Search Results (294)

Endometriosis is a chronic, inflammatory, estrogen-dependent disease that affects approximately 6–10% of women of reproductive age. The present study aimed to investigate the expression of 48 immune-related genes in different types of biological samples from patients with histologically confirmed endometriosis compared to a control group. We analyzed (1) patients’ endometrial tissue, ectopic lesions, and menstrual and venous blood, as well as (2) the control group’s endometrial tissue and menstrual and venous blood. After RNA isolation, expression analysis of 48 immune-related genes was performed using NanoString nCounter^® Elements XT technology. All samples were normalized using nSolver Analysis Software, including control normalization and the use of a reference gene, as well as additional approaches for the detection of reliable differential expression. Expressions of the analyzed genes were similar in venous blood between patients and the controls; no significant dysregulation was found in menstrual blood. Most of the analyzed genes were upregulated in patients’ endometria. Three genes attracted our attention due to their overexpression in ectopic lesions. We were able to demonstrate the differential expression of three genes in ectopic lesions, suggesting their association with the development of endometriosis—THBS1, CHGB, and CYR61. The evidently higher expression of THBS1 in the ectopic lesions nominates this molecule as a potential therapeutic target in endometriosis as well. Full article

Background/Objectives: High-grade serous ovarian cancer (HGSOC) shows variable response to platinum-based neoadjuvant chemotherapy (NACT), with outcomes strongly linked to upfront treatment sensitivity. We evaluated whether oxidative DNA damage in pathologic samples is associated with improved clinical outcomes and reflects tumor–immune interactions. Methods: We analyzed matched pre- and post-NACT tumors from patients with stage III–IV HGSOC using Repair Assisted Damage Detection (RADD) to quantify total and oxidative DNA lesions (oxRADD). Gene expression profiling was performed on a subset of tumors using the NanoString PanCancer I/O 360. Associations with homologous recombination status, platinum sensitivity, recurrence, and survival were assessed. Results: Higher pre-NACT oxidative DNA damage was observed in tumors from patients who later recurred. Among recurrent tumors, elevated oxidative lesions were associated with improved overall survival (61.8 vs. 35.0 months; HR = 0.42, p = 0.037). Oxidative damage predicted recurrence (AUC = 0.71), supporting its utility in risk stratification. Tumors with serious oxidative damage showed reduced IDO1 and TGFβ signaling signatures, along with decreased B cell- and T cell-associated TIGIT signatures after NACT. Conclusions: These findings identify oxidative DNA damage as a potential pretreatment biomarker associated with recurrence, survival, and tumor–immune state, supporting its potential to impact therapeutic decision-making in HGSOC. Full article

Background/Objectives: Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoma and one of the most common hematological neoplasia. Entropy is a statistical measure of randomness that characterizes the texture of an input image and measures tissue complexity. Methods: Image processing and computer vision analysis were performed on a series of 114 diagnostic DLBCL cases and 44 reactive lymphoid tissues stained with hematoxylin and eosin (H&E). Histological entropy was measured to differentiate between reactive lymphoid tissue and DLBCL and predict clinical evolution. At protein level, immunohistochemistry analyzed Ki67, LMO2, MYC, MDM2, CDK6, E2F1, BCL2, CASP8, MYOB, TP53, cPARP, cCASP3, ISY1, TNFAIP8, CSF1R, CD163, PD-L1 and IL-10 markers. Gene expression analysis using the NanoString nCounter PanCancer Immune Profiling Panel was performed in 29 cases. Results: In comparison with reactive lymphoid tissue, DLBCL was characterized by lower entropy (7.32 ± 0.16 vs. 6.82 ± 0.44, respectively; p < 0.001). Within the DLBCL diagnostic category, higher entropy was associated with poor overall survival and death events within the first 2 years (hazard-risk = 2.4, p = 0.004) and lower entropy with a moderate and more favorable outcome (hazard-risk = 0.4, p = 0.004). High entropy was also correlated with ECOG performance status ≥ 2, lower protein expression of apoptosis markers of cPARP and cCASP3, and upregulation of specific immuno-oncology genes such as STAT3, BTK, CASP8, CD47, VCAM1, and MYD88. The prognostic value of entropy was independent of the international prognostic index (IPI), Epstein–Barr virus (EBER), and cell of origin (Hans). Conclusions: The histological evaluation of entropy is useful for the differential diagnosis of reactive lymphoid tissue and DLBCL and is a predictive factor of DLBCL prognosis. Full article

