Yassine Zouaghi

All Publications

• Microglia Rank signaling regulates GnRH neuronal function and the hypothalamic-pituitary-gonadal axis. Science (New York, N.Y.) Collado-Sole, A., Borjini, N., Zhai, J., Ruiz-Pino, F., Soria-Alcaide, G., Folgueira, C., García-Vilela, C., Romero-de la Rosa, B., Lopez, V., Zouaghi, Y., Jacobs, A., Mora-Romero, B., Barranco, A., Yoldi, G., Rizzoti, K., Sabio, G., Perez-Chacon, G., Santamaria, P. G., Esteban, J. A., Journiac, N., Prevot, V., Pascual, A., Fernández-Chacón, R., Tena-Sempere, M., Pitteloud, N., Gonzalez-Suarez, E. 2026: eaeb6999

  Abstract

  The hypothalamic-pituitary-gonadal axis (HPG) controls pubertal development, sexual maturation, and fertility. We identified a role of hypothalamic microglia in controlling the HPG axis through receptor activator of nuclear factor κβ (Rank) signaling. Whole-body and microglia Rank depletion led to hypogonadotropic hypogonadism (HH) resulting from an alteration in gonadotropin-releasing hormone (GnRH) neuron function. In addition, we identified rare gene variants of RANK in patients with HH. Transcriptional profiling upon Rank loss revealed defective microglia activation and morphological alterations in the median eminence, decreasing the contacts and engulfment of GnRH terminal projections and impairing GnRH neuronal responses to kisspeptin. Overall, our data uncover the microglia as regulator of GnRH neuronal function through Rank signaling, with potential implications for reproductive maturation and fertility.

  View details for DOI 10.1126/science.aeb6999

  View details for PubMedID 41818388

• Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation. bioRxiv : the preprint server for biology Metzl-Raz, E., Zhao, R., Deshpande, S., Powell, J., Porter, E. G., Zouaghi, Y., Liu, B. B., Kim, S. H., Abdi, I., Evergreen, I., Agarwal, M., Sheth, M. U., Rico, J., Miyamoto, M., Sanchez, J. M., Engreitz, J. M., Kundaje, A., Greenleaf, W. J., Gifford, C. A. 2025

  Abstract

  Defining the temporal gene regulatory programs that drive human organogenesis is essential for understanding the origins of congenital disease. We combined a time-resolved, single-cell multi-omic atlas of human iPSC-derived cardiac organoids with deep learning models that predict chromatin accessibility from DNA sequence, enabling the discovery of the regulatory syntax underlying early heart development. This framework uncovered cell-state-specific rules of cardiogenesis, including context-dependent activities of TEAD, HAND, and TBX transcription factor families, and linked these motifs to their target genes. We identified distinct programs guiding lineage divergence, such as ventricular versus pacemaker cardiomyocytes, and validated predictions by perturbing Myocardin (MYOCD), establishing its essential role in ventricular specification. Integration of chromatin, transcriptional, and genetic data further highlighted regulatory regions and disease-associated variants that perturb differentiation state transitions, supporting evidence that suggests congenital heart disease emerges early in development. This work bridges developmental gene regulation with disease genetics, providing a foundation for mechanistic and therapeutic insights into congenital diseases.

