Recombinant Mouse Coiled-coil domain-containing protein 107 (Ccdc107)

What is the molecular structure and basic properties of Mouse Ccdc107?

Mouse Ccdc107 is a coiled-coil domain-containing protein encoded by the Ccdc107 gene (Gene ID: 203260) . The protein has the UniProt accession number Q9DCC3 . As suggested by its name, it contains coiled-coil domains, which are structural motifs that mediate protein-protein interactions. The mature protein functions as a precursor and is characterized by:

• Gene alias: MGC31967

• Accession Number: NM_174923.3

• Protein category: organism-gene

• Short label: mCCDC107

The protein's coiled-coil domains likely play an important role in protein-protein interactions and potentially in cellular structural organization, though the complete structural characterization requires further investigation using techniques such as X-ray crystallography or cryo-electron microscopy.

How does the expression profile of Ccdc107 vary across different mouse tissues?

While the search results don't provide comprehensive tissue-specific expression data for mouse Ccdc107, research methodologies to determine this would involve:

• Quantitative PCR (qPCR) to measure mRNA expression levels across different tissues

• Western blotting to quantify protein expression

• Immunohistochemistry to visualize protein localization in tissue sections

• RNA-seq analysis of tissue-specific transcriptomes

By analogy to human CCDC107 expression patterns, which show variable expression across different tissues as indicated in the Human Protein Atlas , mouse Ccdc107 likely has differential expression across various tissues, suggesting tissue-specific functions. To characterize this definitively, researchers should employ a combination of the above techniques on a panel of mouse tissues.

What are the most effective methods for producing recombinant Mouse Ccdc107 protein?

Based on the available research tools, several approaches can be used for producing recombinant Mouse Ccdc107:

The production protocol typically involves:

• Cloning the Ccdc107 gene sequence into an appropriate expression vector

• Transformation/transfection into the chosen expression system

• Induction of protein expression

• Cell lysis and protein purification using affinity tags (His-tag commonly used)

• Validation of protein identity and purity via SDS-PAGE and Western blotting

• Quality control testing including functional assays and endotoxin testing

The choice of expression system should be guided by the intended downstream applications of the recombinant protein.

What are the recommended techniques for detecting endogenous versus recombinant Ccdc107?

Detection methods differ slightly for endogenous versus recombinant Ccdc107:

For endogenous Ccdc107:

• RT-qPCR using gene-specific primers to quantify mRNA expression

• Western blotting with validated antibodies against native Ccdc107

• Immunohistochemistry/immunofluorescence for tissue localization

For recombinant Ccdc107:

• Western blotting using tag-specific antibodies (e.g., anti-His tag)

• ELISA with either tag-specific or protein-specific antibodies

• Mass spectrometry for protein identification and characterization

When comparing expression between samples, RT-qPCR is commonly used, as demonstrated in the colorectal cancer studies that examined differential expression of CCDC107 .

How can CRISPR-Cas9 technology be optimized for Ccdc107 knockout studies?

CRISPR-Cas9 technology offers precise genetic manipulation for Ccdc107 functional studies. The following methodology is recommended based on available CRISPR resources:

• gRNA Design: Select effective guide RNAs targeting Ccdc107 exons. The guide RNAs should be designed to minimize off-target effects while maximizing on-target efficiency. Feng Zhang's laboratory at the Broad Institute has designed validated gRNAs specifically targeting CCDC107 .

• Delivery Method Selection:

  • Plasmid-based delivery for stable cell lines

  • Ribonucleoprotein (RNP) complex for transient editing with minimal off-target effects

  • Viral vectors (lentivirus, adenovirus) for difficult-to-transfect cells

• Validation of Knockout Efficiency:

  • PCR amplification followed by Sanger sequencing to confirm the presence of indels

  • CRISPR Cas9 Cleavage Detection Kits (such as ABM's Screen It™)

  • Western blotting to verify the absence of protein expression

  • Functional assays to confirm phenotypic changes

• Clone Selection: Isolate and expand monoclonal populations with confirmed knockouts rather than using heterogeneous populations, which may contain cells with varying editing efficiencies .

