Sapient Launches Tumor Protein Mapping Platform to Characterize Functional Biology Across Critical Dimensions in Human Tumors

Platform includes SurfaceSeek™ to identify druggable tumor cell surface proteins, SignalingSeek™ to measure signaling pathway activation, and ImmuneSeek™ and ResistanceSeek to map immune and resistance biology – directly in fresh-frozen and FFPE human tumors

Sapient, a leader in multi-omics data generation for biomarker discovery and clinical insight delivery, has announced the launch of its Tumor Protein Mapping Platform as a suite of mass spectrometry-based discovery proteomics workflows designed to map functional tumor biology across four critical dimensions: the druggable cell surface proteome, phosphorylation-driven signaling pathways, the tumor immune microenvironment, and therapeutic resistance mechanisms. The platform is now available to biopharma sponsors and comprises four purpose-built workflows – SurfaceSeek™, SignalingSeek™, ImmuneSeek™, and ResistanceSeek™ – each optimized for both fresh-frozen and FFPE human tumor samples.

Central to the platform is SurfaceSeek, which directly measures proteins that are functionally deployed on the tumor cell surface to enable confident identification and validation of druggable targets for ADC, T-cell engager, and radioligand therapies. The workflow combines Sapient’s mass spectrometry-based discovery proteomics with selective enrichment of mature N-linked glycoproteins to preferentially identify proteins that have completed intracellular trafficking and are exposed on the extracellular surface. This enables direct characterization of surface target accessibility, density, and tumor selectivity, and brings peptide-level resolution to identify protein isoforms and post-translationally modified proteoforms bearing extracellular domains compatible with therapeutic binding.

The platform's additional workflows complement and extend SurfaceSeek findings by mapping functional tumor biology that determines therapeutic outcome. SignalingSeek quantifies tumor signaling pathway activation via the measurement of phosphorylation events across critical oncogenic pathways, enabling direct assessment of on-target pathway modulation as well as identification of adaptive signaling and resistance pathways. ImmuneSeek measures functionally active tumor immune cells and the immune pathways that are driving therapeutic response, immune evasion, or suppression, while ResistanceSeek identifies the coordinated protein networks through which tumors adapt to therapeutic pressure across modalities.

"Building upon our next-generation FFPE Proteomics offering, we have developed specialized workflows that enable precise, multi-dimensional characterization of tumor biology at the protein level – and directly in human tumor tissue," said Jeramie Watrous, PhD, Co-Founder and Head of Analytical R&D at Sapient. "The key technical innovation is that these workflows – including SurfaceSeek's selective glycoprotein enrichment and SignalingSeek's deep phosphoproteomics – perform with exceptional concordance in both fresh-frozen and FFPE samples. This means we can apply them retrospectively to the vast biorepositories of archived tissue already collected, unlocking dimensions of functional tumor biology that were previously inaccessible in these samples."

"Tumors are not defined by a single biological dimension. They are complex and changing systems where surface target accessibility, signaling pathway activation, immune function, and resistance mechanisms all interact to determine therapeutic outcome," said Mo Jain, MD, PhD, Founder and Chief Scientific Officer at Sapient. "By mapping each of these dimensions directly at the protein level, we give drug development teams a comprehensive, unified view of what is actually governing drug response – moving oncology development beyond genomic inference alone, adding new layers of insight derived from the direct measurement of dynamic human tumor biology."

"This platform was shaped by many conversations with oncology leaders where we kept hearing the same thing: they were navigating some of the highest-stakes decisions in drug development, such as which targets to pursue, without the ability to directly measure those targets or the mechanisms that influence therapeutic outcome,” added Jonathan Usuka, PhD, MBA, Chief Executive Officer at Sapient. “We designed the workflows to interrogate key dimensions of tumor biology that determine whether a drug will succeed, so our clients can advance their programs with direct evidence rather than inference."

All four workflows are available as standalone services or can be delivered in combination to provide integrated, multi-dimensional tumor characterization, and may be supported by Sapient's DynamiQ™ Tumor-Tissue virtual biobank which offers streamlined access to annotated FFPE tumors and tissues.