Periodic Reporting for period 1 - TRANSCEND (Translational specialization of cellular identity in embryonic development and disease)
Reporting period: 2023-03-01 to 2025-08-31
A central question in developmental biology is how genetic information is differentially interpreted to program cell-fate decisions essential for embryogenesis. The success of developmental cell-fate decisions relies on the accurate rewiring of the proteome to support rapid cellular identity changes. Here, we will address the fundamental question: How is the developmental transcriptome differentially translated in time and space to program cell-fate decisions? I hypothesize that the developmental competence for cell-fate decisions is controlled by fate-specific translational specialization factors (TSFs). TSFs program the selective and privileged translation of developmental genes in defined time windows to enable the acquisition of cell fate and maintenance of cellular identity. Notably, in a proof-of-principle study, we discovered that translational specialization in pluripotency poises future lineage choices in humans. The research program TRANSCEND has four work packages: (1) identifying candidate TSFs engineering cardiac fate at critical cell-fate transitions by cell-fate specific, systematic cataloging TSFs on ribosomal complexes; (2) dissecting the molecular and functional role of TSFs in cardiac cell-fate specification by combining targeted CRISPR screens and tethered functional approaches; (3) decoding the mechanisms, modalities, and design principles by which TSFs program cardiac identity by using a holistic approach, including loss-of-function studies in cardiac 2D, organoid, and mouse models along with systems-wide methods such as eCLIP-seq and TCP-seq; and (4) engineering translation specialization modules to ameliorate pathological cardiac hypertrophy using patient-derived in vitro and murine in vivo models. Ultimately, the proposed research program TRANSCEND aims at transforming our current understanding of translational control over cell-fate decisions and opening up innovative avenues for controlled therapeutic restoration of cardiac function.
Project TRANSCEND has made progress towards uncovering how translational control shapes human cardiac development and disease. During the first half of the project, we established a comprehensive experimental platform combining advanced proteomics, RNA biology, and functional genomics. This includes the development of a highly sensitive method to profile protein phosphorylation on ribosomal complexes from minimal sample amounts, the generation of versatile stem cell–based reporter models to trace cardiac differentiation, and the successful execution of a whole-genome CRISPR screen to systematically identify factors controlling translational states. We also launched a machine learning–guided therapeutic pipeline targeting stress-responsive translation regulators. These advances place our work at the intersection of systems biology, disease modeling, and developmental biology. Our interdisciplinary team has grown into a vibrant, international group and is now applying these tools to chart how translational programs control human cell fate and how they are reprogrammed in disease.
Currently, the project is ongoing. The TRANSCEND project aims to establish a comprehensive framework for understanding how mRNA translation governs human cardiac development and how its dysregulation contributes to disease. By integrating high-resolution profiling of translational complexes, spatial RNA localization, functional genomics, and proteome/phosphoproteome dynamics, we seek to uncover how ribosome associated proteins and translation specialization factors program cell fate transitions, regulate developmental gene expression, and control the assembly of lineage-specific translational machinery. In parallel, we are exploring how these mechanisms become pathologically reprogrammed in conditions such as cardiac hypertrophy. The long-term objective is to define the principles by which translational control shapes organ development and function, and to identify molecular nodes within the translational apparatus that may be leveraged therapeutically to restore homeostasis in cardiac pathologies.