SOX17 Antibody

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Description

Definition and Biological Significance

SOX17 functions as a master regulator of definitive endoderm specification during embryogenesis, acting downstream of TGF-β/Activin and Wnt3a signaling . Its dysregulation associates with:

  • Pulmonary arterial hypertension (PAH) via ECM pathway alterations

  • Developmental defects in mesoendodermal differentiation

  • Tumor progression in ovarian/gastrointestinal cancers

Antibodies targeting SOX17 (e.g., AF1924, MAB1924, ab224637) enable detection across species, with ≤1% cross-reactivity to SOX18 .

Table 1: Key Antibody Performance Characteristics

CloneHostApplications (Concentration)ReactivitySpecificity Confirmation
AF1924 GoatWB (1-2 µg/mL), ChIP (5 µg), ICC (5-15 µg/mL)Human, Mouse55 kDa band in BG01V hESCs
MAB1924 MouseICC (8-25 µg/mL)Human, MouseEndodermal progenitor staining
ab224637 RabbitWB (1:1000), IP, ICC/IFHuman, Mouse, RatKO validation in HeLa cells

Key Findings Using SOX17 Antibodies:

  • Chromatin Immunoprecipitation: Identified p21 promoter binding in endoderm-differentiated mouse ESCs using AF1924 .

  • PAH Pathogenesis: Risk alleles in SOX17 enhancers reduce endothelial expression by disrupting HOXA5/ROR-α binding, increasing apoptosis/proliferation in hPAECs .

  • Pluripotency Regulation: SOX17+/OCT4+ cells mark primordial germ cell-like cells in iPSC models .

Table 2: Antibody Validation Metrics

ParameterAF1924 ab224637
Host SpeciesGoat polyclonalRabbit monoclonal
PurityAffinity-purifiedProtein A/G purified
Storage-20°C to -70°C-20°C, avoid freeze-thaw
Cross-reactivity<1% SOX18 None in KO lysates
Band Size55 kDa 51 kDa

Disease Relevance and Therapeutic Insights

  • PAH Mechanisms: SOX17 knockdown in hPAECs dysregulates 198 plasma proteins (IL-5, SPARC, COL18A1) linked to vascular remodeling .

  • Pharmacological Targets: Connectivity mapping identified compounds reversing SOX17-deficient transcriptomes .

  • Developmental Models: SOX17 enhancer KO mice exhibit exacerbated hypoxia-induced pulmonary hypertension .

Best Practices for Experimental Use

  • Western Blotting: Use RIPA lysates from endoderm-differentiated BG01V hESCs with 1 µg/mL AF1924 .

  • Immunocytochemistry: Optimize fixation (4% PFA) and permeabilization (0.1% Triton X-100) for nuclear SOX17 detection .

  • Controls: Include SOX17-KO HeLa cells (ab265744) and verify with GAPDH loading controls .

Product Specs

Buffer
Liquid in PBS containing 50% glycerol, 0.5% BSA, and 0.02% sodium azide.
Form
Liquid
Lead Time
Typically, we are able to ship products within 1-3 business days of receiving your order. The exact delivery time may vary depending on the purchasing method or location. Please consult your local distributor for specific delivery timeframes.
Synonyms
FLJ22252 antibody; SOX17 antibody; SOX17_HUMAN antibody; SRY (sex determining region Y) box 17 antibody; SRY box 17 antibody; SRY related HMG box transcription factor SOX17 antibody; Transcription factor SOX-17 antibody; Transcription factor SOX17 antibody; VUR3 antibody
Target Names
Uniprot No.

Target Background

Function
SOX17 functions as a transcription regulator that interacts with target promoter DNA, inducing DNA bending. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX17 modulates transcriptional regulation through the Wnt3a pathway, inhibiting Wnt signaling. It promotes the degradation of activated β-catenin (CTNNB1). SOX17 plays a crucial role in the regulation of embryonic development. It is essential for the normal development of the definitive gut endoderm and the proper looping of the embryonic heart tube. SOX17 is also critical for embryonic and postnatal vascular development, including the formation of arteries. In postnatal angiogenesis, it works in conjunction with SOX18. SOX17 is required for the generation and maintenance of fetal hematopoietic stem cells and for fetal hematopoiesis. It is likely a transcriptional activator in premeiotic germ cells.
Gene References Into Functions
  1. Case-control analyses reveal a significant overrepresentation of rare variants in ATP13A3, AQP1, and SOX17. These findings provide independent validation of the critical role of GDF2 in heritable pulmonary arterial hypertension. PMID: 29650961
  2. This research strongly implicates SOX17 as a novel risk gene contributing to Pulmonary arterial hypertension-congenital heart disease. PMID: 30029678
  3. This study demonstrated that one of four SNPs located near the SOX17 gene, rs1072737, was statistically associated with intracranial aneurysm (IA) formation in a Korean population. The Minor Allele Frequency (MAF) of this variant (minor allele, C) exhibited a significant ethnic difference between Korean and European populations. Two SNPs, rs10958409 and rs9298506, showed statistically significant associations with increased IA risk in the current meta-analysis. PMID: 29191544
  4. The combination of methylated SOX17 with cytology provided a more accurate prediction of neoplastic grade compared to cytology alone. PMID: 28148542
  5. SOX17 acts as a tumor suppressor in cholangiocarcinoma. Restoring its genetic, molecular, and/or pharmacological function may represent a promising new therapeutic strategy. PMID: 28237397
  6. The findings suggest that decreasing SOX17 levels may promote endothelial cell (EC) development and progression. By downregulating MAML3 expression and Wnt signaling, SOX17 acts as a tumor suppressor, potentially improving outcomes for patients with EC. PMID: 27738313
  7. SOX2 repression in TCam-2 cells can be reversed by recruiting the constitutively expressed H3K27 demethylase UTX to the SOX2 promoter through retinoid signaling, leading to the expression of neuronal and other lineage genes. SOX17 has been shown to initiate human primordial germ cell (PGC) specification, with its target PRDM1 suppressing mesendodermal genes. PMID: 27132888
  8. Dedifferentiation of fibroblasts to CD34(+) progenitor cells gives rise to endothelial cells and erythroblasts in a SOX17-dependent manner. PMID: 28381471
  9. The study extracted and analyzed experimentally validated 3D models of the SOX17-HMG domain and β-catenin. The research investigated the molecular level disturbance in these two essential human proteins upon M76A and G103R mutations of SOX17. These mutations further hinder cell signaling phenomena crucial for human cytological development, starting from gastrulation and endoderm formation. PMID: 28132771
  10. The SOX17 promoter is highly methylated in primary tumors and in corresponding plasma samples, both in operable and advanced non-small cell lung cancer. PMID: 26741346
  11. The definitive endoderm and foregut endoderm differentiation capabilities of Wnt pathway-modulated cells were determined based on the expression levels of the endodermal transcription factors SOX17 and FOXA2, and those of the transcription activator GATA4 and the α-fetoprotein (AFP) gene, respectively. PMID: 26861571
  12. Knockdown of OCT4 during differentiation inhibits mesendoderm formation and removal of the H3K27me3 mark from the SOX17 promoter, suggesting that OCT4 acts to induce removal of the Polycomb2 complex. PMID: 26411902
  13. High expression of the Sox17-associated pathway in medium and small arteries indicates that brain arteriovenous malformation vessels are intrinsically active. PMID: 26463399
  14. SOX17 demethylation induced miR-371-5p expression and consequently suppressed its direct target SOX2. This study identified a novel mechanism of the SOX17/miR-371-5p/SOX2 axis involved in the regulation of epithelial-mesenchymal transition (EMT), stemness, and metastasis. PMID: 25868860
  15. Decreased expression of SOX17 is associated with tumor progression in breast cancer. PMID: 25971583
  16. In this study, oligodendroglioma patients with 1p/19q loss of heterozygosity (LOH) and Sox17 protein expression had a better prognosis. PMID: 25674225
  17. SOX17 might play a role in the development of Ovarian Cancer and may be a therapeutic target in OC. PMID: 25953442
  18. Decreased Sox17 expression is correlated with melanoma progression, an unfavorable survival of melanoma patients, and is an independent molecular prognostic factor for melanoma. PMID: 25310020
  19. The possible association of SOX-17 and RBBP8 with brain arteriovenous malformations, genes involved in cell cycle progression, warrants further investigation. PMID: 25053769
  20. Promoter methylation may play a significant role in breast cancer progression and could serve as a prognostic biomarker to identify patients at risk of developing metastasis or recurrence after mastectomy. PMID: 25789956
  21. Human intracranial aneurysm samples exhibited reduced Sox17 expression and impaired endothelial integrity. PMID: 25596186
  22. Low Sox17 expression is associated with hepatocellular carcinoma. PMID: 25106407
  23. SOX17 is the key regulator of human primordial germ cells-like cell (hPGCLC) specification, while BLIMP1 represses endodermal and other somatic genes during hPGCLC specification. PMID: 25543152
  24. Hypermethylation of the SOX17 promoter may be one of the early events in the development of myelodysplastic syndrome and predicts poor prognosis. PMID: 25291942
  25. Low SOX17 expression is associated with esophageal cancer progression. PMID: 24407731
  26. Experimental confirmation of miRNA-mRNA interactions established a critical role of miR-200a in regulating both EMT and definitive endoderm formation, through direct repression of ZEB2 and SOX17, during early stage differentiation. PMID: 23813959
  27. In multiple sclerosis tissue, Sox17 was primarily detected in actively demyelinating lesions and periplaque white matter. PMID: 23918253
  28. Immunofluorescence analysis of human pancreatic tissue arrays revealed the presence of tuft cells in metaplasia and early-stage tumors, along with SOX17 expression, consistent with a biliary phenotype. PMID: 23999170
  29. Overall survival of patients with gastric cancer was found to be significantly associated with SOX17 promoter methylation. PMID: 23403728
  30. After electrostatic interactions attract Sox17 to DNA, Asn73, Ser99, and Trp106 form hydrogen bonds with DNA. Arg70, Lys80, Arg83, His94, and Asn95 on Sox17 undergo conformational changes and form hydrogen bonds with DNA. PMID: 23061670
  31. Recombinant Sox17 mediates modulation of the Wnt pathway through changes in β-catenin, SFRP1, and Wnt/Frizzled expression. PMID: 23474492
  32. The SOX17 promoter region is frequently methylated in primary breast tumors, in circulating tumor cells (CTCs) isolated from patients with breast cancer, and in corresponding cell-free DNA (cfDNA) samples. PMID: 23136251
  33. SOX17 plays a key role in priming hemogenic potential in endothelial cells, thereby regulating hematopoietic development from stem cells. PMID: 23169777
  34. SOX17 acts as a Wnt signaling inhibitor. PMID: 22846201
  35. These findings establish Sox17 as a key regulator of tumor angiogenesis and tumor progression. PMID: 23241958
  36. SOX17 was frequently methylated in human papillary thyroid carcinoma (PTC). Loss of SOX17 expression was induced by promoter region hypermethylation. SOX17 inhibited thyroid cancer proliferation. Methylation of SOX17 activated the Wnt signaling pathway in human thyroid cancer. PMID: 23044318
  37. The SOX17 promoter region is frequently methylated in esophageal cancer and in a progression tendency during esophageal carcinogenesis. PMID: 22921431
  38. This research provided further evidence to support the previously reported association of intracranial aneurysm with single nucleotide polymorphism in SOX17. PMID: 22961961
  39. New sequence variations in SOX17 were identified, but all correspond to nonpathogenic variants, suggesting that SOX17 is not involved in Usher syndrome type 1 (UHL) phenotype. PMID: 22348788
  40. Silencing of Sox17 occurs frequently in early gastric cancer. PMID: 22161215
  41. Downstream targets of Sox17 define signaling pathways and molecular mechanisms in oligodendrocyte progenitor cells that are regulated by Sox17 during cell cycle exit and differentiation in oligodendrocyte development. PMID: 21957254
  42. A stage-specific transduction of SOX17 in the primitive endoderm or mesendoderm promotes directive extraembryonic endoderm or definitive endoderm differentiation by SOX17 transduction, respectively. PMID: 21760905
  43. Sox17 may be a key transcription factor controlling CD133 expression, and it might also play a role in the control of gastric tumor progression. PMID: 21457403
  44. SOX17(+)-human embryonic stem cell progeny expressed endodermal markers. PMID: 21362573
  45. Data indicate that down-regulated by Sox17 expressing HepG2 cells is a set of genes that are expressed in the developing liver, suggesting that one function of Sox17 is the repression of liver gene expression. PMID: 21305474
  46. Sox17 prominently contributes to gastric cancer progression through regulating proliferation and cell cycle, indicating a novel diagnosis and prognosis biomarker as well as a potential therapeutic target in gastric cancer. PMID: 21514720
  47. SOX17 negatively regulates the canonical WNT/β-catenin signaling pathway and inhibits human hepatocellular carcinoma (HCC) cells growth. PMID: 20716954
  48. These data indicate a role of SOX17 in human kidney and urinary tract development and implicate the SOX17-p.Y259N mutation as a causative factor in congenital anomalies of the kidney and the urinary tract. PMID: 20960469
  49. Sox17 may be a valuable biomarker for the study of breast cancer carcinogenesis and progression. PMID: 19301122
  50. SOX17 silencing due to promoter hypermethylation is an early event during tumorigenesis and may contribute to aberrant activation of Wnt signaling in colorectal cancer. PMID: 18413743

