Proteomic-based informatics highlights FNBP4 as a prognostically relevant cytoskeletal protein in Breast Cancer

Proteomic-based informatics highlights FNBP4 as a prognostically relevant cytoskeletal protein in Breast Cancer | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Proteomic-based informatics highlights FNBP4 as a prognostically relevant cytoskeletal protein in Breast Cancer Rashmi Shrivastava, Kavita Kavita, Krishnakant Dalai, Dr. Manjula Kiran, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9039049/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 6 You are reading this latest preprint version Abstract Formin Binding Protein 4 (FNBP4) is a cytoskeletal regulator implicated in actin dynamics, cell migration, and metastasis; however, its prognostic relevance in breast cancer remains poorly defined. This study employed a proteomics-based informatics approach to evaluate the clinical significance of FNBP4 at the protein level and to assess its potential as a prognostic biomarker and therapeutic target. Protein expression patterns of FNBP4 across breast cancer subtypes were analysed using CPTAC, UALCAN, and the Human Protein Atlas (HPA), while survival associations linked to differential protein expression were examined using KM Plotter. Protein–protein interaction networks were constructed using the IntAct database to identify functional partners and elucidate potential mechanistic pathways. FNBP4 was found to exhibit a structurally stable protein conformation with dual cytoplasmic and nuclear localization and moderate nuclear expression in breast cancer tissues. Elevated FNBP4 protein expression was significantly associated with poor overall survival and was particularly enriched in invasive ductal carcinoma and triple-negative breast cancer subtypes. Increased FNBP4 levels correlated with somatic alterations across major oncogenic signalling pathways. Interaction network analysis revealed strong predicted associations with KHDRBS1, SYNJ1, and CSNK2A1, suggesting involvement in RNA regulation, endocytic signalling, and kinase-mediated cellular control. Collectively, these findings identify FNBP4 as a prognostically relevant cytoskeletal protein in breast cancer and provide a strong rationale for its further experimental validation and exploration as a therapeutic target. FNBP4 Formin Binding proteins Formins Cytoskeletal Regulation Cancer Informatics Breast cancer Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 INTRODUCTION Formins are a family of proteins that are crucial for controlling actin filaments formation and organisation within cells 1 . Dysregulation of formins may contribute to the increased motility and invasive properties of cancer cells, facilitating their spread to surrounding tissues 2 . Formin-binding proteins (FNBPs) are a group of proteins that interact with formins to regulate, fine-tune or modulate their activity or functions 3 . The gene for FNBP4(also known as FBP30) is located on chromosome 11p14. This protein contains two tryptophan-rich WW domains, which specifically interact with the proline-rich formin homology 1(FH1) domains found in members of the formin protein family. Despite being the shortest known domains with highly conserved structures, WW domains are known to participate in a diverse array of cellular processes, such as transcription, splicing, organ development, tumorigenesis, ubiquitylation, and much more 4 . Sequence variation confers characteristic ligand specificity to these domains, thus making them capable of binding to different partners and providing the platform for protein-protein interactions. A few of the WW domain-containing formin binding proteins are known to be components of the eukaryotic transcription and splicing machinery as well 5,6,7 . FNBP4 had initially gained attention from a study describing its regulation by p53 8 . Over time, researchers further explored the roles of formin binding proteins across various cancer types 9,10,11 and studied them in relation to their structural characteristics and function ,12,13,14,15 .However, the expression of FNBP4 in breast cancer and its potential link to patient prognosis remains unclear. Breast cancer is among the most common types of cancer diagnosed in women and remains a leading cause of cancer-related deaths globally 16 . The high death rate is mainly due to the spread of tumor cells to distant organs through metastasis. Metastasis involves a complex sequence of events, including detachment from the primary tumor, invasion through the extracellular matrix, intravasation, survival in the circulation, extravasation, and colonization of distant tissues 17 . Regulating the process of actin remodelling is one of the key steps in the progression of cancer; hence, studying the key components of Epithelial-Mesenchymal Transition ( EMT) and Mesenchymal-Epithelial Transition (MET), as well as examining their role in tumor progression 18 , can have therapeutic implications, particularly in devising interventions that prevent metastasis 19 . In the current study, we focused specifically on the protein-level expression of FNBP4 to evaluate its potential role in breast cancer. Protein-level analysis provides functionally relevant insights, as proteins are the principal executors of cellular functions. To achieve a comprehensive understanding, multiple publicly available proteomic and interaction databases were utilized. Protein expression data retrieved from the Human Protein Atlas (HPA) 20 and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), accessed via the UALCAN portal 21 , provides quantitative protein profiles across diverse tumor subtypes and clinical conditions. To explore FNBP4's functional landscape, the IntAct Molecular Interaction Database 22 was used to identify its potential protein–protein interaction partners, shedding light on its involvement in key cellular pathways. Furthermore, the Kaplan–Meier Plotter (KM Plotter) tool 23 was employed to assess the correlation between FNBP4 protein expression and patient survival outcomes, thereby evaluating its prognostic significance. METHODOLOGY Human Protein Atlas (HPA) HPA was utilized to gather comprehensive information on FNBP4, including its protein expression levels, subcellular localization, and predicted functional roles. The University of ALabama at Birmingham CANcer data analysis Portal (UALCAN-CPTAC) To investigate the differential protein expression of Formin-binding protein 4 (FNBP4) in breast cancer, the UALCAN portal 24 , an interactive web resource for analysing cancer omics data, was utilized. Protein expression data were accessed specifically from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) module integrated into UALCAN. The analysis was restricted to the “Breast Invasive Carcinoma” dataset available in CPTAC. FNBP4 protein expression (measured by mass spectrometry-based proteomics) was assessed across normal breast tissue and primary tumor samples. Expression was further stratified based on molecular subtypes (luminal A, luminal B, HER2-enriched, and basal-like) and proteomic subtypes (K1-K10 & S1-S-11), allowing for insights into expression heterogeneity and the probable role in oncogenic pathways. Kaplan-Meier Plotter: To evaluate the prognostic relevance of FNBP4 expression in breast cancer, Kaplan-Meier survival analysis using the Kaplan-Meier Plotter tool 25 , a publicly available resource that integrates gene expression and survival data were performed. IntAct Molecular Interaction Database (IntAct) To investigate the potential interactome of FNBP4, IntAct Database (https://www.ebi.ac.uk/intact/) was employed—it is a manually curated repository of experimentally validated protein–protein interactions derived from peer-reviewed scientific literature. “FNBP4” was used as the query term, and the search was restricted to interactions specific to Homo sapiens, except for one isoform where data was available only for Mus musculus. Interactions with a MIscore greater than 0.35 were selected, prioritizing those categorized as direct interactions or physical associations. The MIscore reflects the confidence level of each interaction, which increases proportionally with the number and quality of supporting experimental evidence. This analysis aimed to reveal functionally relevant partners that may contribute to FNBP4’s role in breast cancer pathophysiology. Results FNBP4 Exhibits Stable Structure, Dual Subcellular Localization, and Moderate Nuclear Expression in Breast Cancer Tissues HPA provided valuable information regarding FNBP4. Alpha Fold-based structural prediction (A) of FNBP4 revealed a high degree of confidence in most regions of the protein, indicated by the prevalence of blue (pLDDT > 90) and light blue (pLDDT > 70) segments. Western blot analysis (B) confirmed recombinant expression of FNBP4, overexpressed in HEK293T cells co-transfected with the expression vector, showing a protein band with minimal non-specific bands. The higher-than-expected molecular weight (~ 110.3 kDa) in Lane 3 may represent a post-translationally modified protein; however, the presence of a clear band supports the specificity of the antibody and successful overexpression of the tagged FNBP4 protein. Immunofluorescence analysis (C)using independent antibodies in U2OS cells demonstrated consistent localization of FNBP4 to the nucleoplasm. Immunohistochemical (IHC) (D - E) staining in breast cancer tissue microarrays provided further evidence of FNBP4’s subcellular localization. Image D showed moderate nuclear staining in tumor cells, while Image E indicated cytoplasmic membranous localization with low staining intensity. Comparative analysis of FNBP4 protein expression across various cancers (F) indicated weak to moderate nuclear positivity with additional cytoplasmic staining in breast cancer tissues. These findings suggest a dual distribution of FNBP4, potentially indicating a shuttling mechanism between the cytoplasm and nucleus or context-dependent functional shifts. Among the twenty cancer types analysed, breast cancer exhibited a notable level of FNBP4 positivity, supporting its relevance in tumor progression. Poor overall survival at high expression of FNBP4 protein KM survival plot shows the relationship between the expression levels of the FNBP4 protein (with UniProt ID: Q8N3X1) and patient survival over time, measured in months. The survival rate was assessed using the Tang (2018) 23 dataset (65 samples). The hazard ratio found was 2.86 with a P value of 0.0092 (Fig. 2 ). Patients with low FNBP4 expression showed a higher probability of survival over time compared to those with high expression levels. High protein expression in Invasive Ductal Carcinoma and TNBC cancer subclass of breast cancer FNBP4 protein expression analysis was performed using CPTAC data available on the UALCAN platform, evaluating its differential expression across various clinical parameters including sample types, cancer stages, molecular subtypes, and histological categories (Fig. 3 ; A-D). The analysis revealed notably higher FNBP4 expression in Invasive Ductal Carcinoma (IDC) and Triple Negative Breast Cancer (TNBC) subtypes, indicating its potential association with aggressive clinical features in breast cancer. Elevated FNBP4 Protein Expression Correlates with Somatic Alterations in Key Oncogenic Signalling Pathways FNBP4 expression has been systematically assessed in the context of somatic pathway alterations by integrating proteomic profiles with whole-exome sequencing and copy number alteration (CNA) data. This integrative multi-omics analysis enabled the identification of pathway-level perturbations and gene-specific alterations associated with FNBP4, providing insights into its potential role in key oncogenic signalling events within breast cancer. Figure 4 presents the Z-score normalized expression pattern of FNBP4 protein across various cancer-associated signalling pathways in CPTAC breast cancer samples, comparing normal tissues, pathway-altered tumors, and other tumors. FNBP4 expression for proteome-based molecular subtypes (K1-K11, S1-S11) and associated mRNA class, notable features for each class, were checked to gain more insights into probable pathways they might be associated with. (Fig. 5 and Table 1 ) Table 1 Integrated Proteogenomic Subtypes (K1-K10/S1-S11/associated mRNA class c1-c10) for interpreting FNBP4 Expression in Breast Cancer. K Subtype S Subtype n (K) n (S) Associated mRNA Class Molecular Features FNBP4 Z-Value (K) FNBP4 Z-Value (S) Interpretation K1 S1 2 1 c1 Proteasome, glycolysis, PPP ~+0.5 ~+0.8 Mildly elevated expression in both, likely reflecting proteasome and glycolytic activity. K2 S2 12 6 c3, c10 Adaptive immune, MHC proteins ~+1.2 ~–0.5 Discordant expression; likely reflects microenvironmental diversity (immune-driven K2 vs suppressed S2). K3 – 5 – c3, c10 Innate immune, hypoxia, complement system ~–1.5 – Strong downregulation; may represent suppressed immune or hypoxic subtypes not well captured in S-type. K4 S3 29 24 c5 Basal-like, MYC/YAP1 targets ~+2.0 ~+0.9 Consistently high expression suggests a strong MYC/YAP1-driven basal-like phenotype. K5 S4 18 25 c6 Epithelial, normoxia, TCA/OXPHOS ~+1.0 ~+0.5 Moderate concordance; reflects epithelial phenotype with metabolic activity. – S5 – – – B cells, MMPs, eosinophils, complement – Not available Likely heterogeneous, may overlap with immune-stromal mixed types (K3, K6). K6 – 14 – c7 Stromal, MMPs, Wnt/Notch, hypoxia ~–1.0 – Consistently downregulated; reflects desmoplastic or hypoxic stromal context. K7 S6 31 30 c8 Stromal, collagen VI, Wnt/Notch ~+0.3 ~–0.5 Slight disagreement; may indicate functional subclusters in stromal response. – S7 – 4 – Axon guidance, frizzled binding – ~+0.6 Moderately upregulated; potential neural/migratory component. – S8 – 5 – RCC only, haemoglobin proteins – ~–1.0 Not relevant to breast cancer; downregulated in RCC cases. K10 S9 14 17 – ER-related, steroid biosynthesis ~–0.5 ~–0.3 Mild downregulation; similar hormonal profile suggests functional similarity. – S10 – 12 – DNA repair, MYC, Wnt, Hippo pathway – ~+1.5 to + 2.5 High expression; resembles K4 biologically—potentially an aggressive subtype. – S11 – – – Synapse, metabolism (TCA, glycolysis, FA) – Not shown Predicted high expression due to metabolic activity; parallels K5 or K4. Direct molecular interactions with KHDRBS1 (KH domain-containing, RNA-binding, signal transduction-associated protein 1) and SYNJ1 (Synaptojanin 1) with the highest probability The IntAct molecular interaction database ( https://www.ebi.ac.uk/intact ) is a curated resource of molecular interactions, derived from the scientific literature and direct data depositions. IntAct curates’ molecular interaction data derived from experimental studies published in scientific literature. The interacting partners of FNBP4 were determined to integrate it into a broader protein interaction network, thereby elucidating its functional context and the biological pathways it may be involved in. These are identified using methods involving purified components, excluding cell extracts or complex mixtures, to ensure no hidden intermediaries are present. Enzymatic reactions (e.g., phosphorylation) were also included in this category, provided purified participants were used, though they are depicted as specific reaction events. A higher MiS score indicates the level of confidence in predicting the specific interaction based on the standardised dataset with a higher number of experimental evidences in support of the claim (Table 2 ). Table 2 Experimentally Determined Interaction Partners of FNBP4 and Its Isoforms S. No Interactive partner (uniProt) Host Organism Detection Method Interaction type Mi Score Publication Id A. Q8N3X1 (homo sapiens species) 1 KHDRBS1 Q07666 In vitro filter binding Direct interaction 0.54 10748127 2 PRPF40A O75400 Saccharomyces cerevisiae (Baker's yeast) 2 hybrid Physical association 0.55 15231748 3 H2BC21 Q16778 Homo sapiens U2OS osteosarcoma cell crosslink Physical association 0.4 30021884 4 HTT P42858 Saccharomyces cerevisiae (Baker's yeast) 2 hybrid Physical association 0.37 17500595 5 HSCB Q8IWL3 Saccharomyces cerevisiae (Baker's yeast) 2 hybrid Physical association 0.37 24606901 6 PLXNA2 O75051 Saccharomyces cerevisiae (Baker's yeast) 2 hybrid Physical association 0.37 12421765 B. Q8N3X1-1 (Isoform) (homo sapiens species) 1 CSNK2A1 P68400 In vitro protein kinase assay Physical association 0.44 22113938 C. Q8N3X1-2 (Isoform) (homo sapiens species) 1 DDX17 Q92841-4 Homo sapiens HEK293T embryonic kidney cell anti tag co ip association 0.35 28514442 2 ZC3H18 Q86VM9 Homo sapiens HEK293T embryonic kidney cell anti tag co ip association 0.35 28514442 D. Q6ZQ03 (Isoform) (with Mus musculus species) 1 SYNJ1 O43426 In vitro phage display direct interaction 0.56 11292345 2 Cdk9 Q99J95 Mus musculus pull down association 0.35 20593818 DISCUSSION Cytoskeletal regulators are central drivers of cancer metastasis. Their dysregulation enhances cellular motility, invasiveness, and metastatic potential 26 . Among these regulators, formins and their binding partners play essential roles in actin remodelling. Although direct evidence on the role of FNBP4 in breast cancer remains limited, its Increasing interest stems from emerging proteomic data suggesting its involvement in both clinical aggressiveness and oncogenic signalling pathways. Proteomic analysis using CPTAC datasets demonstrates a consistent upregulation of FNBP4 in