SH2D1B Human

What is the molecular structure and function of human SH2D1B?

SH2D1B (also known as EAT2) functions as a cytoplasmic adapter protein that regulates receptors of the signaling lymphocytic activation molecule (SLAM) family, including CD84, SLAMF1, LY9, and CD244. The protein contains an SH2 domain that binds phosphotyrosines, enabling it to regulate signal transduction through receptors expressed on antigen-presenting cells. In SLAM signaling, SH2D1B appears to cooperate with SH2D1A (SAP) . The protein structure features the characteristic SH2 domain fold, which is conserved across different species and is crucial for phosphotyrosine recognition and immune signaling modulation.

How does SH2D1B differ from other SH2 domain-containing proteins?

SH2D1B belongs to a distinct family among the 38 discrete SH2 domain families identified across 21 species . While all SH2 domains function as primary phosphotyrosine recognition modules, SH2D1B has specialized functions in immune cell signaling. Unlike many other SH2 domain proteins, SH2D1B specifically regulates natural killer (NK) cell functions without affecting receptor tyrosine phosphorylation. It instead controls distal signaling events, particularly through CD244/2B4, involving PLCG1 and ERK activation pathways . An important paralog is INPPL1, which has a different cellular function .

What are the key protein interaction partners of SH2D1B?

SH2D1B primarily interacts with members of the SLAM family of receptors:

In dendritic cells, SH2D1B negatively regulates CD40-induced cytokine production by activating the PI3K pathway, which inhibits p38 MAPK and JNK activation .

What are optimal techniques for detecting SH2D1B expression in human tissues?

For detecting SH2D1B expression in human tissues, researchers should consider:

• RNA-based methods:

  • RT-qPCR targeting SH2D1B mRNA using validated primers

  • RNA-Seq for transcript quantification and splice variant detection

• Protein-based methods:

  • Western blotting using antibodies against SH2D1B (UniProtKB/Swiss-Prot: O14796)

  • Immunohistochemistry for tissue localization

  • Flow cytometry for immune cell expression profiling

• Single-cell approaches:

  • scRNA-Seq for cell-type specific expression patterns

  • Mass cytometry for protein expression in heterogeneous samples

When designing primers or selecting antibodies, researchers should be aware of the gene's chromosomal location and potential splice variants to ensure specific detection .

How can researchers effectively assess SH2D1B phosphotyrosine binding specificity?

Assessing SH2D1B phosphotyrosine binding specificity requires multiple complementary approaches:

• In vitro binding assays:

  • Peptide arrays with various phosphotyrosine motifs

  • Surface plasmon resonance (SPR) for binding kinetics

  • Isothermal titration calorimetry (ITC) for thermodynamic parameters

• Structural approaches:

  • X-ray crystallography of SH2D1B in complex with phosphopeptides

  • NMR spectroscopy for dynamic binding information

• Cellular validation:

  • Proximity ligation assays (PLA) to detect interactions in situ

  • FRET/BRET assays for dynamic interaction monitoring

  • Immunoprecipitation followed by mass spectrometry

Binding specificity should be analyzed in the context of SLAM family receptors, as SH2D1B has evolved to regulate these specific signaling pathways .

What is the current evidence linking SH2D1B to human disease?

SH2D1B has been associated with several diseases:

While specific disease mechanisms are still being elucidated, SH2D1B's central role in immune signaling suggests its dysregulation could contribute to immunodeficiencies and potentially to cancer through altered NK cell function .

How does SH2D1B affect natural killer cell cytotoxicity in the context of cancer immunology?

SH2D1B plays a critical role in regulating NK cell cytotoxicity, which has significant implications for cancer immunology:

Researchers investigating SH2D1B in cancer immunotherapy should focus on how its modulation might enhance NK cell-mediated tumor clearance without triggering autoimmunity.

How has SH2D1B evolved across species compared to other SH2 domain proteins?

SH2D1B belongs to the broader evolutionary expansion of SH2 domain-containing proteins, which have increased in number throughout metazoan evolution. Comparative genomic analysis across 21 species reveals:

• Evolutionary trajectory:

  • Simple unicellular organisms like yeast contain only one SH2 protein

  • Complex multicellular organisms like humans have 111 SH2 domain-containing proteins

  • This expansion correlates with increasing complexity of intercellular communication

• SH2D1B conservation:

  • SH2D1B and its paralog SH2D1A (SAP) are regulators of immune signaling

  • They represent a specialized branch of SH2 domain evolution linked to adaptive immunity

  • The proteins appear to have undergone functional specialization after gene duplication

The evolutionary history of SH2D1B reflects the broader pattern of domain shuffling and gene duplication that placed modular SH2 domains in diverse protein contexts, allowing them to participate in varied cellular processes .

