ATP6V1F Human

What is ATP6V1F and what is its role in cellular physiology?

ATP6V1F encodes a constituent of vacuolar ATPase (V-ATPase), a multi-subunit enzyme complex responsible for acidification of various cellular organelles. This proton pump is critical for maintaining pH homeostasis within organelles such as lysosomes, endosomes, and secretory vesicles. V-ATPase-mediated acidification is required for numerous essential cellular processes including:

• Receptor-mediated endocytosis

• Zymogen activation

• Protein sorting and degradation

• Generation of proton gradients in synaptic vesicles

Methodologically, researchers investigating ATP6V1F function typically employ techniques including:

• Gene silencing or overexpression to assess functional consequences

• pH-sensitive fluorescent probes to measure organelle acidification

• Co-immunoprecipitation to identify protein-protein interactions

• Subcellular fractionation to determine localization patterns

How is ATP6V1F expression distributed across human tissues?

ATP6V1F shows variable expression across tissues, with particularly high expression noted in metabolically active organs. Research approaches to characterize tissue-specific expression include:

• Analysis of RNA-seq data from repositories like TCGA

• Immunohistochemistry with validated antibodies

• Western blotting of tissue lysates

• Single-cell RNA sequencing to assess cell-type specific expression

Multiple database analyses (including TIMER, HCCDB, and GEPIA) have confirmed ATP6V1F expression across numerous tissue types, with significantly elevated levels observed in multiple cancer types compared to matched normal tissues .

What experimental approaches are used to modulate ATP6V1F activity?

Researchers employ several strategies to investigate ATP6V1F function:

Genetic approaches:

• CRISPR/Cas9-mediated gene editing for knockout or knock-in models

• siRNA or shRNA for transient or stable knockdown

• Expression vectors for wild-type or mutant ATP6V1F overexpression

Pharmacological approaches:

• V-ATPase inhibitors (e.g., bafilomycin A1, concanamycin)

• pH-modulating compounds to assess compensatory mechanisms

Validation methods:

• qRT-PCR and western blotting to confirm expression changes

• Functional assays measuring organelle acidification

• Phenotypic assessments (proliferation, migration, apoptosis)

How does ATP6V1F contribute to hepatocellular carcinoma pathogenesis?

ATP6V1F has been identified as overexpressed in hepatocellular carcinoma (HCC) with significant implications for disease progression. Research has revealed that:

Mechanistically, in vitro experiments have demonstrated that ATP6V1F promotes HCC progression through:

• Enhanced cell proliferation and metastatic capacity

• Inhibition of apoptotic pathways

• Altered tumor microenvironment (TME) acidity

• Modulation of immune cell infiltration patterns

Research approaches to investigate these mechanisms include:

• Wound healing and Transwell invasion assays

• Apoptosis detection methods (flow cytometry, TUNEL assay)

• Xenograft models with ATP6V1F modulation

• Co-culture systems with immune cells

What is the relationship between ATP6V1F expression and immune checkpoint inhibitor therapy?

The potential role of ATP6V1F in immunotherapy response represents an emerging research area with clinical implications. Current evidence suggests:

• ATP6V1F expression correlates with infiltration patterns of specific immune cell populations

• High ATP6V1F expression is associated with altered expression of multiple immune checkpoints, including CTLA4, TIGIT, PDCD1, SIGLEC15, CD274, HAVCR2, LAG3, and PDCD1LG2

• The Tumor Immune Dysfunction and Exclusion (TIDE) algorithm has been utilized to predict differential responses to immune checkpoint inhibitors based on ATP6V1F expression levels

Methodological approaches for investigating this relationship include:

• Multiplex immunohistochemistry

• Flow cytometry of tumor-infiltrating lymphocytes

• Single-cell RNA sequencing of tumor microenvironment

• Immune checkpoint blockade models with ATP6V1F manipulation

What signaling pathways mediate ATP6V1F's effects in cancer cells?

Research using Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO), and KEGG pathway analyses has identified several potential signaling mechanisms through which ATP6V1F may influence cellular behavior:

• mTORC1 signaling pathway involvement

• Autophagy regulation pathways

• Lysosomal function pathways

• Cell migration and invasion pathways

Experimental approaches to investigate these pathways include:

• Western blotting for pathway component activation

• Pathway inhibitor studies

• Proximity ligation assays for protein interactions

• Phosphoproteomic analyses

What are optimal controls when studying ATP6V1F in cellular models?