Background: High-grade serous ovarian carcinoma (HGSOC) can be subdivided into four prognostic molecular subtypes based on gene expression: C1/Mesenchymal (C1.MES), C2/Immunoreactive (C2.IMM), C4/Differentiated (C4.DIF) and C5/Proliferative (C5.PRO), each representing distinct biological characteristics with immune and stromal microenvironments. PrOTYPE enables prognosis and treatment guidance from biopsy material. Metastatic biopsies are often more accessible than primary adnexal sampling; their utility assumes stable tumor-intrinsic properties relative to the primary. Metastases may diverge due to microenvironmental pressure as well as the site-specific subtype dynamics. Methods: Treatment-naïve HGSOC specimens from 138 patients were profiled using the 55-gene nanostring PrOTYPE assay at adnexal, contralateral adnexal, and/or metastatic sites. Results: Adnexal PrOTYPE yielded expected distributions (21% C1.MES, 31% C2.IMM, 23% C4.DIF, 25% C5.PRO) with moderate reproducibility (κ = 0.49). Same-site replicate analysis showed substantial reproducibility (κ = 0.7). Non-adnexal sites were enriched for immune/mesenchymal subtypes (C1.MES/C2.IMM, 36/63 cases), most prominently at the omentum (24/32 C1.MES). C5.PRO was distinctly underrepresented at non-adnexal sites. Subtype shifts from adnexal to extra-adnexal sites were enriched for the second-place adnexal type prediction (p < 0.001). Detailed 55-gene analysis showed POSTN/CTSK were most commonly upregulated across metastatic sites. EMT pathway enrichment increased with metastatic distance (from adnexa to omentum, adj p < 0.05), paralleling—but independent of—C1.MES predominance. Conclusions: Adnexal PrOTYPE showed good stability. However, non-random subtype shifts and EMT enrichment at metastatic sites suggest dissemination selects pre-existing transcriptional plasticity rather than acquiring states de novo as HGSOC adapts to new microenvironments. Microenvironment changes may help predict metastatic potential and should be considered for precision medicine targeting. Full article

There is no proven therapy for Long COVID, a post-acute condition characterized by persistent symptoms following SARS-CoV-2 infection. Extracellular vesicles (EVs) are emerging as mediators of disease pathogenesis through their molecular cargo. We investigated whether EV glycosylation is altered in Long COVID plasma and whether these vesicles can be selectively targeted using a glycan-binding affinity resin. Large (100–500 nm) and small (40–200 nm) EVs were isolated from post-acute COVID-19 plasma and analyzed by nanoparticle flow cytometry to assess surface glycosylation. Small EV capture assays were performed using Galanthus nivalis agglutinin (GNA) affinity resin. Plasma miRNA profiles before and after GNA treatment were evaluated using NanoString nCounter analysis, and potential downstream pathway effects were computationally inferred using validated miRNA–mRNA interactions and PROGENy. Mannose-positive large EVs were significantly increased in Long COVID compared to recovered controls (p < 0.05). GNA-mediated small EV capture correlated with mannose-positive EV abundance (r = 0.341, p < 0.05), and seven miRNAs were significantly reduced following treatment. Computational pathway analysis suggested modulation of key signaling pathways, including JAK-STAT, Estrogen, VEGF, and PI3K. These findings suggest a glycan-associated EV signature in Long COVID and support further investigation of lectin-based capture as a potential strategy to target vesicle-associated molecular cargo. Full article

