Biology subjects

Gaida, M. M.

Publications and source records attributed to Gaida, M. M..

7 recordsLinked to original sources

bioRxiv2026

Targeting soluble immunoglobulins ameliorates idiopathic multicentric Castleman disease in a mouse model

Idiopathic multicentric Castleman disease (iMCD) is a rare lymphoproliferative disorder that affects lymph nodes at multiple sites and can progress to life-threatening organ dysfunction. While curative therapies remain unavailable, largely due to a critical gap in understanding the diseases underlying etiology, the cytokine interleukin-6 (IL-6) is recognized as a major pathogenic driver, particularly in iMCD patients with plasmacytic lymphadenopathy. Here, we demonstrate the presence of Foxp3-expressing cells alongside plasma cells within germinal centers of lymph nodes from such iMCD patients. Based on this observation, we directed IL-6 overexpression specifically to Foxp3+ Treg cells and established a novel preclinical mouse model of iMCD. This targeted approach successfully recapitulated the key characteristics of iMCD in mice, including multifocal lymphadenopathy, splenomegaly, anemia, thrombocytopenia, marked plasmacytosis, and mortality in young adults. Advanced disease was characterized by renal pathology, including proteinuria and elevated creatinine levels. In this model, IL-6 directly promoted plasmacytosis, resulting in profound IgG1 hyperimmunoglobulinemia. Genetic ablation of soluble immunoglobulin production ameliorated iMCD symptoms, prevented renal dysfunction, and significantly extended survival. Our findings identify IL-6-driven IgG1 plasmacytosis as a critical pathogenic factor in iMCD, shedding light on the mechanisms underlying its development. Key pointsO_LITransgenic IL-6 expression in Foxp3+ cells models iMCD in mice and drives lethal IgG1 plasmacytosis C_LIO_LILoss of soluble immunoglobulins prevented renal impairment and prolonged survival in iMCD-like mice C_LI

immunology↗

bioRxiv2026

Computing tumor specificity of cancer antigen targets by k-mer indexing of healthy tissue transcriptomes

Individualized cancer immunotherapies rely on tumor-specific T-cell antigens, often predicted from somatic mutations as neoantigens. For tumors with low mutational burden, mRNA transcript variants, including gene fusions and novel splice junctions, can serve as important alternative targets. A main challenge in their identification from tumor RNA-seq is to confirm that their expression is tumor-restricted. Although large public collections of healthy-tissue RNA-seq exist, verifying tumor-specific expression requires computationally expensive re-analysis of these data for every novel candidate. To address this, we benchmarked nine k-mer indexing algorithms and developed k4neo, which leverages k-mer indexing of raw RNA-seq reads to compute the tumor specificity of any transcript variant. This mapping-free and transcript-class agnostic approach screens any candidate sequence against 18,960 samples across 51 healthy tissue types. We confirmed k4neos detection accuracy with qRT-PCR and showed that k4neo accurately classifies somatic and germline variants, gene fusions, and isoforms by tumor specificity. Applied to nine tumor cohorts, it nominated a median of 4-80 tumor-specific splice junctions per patient, including recurrent, long-read-confirmed novel antigen candidates. Together, k4neo enables efficient access to large-scale sequencing cohorts and accurately computes tumor specificity for any input transcript sequence, thereby expanding the repertoire of individual and shared cancer antigen targets.

bioinformatics↗

bioRxiv2026

Lung-targeted cytokine-coding RNA-lipoplexes induce T and NK cell-mediated anti-tumor immune response

Lung is a major site of metastases for many primary cancers associated with poor outcomes. A central challenge in cancer immunotherapy is overcoming tumor immune evasion, which limits effective antitumor responses. Here, we investigated whether combinatorial mRNA-encoded cytokine therapy can overcome tumor immune evasion by coordinately engaging innate and adaptive immunity, using murine models of pulmonary metastases. We employed intravenously administered cationic nucleoside-modified mRNA-lipoplexes (RNA-LPX) for targeted delivery of mRNA-encoded cytokines to the lung. The cytokine mix containing interferon-, half-life extended interleukin (IL)-7, and a half-life extended IL-2 variant with reduced CD25-binding modulated the tumor immune microenvironment resulting in a potent and broad anti-tumor response and prolonged survival with good tolerability at the conditions tested. Using cell depletion experiments, we demonstrated that both T and natural killer (NK) cells are crucial mediators of the observed anti-tumor efficacy of the cytokine RNA mix, which induced activation and effector function of NK and T cells, coupled with reduced regulatory T cells (Treg) numbers and Treg activation in the lung. Importantly, antitumor efficacy was maintained in models of impaired antigen presentation, including loss of an immunodominant tumor antigen and MHC class I deficiency, where NK cells served as the primary effectors. The cytokine RNA mix induced immune cell activation in the primary human lung tumor culture, suggesting potential for translational application. Collectively, these findings demonstrate that combinatorial cytokine therapy can drive both antigen-dependent and antigen-independent tumor control for the treatment of lung metastases.

immunology↗

bioRxiv2025

Reprogramming Immunosuppressive Bone Marrow Derived Cells via CD44 Targeting Impacts Pancreatic Cancer Metastasis

