buněk pomocí siRNA za účelem knock-downu vybraných genů, Western blotting a analýzu genové exprese pomocí RT-qPCR. Závěrem navrhované DP bude popsat vliv mechanické stimulace na regulaci sestřihu RNA v hiPSC a jejich poziční identitu.
Supervisor: Mgr. Pavel Šimara, Ph.D.
UČO MUNI: 67594
contact: [email protected]
link to full annotation at Masaryk University
BSc topic
Splicing regulation via mechanical signalling (Regulace sestřihu RNA pomocí mechanického signálování)
Anotace
Mechanické signálování hraje důležitou roli v lidských buňkách při vnímání okolí a reakci změny mikroprostředí. Přenos signálu a klíčové proteiny (např. YAP) byly nedávno popsány a byl zdokumentován vliv mechanosensingu na buněčnou expresi. Méně informací máme o vlivu mechanických podnětů na sestřih RNA a vznik různých izoforem proteinů. Regulace sestřihu RNA je přitom zásadní, mimo jiné, při vzniku a rozvoji onemocnění. Student(ka) se v bakalářské práci bude věnovat popisu mechanismu sestřihu RNA, jeho regulaci, popisu mechanického signálování a uvede příklady sestřihových abnormalit, které vedou ke konkrétním onemocněním. Popsány budou též techniky, které se ve výzkumu nejčastěji používají.
Jazyk práce: český
Supervisor: Mgr. Pavel Šimara, Ph.D.
UČO MUNI: 67594
contact: [email protected]
link to full annotation at Masaryk University