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Database Links

HGNC: 18122

OMIM: 610928

KEGG: hsa:64321

STRING: 9606.ENSP00000297316

UniGene: Hs.98367

Involvement In Disease
Vesicoureteral reflux 3 (VUR3)
Subcellular Location
Nucleus.
Tissue Specificity
Expressed in adult heart, lung, spleen, testis, ovary, placenta, fetal lung, and kidney. In normal gastrointestinal tract, it is preferentially expressed in esophagus, stomach and small intestine than in colon and rectum.

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Applications : Immunoblot analysis

Sample type: cell

Review: Schematic diagram of entoderm differentiation. Representative immunostaining images and quantification of SOX17+ (red) and DAPI (blue) in PSC to entoderm stage treated with or without Dox. Scale bars, 200 μm. Data were shown as Mean ± SEM (n = 3, ***p < 0.001 compared with the +Dox group).

Q&A

What is SOX17 and why is it important in developmental biology research?

SOX17 (SRY-box transcription factor 17) is a critical DNA-binding protein that belongs to the SOX family of transcription factors. It is a 44.1 kilodalton protein that plays essential roles in several developmental processes, particularly endoderm formation and vascular development . As a key transcriptional regulator, SOX17 contributes to:

  • Definitive endoderm specification during early embryogenesis

  • Vascular development and maintenance

  • Cell fate determination during organogenesis

  • Regulation of canonical Wnt signaling pathways

In developmental biology research, SOX17 serves as a critical marker for identifying specific cell populations, including arterial endothelial cells and definitive endoderm cells . It is frequently used to monitor differentiation of pluripotent stem cells, particularly their commitment to endodermal lineages that eventually form organs such as the liver, pancreas, and intestines.