breast tumors compared with normal breast tissue. Stage-wise comparison reveals rising levels from stage II onward, indicating a link with tumor progression. Subtype-specific analysis highlights the highest FNBP4 expression in triple-negative breast cancer (TNBC), followed by luminal and HER2-positive subtypes, suggesting a stronger association with aggressive and therapy-refractory disease. Histological assessment shows substantial upregulation in infiltrating ductal carcinoma, while levels remain comparatively lower in infiltrating lobular carcinoma and mucinous variants. Survival analysis using Kaplan–Meier Plotter reveals that high FNBP4 protein expression correlates with significantly poorer patient outcomes (HR = 2.86), positioning FNBP4 as a potential marker of increased mortality risk. Complementary data from the Human Protein Atlas indicate that FNBP4 predominantly localizes to the nucleoplasm and cytoplasm, implicating it in processes such as RNA metabolism, chromatin organization, and transcriptional regulation—mechanisms frequently altered in cancer. Its dual localization suggests dynamic shuttling or context-dependent functions, which may be particularly relevant in rapidly evolving tumor environments such as TNBC, where cytoskeletal flexibility and transcriptional adaptability are essential for tumor plasticity and metastasis. Beyond clinicopathological features, FNBP4 expression shows strong associations with oncogenic pathway alterations. Tumors with somatic changes in pathways such as RTK, WNT, PI3K/AKT/mTOR, MYC/MYCN, p53/Rb, and Hippo exhibit significantly elevated FNBP4 levels. This enrichment suggests that FNBP4 may act as a downstream effector or functional contributor within these pathways, propagating cancer-driving signals that promote cell proliferation, survival, and migration. The highest increases occur in tumors altered in NRF2, MYC/MYCN, RTK, and p53/Rb pathways, emphasising its integration into multiple cancer-relevant networks. Additionally, high copy number alteration (CNA) burden correlates with increased FNBP4 levels, particularly in contexts involving hormone receptor signalling, histone modification, and DNA repair, reinforcing its potential role in the cellular response to genomic instability. Unsupervised clustering studies further support the variable involvement of FNBP4 across molecular tumor subtypes. Large-scale proteome-based analyses have defined multiple subtypes (K1–K10 and S1–S11) 27,28 , each representing distinct biological programs. FNBP4 expression peaks in subtype K4, characterized by basal-like features and activation of MYC and YAP1 pathways—both powerful regulators of transcriptional amplification, cytoskeletal remodelling, and epithelial-mesenchymal transition (EMT) 29 . Moderately elevated levels appear in K2 and K5 subtypes associated with immune and metabolic signatures, respectively. Conversely, subtypes defined by innate immune activation or hypoxia show reduced expression, indicating subtype-specific functional relevance. To elucidate FNBP4’s mechanistic roles, protein–protein interaction (PPI) mapping was performed using IntAct. The canonical FNBP4 isoform in humans shows eight experimentally validated interactions detected through methods such as two-hybrid assays, crosslinking, and filter binding. Several interactions exhibit moderate to high confidence with MI scores ranging from 0.35 to 0.55. Among these, KHDRBS1 (Sam68) emerges as a strong interactor (MI score 0.54), implicating FNBP4 in RNA splicing and transcriptional regulation. KHDRBS1 regulates alternative splicing events that influence cell adhesion, migration, and apoptosis, often promoting tumor progression 30,31,32 Isoform-specific interactions include CSNK2A1 (CK2α) for isoform Q8N3X1-1, identified through kinase assays, suggesting post-translational modulation of FNBP4 by phosphorylation. CSNK2 (CK2) is a well-known oncogenic kinase that drives survival signalling, cytoskeletal reorganization, and adaptation to stress 33,34,35 Isoform Q8N3X1-2 interacts with DDX17and ZC3H18, both involved in RNA helicase activity and transcriptional regulation 36,37 . In murine models, the Q6ZQ03 isoform interacts strongly with SYNJ1 and moderately with CDK9, linking FNBP4 to vesicle trafficking and cell-cycle control. SYNJ1 contributes to altered membrane trafficking and receptor recycling, facilitating enhanced motility and invasive capacity 38,39,40,41. Evidently, all these interactors themselves play established roles in breast cancer. Through these interactions, FNBP4 may serve as a scaffold that integrates pathways involving RNA metabolism, cytoskeletal restructuring, and vesicular dynamics-functions that collectively support tumor aggressiveness. Cross-species conservation and high-confidence interactions further underscore the biological significance of FNBP4 in breast cancer progression CONCLUDING REMARKS The use of large-scale proteomic datasets offers a valuable, systems-level perspective, facilitating the identification of clinically relevant targets. The availability of global cancer databases has significantly enhanced the understanding of tumorigenesis. This study leverages multiple proteomic and clinical datasets to comprehensively examine FNBP4’s role in breast cancer, revealing its potential impact on disease progression and clinical outcomes. Protein-level database analysis is crucial for biomarker discovery and validating targets because it reflects dynamic cellular states and biological function Moving forward, rigorous experimental validation through in-vitro and in-vivo models is essential to confirm these associations, decipher the underlying molecular mechanisms, and translate these bioinformatic insights into clinical applications for breast cancer management. Declarations Author Contribution RS: Substantial contributions to the conception, design of work; acquisition, analysis, interpretation of data, drafting KK: review, formattingKD: review, formattingMK: critical reviewing, formattingST: Drafting the work, critical reviewing, formattingSM: intellectual inputs, interpretation of dataHC: conception, design of the work, interpretation of data, Supervision, Final approval of the version to be published Acknowledgement The authors acknowledge the publicly available proteomics and bioinformatics resources provided by CPTAC, UALCAN, the Human Protein Atlas, KM Plotter, and the IntAct database, which made this analysis possible. References Chesarone MA, DuPage AG, Goode BL. Unleashing formins to remodel the actin and microtubule cytoskeletons. Nat Rev Mol Cell Biol 11(1): 62-74, 2010. DeWard AD, Eisenmann KM, Matheson SF, et al. The role of formins in human disease. Biochimica et Biophysica Acta (BBA)- Mol Cell Res 1803 (2): 226-233, 2010. 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Cdk1-mediated threonine phosphorylation of Sam68 modulates its RNA binding, alternative splicing activity and cellular functions. Nucleic Acids Res 50(22): 13045-13062, 2022. Mitra P, Yang RM, Sutton J, et al. CDK9 inhibitors selectively target estrogen receptor-positive breast cancer cells through combined inhibition of MYB and MCL-1 expression. Oncotarget 7(8): 9069-9083, 2016. Mustafa EH, Laven-Law G, Kikhtyak Z, et al. Selective inhibition of CDK9 in triple negative breast cancer. Oncogene 43: 202-215, 2024. Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 08 May, 2026 Reviewers agreed at journal 07 May, 2026 Reviewers invited by journal 07 May, 2026 Editor assigned by journal 07 Mar, 2026 Submission checks completed at journal 07 Mar, 2026 First submitted to journal 05 Mar, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9039049","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":641559145,"identity":"6968f2d4-c018-431c-a4f0-e38869700444","order_by":0,"name":"Rashmi Shrivastava","email":"","orcid":"","institution":"National Institute of Biologicals","correspondingAuthor":false,"prefix":"","firstName":"Rashmi","middleName":"","lastName":"Shrivastava","suffix":""},{"id":641559149,"identity":"e3fe0965-2c05-4e8a-b65a-8e9ebc74299c","order_by":1,"name":"Kavita Kavita","email":"","orcid":"","institution":"National Institute of Biologicals","correspondingAuthor":false,"prefix":"","firstName":"Kavita","middleName":"","lastName":"Kavita","suffix":""},{"id":641559153,"identity":"60619514-1a27-453d-b701-bacd5269f747","order_by":2,"name":"Krishnakant Dalai","email":"","orcid":"","institution":"National Institute of Biologicals","correspondingAuthor":false,"prefix":"","firstName":"Krishnakant","middleName":"","lastName":"Dalai","suffix":""},{"id":641559159,"identity":"7816606e-d9b1-41ee-ac13-c4a59105a42d","order_by":3,"name":"Dr. Manjula Kiran","email":"","orcid":"","institution":"National Institute