When using commercially available knockout cell lines like the CCDC107 CRISPR Knockout 293T Cell Line, verification of knockout should still be performed in your laboratory conditions .

What phenotypic changes are observed in Ccdc107 knockout models?

While specific phenotypic changes in Ccdc107 knockout models are not explicitly detailed in the search results, researchers interested in characterizing such models should employ:

• Cellular Analysis:

  • Growth rate and proliferation assessments

  • Cell morphology examination

  • Cell cycle analysis

  • Apoptosis assays

• Molecular Profiling:

  • Transcriptome analysis (RNA-seq) to identify dysregulated pathways

  • Proteomics to detect changes in protein expression and interactions

  • Metabolomics to identify altered metabolic processes

• Functional Assays:

  • Migration and invasion assays (particularly relevant for cancer studies)

  • Stress response evaluations

  • Differentiation capacity assessment

Based on the association between CCDC107 downregulation and colorectal cancer , researchers should pay particular attention to cancer-related phenotypes, including changes in proliferation, apoptosis resistance, and migration capabilities.

How does the relationship between Ccdc107 and RMRP lncRNA influence disease progression?

The relationship between CCDC107 and RMRP lncRNA has been studied in the context of colorectal cancer. Here's what research has revealed:

• Expression Patterns: While CCDC107 is significantly down-regulated in colorectal cancer tissues (p < 0.05), RMRP expression does not show significant alteration in CRC versus normal tissues .

• Diagnostic Value:

  • ROC curve analysis shows area under the curve (AUC) for CCDC107 of 0.871, indicating good diagnostic potential

  • RMRP shows an AUC of only 0.5, suggesting limited diagnostic utility

• Clinical Correlations: CCDC107 downregulation is associated with:

  • Poor disease-free survival

  • Friction genome alteration

  • Surgical margin status

• Staging Relevance: Expression of neither gene changes significantly across different disease stages, suggesting their alterations may be early events in carcinogenesis .

Researchers investigating this relationship should employ:

• Co-expression analysis to determine correlation patterns

• Protein-RNA interaction studies (RIP, CLIP) to identify direct interactions

• Functional studies to determine if RMRP regulates CCDC107 expression

• In vivo models to validate the relationship's impact on disease progression

What are the molecular mechanisms underlying Ccdc107 regulation in normal and disease states?

While the search results don't provide detailed information on Ccdc107 regulatory mechanisms, a comprehensive research approach would include:

• Transcriptional Regulation:

  • Promoter analysis to identify transcription factor binding sites

  • ChIP-seq to identify proteins interacting with the Ccdc107 promoter

  • Epigenetic profiling (DNA methylation, histone modifications)

• Post-transcriptional Regulation:

  • miRNA binding site analysis and validation

  • RNA stability assessments

  • Alternative splicing analysis

• Post-translational Modifications:

  • Phosphorylation, acetylation, ubiquitination analysis

  • Protein half-life determination

  • Subcellular localization studies

The significant downregulation of CCDC107 in colorectal cancer suggests either transcriptional repression, epigenetic silencing, or post-transcriptional regulation by miRNAs or other non-coding RNAs . Understanding these mechanisms could reveal therapeutic targets for diseases where Ccdc107 expression is dysregulated.

How can differential expression of Ccdc107 be leveraged as a biomarker in cancer diagnostics?

The potential of CCDC107 as a cancer biomarker has been demonstrated in colorectal cancer research:

• Diagnostic Performance:

  • CCDC107 shows significantly reduced expression in colorectal tumor samples

  • ROC analysis reveals an AUC of 0.871 for CCDC107, indicating strong diagnostic potential

  • This performance suggests CCDC107 could serve as a valuable biomarker for CRC diagnosis

• Methodological Approach for Biomarker Validation:

  • Sample Collection: Paired tumor and adjacent normal tissues (as used in the study with 72 CRC cases)

  • Expression Analysis: RT-qPCR for quantitative assessment of expression levels

  • Statistical Validation: ROC curve analysis, sensitivity/specificity calculations

  • Clinical Correlation: Association with survival outcomes, tumor characteristics, and treatment response

• Implementation Strategies:

  • Development of standardized RT-qPCR protocols for clinical laboratories

  • Creation of immunohistochemistry assays for tissue biopsies

  • Exploration of blood-based detection methods (if the protein is secreted or if circulating tumor cells express it)

• Combinatorial Approaches:

  • Integration with established biomarkers for improved diagnostic accuracy

  • Development of multi-marker panels that include CCDC107

  • Correlation with imaging and other clinical parameters

Researchers should validate these findings in larger cohorts across different populations to establish the robustness of Ccdc107 as a biomarker.