The protein's expression pattern is highly dynamic during development, with tightly regulated temporal and spatial characteristics that reflect its various developmental functions. Importantly, SOX17 expression is often used as a readout for successful definitive endoderm induction in stem cell differentiation protocols, making SOX17 antibodies indispensable tools for developmental biologists.

What are the key applications where SOX17 antibodies prove most valuable?

SOX17 antibodies find utility across numerous experimental applications, making them versatile tools for diverse research questions:

  • Immunocytochemistry/Immunofluorescence (ICC/IF): SOX17 antibodies excel in visualizing protein expression patterns in cells, particularly in stem cell differentiation studies. They can detect SOX17 in various cell types, including embryonic stem cells differentiated toward endoderm, TiPSCs-derived cells, and established cell lines . Typical working concentrations range from 5-15 μg/mL for optimal staining.

  • Western Blot Analysis: SOX17 antibodies can reliably detect the protein in cell and tissue lysates, typically appearing at approximately 55 kDa under reducing conditions . Recommended concentrations are 1-2 μg/mL for standard Western blot applications .

  • Chromatin Immunoprecipitation (ChIP): SOX17 antibodies effectively immunoprecipitate SOX17-DNA complexes, enabling the identification of genomic binding sites. Successful ChIP experiments typically use 5 μg of antibody per 5 x 10^6 cells .

  • Flow Cytometry: For quantitative analysis of SOX17 expression in heterogeneous cell populations, SOX17 antibodies can be used to determine differentiation efficiency, particularly in stem cell research .

  • Immunohistochemistry: SOX17 antibodies can detect the protein in both frozen and paraffin-embedded tissue sections, revealing expression patterns in embryonic tissues, vascular structures, and adult organs .

These applications are particularly valuable in:

  • Tracking endoderm formation during embryonic development

  • Monitoring differentiation efficiency of pluripotent stem cells

  • Studying vascular development and arterial specification

  • Investigating transcriptional regulatory networks

The versatility of SOX17 antibodies across multiple applications makes them essential components of the developmental biology toolkit.

How should SOX17 antibody conditions be optimized for detecting endoderm differentiation in stem cell cultures?

Optimizing SOX17 antibody conditions for endoderm differentiation detection requires careful consideration of several experimental parameters:

Sample preparation:

  • Fix cells at the optimal time point during differentiation. SOX17 expression typically peaks around day 3-5 of endoderm differentiation protocols .

  • Use 4% paraformaldehyde fixation for 15-20 minutes at room temperature.

  • Ensure thorough permeabilization (0.2-0.5% Triton X-100 for 10-15 minutes) as SOX17 is a nuclear transcription factor.

Antibody selection and dilution:

  • For immunofluorescence applications, use 5-15 μg/mL of SOX17 antibody based on published successful protocols .

  • Begin with the middle of this range (10 μg/mL) and adjust based on signal-to-background ratio.

  • Incubate primary antibody for 3 hours at room temperature or overnight at 4°C for optimal results .

Control inclusion:

  • Always include undifferentiated stem cells as negative controls.

  • Use established endoderm-differentiated cells as positive controls.

  • Consider co-staining with FOXA2, another definitive endoderm marker, to confirm specificity of the signal .

Differentiation protocol considerations:

  • The concentration of endoderm-inducing factors significantly impacts SOX17 expression. Evidence shows that higher concentrations of Activin A (50-100 ng/ml) favor SOX17+ endoderm formation, while lower concentrations (10 ng/ml) may promote alternative lineages .

  • Include CHIR99021 (2 μM) with Activin A for enhanced endoderm induction, as demonstrated in successful differentiation protocols .

Detection system optimization:

  • Use fluorophore-conjugated secondary antibodies with brightness appropriate for the expected expression level.

  • Counter-stain nuclei with DAPI to facilitate identification of all cells in the culture.

  • Capture images at consistent exposure settings across experimental conditions.

This systematic approach ensures reliable detection of SOX17 during endoderm differentiation while minimizing background and false positives.

What controls are essential when using SOX17 antibodies for chromatin immunoprecipitation (ChIP) experiments?

Rigorous controls are critical for generating reliable ChIP data with SOX17 antibodies. The following controls should be implemented:

Antibody-specific controls:

  • Isotype control antibody: Include an isotype-matched control antibody (e.g., normal IgG from the same species as the SOX17 antibody) to assess non-specific binding . This control helps distinguish true SOX17 binding from background signal.

  • Antibody validation: Verify SOX17 protein expression in your experimental cells by Western blot before proceeding with ChIP to confirm the protein is indeed present .

Sample-specific controls:

  • Input DNA control: Reserve 5-10% of the pre-immunoprecipitation chromatin to normalize for variations in starting material and DNA recovery.

  • Cell-type controls:

    • Use endoderm-differentiated stem cells as positive controls where SOX17 is highly expressed .

    • Include undifferentiated cells or SOX17-negative cell lines as negative controls.

Target sequence controls:

  • Positive genomic locus: Include PCR primers for known SOX17 binding sites. The p21 promoter has been validated as a SOX17 target that can be detected after ChIP .