What can the intron-exon structure of SH2D1B tell us about its evolutionary history?

Analysis of the SH2D1B gene structure provides important evolutionary insights:

• Intron-exon boundaries:

  • The "intron/exon code" of SH2 domains offers phylogenetic information when sequence data alone is insufficient

  • A strong correlation exists between domain boundaries and exons across eukaryotic genomes

  • SH2D1B's intron phases and positions can be analyzed using tools like SMART to reveal evolutionary relationships

• Evolutionary mechanisms:

  • Splicing and exon shuffling represent evolutionary mechanisms for conserving critical sequences

  • These mechanisms have been instrumental in preserving SH2 domain function while allowing diversification

  • Domain boundaries often coincide with intron positions, facilitating domain shuffling during evolution

By examining intron positions, phases, and conservation across species, researchers can reconstruct the evolutionary history of SH2D1B and its relationship to other SH2 domain-containing proteins.

How can transcriptomic approaches be used to study SH2D1B in circadian rhythm research?

Recent research on blood transcriptome-based biomarkers for human circadian phase provides methodological insights for studying SH2D1B in this context:

• Sampling strategies:

  • Multiple sampling approaches can be employed, including one-sample, two-sample, or three-sample methods

  • Two-sample differential analysis (samples taken 12 hours apart) provides superior performance compared to single-sample analysis

  • This approach eliminates significant "trait-like" characteristics of the transcriptome and focuses on changes in gene expression state

• Analytical methods:

  • Partial Least Squares Regression (PLSR) models outperform molecular timetable approaches

  • PLSR-based two-sample differential models can predict circadian phase with high accuracy (R² of 0.9)

  • These methods are robust across different sleep conditions, including sleep deprivation

• Application to SH2D1B research:

  • Researchers can investigate whether SH2D1B expression follows circadian patterns

  • Studies can examine whether SH2D1B function in immune cells is affected by circadian regulation

  • The relationship between SH2D1B signaling and sleep disruption can be explored using these methodologies

What CRISPR-Cas9 strategies are most effective for functional studies of SH2D1B?

For CRISPR-Cas9 studies of SH2D1B function, researchers should consider:

• Guide RNA design:

  • Target the SH2 domain-encoding region for complete functional knockout

  • Alternatively, design guides targeting specific functional regions for domain-specific studies

  • Use tools considering the chromosome 1 genomic context of SH2D1B (NCBI Gene ID: 117157)

• Functional validation approaches:

  • Assess effects on NK cell cytotoxicity using standard killing assays

  • Examine polarization of microtubule-organizing center and cytotoxic granules

  • Measure downstream signaling events including PLCG1 and ERK activation

• Cell models for editing:

  • NK cell lines for studying cytotoxic functions

  • Dendritic cells for examining effects on CD40-induced cytokine production

  • Primary immune cells for physiologically relevant validation

Data should be analyzed in the context of SH2D1B's known role in regulating SLAM family receptor signaling and NK cell effector functions.

How does SH2D1B function integrate with broader immune signaling networks?

SH2D1B functions as part of a complex immune signaling network:

• Pathway integration:

  • SH2D1B is involved in the Innate Immune System pathway

  • It participates in Class I MHC mediated antigen processing and presentation

  • These pathways represent critical components of both innate and adaptive immunity

• Functional interactions:

  • In SLAM signaling, SH2D1B cooperates with SH2D1A/SAP

  • In NK cells, it regulates effector functions through CD244/2B4 signaling

  • In dendritic cells, it affects CD40-induced cytokine production via PI3K pathway activation

• Research methodology:

  • Systems biology approaches combining transcriptomics, proteomics, and phosphoproteomics

  • Pathway analysis tools to map SH2D1B-dependent signaling networks

  • Single-cell analysis to understand cell type-specific signaling contributions

Understanding these integrative aspects is essential for developing therapeutic strategies targeting SH2D1B or its associated pathways in immune disorders.

What bioinformatic approaches can predict novel SH2D1B functions or interactions?

To predict novel SH2D1B functions or interactions, researchers should employ multiple bioinformatic approaches:

• Sequence-based prediction:

  • Identify conserved motifs in SH2D1B across species

  • Analyze phosphotyrosine binding pocket residues to predict binding preferences

  • Employ molecular docking to identify potential interaction partners

• Network-based approaches:

  • Construct protein-protein interaction networks incorporating known SH2D1B interactions

  • Apply network analysis algorithms to identify potential functional modules

  • Use guilt-by-association methods to predict functions based on interaction partners

• Expression correlation analysis:

  • Analyze co-expression patterns across diverse tissues and conditions

  • Identify genes with expression profiles similar to SH2D1B

  • Integrate with pathway enrichment analysis to suggest functional associations

These computational approaches should be validated through targeted experimental studies to confirm predicted functions and interactions.