GO:0035148 tube formation: Angiogenesis and Neural Tube Morphogenesis, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0035148 (tube formation) is the biological process that creates the central hole of a tube in an anatomical structure through which gases and/or liquids flow [QuickGO definition].
• Tube formation is central to both vascular angiogenesis and embryonic neural tube closure, and is widely modeled in vitro using endothelial tube formation assays.
• Endothelial tube formation is regulated by signaling pathways including STAT3 phosphorylation, TGF-beta/Smad2/3, and VEGF.
• Neural tube formation depends on NMDA receptor signaling and embryonic metabolism, and its failure causes neural tube defects.
• Plant corolla tube formation is controlled by the tasiRNA-ARF pathway, showing the process is conserved across kingdoms.
• CRISPR knockout, knock-in, point-mutation and overexpression models are essential to dissect the causal genes driving tube formation in health and disease.
Description
Tube formation (GO:0035148) is the biological process that creates the central hole of a tube in an anatomical structure through which gases and/or liquids flow [QuickGO]. This process is fundamental to the development and function of tubular organs across species, from the vascular tubes that carry blood in vertebrates to the neural tube that gives rise to the central nervous system, and even to the corolla tubes of flowers. In vitro endothelial tube formation assays are among the most widely used models for studying angiogenesis, and improvements to these models have enabled precise investigation of hypoxia and other microenvironmental stresses. Because tube formation is a multi-step morphogenetic event, it is regulated by a complex interplay of growth factors, receptors, and intracellular signaling cascades. Dysregulation of tube formation underlies major human pathologies, including cancer angiogenesis, stroke, and neural tube defects. Understanding the genes and mechanisms that control tube formation is therefore a central goal of developmental biology, vascular biology, and oncology research.
tube formation At A Glance
| GO ID | GO:0035148 |
|---|---|
| GO term | tube formation |
| Ontology | biological_process |
| Synonym | lumen formation in an anatomical structure; tube lumen formation |
| Definition | Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow. |
| Major function | Generation of tubular lumens for gas and fluid transport in vascular, neural, and other anatomical structures. |
| Related processes | Angiogenesis, neural tube closure, lumen formation, epithelial morphogenesis. |
| Model systems | Endothelial tube formation assays, neural tube explants, plant corolla tube models. |
What Is GO:0035148?
According to the Gene Ontology, GO:0035148 (tube formation) is defined as the creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow. Synonyms include lumen formation in an anatomical structure and tube lumen formation. This process encompasses the cellular and molecular events that generate a hollow, conduit-like structure, enabling the transport of gases or fluids within tissues and organs.
Why Is tube formation Important in Cell Biology?
Tube formation is essential for the development and homeostasis of nearly all tubular organs. In the vasculature, endothelial tube formation is the culminating step of angiogenesis, enabling oxygen and nutrient delivery to tissues; its dysregulation contributes to tumor growth, ischemic disease, and stroke. In the embryo, neural tube formation is a critical early morphogenetic event, and its failure leads to neural tube defects such as spina bifida and anencephaly. Because tube formation is a highly conserved process, findings from model organisms and in vitro assays inform human disease mechanisms and therapeutic strategies.
• Tube formation is the final common step of angiogenesis, required for tumor vascularization and metastatic spread.
• Endothelial tube formation assays are a standard in vitro model for anti-angiogenic drug discovery.
• Neural tube formation is a critical embryonic event; its failure causes neural tube defects.
• NMDA receptor signaling is important for neural tube formation and preventing antiepileptic drug-induced defects.
• Embryonic metabolism influences neural tube closure, linking metabolic status to morphogenesis.
• TGF-beta/Smad2/3 signaling from microglial extracellular vesicles promotes angiogenesis and tube formation after stroke.
• STAT3 phosphorylation regulated by KPNA2 promotes angiogenesis and tube formation.
• Plant corolla tube formation is controlled by the tasiRNA-ARF pathway, demonstrating evolutionary conservation.
• Ginsenoside Rg3 inhibits tube formation in renal cell carcinoma, highlighting therapeutic targeting.
• Beta-caryophyllene inhibits endothelial tube formation by downregulating VEGF in hypoxic lung cancer cells.
What Happens During tube formation?
Initiation and endothelial cell activation
In simple terms: Cells that will form the tube first receive signals telling them to start the process.
Tube formation begins when endothelial or epithelial cells are activated by pro-angiogenic or morphogenetic signals. In endothelial cells, growth factors such as VEGF and cytokines activate intracellular pathways, including STAT3 phosphorylation, which is regulated by KPNA2 and promotes angiogenesis. Hypoxia-preconditioned microglia release extracellular vesicles that activate TGF-beta/Smad2/3 signaling in endothelial cells, initiating tube formation. These activation events prime cells for migration and rearrangement.
Cell migration and alignment
In simple terms: Cells move and line up to form the outline of the future tube.
Following activation, cells migrate and align along a common axis. In in vitro tube formation assays, endothelial cells plated on extracellular matrix migrate toward each other and form cord-like structures that subsequently develop lumens. This step is sensitive to oxygen tension; acute hypoxia modulates the tube formation process in vitro. The alignment of cells is a prerequisite for the creation of a continuous central hole.
Lumen creation and tube hollowing
In simple terms: The solid cord of cells opens up in the middle to create a hollow channel.
The central event of GO:0035148 is the creation of the central hole through which gases and/or liquids flow. In endothelial tubes, lumen formation involves the reorganization of cell-cell junctions and the establishment of apical-basal polarity, leading to a hollow conduit. In the neural tube, the lumen forms as the neural plate folds and fuses, creating the central canal filled with cerebrospinal fluid. This step is tightly regulated by signaling pathways and metabolic cues.
Maturation and stabilization
In simple terms: The new tube is reinforced and stabilized so it can carry fluids reliably.
After lumen formation, the tube matures and stabilizes. In angiogenesis, this involves recruitment of pericytes and deposition of basement membrane components, processes supported by sustained signaling such as STAT3 and TGF-beta/Smad2/3. In neural tube closure, the tube must fuse properly to prevent defects; NMDA receptor signaling is important for this closure and for preventing antiepileptic drug-induced neural tube defects. Embryonic metabolism also influences neural tube closure, linking energy status to stabilization.
Regulation by extracellular signals and pharmacological modulators
In simple terms: Outside signals can speed up or slow down tube formation, and drugs can interfere with it.
Tube formation is modulated by a variety of extracellular signals. Beta-caryophyllene inhibits endothelial tube formation by modulating the secretome of hypoxic lung cancer cells, with a possible role of VEGF downregulation. Ginsenoside Rg3 inhibits tube formation in renal cell carcinoma through DNA demethylation and histone acetylation. These examples demonstrate that tube formation is a druggable process and a target for therapeutic intervention.
Key Genes Involved in GO:0035148 tube formation
The following genes and proteins have been experimentally implicated in tube formation across vascular, neural, and plant model systems.
| Gene | Major Role | Research Relevance |
|---|---|---|
| KPNA2 | Regulates STAT3 phosphorylation to promote angiogenesis and tube formation | Target for anti-angiogenic therapy; studied in endothelial tube assays |
| STAT3 | Transcription factor activated by phosphorylation; promotes angiogenesis | Key signaling node in tube formation; modulated by KPNA2 |
| TGF-beta | Cytokine that activates Smad2/3 signaling in endothelial cells | Mediates microglial EV-induced angiogenesis after stroke |
| Smad2/3 | Intracellular effectors of TGF-beta signaling | Promote tube formation and repress apoptosis in stroke models |
| VEGF | Major pro-angiogenic growth factor | Downregulated by beta-caryophyllene to inhibit tube formation |
| NMDA receptor | Glutamate-gated ion channel important for neural tube formation | Prevents antiepileptic drug-induced neural tube defects |
| ARF | Auxin response factor; regulated by tasiRNA | Controls corolla tube formation in plants |
| tasiRNA | Small RNA that regulates ARF expression | Part of the tasiRNA-ARF pathway in corolla tube formation |
| Rg3 target genes | Mediate DNA demethylation and histone acetylation | Ginsenoside Rg3 inhibits tube formation in renal cell carcinoma |
| Hypoxia-inducible factors | Respond to low oxygen and modulate angiogenesis | Acute hypoxia affects in vitro tube formation |
| Extracellular vesicle cargo | Microglial EVs carry TGF-beta/Smad2/3 signals | Promote angiogenesis and tube formation in stroke mice |
| Beta-caryophyllene targets | Modulate secretome of hypoxic lung cancer cells | Inhibit endothelial tube formation via VEGF downregulation |
| Neural tube closure genes | Coordinate neural plate folding and fusion | Linked to neural tube defects and antiepileptic drug effects |
| Metabolic enzymes | Support embryonic metabolism for neural tube closure | Influence neural tube formation |
| Endothelial junction proteins | Form cell-cell contacts during lumen creation | Required for tube hollowing in vitro |
| Matrix metalloproteinases | Remodel extracellular matrix during angiogenesis | Facilitate endothelial cell migration in tube formation |
| Pericyte recruitment factors | Stabilize newly formed tubes | Support maturation of vascular tubes |
| Apoptosis regulators | Control cell survival during tube morphogenesis | TGF-beta/Smad2/3 represses apoptosis in stroke |
How Is tube formation Regulated?
Tube formation is regulated by a network of signaling pathways and environmental cues. STAT3 phosphorylation, controlled by KPNA2, promotes angiogenesis and tube formation. TGF-beta/Smad2/3 signaling from hypoxia-preconditioned microglial extracellular vesicles promotes angiogenesis and represses apoptosis in stroke mice. VEGF signaling is a central regulator; its downregulation by beta-caryophyllene inhibits endothelial tube formation. Acute hypoxia modulates in vitro tube formation, indicating oxygen tension as a regulatory input. In neural tube formation, NMDA receptor signaling is important for closure and for preventing antiepileptic drug-induced defects, and embryonic metabolism influences neural tube closure. In plants, the tasiRNA-ARF pathway regulates corolla tube formation. Pharmacological agents such as ginsenoside Rg3 modulate tube formation through epigenetic mechanisms.
tube formation and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| KPNA2 | Cancer angiogenesis | Endothelial tube formation assay with KPNA2 knockout |
| STAT3 | Cancer, angiogenesis | STAT3 point-mutation knock-in in endothelial cells |
| TGF-beta/Smad2/3 | Stroke, angiogenesis | Microglial EV treatment in stroke mouse models |
| VEGF | Lung cancer, angiogenesis | Hypoxic lung cancer cell secretome transfer to endothelial cells |
| NMDA receptor | Neural tube defects | Neural tube explant culture with NMDA receptor knockout |
Cancer and tumor angiogenesis
Tube formation is a hallmark of tumor angiogenesis, providing the vascular network that supports tumor growth and metastasis. KPNA2 promotes angiogenesis by regulating STAT3 phosphorylation, making it a potential target for anti-angiogenic therapy. Beta-caryophyllene inhibits endothelial tube formation by modulating the secretome of hypoxic lung cancer cells, with a possible role of VEGF downregulation. Ginsenoside Rg3 inhibits renal cell carcinoma cell migration, invasion, colony formation, and tube formation, and enhances apoptosis through promoting DNA demethylation and histone acetylation. These studies highlight tube formation as a therapeutic target in oncology.
Stroke and ischemic disease
After stroke, promoting angiogenesis and tube formation can support recovery. Extracellular vesicles from hypoxia-preconditioned microglia promote angiogenesis and repress apoptosis in stroke mice via the TGF-beta/Smad2/3 pathway. This suggests that modulating tube formation could be a strategy for stroke therapy.
Neural tube defects
Failure of neural tube formation leads to neural tube defects such as spina bifida and anencephaly. NMDA receptor signaling is important for neural tube formation and for preventing antiepileptic drug-induced neural tube defects. Embryonic metabolism also influences neural tube closure, linking metabolic status to this morphogenetic process. Understanding these mechanisms may inform prevention strategies.
Plant development and corolla tube formation
Although not a human disease, corolla tube formation in plants is regulated by the tasiRNA-ARF pathway, demonstrating the broad relevance of tube formation mechanisms across kingdoms. This knowledge can inform agricultural and developmental biology research.
From tube formation-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X promote endothelial tube formation? | CRISPR knockout of gene X in HUVECs followed by tube formation assay |
| Does a point mutation in gene Y affect neural tube closure? | CRISPR point-mutation knock-in in mouse embryos |
| Does overexpression of gene Z enhance angiogenesis? | Lentiviral overexpression of gene Z in endothelial cells |
| Does a tagged version of protein W localize to the tube lumen? | Knock-in of fluorescent tag at endogenous locus |
| Does a drug inhibit tube formation? | In vitro tube formation assay with drug treatment |
| Does a microRNA regulate tube formation? | CRISPR knockout of miRNA or target site knock-in |
How to Study the tube formation Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Endothelial tube formation assay | Capillary-like tube structures in vitro | Angiogenesis drug screening |
| CRISPR knockout | Loss-of-function effects on tube formation | Causal gene validation |
| CRISPR knock-in | Precise mutation or tag introduction | Modeling point mutations or localization |
| Overexpression | Gain-of-function effects | Testing sufficiency of pro-angiogenic genes |
| Western blot | Protein phosphorylation and expression | STAT3, Smad2/3 signaling |
| Live-cell imaging | Dynamic tube formation and lumen creation | Morphogenesis studies |
| Neural tube explant culture | Neural tube closure ex vivo | Neural tube defect research |
| Metabolic assays | Embryonic metabolism during closure | Linking metabolism to neural tube formation |
In vitro tube formation assay
The endothelial tube formation assay is a widely used method to study angiogenesis in vitro. Cells are plated on extracellular matrix and monitored for the formation of capillary-like structures. Improvements to this model allow the study of acute hypoxia and other conditions. This assay is used to test pro- and anti-angiogenic compounds.
Genetic knockout and knock-in models
CRISPR-Cas9 knockout and knock-in models enable causal testing of genes in tube formation. For example, KPNA2 knockout can assess its role in STAT3 phosphorylation and angiogenesis. Point mutations can model neural tube defects. Overexpression models can test sufficiency of a gene to drive tube formation.
Imaging and morphometrics
Live-cell imaging and morphometric analysis quantify tube length, branching, and lumen formation. These methods are applied to endothelial cells in vitro and to neural tube closure in embryos.
Molecular signaling assays
Western blotting, immunoprecipitation, and reporter assays measure signaling pathway activation, such as STAT3 phosphorylation and TGF-beta/Smad2/3 activity, during tube formation.
How CRISPR Can Be Used to Study GO:0035148 tube formation
Knockout
CRISPR knockout is used to delete genes suspected to be essential for tube formation. For example, knocking out KPNA2 in endothelial cells can test its role in STAT3 phosphorylation and angiogenesis. Knockout of NMDA receptor components can reveal their requirement for neural tube formation.
Point Mutation
CRISPR point mutation introduces specific nucleotide changes to model disease-associated variants. This is particularly useful for studying neural tube defects where subtle mutations in genes like NMDA receptor subunits may impair closure. Point mutations can also dissect phosphorylation sites in STAT3.
Knock-in
Knock-in strategies insert tags, reporters, or human disease alleles at endogenous loci. Tagging junction proteins can visualize lumen formation in real time. Knock-in of disease alleles can model neural tube defects.
Overexpression
Overexpression models test whether a gene is sufficient to drive tube formation. For example, overexpressing TGF-beta/Smad2/3 components can enhance angiogenesis. Overexpression of VEGF can promote tube formation, while its downregulation inhibits it.
How EDITGENE Supports tube formation Research
Researchers studying tube formation-related genes often need to determine whether a candidate gene is causally involved in lumen creation, angiogenesis, or neural tube closure. EDITGENE provides a comprehensive suite of CRISPR-based services to accelerate this research, from knockout to precise point mutations and overexpression models.