  • Negative genomic locus: Include primers for regions not expected to bind SOX17 (e.g., gene desert regions or housekeeping genes not regulated by SOX17).

Technical controls:

  • Sonication efficiency: Verify chromatin fragmentation to 200-500 bp by agarose gel electrophoresis before immunoprecipitation.

  • IP efficiency: Assess immunoprecipitation efficiency by Western blot of the immunoprecipitated material when possible.

Protocol-specific considerations:

  • For SOX17 ChIP, successful protocols have used 5 μg of antibody per ChIP reaction with endoderm-differentiated stem cells .

  • An effective approach involves capturing immunocomplexes using biotinylated secondary antibodies followed by streptavidin ferrofluid, as demonstrated in published protocols .

Implementing these controls enables confident interpretation of SOX17 ChIP data and distinguishes genuine binding events from technical artifacts.

What are the optimal cell and tissue fixation protocols for SOX17 immunostaining?

Optimal fixation protocols for SOX17 immunostaining vary depending on sample type and experimental goals. Below are evidence-based recommendations for different specimen types:

For cultured cells (e.g., stem cells, cell lines):

  • Adherent cells on coverslips:

    • Rinse gently with PBS to remove medium components

    • Fix with 4% paraformaldehyde in PBS for 15-20 minutes at room temperature

    • Permeabilize with 0.2-0.5% Triton X-100 in PBS for 10 minutes

    • Block with 5-10% normal serum from the secondary antibody species

  • Embryoid bodies or 3D structures:

    • Fix with 4% paraformaldehyde for slightly longer (20-30 minutes)

    • Consider using 0.5% Triton X-100 with extended permeabilization time (15-20 minutes)

    • Section larger structures (>200 μm) prior to staining for better antibody penetration

For tissue sections:

  • Frozen sections:

    • Fix fresh tissues in 4% paraformaldehyde for 2-4 hours (small samples) or overnight (larger samples)

    • Cryoprotect in 30% sucrose solution until tissue sinks

    • Embed in OCT compound and freeze at -80°C

    • Cut 8-12 μm sections and mount on positively charged slides

    • Post-fix slides briefly (10 minutes in 4% paraformaldehyde) before staining

  • Paraffin-embedded sections:

    • Fix tissues in 10% neutral buffered formalin for 24-48 hours

    • Process and embed in paraffin using standard histology protocols

    • Section at 5-7 μm thickness

    • Perform heat-induced epitope retrieval using citrate buffer (pH 6.0) for 20 minutes

    • This approach has been successful for detecting SOX17 in endometrial tissue, where it localizes to glandular and luminal epithelium

Special considerations:

  • SOX17 is primarily a nuclear protein, so ensure adequate nuclear permeabilization in all protocols

  • Extended fixation can mask epitopes; if signal is weak, reduce fixation time or try alternative fixatives

  • For co-staining with other markers, select a fixation protocol compatible with all target antigens

  • When staining embryonic tissues, age-appropriate fixation times are critical (younger tissues require shorter fixation)

These protocols have been validated in various research contexts, including stem cell differentiation studies and tissue analysis , providing a solid foundation for successful SOX17 immunostaining.

How can researchers address inconsistent SOX17 staining patterns in differentiated stem cell cultures?

Inconsistent SOX17 staining patterns in differentiated stem cell cultures represent a common challenge that can be systematically addressed through the following approaches:

Differentiation protocol optimization:

  • Standardize induction factors and their concentrations. Evidence shows dramatic differences in SOX17 expression depending on Activin A concentrations—50-100 ng/ml promotes robust SOX17+ endoderm formation, while lower concentrations may yield mixed populations .

  • Ensure consistent timing of differentiation. SOX17 expression is highly dynamic; analyze cells at standardized time points (typically day 3-5 for endoderm) to capture peak expression.

  • Control cell density at initiation of differentiation. Seeding density affects differentiation efficiency; maintain consistent plating densities across experiments (typically 1-2 × 10^5 cells/cm²).

Technical staining considerations:

  • Optimize fixation and permeabilization. Nuclear transcription factors like SOX17 require thorough nuclear permeabilization:

    • Test increased Triton X-100 concentrations (0.3-0.5%)

    • Consider alternative permeabilization methods like methanol fixation (-20°C for 10 minutes)

    • Ensure consistent fixation timing across samples

  • Address colony architecture issues:

    • For dense colonies, extend antibody incubation times (overnight at 4°C)

    • Ensure even distribution of cells when plating to avoid overcrowded regions

    • Consider gentle dissociation to single cells before fixation for highly compact colonies

Antibody-related factors:

  • Validate antibody performance with positive controls (e.g., SOX17-expressing cell lines) .

  • Test multiple SOX17 antibody clones if inconsistency persists.

  • Implement CRISPR/Cas9 SOX17 knockdown controls to confirm specificity, as demonstrated in published research .

Heterogeneity assessment:

  • Quantify staining patterns using imaging software to objectively measure intensity variations.

  • Consider flow cytometry analysis for SOX17 to determine the percentage of positive cells and expression level distribution .

  • Implement single-cell analysis approaches to characterize subpopulations within cultures.

