Description of the PhD thesis project
We are investigating in vivo functions and
mechanisms of action of long noncoding RNAs (lncRNAs) that have emerged as key
regulators of diverse biological phenomena and are implicated in many human
cancers including melanoma.
Metastatic skin melanoma is among the cancers
with the highest mortality despite recent progress in targeted and immune-check
point therapies. While lncRNAs represent an untapped source of therapeutic
targets, their precise molecular functions during cancer initiation and
progression remain elusive, often due to the lack of suitable molecular tools
and in vivo models.
Using an inducible zebrafish skin cancer
system that closely parallels the process of skin cancer development in humans,
we discovered a lncRNA that altered melanomagenesis by accelerating melanoma
initiation, increased tumor progression (i.e. tumors reached earlier a more
advanced tumor stage) and spread of metastasis in vivo. Remarkably, the human
lncRNA ortholog has been found to be misregulated in human metastatic melanoma
compared to primary melanoma and its expression in the zebrafish lncRNA mutant
inhibited accelerated melanoma progression, indicating that its molecular
function is highly conserved throughout evolution.
Our project aims to investigate the molecular
mechanism that underlies the conserved tumor suppressor function of this lncRNA
during melanomagenesis with the overarching goal of defining functional lncRNA
motifs that may serve as therapeutic target sites.
To achieve our goals, we use a combination of
in vivo models and molecular tools including our novel incPRINT technology for
identification of RNA-protein interactions and their targeting with small
molecule inhibitors. We will test the functionality of the identified lncRNA
motifs using relevant human melanoma cell lines and zebrafish.
Thus, our research program will
provide critical molecular insights into the biology of lncRNA motifs,
potentially uncovering novel drug target sites for melanoma patients.
International, interdisciplinary &
intersectoral aspects of the project
The project is based on interdisciplinary
approaches at the forefront of RNA biology, comparative genomics, cancer cell
biology, advanced high throughput biochemical methods and first steps towards
unbiased drug discovery.
The student will develop specific skills in
all mentioned above disciplines. It includes collaborations with the
international experts in comparative genomics (Weizmann Institute, Israel) and
with the experts in normal and pathological development of melanocytes (IC).
Discovery of drugs targeting RNA-protein interaction will be elaborated through
collaborations with chemists.
The student will be exposed to the ongoing
spin-off creation specializing on drugs targeting RNA-protein interactions and
will interact with a Versailles-based company on advanced CRISPR-Cas9 tools.
1) Pérez Rico YA, Barillot E, Shkumatava A. Demarcation of
topologically associating domains is uncoupled from enriched CTCF binding in
developing zebrafish. iScience, 2020 May 22;23(5):101046. doi:
2) Graindorge A, Pinheiro I, Nawrocka A,
Mallory AC, Tsvetkov P, Gil N, Carolis C, Buchholz F, Ulitsky I, Heard E,
Taipale M, Shkumatava A. In-cell
identification and measurement of RNA-protein interactions. Nature Communications.
2019 Nov 22;10(1):5317. doi: 10.1038/s41467-019-13235-w.
3) Lavalou P, Eckert E, Damy L, Constanty F,
Majello S, Bitetti A, Graindorge A, Shkumatava
A. Strategies for genetic inactivation of long noncoding RNAs in zebrafish.
RNA, 2019 May 1. pii: rna.069484.118. doi: 10.1261/rna.069484.118.
A, Mallory AC, Carrieri C, Golini E, Carreño Gutierrez H, Perlas E, Pérez-Rico
YA, Tocchini-Valentini GP, Enright AJ, Norton WHJ, Mandillo S, O’Carroll D, Shkumatava A. MicroRNA degradation by a
conserved target RNA regulates animal behavior. Nat Struct Mol Biol. 2018 Feb;
5) Pérez Rico YA, Boeva V, Mallory AC,
Bitetti A, Majello S, Barillot E,
Shkumatava A. Comparative analyses of super-enhancers reveal conserved
elements in vertebrate genomes. Genome Res. 2017 Feb;27(2):259-268. doi: