Long-read sequencing reveals increased isoform diversity in key transcription factor effectors of intercellular signalling at the invertebrate-vertebrate transition
BackgroundSeveral intercellular signalling pathways (including wingless (Wnt), hedgehog (Hh), and bone morphogenetic protein (BMP)) are used repeatedly in animals throughout development and evolution and are also frequent targets for disease-associated disruptions. We have previously shown that the major transcriptional effectors of β-catenin-dependent Wnt signalling, the TCF/LEF proteins, in contrast to other pathway components, have a higher gene number and isoform diversity in vertebrates versus invertebrates, but this increased diversity has only been poorly quantified. Considering that isoform diversity correlates with organism complexity, any increase in major signalling effectors is likely to have made a significant contribution to vertebrate evolution.ResultsUsing de novo long-read transcriptomes, we compared isoform number per gene for the chordates Ciona intestinalis, Lampetra planeri and Xenopus tropicalis, thus encompassing the invertebrate sister group to vertebrates, as well as a cyclostome and a gnathostome vertebrate. We find a significant increase in the number of transcript isoforms per gene expressed during embryo development and organogenesis at the invertebrate-to-vertebrate transition, specifically for the main transcription factor effectors of the Wnt/β-catenin, Hh and BMP pathways, i.e. TCF/LEF, GLI and SMAD.ConclusionsOur results implicate an increase in isoform diversity of the transcription factors of major intercellular signalling pathways as having a disproportionate role in the evolutionary origin and diversification of vertebrates.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12915-026-02522-w.
- Front Matter
23
- 10.1053/j.gastro.2007.07.018
- Sep 1, 2007
- Gastroenterology
BMP Signaling in the Intestine: Cross-Talk Is Key
- Research Article
217
- 10.1242/dev.02680
- Nov 1, 2006
- Development
Bone morphogenetic protein (BMP) signaling pathways are essential regulators of chondrogenesis. However, the roles of these pathways in vivo are not well understood. Limb-culture studies have provided a number of essential insights, including the demonstration that BMP pathways are required for chondrocyte proliferation and differentiation. However, limb-culture studies have yielded contradictory results; some studies indicate that BMPs exert stimulatory effects on differentiation, whereas others support inhibitory effects. Therefore, we characterized the skeletal phenotypes of mice lacking Bmpr1a in chondrocytes (Bmpr1a(CKO)) and Bmpr1a(CKO);Bmpr1b+/- (Bmpr1a(CKO);1b+/-) in order to test the roles of BMP pathways in the growth plate in vivo. These mice reveal requirements for BMP signaling in multiple aspects of chondrogenesis. They also demonstrate that the balance between signaling outputs from BMP and fibroblast growth factor (FGF) pathways plays a crucial role in the growth plate. These studies indicate that BMP signaling is required to promote Ihh expression, and to inhibit activation of STAT and ERK1/2 MAPK, key effectors of FGF signaling. BMP pathways inhibit FGF signaling, at least in part, by inhibiting the expression of FGFR1. These results provide a genetic in vivo demonstration that the progression of chondrocytes through the growth plate is controlled by antagonistic BMP and FGF signaling pathways.
- Research Article
76
- 10.1038/bjc.2014.560
- Nov 13, 2014
- British Journal of Cancer
Background:Constitutive Wnt activation is essential for colorectal cancer (CRC) initiation but also underlies the cancer stem cell phenotype, metastasis and chemosensitivity. Importantly Wnt activity is still modulated as evidenced by higher Wnt activity at the invasive front of clonal tumours termed the β-catenin paradox. SMAD4 and p53 mutation status and the bone morphogenetic protein (BMP) pathway are known to affect Wnt activity. The combination of SMAD4 loss, p53 mutations and BMP signalling may integrate to influence Wnt signalling and explain the β-catenin paradox.Methods:We analysed the expression patterns of SMAD4, p53 and β-catenin at the invasive front of CRCs using immunohistochemistry. We activated BMP signalling in CRC cells in vitro and measured BMP/Wnt activity using luciferase reporters. MTT assays were performed to study the effect of BMP signalling on CRC chemosensitivity.Results:Eighty-four percent of CRCs with high nuclear β-catenin staining are SMAD4 negative and/or p53 aberrant. BMP signalling inhibits Wnt signalling in CRC only when p53 and SMAD4 are unaffected. In the absence of SMAD4, BMP signalling activates Wnt signalling. When p53 is lost or mutated, BMP signalling no longer influences Wnt signalling. The cytotoxic effects of 5-FU are influenced in a similar manner.Conclusions:The BMP signalling pathway differentially modulates Wnt signalling dependent on the SMAD4 and p53 status. The use of BMPs in cancer therapy, as has been proposed by previous studies, should be targeted to individual cancers based on the mutational status of p53 and SMAD4.
