Publications 2024

Papers including work performed at the Genomics Platform

Alphabetical order of first authors names

• Abassah-Oppong S, Zoia M, Mannion BJ, Rouco R, Tissières V, Spurrell CH, Roland V, Darbellay F, Itum A, Gamart J, Festa-Daroux TA, Sullivan CS, Kosicki M, Rodríguez-Carballo E, Fukuda-Yuzawa Y, Hunter RD, Novak CS, Plajzer-Frick I, Tran S, Akiyama JA, Dickel DE, Lopez-Rios J, Barozzi I, Andrey G, Visel A, Pennacchio LA, Cobb J, Osterwalder M. A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival. Nat Commun. 2024 Oct 10;15(1):8793. doi: 10.1038/s41467-024-53009-7. PMID: 39389973; PMCID: PMC11467299.

• Abe P, Lavalley A, Morassut I, Santinha AJ, Roig-Puiggros S, Javed A, Klingler E, Baumann N, Prados J, Platt RJ, Jabaudon D. Molecular programs guiding arealization of descending cortical pathways. Nature. 2024 Oct;634(8034):644-651. doi: 10.1038/s41586-024-07895-y. Epub 2024 Sep 11. PMID: 39261725.

• Darbellay F, Ramisch A, Lopez-Delisle L, Kosicki M, Rauseo A, Jouini Z, Visel A, Andrey G. Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development. Nat Commun. 2024 Jun 6;15(1):4820. doi: 10.1038/s41467-024-49203-2. PMID: 38844479; PMCID: PMC11156918.

• Diman A, Panis G, Castrogiovanni C, Prados J, Baechler B, Strubin M. Human Smc5/6 recognises transcription-generated positive DNA supercoils. Nat Commun. 2024 Sep 6;15(1):7805. doi: 10.1038/s41467-024-50646-w. PMID: 39242537; PMCID: PMC11379904.

• Docquier M, Nouspikel T, Blouin JL, Abramowicz M, Seebach JD, Spoerl D. Detection of TPSAB1 copy number variation for the diagnosis of hereditary alpha-tryptasemia by quantitative PCR. Clin Exp Allergy. 2024 Jan;54(1):82-85. doi: 10.1111/cea.14413. Epub 2023 Oct 18. PMID: 37853996.

• Dos Santos S, Diene SM, Benouda A, Zerouali K, Ghaith DM, El-Mahdy RH, El Tayeb SHM, Boutiba I, Hammami A, Chrabieh R, Daoud Z, Mereghetti L, Francois P, Van Der Mee-Marquet N; consortium. Carbapenem- and colistin-resistant Enterobacterales in intensive care unit patients in Mediterranean countries, 2019. Front Microbiol. 2024 Apr 12;15:1370553. doi: 10.3389/fmicb.2024.1370553. PMID: 38680922; PMCID: PMC11045966.

• Dos Santos S, Moussounda M, Togola M, Avoune Nguema E, Matteya C, Bignoumba M, Onanga R, Lekana-Douki JB, François P, van der Mee-Marquet N. Carbapenem-producing Enterobacteriaceae in mothers and newborns in southeast Gabon, 2022. Front Cell Infect Microbiol. 2024 Feb 8;14:1341161. doi: 10.3389/fcimb.2024.1341161. PMID: 38390622; PMCID: PMC10881798.

• Idris T, Bachmann M, Bacchetta M, Wehrle-Haller B, Chanson M, Badaoui M. Akt-driven TGF-β and DKK1 Secretion Impairs F508del CF Airway Epithelium Polarity. Am J Respir Cell Mol Biol. 2024 Mar 26. doi: 10.1165/rcmb.2023-0408OC. Epub ahead of print. PMID: 38531016.

• Larrue C, Mouche S, Angelino P, Sajot M, Birsen R, Kosmider O, Mckee T, Vergez F, Recher C, Mas VM, Gu Q, Xu J, Tsantoulis P, Sarry JE, Tamburini J. Targeting ferritinophagy impairs quiescent cancer stem cells in acute myeloid leukemia in vitro and in vivo models. Sci Transl Med. 2024 Jul 24;16(757):eadk1731. doi: 10.1126/scitranslmed.adk1731. Epub 2024 Jul 24. PMID: 39047119.

• Lefrançois LH, Nitschke J, Wu H, Panis G, Prados J, Butler RE, Mendum TA, Hanna N, Stewart GR, Soldati T. Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals the genetic requirement for virulence and survival in amoebae and microglial cells. mSystems. 2024 Feb 20;9(2):e0132623. doi: 10.1128/msystems.01326-23. Epub 2024 Jan 25. PMID: 38270456; PMCID: PMC10878075.

