AST: Adherent-to-Suspension Transcriptomics

A TUCCA computational project using time-series transcriptomics to dissect the adherent-to-suspension transition (AST): how cells adapt from anchored to free-floating growth, a key bottleneck for scaling cultivated meat. The work used the chicken (Gallus gallus) embryonic fibroblast line DF-1, comparing adherent DF-1 against a suspension-adapted derivative.

The challenge

Scaling cultivated meat means growing large quantities of cells efficiently. Many research cell lines grow attached to a surface (adherent), which caps the cell yield at the available surface area: scaling up means more flasks or microcarriers, and that gets expensive and labour-intensive fast. Cells grown floating in suspension instead fill the whole volume of a stirred-tank bioreactor, the same equipment industrial fermentation already runs at scale, so production scales with tank volume rather than surface area. That volumetric scale-up is what brings cultivated-meat cost targets within reach, so industrial production favours suspension cells. The adherent-to-suspension transition is a hard biological process, though, and engineering it requires understanding the transcriptomic changes that let cells survive and grow without attachment.

The computational approach

Time-series bulk RNA sequencing captured the transcriptional dynamics at five stages of adaptation (n = 4 per timepoint). An early development version of tucca-rna-seq served as the analytical engine: quality control (FastQC, Qualimap), alignment (STAR), quantification (Salmon), aggregation (MultiQC), differential expression (DESeq2), and functional enrichment (clusterProfiler ORA/GSEA). These fed custom downstream analyses including time-series soft clustering (Mfuzz).

Key findings

• An acute, transient stress response at the point of transition (autophagy, MAPK signaling up; DNA replication down).
• Permanent reprogramming of suspension-adapted cells: suppressed metabolism and a committed, anchorage-independent adhesion profile.
• A proposed molecular mechanism for suspension proficiency: oxidative stress → MAPK p38δ → TEAD sequestration → a YAP–FoxO1 complex driving antioxidant production and adhesion-gene downregulation.

Data

NCBI BioProject PRJNA1331774 Raw RNA-seq reads (Gallus gallus, DF-1 cell line) for the adherent-to-suspension time series.

Read the paper

Comparative transcriptomics of adherent and suspension chicken fibroblast cell lines for the optimization of cultivated meat processes Contreras, Nagarajan, Bromberg, Villegas & Kaplan (2026), Food Research International. Full study writeup, findings, and links.