- Research Article
36
- 10.1016/j.devcel.2007.11.006
- Dec 1, 2007
- Developmental Cell
Opposing Effects of Wnt and MAPK on BMP/Smad Signal Duration
- Research Article
12
- 10.1074/jbc.m110.177907
- Feb 1, 2011
- Journal of Biological Chemistry
Epidermal differentiation in the ventral ectoderm of Xenopus embryos is regulated by the bone morphogenetic protein (BMP) pathway. However, it remains unclear how the BMP pathway is activated and induces the epidermal fate in the ventral ectoderm. Here, we identify a novel player in the BMP pathway that is required for epidermal differentiation during Xenopus early embryonic development. We show that Xenopus EIG121L (xEIG121L) protein, an evolutionarily conserved transmembrane protein, is expressed in the ventral ectoderm at the gastrula and neurula stages. Almost complete knockdown of xEIG121L protein with antisense morpholino oligonucleotides in early Xenopus embryos results in severe developmental defects, including the inhibition of epidermal differentiation and the induction of neural genes. Remarkably, our analysis shows that BMP/Smad1 signaling is severely suppressed in the xEIG121L knockdown ectoderm. Moreover, immunoprecipitation and immunostaining experiments suggest that xEIG121L protein physically interacts, and co-localizes, with BMP receptors. Thus, our results identify a novel regulator of the BMP pathway that has a positive role in BMP signaling and plays an essential role in epidermal differentiation during early embryonic development.
- Research Article
4
- 10.1111/1750-3841.13775
- Jun 13, 2017
- Journal of food science
Solanum muricatum (SM), also known as pepino, is known for its antioxidative and anti-inflammatory effects. The aim of this study was to evaluate the effects of SM extract in promoting osteogenic differentiation and regulating the Wnt and bone morphogenetic protein (BMP) signaling pathways. Ingredients of pepino were extracted and identified. SM extracts were used to treat rat bone marrow stromal cells (BMSCs), followed by evaluating alkaline phosphatase activities and mineralization levels. The mRNA levels of osteogenic biomarkers, including OPN and Collagen I, were also evaluated with real-time polymerase chain reaction. After treatment with SM extracts, the expressions of key proteins in the Wnt and BMP signaling pathways were assessed. DKK-1 and noggin, which are Wnt and BMP inhibitors, respectively, were added with SM extracts to investigate the role of Wnt and BMP pathways in the ameliorating effects of SM extract in osteogenesis. Treatment of BMSCs with SM extract promoted osteogenesis. Meanwhile, upregulations in the Wnt and BMP pathways were also observed. However, inhibiting both pathways compromised the effects of SM extract in promoting osteogenic differentiation. SM extract promotes osteogenic differentiation in BMSCs via promoting the Wnt and BMP signaling pathways.
- Research Article
- 10.1096/fasebj.29.1_supplement.553.4
- Apr 1, 2015
- The FASEB Journal
Calcific Aortic Valve Disease (CAVD) affects >2% of the elderly population for whom the standard of care is valve replacement surgery. Unfortunately, the pathogenic mechanisms of CAVD, which could serve as potential therapeutic targets, remain unknown. Klotho‐null mice exhibit accelerated aging and aortic valve (AoV) calcification similar to human CAVD. Notably, phosphorylation of Smads1/5/8, Bone Morphogenetic Protein (BMP) pathway effectors essential for bone calcification, precedes and later localizes with calcific nodules in Klotho‐null AoV. Our hypothesis is that BMP pathway activation promotes AoV calcification. Our goal is to determine the role of the BMP pathway in the pathogenesis of CAVD and to use a pharmacologic inhibitor of BMP signaling as a potential treatment for CAVD in vivo. Our current studies demonstrate that osteochondrogenic factors involved in bone and cartilage formation are significantly increased in Klotho‐null AoV. In addition, BMP pathway components, including BMP2/4, Smad6 and Noggin, are significantly up‐regulated in Klotho‐null AoV. Moreover, in porcine AoV interstitial cells cultured in vitro, osteogenic media treatment induces osteochondrogenic gene expression and activation of the BMP‐pSmad1/5/8 pathway, as well as formation of calcific nodules. Interestingly, treatment with LDN‐193189, a BMP pathway inhibitor, decreases osteochondrogenic gene induction and prevents calcific nodule formation in the presence of osteogenic media. Together these data support an active role for BMP signaling during osteochondrogenic gene induction and the development of AoV calcification.AHA Pre‐doctoral Fellowship 13PRE1623006 ‐MVGNIH R01 HL114682 ‐KEY.