Pancreatic ductal adenocarcinoma (PDAC) is characterized by early dissemination and an aggressive metastatic course. In order to establish in the liver, metastatic cells require a metastatic niche providing pro-survival signals. Here, we demonstrate that bone marrow-derived cells (BMDCs) establish immunosuppressive niches in the liver that promote metastatic colonization in PDAC. Using an immunocompetent orthotopic PDAC mouse model, we show that BMDCs form clusters enriched in myeloid progenitors and display upregulation of migratory, adhesive, and immunoregulatory programs in response to tumor-derived cues. CD44 and its splice variant CD44v6 are found to be highly expressed on these cells. Hematopoietic-specific deletion of Cd44 or Cd44v6 using Cd44/Cd44v6fl/fl;VavCreERT2mice markedly impairs BMDC clustering, reshapes the BMDC transcriptome, disrupting pathways critical for migration, adhesion, and immunosuppression thereby reducing metastatic burden. Mechanistically, CD44 inhibition blocks BMDC migration toward CCL2, CCL5, and CXCL12, and impairs adhesion to VCAM-1 and fibronectin. Functionally, Cd44-deficient BMDCs exhibit reduced expression of immunosuppressive mediators such as Arginase 1, Ido1, and Il10, and fail to suppress T cell proliferation. Our findings position CD44 as a pleiotropic regulator of BMDC-mediated metastatic niche formation and identify it as a promising therapeutic target to disrupt the pro-metastatic microenvironment in PDAC.

cancer biology↗

bioRxiv2025

Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+ Treg cells

Regulatory T (Treg) cells, a subset of CD4+ T cells, play a crucial role in immunoregulation. Notably, CCR8-expressing Treg cells in tissues also contribute to organ homeostasis and repair. To determine whether these tissue-regenerative programs are active in the tumor microenvironment, we employed single-cell chromatin accessibility and genome-wide DNA methylation analyses to investigate CCR8+ tissue Treg cells isolated from human tumor and adjacent tumor-free tissues. Our findings indicate that CCR8+ tissue Treg cells from tumor and corresponding tumor-free tissues exhibit a high degree of similarity, suggesting that the tumor microenvironment may harbor highly activated tissue Treg cells. This observation was consistent across various tumor types and origins, including primary tumors and metastases. Using quantitative proteomics, we identified several candidate factors associated with the regenerative and suppressive programs of Treg cells, which may serve as potential reservoir of druggable targets for future therapeutic interventions.

immunology↗

bioRxiv2021

Deep molecular characterization linked to drug response profiling of pancreatic ductal adenocarcinoma using patient-derived organoids.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by high drug resistance and poor prognosis. Novel therapeutic and stratification strategies are urgently needed. Here, we present an integration of in-depth genomic and transcriptomic characterization with drug screening and clinical outcome based on a catalogue of 51 patient-derived tumor organoids (PDOs) from resected PDAC. Known PDAC molecular subtypes and their prognostic value are conserved in organoids. Integration of transcriptomic and drug response profiles suggest a metabolism-mediated modulations of drug resistance. Copy number alterations on chromosome 13q and wild-type status of TP53 emerged as potential novel genomic biomarkers for sensitivity to 5-FU and oxaliplatin treatment, respectively. Functional testing of targeted drugs in PDOs revealed its additional value for genome-driven personalized oncology. Co-deletion of TP53/POLR2A increased vulnerability to RNA polymerase II inhibition, pointing to a promising target for personalized treatment in PDAC. SignificancePatient-derived PDAC organoids hold great promise as surrogate tumor models for personalized oncology. By integrating highly granular molecular, drug sensitivity and clinical data, we demonstrate that PDOs are valid models for molecular characterization and response prediction that also enable identification of novel drug sensitivity biomarkers and resistance mechanisms in PDAC.

cancer biology↗

bioRxiv2021

Inflammation induces pro-NETotic neutrophils via TNFR2 signaling

Cytokines released during chronic inflammatory diseases induce pro-inflammatory properties in polymorphonuclear neutrophils (PMN). Here we show that in vitro cytokine treatment leads to the development of a subgroup of human PMN expressing CCR5, termed CCR5+ cytokine-induced PMN (CCR5+ cPMN). Auto/paracrine TNF signaling increases intracellular neutrophil elastase (ELANE) abundance and induces NETosis in CCR5+ cPMN. Triggering of CCR5 amplifies NETosis. Membranous TNF (mTNF) outside-in signaling induces the formation of reactive oxygen species, a known activator of NETosis. In vivo, we find an increased number of CCR5+ cPMN in the peripheral blood and inflamed lamina propria of patients with ulcerative colitis (UC) but not Crohns disease (CD). Notably, failure of anti-TNF therapy is associated with higher frequencies of CCR5+ cPMN. In conclusion, we identify a phenotype of pro-NETotic, CCR5 positive PMN present in inflamed tissue in vivo and inducible in vitro. These cells may reflect an important component of tissue damage during chronic inflammation and could be of diagnostic value.

immunology↗