Biology subjects

Abebayehu, D.

Publications and source records attributed to Abebayehu, D..

5 recordsLinked to original sources

bioRxiv2026

Microporous annealed particle scaffolds avoid foreign body response by down regulating complement-fibroblast-macrophage signaling loop

Biomaterial implantation can trigger a foreign body response (FBR) that impedes tissue-implant integration. To investigate how implant porosity influences this response, we compared the immune response to subcutaneous implants of microporous annealed particle (MAP) scaffolds and nanoporous hydrogels using mass cytometry, single-cell RNA sequencing, and multiplex cytokine assays. MAP scaffolds promoted vascularization and tissue integration, marked by increased endothelial and regulatory T cells, and reduced proinflammatory immune cells and cytokines. In contrast, nanoporous hydrogels demonstrated enrichment of basophils, natural killer cells, and macrophage populations associated with fibrosis. Transcriptomic and proteomic analyses revealed that MAP scaffolds suppressed activation of the complement-fibroblast-macrophage signaling loop, particularly the C5a signaling crosstalk pathway. This was confirmed using C5-deficient mice, where complement-driven cytokine production was significantly reduced only in nanoporous implants. These findings demonstrate that scaffold porosity modulates immune and complement responses, identifying a key mechanism by which MAP scaffolds reduce FBR and improve biomaterial integration.

bioengineering↗

bioRxiv2024

Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs

Dysregulation of the cellular mechanisms that coordinate the interpretation and transduction of microenvironmental biophysical signals are a unifying feature of tissue remodeling pathologies such as fibrosis and cancer. While genomic regulation downstream of normal mechanotransduction (i.e. cases where cells sense soft and stiff appropriately) is well studied, significantly less is known about the consequences of abnormal mechanoperception and subsequent misinterpretation of the mechanical environment. Leveraging Thy-1 (a.k.a. CD90) loss as a model of impaired mechanoperception, we employed ATAC- and RNA-sequencing in parallel to characterize the changes in lung fibroblast genomic activity in response to a combination of substrate stiffness and culture time. Notably, we find perturbed mechanoperception elicits a near-complete shutdown of HOXA5, a transcription factor responsible for pattern specification and development in the nascent lung. In vitro investigation of HOXA5 expression reveals a potential mechanism connecting increased v integrin signaling, cytoskeletal tension, and SRC kinase activity to HOXA5 silencing. These results establish novel links between integrin signaling and the expression dynamics of genes necessary for tissue formation and regeneration in the injured and/or developing lung, particularly HOXA5.

cell biology↗

bioRxiv2022

A unique Thy-1-negative immuno-fibroblast population emerges as a key determinant of fibrotic outcomes to biomaterials

Microporous annealed particle (MAP) hydrogels are an exciting new development in biomaterial design. They regulate innate and acquired immunity which has been linked to their ability to evade normal host-material fibrosis. Yet, resident stromal fibroblasts, not immune cells, are the arbiters of the extracellular matrix assembly that characterizes fibrosis. In other idiopathic fibrotic disorders, a fibroblast subpopulation defined by its loss of cell surface Thy-1 expression is strongly correlated with degree of fibrosis. We have previously shown that Thy-1 is a critical v{beta}3 integrin regulator that enables normal fibroblast mechanosensing and here, leveraging non-fibrosing MAP gels, we demonstrate that Thy-1-/- mice mount a robust response to MAP gels that remarkably resembles a classical foreign body response. We further find that within the naive, Thy-1+ fibroblast population exists a distinct and cryptic SMA+ Thy-1- population that emerges in response to IL-1{beta} and TNF. Employing single-cell RNA sequencing, we find that IL-1{beta}/TNF-induced Thy-1- fibroblasts actually consist of two distinct subpopulations, both of which are strongly pro-inflammatory. These findings illustrate the emergence of a unique pro-inflammatory, pro-fibrotic fibroblast subpopulation that is central to material-associated fibrosis likely through amplifying local inflammatory signaling. Significance StatementDespite decades of research, implanted biomaterials are still significantly hampered by the foreign body response and fibrotic encapsulation. Advancements in material design and immunomodulation have made positive impacts, yet, a fuller mechanistic understanding of aberrant ECM remodeling in the biomaterial microenvironment could improve approaches in biomaterial-host interactions. Here, we leverage anti-fibrotic MAP hydrogels and demonstrate that their ability to evade fibrosis is linked to fibroblast Thy-1 (CD90) surface expression. Thy-1-/- mice exhibit elevated NF{kappa}B signaling and elevated fibrosis in response to MAP gel implantation. Interestingly, pro-inflammatory cytokines elicit a Thy-1-/SMA+ myofibroblast subpopulation. Single-cell RNA-Seq more fully identifies an immunofibroblast subpopulation defined by Thy-1 loss and a pro-inflammatory/fibrotic cytokine, chemokine, and cytokine receptor expression profile, suggesting a self-perpetuating pro-fibrotic subpopulation.

