Intitulé du sujet: Harnessing knowledge on mechanisms of Biliary Atresia from cutting edge genomic analyses to functional studies in patient derived organoid models

Sujet

Codirection: No co-direction, the only Thesis director in the host lab is Dr. Muriel GIRARD, MD-PhD, MCU-PH, HDR

Nombre de mois: 48 mois

Ecole Doctorale: ED 562 - Bio Sorbonne Paris Cité

Unité de recherche et équipe:

INSERM U1151/CNRS UMR 8253, Institute Necker Enfants Malades (INEM, http://www.institut-necker-enfants-malades.fr/)

Laboratory of Nutrient Sensing Mechanisms (www.panasyuklab.fr)

Coordonnées de l’équipe:

Laboratory of Nutrient Sensing Mechanisms, Team 17

156-160 Rue Vaugirard,
Paris 75015,
France
WEB: www.panasyuklab.fr

Secteur: Sciences de la vie / Life Sciences

Langue attendue: Anglais

Niveau de langue attendu: B2

Description

Description du sujet:

In the Panasyuk Lab we want to know: How the detrimental alterations in nutrient sensing signaling and altered cellular metabolic activities could lead to human diseases? We focus on central for metabolic control signaling pathways controlled by PI3K and mTOR kinases and we aim to harness new knowledge about their implication in rare diseases such as lysosomal storage diseases and hepatobiliary diseases (www.panasyuklab.fr). The research program that we develop is funded by highly prestigious EU ERC grant as well as national funding agencies (ANR, FRM). Our leadership is validated by the publications in the high-ranking journals including Nature Cell Biology, Nature Comm, JCI.

In frame of the on-going funded research in the lab, the proposed PhD project aims to understand the causes and the mechanisms of rare hepatobiliary disease – Biliary Atresia (BA). BA is a severe uncurable pediatric liver disease manifested as a fibroinflammatory destruction of the biliary ducts. There are no drugs for BA making it the most common cause of liver transplantation in children. Despite its serious health impact and high socioeconomic cost, there is no consensus about the molecular mechanisms underlying failed cholangiocyte and hepatocyte homeostasis in BA.  Prior genetic analyses in BA concluded that its inheritance is not Mendelian. Potential mutations in ADD3, GPC1, EFEMP1 and ARF6 genes have been associated with BA in different populations and mutations in the PKD1L1 gene have been found in rare patients with a syndromic form. However, no follow-up functional studies validated their contribution to BA with the most recent exception of PKD1L1. Yet, the PKD1L1 variant is only identified in extremely rare cases, thus cannot be generalized as causative in BA. Moreover, recent advances in whole exome sequencing in different populations pointed to potential alterations in primary cilia and cytoskeleton genes did not reveal a unique genetic alteration profile in BA. In sum, although these studies identified several predisposition loci and rare gene variants associated with BA pointing it out as a polygenic disease, they did not propose a unifying mechanistic picture of its pathogenicity. Thus, we hypothesized that the genetic analyses in the patient population with the highest incidence of disease could be much more informative due to patient homogenous genetic background. This idea is backed by our unpublished observations of GWAS analyses in the unique cohort of BA patients from French Polynesia that show extremely elevated rate of BA compared to the French European population or the rest of the world (1:7000 instead of 1:20 000). These analyses pointed to interesting genetic alteration in a locus that was not suggested by previous works. Thus, we now wish to conduct in this cohort of BA patients the whole genome sequencing that may point to unanticipated potentially disease-causing genetic alterations. To this end, we are seeking for a motivated PhD candidate to develop an interdisciplinary highly translational research program addressing an urgent need to understand Biliary Atresia through combining genetic analyses in patients, cell biology and molecular analyses in the organoid models derived from available on-site patient liver material coupled with multi-omics analyses.

The PhD project will be developed under the supervision of MD-PhD, an expert in medical genetics and leading BA hepatologist on Necker Hospital campus.

The PhD project will focus on following three major axes:

(1) To perform whole genome analyses in the cohort of patients with BA from French Polynesia (samples available). These will be followed by functional analyses of identified targets;

(2) To conduct the functional studies in cellular pre-clinical models of BA. To this end the unique patient derived cholangiocyte and hepatocyte organoid 3D culture models will be established (samples available and expertise present on site);

(3) To explore multi-omics analyses in liver tissue, in organoid models of BA patients as well as in liver and biliary tissue from available mouse models of BA disease. These will be complemented by the functional analyses following data integration to evaluate contribution of identified pathways/gene targets (the host lab has a validated by high-profile publications expertise in conducting mechanistic studies).

