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Article ; Online: Production of kidney organoids arranged around single ureteric bud trees, and containing endogenous blood vessels, solely from embryonic stem cells.

Palakkan, Anwar A / Tarnick, Julia / Waterfall, Martin / Sallam, May / Glykofrydis, Fokion / Elhendawi, Mona / Davies, Jamie A

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12573

Abstract: There is intense worldwide effort in generating kidney organoids from pluripotent stem cells, for research, for disease modelling and, perhaps, for making transplantable organs. Organoids generated from pluripotent stem cells (PSC) possess accurate micro- ...

Abstract	There is intense worldwide effort in generating kidney organoids from pluripotent stem cells, for research, for disease modelling and, perhaps, for making transplantable organs. Organoids generated from pluripotent stem cells (PSC) possess accurate micro-anatomy, but they lack higher-organization. This is a problem, especially for transplantation, as such organoids will not be able to perform their physiological functions. In this study, we develop a method for generating murine kidney organoids with improved higher-order structure, through stages using chimaeras of ex-fetu and PSC-derived cells to a system that works entirely from embryonic stem cells. These organoids have nephrons organised around a single ureteric bud tree and also make vessels, with the endothelial network approaching podocytes.
MeSH term(s)	Animals ; Cell Differentiation/physiology ; Embryonic Stem Cells ; Kidney ; Mice ; Organoids ; Podocytes
Language	English
Publishing date	2022-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16768-1
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Article ; Online: Immune responses in genomically simple SWI/SNF-deficient cancers.

Leruste, Amaury / Chauvin, Céline / Pouponnot, Celio / Bourdeaut, Franck / Waterfall, Joshua J / Piaggio, Eliane

Cancer

2020 Volume 127, Issue 2, Page(s) 172–180

MeSH term(s)	Animals ; Combined Modality Therapy/methods ; DNA Helicases/deficiency ; DNA Helicases/genetics ; DNA-Binding Proteins/deficiency ; DNA-Binding Proteins/genetics ; Disease Models, Animal ; Humans ; Immune Checkpoint Inhibitors/therapeutic use ; Immunity ; Mice ; Mutation ; Neoplasms/drug therapy ; Neoplasms/immunology ; Neoplasms/metabolism ; Neoplasms/radiotherapy ; Nuclear Proteins/deficiency ; Nuclear Proteins/genetics ; Polymorphism, Single Nucleotide ; SMARCB1 Protein/deficiency ; SMARCB1 Protein/genetics ; Transcription Factors/deficiency ; Transcription Factors/genetics ; Treatment Outcome
Chemical Substances	DNA-Binding Proteins ; Immune Checkpoint Inhibitors ; Nuclear Proteins ; PBRM1 protein, human ; SMARCB1 Protein ; SMARCB1 protein, human ; Transcription Factors ; SMARCA4 protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
Keywords	covid19
Language	English
Publishing date	2020-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1429-1
ISSN	1097-0142 ; 0008-543X ; 1934-662X
ISSN (online)	1097-0142
ISSN	0008-543X ; 1934-662X
DOI	10.1002/cncr.33172
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Article: Cell-Free DNA Extracted from CSF for the Molecular Diagnosis of Pediatric Embryonal Brain Tumors.

Chicard, Mathieu / Iddir, Yasmine / Masliah Planchon, Julien / Combaret, Valérie / Attignon, Valéry / Saint-Charles, Alexandra / Frappaz, Didier / Faure-Conter, Cécile / Beccaria, Kévin / Varlet, Pascale / Geoerger, Birgit / Baulande, Sylvain / Pierron, Gaelle / Bouchoucha, Yassine / Doz, François / Delattre, Olivier / Waterfall, Joshua J / Bourdeaut, Franck / Schleiermacher, Gudrun

Cancers

2023 Volume 15, Issue 13

Abstract: Background: Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA ...

Abstract	Background: Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA might be more informative than plasma cfDNA. Here, we assess the use of CSF cfDNA in pediatric embryonal brain tumors (EBT) for molecular diagnosis. Methods: The CSF cfDNA of pediatric patients with medulloblastoma ( Results: 15/25 CSF cfDNA samples yielded informative results, with informative CNA and SNVs in 11 and 15 cases, respectively. For cases with paired tumor and CSF cfDNA WES ( Conclusion: CSF cfDNA sequencing yielded informative results in 60% (15/25) of all cases, with informative results in 83% (15/18) of all cases analyzed by WES. These results pave the way for the implementation of these novel approaches for molecular diagnosis and minimal residual disease monitoring.
Language	English
Publishing date	2023-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15133532
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Article: Immune responses in genomically simple SWI/SNF-deficient cancers

Leruste, Amaury / Chauvin, Céline / Pouponnot, Celio / Bourdeaut, Franck / Waterfall, Joshua J / Piaggio, Eliane

Cancer

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #33079397
Database	COVID19

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Article ; Online: Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions.