Contact EDITGENE today to design your custom CRISPR model for tube formation research.
Frequently Asked Questions About tube formation
What is GO:0035148 tube formation?
GO:0035148 is a Gene Ontology biological process term defined as the creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow [QuickGO].
What genes are involved in tube formation?
Genes such as KPNA2, STAT3, TGF-beta, Smad2/3, VEGF, NMDA receptor, and ARF have been experimentally implicated in tube formation.
How is tube formation studied in the lab?
Common methods include endothelial tube formation assays, CRISPR knockout and knock-in models, imaging, and signaling assays.
What diseases are linked to defective tube formation?
Defective tube formation is linked to cancer angiogenesis, stroke, and neural tube defects.
What is the role of STAT3 in tube formation?
STAT3 phosphorylation, regulated by KPNA2, promotes angiogenesis and tube formation.
How does hypoxia affect tube formation?
Acute hypoxia modulates in vitro tube formation, and hypoxia-preconditioned microglia promote angiogenesis via TGF-beta/Smad2/3.
Can tube formation be inhibited pharmacologically?
Yes, compounds such as beta-caryophyllene and ginsenoside Rg3 inhibit tube formation in cancer models.
What is the difference between tube formation and angiogenesis?
Tube formation is the specific step of creating the tubular lumen, while angiogenesis encompasses the broader process of new blood vessel formation.
What is the role of NMDA receptor in neural tube formation?
NMDA receptor signaling is important for neural tube formation and for preventing antiepileptic drug-induced neural tube defects.
How does embryonic metabolism influence neural tube closure?
Embryonic metabolism affects neural tube closure, linking metabolic status to morphogenesis.
Conclusion
GO:0035148 tube formation is a fundamental biological process that creates tubular lumens for gas and fluid transport across diverse anatomical structures. From endothelial angiogenesis to neural tube closure and plant corolla development, tube formation is regulated by conserved signaling pathways and is implicated in major human diseases including cancer, stroke, and neural tube defects. Continued research using CRISPR models and in vitro assays will further illuminate the genetic and molecular basis of tube formation, offering new therapeutic opportunities.
References
- 1. Jia Y et al.. 2022. KPNA2 promotes angiogenesis by regulating STAT3 phosphorylation.. J Transl Med 20(1):627 PMID: 36578083
- 2. Li F et al.. 2022. Improvement of tube formation model of cell: Application for acute hypoxia in in vitro study of angiogenesis.. Microvasc Res 140:104297 PMID: 34890690
- 3. Zhang L et al.. 2021. Extracellular vesicles from hypoxia-preconditioned microglia promote angiogenesis and repress apoptosis in stroke mice via the TGF-β/Smad2/3 pathway.. Cell Death Dis 12(11):1068 PMID: 34753919
- 4. Ding B et al.. 2020. Developmental Genetics of Corolla Tube Formation: Role of the tasiRNA-ARF Pathway and a Conceptual Model.. Plant Cell 32(11):3452-3468 PMID: 32917737
- 5. Wittig F et al.. 2024. β-Caryophyllene Inhibits Endothelial Tube Formation by Modulating the Secretome of Hypoxic Lung Cancer Cells-Possible Role of VEGF Downregulation.. Int J Mol Sci 25(2) PMID: 38255884
- 6. Ma Z et al.. 2023. Ginsenoside Rg3 inhibits renal cell carcinoma cell migration, invasion, colony formation, and tube formation and enhances apoptosis through promoting the DNA demethylation and histone acetylation.. J Pharm Pharmacol 75(1):76-86 PMID: 36264186
- 7. Sequerra EB et al.. 2018. NMDA Receptor Signaling Is Important for Neural Tube Formation and for Preventing Antiepileptic Drug-Induced Neural Tube Defects.. J Neurosci 38(20):4762-4773 PMID: 29712790
- 8. Yamaguchi Y et al.. 2017. Neural tube closure and embryonic metabolism.. Congenit Anom (Kyoto) 57(5):134-137 PMID: 28295633