  View details for DOI 10.1101/2025.10.15.680997

  View details for PubMedID 41279701

  View details for PubMedCentralID PMC12632746

• Publisher Correction: Understanding the genetic complexity of puberty timing across the allele frequency spectrum. Nature genetics Kentistou, K. A., Kaisinger, L. R., Stankovic, S., Vaudel, M., Mendes de Oliveira, E., Messina, A., Walters, R. G., Liu, X., Busch, A. S., Helgason, H., Thompson, D. J., Santoni, F., Petricek, K. M., Zouaghi, Y., Huang-Doran, I., Gudbjartsson, D. F., Bratland, E., Lin, K., Gardner, E. J., Zhao, Y., Jia, R. Y., Terao, C., Riggan, M. J., Bolla, M. K., Yazdanpanah, M., Yazdanpanah, N., Bradfield, J. P., Broer, L., Campbell, A., Chasman, D. I., Cousminer, D. L., Franceschini, N., Franke, L. H., Girotto, G., He, C., Järvelin, M. R., Joshi, P. K., Kamatani, Y., Karlsson, R., Luan, J., Lunetta, K. L., Mägi, R., Mangino, M., Medland, S. E., Meisinger, C., Noordam, R., Nutile, T., Concas, M. P., Polašek, O., Porcu, E., Ring, S. M., Sala, C., Smith, A. V., Tanaka, T., van der Most, P. J., Vitart, V., Wang, C. A., Willemsen, G., Zygmunt, M., Ahearn, T. U., Andrulis, I. L., Anton-Culver, H., Antoniou, A. C., Auer, P. L., Barnes, C. L., Beckmann, M. W., Berrington de Gonzalez, A., Bogdanova, N. V., Bojesen, S. E., Brenner, H., Buring, J. E., Canzian, F., Chang-Claude, J., Couch, F. J., Cox, A., Crisponi, L., Czene, K., Daly, M. B., Demerath, E. W., Dennis, J., Devilee, P., De Vivo, I., Dörk, T., Dunning, A. M., Dwek, M., Eriksson, J. G., Fasching, P. A., Fernandez-Rhodes, L., Ferreli, L., Fletcher, O., Gago-Dominguez, M., García-Closas, M., García-Sáenz, J. A., González-Neira, A., Grallert, H., Guénel, P., Haiman, C. A., Hall, P., Hamann, U., Hakonarson, H., Hart, R. J., Hickey, M., Hooning, M. J., Hoppe, R., Hopper, J. L., Hottenga, J. J., Hu, F. B., Huebner, H., Hunter, D. J., Jernström, H., John, E. M., Karasik, D., Khusnutdinova, E. K., Kristensen, V. N., Lacey, J. V., Lambrechts, D., Launer, L. J., Lind, P. A., Lindblom, A., Magnusson, P. K., Mannermaa, A., McCarthy, M. I., Meitinger, T., Menni, C., Michailidou, K., Millwood, I. Y., Milne, R. L., Montgomery, G. W., Nevanlinna, H., Nolte, I. M., Nyholt, D. R., Obi, N., O'Brien, K. M., Offit, K., Oldehinkel, A. J., Ostrowski, S. R., Palotie, A., Pedersen, O. B., Peters, A., Pianigiani, G., Plaseska-Karanfilska, D., Pouta, A., Pozarickij, A., Radice, P., Rennert, G., Rosendaal, F. R., Ruggiero, D., Saloustros, E., Sandler, D. P., Schipf, S., Schmidt, C. O., Schmidt, M. K., Small, K., Spedicati, B., Stampfer, M., Stone, J., Tamimi, R. M., Teras, L. R., Tikkanen, E., Turman, C., Vachon, C. M., Wang, Q., Winqvist, R., Wolk, A., Zemel, B. S., Zheng, W., van Dijk, K. W., Alizadeh, B. Z., Bandinelli, S., Boerwinkle, E., Boomsma, D. I., Ciullo, M., Chenevix-Trench, G., Cucca, F., Esko, T., Gieger, C., Grant, S. F., Gudnason, V., Hayward, C., Kolčić, I., Kraft, P., Lawlor, D. A., Martin, N. G., Nøhr, E. A., Pedersen, N. L., Pennell, C. E., Ridker, P. M., Robino, A., Snieder, H., Sovio, U., Spector, T. D., Stöckl, D., Sudlow, C., Timpson, N. J., Toniolo, D., Uitterlinden, A., Ulivi, S., Völzke, H., Wareham, N. J., Widen, E., Wilson, J. F., Pharoah, P. D., Li, L., Easton, D. F., Njølstad, P. R., Sulem, P., Murabito, J. M., Murray, A., Manousaki, D., Juul, A., Erikstrup, C., Stefansson, K., Horikoshi, M., Chen, Z., Farooqi, I. S., Pitteloud, N., Johansson, S., Day, F. R., Perry, J. R., Ong, K. K. 2024