- Research Article
162
- 10.1074/jbc.m509205200
- Apr 1, 2006
- Journal of Biological Chemistry
C57BL/6J (B6), but not C3H/HeJ (C3H), mice responded to mechanical loading with an increase in bone formation. A 30-min steady fluid shear of 20 dynes/cm(2) increased [(3)H]thymidine incorporation and alkaline phosphatase activity and up-regulated the expression of early mechanoresponsive genes (integrin beta1 (Igtb1) and cyclooxygenase-2 (Cox-2)) in B6 but not C3H osteoblasts, indicating that the differential mechanosensitivity was intrinsic to osteoblasts. In-house microarray analysis with 5,500 gene fragments revealed that the expression of 669 genes in B6 osteoblasts and 474 genes in C3H osteoblasts was altered 4 h after the fluid shear. Several genes associated with the insulin-like growth factor (IGF)-I, the estrogen receptor (ER), the bone morphogenetic protein (BMP)/transforming growth factor-beta, and Wnt pathways were differentially up-regulated in B6 osteoblasts. In vitro mechanical loading also led to up-regulation of these genes in the bones of B6 but not C3H mice. Pretreatment of B6 osteoblasts with inhibitors of the Wnt pathway (endostatin), the BMP pathway (Noggin), or the ER pathway (ICI182780) blocked the fluid shear-induced proliferation. Inhibition of integrin and Cox-2 activation by echistatin and indomethacin, respectively, each blocked the fluid shear-induced up-regulation of genes associated with these four pathways. In summary, up-regulation of the IGF-I, ER, BMP, and Wnt pathways is involved in mechanotransduction. These four pathways are downstream to the early mechanoresponsive genes, i.e. Igtb1 and Cox-2. In conclusion, differential up-regulation of these anabolic pathways may in part contribute to the good and poor response, respectively, in the B6 and C3H mice to mechanical loading.
- Research Article
22
- 10.3109/03008207.2014.923867
- Aug 15, 2014
- Connective Tissue Research
Odontoblast differentiation during physiological and reparative dentinogenesis is dependent upon multiple signaling molecules, including fibroblast growth factors (FGFs), bone morphogenetic proteins (BMPs) and Wingless/Integrated (Wnt) ligands. Recent studies in our laboratory showed that continuous exposure of primary dental pulp cultures to FGF2 exerted biphasic effects on the expression of markers of dentinogenesis. In the present study, we examined the possible involvement of the BMP and Wnt signaling pathways in mediating the effects of FGF2 on dental pulp cells. Our results showed that stimulatory effects of FGF2 on dentinogenesis during the proliferation phase of growth were associated with increased expression of the components of the BMP (Bmp2, Dlx5, Msx2, Osx) and Wnt (Wnt10a, Wisp2) pathways, and decreased expression of an inhibitor of the Wnt signaling, Nkd2. Further addition of FGF2 during the differentiation/mineralization phase of growth resulted in decreased expression of components of the BMP signaling (Bmp2, Runx2, Osx) and increased expression of inhibitors of the Wnt signaling (Nkd2, Dkk3). This suggests that both BMP and Wnt pathways may be involved in mediating the effects of FGF2 on dental pulp cells.
- Research Article
- 10.1002/mnfr.70387
- Jan 1, 2026
- Molecular nutrition & food research
The intestinal bone morphogenetic protein (BMP) pathway counteracts the Wnt pathway, which is overactivated in 90% of colorectal cancers (CRC) due to mutations in the adenomatous polyposis coli (APC) gene. Our study aimed to identify a polyphenol that acts on the colonic BMP pathway and to evaluate its ability to mitigate the harmful effects of 4-hydroxynonenal (HNE), a dietary genotoxic molecule, on normal colonocytes. We first evaluated the effect of 10 polyphenols on the expression of BMP pathway actors using a normal mouse colonocyte and fibroblast culture model. Apigenin (Apig) and resveratrol (Res) increased the production of BMP4 ligand and reduced expression of the Gremlin1 (Grem1) antagonist in fibroblasts. Apig also enhanced the expression of the bone morphogenetic protein receptor type 2 (Bmpr2) in fibroblasts and that of the Smad1 effector in colonocytes. Finally, Apig inhibited the phenotypic transformation of colonocytes induced by HNE through a mechanism that involved the BMP pathway in both fibroblasts and colonocytes. Our findings suggest that targeting the colonic BMP signaling pathway through dietary factors could contribute to the prevention of CRC. Apig-rich foods or supplements may play a role in this preventive nutrition, although further in vivo experiments are needed to confirm this potential.
