Genetics and Molecular Biology

ALESSANDRO ROSA

The course aims to provide knowledge on the fundamental properties of stem cells, with particular focus on the molecular mechanisms that regulate their capacity of self-renewal and differentiation. The course also intends to clarify the potential of somatic cell reprogramming to induced pluripotent stem cells (iPS), providing notions about the epigenetic mechanisms underlying the reprogramming process. Examples of the use of stem cells for the creation of in vitro model systems of different human diseases and regenerative medicine will be provided.
The student is guided along the path to arrive at an understanding of the processes that determine the peculiar capacities of stem cells to give rise to the different types of differentiated cells that build up organs and tissues.

There are no laboratory activities.

Knowledge and understanding
The student:
- Knows correctly the terminology related to stem cells;
- Knows the molecular basis of biological processes that regulate self-renewal and differentiation of stem cells;
- Knows the different levels of epigenetic regulation of stem cell differentiation;
- Knows the basic techniques for the study of stem cells

Ability to apply knowledge and understanding
The student:
- knows how to properly use stem cell terminology
- can distinguish the different types of stem cells, also based on their differentiation potential
- can evaluate the possible use of stem cells as model systems in biology;
- knows how to evaluate the possible applications of stem cells
- is able to use the knowledge on the techniques for the study of stem cells to design an experiment in the laboratory.

At the end of the course, the student will have acquired an in-depth knowledge of the main concepts and processes that regulate stem cell biology, with particular emphasis on differentiation potential and self-renewal, as well as on the mechanisms of reprogramming and transdifferentiation.
They will be able to critically understand the molecular bases that determine cell identity and plasticity, analyzing the dynamics of the transcriptional, epigenetic, and post-transcriptional circuits that govern these phenomena. Moreover, they will be able to place this knowledge within the context of basic and biomedical research and regenerative medicine, assessing the potential and limitations of stem cell-based therapeutic applications.

The student will be able to apply the theoretical knowledge acquired to interpret data and experimental protocols related to the study of stem cells. In particular, they will be able to use and critically evaluate molecular biology techniques and experimental approaches aimed at analyzing pluripotency, differentiation, and cellular reprogramming. They will recognize the factors that influence the efficiency of differentiation processes and propose improvement strategies, demonstrating operational mastery of theoretical concepts and a rigorous methodological approach.

From a critical standpoint, the course aims to develop in the student a solid scientific autonomy of judgment. They will be able to analyze the relevant literature, compare different models of pluripotency and reprogramming, discuss experimental evidence in a reasoned manner, and evaluate the ethical and social implications related to the use of stem cells and genome editing technologies. Learning will be oriented toward stimulating the ability to evaluate complex data, formulate coherent hypotheses, and design experimental verification pathways.

From a communicative perspective, the student will develop the ability to clearly and rigorously present and discuss concepts, data, and results related to stem cell biology. They will be able to communicate using appropriate technical language and adapt their communication to the context, whether academic or interdisciplinary. These communication skills will form an essential basis for participation in research groups and high-level scientific discussions.

Finally, the course will enhance the student’s ability for autonomous learning. They will be able to independently update their knowledge in relation to the most recent advances in stem cell research, integrate information from related disciplines such as genetics, epigenetics, and biotechnology, and independently design a study or research project on emerging topics such as organoid generation, genome editing applications, or personalized regenerative medicine strategies.

Prerequisites (“propedeuticità”) are not required. However, the student must have basic notions of cellular and molecular biology.

1) Introduction and Background (8 hours)
- Adult and embryonic stem cells; differentiation potential; stem cell niche; examples of adult stem cells; epigenetics.
- Molecular biology techniques for the study of stem cells.

2) Molecular basis of pluripotency (20 hours)
- Origin of embryonic stem cells; regulatory circuits in the formation of the mammalian blastocyst.
- Regulation of pluripotency: signaling, "naive" and "primed" states of pluripotency, transcriptional and post-transcriptional regulatory networks, epigenetic control of pluripotency, regulation by microRNAs and lncRNAs.
- Molecular basis of pluripotent stem cell differentiation; examples of differentiation to generate cell types for therapy and research; strategies to improve the efficiency of differentiation.
- Pluripotent stem cells in basic research and regenerative medicine.

3) Cell reprogramming and transdifferentiation (20 hours)
- From nuclear transfer to iPS cells;
- Molecular mechanisms of reprogramming; deterministic and stochastic models; early, intermediate and late phases in reprogramming; epigenetic memory.
- Patient-specific iPS cells; applications of reprogramming in basic research and regenerative medicine; "genome editing" techniques to correct mutations; generation of organoids in vitro.
- Transdifferentiation: methods and applications; epigenetic basis of transdifferentiation; examples of transdifferentiation to obtain cells of therapeutic interest (muscle, neurons).

Reference scientific articles and other teaching material will be indicated during the lectures. The teacher will also make available the powerpoint presentations of the lessons on the Sapienza Elearning platform.