On completion, the proposed PhD project will bring advances in understanding the mechanisms driving to liver failure manifested by severe form of hepato-biliary fibrosis in BA, the knowledge that potentially could be translated to other rare hepatobiliary diseases and might lead to development of novel therapies in future.

More details on the project will be provided during the interview with the interested candidates.

Environment: The Panasyuk Lab is proud to belong to INSERM, which is a widely known, public organisation for fundamental and translational medical research. Our laboratory is based in central Paris, on the campus of internationally renowned Necker Hospital. Our lab fully exploits the exceptional translational opportunities of Necker campus, such as close working relationships with the Clinical Biochemistry and Hepatobiliary disease units of Necker Hospital, and tight interaction with rare disease patient associations. We belong to a multidisciplinary international research centre of molecular medicine – the Institute Necker Enfants Malades (INEM, https://institut-necker-enfants-malades.fr) which is located in newly refurbished premises of Paris Descartes University Medical School (University Paris Cite). INEM provides excellent institute infrastructure (modern spacious lab layout, library, on-site restaurant and gym for staff) as well as access to 17 on-site state-of-the-art core facilities (https://www.sfr-necker.fr/), all to promote an engaging international work environment to conduct collaborative translational research. The PhD trainee will be trained in a highly dynamic scientifically stimulating English working language environment hand-in-hand with fellows from all over the world (www.panasyuklab.fr). The trainee will thrive on the opportunities to communicate with researchers of different levels and diverse research fields as well as from the training of both hard and soft skills through multiple available courses at University Paris Cite and INSERM.

Compétences requises:

We aim to recruit an enthusiastic, creative, scientifically driven PhD trainee motivated in conducting collaborative research employing a wide range of wet lab and computational approaches. This project is for you is you are interested in becoming proficient with unbiased genomic analyses, medical genetics and disease modelling in patient derived organoid models. We are looking for a trustworthy team player with the ability to work with others in a collegiate, and collaborative environment. You are expected to have MSc qualification in areas of Cell Physiology, Cell Biology, Genetics or Molecular Biology. We invite applications from individuals with a strong background and training in physiology and pathophysiology, expertise in employing cellular and animal models to model disease and conduct mechanistic studies. As a successful candidate you should have confirmed lab experience in conducting research projects that dissected regulatory mechanisms both in cell models and in in vivo models (generation and phenotyping of animal models of disease, sample handling for histological and molecular analyses). The confirmed experience in routine molecular biology and cell biology techniques for protein and gene expression analyses is a must, including techniques such as immunoblot; DNA, RNA and protein extraction; RT-qPCR; cell imaging by immunofluorescent microscopy. Prior experience with isolation and culture of hepatocyte and/or cholangiocyte-derived organoids will be a great bonus, although the training will be also provided on site. First-hand experience with analysing and integration of -omics datasets (NGS, RNA-Seq, ChIP-Seq) is an advantage, yet the training will be available on site. To excel in this project, you should have great communication skills, ability to effectively prioritize, multi-task and work autonomously with a strong work ethic. As we are an international lab, proficiency in English language is a requirement.

Références bibliographiques:

The selected publication of the laboratory:

1. Alkhoury, C., Henneman, N.F., et al. Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis. Nat Cell Biol 25, 975–988 (2023). https://doi.org/10.1038/s41556-023-01171-3
2. Iershov A, et al. The class 3 PI3K coordinates autophagy and mitochondrial lipid catabolism by controlling nuclear receptor PPARα. Nat Commun. 2019, Apr 5;10(1):1566.
3. Nemazanyy I, et al., Class III PI3K controls hepatic insulin receptor function on whole body glucose homeostasis by a retrograde signalling mechanism. Nat. Comm. 2015; 6:8283
4. Patitucci C, et al., Hepatocyte nuclear factor 1α suppresses steatosis-associated liver cancer by inhibiting PPARγ transcription. J Clin Invest. (2017) 127(5): 1873-1888.
5. Shibayama Y, et al. Class 3 phosphoinositide 3-kinase promotes hepatic glucocorticoid receptor stability and transcriptional activity. Acta Physiol (Oxf) 2022;e13793. doi: 10.1111/apha.13793.

