Chemical Biology of Cancer

“Nature is dominated by chemically favoured processes. While biology is prone to evolution, universal principles of physical chemistry are not (at least not on the same time scale). It is my opinion that life has evolved mechanisms to circumvent undesired chemistry’’ -Raphaël Rodriguez-

Congratulations to Raphaël for the Tetrahedron Young Investigator Award for Bioorganic and Medicinal Chemistry 2019.

Other recent prizes of Raphaël Rodriguez:
2019 Grand Prix de l’Institut de France ‘Charles Defforey’
2019 SUNRISE Cancer Stem Cell Award
2019 i-Lab Award for the company SideROS

Our laboratory has adopted ‘the small molecule approach’ to biology. We study cell biology at the molecular level using an integrated approach combining synthetic organic chemistry and molecular biology techniques. We custom design new probes and protocols to delineate mechanisms of action of small molecules. These includes cutting-edge small molecule imaging in cells by means of click chemistry, next generation sequencing and quantitative proteomics. During the course of our studies, these unbiased methods have led to the identification of novel therapeutic targets such as the lysine acetyl transferase NAT10 as a master regulator of ageing, iron homeostasis has a druggable network in mesenchymal cancer cells and new anti-cancer strategies that consist of altering the chromatin landscape to control genome targeting with cisplatin drugs. The lab is currently focused on developing methods for personalised cancer treatments and elucidating roles of iron in the maintenance of mesenchymal cancer cells. The group seeks to employ universal principles of physical chemistry and knowledge of biology to impact human medicine.


Selected publications

PML-dependent metabolic heterogeneity enhances chemosensitivity in human ovarian cancers. Géraldine Gentric, Yann Kieffer, O. Goundiam, V. Mieulet, C. Bonneau, F. Nemati, Ilse Hurbain, Graça Raposo, T. Popova, M.-H. Stern, V. Lallemand-Breitenbach, A. Vincent-Salomon, H. de Thé, R. Rossignol, Sebastian Müller, Tatiana Cañeque,Raphaël Rodriguez and Fatima Mechta-Grigoriou. Cell Metabolism, 2019, 8, 156-173.

Diverse engineering. Tatiana Cañeque and Raphaël Rodriguez*. News & Views in Nature Chem. (2019), 11, 499-500.

Visualizing biologically active small molecules in cells using click chemistry. Tatiana Cañeque, Sebastian Müller, Raphaël Rodriguez*. Nature Rev. Chem. (2018), 2,  202–215.

Targeting NAT10 enhances healthspan and lifespan in a mouse model of human accelerated aging syndrome. Gabriel Balmus, Delphine Larrieu, Ana C. Barros, Casey Collins, Monica Abrudan, Mukerrem Demir, Nicola Geisler, Christopher J. Lelliott, Jacqui White, Natasha A. Karp, James Atkinson, Andrea Kirton, Matt Jacobsen, Dean Clift, Sanger Mouse Genetics Project, Raphaël Rodriguez, David J. Adams, Stephen P. Jackson. Nature Comm. 9, (2018).

Click chemistry enables preclinical evaluation of targeted epigenetic therapies. Dean S. Tyler, Johanna Vappiani, Tatiana Cañeque, Enid Y. N. Lam, Aoife Ward, Omer Gilan, Yih-Chih Chan, Antje Hienzsch, Anna Rutkowska, Thilo Werner, Anne J. Wagner, Dave Lugo, Richard Gregory, Cesar Ramirez Molina, Neil Garton, Christopher R. Wellaway, Susan Jackson, Laura MacPherson, Margarida Figueiredo, Sabine Stolzenburg, Charles C. Bell, Colin House, Sarah-Jane Dawson, Edwin D. Hawkins, Gerard Drewes, Rab K. Prinjha, Raphaël Rodriguez, Paola Grandi, Mark A. Dawson. Science, 356, 1397-1401 (2017), Highlighted in Nature.

Chromatin regulates genome targeting with cisplatin. Emmanouil Zacharioudakis, Poonam Agarwal, Alexandra Bartoli, Nathan Abell, Lavaniya Kunalingam, Valérie Bergoglio, Blerta Xhemalce, Kyle M. Miller*, Raphaël Rodriguez*. Angew. Chem. Int. Ed. 56, 6483-6487 (2017).

Salinomycin kills cancer stem cells by sequestering iron in lysosomes. Trang Thi Mai, Ahmed Hamaï, Antje Hienzsch, Tatiana Cañeque, Sebastian Müller, Julien Wicinski, Olivier Cabaud, Christine Leroy, Amandine David, Verónica Acevedo, Akihide Ryo, Christophe Ginestier, Daniel Birnbaum, Emmanuelle Charafe-Jauffret, Patrice Codogno, Maryam Mehrpour*, Raphaël Rodriguez*. Nature Chem. 9,1025–1033 (2017), Highlighted in chemical & engineering news.

