Knockdown of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection
4 affiliations
- 1IISc Mathematics Initiative, Indian Institute of Science, Bangalore, India
- 2Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- 3Department of Biochemistry, Indian Institute of Science, Bangalore, India
- 4Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
Abstract
Macrophages are driven to form distinct functional phenotypes in response to different immunological stimuli, in a process widely referred to as macrophage polarization. Transcriptional regulators that guide macrophage polarization in response to a given trigger remain largely unknown. In this study, we interrogate the programmable landscape in macrophages to find regulatory panels that determine the precise polarization state that a macrophage is driven to. Toward this, we configure an integrative network analysis pipeline that utilizes macrophage transcriptomes in response to 28 distinct stimuli, reconstructs contextualized human gene regulatory networks, and identifies epicenters of perturbations in each case. We find that these contextualized regulatory networks form a spectrum of 13 distinct clusters, with M1 and M2 at the two ends. Using our computational pipeline, we identify combinatorial panels of epicentric regulatory factors (RFs) for each polarization state. We demonstrate that a set of three RFs, that is, CEBPB, NFE2L2, and BCL3, is sufficient to change the polarization destination from M1 to M2. siRNA knockdown of the 3-RF-set in THP1-derived M0 cells, despite exposure to an M1 stimulant, significantly attenuated the shift to M1 phenotype and instead increased the expression of M2 markers. Single knockdown of each RF also showed a similar trend. The siRNA-mediated knockdown of the 3-RF-set rendered the macrophages hyper-susceptible to Staphylococcus aureus infection, demonstrating the importance of these factors in modulating immune responses. Overall, our results provide insights into the transcriptional mechanisms underlying macrophage polarization and identify key RFs that may be targeted to modulate immune responses.
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BibTeX
@article{ravichandran2026knockdown,
title = {{Knockdown of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection}},
author = {Sathyabaarathi Ravichandran and Bharath Bhatt and Awantika Shah and Debajyoti Das and Kithiganahalli Narayanaswamy Balaji and Nagasuma Chandra},
journal = {eLife},
year = {2026},
month = nov,
doi = {10.7554/elife.91547},
url = {https://elifesciences.org/articles/91547},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Knockdown of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection
AU - Sathyabaarathi Ravichandran
AU - Bharath Bhatt
AU - Awantika Shah
AU - Debajyoti Das
AU - Kithiganahalli Narayanaswamy Balaji
AU - Nagasuma Chandra
PY - 2026
DA - 2026/11/02
JO - eLife
DO - 10.7554/elife.91547
UR - https://elifesciences.org/articles/91547
AB - Macrophages are driven to form distinct functional phenotypes in response to different immunological stimuli, in a process widely referred to as macrophage polarization. Transcriptional regulators that guide macrophage polarization in response to a given trigger remain largely unknown. In this study, we interrogate the programmable landscape in macrophages to find regulatory panels that determine the precise polarization state that a macrophage is driven to. Toward this, we configure an integrative network analysis pipeline that utilizes macrophage transcriptomes in response to 28 distinct stimuli, reconstructs contextualized human gene regulatory networks, and identifies epicenters of perturbations in each case. We find that these contextualized regulatory networks form a spectrum of 13 distinct clusters, with M1 and M2 at the two ends. Using our computational pipeline, we identify combinatorial panels of epicentric regulatory factors (RFs) for each polarization state. We demonstrate that a set of three RFs, that is, CEBPB, NFE2L2, and BCL3, is sufficient to change the polarization destination from M1 to M2. siRNA knockdown of the 3-RF-set in THP1-derived M0 cells, despite exposure to an M1 stimulant, significantly attenuated the shift to M1 phenotype and instead increased the expression of M2 markers. Single knockdown of each RF also showed a similar trend. The siRNA-mediated knockdown of the 3-RF-set rendered the macrophages hyper-susceptible to Staphylococcus aureus infection, demonstrating the importance of these factors in modulating immune responses. Overall, our results provide insights into the transcriptional mechanisms underlying macrophage polarization and identify key RFs that may be targeted to modulate immune responses.
SN - 2050-084X
ER -