Molecular and Cellular Function of Transcription Factor 4 in Pitt-Hopkins Syndrome

Chen, Huei Ying; Bohlen, Joseph F.; Maher, Brady J.

doi:10.1159/000516666

Cited by 24 publications

(8 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Haploinsufficiency of these genes is associated with neurodevelopmental disorders and diseases, including Bosch-Boonstra-Schaaf optic atrophy syndrome ( Nr2f1 ), Pitt-Hopkins Syndrome ( Tcf4 ), FOXG1 syndrome ( Foxg1 ) and TBR1 syndrome ( Tbr1 ). These transcription factors play critical roles in cortical neuronal differentiation and progenitor maintenance, regional patterning, neuronal migration, and circuit assembly through the regulation of networks of other transcription factors (Chen et al, 2021; Greig et al ., 2013; Hou et al, 2020). Most of their expression spans from embryonic to postnatal stages: Tcf4 and Nr2f1 are broadly expressed in most cell types, whereas Foxg1 and Tbr1 expression is restricted to subclasses of neurons including deep layer projection neurons and immature neurons ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Massively parallelin vivoPerturb-seq reveals cell type-specific transcriptional networks in cortical development

Zheng,

Wu,

Liu

et al. 2023

Preprint

View full text Add to dashboard Cite

Systematic analysis of gene function across diverse cell types in vivo is hindered by two challenges: obtaining sufficient cells from live tissues and accurately identifying each cell's perturbation in high-throughput single-cell assays. Leveraging AAV's versatile cell type tropism and high labeling capacity, we expanded the resolution and scale of in vivo CRISPR screens: allowing phenotypic analysis at single-cell resolution across a multitude of cell types in the embryonic brain, adult brain, and peripheral nervous system. We undertook extensive tests of 86 AAV serotypes, combined with a transposon system, to substantially amplify labeling and accelerate in vivo gene delivery from weeks to days. Using this platform, we performed an in utero genetic screen as proof-of-principle and identified pleiotropic regulatory networks of Foxg1 in cortical development, including Layer 6 corticothalamic neurons where it tightly controls distinct networks essential for cell fate specification. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% (mediated by lentivirus), and achieve analysis of over 30,000 cells in one experiment, thus enabling massively parallel in vivo Perturb-seq. Compatible with various perturbation techniques (CRISPRa/i) and phenotypic measurements (single-cell or spatial multi-omics), our platform presents a flexible, modular approach to interrogate gene function across diverse cell types in vivo, connecting gene variants to their causal functions.

show abstract

Section: Resultsmentioning

confidence: 99%

Massively parallelin vivoPerturb-seq reveals cell type-specific transcriptional networks in cortical development

Zheng,

Wu,

Liu

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…1b, d ; Supplementary Data 1 ), which we used for further functional validation. The selected candidates are involved in various cellular functions and components, including cytoskeleton structure ( MYH9 ) 27 , cell adhesion ( CD93 , ADGRL4 (also known as ELTD1 )) 28 , 29 , gap junctions ( GJA1 ) 30 , or regulation of gene expression ( TCF4 , transcription factor 4 31 ; CCDC85B , putative transcriptional repressor 32 ). All selected candidates are not or only minimally characterized by a function in ECs.…”

Section: Resultsmentioning

confidence: 99%

Prioritization and functional validation of target genes from single-cell transcriptomics studies

et al. 2023

View full text Add to dashboard Cite

Translation of academic results into clinical practice is a formidable unmet medical need. Single-cell RNA-sequencing (scRNA-seq) studies generate long descriptive ranks of markers with predicted biological function, but without functional validation, it remains challenging to know which markers truly exert the putative function. Given the lengthy/costly nature of validation studies, gene prioritization is required to select candidates. We address these issues by studying tip endothelial cell (EC) marker genes because of their importance for angiogenesis. Here, by tailoring Guidelines On Target Assessment for Innovative Therapeutics, we in silico prioritize previously unreported/poorly described, high-ranking tip EC markers. Notably, functional validation reveals that four of six candidates behave as tip EC genes. We even discover a tip EC function for a gene lacking in-depth functional annotation. Thus, validating prioritized genes from scRNA-seq studies offers opportunities for identifying targets to be considered for possible translation, but not all top-ranked scRNA-seq markers exert the predicted function.

show abstract

“…The structure of the TCF4 gene is very complex: through the subsequent mapping of more alternative 5'exons [20 in total, not shown in Figure 1B], the demonstration of 20 coding exons and the confirmation of one previously unreported 3'-terminal non-protein-coding exon [Figure 1B], the total number of exons in TCF4 has now risen to 41 [67] (for the equal complexity of mouse Tcf4 alternative transcripts, see Ref. [68] ; for subsequent reviews, see Refs. [9,69] ; also note that Ensembl lists 48 transcripts) and the size of the human gene accordingly to > 400 kb.…”

Section: Tcf4 Protein/gene Structurementioning

confidence: 99%

Different E-box binding transcription factors, similar neuro-developmental defects: ZEB2 (Mowat-Wilson syndrome) and TCF4 (Pitt-Hopkins syndrome)

Meert¹,

Birkhoff²,

Conidi³

et al. 2022

Rare Dis Orphan Drugs J

View full text Add to dashboard Cite

ZEB2 and TCF4 are transcription factors (TFs) whose locations in embryos overlap in many sites and developmental phases, including in the forebrain and its cortical neurons. De novo mutations cause the phenotypically overlapping, haploinsufficient Mowat-Wilson (MOWS, in the ZEB2 gene) and Pitt-Hopkins (PTHS, in TCF4) syndromes, which currently cannot be cured. Mutant alleles have been mapped and defects documented (also in brain function) in MOWS and PTHS patients. Appropriately designed mouse models and cells derived from these, as well as cellular models including cultured pluripotent cells, enable investigating the genetic and molecular mechanisms underlying the developmental deficiencies that manifest after birth in the nervous systems and their multiple cell types, as well as those of organs other than the brain, in MOWS and PTHS. Biochemical analyses of cell type-specific transcriptomic changes in these perturbation models as compared to control cells, the identification of the intact-factor dependent and direct target genes, and of partner proteins including chromatin modulators, are revealing complex and multiple modes of action that eventually will explain target gene selectivity for these TFs. Both TFs have also been found to operate in acute and chronic diseases and cell-based repair processes after tissue or organ injury. In addition, the defective function also arises from their aberrant gene expression, which will require a deeper investigation of how the transcription of these TF genes is regulated. Furthermore, these two factors genetically and biochemically interact. This review combines the essentials and recent progress for both TFs for the first time, with a focus on MOWS and PTHS.

show abstract

Molecular and Cellular Function of Transcription Factor 4 in Pitt-Hopkins Syndrome

Cited by 24 publications

References 58 publications

Massively parallelin vivoPerturb-seq reveals cell type-specific transcriptional networks in cortical development

Massively parallelin vivoPerturb-seq reveals cell type-specific transcriptional networks in cortical development

Prioritization and functional validation of target genes from single-cell transcriptomics studies

Different E-box binding transcription factors, similar neuro-developmental defects: ZEB2 (Mowat-Wilson syndrome) and TCF4 (Pitt-Hopkins syndrome)

Contact Info

Product

Resources

About