Environmental variables:

  • Control oxygen levels during differentiation, as HIF-1 alpha activation has been shown to upregulate SOX17 expression .

  • Maintain consistent temperature and CO₂ levels throughout differentiation.

  • Use defined media components rather than serum or conditioned media to reduce variability.

By systematically addressing these factors, researchers can significantly improve the consistency of SOX17 staining patterns and more accurately assess endoderm differentiation efficiency.

Why might Western blot detection of SOX17 fail despite confirmed mRNA expression?

Western blot detection of SOX17 may fail despite confirmed mRNA expression due to several technical and biological factors. This disconnect between mRNA and protein detection requires systematic troubleshooting:

Protein extraction optimization:

  • SOX17 is primarily a nuclear transcription factor, requiring effective nuclear protein extraction methods:

    • Use RIPA buffer supplemented with nuclear extraction components

    • Include sonication steps (3-5 cycles of 10 seconds each) to shear genomic DNA and enhance nuclear protein release

    • Add freshly prepared protease inhibitor cocktail to prevent degradation

    • Consider specialized nuclear extraction kits for challenging samples

Western blot technical adjustments:

  • Protein migration considerations:

    • SOX17 appears at approximately 55 kDa in Western blots, higher than its calculated molecular weight of 44.1 kDa , likely due to post-translational modifications

    • Use appropriate molecular weight markers spanning 40-70 kDa range

    • Extend running time to improve band separation

  • Membrane and transfer optimization:

    • Use PVDF membranes which have been successfully used for SOX17 detection

    • Employ reducing conditions as specified in validated protocols

    • Consider wet transfer methods for improved transfer of nuclear proteins

  • Detection system sensitivity:

    • Increase primary antibody concentration to 1-2 μg/mL as recommended

    • Extend primary antibody incubation to overnight at 4°C

    • Use enhanced chemiluminescence (ECL) detection systems with increased sensitivity

    • Consider longer exposure times during imaging

Biological and sample-specific factors:

  • Protein stability and half-life:

    • SOX17 protein may have a shorter half-life than its mRNA

    • Consider treating cells with proteasome inhibitors (e.g., MG132) prior to lysis

  • Post-translational modifications:

    • SOX17 undergoes modifications that might affect antibody recognition

    • Test multiple antibodies recognizing different epitopes

  • Expression levels:

    • SOX17 might be expressed at levels below Western blot detection limits

    • Increase protein loading amount (50-100 μg total protein)

    • Consider immunoprecipitation to enrich SOX17 before Western blot

Control experiments:

  • Include positive controls known to express SOX17 protein:

    • Endoderm-differentiated embryonic stem cells

    • Cell lines with confirmed SOX17 expression (e.g., certain ovarian cancer cell lines like SK-OV-3 and OVCAR-3)

  • Verify antibody functionality:

    • Test the antibody on recombinant SOX17 protein

    • Consider alternative detection methods like immunofluorescence to confirm antibody reactivity

By systematically addressing these factors, researchers can overcome technical hurdles and successfully detect SOX17 protein by Western blot, reconciling the disconnect between mRNA and protein detection.

How can researchers design ChIP-seq experiments to map genome-wide SOX17 binding profiles?

Designing a robust ChIP-seq experiment to map genome-wide SOX17 binding profiles requires careful planning of each experimental step:

Experimental design and sample preparation:

  • Cell selection and verification:

    • Choose cells with confirmed SOX17 expression (e.g., differentiated endoderm cells, arterial endothelial cells)

    • Verify protein expression by Western blot before proceeding

    • Consider enhancing SOX17 levels where appropriate; for instance, HIF-1 alpha activation has been shown to increase SOX17 expression in endothelial cells

  • Cell number and chromatin preparation:

    • Scale up to obtain sufficient starting material (≥10 million cells per condition)

    • Optimize crosslinking conditions (1% formaldehyde for 10 minutes at room temperature)

    • Verify chromatin fragmentation to 200-500 bp by gel electrophoresis

Immunoprecipitation strategy:

  • Antibody selection and validation:

    • Choose antibodies validated for ChIP applications (search results indicate successful ChIP with 5 μg of SOX17 antibody)

    • Verify antibody specificity by Western blot and immunoprecipitation-Western blot

    • Consider antibodies targeting different epitopes for complementary experiments

  • IP protocol optimization:

    • Implement the validated approach using biotinylated secondary antibodies followed by streptavidin ferrofluid capture

    • Include appropriate controls:

      • Input chromatin (non-immunoprecipitated)

      • IgG control (isotype-matched non-specific antibody)

      • Known SOX17 target regions (e.g., p21 promoter)

Sequencing considerations:

  • Library preparation:

    • Prepare libraries from:

      • SOX17 ChIP DNA

      • Input control DNA

      • IgG control DNA

    • Use library preparation kits designed for low DNA input if necessary

    • Include library amplification controls to prevent over-amplification

  • Sequencing parameters:

    • Sequence to sufficient depth (≥20 million uniquely mapping reads per sample)

    • Consider paired-end sequencing for improved mapping accuracy

    • Include spike-in controls for quantitative comparisons between samples

Data analysis pipeline:

  • Primary analysis:

    • Align reads to the appropriate reference genome

    • Call peaks using established algorithms (e.g., MACS2)

    • Filter peaks based on fold enrichment over input and IgG controls

  • Secondary analyses:

    • Perform motif discovery to identify SOX17 binding motifs

    • Annotate peaks to genomic features (promoters, enhancers, etc.)