• Liberini E, Fan SH, Bayer AS, Beck C, Biboy J, François P, Gray J, Hipp K, Koch I, Peschel A, Sailer B, Vollmer D, Vollmer W, Götz F. Staphylococcus aureus Stress Response to Bicarbonate Depletion. Int J Mol Sci. 2024 Aug 26;25(17):9251. doi: 10.3390/ijms25179251. PMID: 39273203; PMCID: PMC11394868.

• Lo Giudice Q, Wagener RJ, Abe P, Frangeul L, Jabaudon D. Developmental emergence of first- and higher-order thalamic neuron molecular identities. Development. 2024 Sep 15;151(18):dev202764. doi: 10.1242/dev.202764. Epub 2024 Sep 30. PMID: 39348458; PMCID: PMC11463969.

• Maas-Bauer K, Köhler N, Stell AV, Zwick M, Acharya S, Rensing-Ehl A, König C, Kroll J, Baker J, Koßmann S, Pradier A, Wang S, Docquier M, Lewis DB, Negrin RS, Simonetta F. Single-cell transcriptomics reveal different maturation stages and sublineage commitment of human thymic invariant natural killer T cells. J Leukoc Biol. 2024 Jan 19;115(2):401-409. doi: 10.1093/jleuko/qiad113. PMID: 37742056; PMCID: PMC10799303.

• Martischang R, Seth-Smith H, Verschuuren TD, Héquet D, Gaïa N, François P, Fluit AC, Kluytmans JAJW, Seiffert SN, Tacconelli E, Cherkaoui A, Harbarth S, Egli A, Kohler P. Regional spread of an atypical ESBL-producing Escherichia coli ST131H89 clone among different human and environmental reservoirs in Western Switzerland. Antimicrob Agents Chemother. 2024 Feb 7;68(2):e0092523. doi: 10.1128/aac.00925-23. Epub 2024 Jan 3. PMID: 38169291; PMCID: PMC10848748.

• Noireterre A, Soudet J, Bagdiul I, Stutz F. The cullin Rtt101 promotes ubiquitin-dependent DNA-protein crosslink repair across the cell cycle. Nucleic Acids Res. 2024 Sep 9;52(16):9654-9670. doi: 10.1093/nar/gkae658. PMID: 39077933; PMCID: PMC11381328.

• Padayachy L, Ntallis SG, Halazonetis TD. RECQL4 is not critical for firing of human DNA replication origins. Sci Rep. 2024 Apr 2;14(1):7708. doi: 10.1038/s41598-024-58404-0. PMID: 38565932; PMCID: PMC10987555.

• Perez-Frances M, Bru-Tari E, Cohrs C, Abate MV, van Gurp L, Furuyama K, Speier S, Thorel F, Herrera PL. Regulated and adaptive in vivo insulin secretion from islets only containing β-cells. Nat Metab. 2024 Sep;6(9):1791-1806. doi: 10.1038/s42255-024-01114-8. Epub 2024 Aug 21. PMID: 39169271; PMCID: PMC11422169.

• Petropoulos M, Karamichali A, Rossetti GG, Freudenmann A, Iacovino LG, Dionellis VS, Sotiriou SK, Halazonetis TD. Transcription-replication conflicts underlie sensitivity to PARP inhibitors. Nature. 2024 Apr;628(8007):433-441. doi: 10.1038/s41586-024-07217-2. Epub 2024 Mar 20. PMID: 38509368; PMCID: PMC11006605.

• Rossetti GG, Dommann N, Karamichali A, Dionellis VS, Asensio Aldave A, Yarahmadov T, Rodriguez-Carballo E, Keogh A, Candinas D, Stroka D, Halazonetis TD. In vivo DNA replication dynamics unveil aging-dependent replication stress. Cell. 2024 Oct 31;187(22):6220-6234.e13. doi: 10.1016/j.cell.2024.08.034. Epub 2024 Sep 17. PMID: 39293447.

• Tankov S, Petrovic M, Lecoultre M, Espinoza F, El-Harane N, Bes V, Chliate S, Bedoya DM, Jordan O, Borchard G, Migliorini D, Dutoit V, Walker PR. Hypoxic glioblastoma-cell-derived extracellular vesicles impair cGAS-STING activity in macrophages. Cell Commun Signal. 2024 Feb 22;22(1):144. doi: 10.1186/s12964-024-01523-y. PMID: 38389103; PMCID: PMC10882937.

• Wang C, Zeng Q, Gül ZM, Wang S, Pick R, Cheng P, Bill R, Wu Y, Naulaerts S, Barnoud C, Hsueh PC, Moller SH, Cenerenti M, Sun M, Su Z, Jemelin S, Petrenko V, Dibner C, Hugues S, Jandus C, Li Z, Michielin O, Ho PC, Garg AD, Simonetta F, Pittet MJ, Scheiermann C. Circadian tumor infiltration and function of CD8⁺ T cells dictate immunotherapy efficacy. Cell. 2024 May 23;187(11):2690-2702.e17. doi: 10.1016/j.cell.2024.04.015. Epub 2024 May 8. PMID: 38723627.