Biology subjects

Anufrieva, K. S.

Publications and source records attributed to Anufrieva, K. S..

5 recordsLinked to original sources

bioRxiv2025

Fibroblasts sense spatial proximity via an EGFR CREB5 axis to restore quiescent synovial lining in remission rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic inflammatory disease where the synovial lining membrane undergoes pathological changes resulting in joint destruction. In healthy joints, the synovial lining is essential for joint homeostasis, forming a selective barrier and secreting lubricating molecules, yet the mechanisms that restores homeostatic synovial lining during RA remission remains poorly understood. Here, we applied spatial transcriptomics to examine biopsies of RA patients in remission to identify a mechanism that orchestrates a phenotypic switch specifying synovial quiescent lining fibroblast differentiation. Spatial transcriptomics revealed a proximity-sensing program where at low cell-density, fibroblasts adopt proliferative and fibrotic transcriptional state characterized by expression of MKI67, COL1A2 and COL6A2, whereas at high cell-density, fibroblasts induce a quiescent lining fibroblast transcriptional program characterized by PRG4, CLU and PDPN. Mechanistically, fibroblasts sense spatial proximity through HB-EGF-EGFR signaling, which leads to phosphorylation of transcription factor CREB5. Perturbation of the EGFR-CREB5 axis abolishes fibroblast proximity-sensing and blocks synovial lining fibroblast differentiation. Conversely, EGFR activation by the ligand HB-EGF or pharmacologic activation of CREB5 is sufficient to induce synovial lining fibroblast differentiation. Together, our findings define a novel spatial proximity-sensing pathway underlying a return to homoeostatic fibroblast function during RA remission. By sensing their spatial proximity to neighboring fibroblasts, synovial fibroblasts translate these positional cues into signals that lead to restoration of normal, steady-state synovial lining membrane.

genomics↗

bioRxiv2025

A Spatially Coordinated Keratinocyte-Fibroblast Circuit Recruits MMP9+ Myeloid Cells to Drive IFN-I-Driven Inflammation in Photosensitive Autoimmunity

Photosensitivity is a hallmark of cutaneous lupus erythematosus (CLE) and dermatomyositis (DM), yet the mechanisms linking ultraviolet B (UVB) exposure to tissue-specific autoimmunity remain incompletely defined. Here, we use an integrative human-based approach, including single-cell RNA sequencing, spatial transcriptomics (seqFISH+), in vivo UVB provocation, and in vitro modeling, to uncover a spatially coordinated inflammatory circuit that underlies interferon-I (IFN-I)-amplified skin pathology. We identify MMP9+ CD14+ myeloid cells as central effectors of photosensitivity in both CLE and DM. These cells are markedly expanded in lesional skin, serve as the dominant source of IFN-{beta}, and colocalize with cytotoxic CD4+ T cells at the dermal-epidermal junction. Spatial transcriptomics further reveals a keratinocyte-fibroblast-myeloid axis, wherein keratinocytes activate discrete subsets of pro-inflammatory fibroblasts in the superficial dermis to produce monocyte-attracting chemokines, including CCL2, CCL19, CCL7, CCL8, and CXCL12, directing MMP9+ CD14+ cell recruitment toward the interface. In our in-vitro model, IFN-I-primed basal keratinocytes undergo heightened UVB-induced cell death and release membrane-associated cytokines such as TNF-, IL-1, which activate monocyte-derived dendritic cells (moDCs) and induce transcriptional programs mirroring those of MMP9+ CD14+ cells in vivo. In vivo, UVB irradiation of non-lesional DM skin, but not healthy controls, elicits rapid infiltration of these myeloid cells, confirming their disease-specific responsiveness to UVB. Finally, in a proof-of-concept clinical study, treatment with anifrolumab (anti-IFN-I receptor) blocked UVB-induced MMP9+ CD14+ infiltration and attenuated photosensitivity in CLE. Together, these findings define a multicellular inflammatory cascade linking keratinocyte injury, fibroblast chemotactic programming, and myeloid effector function in IFN-I-driven skin autoimmunity and nominate MMP9+ CD14+ cells as actionable targets in photosensitive dermatoses. Photosensitivity is central to cutaneous lupus erythematosus (CLE) and dermatomyositis (DM), but the mechanisms linking UVB exposure to tissue-specific autoimmunity are poorly defined. Using single-cell RNA sequencing, spatial transcriptomics, UVB provocation, and in vitro modeling, we identify MMP9+ CD14+ myeloid cells as critical mediators of photosensitivity. These cells expand significantly in lesional skin, produce IFN-{beta}, and colocalize with cytotoxic CD4+ T cells at the dermal-epidermal junction. Keratinocytes activate fibroblasts in the superficial dermis, prompting them to release chemokines (CCL2, CCL19, CCL7, CCL8, CXCL12) that recruit MMP9+ CD14+ cells. IFN-I-primed keratinocytes exposed to UVB release cytokines activating dendritic cells, mirroring in vivo responses. UVB irradiation of non-lesional DM skin rapidly recruits these myeloid cells. In a clinical proof-of-concept study, anti-IFN-I treatment with anifrolumab prevented UVB-induced myeloid infiltration and reduced photosensitivity. Thus, targeting MMP9+ CD14+ cells may offer therapeutic potential for managing photosensitive autoimmune skin conditions.

