Endogenous Bioid Elucidates TCF7L1 Interactome Modulation Upon GSK-3 Inhibition in Mouse ESCs

Moreira, Steven; Seo, Caleb; Gordon, Victor; Xing, Sansi; Wu, Renyi; Polena, Enio; Fung, Vincent; Ng, Deborah; Wong, Cassandra; Larsen, Brett; Raught, Brian; Gingras, Anne‐Claude; Lu, Y. P.; Doble, Bradley W.

doi:10.2139/ssrn.3348349

Cited by 5 publications

(8 citation statements)

References 45 publications

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“…For example, the abundance of ID1, a transcription factor critical in the maintenance of ES cell self-renewal and regulation of lineage commitment (Romero-Lanman et al, 2012), covaries significantly (positively and negatively) with chromatin accessibility at 112 ATAC-seq peaks across the genome (Fig 3A). Other proteins with potential roles in pluripotency maintenance include: AHDC1, a putative DNA-binding protein previously shown to physically interact with TCF7L1 (TCF3), a transcription factor involved in pluripotency regulation (Moreira et al, 2018; Wray et al, 2011); and UHRF2, a ubiquitin ligase identified as a target of epigenetic control during self-renewal (Walker et al, 2010). For almost half of these proteins, we find that their covarying ATAC-seq peaks are overrepresented in binding sites active in ESCs for TRP53 (n = 28) and naïve pluripotency factors NANOG, ESRRB, and PRDM14 (n = 19, 18, 16 at FDR < 0.05) (Kalkan et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

Genetic dissection of the pluripotent proteome through multi-omics data integration

Aydin

Pham

Zhang

et al. 2022

Preprint

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Genetic background is a major driver of phenotypic variability in pluripotent stem cells (PSCs). Most studies of variation in PSCs have relied on transcript abundance as the primary molecular readout of cell state. However, little is known about how proteins, the primary functional units in the cell, vary across genetically diverse PSCs, how protein abundance relates to variation in other cell characteristics, and how genetic background confers these effects. Here we present a comprehensive genetic study characterizing the pluripotent proteome of 190 unique mouse embryonic stem cell lines (mESCs) derived from genetically heterogeneous Diversity Outbred (DO) mice. The quantitative proteome is highly variable across DO mESCs, and we identified differentially activated pluripotency-associated pathways in the proteomics data that were not evident in transcriptome data from the same cell lines. Comparisons of protein abundance to transcript levels and chromatin accessibility show broad co-variation across molecular layers and variable correlation across samples, with some lines showing high and others low correlation between these multi-omics datasets. Integration of these three molecular data types using multi-omics factor analysis revealed shared and unique drivers of quantitative variation in pluripotency-associated pathways. QTL mapping localized the genetic drivers of this quantitative variation to a number of genomic hotspots, and demonstrated that multi-omics data integration consolidates the influence of genetic signals shared across molecular traits to increase QTL detection power and overcome the limitations inherent in mapping individual molecular features. This study reveals transcriptional and post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome, and in so doing provides a regulatory map for mouse ESCs that can provide a rational basis for future mechanistic studies, including studies of human PSCs.

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Section: Resultsmentioning

confidence: 99%

Genetic dissection of the pluripotent proteome through multi-omics data integration

