Sophia Julia Häfner – University of Copenhagen

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Sophia Julia Häfner (ER3)

Nationality: German

Main Host Institution:

Academic Background: PhD in Genomes, Epigenomes and Cell Fate (2014, Université Paris Diderot, Paris, France)

Project title:
Project nb. 1: Long noncoding RNAs in normal and pathological pluripotency
Project nb. 2: 2’O-methylations of the human ribosomal RNA and their functional impact

Project background:
Project 1: Gaining stemness properties has been shown to grant cancer cells various advantages such as better survival and dissemination, the ability to remain quiescent and greater resistance to treatments. Thus, cancer stem cells or highly aggressive cancer forms have been shown to display a protein profile very similar to “normal” stem cells, such as embryonic stem cells (ESCs).

Long noncoding RNAs (lncRNAs) are a huge class of recently discovered transcripts, which are implicated in virtually every cellular mechanism. Despite the fact that the huge majority is not yet functionally characterized, many lncRNAs have been identified to be crucial for the maintain of the ESC identity, and numerous ones have been shown to be deregulated in cancer. However, no study has systematically investigated the putative role of stemness-specific lncRNAs in dedifferentiated and aggressive cancers.

Project 2: Ribosomal RNA (rRNA) carries numerous modifications, among them 2’-O-methylations. Located in functionally important regions of the ribosome, they are essential for correct folding and translational fidelity. A specific class of small nucleolar RNAs (snoRNAs), the box C/D class snoRNAs, guides methylases to the nucleotides to be methylated during ribosome biogenesis.

In contrast to previous beliefs, ribosomes are not all identical and do not carry all the same set of modifications. Recent research seems to indicate that either several pools of ribosomes exist in the same cell or that different cell types possess different sets of ribosomes, favouring eventually the translation of different transcripts or varying in translation efficiency and fidelity.

Notably cancer cells might possess ribosomes displaying characteristic modifications, which favour the translation of a cancer-specific proteome and lack fidelity (the cancer-ribosome).

In collaboration with the team of Henrik Nielsen (Copenhagen), we developed and optimized the MethSeq technique, allowing us to detect and quantify 2’-O-mehylations at the scale of the entire ribosomal RNA.

Project Aim: 
The first step of the project consists in the collection and bioinformatic treatment of publicly available data (ENCODE, GEO…) leading to the generation of a list of normal stemness related lnRNA, which is crossed in turn with sequencing data of cancer forms displaying dedifferentiation features.

Once a list of candidates has been established, they will be confirmed in adequate models and their role in normal and pathological pluripotency investigated experimentally via current gain and loss of function techniques, as well as the molecular mechanisms elucidated (binding partners etc.).

In a close future, I will also examine the global profile of rRNA modifications in different cellular contexts, starting with human embryonic stem cells at the pluripotent state and during differentiation into the three germ layers.

Expected outcome:
Project 1: Identify and characterize functionally and mechanistically lncRNAs specific for stemness features that are hijacked by cancer cells in order to acquire features increasing their survival, invasiveness and aggressiveness in order to identify novel therapeutic targets and biomarkers.

Project 2: Deciphering the ribosome-code. What modification profile corresponds to which cellular context, and what is the functional readout of specific modifications. Vice-versa, can we manipulate the proteome and the cellular state via the ribosomal methylation profile?