What therapeutic strategies could target Ccdc107 or its regulatory pathways?

While the search results don't directly address therapeutic targeting of Ccdc107, several approaches warrant investigation based on its downregulation in cancer:

• Expression Restoration Strategies:

  • Gene therapy approaches to reintroduce functional Ccdc107

  • Epigenetic modifiers to reverse potential silencing mechanisms

  • Small molecules that can induce Ccdc107 expression

• Targeting Regulatory Pathways:

  • Inhibition of transcriptional repressors that may downregulate Ccdc107

  • Anti-miRNA approaches if miRNAs are identified that target Ccdc107

  • Modulation of signaling pathways that regulate Ccdc107 expression

• Protein Stabilization Approaches:

  • Small molecules that can bind to and stabilize Ccdc107 protein

  • Inhibitors of proteolytic pathways that may degrade Ccdc107

• Combination Therapies:

  • Integration with standard treatments for synergistic effects

  • Sequential therapeutic approaches based on molecular response

How conserved is Ccdc107 across species, and what does this suggest about its function?

While the search results provide limited information on conservation, the following methodological approach would determine conservation and functional implications:

• Sequence Alignment Analysis:

  • Perform multiple sequence alignments of Ccdc107 protein sequences from various species

  • Calculate percent identity and similarity between mouse and human orthologs

  • Identify conserved domains and motifs across species

• Phylogenetic Analysis:

  • Construct phylogenetic trees to understand evolutionary relationships

  • Determine when in evolutionary history the gene emerged

  • Identify species-specific adaptations in the protein sequence

• Structural Conservation:

  • Compare predicted or determined 3D structures across species

  • Identify conserved structural elements that may be critical for function

  • Analyze conservation of protein interaction surfaces

• Functional Conservation Testing:

  • Cross-species complementation experiments

  • Comparing knockout phenotypes across model organisms

  • Evaluation of conserved interaction partners

High conservation across species would suggest fundamental cellular functions for Ccdc107, while divergence might indicate species-specific adaptations. The known association with colorectal cancer in humans suggests at least some functional conservation in cellular processes relevant to cancer development .

What are the most promising avenues for future research on Ccdc107?

Based on current knowledge and gaps identified in the search results, the following research directions warrant investigation:

• Structural and Functional Characterization:

  • Comprehensive structural analysis using X-ray crystallography or cryo-EM

  • Identification of functional domains through mutagenesis studies

  • Determination of binding partners through proteomics approaches

• Regulatory Network Mapping:

  • Identification of transcription factors controlling Ccdc107 expression

  • Characterization of non-coding RNAs regulating Ccdc107

  • Analysis of epigenetic mechanisms affecting gene expression

• Role in Cancer Biology:

  • Expanded analysis across multiple cancer types

  • Mechanistic studies of how Ccdc107 loss contributes to tumorigenesis

  • Investigation of potential tumor suppressor functions

• Therapeutic Development:

  • High-throughput screening for compounds that modulate Ccdc107 expression

  • Development of targeted therapies based on Ccdc107 pathways

  • Exploration of biomarker-guided treatment approaches

• Mouse Models:

  • Development of tissue-specific conditional knockout models

  • Creation of transgenic models with fluorescent-tagged Ccdc107 for in vivo tracking

  • Analysis of Ccdc107 in mouse models of colorectal cancer

These research directions would address current knowledge gaps and potentially lead to clinically relevant applications in diagnostics and therapeutics.