of Biologicals","correspondingAuthor":false,"prefix":"Dr.","firstName":"Manjula","middleName":"","lastName":"Kiran","suffix":""},{"id":641559160,"identity":"024e412a-1c0a-4392-8525-becf6e9260ea","order_by":4,"name":"Shalini Tewari","email":"","orcid":"","institution":"National Institute of Biologicals","correspondingAuthor":false,"prefix":"","firstName":"Shalini","middleName":"","lastName":"Tewari","suffix":""},{"id":641559162,"identity":"cb1fcd82-9680-44ce-9d54-b3a2c4de5b59","order_by":5,"name":"Dr. Sankar Maiti","email":"","orcid":"","institution":"Indian Institute of Science Education and Research Kolkata","correspondingAuthor":false,"prefix":"Dr.","firstName":"Sankar","middleName":"","lastName":"Maiti","suffix":""},{"id":641559165,"identity":"cf8d2e69-6063-4abc-ad07-d336ef94365e","order_by":6,"name":"Dr. Harish Chander","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABDklEQVRIie3RPUvEMBjA8acUrkvarg0H9xkeCBQOi5/lQqEuUg+E46YSEHKL6NpP4pwja+18UoebnAUXXwqaIohK652bSP5DCEl+JBAAm+0vpogZEGYA3WQEEIIj37fcfQkVexH4RFB14w8FzfX6YTkvcvDMZL5ITlhzJrfwnHDh+aqP0DpPaYX6FEiejss6m17drlfoXGRcuMGsj2BFkApUXEQEx77UGG+4jJxzzcAlOEDYk8CiI+zFl6/Iyt0kNre4HYnNLQoxMgQe9WSIUEOmAjWX5Dg+IHWK0YavkItsMhoggXnYjWgLfulVrCGLQwzLo7vtfZuQMKx6yUdf/4LL7yu7a3953maz2f5zb4SpWGLwAugJAAAAAElFTkSuQmCC","orcid":"","institution":"National Institute of Biologicals","correspondingAuthor":true,"prefix":"Dr.","firstName":"Harish","middleName":"","lastName":"Chander","suffix":""}],"badges":[],"createdAt":"2026-03-05 10:26:30","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9039049/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9039049/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":109452242,"identity":"bb54cfa8-461b-4cca-b8ea-ad49462ef9b2","added_by":"auto","created_at":"2026-05-18 09:12:21","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":593750,"visible":true,"origin":"","legend":"\u003cp\u003eA- Predicted structure; B- Enhanced recombinant expression based on predicted size; C, D, E- Antibody staining showing nuclear and cytoplasmic membranous location; F- weak to moderate nuclear positivity with additional cytoplasmic staining across different cancers\u003csup\u003e21\u003c/sup\u003e.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-9039049/v1/be7dbfd6c5e61ff46779b4e5.png"},{"id":109452237,"identity":"ce88b92f-c50d-4229-b764-ffa093ad8127","added_by":"auto","created_at":"2026-05-18 09:12:17","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":73245,"visible":true,"origin":"","legend":"\u003cp\u003eSurvival plots. The KM survival plot shows the relationship between the expression levels of the FNBP4 protein (UniProt ID: Q8N3X1) and patient survival over time, measured in months (Hazard ratio= 2.86, P value= 0.0092).\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-9039049/v1/3e1d5c389669cd5bb2476fce.png"},{"id":109452243,"identity":"0ae9303f-9da8-47be-8a1a-abb94ab698b1","added_by":"auto","created_at":"2026-05-18 09:12:21","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":126646,"visible":true,"origin":"","legend":"\u003cp\u003eUALCAN-CPTAC data. (A) Expression of protein levels of FNBP4 in normal tissue and primary breast cancer. (B) Expression of FNBP4 protein levels in distinct stages of breast cancer. (C)) Expression of protein levels of FNBP4 in different breast cancer subclasses. (D) Expression of FNBP4 protein levels in breast cancer based on histological subtypes.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-9039049/v1/63d2643098077ba6cfafd842.png"},{"id":109452169,"identity":"4af599b4-cf16-4268-9111-96cd221560d4","added_by":"auto","created_at":"2026-05-18 09:12:08","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":203207,"visible":true,"origin":"","legend":"\u003cp\u003eThe expression pattern of FNBP4 protein (Z-score normalized) across various cancer-altered signalling pathways in CPTAC breast cancer samples, comparing normal tissue, pathway-altered tumors, and other tumors.\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-9039049/v1/305eea655274f3745a0d39c8.png"},{"id":109452235,"identity":"27902386-c934-439d-bdf7-6fb151c3537d","added_by":"auto","created_at":"2026-05-18 09:12:14","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":130265,"visible":true,"origin":"","legend":"\u003cp\u003eFNBP4 protein expression based on Proteome-based Molecular subtype a) (K1-K10) in breast cancer; b) K1-K10 in Pan cancer; c) Molecular subtype 2 (S1-S10) in breast cancer; d) S1-S11 in Pan cancer.\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-9039049/v1/82c0904827e973acac4ea1c8.png"},{"id":109759962,"identity":"82c1b76f-7c0e-434f-b2c8-c98f67e763c5","added_by":"auto","created_at":"2026-05-22 07:27:59","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1236175,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9039049/v1/ab0253fe-2bf3-418f-b20a-09007c7a1879.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Proteomic-based informatics highlights FNBP4 as a prognostically relevant cytoskeletal protein in Breast Cancer","fulltext":[{"header":"INTRODUCTION","content":"\u003cp\u003eFormins are a family of proteins that are crucial for controlling actin filaments formation and organisation within cells\u003csup\u003e1\u003c/sup\u003e. Dysregulation of formins may contribute to the increased motility and invasive properties of cancer cells, facilitating their spread to surrounding tissues\u003csup\u003e2\u003c/sup\u003e.\u0026nbsp;Formin-binding proteins (FNBPs) are a group of proteins that interact with formins to regulate, fine-tune or modulate their activity or functions\u003csup\u003e3\u003c/sup\u003e. \u0026nbsp;The gene for FNBP4(also known as FBP30) is located on chromosome 11p14. This protein contains two tryptophan-rich WW domains, which specifically interact with the proline-rich formin homology 1(FH1) domains found in members of the formin protein family. Despite being the shortest known domains with highly conserved structures, WW domains are known to participate in a diverse array of cellular processes, such as transcription, splicing, organ development, tumorigenesis, ubiquitylation, and much more\u003csup\u003e4\u003c/sup\u003e. Sequence variation confers characteristic ligand specificity to these domains, thus making them capable of binding to different partners and providing the platform for protein-protein interactions. A few of the WW domain-containing formin binding proteins are known to be components of the eukaryotic transcription and splicing machinery as well\u003csup\u003e5,6,7\u003c/sup\u003e.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eFNBP4 had initially gained attention from a study describing its regulation by p53\u003csup\u003e8\u003c/sup\u003e. Over time, researchers further explored the roles of formin binding proteins across various cancer types \u003csup\u003e9,10,11\u003c/sup\u003e and studied them in relation to their structural characteristics and function\u003csup\u003e,12,13,14,15\u003c/sup\u003e.However, the expression of FNBP4 in breast cancer and its potential link to patient prognosis remains unclear.\u003c/p\u003e\n\u003cp\u003eBreast cancer is among the most common types of cancer diagnosed in women and remains a leading cause of cancer-related deaths globally\u003csup\u003e16\u003c/sup\u003e. The high death rate is mainly due to the spread of tumor cells to distant organs through metastasis. Metastasis involves a complex sequence of events, including detachment from the primary tumor, invasion through the extracellular matrix, intravasation, survival in the circulation, extravasation, and colonization of distant tissues\u003csup\u003e17\u003c/sup\u003e. Regulating the process of actin remodelling is one of the key steps in the progression of cancer; hence, studying the key components of Epithelial-Mesenchymal Transition\u003cs\u003e\u0026nbsp;(\u003c/s\u003eEMT) and Mesenchymal-Epithelial Transition (MET), as well as examining their role in tumor progression\u003csup\u003e18\u003c/sup\u003e, can have therapeutic implications, particularly in devising interventions that prevent metastasis\u003csup\u003e19\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003eIn the current study, we focused specifically on the protein-level expression of FNBP4 to evaluate its potential role in breast cancer. Protein-level analysis provides functionally relevant insights, as proteins are the principal executors of cellular functions. To achieve a comprehensive understanding, multiple publicly available proteomic and interaction databases were utilized. Protein expression data retrieved from the Human Protein Atlas (HPA)\u003csup\u003e20\u003c/sup\u003e and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), accessed via the UALCAN portal\u003csup\u003e21\u003c/sup\u003e, provides quantitative protein profiles across diverse tumor subtypes and clinical conditions. To explore FNBP4's functional landscape, the IntAct Molecular Interaction Database\u003csup\u003e22\u003c/sup\u003e was used to identify its potential protein–protein interaction partners, shedding light on its involvement in key cellular pathways. Furthermore, the Kaplan–Meier Plotter (KM Plotter) tool\u003csup\u003e23\u003c/sup\u003e was employed to assess the correlation between FNBP4 protein expression and patient survival outcomes, thereby evaluating its prognostic significance.