Vibert, Julien / Saulnier, Olivier / Collin, Céline / Petit, Floriane / Borgman, Kyra J E / Vigneau, Jérômine / Gautier, Maud / Zaidi, Sakina / Pierron, Gaëlle / Watson, Sarah / Gruel, Nadège / Hénon, Clémence / Postel-Vinay, Sophie / Deloger, Marc / Raynal, Virginie / Baulande, Sylvain / Laud-Duval, Karine / Hill, Véronique / Grossetête, Sandrine /

Dingli, Florent / Loew, Damarys / Torrejon, Jacob / Ayrault, Olivier / Orth, Martin F / Grünewald, Thomas G P / Surdez, Didier / Coulon, Antoine / Waterfall, Joshua J / Delattre, Olivier

Molecular cell

2022 Volume 82, Issue 13, Page(s) 2458–2471.e9

Abstract: Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and ... ...

Abstract	Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neogenes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, we show that hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, this study identifies the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer.
MeSH term(s)	Carcinogenesis/genetics ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic/genetics ; Gene Silencing ; Genome/genetics ; Genomics ; Humans ; Oncogene Proteins, Fusion/genetics ; Oncogene Proteins, Fusion/metabolism ; Oncogenes/genetics ; Proto-Oncogene Protein c-fli-1/genetics ; Proto-Oncogene Protein c-fli-1/metabolism ; Sarcoma, Ewing/genetics ; Sarcoma, Ewing/metabolism ; Sarcoma, Ewing/pathology ; Transcription Factors/genetics ; Transcription, Genetic/genetics
Chemical Substances	Oncogene Proteins, Fusion ; Proto-Oncogene Protein c-fli-1 ; Transcription Factors
Language	English
Publishing date	2022-05-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.04.019
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Article ; Online: Rapid and reversible suppression of ALT by DAXX in osteosarcoma cells.

Yost, Kathryn E / Clatterbuck Soper, Sarah F / Walker, Robert L / Pineda, Marbin A / Zhu, Yuelin J / Ester, Corbin D / Showman, Soyeon / Roschke, Anna V / Waterfall, Joshua J / Meltzer, Paul S

Scientific reports

2019 Volume 9, Issue 1, Page(s) 4544

Abstract: Many tumors maintain chromosome-ends through a telomerase-independent, DNA-templated mechanism called alternative lengthening of telomeres (ALT). While ALT occurs in only a subset of tumors, it is strongly associated with mutations in the genes ATRX and ... ...

Abstract	Many tumors maintain chromosome-ends through a telomerase-independent, DNA-templated mechanism called alternative lengthening of telomeres (ALT). While ALT occurs in only a subset of tumors, it is strongly associated with mutations in the genes ATRX and DAXX, which encode components of an H3.3 histone chaperone complex. The role of ATRX and DAXX mutations in potentiating the mechanism of ALT remains incompletely understood. Here we characterize an osteosarcoma cell line, G292, with wild-type ATRX but a unique chromosome translocation resulting in loss of DAXX function. While ATRX and DAXX form a complex in G292, this complex fails to localize to nuclear PML bodies. We demonstrate that introduction of wild type DAXX suppresses the ALT phenotype and restores the localization of ATRX/DAXX to PML bodies. Using an inducible system, we show that ALT-associated PML bodies are disrupted rapidly following DAXX induction and that ALT is again restored following withdrawal of DAXX.
MeSH term(s)	Bone Neoplasms/genetics ; Bone Neoplasms/pathology ; Co-Repressor Proteins/genetics ; Humans ; Molecular Chaperones/genetics ; Mutation ; Osteosarcoma/genetics ; Osteosarcoma/pathology ; Phenotype ; Telomerase/genetics ; Telomerase/metabolism ; Telomere Homeostasis ; Tumor Cells, Cultured
Chemical Substances	Co-Repressor Proteins ; DAXX protein, human ; Molecular Chaperones ; TERT protein, human (EC 2.7.7.49) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2019-03-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-41058-8
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Article ; Online: Evolution of synchronous female bilateral breast cancers and response to treatment.

Hamy, Anne-Sophie / Abécassis, Judith / Driouch, Keltouma / Darrigues, Lauren / Vandenbogaert, Mathias / Laurent, Cecile / Zaccarini, Francois / Sadacca, Benjamin / Delomenie, Myriam / Laas, Enora / Mariani, Odette / Lam, Thanh / Grandal, Beatriz / Laé, Marick / Bieche, Ivan / Vacher, Sophie / Pierga, Jean-Yves / Brain, Etienne / Vallot, Celine /

Hotton, Judicael / Richer, Wilfrid / Rocha, Dario / Tariq, Zakia / Becette, Veronique / Meseure, Didier / Lesage, Laetitia / Vincent-Salomon, Anne / Filmann, Natalie / Furlanetto, Jenny / Loibl, Sibylle / Dumas, Elise / Waterfall, Joshua J / Reyal, Fabien

Nature medicine

2023 Volume 29, Issue 3, Page(s) 646–655

Abstract: Synchronous bilateral breast cancer (sBBC) occurs after both breasts have been affected by the same germline genetics and environmental exposures. Little evidence exists regarding immune infiltration and response to treatment in sBBCs. Here we show that ... ...