Click quantitative mass spectrometry identifies PIWIL3 as a mechanistic target of RNA interference activator enoxacin in cancer cells. Nathan S. Abell, Marvin Mercado, Tatiana Cañeque, Raphaël Rodriguez*, Blerta Xhemalce*. J. Am. Chem. Soc. 139, 1400-1403 (2017).

Chromatin dynamics during the cell cycle at centromeres. Sebastian Müller & Geneviève Almouzni. Nature Rev. Genet. 18, 192–208 (2017).

Targeting cancer stem cells with small molecules. Sebastian Müller, Tatiana Cañeque, Verónica Acevedo, Raphaël Rodriguez*. Isr. J. Chem. DOI: 10.1002/ijch.201600109. Special Stuart L. Schreiber & Kyriacos C. Nicolaou Wolf Prize special issue.

Synthesis of marmycin A and investigation into its cellular activity. Tatiana Cañeque, Filipe Gomes, Trang Thi Mai, Giovanni Maestri, Max Malacria, Raphaël Rodriguez*. Nature Chem. 7, 744-751 (2015).

Unravelling the genomic targets of small molecules using high-throughput sequencing. Raphaël Rodriguez*, Kyle M. Miller*. Nature Rev. Genet. 15, 783-796 (2014).

Chemical inhibition of NAT10 corrects defects of laminopathic cells. Delphine Larrieu, Sébastien Britton, Mukerrem Demir, Raphaël Rodriguez*, Stephen P. Jackson*. Science 344, 527-532 (2014), Highlighted in chemical & engineering news.

Modular construction of dynamic nucleodendrimers. Valentina Abet, Robert Evans, Florian Guibbal, Stefano Caldarelli, Raphaël Rodriguez*. Angew. Chem. Int. Ed. 53, 4862-4866 (2014).

Selective RNA versus DNA G-quadruplex targeting by in situ click chemistry. Marco Di Antonio, Giulia Biffi, Angelica Mariani, Eun-Ang Raiber, Raphaël Rodriguez*, Shankar Balasubramanian*. Angew. Chem. Int. Ed. 51, 11073-11078 (2012).

Small molecule-induced DNA damage identifies alternative DNA structures in human genes. Raphaël Rodriguez, Kyle M. Miller, Josep V. Forment, Charles R. Bradshaw, Sébastien Britton, Tobias Oelschlaegel, Mehran Nikan, Blerta Xhemalce, Shankar Balasubramanian, Stephen P. Jackson. Nature Chem. Biol. 8, 301-310 (2012). Highlights in Nature Chem. Biol. and F1000; Most Accessed Article.

A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands. Deepak Koirala, Soma Dhakal, Beth Ashbridge, Yuta Sannohe, Raphaël Rodriguez, Hiroshi Sugiyama, Shankar Balasubramanian, Hanbin Mao. Nature Chem. 3, 782-787 (2011).

The transcription factor FOXM1 is a cellular target of the natural product thiostrepton. Nagaratna S. Hegde, Deborah A. Sanders, Raphaël Rodriguez, Shankar Balasubramanian. Nature Chem. 3, 725-731 (2011).

G-quadruplex-binding benzo[a]phenoxazines down-regulate c-KIT expression in human gastric carcinoma cells. Keith I. E. McLuckie, Zoë A. E. Waller, Deborah A. Sanders, David Alves, Raphaël Rodriguez, Jyotirmayee Dash, Grahame J. McKenzie, Ashok R. Venkitaraman, Shankar Balasubramanian. J. Am. Chem. Soc. 133, 2658-2663 (2011).

Small-molecule-mediated G-quadruplex isolation from human cells. Sebastian Müller, Sunita Kumari, Raphaël Rodriguez*, Shankar Balasubramanian*. Nature Chem. 2, 1095-1098 (2010). Highlight in F1000.

A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres. Raphaël Rodriguez, Sebastian Müller, Justin A. Yeoman, Chantal Trentesaux, Jean-François Riou, Shankar Balasubramanian. J. Am. Chem. Soc. 130, 15758-15759 (2008).

Exploring the differential recognition of DNA G-quadruplex targets by small molecules using dynamic combinatorial chemistry. Anthony Bugaut, Katja Jantos, Jean-Luc Wietor, Raphaël Rodriguez, Jeremy K. M. Sanders, Shankar Balasubramanian. Angew. Chem. Int. Ed. 47, 2677-2680 (2008).

Tri-substituted isoalloxazines as a new class of G-quadruplex binding ligands: small molecule regulation of c-kit oncogene expression. Mallesham Bejugam, Sven Sewitz, Pravin S. Shirude, Raphaël Rodriguez, Ramla Shahid, Shankar Balasubramanian. J. Am. Chem. Soc. 129, 12926-12927 (2007).