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Dröscher, A. (2014). Images of cell trees, cell lines, and cell fates: the legacy of Ernst Haeckel and August Weismann in stem cell research. HPLS, 36, 157–186. https://doi.org/10.1007/s40656-014-0028-8

Hsu, Y.-C. & Fuchs, E. (2012). A family business: stem cell progeny join the niche to regulate homeostasis. Nat Rev Mol Cell Biol, 13, 103–114.

Zernicka-Goetz, M., Morris, S. A. & Bruce, A. W. (2009). Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo. Nat Rev Genet, 10, 467–477.

Evans, M. (2011). Discovering pluripotency: 30 years of mouse embryonic stem cells. Nat Rev Mol Cell Biol, 12, 680–686.

Bermejo-Alvarez, P., Ramos-Ibeas, P. & Gutierrez-Adan, A. (2012). Solving the ‘x’ in embryos and stem cells. Stem Cells Dev, 21, 1215–1224.

Jaenisch, R. & Young, R. (2008). Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell, 132, 567–582.

Gonzales, K. A. U. & Ng, H.-H. (2011). Choreographing pluripotency and cell fate with transcription factors. Biochim Biophys Acta, 1809, 337–349.

Boyer, L. A. et al. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122, 947–956.

Cole, M. F., Johnstone, S. E., Newman, J. J., Kagey, M. H. & Young, R. A. (2008). Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev, 22, 746–755.

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I. & Young, R. A. (2013). Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153, 307–319.

Spivakov, M. & Fisher, A. G. (2007). Epigenetic signatures of stem-cell identity. Nat Rev Genet, 8, 263–271.

Mattout, A. & Meshorer, E. (2010). Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Curr Opin Cell Biol, 22, 334–341.

Jones, A. & Wang, H. (2010). Polycomb repressive complex 2 in embryonic stem cells: an overview. Protein Cell, 1, 1056–1062.

Gaspar-Maia, A., Alajem, A., Meshorer, E. & Ramalho-Santos, M. (2011). Open chromatin in pluripotency and reprogramming. Nat Rev Mol Cell Biol, 12, 36–47.

Li, M., Liu, G.-H. & Izpisúa Belmonte, J. C. (2012). Navigating the epigenetic landscape of pluripotent stem cells. Nat Rev Mol Cell Biol, 13, 524–535.

Young, R. A. (2011). Control of the embryonic stem cell state. Cell, 144, 940–954.

Voigt, P. et al. (2013). A double take on bivalent promoters. Genes Dev, 27, 1318–1338.

White, J. & Dalton, S. (2005). Cell cycle control of embryonic stem cells. Stem Cell Reviews, 1, 131–138.

Conklin, J. F. & Sage, J. (2009). Keeping an eye on retinoblastoma control of human embryonic stem cells. J Cell Biochem, 108, 1023–1030.

Rosa, A. & Brivanlou, A. H. (2009). microRNAs in early vertebrate development. Cell Cycle, 8.

Wang, Y. & Blelloch, R. (2009). Cell cycle regulation by microRNAs in embryonic stem cells. Cancer Res, 69, 4093–4096.

Rosa, A. & Brivanlou, A. H. (2013). Regulatory non-coding RNAs in pluripotent stem cells. Int J Mol Sci, 14, 14346–14373.

Rosa, A. & Ballarino, M. (2016). Long noncoding RNA regulation of pluripotency. Stem Cells Int, 2016:1797692.

Fatica, A. & Bozzoni, I. (2014). Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet, 15, 7–21.

Karus, M., Blaess, S. & Brüstle, O. (2014). Self-organization of neural tissue architectures from pluripotent stem cells. J Comp Neurol, 522, 2831–2844.

Gurdon, J. B. & Melton, D. A. (2008). Nuclear reprogramming in cells. Science, 322, 1811–1815.

Gurdon, J. (2009). Nuclear reprogramming in eggs. Nature Medicine. doi:10.1038/nm1009-1141.

Gurdon, J. B. & Byrne, J. A. (2004). The first half-century of nuclear transplantation. Biosci Rep, 24, 545–557.

Yamanaka, S. (2008). Pluripotency and nuclear reprogramming. Philos Trans R Soc Lond B Biol Sci, 363, 2079–2087.

Graf, T. (2011). Historical origins of transdifferentiation and reprogramming. Cell Stem Cell, 9, 504–516.

Takahashi, K. & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126, 663–676.

Martello, G. & Smith, A. (2014). The nature of embryonic stem cells. Annu Rev Cell Dev Biol, 30, 647–675.

Ohtsuka, S. & Dalton, S. (2008). Molecular and biological properties of pluripotent embryonic stem cells. Gene Ther, 15, 74–81.

Pera, M. F. & Tam, P. P. L. (2010). Extrinsic regulation of pluripotent stem cells. Nature, 465, 713–720.

Dreesen, O. & Brivanlou, A. H. (2007). Signaling pathways in cancer and embryonic stem cells. Stem Cell Reviews, 3, 7–17.

