Humphries, E. M. | Search bioRxiv

bioRxiv2026

An organ-resolved rat FFPE phosphoproteome map enables directional kinase activity inference

Formalin-fixed paraffin-embedded (FFPE) tissue is the dominant clinical pathology resource yet whether it faithfully preserves organ signalling biology and supports directional regulatory analysis remains unquantified. We generated a phosphoproteome map from eight healthy rat organs, separating preservation effects from biological variation. Using mass spectrometry, we quantified 54,710 phosphosites on 5,994 proteins across receptors, kinase cascades and nuclear regulators. Organ-specific phosphosite signatures matched known physiological and proliferative states. Paired antagonistic phosphosites converted into "activating-minus-inhibitory" indices that quantified net tissue-specific pathway activity, while a "kinase-by-organ activity" matrix resolved functional hierarchies. Joint analysis with an external fresh-frozen phosphoproteome dataset yielded 58,631 phosphosites total, recovering 86% of the 28,888 sites detected in the frozen dataset. Organ identity explained over 92% of the total variance after batch correction, versus under 0.5% for preservation method. Per-organ phosphosite intensities agreed closely between preservation modes except in brain. This establishes that archived pathology tissue supports biologically faithful phosphoproteome analysis at organ, pathway, and site resolution, providing a framework for retrospective signalling studies in clinical archives. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/741173v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@191c1a2org.highwire.dtl.DTLVardef@3f8d21org.highwire.dtl.DTLVardef@4a8525org.highwire.dtl.DTLVardef@6b4b91_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a secure cloud-based environment where research and education communities can analyze genomic and biomedical data. The platform supports a wide range of data analysis as well as the ability to safely store and access data in compliance with NIH policies. Work on the AnVIL platform can be easily shared to promote reproducible science and collaboration. The purpose of this study is to better understand the current user base of the AnVIL platform. The AnVIL Community Poll aimed to collect baseline information, identify development opportunities, guide the prioritization of user support strategies, and succinctly but comprehensively describe the current AnVIL Community. The AnVIL Team disseminated the inaugural AnVIL Community Poll by sharing it broadly on social media and through AnVIL and related consortia mailing lists. We categorized respondents as either returning or potential users of the AnVIL platform (based on their provided usage description) and examined user experiences: specifically user backgrounds, technological comfort, research interests, computational needs, and preferences for training and support. Our sample of the AnVIL community found opportunities for platform adoption beyond the current user base and identified areas where training should be enhanced, training preferences, and user computational needs. Specifically, while most respondents were involved in human genomics research, there may be potential for growth in adoption of the platform by prioritizing materials to support clinical researchers. All respondents felt availability of specific tools or datasets was a key feature of the platform. The broader community may also benefit from further development or showcasing of resources to facilitate cost management, finding and incorporating analysis tools, and data import. Our sample greatly preferred virtual training opportunities and returning users of the platform foresaw needing large amounts of storage. This poll provided an insightful snapshot of the current state of the AnVIL and demonstrated areas where the AnVIL Team can take specific steps to address barriers related to platform adoption and further support the existing and varied AnVIL Community. This work can be built upon through user interviews, community discussion, and coordinating a recurring poll.

scientific communication and education↗