Loh, D. | bioRxiv Science

bioRxiv2026

Multiaxial Biophysical Control of Oncogenic Phase Separation by Indoleamines: A Proof-of-Concept Synthesis of Landscape-Level Regulation

ABSTRACTO_ST_ABSBackgroundC_ST_ABSPhase-separated oncogenic condensates act as biophysical sanctuaries, stabilizing transcriptional and survival programs to drive cancer progression. While individual proteins within these assemblies are well-documented, a universal regulator capable of orchestrating the integrated biophysical axes governing cellular phase behavior has remained elusive. We propose a paradigm of landscape-level regulation mediated by the indoleamine scaffold. MethodsA systematic synthesis and integrative bioinformatics analysis were performed to identify the intersection between melatonin-responsive genes and the phase-separation proteome. A gene set of 121 phase separation-related molecules was validated via PhaSepDB and intersected with 134 melatonin-modulated genes identified across diverse cancer models. Clinical relevance was assessed using TCGA survival datasets. ResultsWe identified a conserved network of 26 core genes--including AR, BCL2, CGAS, CTNNB1, EP300, EZH2, EGFR, IKBKG (NEMO), KEAP1, KDM1A (LSD1), LEF1, MYC, NANOG, PRNP, SMAD3, SOX9, SQSTM1, TFEB, TFAM, TP53, TWIST1, USP10, WWTR1 (TAZ), VIM, YAP1, and YTHDF3--at the intersection of melatonin signaling and PS architecture. Network analysis revealed high-confidence interactions predominantly localized to the nucleoplasm and stress granules. Melatonin significantly suppressed the majority of these oncogenic drivers, targeting pathways associated with EMT, glycolysis, and hypoxia. Furthermore, higher expression of this melatonin-responsive phase separation-network correlated with poorer overall survival in breast and gastric cancers. ConclusionsThis proof-of-concept synthesis positions melatonin as a remarkably versatile regulator of phase-separated oncogenic networks, capable of simultaneously modulating the integrated biophysical axes that govern cellular phase behavior. We propose that melatonin utilizes a tri-lever framework--comprising redox switching, structural intercalation, and dielectric tuning--to recalibrate the cellular solvation and fluidity landscape. By enforcing fundamental physicochemical constraints rather than targeting discrete signaling nodes, melatonin destabilizes the biophysical sanctuaries that shield oncogenic programs. This landscape-level regulation offers a strategic platform for disrupting condensate-driven malignancy, providing a biophysical logic that circumvents the diverse evasion mechanisms of the malignant cell.

cancer biology↗

bioRxiv2020

Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator

Coupling recent advancements in genetic engineering of diverse microbes and gas-driven fermentation provides a path towards sustainable commodity chemical production. Cupriavidus necator H16 is a suitable species for this task because it effectively utilizes H2 and CO2 and is genetically tractable. Here, we demonstrate the versatility of C. necator for chemical production by engineering it to produce three products from CO2 under lithotrophic conditions: sucrose, polyhydroxyalkanoates (PHAs), and lipochitooligosaccharides (LCOs). We engineered sucrose production in a co-culture system with heterotrophic growth 30 times that of WT C. necator. We engineered PHA production (20-60% DCW) and selectively altered product composition by combining different thioesterases and phaCs to produce copolymers directly from CO2. And, we engineered C. necator to convert CO2 into the LCO, a plant growth enhancer, with titers of [~]1.4 mg/L--equivalent to yields in its native source, Bradyrhizobium. We applied the LCOs to germinating seeds as well as corn plants and observed increases in a variety of growth parameters. Taken together, these results expand our understanding f how a gas-utilizing bacteria can promote sustainable production.

synthetic biology↗

bioRxiv2018

Electrospray sample injection for single-particle imaging with X-ray lasers

The possibility of imaging single proteins constitutes an exciting challenge for X-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available X-ray lasers and, as we demonstrate here, contamination of the aerosolised molecules by non-volatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet-size during aerosolisation. Here we show that with our electrospray injector we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next generation X-ray lasers, constitute an important stepping stone towards the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.

biophysics↗