  View details for DOI 10.1038/s41588-024-01857-w

  View details for PubMedID 38982295

• Understanding the genetic complexity of puberty timing across the allele frequency spectrum. Nature genetics Kentistou, K. A., Kaisinger, L. R., Stankovic, S., Vaudel, M., Mendes de Oliveira, E., Messina, A., Walters, R. G., Liu, X., Busch, A. S., Helgason, H., Thompson, D. J., Santoni, F., Petricek, K. M., Zouaghi, Y., Huang-Doran, I., Gudbjartsson, D. F., Bratland, E., Lin, K., Gardner, E. J., Zhao, Y., Jia, R. Y., Terao, C., Riggan, M. J., Bolla, M. K., Yazdanpanah, M., Yazdanpanah, N., Bradfield, J. P., Broer, L., Campbell, A., Chasman, D. I., Cousminer, D. L., Franceschini, N., Franke, L. H., Girotto, G., He, C., Järvelin, M. R., Joshi, P. K., Kamatani, Y., Karlsson, R., Luan, J., Lunetta, K. L., Mägi, R., Mangino, M., Medland, S. E., Meisinger, C., Noordam, R., Nutile, T., Concas, M. P., Polašek, O., Porcu, E., Ring, S. M., Sala, C., Smith, A. V., Tanaka, T., van der Most, P. J., Vitart, V., Wang, C. A., Willemsen, G., Zygmunt, M., Ahearn, T. U., Andrulis, I. L., Anton-Culver, H., Antoniou, A. C., Auer, P. L., Barnes, C. L., Beckmann, M. W., Berrington de Gonzalez, A., Bogdanova, N. V., Bojesen, S. E., Brenner, H., Buring, J. E., Canzian, F., Chang-Claude, J., Couch, F. J., Cox, A., Crisponi, L., Czene, K., Daly, M. B., Demerath, E. W., Dennis, J., Devilee, P., De Vivo, I., Dörk, T., Dunning, A. M., Dwek, M., Eriksson, J. G., Fasching, P. A., Fernandez-Rhodes, L., Ferreli, L., Fletcher, O., Gago-Dominguez, M., García-Closas, M., García-Sáenz, J. A., González-Neira, A., Grallert, H., Guénel, P., Haiman, C. A., Hall, P., Hamann, U., Hakonarson, H., Hart, R. J., Hickey, M., Hooning, M. J., Hoppe, R., Hopper, J. L., Hottenga, J. J., Hu, F. B., Huebner, H., Hunter, D. J., Jernström, H., John, E. M., Karasik, D., Khusnutdinova, E. K., Kristensen, V. N., Lacey, J. V., Lambrechts, D., Launer, L. J., Lind, P. A., Lindblom, A., Magnusson, P. K., Mannermaa, A., McCarthy, M. I., Meitinger, T., Menni, C., Michailidou, K., Millwood, I. Y., Milne, R. L., Montgomery, G. W., Nevanlinna, H., Nolte, I. M., Nyholt, D. R., Obi, N., O'Brien, K. M., Offit, K., Oldehinkel, A. J., Ostrowski, S. R., Palotie, A., Pedersen, O. B., Peters, A., Pianigiani, G., Plaseska-Karanfilska, D., Pouta, A., Pozarickij, A., Radice, P., Rennert, G., Rosendaal, F. R., Ruggiero, D., Saloustros, E., Sandler, D. P., Schipf, S., Schmidt, C. O., Schmidt, M. K., Small, K., Spedicati, B., Stampfer, M., Stone, J., Tamimi, R. M., Teras, L. R., Tikkanen, E., Turman, C., Vachon, C. M., Wang, Q., Winqvist, R., Wolk, A., Zemel, B. S., Zheng, W., van Dijk, K. W., Alizadeh, B. Z., Bandinelli, S., Boerwinkle, E., Boomsma, D. I., Ciullo, M., Chenevix-Trench, G., Cucca, F., Esko, T., Gieger, C., Grant, S. F., Gudnason, V., Hayward, C., Kolčić, I., Kraft, P., Lawlor, D. A., Martin, N. G., Nøhr, E. A., Pedersen, N. L., Pennell, C. E., Ridker, P. M., Robino, A., Snieder, H., Sovio, U., Spector, T. D., Stöckl, D., Sudlow, C., Timpson, N. J., Toniolo, D., Uitterlinden, A., Ulivi, S., Völzke, H., Wareham, N. J., Widen, E., Wilson, J. F., Pharoah, P. D., Li, L., Easton, D. F., Njølstad, P. R., Sulem, P., Murabito, J. M., Murray, A., Manousaki, D., Juul, A., Erikstrup, C., Stefansson, K., Horikoshi, M., Chen, Z., Farooqi, I. S., Pitteloud, N., Johansson, S., Day, F. R., Perry, J. R., Ong, K. K. 2024

