Vora, M. | Search bioRxiv

bioRxiv2024

Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion

Smads and their transcription factor partners mediate the transcriptional responses of target cells to secreted ligands of the Transforming Growth Factor-{beta} (TGF-{beta}) family, including those of the conserved bone morphogenetic protein (BMP) family, yet only a small number of direct target genes have been well characterized. In C. elegans, the BMP2/4 ortholog DBL-1 regulates multiple biological functions, including body size, via a canonical receptor-Smad signaling cascade. Here, we identify functional binding sites for SMA-3/Smad and its transcriptional partner SMA-9/Schnurri based on ChIP-seq peaks (identified by modEncode) and expression differences of nearby genes identified from RNA-seq analysis of corresponding mutants. We found that SMA-3 and SMA-9 have both overlapping and unique target genes. At a genome- wide scale, SMA-3/Smad acts as a transcriptional activator, whereas SMA-9/Schnurri direct targets include both activated and repressed genes. Mutations in sma-9 partially suppress the small body size phenotype of sma-3, suggesting some level of antagonism between these factors and challenging the prevailing model for Schnurri function. Functional analysis of target genes revealed a novel role in body size for genes involved in one-carbon metabolism and in the endoplasmic reticulum (ER) secretory pathway, including the disulfide reductase dpy-11. Our findings indicate that Smads and SMA-9/Schnurri have previously unappreciated complex genetic and genomic regulatory interactions that in turn regulate the secretion of extracellular components like collagen into the cuticle to mediate body size regulation.

genomics↗

bioRxiv2021

The Hypoxia Response Pathway Promotes PEP Carboxykinase Expression And Gluconeogenesis

Actively dividing cells, including some cancers, rely on aerobic glycolysis rather than oxidative phosphorylation to generate energy, a phenomenon termed "the Warburg effect1." Constitutive activation of the Hypoxia Inducible Factor (HIF-1), a transcription factor known for mediating an adaptive response to oxygen deprivation (hypoxia), is a hallmark of the Warburg effect2. HIF-1 is thought to promote glycolysis and suppress oxidative phosphorylation. Here, we show instead that HIF-1 can promote gluconeogenesis. Using a multiomics approach, we determined the genomic, transcriptomic, and metabolomic landscapes regulated by constitutively active HIF-1 in C. elegans. We performed RNA-seq and ChIP-seq under aerobic conditions in mutants lacking EGL-9, a key negative regulator of HIF-1, and then integrated these approaches to identify over a hundred genes directly and functionally upregulated by HIF-1. We show that HIF-1 directly promotes the expression of PCK-1, a PEP carboxykinase that is a rate-limiting mediator of gluconeogenesis3. This activation of PCK-1 by HIF-1 promotes survival in response to both oxidative and hypoxic stress. Our work is the first to identify functional direct targets of HIF-1 in vivo, and it describes the first complete metabolome induced by constitutive HIF-1 activation in any organism.

genetics↗

bioRxiv2018

C. elegans models of Marfan and Marfan-like Syndromes reveal trafficking defects of the type II TGFβ receptor as a potential novel disease mechanism

The transforming growth factor-{beta} (TGF{beta}) family plays an important role in many developmental processes and when mutated often contributes to various diseases. Marfan syndrome is a genetic disease with an occurrence of approximately 1 in 5,000. The disease is caused by mutations in fibrillin, which lead to an increase in TGF{beta} ligand activity, resulting in abnormalities of connective tissues which can be life-threatening. Mutations in other components of TGF{beta} signaling (receptors, Smads, Schnurri) lead to similar diseases with attenuated phenotypes relative to Marfan syndrome. In particular, mutations in TGF{beta} receptors, most of which are clustered at the C-terminal end, result in Marfan-like (MFS-like) syndromes. Even though it was assumed that many of these receptor mutations would reduce or eliminate signaling, in many cases signaling is active. From our trafficking work in C. elegans, we noticed that many of these receptor mutations that lead to Marfan-like syndromes overlap with mutations that cause mis-trafficking of the receptor, suggesting a link between Marfan-like syndromes and TGF{beta} receptor trafficking. To test this hypothesis, we introduced some of these key MFS and MFS-like mutations into the C. elegans TGF{beta} receptor and asked if receptor trafficking is altered. We find that some of the mutated receptors localize to the apical surface rather than basolateral surface of the polarized intestinal cells. Further, we find that these mutations result in longer animals, a phenotype due to over-stimulation of the pathway and, importantly, indicating that function of the receptor is not abrogated in these mutants. Our nematode models of Marfan syndrome suggest that MFS and MFS-like mutations in the type II receptor lead to mis-trafficking of the receptor and possibly provides an explanation for the disease, a phenomenon which might also occur in some cancers that possess the same mutations within the type II receptor (e.g. colon cancer). Author SummaryThe transforming growth factor-{beta} (TGF{beta}) family plays an important role in many basic biological processes and when mutated often contributes to various diseases. Marfan syndrome (MFS) is a genetic disease with an occurrence of approximately 1 in 5,000. The disease is caused by mutations in fibrillin, which lead to an increase in TGF{beta} ligand activity, resulting in abnormalities of connective tissues which can be life-threatening. However, some patients with normal fibrillin genes also show symptoms and pathologies associated with Marfan syndrome, known collectively as Marfan-like Syndromes (MFS-like). When these patients were assessed for mutations in other components of the TGF{beta} pathway, several mutations clustered in a small region of the receptors, primarily in the type II TGF{beta} receptor were found. We find that mimicking these mutations in the nematode type II TGF{beta} receptor causes the mutant receptor to move to regions of the cell where it is not normally found. Importantly, these mutations do not abrogate the function of the receptor, suggesting that mis-localization of the receptor might be previously unknown cause of disease etiology. We hypothesize that receptor mutations present at the LTA lead to disruptions in interactions with trafficking regulators leading to symptoms of MFS/MFS-like syndromes - a novel disease mechanism of MFS/MFS-like syndromes that might also extend to other cancers bearing similar mutations.

cancer biology↗