\u003c/p\u003e"},{"header":"METHODOLOGY","content":"\u003col\u003e\n \u003cli\u003eHuman Protein Atlas (HPA)\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eHPA was utilized to gather comprehensive information on FNBP4, including its protein expression levels, subcellular localization, and predicted functional roles.\u003c/p\u003e\n\u003col start=\"2\"\u003e\n \u003cli\u003eThe University of ALabama at Birmingham CANcer data analysis Portal (UALCAN-CPTAC)\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eTo investigate the differential protein expression of Formin-binding protein 4 (FNBP4) in breast cancer, the UALCAN portal\u003csup\u003e24\u003c/sup\u003e, an interactive web resource for analysing cancer omics data, was utilized. Protein expression data were accessed specifically from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) module integrated into UALCAN. The analysis was restricted to the “Breast Invasive Carcinoma” dataset available in CPTAC. FNBP4 protein expression (measured by mass spectrometry-based proteomics) was assessed across normal breast tissue and primary tumor samples. Expression was further stratified based on molecular subtypes (luminal A, luminal B, HER2-enriched, and basal-like) and proteomic subtypes (K1-K10 \u0026amp; S1-S-11), allowing for insights into expression heterogeneity and the probable role in oncogenic pathways.\u003c/p\u003e\n\u003col start=\"3\"\u003e\n \u003cli\u003eKaplan-Meier Plotter:\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eTo evaluate the prognostic relevance of FNBP4 expression in breast cancer, Kaplan-Meier survival analysis using the Kaplan-Meier Plotter tool\u003csup\u003e25\u003c/sup\u003e, a publicly available resource that integrates gene expression and survival data were performed.\u003c/p\u003e\n\u003col start=\"4\"\u003e\n \u003cli\u003eIntAct Molecular Interaction Database (IntAct)\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eTo investigate the potential interactome of FNBP4, IntAct Database (https://www.ebi.ac.uk/intact/) was employed—it is a manually curated repository of experimentally validated protein–protein interactions derived from peer-reviewed scientific literature. “FNBP4” was used as the query term, and the search was restricted to interactions specific to Homo sapiens, except for one isoform where data was available only for Mus musculus. Interactions with a MIscore greater than 0.35 were selected, prioritizing those categorized as direct interactions or physical associations. The MIscore reflects the confidence level of each interaction, which increases proportionally with the number and quality of supporting experimental evidence. This analysis aimed to reveal functionally relevant partners that may contribute to FNBP4’s role in breast cancer pathophysiology.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eFNBP4 Exhibits Stable Structure, Dual Subcellular Localization, and Moderate Nuclear Expression in Breast Cancer Tissues\u003c/h2\u003e \u003cp\u003eHPA provided valuable information regarding FNBP4. Alpha Fold-based structural prediction (A) of FNBP4 revealed a high degree of confidence in most regions of the protein, indicated by the prevalence of blue (pLDDT\u0026thinsp;\u0026gt;\u0026thinsp;90) and light blue (pLDDT\u0026thinsp;\u0026gt;\u0026thinsp;70) segments. Western blot analysis (B) confirmed recombinant expression of FNBP4, overexpressed in HEK293T cells co-transfected with the expression vector, showing a protein band with minimal non-specific bands. The higher-than-expected molecular weight (~\u0026thinsp;110.3 kDa) in Lane 3 may represent a post-translationally modified protein; however, the presence of a clear band supports the specificity of the antibody and successful overexpression of the tagged FNBP4 protein. Immunofluorescence analysis (C)using independent antibodies in U2OS cells demonstrated consistent localization of FNBP4 to the nucleoplasm. Immunohistochemical (IHC) (D - E) staining in breast cancer tissue microarrays provided further evidence of FNBP4\u0026rsquo;s subcellular localization. Image D showed moderate nuclear staining in tumor cells, while Image E indicated cytoplasmic membranous localization with low staining intensity. Comparative analysis of FNBP4 protein expression across various cancers (F) indicated weak to moderate nuclear positivity with additional cytoplasmic staining in breast cancer tissues. These findings suggest a dual distribution of FNBP4, potentially indicating a shuttling mechanism between the cytoplasm and nucleus or context-dependent functional shifts. Among the twenty cancer types analysed, breast cancer exhibited a notable level of FNBP4 positivity, supporting its relevance in tumor progression.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003ePoor overall survival at high expression of FNBP4 protein\u003c/h3\u003e\n\u003cp\u003eKM survival plot shows the relationship between the expression levels of the FNBP4 protein (with UniProt ID: Q8N3X1) and patient survival over time, measured in months. The survival rate was assessed using the Tang (2018)\u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e dataset (65 samples). The hazard ratio found was 2.86 with a P value of 0.0092 (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Patients with low FNBP4 expression showed a higher probability of survival over time compared to those with high expression levels.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e\n\u003ch3\u003eHigh protein expression in Invasive Ductal Carcinoma and TNBC cancer subclass of breast cancer\u003c/h3\u003e\n\u003cp\u003eFNBP4 protein expression analysis was performed using CPTAC data available on the UALCAN platform, evaluating its differential expression across various clinical parameters including sample types, cancer stages, molecular subtypes, and histological categories (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e; A-D). The analysis revealed notably higher FNBP4 expression in Invasive Ductal Carcinoma (IDC) and Triple Negative Breast Cancer (TNBC) subtypes, indicating its potential association with aggressive clinical features in breast cancer.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e\n\u003ch3\u003eElevated FNBP4 Protein Expression Correlates with Somatic Alterations in Key Oncogenic Signalling Pathways\u003c/h3\u003e\n\u003cp\u003eFNBP4 expression has been systematically assessed in the context of somatic pathway alterations by integrating proteomic profiles with whole-exome sequencing and copy number alteration (CNA) data. This integrative multi-omics analysis enabled the identification of pathway-level perturbations and gene-specific alterations associated with FNBP4, providing insights into its potential role in key oncogenic signalling events within breast cancer. Figure\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e presents the Z-score normalized expression pattern of FNBP4 protein across various cancer-associated signalling pathways in CPTAC breast cancer samples, comparing normal tissues, pathway-altered tumors, and other tumors.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eFNBP4 expression for proteome-based molecular subtypes (K1-K11, S1-S11) and associated mRNA class, notable features for each class, were checked to gain more insights into probable pathways they might be associated with. (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e and Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e)\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eIntegrated Proteogenomic Subtypes (K1-K10/S1-S11/associated mRNA class c1-c10) for interpreting FNBP4 Expression in Breast Cancer.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"9\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK\u003c/p\u003e \u003cp\u003eSubtype\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS\u003c/p\u003e \u003cp\u003eSubtype\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003en\u003c/p\u003e \u003cp\u003e(K)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003en\u003c/p\u003e \u003cp\u003e(S)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAssociated mRNA Class\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMolecular Features\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eFNBP4 Z-Value (K)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eFNBP4 Z-Value (S)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c9\"\u003e \u003cp\u003eInterpretation\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eProteasome, glycolysis, PPP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~+0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~+0.