  Abstract

  Pubertal timing varies considerably and is associated with later health outcomes. We performed multi-ancestry genetic analyses on ~800,000 women, identifying 1,080 signals for age at menarche. Collectively, these explained 11% of trait variance in an independent sample. Women at the top and bottom 1% of polygenic risk exhibited ~11 and ~14-fold higher risks of delayed and precocious puberty, respectively. We identified several genes harboring rare loss-of-function variants in ~200,000 women, including variants in ZNF483, which abolished the impact of polygenic risk. Variant-to-gene mapping approaches and mouse gonadotropin-releasing hormone neuron RNA sequencing implicated 665 genes, including an uncharacterized G-protein-coupled receptor, GPR83, which amplified the signaling of MC3R, a key nutritional sensor. Shared signals with menopause timing at genes involved in DNA damage response suggest that the ovarian reserve might signal centrally to trigger puberty. We also highlight body size-dependent and independent mechanisms that potentially link reproductive timing to later life disease.

  View details for DOI 10.1038/s41588-024-01798-4

  View details for PubMedID 38951643

  View details for PubMedCentralID 6185946

• Understanding the genetic complexity of puberty timing across the allele frequency spectrum. medRxiv : the preprint server for health sciences Kentistou, K. A., Kaisinger, L. R., Stankovic, S., Vaudel, M., de Oliveira, E. M., Messina, A., Walters, R. G., Liu, X., Busch, A. S., Helgason, H., Thompson, D. J., Santon, F., Petricek, K. M., Zouaghi, Y., Huang-Doran, I., Gudbjartsson, D. F., Bratland, E., Lin, K., Gardner, E. J., Zhao, Y., Jia, R., Terao, C., Riggan, M., Bolla, M. K., Yazdanpanah, M., Yazdanpanah, N., Bradfield, J. P., Broer, L., Campbell, A., Chasman, D. I., Cousminer, D. L., Franceschini, N., Franke, L. H., Girotto, G., He, C., Järvelin, M. R., Joshi, P. K., Kamatani, Y., Karlsson, R., Luan, J., Lunetta, K. L., Mägi, R., Mangino, M., Medland, S. E., Meisinger, C., Noordam, R., Nutile, T., Concas, M. P., Polašek, O., Porcu, E., Ring, S. M., Sala, C., Smith, A. V., Tanaka, T., van der Most, P. J., Vitart, V., Wang, C. A., Willemsen, G., Zygmunt, M., Ahearn, T. U., Andrulis, I. L., Anton-Culver, H., Antoniou, A. C., Auer, P. L., Barnes, C. L., Beckmann, M. W., Berrington, A., Bogdanova, N. V., Bojesen, S. E., Brenner, H., Buring, J. E., Canzian, F., Chang-Claude, J., Couch, F. J., Cox, A., Crisponi, L., Czene, K., Daly, M. B., Demerath, E. W., Dennis, J., Devilee, P., Vivo, I. D., Dörk, T., Dunning, A. M., Dwek, M., Eriksson, J. G., Fasching, P. A., Fernandez-Rhodes, L., Ferreli, L., Fletcher, O., Gago-Dominguez, M., García-Closas, M., García-Sáenz, J. A., González-Neira, A., Grallert, H., Guénel, P., Haiman, C. A., Hall, P., Hamann, U., Hakonarson, H., Hart, R. J., Hickey, M., Hooning, M. J., Hoppe, R., Hopper, J. L., Hottenga, J. J., Hu, F. B., Hübner, H., Hunter, D. J., Jernström, H., John, E. M., Karasik, D., Khusnutdinova, E. K., Kristensen, V. N., Lacey, J. V., Lambrechts, D., Launer, L. J., Lind, P. A., Lindblom, A., Magnusson, P. K., Mannermaa, A., McCarthy, M. I., Meitinger, T., Menni, C., Michailidou, K., Millwood, I. Y., Milne, R. L., Montgomery, G. W., Nevanlinna, H., Nolte, I. M., Nyholt, D. R., Obi, N., O'Brien, K. M., Offit, K., Oldehinkel, A. J., Ostrowski, S. R., Palotie, A., Pedersen, O. B., Peters, A., Pianigiani, G., Plaseska-Karanfilska, D., Pouta, A., Pozarickij, A., Radice, P., Rennert, G., Rosendaal, F. R., Ruggiero, D., Saloustros, E., Sandler, D. P., Schipf, S., Schmidt, C. O., Schmidt, M. K., Small, K., Spedicati, B., Stampfer, M., Stone, J., Tamimi, R. M., Teras, L. R., Tikkanen, E., Turman, C., Vachon, C. M., Wang, Q., Winqvist, R., Wolk, A., Zemel, B. S., Zheng, W., van Dijk, K. W., Alizadeh, B. Z., Bandinelli, S., Boerwinkle, E., Boomsma, D. I., Ciullo, M., Chenevix-Trench, G., Cucca, F., Esko, T., Gieger, C., Grant, S. F., Gudnason, V., Hayward, C., Kolčić, I., Kraft, P., Lawlor, D. A., Martin, N. G., Nøhr, E. A., Pedersen, N. L., Pennell, C. E., Ridker, P. M., Robino, A., Snieder, H., Sovio, U., Spector, T. D., Stöckl, D., Sudlow, C., Timpson, N. J., Toniolo, D., Uitterlinden, A., Ulivi, S., Völzke, H., Wareham, N. J., Widen, E., Wilson, J. F., Pharoah, P. D., Li, L., Easton, D. F., Njølstad, P., Sulem, P., Murabito, J. M., Murray, A., Manousaki, D., Juul, A., Erikstrup, C., Stefansson, K., Horikoshi, M., Chen, Z., Farooqi, I. S., Pitteloud, N., Johansson, S., Day, F. R., Perry, J. R., Ong, K. K. 2023

  Abstract

  Pubertal timing varies considerably and has been associated with a range of health outcomes in later life. To elucidate the underlying biological mechanisms, we performed multi-ancestry genetic analyses in ~800,000 women, identifying 1,080 independent signals associated with age at menarche. Collectively these loci explained 11% of the trait variance in an independent sample, with women at the top and bottom 1% of polygenic risk exhibiting a ~11 and ~14-fold higher risk of delayed and precocious pubertal development, respectively. These common variant analyses were supported by exome sequence analysis of ~220,000 women, identifying several genes, including rare loss of function variants in ZNF483 which abolished the impact of polygenic risk. Next, we implicated 660 genes in pubertal development using a combination of in silico variant-to-gene mapping approaches and integration with dynamic gene expression data from mouse embryonic GnRH neurons. This included an uncharacterized G-protein coupled receptor GPR83, which we demonstrate amplifies signaling of MC3R, a key sensor of nutritional status. Finally, we identified several genes, including ovary-expressed genes involved in DNA damage response that co-localize with signals associated with menopause timing, leading us to hypothesize that the ovarian reserve might signal centrally to trigger puberty. Collectively these findings extend our understanding of the biological complexity of puberty timing and highlight body size dependent and independent mechanisms that potentially link reproductive timing to later life disease.

  View details for DOI 10.1101/2023.06.14.23291322

  View details for PubMedID 37503126

  View details for PubMedCentralID PMC10371120