final

.gitignore

@@ -0,0 +1,8 @@
+*.nav
+*.snm
+*.xml
+*.bbl
+*.DS_Store
+*.gz
+*.out
+*.fls

presentation.tex

@@ -120,7 +120,8 @@
     \egroup
 }
 %Page de titre:
-\title[]{\emoji{dna} Genetic alterations in ChIP-seq}
+\title[]{\emoji{dna} TREC mediated oncogenesis in human immature T lymphoid malignancies
+preferentially involves \textit{ZFP36L2} --- Molecular Cancer}
 
 \author{Dr. Thomas Steimlé}
 
@@ -154,14 +155,14 @@
     the antigen receptor (TCR) is acquired.
   \end{itemize}
   \centering
-    \includegraphics<1>[width=.4\textwidth]{Images/dev_thym.png}
+    \includegraphics<1>[width=.5\textwidth]{Images/dev_thym.png}
     \includegraphics<2>[width=.6\textwidth]{Images/Tcr_str.png}
 \end{frame}
 
 \begin{frame}{\emoji{drop-of-blood} Background --- V(D)J recombination}
   \begin{itemize}
     \item<1-> This process involves a series of genome recombination of the different TCR loci 
-    followed by \alert{proliferation selection of functionnal non self-reacting receptors}.
+    followed by \alert{proliferation and selection of functionnal non self-reacting TCR}.
   \end{itemize}
   \centering
     \includegraphics<1>[width=.7\textwidth]{Images/MaturLt.png}
@@ -175,7 +176,7 @@
         \item V(D)J recombination is a \alert{threat to genomic stability}, 
         prone to induce \alert{DSB occurring in genes outside of the TCR loci}, 
         followed by erroneous repair resultating in SV.
-        \item This oncogenesis process is responsible of well known genetic alterations 
+        \item This oncogenetic process is responsible of well known genetic alterations 
         in T-ALL (particulary translocations accountable of ectopic expression of oncogenes 
         \textit{TLX1}, \textit{TAL1} etc\dots)$^1$.
 
@@ -206,8 +207,8 @@
     \begin{column}{.5\textwidth}
       \begin{itemize}
         \item During recombination deleted parts of the loci are circulized into TRECs.
-        \item Like tansposons the reintegration of TRECs as been suspect to cause 
-        \alert{deregulation of targeted genes}.
+        \item Similar to transposons, the reintegration of TRECs has been implicated in the 
+        \alert{deregulation or inactivation of targeted genes}.
       \end{itemize}
     \end{column}
   \end{columns}
@@ -224,14 +225,14 @@
   \metroset{block=fill}
   \begin{alertblock}{{\centering \large Hypothesis} }
     \begin{itemize}
-      \item In T-ALL, we could find with molecular biolgy tools insertions of those TRECs.
-      \item With the same tools we also could also find all the translocations which involves the TCR.
+      \item In T-ALL, we could find with molecular biology tools insertions of those TRECs.
+      \item With the same tools we could also find all the translocations which involves the TCR.
     \end{itemize}
   \end{alertblock}
 \end{frame}
 }
 
-\begin{frame}{\emoji{up-arrow} Material \& Method}
+\begin{frame}{\emoji{triangular-ruler} Material \& Method}
   \begin{itemize}
     \item<1-> We used our extensed collection of \alert{T-ALL samples at diagnostic n = 1533}.
     \item<2-> We designed a NGS capture assay with \alert{capture probes} mapped at multiple parts of de TCR \delta { } locus.
@@ -239,12 +240,12 @@
   \end{itemize}
   \begin{figure}
     \centering
-    \includegraphics<2>[width=.8\textwidth]{Images/Probes_TRD.png}
+    \includegraphics<2>[width=\textwidth]{Images/Probes_TRD.png}
     \includegraphics<3>[width=.8\textwidth]{Images/assemblage.png}
   \end{figure}
 \end{frame}
 