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with limited publicly available spatial transcriptomic resources, particularly for extensive-stage disease (ES-SCLC), which remains absent from major initiatives such as The Cancer Genome Atlas (TCGA). To improve accessibility, interoperability, and downstream analytical utility of existing spatial transcriptomic data, SCAPeSCLC was developed as a harmonized dataset derived from two publicly available Gene Expression Omnibus (GEO) series, GSE261345 and GSE261348, generated using the NanoString GeoMx Digital Spatial Profiler platform. The resource integrates normalized expression measurements from 296 tumor regions of interest (ROI) across 58 ES-SCLC patients treated with first-line chemoimmunotherapy. Normalized expression matrices were reformatted into survival-ready column-based datasets at both ROI and patient levels following log₂-transformation and standardization. Clinical metadata were curated and harmonized, and progression-free survival (PFS), disease-specific survival (DSS), overall survival (OS), time-on-treatment (ToT), follow-up intervals, and censoring indicators were reconstructed from the original clinical records. Biological pathway (BP) activity scores were generated using Cancer Transcriptome Atlas (CTA) annotations encompassing 106 BPs. To account for variable ROI sampling across patients, Bayesian hierarchical modeling was applied to estimate patient-level pathway activity, yielding posterior estimates and corresponding credible intervals. The resulting resource includes harmonized expression matrices, pathway enrichment profiles, Bayesian posterior estimates, survival-ready clinical annotations, and standardized Cox proportional hazards modeling outputs, along with a dedicated GitHub repository. SCAPeSCLC is intended to facilitate confirmatory analyses, integrative statistical modeling, methodological benchmarking, and reproducible exploration of spatial transcriptomic determinants of survival in ES-SCLC. Full article

Background/Objectives: Mucinous adenocarcinoma (MAC) is a rare and clinically problematic subtype of rectal cancer, tending to present at an advanced stage and to respond poorly to neoadjuvant therapy. The consistently worse prognosis than that of not-otherwise-specified adenocarcinoma (NOS-AC) is not fully understood, potentially owing to intrinsically more aggressive biology or specific immune evasion mechanisms. We used the IMMUNOREACT multicentre cohort, with external validation in TCGA, to investigate the clinical and immunological features of rectal MAC in detail. Methods: Two hundred patients with rectal adenocarcinoma (16 MAC, 184 NOS-AC) from the IMMUNOREACT 1 (NCT04915326) and IMMUNOREACT 2 (NCT04917263) prospective cohorts were included. To account for the imbalance in baseline characteristics, propensity score matching (PSM) was performed on age, sex, neoadjuvant treatment and TNM stage. The immune microenvironment was characterised using immunohistochemistry (CD3, CD4, CD8, CD8β, Tbet, FoxP3, PD-L1, MSH6, PMS2, CD80), flow cytometry and NanoString PanCancer IO 360™ transcriptomics of adjacent healthy mucosa. Findings were externally validated against TCGA rectal and colon adenocarcinoma datasets. Results: MAC presented at significantly more advanced stage than NOS-AC across all TNM parameters: higher T stage (p = 0.006), N stage (p < 0.001), M stage (p = 0.039) and overall TNM stage (p < 0.001). In the unmatched cohort, MAC was associated with worse overall survival (HR 2.53; 95% CI 1.03–6.23; p = 0.043) and disease-free survival (HR 2.86; 95% CI 1.25–6.55; p = 0.013), but both differences became non-significant after PSM. MAC patients had higher haemoglobin after adjusting for confounders (mean difference [MD] 1.26 g/dL, 95% CI 0.30–2.31, p = 0.012), consistent with a hypothesis of reduced chronic rectal bleeding as a possible mechanism for late presentation. Transcriptomically, MAC showed suppression of HLA class II antigen presentation genes (HLA-DQA1, HLA-DQB1, HLA-DRB1) and myeloid activation genes (S100A8/A9/A12) in adjacent healthy mucosa. Loss of MMR proteins MSH6 and PMS2 in histologically normal mucosa was significantly more frequent in MAC. These findings were replicated in the TCGA cohort, which also showed lower tumour mutational burden and a distinct mucin-associated transcriptomic profile in MAC. Conclusions: The worse outcomes of rectal MAC appear to be driven largely by late-stage presentation, possibly owing to later diagnosis. MAC nonetheless carries a distinct immune phenotype, detectable even in histologically normal surrounding mucosa, that likely contributes to its treatment resistance. These observations provide a basis for developing histotype-specific approaches to both early detection and treatment in this uncommon but clinically challenging tumour subtype. Full article

