CIPHER-seq Maps RNA-to-Protein Timing in Single Immune Cells

Linking gene activity to actual protein output gives a truer read on immune signals with potential to guide immunotherapy research.

Overview

CIPHER-seq, which researchers published Wednesday in Scientific Reports, enables simultaneous RNA and protein readouts from the same immune cell.
The platform measures genome-wide RNA, surface proteins, intracellular proteins, and cytokines still trapped inside the cell for a fuller snapshot of activity.
In stimulated blood immune cells, it captured strong interferon-gamma and tumor necrosis factor signals and showed RNA rising before protein during activation.
Compared with standard single-cell workflows, the method produced far fewer mitochondrial stress signatures, indicating gentler handling and cleaner data.
The team positions this as a research tool for cancer, inflammation, and treatment-resistance studies with possible use in therapy design and patient prediction, though it has not been tested in clinical cohorts.