Rigorous experimental design for ATP6V1F studies should include:

For genetic manipulation experiments:

• Empty vector controls (for overexpression studies)

• Non-targeting siRNA/shRNA (for knockdown studies)

• Rescue experiments with wild-type ATP6V1F

• Isogenic cell line pairs differing only in ATP6V1F status

For functional assays:

• V-ATPase inhibitor controls

• pH-matched controls when assessing acidification-dependent phenotypes

• Time course experiments to detect temporal dynamics

• Multiparameter assays to assess specificity of effects

How can researchers differentiate direct ATP6V1F effects from general V-ATPase dysfunction?

Distinguishing ATP6V1F-specific effects from general V-ATPase dysfunction requires:

• Comparative analysis with manipulation of other V-ATPase components

• Structure-function studies with domain-specific mutations

• Complementation assays with other V-ATPase subunits

• Temporal control of ATP6V1F modulation (e.g., inducible systems)

• Dose-response studies to identify threshold effects

What cellular models are most appropriate for ATP6V1F research?

Selection of experimental models should consider:

Cell line considerations:

• HCC cell lines for cancer studies (e.g., HepG2, Huh7, MHCC97H)

• Cell lines with varying baseline ATP6V1F expression

• Primary cells to validate findings from established lines

• 3D culture systems to better recapitulate in vivo conditions

In vivo model considerations:

• Tissue-specific conditional knockout models

• Patient-derived xenografts

• Genetically engineered mouse models with ATP6V1F alterations

• Models that allow assessment of immune components (for TME studies)

How should researchers interpret ATP6V1F expression data across different cancer types?

ATP6V1F expression patterns vary across cancer types, requiring careful interpretation:

• ATP6V1F is significantly overexpressed in multiple cancers, including BLCA, BRCA, CHOL, HNSC, ESCA, KICH, LIHC, KIRP, LUSC, READ, PRAD, SKCM, THCA, STAD, and UCEC

• The prognostic significance of ATP6V1F differs by cancer type, with high expression predicting:

  • Poorer OS and DFS in kidney renal papillary cell carcinoma (KIRP)

  • Better OS and DFS in brain lower grade glioma (LGG)

  • Worse OS and DFS in liver hepatocellular carcinoma (LIHC)

Analytical approaches should include:

• Multi-cohort validation

• Multivariate analyses controlling for confounding variables

• Stratification by molecular subtypes

• Integration with clinical parameters

What methods are recommended for integrating ATP6V1F data with broader V-ATPase complex function?

Understanding ATP6V1F in the context of the complete V-ATPase complex requires:

• Co-expression network analysis with other V-ATPase subunits

• Protein-protein interaction studies

• Comparative phenotypic analysis across V-ATPase subunit alterations

• Systems biology approaches integrating transcriptomic, proteomic, and functional data

Research has shown that different V-ATPase subunits can be associated with distinct clinical entities:

• ATP6V0A1 mutations cause developmental and epileptic encephalopathy

• ATP6V1C1 and ATP6V1B2 variants are linked to DOORS syndrome and related disorders

How can researchers address contradictory findings regarding ATP6V1F function?

When encountering seemingly contradictory results across studies, consider:

• Tissue-specific or context-dependent effects

• Differences in experimental models or conditions

• Technical variations in ATP6V1F detection or modulation

• Threshold effects in ATP6V1F expression levels

• Compensatory mechanisms within the V-ATPase complex

Methodological approaches to resolve contradictions include:

• Systematic replication studies

• Meta-analysis of published data

• Direct comparison of experimental conditions

• Exploration of biological variables (cell type, genetic background)

What are the challenges in detecting and quantifying ATP6V1F protein?

Accurate ATP6V1F protein analysis requires attention to:

• Antibody validation (using knockout controls)

• Appropriate subcellular fractionation techniques

• Consideration of post-translational modifications

• Comparative analysis of protein vs. mRNA levels

Recommended approaches include:

• Multiple antibody validation

• Inclusion of recombinant protein standards

• Mass spectrometry-based quantification

• Assessment of protein complex assembly

How should researchers design experiments to investigate ATP6V1F interaction with the immune system?

Investigating the immunomodulatory effects of ATP6V1F requires:

• Co-culture systems with relevant immune cell populations

• Flow cytometry to characterize immune infiltrates

• Cytokine profiling before and after ATP6V1F modulation

• In vivo models with intact immune systems

Data from HCC studies suggest significant correlations between ATP6V1F expression and immune checkpoint molecules, indicating complex interactions with the immune microenvironment that warrant careful experimental design .