Affinity purification coupled with mass spectrometry (AP–MS) and proximity-dependent biotinylation identification (BioID) methods have made substantial contributions to interaction proteomics studies. We have developed a GFP-tag AP-MS workflow to study the virus-host interactions of several medically and economically important viruses in Thailand. We are currently developing a proteomics platform for the dynamic visualization of signalosome landscape, where we combine the CRISPR-Cas9 genome editing with the BioID system. Cells will be engineered to produce the biotin ligase-tagged signaling protein of interest and BioID will be performed following the activation of the signaling pathway in a time-course manner. When paired with quantitative proteomics approach, the assay will be able to provide snapshots of both core and transient protein landscape of the signaling pathway over time.

1.Expanding the Flaviviral NS5 Interactome: A Proteomic Insight into Host-Pathogen Interactions

Kovanich D, Saisawang C, Sittipaisankul P, Ramphan S, Kalpongnukul N, Somparn P, Pisitkun T, Smith DR. Analysis of the Zika and Japanese Encephalitis Virus NS5 Interactomes. J Proteome Res. 2019 Aug 2;18(8):3203-3218.

Mosquito-borne flaviviruses, including dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV), remain significant global health threats. Among flaviviral proteins, nonstructural protein 5 (NS5) is the largest, most conserved, and enzymatically vital component of the viral replication complex, making it an attractive target for broad-spectrum antiviral strategies. Understanding NS5-host protein interactions is critical for unveiling the molecular mechanisms that underpin flavivirus infection and replication.

In this study, our team conducted a comprehensive proteomic analysis to map the JEV- and ZIKV-NS5 interactomes. Using EGFP immunoprecipitation and label-free quantitative mass spectrometry, we identified 137 NS5 interactors, with a pronounced enrichment in spliceosomal and transcriptional regulatory proteins, suggesting that NS5 plays a key role in modulating host RNA processing. Notably, we identified the transcription complex Paf1C and phosphatase 6 as conserved NS5-associated complexes, providing novel mechanistic insights into viral replication. Interestingly, PAF1, a core component of Paf1C, exhibited opposing roles in JEV and ZIKV infections, emphasizing virus-specific host dependencies. Our findings contributed to subsequent discoveries by other research groups, who later characterized the functional roles of Paf1C in flavivirus infection. This independent validation underscores the broader significance of our proteomic dataset in unraveling critical host pathways manipulated by flaviviruses.

https://www.mdpi.com/1999-4915/15/5/1032
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010100

2.Unraveling the Nuclear Role of PDE3A2 in Cardiac Myocyte Hypertrophy: A Proteomics-Driven Discovery

Subramaniam G, Schleicher K, Kovanich D, Zerio A, Folkmanaite M, Chao YC, Surdo NC, Koschinski A, Hu J, Scholten A, Heck AJR, Ercu M, Sholokh A, Park KC, Klussmann E, Meraviglia V, Bellin M, Zanivan S, Hester S, Mohammed S, Zaccolo M. Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy. Circ Res. 2023 Mar 31;132(7):828-848.

Cardiovascular diseases remain a leading cause of morbidity and mortality worldwide, with cardiac hypertrophy being a key pathological adaptation to chronic stressors. In a groundbreaking study, “Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy,” we employed state-of-the-art proteomics and Förster Resonance Energy Transfer (FRET) imaging approaches to uncover a previously unrecognized nuclear function of phosphodiesterase 3A2 (PDE3A2) in cardiac myocytes.

Through a comprehensive integration of interaction proteomics, phosphoproteomics, and FRET imaging, , the study demonstrated that PDE3A2, classically known for its cytoplasmic role in cyclic nucleotide signaling, localizes to the nucleus where it exerts a direct regulatory influence on transcriptional programs associated with myocyte hypertrophy. Our findings reveal a novel mechanistic paradigm, in which nuclear PDE3A2 modulates hypertrophic gene expression by interacting with key nuclear proteins, ultimately shaping the cellular landscape of pathological remodeling.

This study not only expands our fundamental understanding of cardiac signaling but also positions nuclear PDE3A2 as a promising therapeutic target for hypertrophic heart disease. By bridging high-resolution proteomics with cellular functional analyses, our work paves the way for innovative therapeutic strategies aimed at mitigating maladaptive cardiac growth at the nuclear level.

3.A Comprehensive Review of Nanodomain cAMP Signaling in Cardiac Pathophysiology: From Fundamental Insights to Targeted Therapeutic Strategies

Zaccolo M, Kovanich D. Nanodomain cAMP signaling in cardiac pathophysiology: potential for developing targeted therapeutic interventions. Physiol Rev. 2025 Apr 1;105(2):541-591.

Cyclic adenosine monophosphate (cAMP) signaling is a cornerstone of cardiac physiology, orchestrating a diverse array of cellular processes that regulate heart function. Over the past decades, research has shifted from viewing cAMP as a diffusible second messenger to recognizing its highly compartmentalized nature, with spatially confined nanodomains that enable precise regulation of cardiac signaling pathways. Understanding these localized cAMP signaling microdomains is critical for developing targeted therapeutic strategies for cardiovascular diseases.

In this comprehensive review, we provide an in-depth examination of the evolution of compartmentalized cAMP signaling, tracing its conceptual development from early models of global diffusion to contemporary insights into nanodomain organization. We discuss how cAMP-hydrolyzing enzymes, phosphodiesterases (PDEs), and the A-kinase anchoring protein (AKAP) family work together to finely tune cAMP gradients within cardiac cells. These spatiotemporal regulatory mechanisms ensure the precise control of downstream effectors such as protein kinase A (PKA) and exchange proteins directly activated by cAMP (Epac), which are integral to maintaining normal cardiac function.

Furthermore, we explore the pathophysiological implications of disrupted nanodomain cAMP signaling in conditions such as heart failure, arrhythmias, and cardiomyopathies. Dysregulation of localized cAMP compartments can lead to aberrant signaling cascades that contribute to disease progression, making these microdomains promising therapeutic targets. We highlight recent advancements in the development of PDE inhibitors, AKAP disruptors, and compartment-specific modulators, which offer potential for precision medicine approaches in treating cardiac disorders.

By synthesizing past and present research, this review serves as a definitive resource on nanodomain cAMP signaling in cardiac pathophysiology. We emphasize the importance of spatially targeted interventions and advocate for the continued exploration of compartmentalized signaling mechanisms as a means to develop more effective and selective cardiac therapies.