Ligand-driven G-quadruplex conformational switching by using an unusual mode of interaction. Raphaël Rodriguez, G. Dan Pantoş, Diana P. N. Gonçalves, Jeremy K. M. Sanders, Shankar Balasubramanian. Angew. Chem. Int. Ed. 46, 5405-5407 (2007).

Oxazole-based peptide macrocycles: a new class of G-quadruplex binding ligands. Katja Jantos, Raphaël Rodriguez, Sylvain Ladame, Pravin S. Shirude, Shankar Balasubramanian. J. Am. Chem. Soc. 128, 13662-13663 (2006).


Key words: small molecules, chromatin biology, epigenetics, traffic, signaling, cancer, EMT, iron metabolism, cell imaging, next generation sequencing, proteomics

Role of chromatin in genotoxic drug responses: Genotoxic agents represent a major class of drugs used in the clinical management of cancer. We seek to establish unbiased protocols based on DNA target pull down coupled to next generation sequencing (e.g. ChIP-Seq, Click-Seq) and quantitative proteomics (e.g. SILAC) to identify genomic targets of these drugs and further delineate and control drug responses. We aim to pharmacologically alter the structure of chromatin to orchestrate the genomic responses of genotoxic agents. We have previously employed small molecule imaging in cells to screen for potential regulators of genome targeting and identified DNMT and HDAC inhibitors that altered genome targeting with cisplatin, activating translesion synthesis and apoptosis. Ultimately, we aim to exploit these technologies to predict and modulate drug responses, a step forward towards personalised medicine.

A) Detection of labeled DNA-Pt in U2OS cells. B) Schematic representation of a strategy for enhancing the detection of DNA-Pt in cells. C) Detection of labeled DNA-Pt in U2OS cells subjected to pre-extraction. Cells were treated with APPA (250 mm for 3 h). Zoomed images are 3x . Scale bar, 20 μm. Unt., untreated.
A) Detection of labeled DNA-Pt in U2OS cells. B) Schematic representation of a strategy for enhancing the detection of DNA-Pt in cells. C) Detection of labeled DNA-Pt in U2OS cells subjected to pre-extraction.

Iron metabolism in EMT and mesenchymal cancer cell maintenance: During embryogenesis, epithelial cells undergo extensive epigenetic reprogramming, allowing them to transdifferentiate and to acquire physical properties of mesenchymal cells, a process called epithelial-to-mesenchymal transition (EMT). In this manner, cells can detach from primary tissues and migrate to distant locations. Theres is a subpopulations of cells able to harness similar mechanisms to disseminate, initiate and sustain tumour growth. We have recently identified iron homeostasis as a druggable network in CSCs, raising a putative role of iron in these cells. Thus, we seek to characterise features of iron homeostasis in CSCs and elucidate its role in the maintenance of these cells.

Salinomycin targets mesenchymal cancer cells by sequestering iron in lysosomes, leading to ROS production and ferroptosis.

Selective targeting of the lysosomal compartment with small molecules: Our laboratory has recently established the first synthetic scheme towards the production of the complex natural products Marmycin A and B in 18 steps. Contrary to belief, we have discovered that these natural products do not target genomic DNA but quantitatively accumulates in lysosomes and enter cells by means of endocytosis. We have taken advantage of this finding to physically drive other small molecules (the effector) inside this organelle by chemically linking these structures to the scaffold of Marmycin (the driver), a strategy we have termed ‘molecular driver’. This strategy enables to virtually deliver any effector in the lysosomal compartment given that hybrid structures also target the plasma membrane in a similar manner thanks to the driver. Proof-of-concept was established through the conception of the hybrid structure we named Artesumycin, a dimer of the natural products Artemisinin and Marmycin A. While Artemisinin does not in itself quantitatively target the lysosomal compartments, we found that Artesumycin, effectively target lysosomes and chemically react with lysosomal iron to produce toxic free radicals. We seek to elaborate on this strategy to target iron homeostasis in the context of cancer.

Artesumycin, a hybrid between Artemisinin and Marmycin that targets the lysosomal compartement.
Artesumycin, a hybrid of Artemisinin and Marmycin that targets the lysosomal compartement.

Key publications

Year of publication 2020

Sebastian Müller, Fabien Sindikubwabo , Tatiana Cañeque, Anne Lafon, Antoine Versini, Bérangère Lombard, Damarys Loew, Ting-Di Wu, Christophe Ginestier, Emmanuelle Charafe-Jauffret, Adeline Durand, Céline Vallot, Sylvain Baulande, Nicolas Servant, Raphaël Rodriguez (2020 Oct 1)

CD44 regulates epigenetic plasticity by mediating iron endocytosis

Nature Chemistry : 12 : 929-938 : DOI : 10.1038/s41557-020-0513-5