    • Integrate with transcriptomic data to correlate binding with gene expression

Validation experiments:

  • ChIP-qPCR validation:

    • Select several peaks of varying strengths for validation

    • Design primers for these regions and negative control regions

    • Perform qPCR on independent ChIP samples

  • Functional validation:

    • Select candidate target genes for functional studies

    • Use reporter assays or CRISPR-based approaches to confirm regulatory relationships

This comprehensive approach enables reliable genome-wide mapping of SOX17 binding sites, providing insights into its transcriptional regulatory networks and biological functions.

How can SOX17 antibodies be integrated with single-cell analysis technologies to study heterogeneity in endoderm differentiation?

Integrating SOX17 antibodies with single-cell technologies provides powerful approaches to dissect heterogeneity in endoderm differentiation, revealing developmental trajectories and cell fate decisions with unprecedented resolution:

Flow cytometry-based approaches:

  • Index sorting with transcriptomic analysis:

    • Use fluorophore-conjugated SOX17 antibodies for cell sorting

    • Perform index sorting to record SOX17 protein levels for each individual sorted cell

    • Process sorted cells for single-cell RNA sequencing

    • Correlate SOX17 protein levels with transcriptomic profiles to identify gene expression patterns associated with different SOX17 expression levels

    • This approach has proven valuable when studying heterogeneous differentiation outcomes influenced by varying Activin A concentrations

  • Multi-parameter protein analysis:

    • Combine SOX17 antibodies with other lineage markers (FOXA2, GATA4/6, CXCR4)

    • Include markers for alternative lineages (e.g., Brachyury for mesoderm, Nestin for ectoderm) to identify mixed populations

    • Use fluorescence-activated cell sorting to isolate distinct subpopulations for further characterization

Mass cytometry (CyTOF) implementation:

  • High-dimensional protein profiling:

    • Conjugate SOX17 antibodies with metal isotopes for CyTOF analysis

    • Combine with 30+ additional protein markers covering:

      • Other transcription factors (FOXA2, GATA factors)

      • Signaling pathway components (phospho-SMAD2/3, β-catenin)

      • Cell cycle and proliferation markers

    • Apply dimensionality reduction and clustering algorithms to identify discrete cell populations

    • This approach captures proteomic heterogeneity at unprecedented resolution

CITE-seq and related technologies:

  • Simultaneous protein and RNA profiling:

    • Label SOX17 antibodies with oligonucleotide barcodes

    • Combine with other barcoded antibodies against relevant markers

    • Perform single-cell RNA sequencing that captures both transcriptome and antibody-derived barcodes

    • This provides concurrent measurement of SOX17 protein expression and whole-transcriptome analysis in the same cells

    • Particularly valuable for correlating SOX17 protein levels with expression of genes not amenable to antibody detection

In situ approaches for spatial context:

  • Multiplexed imaging:

    • Use SOX17 antibodies in sequential immunofluorescence or imaging mass cytometry

    • Apply to embryoid bodies, gastruloids, or tissue sections

    • Preserve spatial information critical for understanding developmental patterning

    • The validated immunofluorescence protocols for SOX17 can be adapted for multiplexed approaches

Experimental design considerations:

  • Differentiation protocol variables:

    • Design experiments with varying induction conditions to capture diverse differentiation trajectories

    • The search results demonstrate that Activin A concentration significantly affects differentiation outcomes and SOX17 expression patterns

    • Include time-course sampling to capture transient cell states

  • Analysis framework:

    • Apply trajectory inference algorithms to reconstruct developmental progressions

    • Identify branch points where cells diverge toward different endodermal fates

    • Correlate SOX17 expression levels with trajectory positioning

These integrated approaches provide multidimensional insights into endoderm differentiation heterogeneity, revealing how quantitative differences in SOX17 expression influence cell fate decisions and developmental trajectories.

What are the challenges in detecting post-translational modifications of SOX17 using current antibodies?

Detecting post-translational modifications (PTMs) of SOX17 presents several significant challenges that researchers must navigate:

Current detection limitations:

  • Epitope masking and accessibility:

    • PTMs can directly block antibody binding sites or alter protein conformation

    • Standard SOX17 antibodies may exhibit variable binding depending on the modification status of their target epitopes

    • Evidence suggests SOX17 migrates at approximately 55 kDa in Western blots, higher than its predicted 44.1 kDa size, indicating the presence of significant PTMs

  • Modification-specific antibody scarcity:

    • Few commercially available antibodies specifically recognize modified forms of SOX17

    • Developing such antibodies requires:

      • Identification of specific modification sites

      • Generation of modified peptide antigens

      • Extensive validation across multiple applications

  • Dynamic nature of modifications:

    • PTMs are often transient and context-dependent

    • Modification patterns may vary during differentiation stages or in response to signaling events