Frequently Asked Questions for Researchers on Recombinant Mouse Coiled-coil domain-containing protein 107 (Ccdc107)

Recombinant Mouse Coiled-coil domain-containing protein 107 (Ccdc107) has emerged as a significant protein of interest in various research domains, particularly in cancer studies. This comprehensive FAQ guide addresses common questions that researchers encounter when working with this protein.

What is the molecular structure and basic properties of Mouse Ccdc107?

Mouse Ccdc107 is a coiled-coil domain-containing protein encoded by the Ccdc107 gene (Gene ID: 203260) . The protein has the UniProt accession number Q9DCC3 . As suggested by its name, it contains coiled-coil domains, which are structural motifs that mediate protein-protein interactions. The mature protein functions as a precursor and is characterized by:

• Gene alias: MGC31967

• Accession Number: NM_174923.3

• Protein category: organism-gene

• Short label: mCCDC107

The protein's coiled-coil domains likely play an important role in protein-protein interactions and potentially in cellular structural organization, though the complete structural characterization requires further investigation using techniques such as X-ray crystallography or cryo-electron microscopy.

How does the expression profile of Ccdc107 vary across different mouse tissues?

While the search results don't provide comprehensive tissue-specific expression data for mouse Ccdc107, research methodologies to determine this would involve:

• Quantitative PCR (qPCR) to measure mRNA expression levels across different tissues

• Western blotting to quantify protein expression

• Immunohistochemistry to visualize protein localization in tissue sections

• RNA-seq analysis of tissue-specific transcriptomes

By analogy to human CCDC107 expression patterns, which show variable expression across different tissues as indicated in the Human Protein Atlas , mouse Ccdc107 likely has differential expression across various tissues, suggesting tissue-specific functions. To characterize this definitively, researchers should employ a combination of the above techniques on a panel of mouse tissues.

What are the most effective methods for producing recombinant Mouse Ccdc107 protein?

Based on the available research tools, several approaches can be used for producing recombinant Mouse Ccdc107:

The production protocol typically involves:

• Cloning the Ccdc107 gene sequence into an appropriate expression vector

• Transformation/transfection into the chosen expression system

• Induction of protein expression

• Cell lysis and protein purification using affinity tags (His-tag commonly used)

• Validation of protein identity and purity via SDS-PAGE and Western blotting

• Quality control testing including functional assays and endotoxin testing

The choice of expression system should be guided by the intended downstream applications of the recombinant protein.

What are the recommended techniques for detecting endogenous versus recombinant Ccdc107?

Detection methods differ slightly for endogenous versus recombinant Ccdc107:

For endogenous Ccdc107:

• RT-qPCR using gene-specific primers to quantify mRNA expression

• Western blotting with validated antibodies against native Ccdc107

• Immunohistochemistry/immunofluorescence for tissue localization

For recombinant Ccdc107:

• Western blotting using tag-specific antibodies (e.g., anti-His tag)

• ELISA with either tag-specific or protein-specific antibodies

• Mass spectrometry for protein identification and characterization

When comparing expression between samples, RT-qPCR is commonly used, as demonstrated in the colorectal cancer studies that examined differential expression of CCDC107 .

How can CRISPR-Cas9 technology be optimized for Ccdc107 knockout studies?

CRISPR-Cas9 technology offers precise genetic manipulation for Ccdc107 functional studies. The following methodology is recommended based on available CRISPR resources:

• gRNA Design: Select effective guide RNAs targeting Ccdc107 exons. The guide RNAs should be designed to minimize off-target effects while maximizing on-target efficiency. Feng Zhang's laboratory at the Broad Institute has designed validated gRNAs specifically targeting CCDC107 .

• Delivery Method Selection:

  • Plasmid-based delivery for stable cell lines

  • Ribonucleoprotein (RNP) complex for transient editing with minimal off-target effects

  • Viral vectors (lentivirus, adenovirus) for difficult-to-transfect cells

• Validation of Knockout Efficiency:

  • PCR amplification followed by Sanger sequencing to confirm the presence of indels

  • CRISPR Cas9 Cleavage Detection Kits (such as ABM's Screen It™)

  • Western blotting to verify the absence of protein expression

  • Functional assays to confirm phenotypic changes

• Clone Selection: Isolate and expand monoclonal populations with confirmed knockouts rather than using heterogeneous populations, which may contain cells with varying editing efficiencies .