-\begin{frame}{\emoji{up-arrow} Results --- \textit{TRD} translocations --- Validation cohort}
+\begin{frame}{\emoji{bar-chart} Results --- \textit{TRD} translocations --- Validation cohort}
   \begin{itemize}
     \item To validate our method, we used a previously published cohort of 264 cases analysed with \alert{\textit{TRD} 
     dual-color FISH probe}$^1$.
@@ -264,7 +265,7 @@
   }
 \end{frame}
 
-\begin{frame}{\emoji{up-arrow} Results --- \textit{TRD} translocations --- Discovery cohort}
+\begin{frame}{\emoji{bar-chart} Results --- \textit{TRD} translocations --- Discovery cohort}
   \begin{figure}
     \includegraphics[height=.8\textheight]{Images/distribution.png}
   \end{figure}
@@ -282,7 +283,7 @@
   }
 \end{frame}
 
-\begin{frame}{\emoji{dart} Results --- \textit{TRD} translocations --- Discovery cohort}
+\begin{frame}{\emoji{round-pushpin} Results --- \textit{TRD} translocations --- Discovery cohort}
   We confirmed all TRECs insertions with sanger sequencing and OGM.
   \begin{figure}
     \includegraphics[width=\textwidth]{Images/ZFP36L2_lolli.pdf}
@@ -302,8 +303,8 @@
       any additional costs.
       \item Our findings provide confirmation that \alert{recurrent TRECs insertions} are present in cases of 
       T-ALL.
-      \item Using our method, we have observed that these recurrent TRECs insertions predominantly 
-      disrupt the \textit{ZFP36L2} genes.
+      \item Using our method, we have observed that these recurrent \alert{TRECs insertions predominantly 
+      disrupt the \textit{ZFP36L2} gene}.
       \item The tumor suppressor \textit{ZFP36L2} is well-established to be involved in V(D)J recombination, 
       but further clarifications are needed regarding its specific role in oncogenesis. Our findings will 
       help in the characterization of this tumor suppressor.
@@ -312,38 +313,152 @@
 \end{frame}
 }
 