    • Evidence shows SOX17 regulation by estrogen/progesterone in endometrial cells and by HIF-1 alpha in endothelial cells, suggesting condition-specific modifications

Methodological approaches to address these challenges:

  • Modification-enrichment strategies:

    • For phosphorylation: Use phosphatase inhibitors during sample preparation and phospho-protein enrichment methods

    • For ubiquitination: Include deubiquitinase inhibitors and consider immunoprecipitation under denaturing conditions

    • For SUMOylation: Use SUMO-specific proteases inhibitors and specialized lysis conditions

  • Mass spectrometry-based approaches:

    • Immunoprecipitate SOX17 using validated antibodies

    • Perform tandem mass spectrometry to identify modification sites

    • Quantify modification stoichiometry across different conditions

    • This approach avoids antibody-based detection biases

  • Combinatorial antibody strategies:

    • Use multiple antibodies targeting different SOX17 epitopes

    • Compare detection patterns to infer modification status

    • Combine with enzymatic treatments (phosphatases, deubiquitinases) to confirm modification types

  • In-cell verification approaches:

    • Use proximity ligation assays to detect specific modifications in situ

    • Combine with knock-in systems expressing tagged SOX17 variants with mutation of potential modification sites

Functional significance considerations:

  • Correlation with activity:

    • Compare SOX17 modification status with functional readouts:

      • DNA binding capacity (ChIP efficiency)

      • Transcriptional activity (reporter assays)

      • Protein-protein interactions (co-immunoprecipitation)

  • Context-dependent regulation:

    • Investigate modification patterns across developmental contexts

    • Examine modifications in response to signaling pathway activators/inhibitors

    • Compare modifications between normal and disease states

These multifaceted approaches help overcome the significant technical challenges in detecting SOX17 PTMs, providing insights into their regulatory roles in development and disease.

How might advancing SOX17 antibody technology improve our understanding of early embryonic development?

Advancing SOX17 antibody technology holds transformative potential for embryonic development research through several innovative approaches:

Enhanced epitope targeting and detection sensitivity:

  • Single-domain antibodies and nanobodies:

    • Develop smaller SOX17-binding reagents with superior tissue penetration

    • Enable live-cell imaging of SOX17 dynamics during embryogenesis

    • Improve detection in complex 3D structures like embryoid bodies and gastruloids

    • Current antibodies have demonstrated efficacy in fixed samples , but live imaging capabilities would reveal dynamic processes

  • Multi-epitope recognition strategies:

    • Design antibody panels targeting different SOX17 domains

    • Create comprehensive "fingerprinting" of SOX17 conformational states

    • Distinguish between functionally distinct SOX17 populations based on protein interactions or modifications

    • This would extend beyond current capabilities that primarily detect SOX17 presence/absence

Technological integration for multidimensional analysis:

  • Spatially-resolved antibody technologies:

    • Adapt SOX17 antibodies for Spatial Transcriptomics and Imaging Mass Cytometry

    • Map SOX17 expression in relation to tissue architecture and morphogen gradients

    • Correlate protein expression with positional information in the developing embryo

    • Current immunofluorescence applications could be extended to provide spatial context at higher resolution

  • Temporal dynamics monitoring:

    • Develop split-fluorescent protein systems for SOX17 to enable real-time visualization

    • Track SOX17 expression kinetics in response to developmental signals

    • Correlate expression timing with developmental milestones

    • Current approaches provide static snapshots rather than continuous monitoring

Functional investigation capabilities:

  • Conformation-specific antibodies:

    • Generate antibodies recognizing DNA-bound versus unbound SOX17

    • Distinguish between active and inactive protein states

    • Provide insight into the regulation of SOX17 transcriptional activity

    • Extend beyond current ChIP applications to characterize the active fraction of SOX17

  • Intracellular blocking antibodies:

    • Develop cell-permeable antibodies that selectively inhibit specific SOX17 domains

    • Create temporally-controlled functional perturbation

    • Study domain-specific functions without genetic manipulation

    • Complementary to current genetic knockdown approaches mentioned in search results

Developmental biology implications:

  • Lineage specification mechanisms:

    • Better characterize the threshold levels of SOX17 required for endoderm commitment

    • Identify cell-autonomous versus non-autonomous effects of SOX17 expression

    • Evidence shows varying Activin A concentrations dramatically affect SOX17-dependent differentiation outcomes

  • Species-comparative developmental biology:

    • Develop cross-species reactive antibodies to compare SOX17 functions across evolutionary distance

    • Identify conserved versus divergent aspects of SOX17 biology

    • Current antibodies show reactivity with human, mouse, and rat SOX17 , but broader cross-reactivity would enable evolutionary studies

  • Developmental disorder insights:

    • Apply advanced SOX17 antibody technologies to developmental disorder models

    • Correlate abnormal SOX17 expression patterns with phenotypic outcomes

    • Identify potential therapeutic targets for SOX17-related developmental conditions

These advanced antibody technologies would transform our ability to track, characterize, and manipulate SOX17 during embryonic development, providing unprecedented insights into the molecular mechanisms governing endoderm specification, vascular development, and organ formation.

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