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Merge pull request #362 from monarch-initiative/curate/rump-research-src-tests-refs-2026-02-16
Add remaining reference cache, research, src, and test updates
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‎references_cache/DOI_10.1016_j.ajhg.2011.01.015.md‎

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reference_id: "DOI:10.1016/j.ajhg.2011.01.015"
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title: Exome Sequencing Identifies Truncating Mutations in Human SERPINF1 in Autosomal-Recessive Osteogenesis Imperfecta
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authors:
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- Jutta Becker
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- Oliver Semler
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- Christian Gilissen
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- Yun Li
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- Hanno Jörn Bolz
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- Cecilia Giunta
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- Carsten Bergmann
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- Marianne Rohrbach
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- Friederike Koerber
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- Katharina Zimmermann
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- Petra de Vries
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- Brunhilde Wirth
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- Eckhard Schoenau
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- Bernd Wollnik
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- Joris A. Veltman
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- Alexander Hoischen
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- Christian Netzer
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journal: The American Journal of Human Genetics
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year: '2011'
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doi: 10.1016/j.ajhg.2011.01.015
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content_type: unavailable
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---
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# Exome Sequencing Identifies Truncating Mutations in Human SERPINF1 in Autosomal-Recessive Osteogenesis Imperfecta
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**Authors:** Jutta Becker, Oliver Semler, Christian Gilissen, Yun Li, Hanno Jörn Bolz, Cecilia Giunta, Carsten Bergmann, Marianne Rohrbach, Friederike Koerber, Katharina Zimmermann, Petra de Vries, Brunhilde Wirth, Eckhard Schoenau, Bernd Wollnik, Joris A. Veltman, Alexander Hoischen, Christian Netzer
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**Journal:** The American Journal of Human Genetics (2011)
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**DOI:** [10.1016/j.ajhg.2011.01.015](https://doi.org/10.1016/j.ajhg.2011.01.015)
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## Content

‎references_cache/DOI_10.1016_j.ijcard.2022.06.019.md‎

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reference_id: "DOI:10.1016/j.ijcard.2022.06.019"
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title: "Outcomes in patients experiencing complications associated with atrial fibrillation ablation: Data from the German Ablation Registry"
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authors:
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- Shinwan Kany
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- Karl-Heinz Kuck
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- Johannes Brachmann
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- Dietrich Andresen
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- Stephan Willems
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- Lars Eckardt
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- Matthias Hochadel
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- Jochen Senges
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- Andreas Metzner
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- Andreas Rillig
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journal: International Journal of Cardiology
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year: '2022'
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doi: 10.1016/j.ijcard.2022.06.019
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content_type: unavailable
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---
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# Outcomes in patients experiencing complications associated with atrial fibrillation ablation: Data from the German Ablation Registry
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**Authors:** Shinwan Kany, Karl-Heinz Kuck, Johannes Brachmann, Dietrich Andresen, Stephan Willems, Lars Eckardt, Matthias Hochadel, Jochen Senges, Andreas Metzner, Andreas Rillig
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**Journal:** International Journal of Cardiology (2022)
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**DOI:** [10.1016/j.ijcard.2022.06.019](https://doi.org/10.1016/j.ijcard.2022.06.019)
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## Content

‎references_cache/DOI_10.1016_j.jbc.2024.107995.md‎

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reference_id: "DOI:10.1016/j.jbc.2024.107995"
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title: Engineered bacterial lipoate protein ligase A (lplA) restores lipoylation in cell models of lipoylation deficiency
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authors:
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- Nolan R. Bick
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- Margaret B. Dreishpoon
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- Ava Perry
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- Anna Rogachevskaya
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- Sylvia S. Bottomley
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- Mark D. Fleming
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- Sarah Ducamp
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- Peter Tsvetkov
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journal: Journal of Biological Chemistry
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year: '2024'
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doi: 10.1016/j.jbc.2024.107995
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content_type: unavailable
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---
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# Engineered bacterial lipoate protein ligase A (lplA) restores lipoylation in cell models of lipoylation deficiency
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**Authors:** Nolan R. Bick, Margaret B. Dreishpoon, Ava Perry, Anna Rogachevskaya, Sylvia S. Bottomley, Mark D. Fleming, Sarah Ducamp, Peter Tsvetkov
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**Journal:** Journal of Biological Chemistry (2024)
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**DOI:** [10.1016/j.jbc.2024.107995](https://doi.org/10.1016/j.jbc.2024.107995)
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## Content