immunology↗

bioRxiv2025

Spatial Transcriptomics Identifies Immune-Stromal Niches Associated with Cancer in Adult Dermatomyositis

Adult-onset dermatomyositis (DM) is an autoimmune inflammatory myopathy with distinct cutaneous manifestations and a strong malignancy association. Through comparative analysis with cutaneous lupus erythematosus (CLE), our integrated spatial and single-cell transcriptomics analysis revealed unique immune and stromal niches associated with DM subtypes. Unexpectedly, we found an association between cancer-associated DM skin lesions and the presence of dispersed immune infiltrates enriched with macrophages, CD8+ T cells, plasma cells, and B cells with preserved vascular architecture. In contrast, non-cancer associated DM skin exhibited dense myeloid cell infiltrates, including neutrophils, monocytes, and macrophages, with elevated expression of IL1B and CXCL10 localized near injured vascular endothelia. Cytokines produced by these myeloid infiltrates together with local tissue hypoxia triggered dramatic stromal remodeling, leading to loss of vascular-associated fibroblasts. In addition to the CXCL10+ myeloid signature, non-cancer-associated DM skin with pDC presence showed the emergence of specific cellular pairs: PD-L1-expressing mregDCs and activated Tregs expressing NFKB2 and TNF receptors. While both DM and CLE showed strong interferon signatures, DM uniquely displayed IFN-{beta} expression. Together, our study provides the first comprehensive spatial mapping of immune and stromal cells in adult-onset DM.

immunology↗

bioRxiv2025

Spatial patterning of fibroblast TGFβ signaling underlies treatment resistance in rheumatoid arthritis

Treatment-refractory rheumatoid arthritis (RA) is a major unmet need, and the mechanisms driving treatment resistance are poorly understood. To identify molecular determinants of RA non-remission, we performed spatial transcriptomic profiling on pre- and post-treatment synovial tissue biopsies from treatment naive patients who received conventional DMARDs or adalimumab for 6 months. In the baseline biopsies of non-remission patients, we identified significant expansion of fibrogenic fibroblasts marked by high expression of COMP, a fibrosis-associated extracellular matrix protein. COMPhi fibroblasts localized to perivascular niches that, unexpectedly, served as transcriptional hubs for TGF{beta} activity. We identified endothelial-derived Notch signaling as an upstream regulator of fibroblast TGF{beta} signaling via its dual role in driving TGF{beta} isoform expression and suppressing TGF{beta} receptors, generating a proximal-distal gradient of TGF{beta} activity. Further, disruption of steady-state Notch signaling in vitro enabled fibrogenic fibroblast activation. Analysis of post-treatment biopsies revealed marked expansion of COMPhi fibroblasts in non-remission RA patients, despite evidence of successful immune cell depletion, suggesting a spatiotemporal process of fibrogenic remodeling linked to treatment resistance. Collectively, our data implicates targeting of TGF{beta} signaling to prevent exuberant synovial tissue fibrosis as a potential therapeutic strategy for refractory RA.

immunology↗

bioRxiv2023

Unlocking DNA Damage Sensitivity of Cancer Cells: The Potential of Splicing Inhibitors

Despite the growing interest in pre-mRNA alternative splicing (AS) as a therapeutic anticancer target, the potential of splicing inhibitors in treating solid tumors remains largely unexplored. We conducted a meta-analysis of transcriptome data from six different tumor types and revealed that splicing inhibitors induced similar patterns of AS, resulting in widespread exon-skipping and intron retention events that often lead to nonsense-mediated decay of the transcripts. Interestingly, in many cases exon skipping is induced by a compensatory cellular response to splicing inhibitor treatment. It involves an upregulation of multiple splicing factors and incomplete recognition of branch points by U2 snRNP. These post transcriptional changes downregulate one-third of essential DNA repair genes, thereby creating a therapeutic vulnerability that can be exploited for cancer treatment. To harness this vulnerability, we proposed a new approach to cancer treatment consisting of sequential addition of a splicing inhibitors followed by a DNA-damaging agent. Our in vitro and in vivo experiments demonstrated that this strategy exhibits promising therapeutic potential for a wide range of tumors.

cancer biology↗