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eMildly elevated expression in both, likely reflecting proteasome and glycolytic activity.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec3, c10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAdaptive immune, MHC proteins\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~+1.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~\u0026ndash;0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eDiscordant expression; likely reflects microenvironmental diversity (immune-driven K2 vs suppressed S2).\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec3, c10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eInnate immune, hypoxia, complement system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~\u0026ndash;1.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eStrong downregulation; may represent suppressed immune or hypoxic subtypes not well captured in S-type.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eBasal-like, MYC/YAP1 targets\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~+2.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~+0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eConsistently high expression suggests a strong MYC/YAP1-driven basal-like phenotype.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eEpithelial, normoxia, TCA/OXPHOS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~+1.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~+0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eModerate concordance; reflects epithelial phenotype with metabolic activity.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eB cells, MMPs, eosinophils, complement\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNot available\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eLikely heterogeneous, may overlap with immune-stromal mixed types (K3, K6).\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStromal, MMPs, Wnt/Notch, hypoxia\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~\u0026ndash;1.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eConsistently downregulated; reflects desmoplastic or hypoxic stromal context.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e31\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003ec8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStromal, collagen VI, Wnt/Notch\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~+0.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~\u0026ndash;0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eSlight disagreement; may indicate functional subclusters in stromal response.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAxon guidance, frizzled binding\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~+0.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eModerately upregulated; potential neural/migratory component.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eRCC only, haemoglobin proteins\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~\u0026ndash;1.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eNot relevant to breast cancer; downregulated in RCC cases.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eK10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eER-related, steroid biosynthesis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e~\u0026ndash;0.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~\u0026ndash;0.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eMild downregulation; similar hormonal profile suggests functional similarity.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eDNA repair, MYC, Wnt, Hippo pathway\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e~+1.5 to +\u0026thinsp;2.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eHigh expression; resembles K4 biologically\u0026mdash;potentially an aggressive subtype.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eS11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eSynapse, metabolism (TCA, glycolysis, FA)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u0026ndash;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eNot shown\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003ePredicted high expression due to metabolic activity; parallels K5 or K4.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eDirect molecular interactions with KHDRBS1 (KH domain-containing, RNA-binding, signal transduction-associated protein 1) and SYNJ1 (Synaptojanin 1) with the highest probability\u003c/b\u003e \u003c/p\u003e \u003cp\u003eThe IntAct molecular interaction database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ebi.ac.uk/intact\u003c/span\u003e\u003cspan address=\"https://www.ebi.ac.uk/intact\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) is a curated resource of molecular interactions, derived from the scientific literature and direct data depositions. IntAct curates\u0026rsquo; molecular interaction data derived from experimental studies published in scientific literature. The interacting partners of FNBP4 were determined to integrate it into a broader protein interaction network, thereby elucidating its functional context and the biological pathways it may be involved in. These are identified using methods involving purified components, excluding cell extracts or complex mixtures, to ensure no hidden intermediaries are present. Enzymatic reactions (e.g., phosphorylation) were also included in this category, provided purified participants were used, though they are depicted as specific reaction events. A higher MiS score indicates the level of confidence in predicting the specific interaction based on the standardised dataset with a higher number of experimental evidences in support of the claim (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eExperimentally Determined Interaction Partners of FNBP4 and Its Isoforms\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eS.\u003c/p\u003e \u003cp\u003eNo\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eInteractive partner (uniProt)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHost\u003c/p\u003e \u003cp\u003eOrganism\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eDetection Method\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eInteraction\u003c/p\u003e \u003cp\u003etype\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMi\u003c/p\u003e \u003cp\u003eScore\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003ePublication\u003c/p\u003e \u003cp\u003eId\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"7\" nameend=\"c7\" namest=\"c1\"\u003e \u003cp\u003eA. Q8N3X1 (homo sapiens species)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e1\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eKHDRBS1\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eQ07666\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eIn vitro\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003efilter binding\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003eDirect interaction\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.54\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e10748127\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e2\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003ePRPF40A\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eO75400\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eSaccharomyces\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003ecerevisiae (Baker's yeast)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003e2 hybrid\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003ePhysical association\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.55\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e15231748\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e3\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eH2BC21\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eQ16778\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eHomo sapiens U2OS\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eosteosarcoma cell\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003ecrosslink\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003ePhysical