‎references_cache/DOI_10.1038_ng1511.md‎

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reference_id: "DOI:10.1038/ng1511"
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title: "A syndrome of altered cardiovascular, craniofacial, neurocognitive and skeletal development caused by mutations in TGFBR1 or TGFBR2"
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authors:
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- Bart L Loeys
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- Junji Chen
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- Enid R Neptune
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- Daniel P Judge
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- Megan Podowski
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- Tammy Holm
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- Jennifer Meyers
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- Carmen C Leitch
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- Nicholas Katsanis
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- Neda Sharifi
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- F Lauren Xu
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- Loretha A Myers
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- Philip J Spevak
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- Duke E Cameron
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- Julie De Backer
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- Jan Hellemans
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- Yan Chen
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- Elaine C Davis
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- Catherine L Webb
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- Wolfram Kress
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- Paul Coucke
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- Daniel B Rifkin
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- Anne M De Paepe
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- Harry C Dietz
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journal: Nature Genetics
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year: '2005'
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doi: 10.1038/ng1511
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content_type: unavailable
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---
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# A syndrome of altered cardiovascular, craniofacial, neurocognitive and skeletal development caused by mutations in TGFBR1 or TGFBR2
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**Authors:** Bart L Loeys, Junji Chen, Enid R Neptune, Daniel P Judge, Megan Podowski, Tammy Holm, Jennifer Meyers, Carmen C Leitch, Nicholas Katsanis, Neda Sharifi, F Lauren Xu, Loretha A Myers, Philip J Spevak, Duke E Cameron, Julie De Backer, Jan Hellemans, Yan Chen, Elaine C Davis, Catherine L Webb, Wolfram Kress, Paul Coucke, Daniel B Rifkin, Anne M De Paepe, Harry C Dietz
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**Journal:** Nature Genetics (2005)
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**DOI:** [10.1038/ng1511](https://doi.org/10.1038/ng1511)
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## Content

‎references_cache/DOI_10.1038_s41431-022-01279-4.md‎

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reference_id: "DOI:10.1038/s41431-022-01279-4"
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title: Truncating variants in the penultimate exon of TGFBR1 escaping nonsense-mediated mRNA decay cause Loeys-Dietz syndrome
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authors:
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- Paola Fortugno
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- Rosanna Monetta
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- Valeria Cinquina
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- Chiara Rigon
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- Francesca Boaretto
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- Chiara De Luca
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- Nicoletta Zoppi
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- Luana Di Leandro
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- Emanuela De Domenico
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- Arianna Di Daniele
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- Rodolfo Ippoliti
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- Francesco Angelucci
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- Ernesto Di Cesare
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- Ruggero De Paulis
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- Leonardo Salviati
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- Marina Colombi
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- Francesco Brancati
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- Marco Ritelli
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journal: European Journal of Human Genetics
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year: '2023'
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doi: 10.1038/s41431-022-01279-4
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content_type: unavailable
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---
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# Truncating variants in the penultimate exon of TGFBR1 escaping nonsense-mediated mRNA decay cause Loeys-Dietz syndrome
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**Authors:** Paola Fortugno, Rosanna Monetta, Valeria Cinquina, Chiara Rigon, Francesca Boaretto, Chiara De Luca, Nicoletta Zoppi, Luana Di Leandro, Emanuela De Domenico, Arianna Di Daniele, Rodolfo Ippoliti, Francesco Angelucci, Ernesto Di Cesare, Ruggero De Paulis, Leonardo Salviati, Marina Colombi, Francesco Brancati, Marco Ritelli
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**Journal:** European Journal of Human Genetics (2023)
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**DOI:** [10.1038/s41431-022-01279-4](https://doi.org/10.1038/s41431-022-01279-4)
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## Content