-\begin{frame}{\emoji{dart} My PhD --- Rationnal}
+\begin{frame}{\emoji{thinking-face} My PhD --- Epigenetic Rationnal}
   \begin{itemize}
-    \item The aforementioned results contribute to the understanding of the dysregulation of proto-oncogenes 
+    \item<1-> The aforementioned results contribute to the \alert{understanding of the dysregulation of proto-oncogenes} 
     such as \textit{TAL1}, \textit{TLX1} or \textit{TLX3}.
-    \item Despite extensive investigation, the molecular mechanisms underlying the dysregulation of these oncogenes, 
-    remain elusive in many cases. 
-    \item 
+    \item<2-> Despite extensive investigation, \alert{the molecular mechanisms} underlying the dysregulation of these oncogenes, 
+    \alert{remain elusive in many cases}. 
+    \item<3-> It has been demonstrated that \alert{tumor cells acquire enhancers}\footnotemark[1] through intergenic 
+    sequence mutations that enable binding of transcription factors.
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics<3>[width=.75\textwidth]{Images/bradner_cis_small.png}
+  \end{figure}
+  \footnotetext[1]{Bradner JE, et al. Cancer. Cell. 2017 Feb 9;168(4):629-643}
+\end{frame}
+
+\begin{frame}{\emoji{thinking-face} My PhD --- Epigenetic Rationnal}
+  \begin{itemize}
+   \item The presence of upstream \alert{indels in \textit{TAL1} leads to the formation of a neo-enhancer}$^1$.
+   \item It has also been shown that the transcription factor \alert{MYB can bind to this neo-enhancers}$^2$.
+  \end{itemize}
+  \begin{figure}
+    \includegraphics[width=.46\textwidth]{Images/tal_ins.png}
+  \end{figure}
+  \footnotetext[1]{
+    \tiny
+    Navarro JM et al. Nat Commun. 2015;6:6094}
+  \footnotetext[2]{
+    \tiny
+    Smith, C et al. “TAL1 activation in T-cell acute lymphoblastic leukemia: a 
+  novel oncogenic 3' neo-enhancer.” Haematologica vol. 108,5 1259-1271. 1 May. 2023}
+\end{frame}
+
+{\setbeamercolor{background canvas}{bg=bgturq}
+\begin{frame}[c]
+  \vspace{.6cm}
+  \metroset{block=fill}
+  \begin{alertblock}{{\centering \large Hypothesis} }
+    \begin{itemize}
+      \item[A]<1-> By taking a pan-genomic approach, it is possible to identify numerous \alert{intergenic 
+      alterations correlated with the cis deregulation of adjacent genes} (correlation between 
+      transcriptome RNA-seq and ChIP-seq).
+      \item[B]<2-> Some of these genes are expected to be known oncogenes, while others have 
+      the potential to be \alert{novel oncogenes} (discovery).
+      \item[C]<3-> It is likely that these specific alterations are the causative factors 
+      for the cis deregulation of adjacent genes (functional experiments).
+      \item[D]<4-> Based on these alterations, it is possible to stratify patients into 
+      groups with similar \alert{prognoses}.
+      \item[E]<5-> The \alert{characterization of the deregulation mechanisms and the discovered oncogenes} 
+      should help identify vulnerabilities that can be targeted by treatment.
+      \item[F]<6-> This treatment may prove to be \alert{more effective with fewer side effects} compared 
+      to the currently prescribed polychemotherapy.
+    \end{itemize}
+  \end{alertblock}
+\end{frame}
+}
+
+\begin{frame}{\emoji{white-check-mark} What's already done}
+  \begin{itemize}
+    \item[\emoji{white-check-mark}] Alignement and copy number analysis of more than 260 RNA-seq
+  \end{itemize}
+  \begin{figure}
+    \includegraphics[width=\textwidth]{Images/fdt_hm.png}
+  \end{figure}
+\end{frame}
+
+\begin{frame}{\emoji{white-check-mark} What's already done}
+  \begin{itemize}
+    \item[\emoji{white-check-mark}]<1-> Alignement and copy number analysis of more than 260 RNA-seq
+    \item[\emoji{white-check-mark}]<1-> Alignement and copy number analysis of 72 ChIP-seq (H3K4me4 and H4K27ac).
+    \item[\emoji{white-check-mark}]<2-> We have developed a high-performance tool that optimizes memory usage and 
+    speed for correlating variably expressed genes with depth of ChIP-seq peaks. Specifically, our tool 
+    efficiently handles a large dataset consisting of 10,036 gene expressions and 84,839 ChIP-seq positions, 
+    resulting in a total of 851,444,204 correlations.
+    \item[\emoji{white-check-mark}]<3-> Calling of genetic alterations sequenced by ChIP-seq.
+  \end{itemize}
+\end{frame}
+
+\begin{frame}{\emoji{dart} First results}
+  With these filters:
+  \begin{itemize}
+    \item Recurrent mutations in the same ChIP-seq peak (> 1 case) with enrichment of the alternative allele (AF > 0.6).
+    \item Cases with the mutations should have correlated genes (Pearson coefficient > 0.7) 
+    significantly upregulated (t-test p value < 0.05)
+  \end{itemize}
+  \begin{figure}
+    \includegraphics[width=\textwidth]{Images/hm_1.png}
+  \end{figure}
+  \vspace{.5cm}
+  \begin{figure}
+    \includegraphics[width=\textwidth]{Images/hm_2.png}
+  \end{figure}
+\end{frame}
+
+\begin{frame}{\emoji{knocked-out-face} Caveats}
+  \begin{itemize}
+    \item<1-> Most of intergenic alterations are \alert{SNPs}.
+    \item<2-> Complexe alterations like \alert{indels and SV are difficult to call with ChIP-seq small reads}.
+    \item[$\rightarrow$]<3-> We are implementing \alert{longreads sequencing} with the Oxford Nanopore Promethion for 
+    resolving complex genomic regions, detecting structural variations, and studying repetitive elements.
+  \end{itemize}
+  \begin{figure}
+    \includegraphics<3>[width=.4\textwidth]{Images/promethion.png}
+  \end{figure}
+\end{frame}
+
+\begin{frame}{\emoji{flying-saucer} Longreads pipeline}
+  \begin{itemize}
+    \item<1-> We will conduct a \alert{whole-genome sequencing of 150 T-ALL cases along with their corresponding constitutional samples}.
+    \item<2-> Our objective is to implement a pipeline capable of \alert{assembling long reads and generating a diploid 
+    reference genome} for each of the cases.
   \end{itemize}
+  \begin{figure}
+    \includegraphics<2->[width=\textwidth]{Images/lr_pipe.png}
+  \end{figure}
+  
+  \footnotetext[1]{
+    \tiny
+    Kolmogorov, Mikhail et al. “Assembly of long, error-prone reads using repeat graphs.” Nature biotechnology 
+    vol. 37,5 (2019): 540-546. doi:10.1038/s41587-019-0072-8}
 \end{frame}
 
