Biology subjects

Khoury, C.

Publications and source records attributed to Khoury, C..

4 recordsLinked to original sources

bioRxiv2026

Paralogous lncRNAs CYTOR and MORRBID share a conserved trans acting function in MEK ERK signaling

Background: Long non-coding RNAs (lncRNAs) exhibit rapid evolutionary turnover, often driven by genomic duplication. How paralogous lncRNAs maintain, partition, or diverge in function across distinct genomic contexts remains poorly understood. The evolutionarily conserved lncRNA MORRBID and its primate-specific paralog CYTOR provide a natural framework to interrogate the functional consequences of lncRNA duplication. Results: Although CYTOR and MORRBID have acquired distinct transcript variants influenced by their divergent genomic environments, we demonstrate that they maintain a robust, shared core function encoded by near-identical dominant two-exon transcripts. Using SNP-based paralog-specific quantification, we found that CYTOR contributes more strongly to the shared transcript pool, while both transcripts localize predominantly to the cytoplasm, consistent with a shared trans-acting function. Simultaneous repression of CYTOR and MORRBID consistently impairs cell adhesion and migration across multiple cancer models. Mechanistically, the shared CYTOR/MORRBID transcript pool associates with MEK2 and sustains MEK-ERK signaling. This signaling axis promotes FOSL1 expression and AP-1-linked transcriptional output, including expression of the downstream effector EPHA4, whose role was supported by rescue experiments. Patient tumor transcriptomes and healthy single-cell datasets further supported the associated mesenchymal, adhesion, and epithelial-mesenchymal transition program. Conclusions: Our findings establish that paralogous lncRNAs can retain a conserved mechanistic core despite context-dependent transcriptional divergence. The CYTOR/MORRBID transcript pool defines a shared lncRNA signaling module that supports MAPK-ERK signaling and adhesion-migration programs across cancer and mesenchymal-like cellular contexts. This defines a unified mechanistic framework for the shared core function of these widely studied paralogous lncRNAs.

genetics↗

bioRxiv2022

No branch left behind: tracking terrestrial biodiversity from a phylogenetic completeness perspective

Biodiversity, as we see it today, ultimately is the outcome of millions of years of evolution; however, biodiversity in its multiple dimensions is changing rapidly due to increasing human domination of Earth. Here, we present the "phylogenetic completeness" (PC) a concept and methodology that intends to safeguard Earths evolutionary heritage by maintaining all branches of the tree of life. We performed a global evaluation of the PC approach using data from five major terrestrial clades and compared the results to an approach in which species are conserved or lost randomly. We demonstrate that under PC, for a given number of species extinctions, it is possible to maximize the protection of evolutionary innovations in every clade. The PC approach is flexible and can be used to conduct a phylogenetic audit of biodiversity under different conservation scenarios. The PC approach complements existing conservation efforts and is linked to the post-2020 Convention of Biodiversity targets.

ecology↗

bioRxiv2020

Specific breeding system and ploidy interactions increase niche adaptability in potatoes

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for sustainability. Niches of crop wild relatives, including wild potatoes (Solanum section Petota), have received attention, however, such information has not been analyzed in combination with phylogenetic histories, genomic composition and reproductive systems. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate niches inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche divergence through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.

ecology↗

bioRxiv2020

The hidden land use cost of widespread cover cropping

Cover cropping is considered a cornerstone practice in sustainable agriculture; however, little attention has been paid to the cover crop production supply chain. In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 3.8% (median 2.0%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.5% and 11.9%, respectively. The latter land requirement is comparable to the annual amount of maize grain lost to disease in the U.S. We highlight avenues for reducing these high land use costs.

ecology↗