When using commercially available knockout cell lines like the CCDC107 CRISPR Knockout 293T Cell Line, verification of knockout should still be performed in your laboratory conditions .

What phenotypic changes are observed in Ccdc107 knockout models?

While specific phenotypic changes in Ccdc107 knockout models are not explicitly detailed in the search results, researchers interested in characterizing such models should employ:

• Cellular Analysis:

  • Growth rate and proliferation assessments

  • Cell morphology examination

  • Cell cycle analysis

  • Apoptosis assays

• Molecular Profiling:

  • Transcriptome analysis (RNA-seq) to identify dysregulated pathways

  • Proteomics to detect changes in protein expression and interactions

  • Metabolomics to identify altered metabolic processes

• Functional Assays:

  • Migration and invasion assays (particularly relevant for cancer studies)

  • Stress response evaluations

  • Differentiation capacity assessment

Based on the association between CCDC107 downregulation and colorectal cancer , researchers should pay particular attention to cancer-related phenotypes, including changes in proliferation, apoptosis resistance, and migration capabilities.

How does the relationship between Ccdc107 and RMRP lncRNA influence disease progression?

The relationship between CCDC107 and RMRP lncRNA has been studied in the context of colorectal cancer. Here's what research has revealed:

• Expression Patterns: While CCDC107 is significantly down-regulated in colorectal cancer tissues (p < 0.05), RMRP expression does not show significant alteration in CRC versus normal tissues .

• Diagnostic Value:

  • ROC curve analysis shows area under the curve (AUC) for CCDC107 of 0.871, indicating good diagnostic potential

  • RMRP shows an AUC of only 0.5, suggesting limited diagnostic utility

• Clinical Correlations: CCDC107 downregulation is associated with:

  • Poor disease-free survival

  • Friction genome alteration

  • Surgical margin status

• Staging Relevance: Expression of neither gene changes significantly across different disease stages, suggesting their alterations may be early events in carcinogenesis .

Researchers investigating this relationship should employ:

• Co-expression analysis to determine correlation patterns

• Protein-RNA interaction studies (RIP, CLIP) to identify direct interactions

• Functional studies to determine if RMRP regulates CCDC107 expression

• In vivo models to validate the relationship's impact on disease progression

What are the molecular mechanisms underlying Ccdc107 regulation in normal and disease states?

While the search results don't provide detailed information on Ccdc107 regulatory mechanisms, a comprehensive research approach would include:

• Transcriptional Regulation:

  • Promoter analysis to identify transcription factor binding sites

  • ChIP-seq to identify proteins interacting with the Ccdc107 promoter

  • Epigenetic profiling (DNA methylation, histone modifications)

• Post-transcriptional Regulation:

  • miRNA binding site analysis and validation

  • RNA stability assessments

  • Alternative splicing analysis

• Post-translational Modifications:

  • Phosphorylation, acetylation, ubiquitination analysis

  • Protein half-life determination

  • Subcellular localization studies

The significant downregulation of CCDC107 in colorectal cancer suggests either transcriptional repression, epigenetic silencing, or post-transcriptional regulation by miRNAs or other non-coding RNAs . Understanding these mechanisms could reveal therapeutic targets for diseases where Ccdc107 expression is dysregulated.

How can differential expression of Ccdc107 be leveraged as a biomarker in cancer diagnostics?

The potential of CCDC107 as a cancer biomarker has been demonstrated in colorectal cancer research:

• Diagnostic Performance:

  • CCDC107 shows significantly reduced expression in colorectal tumor samples

  • ROC analysis reveals an AUC of 0.871 for CCDC107, indicating strong diagnostic potential

  • This performance suggests CCDC107 could serve as a valuable biomarker for CRC diagnosis

• Methodological Approach for Biomarker Validation:

  • Sample Collection: Paired tumor and adjacent normal tissues (as used in the study with 72 CRC cases)

  • Expression Analysis: RT-qPCR for quantitative assessment of expression levels

  • Statistical Validation: ROC curve analysis, sensitivity/specificity calculations