bioengineering↗

bioRxiv2021

Myeloid-mediated IL-1R signaling in immuno-responsive Thy-1 negative fibroblasts is critical for pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a fatal disease with poorly defined pathogenic mechanism and no cure. It is characterized by chronic inflammation, myofibroblast accumulation, and aberrant extracellular matrix (ECM) remodeling. Fibrosis progression is considered to occur due to sustained aberrant fibroblast mechanotransduction: sensing "normal" soft tissue as stiff scarred tissue leading to the overproduction of ECM that then stiffens the microenvironment, thus reinforcing a progressive, stiffness-dependent fibrotic program. How chronic inflammation leads to aberrant mechanotransduction is not well understood. Thy-1 is a regulator of mechanotransduction in fibroblasts. Thy-1 expression is lost in fibroblastic foci, the active sites of fibrosis, although the mechanism of this loss is unknown. We demonstrate that in IPF tissue, the SMA+ fibroproliferative foci express the Type 1 IL-1 receptor (IL-1RI) and IL-1RI-deficient mice did not develop bleomycin-induced pulmonary fibrosis. Using ASC speck formation during inflammasome activation as a marker of mature IL-1{beta} release, we identified the immune compartment as the source of active IL-1{beta} during bleomycin-induced fibrosis. Furthermore, incubating mouse lung fibroblasts on soft (2kPa) hydrogels with IL-1{beta} was sufficient to reduce Thy-1 surface expression and induce v{beta}3 integrin activation. As expected, Thy-1 negative fibroblasts exhibited elevated v{beta}3 integrin activation but surprisingly, Thy-1 negative fibroblasts also expressed higher levels of IL-1RI, potentially linking the immuno-responsive and mechanosensitivity of this fibroblast subpopulation. Leveraging the non-resolving fibrosis that occurs in Thy-1-/- mice, we observed that crossing Thy-1-/- mice onto the IL-1RI-/- background was sufficient to reduce fibrosis. Together, these data indicate that Thy-1 negative fibroblasts are an immuno-responsive subpopulation that also display altered mechanotransduction, potentially serving as the link between the noted inflammation and aberrant mechanotransduction observed in IPF.

cell biology↗

bioRxiv2019

Cachexia and fibrosis are costs of chronic IL-1R-mediated disease tolerance in T. gondii infection

Cachexia is an immune-metabolic disease of progressive muscle wasting that impairs patient survival and quality of life across a range of chronic diseases. T. gondii is a protozoan parasite that causes lifelong infection in many warm-blooded organisms, including humans and mice. Here we show that mice infected with T. gondii develop robust, sustained cachexia and perivascular fibrosis in metabolic tissues. Consistent with an emerging role for the IL-1 axis in disease tolerance, we show that mice deficient in the Type 1 IL-1 receptor (IL-1R) have more severe acute muscle wasting, adipocyte and hepatocyte necrosis, independent of parasite burden. Unexpectedly, IL-1R-/- mice rapidly recover from acute disease, despite sustained parasite infection, and are protected from chronic cachexia as well as perivascular liver and muscle fibrosis. These data are consistent with a model where IL-1R signaling benefits cell survival and tissue integrity over short periods of inflammation, but sustained reliance on IL-1 mediated tolerance programs come at the cost of fibrosis and cachexia.\n\nSummaryIL-1R signaling drives a disease tolerance program that protects mice from tissue pathology during acute Toxoplasma gondii infection. However, extended IL-1R signaling drives chronic cachexia and perivascular fibrosis in the liver and skeletal muscle.

immunology↗