‎references_cache/DOI_10.1056_NEJMoa055695.md‎

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reference_id: "DOI:10.1056/NEJMoa055695"
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title: Aneurysm Syndromes Caused by Mutations in the TGF-β Receptor
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authors:
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- Bart L. Loeys
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- Ulrike Schwarze
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- Tammy Holm
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- Bert L. Callewaert
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- George H. Thomas
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- Hariyadarshi Pannu
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- Julie F. De Backer
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- Gretchen L. Oswald
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- Sofie Symoens
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- Sylvie Manouvrier
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- Amy E. Roberts
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- Francesca Faravelli
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- M. Alba Greco
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- Reed E. Pyeritz
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- Dianna M. Milewicz
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- Paul J. Coucke
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- Duke E. Cameron
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- Alan C. Braverman
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- Peter H. Byers
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- Anne M. De Paepe
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- Harry C. Dietz
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journal: New England Journal of Medicine
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year: '2006'
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doi: 10.1056/NEJMoa055695
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content_type: unavailable
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---
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# Aneurysm Syndromes Caused by Mutations in the TGF-β Receptor
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**Authors:** Bart L. Loeys, Ulrike Schwarze, Tammy Holm, Bert L. Callewaert, George H. Thomas, Hariyadarshi Pannu, Julie F. De Backer, Gretchen L. Oswald, Sofie Symoens, Sylvie Manouvrier, Amy E. Roberts, Francesca Faravelli, M. Alba Greco, Reed E. Pyeritz, Dianna M. Milewicz, Paul J. Coucke, Duke E. Cameron, Alan C. Braverman, Peter H. Byers, Anne M. De Paepe, Harry C. Dietz
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**Journal:** New England Journal of Medicine (2006)
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**DOI:** [10.1056/NEJMoa055695](https://doi.org/10.1056/NEJMoa055695)
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## Content

‎references_cache/DOI_10.3390_antiox13081023.md‎

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reference_id: "DOI:10.3390/antiox13081023"
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title: A Multi-Target Pharmacological Correction of a Lipoyltransferase LIPT1 Gene Mutation in Patient-Derived Cellular Models
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authors:
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- David Gómez-Fernández
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- Ana Romero-González
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- Juan M. Suárez-Rivero
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- Paula Cilleros-Holgado
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- Mónica Álvarez-Córdoba
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- Rocío Piñero-Pérez
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- José Manuel Romero-Domínguez
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- Diana Reche-López
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- Alejandra López-Cabrera
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- Salvador Ibáñez-Mico
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- Marta Castro de Oliveira
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- Andrés Rodríguez-Sacristán
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- Susana González-Granero
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- José Manuel García-Verdugo
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- José A. Sánchez-Alcázar
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journal: Antioxidants
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year: '2024'
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doi: 10.3390/antiox13081023
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content_type: abstract_only
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---
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# A Multi-Target Pharmacological Correction of a Lipoyltransferase LIPT1 Gene Mutation in Patient-Derived Cellular Models
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**Authors:** David Gómez-Fernández, Ana Romero-González, Juan M. Suárez-Rivero, Paula Cilleros-Holgado, Mónica Álvarez-Córdoba, Rocío Piñero-Pérez, José Manuel Romero-Domínguez, Diana Reche-López, Alejandra López-Cabrera, Salvador Ibáñez-Mico, Marta Castro de Oliveira, Andrés Rodríguez-Sacristán, Susana González-Granero, José Manuel García-Verdugo, José A. Sánchez-Alcázar
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**Journal:** Antioxidants (2024)
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**DOI:** [10.3390/antiox13081023](https://doi.org/10.3390/antiox13081023)
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## Content
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Mutations in the lipoyltransferase 1 (LIPT1) gene are rare inborn errors of metabolism leading to a fatal condition characterized by lipoylation defects of the 2-ketoacid dehydrogenase complexes causing early-onset seizures, psychomotor retardation, abnormal muscle tone, severe lactic acidosis, and increased urine lactate, ketoglutarate, and 2-oxoacid levels. In this article, we characterized the disease pathophysiology using fibroblasts and induced neurons derived from a patient bearing a compound heterozygous mutation in LIPT1. A Western blot analysis revealed a reduced expression of LIPT1 and absent expression of lipoylated pyruvate dehydrogenase E2 (PDH E2) and alpha-ketoglutarate dehydrogenase E2 (α-KGDH E2) subunits. Accordingly, activities of PDH and α-KGDH were markedly reduced, associated with cell bioenergetics failure, iron accumulation, and lipid peroxidation. In addition, using a pharmacological screening, we identified a cocktail of antioxidants and mitochondrial boosting agents consisting of pantothenate, nicotinamide, vitamin E, thiamine, biotin, and α-lipoic acid, which is capable of rescuing LIPT1 pathophysiology, increasing the LIPT1 expression and lipoylation of mitochondrial proteins, improving cell bioenergetics, and eliminating iron overload and lipid peroxidation. Furthermore, our data suggest that the beneficial effect of the treatment is mainly mediated by SIRT3 activation. In conclusion, we have identified a promising therapeutic approach for correcting LIPT1 mutations.