association\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.4\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e30021884\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e4\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eHTT\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eP42858\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eSaccharomyces\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003ecerevisiae (Baker's yeast)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003e2 hybrid\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003ePhysical association\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.37\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e17500595\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e5\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eHSCB\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eQ8IWL3\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eSaccharomyces\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003ecerevisiae (Baker's yeast)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003e2 hybrid\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003ePhysical association\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.37\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e24606901\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e6\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003ePLXNA2\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eO75051\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eSaccharomyces\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003ecerevisiae (Baker's yeast)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003e2 hybrid\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003ePhysical association\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.37\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e12421765\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"7\" nameend=\"c7\" namest=\"c1\"\u003e \u003cp\u003eB. Q8N3X1-1 (Isoform) (homo sapiens species)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e1\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eCSNK2A1\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eP68400\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eIn vitro\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003eprotein kinase assay\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003ePhysical association\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.44\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e22113938\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"7\" nameend=\"c7\" namest=\"c1\"\u003e \u003cp\u003eC. Q8N3X1-2 (Isoform) (homo sapiens species)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e1\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eDDX17\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eQ92841-4\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eHomo sapiens\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eHEK293T\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eembryonic kidney cell\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003eanti tag co ip\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003eassociation\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.35\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e28514442\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e2\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eZC3H18\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eQ86VM9\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eHomo sapiens\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eHEK293T\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eembryonic kidney cell\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003eanti tag co ip\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003eassociation\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.35\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e28514442\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"7\" nameend=\"c7\" namest=\"c1\"\u003e \u003cp\u003eD. Q6ZQ03 (Isoform) (with Mus musculus species)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e1\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eSYNJ1\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eO43426\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eIn vitro\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003ephage\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003edisplay\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003edirect interaction\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.56\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e11292345\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e2\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eCdk9\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eQ99J95\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eMus musculus\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003epull\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003edown\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003eassociation\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cb\u003e0.35\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e20593818\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e"},{"header":"DISCUSSION","content":"\u003cp\u003eCytoskeletal regulators are central drivers of cancer metastasis. Their dysregulation enhances cellular motility, invasiveness, and metastatic potential\u003csup\u003e26\u003c/sup\u003e. Among these regulators, formins and their binding partners play essential roles in actin remodelling. Although direct evidence on the role of FNBP4 in breast cancer remains limited, its Increasing interest stems from emerging proteomic data suggesting its involvement in both clinical aggressiveness and oncogenic signalling pathways.\u003c/p\u003e\n\u003cp\u003eProteomic analysis using CPTAC datasets demonstrates a consistent upregulation of FNBP4 in breast tumors compared with normal breast tissue. Stage-wise comparison reveals rising levels from stage II onward, indicating a link with tumor progression. Subtype-specific analysis highlights the highest FNBP4 expression in triple-negative breast cancer (TNBC), followed by luminal and HER2-positive subtypes, suggesting a stronger association with aggressive and therapy-refractory disease. Histological assessment shows substantial upregulation in infiltrating ductal carcinoma, while levels remain comparatively lower in infiltrating lobular carcinoma and mucinous variants.\u003c/p\u003e\n\u003cp\u003eSurvival analysis using Kaplan\u0026ndash;Meier Plotter reveals that high FNBP4 protein expression correlates with significantly poorer patient outcomes (HR = 2.86), positioning FNBP4 as a potential marker of increased mortality risk. Complementary data from the Human Protein Atlas indicate that FNBP4 predominantly localizes to the nucleoplasm and cytoplasm, implicating it in processes such as RNA metabolism, chromatin organization, and transcriptional regulation\u0026mdash;mechanisms frequently altered in cancer. Its dual localization suggests dynamic shuttling or context-dependent functions, which may be particularly relevant in rapidly evolving tumor environments such as TNBC, where cytoskeletal flexibility and transcriptional adaptability are essential for tumor plasticity and metastasis.\u003c/p\u003e\n\u003cp\u003eBeyond clinicopathological features, FNBP4 expression shows strong associations with oncogenic pathway alterations. Tumors with somatic changes in pathways such as RTK, WNT, PI3K/AKT/mTOR, MYC/MYCN, p53/Rb, and Hippo exhibit significantly elevated FNBP4 levels. This enrichment suggests that FNBP4 may act as a downstream effector or functional contributor within these pathways, propagating cancer-driving signals that promote cell proliferation, survival, and migration. The highest increases occur in tumors altered in NRF2, MYC/MYCN, RTK, and p53/Rb pathways, emphasising its integration into multiple cancer-relevant networks. Additionally, high copy number alteration (CNA) burden correlates with increased FNBP4 levels, particularly in contexts involving hormone receptor signalling, histone modification, and DNA repair, reinforcing its potential role in the cellular response to genomic instability.\u003c/p\u003e\n\u003cp\u003eUnsupervised clustering studies further support the variable involvement of FNBP4 across molecular tumor subtypes. Large-scale proteome-based analyses have defined multiple subtypes (K1\u0026ndash;K10 and S1\u0026ndash;S11)\u003csup\u003e27,28\u003c/sup\u003e, each representing distinct biological programs. FNBP4 expression peaks in subtype K4, characterized by basal-like features and activation of MYC and YAP1 pathways\u0026mdash;both powerful regulators of transcriptional amplification, cytoskeletal remodelling, and epithelial-mesenchymal transition (EMT)\u003csup\u003e29\u003c/sup\u003e. Moderately elevated levels appear in K2 and K5 subtypes associated with immune and metabolic signatures, respectively. Conversely, subtypes defined by innate immune activation or hypoxia show reduced expression, indicating subtype-specific functional relevance.