Publications

2026

1. 

   A Multi-Cohort Study of Immunoglobulin G Glycans in Newly Diagnosed Inflammatory Bowel Disease Patients Reveals Accelerated Biological Aging

   Konstantinos Flevaris, Irena Trbojević-Akmačić, David Goh, 16 more authors, and Cleo Kontoravdi

   medRxiv, Apr 2026

   Abs DOI Bib HTML

   People newly diagnosed with inflammatory bowel disease exhibit accelerated biological aging as quantified by the GlycanAge index alongside reduced IgG galactosylation. Machine learning models achieved robust discrimination between non-IBD and IBD groups across multiple cohorts, supporting IgG glycans as potential clinical biomarkers for inflammatory bowel disease.

   @article{flevaris2026glycan,
     title = {A Multi-Cohort Study of Immunoglobulin {G} Glycans in Newly Diagnosed Inflammatory Bowel Disease Patients Reveals Accelerated Biological Aging},
     author = {Flevaris, Konstantinos and Trbojevi{\'c}-Akma{\v{c}}i{\'c}, Irena and Goh, David and Lalli, Juproop Singh and Vu{\v{c}}kovi{\'c}, Frano and {\'C}apin Vilaj, Marija and {\v{S}}tambuk, Jerko and Kri{\v{s}}ti{\'c}, Jasminka and Mijakovac, Anika and Ventham, Nick and Kalla, Rahul and Latiano, Anna and Manetti, Natalia and Li, Dalin and McGovern, Dermot P.B. and Kennedy, Nicholas A. and Annese, Vito and Lauc, Gordan and Satsangi, Jack and Kontoravdi, Cleo},
     journal = {medRxiv},
     year = {2026},
     month = apr,
     doi = {10.64898/2026.04.10.26349930},
   }

2. 

   Interplay between the immune response and the adaptation of metabolic pathways upon infection

   Andriy Goychuk, David Goh, Sergio Eraso, Ruslan Medzhitov, and Arup K. Chakraborty

   bioRxiv, Jan 2026

   Abs DOI Bib HTML

   Glucose is the principal metabolic fuel for the energy needs of most cell types. Upon infection, cytokines secreted by the immune system regulate redistribution of glucose to meet new metabolic needs associated with clearing the pathogen. We develop a mathematical model to describe the dynamics of such adaptation of metabolic pathways mediated by the immune response and its impact on the ability to clear pathogen and restore health. We find that cytokine-regulated redistribution of glucose resources in different tissues is critical for an effective immune response to pathogen as strictly clamping plasma glucose levels to homeostatic levels results in an ineffective immune response. By studying the effects of various parameters in our model, we describe how aberrant regulation of adaptation mechanisms affect outcomes of infection. Too high a glucose consumption rate by innate immune cells to mediate functions results in failure to clear pathogen. Pathogens with a very high replication rate can be controlled to low levels, but at a very high metabolic cost. Too low a pathogen replication rate allows the pathogen to hide from the immune system and rebound to high levels at later times. Finally, the strength of the innate immune response must be regulated to not be too high, not only to limit immunopathogenesis, but also for mediating an effective adaptive immune response.

   @article{goychuk2026immune,
     title = {Interplay between the immune response and the adaptation of metabolic pathways upon infection},
     author = {Goychuk, Andriy and Goh, David and Eraso, Sergio and Medzhitov, Ruslan and Chakraborty, Arup K.},
     journal = {bioRxiv},
     year = {2026},
     month = jan,
     doi = {10.64898/2026.01.02.697260},
   }

2025

1. 

   RNA gradients can guide condensates toward promoters: Implications for enhancer-promoter contacts and condensate-promoter kissing

   David Goh, Deepti Kannan, Pradeep Natarajan, Andriy Goychuk, and Arup K. Chakraborty

   The Journal of Chemical Physics, Sep 2025

   Abs DOI Bib HTML

   We study how protein condensates respond to a site of active RNA transcription (i.e., a gene promoter) due to electrostatic protein–RNA interactions. Our results indicate that condensates can show directed motion toward the promoter, driven by gradients in the RNA concentration. Analytical theory, consistent with simulations, predicts that the droplet velocity has a non-monotonic dependence on the distance to the promoter. We explore the consequences of this gradient-sensing mechanism for enhancer–promoter (E–P) communication using polymer simulations of the intervening chromatin chain. Directed motion of enhancer-bound condensates can, together with loop extrusion by cohesin, collaboratively increase the enhancer–promoter contact probability. Finally, we investigate under which conditions condensates can exhibit oscillations in their morphology and in the distance to the promoter. Oscillatory dynamics are caused by a delayed response of transcription to condensate-promoter contact and negative feedback from the accumulation of RNA at the promoter, which results in charge repulsion.

   @article{goh2025rna,
     title = {{RNA} gradients can guide condensates toward promoters: Implications for enhancer-promoter contacts and condensate-promoter kissing},
     author = {Goh, David and Kannan, Deepti and Natarajan, Pradeep and Goychuk, Andriy and Chakraborty, Arup K.},
     journal = {The Journal of Chemical Physics},
     volume = {163},
     number = {10},
     pages = {104905},
     year = {2025},
     month = sep,
     doi = {10.1063/5.0277838},
   }