  • Clinical Correlation: Association with survival outcomes, tumor characteristics, and treatment response

• Implementation Strategies:

  • Development of standardized RT-qPCR protocols for clinical laboratories

  • Creation of immunohistochemistry assays for tissue biopsies

  • Exploration of blood-based detection methods (if the protein is secreted or if circulating tumor cells express it)

• Combinatorial Approaches:

  • Integration with established biomarkers for improved diagnostic accuracy

  • Development of multi-marker panels that include CCDC107

  • Correlation with imaging and other clinical parameters

Researchers should validate these findings in larger cohorts across different populations to establish the robustness of Ccdc107 as a biomarker.

What therapeutic strategies could target Ccdc107 or its regulatory pathways?

While the search results don't directly address therapeutic targeting of Ccdc107, several approaches warrant investigation based on its downregulation in cancer:

• Expression Restoration Strategies:

  • Gene therapy approaches to reintroduce functional Ccdc107

  • Epigenetic modifiers to reverse potential silencing mechanisms

  • Small molecules that can induce Ccdc107 expression

• Targeting Regulatory Pathways:

  • Inhibition of transcriptional repressors that may downregulate Ccdc107

  • Anti-miRNA approaches if miRNAs are identified that target Ccdc107

  • Modulation of signaling pathways that regulate Ccdc107 expression

• Protein Stabilization Approaches:

  • Small molecules that can bind to and stabilize Ccdc107 protein

  • Inhibitors of proteolytic pathways that may degrade Ccdc107

• Combination Therapies:

  • Integration with standard treatments for synergistic effects

  • Sequential therapeutic approaches based on molecular response

How conserved is Ccdc107 across species, and what does this suggest about its function?

While the search results provide limited information on conservation, the following methodological approach would determine conservation and functional implications:

• Sequence Alignment Analysis:

  • Perform multiple sequence alignments of Ccdc107 protein sequences from various species

  • Calculate percent identity and similarity between mouse and human orthologs

  • Identify conserved domains and motifs across species

• Phylogenetic Analysis:

  • Construct phylogenetic trees to understand evolutionary relationships

  • Determine when in evolutionary history the gene emerged

  • Identify species-specific adaptations in the protein sequence

• Structural Conservation:

  • Compare predicted or determined 3D structures across species

  • Identify conserved structural elements that may be critical for function

  • Analyze conservation of protein interaction surfaces

• Functional Conservation Testing:

  • Cross-species complementation experiments

  • Comparing knockout phenotypes across model organisms

  • Evaluation of conserved interaction partners

High conservation across species would suggest fundamental cellular functions for Ccdc107, while divergence might indicate species-specific adaptations. The known association with colorectal cancer in humans suggests at least some functional conservation in cellular processes relevant to cancer development .

What are the most promising avenues for future research on Ccdc107?

Based on current knowledge and gaps identified in the search results, the following research directions warrant investigation:

• Structural and Functional Characterization:

  • Comprehensive structural analysis using X-ray crystallography or cryo-EM

  • Identification of functional domains through mutagenesis studies

  • Determination of binding partners through proteomics approaches

• Regulatory Network Mapping:

  • Identification of transcription factors controlling Ccdc107 expression

  • Characterization of non-coding RNAs regulating Ccdc107

  • Analysis of epigenetic mechanisms affecting gene expression

• Role in Cancer Biology:

  • Expanded analysis across multiple cancer types

  • Mechanistic studies of how Ccdc107 loss contributes to tumorigenesis

  • Investigation of potential tumor suppressor functions

• Therapeutic Development:

  • High-throughput screening for compounds that modulate Ccdc107 expression

  • Development of targeted therapies based on Ccdc107 pathways

  • Exploration of biomarker-guided treatment approaches

• Mouse Models:

  • Development of tissue-specific conditional knockout models

  • Creation of transgenic models with fluorescent-tagged Ccdc107 for in vivo tracking

  • Analysis of Ccdc107 in mouse models of colorectal cancer

These research directions would address current knowledge gaps and potentially lead to clinically relevant applications in diagnostics and therapeutics.