Aydin

Pham

Zhang

et al. 2022

Preprint

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“…Gene ontology analysis of these hits revealed that FOXQ1 proximal proteins are primarily involved in mRNA processing, chromatin remodelling, and transcription regulation, but notably also β-catenin/TCF complex assembly (Fig EV3E, and Table 1). To identify common interactors of FOXQ1 and the Wnt transcriptional complex, we included a published BioID dataset of Tcf7l1 interactors in CHIR99021-treated or control mouse embryonic stem cells (Moreira et al , 2018) in our analyses. Following stringent, uniform data filtration and analysis, we observed that numerous candidate FOXQ1 interactors were shared with Tcf7l1 (Fig 3E, and Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…Processed mass spectrometry data were analysed further using SAINTexpress v3.6.3 (Teo et al , 2014). The resulting output file was merged with a dataset of Tcf7l1 interactors in mouse embryonic stem cells ((Moreira et al ., 2018), their Supplemental Table S1), following mouse-to-human gene name conversion using the biomaRt R package (Durinck et al , 2009). Data were filtered against common mass spectrometry contaminants using the CRAPome repository (Mellacheruvu et al , 2013) with Frequency cut-off 0.2 or PSM ratio cut-off 3.…”

Section: Methodsmentioning

confidence: 99%

The oncogene FOXQ1 is a selective activator of Wnt/β-catenin signalling

Pizzolato

Moparthi

Söderholm

et al. 2022

Preprint

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The forkhead box transcription factor FOXQ1 is aberrantly induced in various cancers, and contributes to tumour growth and metastasis. It has been suggested that FOXQ1 exacerbates cancer by activating the oncogenic Wnt/β-catenin signalling pathway. However, the mode of action of FOXQ1 in the Wnt pathway remains to be resolved. Here, we report that FOXQ1 is a bimodal transcriptional activator of Wnt target gene expression in normal and cancer cells. Using co-immunoprecipitation, proximity proteomics, and reporter assays, we show that FOXQ1 engages the Wnt transcriptional complex to promote gene expression via TCF/LEF transcription factors. In parallel, FOXQ1 differentially regulates the expression of Wnt target genes independently of β-catenin and TCF/LEFs, which is facilitated by spatially separated activator and repressor domains. Our results suggest that FOXQ1 is a novel component of the Wnt transcriptional complex that reinforces and specifies Wnt signalling in a context-dependent manner.

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“…We then asked to what extent the tested FOXs are associated with the same protein complexes as TCF/LEF. For this, we performed an enrichment analysis against a dataset of curated human protein complexes ( 26 ), including previously identified Tcf7l1, FOXQ1, and FOXB2 interactors ( 27, 28 ). We observed that FOXQ1, FOXN4, FOXDI, and FOXI1, in particular, share a substantial number of interacting complexes with one another and Tcf7l1 (Fig.…”

Section: Resultsmentioning

confidence: 99%

FOX transcription factors are common regulators of Wnt/β-catenin signaling

Moparthi

Koch

2022

Preprint

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The Wnt/β-catenin signaling pathway is a critical regulator of development and stem cell maintenance. Mounting evidence suggests that the context-specific outcome of Wnt signaling is determined by the collaborative action of multiple transcription factors, including members of the highly conserved forkhead box (FOX) protein family. However, the contribution of FOX transcription factors to Wnt signaling has not been investigated in a systematic manner. Here, we performed uniform gain-of-function screens of all 44 human FOX transcription factors to identify and classify new regulators of the Wnt/β-catenin pathway. By combining β-catenin reporter assays with Wnt pathway-focused qPCR arrays and proximity proteomics of selected FOX family members, we determine that most FOX proteins are involved in the regulation of Wnt pathway activity and the expression of Wnt ligands and target genes. Moreover, as a proof of principle we characterize class D and I FOX transcription factors as physiologically relevant positive and negative regulators of Wnt/β-catenin signaling, respectively. We conclude that FOX proteins are common regulators of the Wnt/β-catenin pathway that may control the outcome of Wnt signaling in a tissue-specific manner.

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Endogenous Bioid Elucidates TCF7L1 Interactome Modulation Upon GSK-3 Inhibition in Mouse ESCs

Cited by 5 publications

References 45 publications

Genetic dissection of the pluripotent proteome through multi-omics data integration

Genetic dissection of the pluripotent proteome through multi-omics data integration

The oncogene FOXQ1 is a selective activator of Wnt/β-catenin signalling

FOX transcription factors are common regulators of Wnt/β-catenin signaling

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