Nichols, J. & Smith, A. (2009). Naive and primed pluripotent states. Cell Stem Cell, 4, 487–492.

Yamanaka, S. (2007). Strategies and new developments in the generation of patient-specific pluripotent stem cells. Cell Stem Cell, 1, 39–49.

Zhao, R. & Daley, G. Q. (2008). From fibroblasts to iPS cells: induced pluripotency by defined factors. J Cell Biochem, 105, 949–956.

Wernig, M. et al. (2007). In vitro reprogramming of fibroblasts into a pluripotent nES-cell-like state. Nature, 448, 318–324.

Vierbuchen, T. & Wernig, M. (2012). Molecular roadblocks for cellular reprogramming. Mol Cell, 47, 827–838.

Papp, B. & Plath, K. (2011). Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape. Cell Res, 21, 486–501.

Stadtfeld, M. & Hochedlinger, K. (2010). Induced pluripotency: history, mechanisms, and applications. Genes Dev, 24, 2239–2263.

Buganim, Y., Faddah, D. A. & Jaenisch, R. (2013). Mechanisms and models of somatic cell reprogramming. Nat Rev Genet, 14, 427–439.

Sancho-Martinez, I. & Izpisúa Belmonte, J. C. (2013). Stem cells: Surf the waves of reprogramming. Nature, 493, 310–311.

Silva, J., Nichols, J., Theunissen, T. W., Guo, G., van Oosten, A. L., Barrandon, O., Wray, J., Yamanaka, S., Chambers, I. & Smith, A. (2009). Nanog is the gateway to the pluripotent ground state. Cell, 138, 722–737.

Kiskinis, E. & Eggan, K. (2010). Progress toward the clinical application of patient-specific pluripotent stem cells. J Clin Invest, 120, 51–59.

Pera, M. F. (2011). Stem cells: The dark side of induced pluripotency. Nature, 471, 46–47.

Drews, K., Jozefczuk, J., Prigione, A. & Adjaye, J. (2012). Human induced pluripotent stem cells—from mechanisms to clinical applications. J Mol Med, 90, 735–745.

Sandoe, J. & Eggan, K. (2013). Opportunities and challenges of pluripotent stem cell neurodegenerative disease models. Nat Neurosci, 16(7), 780–789.

Bilic, J. & Izpisúa Belmonte, J. C. (2012). Concise review: Induced pluripotent stem cells versus embryonic stem cells: close enough or yet too far apart? Stem Cells, 30, 33–41.

Rowe, R. G. & Daley, G. Q. (2019). Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet, 20, 377–388.

Vierbuchen, T. & Wernig, M. (2011). Direct lineage conversions: unnatural but useful? Nat Biotechnol, 29, 892–907.

The course takes place through a series of lectures and seminars.

Attendance is optional but strongly recommended

Assessment method: only oral exam to be held after the end of the course. The objective of the test is to verify the knowledge acquired, in line with the training objectives. The questions will be open and with an open answer. The duration of the oral exam will be approximately 30 minutes. The following elements will be considered for evaluation: acquisition of knowledge and autonomous reasoning skills. These aspects contribute in equal measure to the formulation of the final score.

- Phases of the reprogramming process
- Regulation of pluripotency and differentiation by non-coding RNAs
- Transcription factors involved in maintaining pluripotency
- Bivalent chromatin domains

• Lectures 1–3. Introduction to the course. Historical background. Fundamental properties of stem cells. Adult stem cells and the stem cell niche. Examples of adult stem cells: satellite cells, corneal stem cells, intestinal stem cells.


• Lectures 4–9. Techniques for studying stem cells; differentiation potential of stem cells. Mouse embryonic stem cells: embryonic origin and fundamental characteristics, derivation, stem cell potential, pluripotency assays, signaling pathways. Human embryonic stem cells: derivation, stem cell potential, signaling pathways. Naive and primed pluripotency states.


• Lectures 10–13. Transcription factors associated with pluripotency; the “core” transcriptional regulatory network. Bivalent chromatin domains; epigenetic factors of pluripotency. Cell cycle regulation in embryonic stem cells; ESCC microRNAs. Non-coding RNAs regulating pluripotency and differentiation (miRNAs; lncRNAs).


• Lectures 14–15. Differentiation of embryonic stem cells: principles and applications.


• Lectures 16–21. From nuclear transfer to reprogramming with defined factors. Generation of iPS cells through ectopic expression of reprogramming factors in mouse and human. Cellular and molecular mechanisms of reprogramming: deterministic/elite and stochastic models; early, intermediate, and late phases of the reprogramming process; stochastic and deterministic phases of reprogramming. Applications of human iPS cells in regenerative medicine and disease modeling. Challenges and opportunities.


• Lecture 22. Transdifferentiation: historical background; molecular and cellular bases; applications.


• Seminars 1-2. Satellite cells: niche; role of microRNAs; symmetric and asymmetric divisions; quiescence; Notch pathway. Hematopoietic stem cells.