\u003c/p\u003e\n\u003cp\u003eTo elucidate FNBP4\u0026rsquo;s mechanistic roles, protein\u0026ndash;protein interaction (PPI) mapping was performed using IntAct. The canonical FNBP4 isoform in humans shows eight experimentally validated interactions detected through methods such as two-hybrid assays, crosslinking, and filter binding. Several interactions exhibit moderate to high confidence with MI scores ranging from 0.35 to 0.55. Among these, KHDRBS1 (Sam68) emerges as a strong interactor (MI score 0.54), implicating FNBP4 in RNA splicing and transcriptional regulation. KHDRBS1 regulates alternative splicing events that influence cell adhesion, migration, and apoptosis, often promoting tumor progression\u003csup\u003e30,31,32\u0026nbsp;\u003c/sup\u003eIsoform-specific interactions include CSNK2A1 (CK2\u0026alpha;) for isoform Q8N3X1-1, identified through kinase assays, suggesting post-translational modulation of FNBP4 by phosphorylation. CSNK2 (CK2) is a well-known oncogenic kinase that drives survival signalling, cytoskeletal reorganization, and adaptation to stress\u003csup\u003e33,34,35\u0026nbsp;\u003c/sup\u003eIsoform Q8N3X1-2 interacts with DDX17and ZC3H18, both involved in RNA helicase activity and transcriptional regulation\u003csup\u003e36,37\u003c/sup\u003e. In murine models, the Q6ZQ03 isoform interacts strongly with SYNJ1 and moderately with CDK9, linking FNBP4 to vesicle trafficking and cell-cycle control. SYNJ1 contributes to altered membrane trafficking and receptor recycling, facilitating enhanced motility and invasive capacity \u003csup\u003e38,39,40,41.\u0026nbsp;\u003c/sup\u003eEvidently, all these interactors themselves play established roles in breast cancer. Through these interactions, FNBP4 may serve as a scaffold that integrates pathways involving RNA metabolism, cytoskeletal restructuring, and vesicular dynamics-functions that collectively support tumor aggressiveness. Cross-species conservation and high-confidence interactions further underscore the biological significance of FNBP4 in breast cancer progression\u003c/p\u003e"},{"header":"CONCLUDING REMARKS","content":"\u003cp\u003eThe use of large-scale proteomic datasets offers a valuable, systems-level perspective, facilitating the identification of clinically relevant targets. The availability of global cancer databases has significantly enhanced the understanding of tumorigenesis. This study leverages multiple proteomic and clinical datasets to comprehensively examine FNBP4’s role in breast cancer, revealing its potential impact on disease progression and clinical outcomes. Protein-level database analysis is crucial for biomarker discovery and validating targets because it reflects dynamic cellular states and biological function Moving forward, rigorous experimental validation through \u003cem\u003ein-vitro\u003c/em\u003e and \u003cem\u003ein-vivo\u003c/em\u003e models is essential to confirm these associations, decipher the underlying molecular mechanisms, and translate these bioinformatic insights into clinical applications for breast cancer management.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eRS: Substantial contributions to the conception, design of work; acquisition, analysis, interpretation of data, drafting KK: review, formattingKD: review, formattingMK: critical reviewing, formattingST: Drafting the work, critical reviewing, formattingSM: intellectual inputs, interpretation of dataHC: conception, design of the work, interpretation of data, Supervision, Final approval of the version to be published\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eThe authors acknowledge the publicly available proteomics and bioinformatics resources provided by CPTAC, UALCAN, the Human Protein Atlas, KM Plotter, and the IntAct database, which made this analysis possible.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eChesarone MA, DuPage AG, Goode BL. 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Oncogene 43: 202-215, 2024. \u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"journal-of-proteins-and-proteomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"Learn more about [Journal of Proteins and Proteomics](https://www.springer.com/journal/42485)","snPcode":"42485","submissionUrl":"https://submission.nature.com/new-submission/42485/3","title":"Journal of Proteins and Proteomics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"FNBP4, Formin Binding proteins, Formins, Cytoskeletal Regulation, Cancer Informatics, Breast cancer","lastPublishedDoi":"10.21203/rs.3.rs-9039049/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9039049/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eFormin Binding Protein 4 (FNBP4) is a cytoskeletal regulator implicated in actin dynamics, cell migration, and metastasis; however, its prognostic relevance in breast cancer remains poorly defined. This study employed a proteomics-based informatics approach to evaluate the clinical significance of FNBP4 at the protein level and to assess its potential as a prognostic biomarker and therapeutic target. Protein expression patterns of FNBP4 across breast cancer subtypes were analysed using CPTAC, UALCAN, and the Human Protein Atlas (HPA), while survival associations linked to differential protein expression were examined using KM Plotter. Protein\u0026ndash;protein interaction networks were constructed using the IntAct database to identify functional partners and elucidate potential mechanistic pathways. FNBP4 was found to exhibit a structurally stable protein conformation with dual cytoplasmic and nuclear localization and moderate nuclear expression in breast cancer tissues. Elevated FNBP4 protein expression was significantly associated with poor overall survival and was particularly enriched in invasive ductal carcinoma and triple-negative breast cancer subtypes. Increased FNBP4 levels correlated with somatic alterations across major oncogenic signalling pathways. Interaction network analysis revealed strong predicted associations with KHDRBS1, SYNJ1, and CSNK2A1, suggesting involvement in RNA regulation, endocytic signalling, and kinase-mediated cellular control. Collectively, these findings identify FNBP4 as a prognostically relevant cytoskeletal protein in breast cancer and provide a strong rationale for its further experimental validation and exploration as a therapeutic target.\u003c/p\u003e","manuscriptTitle":"Proteomic-based informatics highlights FNBP4 as a prognostically relevant cytoskeletal protein in Breast Cancer","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-05-18 09:11:28","doi":"10.21203/rs.3.rs-9039049/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2026-05-08T04:29:54+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"21972551357875240084320890659321393032","date":"2026-05-08T03:46:01+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-05-07T14:51:59+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-07T12:26:45+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-07T12:26:30+00:00","index":"","fulltext":""},{"type":"submitted","content":"Journal of Proteins and Proteomics","date":"2026-03-05T10:13:16+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"journal-of-proteins-and-proteomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"Learn more about [Journal of Proteins and Proteomics](https://www.springer.com/journal/42485)","snPcode":"42485","submissionUrl":"https://submission.nature.com/new-submission/42485/3","title":"Journal of Proteins and Proteomics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"f7f187b6-35d1-4c5d-979c-e75fcb6b741a","owner":[],"postedDate":"May 18th, 2026","published":true,"recentEditorialEvents":[{"type":"editorInvitedReview","content":"","date":"2026-05-08T04:29:54+00:00","index":10,"fulltext":""},{"type":"reviewerAgreed","content":"21972551357875240084320890659321393032","date":"2026-05-08T03:46:01+00:00","index":9,"fulltext":""},{"type":"reviewersInvited","content":"3","date":"2026-05-07T14:51:59+00:00","index":"","fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-18T09:11:28+00:00","versionOfRecord":[],"versionCreatedAt":"2026-05-18 09:11:28","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9039049","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9039049","identity":"rs-9039049","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}