Deep Quantitative Proteomics Reveals Extensive Metabolic Reprogramming and Cancer-Like Changes of Ectopic Endometriotic Stromal Cells

Endometriosis is a prevalent health condition in women of reproductive age characterized by ectopic growth of endometrial-like tissue in the extrauterine environment. Thorough understanding of the molecular mechanisms underlying the disease is still incomplete. We dissected eutopic and ectopic endometrial primary stromal cell proteomes to a depth of nearly 6900 proteins using quantitative mass spectrometry with a spike-in SILAC standard. Acquired data revealed metabolic reprogramming of ectopic stromal cells with extensive upregulation of glycolysis and downregulation of oxidative respiration, a widespread metabolic phenotype known as the Warburg effect and previously described in many cancers. These changes in metabolism are additionally accompanied by attenuated aerobic respiration of ectopic endometrial stromal cells as measured by live-cell oximetry and by altered mRNA levels of respective enzyme complexes. Our results additionally highlight other molecular changes of ectopic endometriotic stromal cells indicating reduced apoptotic potential, increased cellular invasiveness and adhesiveness, and altered immune function. Altogether, these comprehensive proteomics data refine the current understanding of endometriosis pathogenesis and present new avenues for therapies

DataSheet1_Evolving a mitigation of the stress response pathway to change the basic chemistry of life.pdf

Despite billions of years of evolution, there have been only minor changes in the number and types of proteinogenic amino acids and the standard genetic code with codon assignments across the three domains of life. The rigidity of the genetic code sets it apart from other aspects of organismal evolution, giving rise to key questions about its origins and the constraints it places on innovation in translation. Through adaptive laboratory evolution (ALE) in Escherichia coli, we aimed to replace tryptophan (Trp) in the genetic code with an analogue L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa). This required Escherichia coli to recruit thienopyrrole instead of indole and allowed reassignment of UGG codons. Crossing the stress response system emerged as a major obstacle for ancestral growth in the presence of [3,2]Tp and Trp limitation. During ALE, a pivotal innovation was the deactivation of the master regulon RpoS, which allowed growth solely in the presence of [3,2]Tp in minimal medium. Notably, knocking out the rpoS gene in the ancestral strain also facilitated growth on [3,2]Tp. Our findings suggest that regulatory constraints, not just a rigid translation mechanism, guard Life’s canonical amino acid repertoire. This knowledge will not only facilitate the design of more effective synthetic amino acid incorporation systems but may also shed light on a general biological mechanism trapping organismal configurations in a status quo.</p