Deconvolution of heterogeneous wound tissue samples into relative macrophage phenotype compositionviamodels based on gene expression

Abstract

Macrophages, the primary cell of the innate immune system, act on a spectrum of phenotypes that correspond to diverse functions. Dysregulation of macrophage phenotype is associated with many diseases. In particular, defective transition from pro-inflammatory (M1) to anti-inflammatory (M2) behavior has been implicated as a potential source of sustained inflammation that prevents healing of chronic wounds such as diabetic ulcers. In order to design effective treatments, an understanding of the relative presence of macrophage phenotypes during tissue repair is necessary. Inferring the relative phenotype composition is currently challenging due to the heterogeneous nature of the macrophages themselves and also of tissue samples. We propose here a method to deconvolute gene expression from heterogeneous tissue samples into the composition of two primary macrophage phenotypes (M1 and M2). Our final method uses gene expression signatures for each phenotype cultivated in vitro as input to a predictive model that infers sample composition with an average error of 0.16, and whose predictions fit known compositions prepared in vitro with an R2 value of 0.90. Finally, we apply this model to describe macrophage behavior in human diabetic ulcer healing using clinically isolated ulcer tissue samples. The model predicted that non-healing diabetic ulcers contained higher proportions of M1 macrophages compared to healing diabetic ulcers, in agreement with numerous studies that have implicated a dysfunctional M1-to-M2 transition in the impaired healing of diabetic ulcers. These results show proof of concept that the model holds utility in making predictions regarding macrophage behavior in heterogeneous samples, with potential application as a wound healing diagnostic.

Ovarian cancer stem cells and macrophages reciprocally interact through the WNT pathway to promote pro-tumoral and malignant phenotypes in 3D engineered microenvironments

“…In our experiments, we found that macrophage-specific inhibition of WNT secretion resulted in a significant reduction in ALDH + enrichment in hetero-spheroids, implying that WNT signaling was likely involved bi-directionally in CSC/macrophage interactions. The lone WNT ligand we found significantly upregulated in M2-like macrophages (compared to monocytes or M0 macrophages) was WNT5B , in line with transcriptomic and gene expression analyses performed on human M2 macrophages by other groups [41, 42]. Interestingly, macrophage WNT5B knockdown resulted in the loss of ALDH + enrichment in the CSC compartment of hetero-spheroids, with an associated loss of IL-6 secretion.…”

Modulating macrophage activities to promote endogenous bone regeneration: Biological mechanisms and engineering approaches

“…Second, macrophages are highly plastic, and their phenotypic change may lead to entirely different immune responses against the implants. Third, recent studies are increasingly uncovering the essential, underestimated roles of macrophages (and their precursor, monocytes) in tissue regeneration and particularly bone development and repair [ 16 , 17 ]. They can not only eliminate debris and regulate bone resorption but, more importantly, act as a powerhouse to secrete an array of cytokines under dynamical control.…”

Human macrophage response to microbial supernatants from diabetic foot ulcers

“…In contrast, M2c macrophages clear apoptotic cell debris and secrete enzymes that remodel the extracellular matrix, while M2a macrophages produce growth factors that stimulate granulation tissue formation . Notably, a timely transition from M1 to M2a is essential for successful wound healing, and dysregulation of macrophage activation is associated with chronic wounds . The timing of M2c activation has not been well characterized, but studies suggest that this phenotype acts at early stages of wound healing …”

“…8 Notably, a timely transition from M1 to M2a is essential for successful wound healing, and dysregulation of macrophage activation is associated with chronic wounds. [9][10][11][12][13] The timing of M2c activation has not been well characterized, but studies suggest that this phenotype acts at early stages of wound healing. 7 One potential mechanism behind dysfunctional macrophage behavior in DFUs is the interaction of macrophages with the colonizing microbiota.…”