- Research Article
81
- 10.1053/j.gastro.2007.08.021
- Aug 14, 2007
- Gastroenterology
The Effect of Statins in Colorectal Cancer Is Mediated Through the Bone Morphogenetic Protein Pathway
- Research Article
30
- 10.1042/bst20160111
- Oct 15, 2016
- Biochemical Society Transactions
The bone morphogenetic protein (BMP) pathway is a major conserved signalling pathway with diverse roles in development and homeostasis. Given that cells exist in three-dimensional environments, one important area is to understand how the BMP pathway operates within such complex cellular environments. The extracellular matrix contains information regarding tissue architecture and its mechanical properties that is transmitted to the cell via integrin receptors. In this review, I describe various examples of modulation of the BMP pathway by integrins. In the case of the Drosophila embryo and some cell line-based studies, integrins have been found to enhance BMP responses through different mechanisms, such as enhancement of BMP ligand-receptor binding and effects on Smad phosphorylation or stability. In these contexts, BMP-dependent activation of integrins is a common theme. However, I also discuss examples where integrins inhibit the BMP pathway, highlighting the context-dependent nature of integrin-BMP cross-talk.
- Research Article
17
- 10.1042/bst20190223
- Mar 13, 2020
- Biochemical Society Transactions
The bone morphogenetic protein (BMP) pathway regulates the fate and proliferation of normal hematopoietic stem cells (HSC) as well as interactions with their niche. While BMP2 and BMP4 promote HSC differentiation, only BMP4 maintains HSC pool and favors interactions with their niche. In myeloid leukemia, we have identified intrinsic and extrinsic dysregulations of the BMP pathway in Chronic Myeloid Leukemia (CML) and Acute Myeloid leukemia (AML) responsible for leukemic stem cells (LSC) survival. In AML, BMP pathway alterations sustain and promote resistant immature-like leukemic cells by activating a new signaling cascade. Binding of BMP4 to BMPR1A leads to ΔNp73 expression, which in turn induces NANOG, altogether associated with a poor patient's prognosis. Despite efficient targeted therapies, like Tyrosine Kinase Inhibitors (TKI) in CML, many patients retain LSCs. Our laboratory demonstrated that the BMP pathway sustains a permanent pool of LSCs expressing high levels of BMPR1B receptor, that evolve upon treatment to progressively implement a BMP4 autocrine loop, leading to TKI-resistant cells. Single cell RNA-Seq analysis of TKI-persisting LSCs showed a co-enrichment of BMP with Jak2-signaling, quiescence and stem cell (SC) signatures. Using a new model of persisting LSCs, we recently demonstrated that BMPR1B+ cells display co-activated Smad1/5/8 and Stat3 pathways and could be targeted by blocking BMPR1B/Jak2 signal. Lastly, a specific BMPR1B inhibitor impaired BMP4-mediated LSC protection against TKIs. Altogether, data based on various studies including ours, indicate that BMP targeting could eliminate leukemic cells within a protective bone marrow microenvironment to efficiently impact residual resistance or persistence of LSCs in myeloid leukemia.
- Abstract
- 10.1182/blood.v128.22.1548.1548
- Dec 2, 2016
- Blood
The Bone Marrow Niche Distinguishes Young and Old Leukemia
- Research Article
65
- 10.1093/carcin/bgs233
- Jul 12, 2012
- Carcinogenesis
Helicobacter pylori infection is the main risk factor for intestinal metaplasia (IM) and gastric cancer development. IM is a pre-neoplastic lesion, induced by the transcription factor CDX2, where the gastric mucosa is converted to an intestinal phenotype. We previously demonstrated that key elements of the bone morphogenetic protein (BMP) pathway co-localize with CDX2 in IM and upregulate CDX2 expression in gastric cell lines. These observations, together with the hypothesis that CDX2 could be repressed by SOX2, led us to test whether H. pylori, through BMPs, SOX2 and CDX2 could participate in a molecular network critical for the development of IM. AGS cells with and without SMAD4 knock-down were co-cultured with H. pylori or BMP2 to assess the expression of BMP pathway members as well as CDX2 and SOX2 by qPCR and western blot. Proximity ligation assay (PLA) was also performed to evaluate SMAD proteins interaction. Immunohistochemistry and western blot were performed in gastric samples from mice infected with Helicobacter spp. to measure Smad4, pSmad1/5/8, Cdx2 and Sox2 expression in vivo. Increased expression and activity of the BMP pathway accompanied by CDX2 upregulation and SOX2 downregulation were observed in AGS cells co-cultured with H. pylori or BMP2. These effects were impaired by downregulation of the BMP pathway. Finally, infected mice present BMP pathway upregulation, focal Cdx2 expression and decreased Sox2. These results provide a novel link between H. pylori infection and the BMP pathway in the regulation of intestinal and gastric-specific genes that might be relevant for gastric IM.
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