ReTuBi Lecture - Eliane Piaggio
On July 16 of 2018, Eliane Piaggio from Institut Curie (France) was the invited speaker as an expert visit with the lecture “High dimensional analysis of immune cells in breast tumor-draining lymph nodes”.
Summary of the Lecture:
Lymph node (LN) invasion by tumor cells correlates with a negative clinical prognosis across different cancer types. It is thought that the metastatic tumor cells invading the LNs exert local immunosuppression, which promotes the loss of tumor immune control. To determine whether tumor-invaded LNs represent tolerogenic sites for T cells, we used a multiscale immune profiling strategy based on multiparametric high-dimensional flow cytometry, RNA sequencing, and T cell receptor (TCR) repertoire analysis, and more recently single-cell RNAseq coupled to TCRseq. We compared CD8+, CD4+ conventional and regulatory T cells in matched tumor-invaded LNs, non-invaded LNs, and primary tumors (TILs) from patients with luminal breast cancer. We found that regulatory T cells in all tissues express higher levels of both positive and negative immunecheckpoints than CD4+ and CD8+ T cells. The T cells in invaded LNs proliferate, produce cytokines, and respond to recall antigens, whereas TILs from the same patients fail to do so. Repertoire analysis shows that CD4+ and CD8+ T cells in LNs and tumors share oligoclonal TCRs, suggesting that tumor-specific T cells traffic between the two sites, but acquire the exhausted phenotype exclusively in tumors. Therefore, in contrast to TILs, tumor-specific T cells within invaded LNs are fully functional. These results suggest that LNs may represent a tumor immunoediting site in which immune-resistant tumor-cell clones are selected, in line with the strong prognosis value of invaded TDLNs for relapse.
Nuclear and mitochondria instability in health and cancer Scientific Symposium
From July 3 to 5, 2018 it was held the "Nuclear and mitochondria instability in health and cancer Scientific Symposium", in Montargil, Portugal. This ReTuBi event had a total of 31 participants from Instituto de Medicina Molecular, Institut Curie and from the Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER).
ReTuBi Lecture - Antonin Morillon
On July 2 of 2018, Antonin Morillon from Institut Curie (France) was the invited speaker as an expert visit with the lecture “The dark side of the genome: pervasive they said”.
Summary of the Lecture:
Among the signals that control the epigenetic landscape, non-coding (nc)RNAs have been identified to play a major role but the generalization and the mechanisms of their activity are still poorly apprehended. Recent data using high-throughput technologies have profoundly changed our view on how the genomes are organized. Indeed transcriptome analyses have shown that large genomic regions are pervasively transcribed producing a broad variety of lncRNA which functions on the epigenome remain to be deciphered. Recent works showed that S. cerevisiae’s genome also supports production of non-coding protein large transcripts, which are strongly controlled by RNA decay pathways. Of specific interest are the lncRNA XUT that we described recently, mostly antisense to class II genes and associated with a consistent regulatory potential through epigenetic modifications. Here, I will present data providing insights on their regulatory activity which is conserved also in S. pombe containing RNAi pathway. The transcription and post-transcription-mediated regulatory activities of antisense transcripts will also be discussed in human cells where we draw an unprecedented landscape of antisense transcription in cancer cell lines and tumors.
Staff exchange between iMM-Curie (2018/06)
From June 25 to 30 of 2018 Marie Ouarné from Cláudio Franco (iMM) made a “ReTuBi Staff Exchange” to Danijela Vignjevic (Institut Curie) with the objectivo to observe the procedures and equipment necessary for surgery and intravital 2-photon imaging in brain of adult mice. This staff exchange was important to study polarization and migration profiles of endothelial cells in mice. It also enabled to study the influence of blood flow on endothelial cell behaviour and if possible replicated the techniques at the iMM, strengthening collaborations to study molecular pathways involved in endothelial response to blood flow.
ReTuBi Lecture - Ingrid Grummt
On June 18 of 2018, Ingrid Grummt from DKFZ (Germany) was the invited speaker as an expert visit with the lecture “DNA:RNA triplexes – a liaison between regulatory RNAs and chromatin”.
Summary of the Lecture:
Nuclear long non-coding RNAs (lncRNAs) have been implicated on most, if not all, chromatin-mediated processes. While cataloging the transcriptional output of sequenced genomes has led to new approaches for the discovery of thousands of bona fide lncRNAs, few of these lncRNAs have been ascribed function and very little is known about their mode of action and regulation. We have discovered a novel long non-coding RNA (lncRNA), Khps1, which is transcribed in antisense orientation to the proto-oncogene SPHK1. Khps1 interacts with a homopurine stretch upstream of the transcription start site of SPHK1, forming a DNA:RNA triplex that tethers Khps1 to SPHK1 and guides Khps1-associated p300/CBP to the SPHK1 promoter to local changes of the chromatin structure that activates SPHK1 transcription. Deletion or mutation of the triplex-forming region diminishes enhancer occupancy of E2F1 and p300, attenuates KHPS1-dependent activation of SPHK1 transcription and impairs cell migration and proliferation.
To examine whether lncRNA-mediated triplex formation is a general mechanism of epigenetic regulation, we have established a genome-wide method that allows genome-wide mapping of RNAs that are engaged in DNA:RNA triplex structures. High-throughput sequencing and computational analysis revealed a large set of triplex-forming RNAs originating from non-coding and coding loci harboring super-enhancer and repeat sequences. In a complementary approach, we have identified DNA sequences that are engaged in DNA:RNA triplex structures. Analysis of DNA-associated RNA regions combined with identification of genomic loci that are targeted by triplex-forming RNAs reveals that DNA:RNA triplex formation is a general mechanism of RNA-mediated target-site recognition.
Joint Lab Retreat on Trafficking and Cell Migration in Cancer
From June 6 to 8, 2018 it was held the Joint Lab Retreat on Trafficking and Cell Migration in Cancer, in Sintra, Portugal. This ReTuBi event had a total of 30 participants from Instituto de Medicina Molecular, Institut Curie and IFOM, the FIRC Institute for Molecular Oncology! Great opportunity to discuss outstanding science!