CIPHER-seq Breakthrough Reveals Real-Time "Crosstalk" of Immune Cells During Treatment

New CIPHER-seq technology from the University of Miami reveals how immune cells talk in real-time by measuring RNA and proteins together for better cancer therapy.

By: AXL Media

Published: Apr 8, 2026, 11:06 AM EDT

Source: Information for this report was sourced from University of Miami Miller School of Medicine

Bridging the Instruction-to-Action Gap in Cancer Immunology

Single-cell RNA sequencing has long been the gold standard for understanding cellular intent, yet it often fails to account for functional reality. In the complex theater of the immune system, RNA acts as a set of instructions, but proteins are the molecules that execute those commands. Researchers at the University of Miami Miller School of Medicine have identified a significant "blind spot": RNA levels for cytokines often do not correlate with the amount of protein actually produced. CIPHER-seq (Cytokine Intracellular Protein High-throughput Expression with RNA sequencing) was developed specifically to bridge this gap, allowing scientists to see not just where a cell is "headed," but where it has actually arrived.

The Four-Layer Snapshot: A New Standard for Multimodal Profiling

Unlike traditional methods that capture a single layer of data, CIPHER-seq provides a comprehensive, four-dimensional snapshot from a single immune cell. The technology concurrently captures:

Transcriptome Data: Genomic RNA across the entire genome.

Surface Markers: Proteins located on the cell exterior.