Abstract	Synchronous bilateral breast cancer (sBBC) occurs after both breasts have been affected by the same germline genetics and environmental exposures. Little evidence exists regarding immune infiltration and response to treatment in sBBCs. Here we show that the impact of the subtype of breast cancer on levels of tumor infiltrating lymphocytes (TILs, n = 277) and on pathologic complete response (pCR) rates (n = 140) differed according to the concordant or discordant subtype of breast cancer of the contralateral tumor: luminal breast tumors with a discordant contralateral tumor had higher TIL levels and higher pCR rates than those with a concordant contralateral tumor. Tumor sequencing revealed that left and right tumors (n = 20) were independent regarding somatic mutations, copy number alterations and clonal phylogeny, whereas primary tumor and residual disease were closely related both from the somatic mutation and from the transcriptomic point of view. Our study indicates that tumor-intrinsic characteristics may have a role in the association of tumor immunity and pCR and demonstrates that the characteristics of the contralateral tumor are also associated with immune infiltration and response to treatment.
MeSH term(s)	Female ; Humans ; Breast Neoplasms/pathology ; Breast/pathology ; Lymphocytes, Tumor-Infiltrating ; Neoadjuvant Therapy ; Gene Expression Profiling
Language	English
Publishing date	2023-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-023-02216-8
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Article ; Online: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups.

Lobón-Iglesias, María-Jesús / Andrianteranagna, Mamy / Han, Zhi-Yan / Chauvin, Céline / Masliah-Planchon, Julien / Manriquez, Valeria / Tauziede-Espariat, Arnault / Turczynski, Sandrina / Bouarich-Bourimi, Rachida / Frah, Magali / Dufour, Christelle / Blauwblomme, Thomas / Cardoen, Liesbeth / Pierron, Gaelle / Maillot, Laetitia / Guillemot, Delphine / Reynaud, Stéphanie / Bourneix, Christine / Pouponnot, Célio /

Surdez, Didier / Bohec, Mylene / Baulande, Sylvain / Delattre, Olivier / Piaggio, Eliane / Ayrault, Olivier / Waterfall, Joshua J / Servant, Nicolas / Beccaria, Kevin / Dangouloff-Ros, Volodia / Bourdeaut, Franck

Nature communications

2023 Volume 14, Issue 1, Page(s) 6669

Abstract: Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26- ... ...

Abstract	Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-Cre
MeSH term(s)	Humans ; Rhabdoid Tumor/genetics ; Multiomics ; SMARCB1 Protein/genetics ; Transcription Factors/genetics ; Brain Neoplasms/genetics ; Diagnostic Imaging ; Teratoma/pathology ; Hedgehog Proteins/genetics
Chemical Substances	SMARCB1 Protein ; Transcription Factors ; SHH protein, human ; Hedgehog Proteins
Language	English
Publishing date	2023-10-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42371-7
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Article ; Online: Author Correction: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans.

Nature communications

2020 Volume 11, Issue 1, Page(s) 700

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-01-30
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-14448-0
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Article ; Online: Splicing Patterns in

Bigot, Jeremy / Lalanne, Ana I / Lucibello, Francesca / Gueguen, Paul / Houy, Alexandre / Dayot, Stephane / Ganier, Olivier / Gilet, Jules / Tosello, Jimena / Nemati, Fariba / Pierron, Gaelle / Waterfall, Joshua J / Barnhill, Raymond / Gardrat, Sophie / Piperno-Neumann, Sophie / Popova, Tatiana / Masson, Vanessa / Loew, Damarys / Mariani, Pascale /

Cassoux, Nathalie / Amigorena, Sebastian / Rodrigues, Manuel / Alsafadi, Samar / Stern, Marc-Henri / Lantz, Olivier

Cancer discovery

2021 Volume 11, Issue 8, Page(s) 1938–1951

Abstract: Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neoantigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In ... ...

Abstract	Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neoantigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In this study, we show that mutations of the splicing factor
MeSH term(s)	Alternative Splicing ; Humans ; Melanoma/genetics ; Phosphoproteins/genetics ; RNA Splicing Factors/genetics ; Uveal Neoplasms/genetics
Chemical Substances	Phosphoproteins ; RNA Splicing Factors ; SF3B1 protein, human
Language	English
Publishing date	2021-04-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-20-0555
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