Background: Neoadjuvant partial breast irradiation using stereotactic body radiotherapy (SBRT) has emerged as a strategy to induce tumor and immune responses in early-stage, low-risk breast cancer. While prior studies have demonstrated encouraging response rates and evidence of immune modulation, the optimal radiotherapy regimen for immune priming remains unclear. SIGNAL 2.0 is a randomized phase II trial designed to compare the biological and immunological impact of a single-fraction versus three-fraction neoadjuvant SBRT. Materials and Methods: Sixty-one postmenopausal patients ≥ 50 years with unifocal, hormone positive, node-negative invasive ductal carcinoma < 3 cm were randomized 1:1 to receive either 21 Gy in one fraction or 30 Gy in three fractions, delivered to the tumor in the prone position. Core biopsies were collected pre-SBRT and 14–20 days post-SBRT at the time of surgery. Immune markers were assessed using tumor-infiltrating lymphocyte (TIL) scoring, NanoString nCounter PanCancer Immune Profiling, and NanoString GeoMx Digital Spatial Profiling (DSP). Results: Available tumor samples from 47 patients underwent paired tissue analysis. Three-fraction SBRT induced 200 differentially expressed genes, including enrichment of pathways related to adaptive immune activation, with significant increases in expression levels of macrophages, dendritic cells, neutrophils and CD8 T-cells. Proteomic profiling also identified a significant increase in the expression levels of neutrophils, Treg cells, macrophages, and NK cells in the tumor microenvironment of the samples from patients receiving the three-fraction regimen. Conclusions: Neoadjuvant SBRT induces measurable immune activation, with three-fraction regimens generating more extensive transcriptional, proteomic, and cellular immune changes than a single fraction. Three-fraction neoadjuvant SBRT may provide superior immune priming, providing a foundation for future trials integrating neoadjuvant radiotherapy with immunomodulatory therapies. Full article

The mammary gland is a heterogeneous organ that modulates ductal morphogenesis and alveolar differentiation. Obesity is a significant risk factor for several cancers, including postmenopausal breast cancer. We and others have described an association between obesity and increased breast cancer growth. However, the effects of obesity on the mammary fat pad microenvironment (MFPME) remain understudied. Here, we investigated the effect of the Western Diet (WD) on immunocompetent female mice and on their MFPME. Our data suggest that the WD increased body, liver, and perigonadal white adipose tissue (pWAT) weight, as well as myeloid cell infiltration into these tissues. Interestingly, we did not find any significant change in CD4⁺ and CD8⁺ T cells in the liver, blood, and pWAT. NanoString data demonstrates that various cellular processes, including the complement system, innate immune system, phagocytic activity, immune metabolism, and NOD-like receptor (NLR) signaling, were upregulated in the MFPME of obese mice. RNA-Seq data suggest that WD significantly modulated MFPME physiology through regulation of gene expression, cellular processes, and signaling pathways. Further investigation is necessary to determine how WD-mediated changes in MFPME modulate breast cancer biology. Full article

Background/Objectives: Chronic myeloid leukemia (CML), essential thrombocythemia (ET), primary myelofibrosis (PMF), and polycythemia vera (PV) are myeloproliferative neoplasms (MPNs) that require precise molecular characterization. Although driver mutations such as BCR-ABL1 and JAK2 are diagnostically important, they do not fully explain disease heterogeneity. The NanoString nCounter^® system enables direct multiplex gene expression analysis without RNA amplification and is suitable for degraded bone marrow specimens. This study aimed to analyze cytokine gene expression in bone marrow mononuclear cells of patients with MPNs and controls using NanoString technology, identify differentially expressed genes (DEGs) among MPN subtypes, and investigate their biological significance. Methods: Bone marrow aspirates were collected from 19 patients with MPNs (CML, ET, PMF, and PV) and 6 control patients. Mononuclear cells were isolated, and RNA expression of a 40-gene cytokine panel was analyzed using the NanoString nCounter^® system with strict quality control and normalization. DEGs were identified for each MPN subtype, followed by Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analyses. Results: CML and PV demonstrated 20 and 12 DEGs, respectively. In contrast, ET showed only one DEG (IRAK2), and PMF showed none. Functional analyses revealed enrichment of cytokine signaling, Toll-like receptor (TLR), and JAK-STAT pathways in CML, indicating immune and inflammatory dysregulation. PV DEGs were associated with TLR signaling, IL-17 pathways, and cytokine–cytokine receptor interactions, suggesting active cytokine-mediated inflammation. Conclusions: CML and PV exhibited distinct cytokine-driven transcriptional signatures, whereas ET and PMF exhibited minimal alterations. These findings support the clinical utility of NanoString technology for bone marrow specimens and highlight disease-specific immune pathways as potential diagnostic biomarkers in MPNs. Full article