The relevant publications of the PhD thesis director

1. Girard M, Douillard C, Debray D et al. Longterm outcome of PMI-CDG patients on D-mannose therapy. J Inherit Metab Dis. 2020;43:1360-1369.
2. Dana J, Girard M, Debray D. Hepatic manifestations of cystic fibrosis. Curr Opin Gastroenterol.2020;36:192-198.
3. Dudoignon B, Huber C, Michot C, et al. Expanding the phenotype in Adams-Oliver syndrome correlating with the genotype. Am J Med Genet A. 2020;182:29–37.
4. Corpechot C, Barbu V, Chazouillères O, et al. Genetic contribution of ABCC2 to Dubin-Johnson syndrome and inherited cholestatic disorders. Liver Int. 2020;40:163–174.
5. Altassan R, Péanne R, Jaeken J et al. International clinical guidelines for the management of phosphomannomutase 2-congenital disorders of glycosylation: Diagnosis, treatment and follow up. 2019.42:577.
6. Brassier A, Krug P, Lacaille F, et al. Long-term outcome of methylmalonic aciduria after kidney, liver, or combined liver-kidney transplantation: The French experience. J Inherit Metab Dis. 2020:43:234-243.
7. Fanna M, Masson G, Capito C, et al. Management of Biliary Atresia in France 1986 to 2015: Long-term Results. J Pediatr Gastroenterol Nutr. 2019.69:416–424.
8. Girard M, Panasyuk G. Genetics in Biliary Atresia. Curr Opin Gastroenterol. 2019 ;35:73-81.
9. Girard M, Poujois A, Fabre M, et al. CCDC115-CDG: A new rare and misleading inherited cause of liver disease. Mol Genet Metab. 2018 ;124:228-235.
10. Girard M, Bizet AA, Lachaux A, Gonzales E, et al. DCDC2 Mutations Cause Neonatal Sclerosing Cholangitis. Hum Mutat. 2016 ;37 :1025-9.
11. Nizery L, Debray D, Sissaoui S, Capito C, Chardot, C, Girard M. Biliary atresia : clinical advences and perspectives. Clinics and research in Hepatology and Gastroenterology.2016 ;40 :281-7.
12. Girard M, Lacaille F, Verkarre V, et al. MYO5B, and BSEP contribute to cholestatic liver disorder in microvillous inclusion disease. Hepatology. 2014;60:301-10
13. Jedraszak G, Girard M, Mellas A, et al. A patient with Simpson-Golabi-Behmel syndrome, biliary cirrhosis and successfull liver transplantation. Am J Med Genet A. 2014 ;164A:774-7.
14. Girard M, Jannot AS, Besnard M, Jacquemin E, Henrion-Caude A. Biliary atresia: Does ethnicity matter? J Hepatol. 2012;57:700-115.
15. Girard M, Franchi-Abella S, Lacaille F, Debray D. Specificities of sclerosing  cholangitis in childhood. Clin Res Hepatol Gastroenterol. 2012. 36:530-5
16. Paganelli M, Stephenne X, Gilis A, Jet al. Neonatal ichthyosis and sclerosing cholangitis syndrome: extremely variable liver disease severity from claudin-1 deficiency. J Pediatr Gastroenterol Nutr. 2011;53:350-4.
17. Girard M, Jannot AS, Besnard M, Leutenegger AL, Jacquemin E, Lyonnet S, Henrion-Caude A. Polynesian ecology determines seasonality of biliary atresia. Hepatology. 2011;54:1893-4.
18. Girard M, Jacquemin E, Munnich A, Lyonnet S, Henrion-Caude A. miR-122 a paradigm for the role of microRNAs in the liver. J Hepatol. 2008:48:648-56.
19. Hermeziu B, Sanlaville D, Girard M, et al. Heterozygous bile salt export pump deficiency: a possible genetic predisposition to strancient neonatal cholestasis. J Pediatr Gastroenterol Nutr. 2006;42:114-6.
20. Girard M, Amiel J, Fabre M, Pariente D, Lyonnet S, Jacquemin E. Adams-Oliver syndrome and hepatoportal sclerosis: occasional association or common mechanism? Am J Med Genet A. 2005;135:186-9.