-\begin{frame}{\emoji{dart} Troisième année de thèse -- Hypothèses E et F}
+\begin{frame}{\emoji{flying-saucer} Longreads pipeline}
   \begin{itemize}
-   \item Selon les oncogènes identifiés lors des étapes précédentes nous explorerons les possibles interventions thérapeutiques
-   \item Possibilité de test phramacologiques \textit{ex vivo} et \textit{in vivo}. 
+    \item<1-> We will conduct a \alert{whole-genome sequencing of 150 T-ALL cases along with their corresponding constitutional samples}.
+    \item<1-> Our objective is to implement a pipeline capable of \alert{assembling long reads and generating a diploid 
+    reference genome} for each of the cases.
+    \item<1-> The alignment of somatic reads on it and the subsequent calling of somatic variants, 
+    especially \alert{structural variations} (SV), will be of significant interest.
+    \item<2-> By aligning our current RNA-seq and ChIP-seq data using this approach, we will be able to \alert{phase gene 
+    expression} and identify \alert{allele-enriched epigenetic marks} more efficiently.
+    \item<3-> We will also have access to \alert{phased methylation of CpG islands} with the same technic.
   \end{itemize}
 \end{frame}
 
 % qrencode https://git.t0m4.fr/Thomas/presentation_projet_inserm/raw/master/presentation.pdf -t SVG | sed  's/"#000000"/"#e3b505"/g' | sed 's/"#ffffff"/"#23373B"/g' | /Applications/Inkscape.app/Contents/MacOS/inkscape -p Images/qr-code.pdf
 \begin{frame}[standout]
-  \alert{\textbf{Questions ?}}\\
-  \vspace*{1.5cm}
-  \emoji{calling}
+  \vspace*{1cm}
+  \textcolor[HTML]{e3b505}{Thank you for listening !}\\
+  \textcolor[HTML]{e3b505}{\textbf{Questions ?}}\\
+  \vspace*{1cm}
   \begin{figure}
     \includegraphics[width=.2\textwidth]{Images/qr-code.pdf}
   \end{figure}
 \end{frame}
 
-% \begin{frame}
-%   \frametitle{\emoji{floppy-disk} Méthodes > Calling > Lancet}
-%   Source code : \url{https://github.com/nygenome/lancet}
-%   \vskip 0.2in
-%   \lstinputlisting[language=bash, caption={lancet -- bash version}, style=mystyle]{Codes/lancet.txt}
-% \end{frame}
+% qrencode https://git.t0m4.fr/Thomas/presentation_projet_inserm/raw/master/presentation.pdf -t SVG | sed  's/"#000000"/"#e3b505"/g' | sed 's/"#ffffff"/"#23373B"/g' | /Applications/Inkscape.app/Contents/MacOS/inkscape -p  --without-gui --export-pdf=Images/qr-code.pdf
 
 \end{document}