Background/Objectives: Triple-negative breast cancer (TNBC) is a candidate for immune checkpoint blockade; however, current biomarkers remain insufficient to predict therapeutic response or capture tumor-intrinsic mechanisms. Enhancer of Zeste Homolog 2 (EZH2)-mediated epigenetic repression has been implicated in immune evasion, yet the contribution of EZH2-repressed genes to anti-tumor immunity and clinical outcomes in TNBC remains unclear. We aimed to identify EZH2-associated epigenetically repressed genes in TNBC and evaluate their relevance as tumor-intrinsic regulators and potential predictors of immunotherapy outcome. Methods: We performed integrative in silico analyses of The Cancer Genome Atlas (TCGA) breast cancer cohorts to identify EZH2-associated hypermethylated genes in TNBC. A composite 30-gene signature (30GS) was defined based on transcriptional repression and promoter hypermethylation. Associations with clinical outcomes, tumor- and immune-related programs, and therapeutic response were evaluated, with validation in the I-SPY2 cohort and an independent TNBC patient cohort. Results: The 30GS was significantly reduced in TNBC and basal-like tumors and associated with improved clinical outcomes and enrichment of tumor- and immune-related signatures. In the I-SPY2 cohort, the 30GS predicted pathological complete response in patients receiving chemo-immunotherapy (AUC = 0.7377, p = 0.0007). Gene-level analysis identified Dual Specificity Phosphatase 5 (DUSP5) as the gene most consistently associated with immune-related parameters. In an independent TNBC cohort, DUSP5-high tumors demonstrated transcriptional programs enriched for inflammatory, immune-related, and signaling pathways within the NanoString Breast Cancer 360 panel. Conclusions: This study defines an EZH2-associated epigenetic program linked to tumor-intrinsic immune programs in TNBC and identifies DUSP5 as a candidate gene associated with immune-related transcriptional states. Full article

Following acute infection, herpes simplex virus type 1 (HSV-1) establishes life-long latency in neurons. Although sensory neurons in trigeminal ganglia (TG) are primary sites for latency, the brainstem is also an important site for latency. The rationale for examining the principal sensory nucleus of the spinal trigeminal tract (Pr5) receives afferent inputs from TG. Notably, the (LC) is indirectly linked to Pr5. Our previous studies revealed that senescent cells and inflammation were detected in the Pr5 and LC of aged mice and young mice that are latently infected with HSV-1. To expand our understanding of how HSV-1 influences senescence and inflammation in Pr5 and LC, NanoString studies in mice latently infected with wild-type HSV-1 or a latency-associated transcript (LAT) null mutant (dLAT2903) was compared to age-matched uninfected C57Bl/6 male and female mice. LAT is the only viral gene abundantly expressed during latency, suggesting it influences cellular gene expression during latency. Cellular genes that regulate neuron differentiation, axonal projection, and pro-inflammatory mediators were more prevalent in mice latently infected with wild-type (wt) HSV-1 and dLAT2903 versus uninfected mice. Finally, these studies revealed that latency in Pr5 and LC is a dynamic process. Full article

The immunological composition of the microenvironment has shown relevance for diagnosis, prognosis, and therapy in solid tumors but remains underexplored in acute leukemias. We investigated the significance of the acute myeloid leukemia (AML) bone marrow microenvironment in predicting chemosensitivity and long-term remission in pediatric patients. We analyzed 32 non-promyelocytic pediatric AML patients at diagnosis using a NanoString PanCancer IO 360 assay, RNA sequencing, and deep-phenotype flow cytometry analyses. The findings were validated using the pediatric TARGET AML dataset. A short signature of three interferon (IFN)-related genes (GBP1, PARP12, and TRAT1) distinguished patients with chemosensitive disease and reduced minimal residual disease after induction chemotherapy. The signature stratified patients overall, and within the clinically defined “standard-risk” group, patients with high gene expression at diagnosis had significantly longer overall survival. The leukemia microenvironment associated with this signature showed enrichment of non-exhausted CD4⁺ and CD8⁺ T cytotoxic lymphocytes and expansion of CD8⁺ T effector memory cells re-expressing CD45RA (TEMRA) in patients with a favorable prognosis. Our results show the importance of the bone marrow microenvironment in pediatric AML and provide tools for a refined stratification of “standard-risk” patients, lacking adequate risk-oriented therapies. They also offer a promising guide for tackling immune pathways and exploiting immune-targeted therapies. Full article