‎references_cache/GEO_GSE104922.md‎

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reference_id: "GEO:GSE104922"
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title: Molecular subtype classification of urothelial carcinoma in Lynch syndrome
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content_type: summary
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# Molecular subtype classification of urothelial carcinoma in Lynch syndrome
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## Content
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We aimed to provide a molecular description of Lynch syndrome-associated urothelial cancer in relation to molecular subtypes of sporadic bladder cancer. Whole genome mRNA expression profiles of 41 tumors and immunohistochemical stainings against FGFR3, KRT5, CCNB1, RB1, and CDKN2A (p16) of 37 tumors from Lynch syndrome patients were generated. Pathological data, microsatellite instability, anatomic location, and overall survival data was analyzed and compared with data from sporadic bladder cancer.

‎references_cache/GEO_GSE106500.md‎

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reference_id: "GEO:GSE106500"
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title: Immune Profiling of Premalignant Lesions in Patients with Lynch Syndrome
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content_type: summary
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# Immune Profiling of Premalignant Lesions in Patients with Lynch Syndrome
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## Content
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mRNA expression from adenomas of patients with Lynch Syndrome and Familial Adenomatous Polyposis

‎references_cache/GEO_GSE157591.md‎

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reference_id: "GEO:GSE157591"
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title: MYC Promotes Bone Marrow Stem Cell Dysfunction in Fanconi Anemia
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content_type: summary
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# MYC Promotes Bone Marrow Stem Cell Dysfunction in Fanconi Anemia
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## Content
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We profiled primary HSPCs from Fanconi anemia (FA) patients for single cell transcriptome (scRNA-seq) to identify additional determinants of HSPC impairment leading to the bone marrow failure,. Trajectory analysis revealed that early hematopoietic differentiation potential is preserved in FA HSPCs. As expected, p53 and TGFβ pathway genes were overexpressed in HSPCs from FA patients. The oncogene MYC was also identified as one of the top over-expressed genes in FA HSPCs. Interestingly, we observed co-existence of “High-TP53” expressing HSPCs and HighMYC expressing HSPCs in FA bone marrow. Inhibition of MYC expression by the BET bromodomain inhibitor (+)-JQ1 reduced the clonogenic potential of primary HSPCs from FA patients but rescued the physiological/genotoxic stress in HSPCs from FA mice. The “High-MYC” expressing HSPCs exhibited a significant downregulation of cell adhesion genes, such as CXCR4. Consistently, HSPCs in FA patients showed a defect in adhesion to their bone marrow niche resulting in egression from the bone marrow into peripheral blood. We speculate that MYC overexpression impairs HSPC function and contributes to exhaustion of HSPCs in FA bone marrow.

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