Emphysema is a well-recognized risk factor for lung cancer; however, its influence on the immunologic tumor microenvironment in lung adenocarcinoma remains poorly defined. In this pilot, hypothesis-generating study, immune-related gene expression profiling was performed using archival formalin-fixed paraffin-embedded tumor specimens from 12 patients with lung adenocarcinoma, including the Never-smoker group (never-smokers without emphysema; n = 4), the Smoker 1 group (smokers without emphysema; n = 3), and the Smoker 2 group (smokers with CT-defined emphysema; n = 5). Expression of 770 immune-related genes was analyzed using the nCounter PanCancer IO 360 Panel (NanoString Technologies, Seattle, WA, USA). Compared with the Never-smoker group, tumors from the Smoker 1 group showed marked upregulation of SFRP1, SERPINB5, and IL6, whereas tumors from the Smoker 2 group exhibited increased expression of KIR2DL3, BLK, and WNT2B. Relative to the Smoker 1 group, the Smoker 2 group demonstrated significant upregulation of MMP7, TDO2, and CCL18. Pathway enrichment analysis revealed cytokine–cytokine receptor interaction as the most prominently enriched pathway in both smoker groups, while the IL-17 signaling pathway was preferentially enriched in the Smoker 2 group. In addition, diffusing capacity for carbon monoxide showed significant correlations with immune-related genes including IL-6 and IL-6R. Collectively, these preliminary findings suggest that lung adenocarcinoma arising in emphysematous lungs may be characterized by a distinct pro-inflammatory immune microenvironment. Given the small sample size and potential confounders, these results should be regarded as hypothesis-generating. Emphysema-associated immune remodeling may nevertheless represent an important biological factor worthy of validation in larger, independent cohorts. Full article

Biological heterogeneity among different breast cancer (BC) subtypes results in markedly varying clinical outcomes. Identification and analysis of key gene biomarkers that are differentially regulated during radiation therapy (RT) may pose multiple clinical challenges for BC treatment. The purpose of the study is to identify and analyze the expression of key gene biomarkers and their networks that are differentially regulated after hypofractionated RT. Patients with BC (cT0-T2, N0, M0) were treated with hypofractionated whole breast RT 25 Gy in five fractions, 4 to 8 weeks before breast conservation surgery (BCS). Biopsy (pre-RT; n = 5) and surgical (post-RT; n = 14 or 15) BC tumor samples were used for NanoString targeted sequencing. We identified 165 and 244 differentially expressed genes (DEGs; p < 0.05) in BC tumor samples from BC patients post-RT using the nCounter BC360 and IO360 panels, respectively. Gene networks and pathway analysis revealed that RT increases the gene signature of tumor inflammation (TIS), cytotoxicity, and apoptosis, while downregulating the gene signatures of tumor cell proliferation, differentiation, and cell adhesion, and increases the claudin-low gene score. RT-induced mammary stemness and enhanced infiltration of stroma, mast, and macrophage cells in the BC tumor microenvironment (TME). Further, the nCounter IO360 (immuno-oncology) panel analysis validated the findings of BC360 and demonstrated that RT increased the myeloid inflammation signature and chemokine expression, modulated B, T, NK, and DC cell activities, and enhanced residual cancer burden (RCB) in BC tumors, thus creating an immunosuppressive TME. Collectively, RT sensitized BC tumors by increasing the gene signature of TIS, cytotoxicity, apoptosis, and mammary stemness. RT facilitated an immunosuppressive environment and increased RCB, suggesting that the therapeutic potential of RT is highly individualized for each patient based on their unique tumor biology, genetic makeup, and TME. Full article