Wolfram Ruf

The immune system leverages B and T cells to recognize specific molecular patterns, known as epitopes, on pathogens and cancer cells to effectively combat infections and diseases. The critical success of immunotherapies in cancer treatment and COVID-19 vaccine development has established precise epitope identification as a central and rapidly growing priority in therapeutic design. Because traditional wet-lab based identification of B- and T-cell epitopes is expensive and timeconsuming, our systematic literature search (2015–2026) identified 148 Artificial Intelligence (AI) based linear B-cell, conformational B-cell, and T-cell epitope prediction models within the stated search scope. However, the true potential of these models remains unclear due to fragmented evaluation practices, with models rarely tested across a comprehensive range of datasets, insufficient comparison with existing predictors, systematic under-utilization of available public databases, and other methodological inconsistencies across five different stages of the predictive pipeline. Moreover, the 7 existing review papers fail to adequately highlight these research gaps or to support the development of robust AI models. This review paper consolidates the computational landscape of B-cell and T-cell epitope recognition and introduces a unified taxonomy that organises the field into twelve prediction tasks: linear and conformational B-cell prediction together with ten T-cell subtasks (T1–T10) that span the antigen-recognition cascade from human leukocyte antigen (HLA) typing to vaccine design. It analyses these twelve tasks across five major stages of a shared predictive pipeline. Within this taxonomy, the recognition sub-tasks (T1–T7) apply to the epitopes of any antigen, whereas neoantigen identification (T8) and tumor T-cell antigen (TTCA) classification (T9) are oncology-specific translational applications and multi-epitope vaccine design (T10) spans infectious-disease and cancer targets. It systematically examines 155 studies published from 2015 to 2026 to perform comprehensive categorization of 43 dedicated epitope/immunology databases, 144 benchmark datasets, 272 representation learning approaches, 148 classifiers, 54 evaluation and optimization approaches, and 148 predictive models accessibility status across all twelve prediction tasks. Additionally, it highlights persistent challenges across each stage of the predictive pipeline and offers key directions for improvement. This comprehensive analysis provides actionable recommendations for developing more robust, generalizable epitope predictors, and it ultimately accelerates the translation of computational predictions into effective immunotherapies against diverse diseases.

BACKGROUND: Endothelial dysfunction is an early event in atherosclerosis development and is centrally linked with insufficient endothelial NO production. However, chronically increased NO levels, including NO from other cellular sources, may induce endothelial dysfunction. Here, we studied how chronically elevated NO production from erythrocytes, achieved by genetic deletion of ARG1 (arginase-1), impacts smooth muscle cell (SMC) lipid accumulation and atherosclerosis progression. METHODS: Primary aortic SMCs from mice lacking ARG1 in red blood cell (RBC.ARG1-knockout [KO]) were subjected to RNA-sequencing, lipidomic, metabolic, and molecular analyses; atherosclerosis burden was quantified en face and at the aortic root. RESULTS: Increased lipid droplet formation in SMCs from RBC.ARG1-KO mice was observed using brightfield and electron microscopy and confirmed by Oil Red O and boron-dipyrromethene lipid dye staining. RNA sequencing revealed the simultaneous overexpression of genes regulating lipid uptake ( Cd36 ), catabolism ( Cpt1a ), and de novo lipogenesis ( Acaca , Fasn [ Fatty acid synthase ]) in RBC.ARG1-KO SMCs, and inhibiting fatty acid translocase (CD36), ACC (acetyl-CoA [coenzyme A] carboxylase), or fatty acid synthase prevented the lipid accumulation in RBC.ARG1-KO SMCs. Increased expression of CD36 downstream of NO and overactivated sGC (soluble guanylyl cyclase)-cyclic guanosine monophosphate signaling was identified as a mediator of increased lipid uptake in RBC.ARG1-KO SMCs. Loss of PDE (phosphodiesterase) 2A, coupling cyclic guanosine monophosphate with cyclic adenosine monophosphate and PKA (protein kinase A) activation, was also observed, resulting in AMPK (5’ AMP-activated protein kinase) inhibition, thus unlocking acetyl-CoA carboxylase, catalyzing the rate-limiting step in fatty acid synthesis. Inhibiting PDE2A recapitulated the RBC.ARG1-KO SMC phenotype, while inhibiting PKA or ATP generation from cyclic adenosine monophosphate abrogated the lipid droplet accumulation in RBC.ARG1-KO SMCs. Increased Oil Red O-positive aortic atherosclerosis burden in hypercholesterolemic apolipoprotein E–deficient RBC.ARG1-KO mice was confirmed by histology and elevated levels of polyunsaturated long-chain cholesterol esters in aortic atheroma by mass spectrometry lipidomics. CONCLUSIONS: Our findings show the importance of erythrocyte-derived NO for metabolically reprogramming SMCs toward increased fatty acid uptake and lipogenesis, and identify PDE2A as a molecular switch linking chronically activated NO signaling with lipid accumulation and atheroma progression.

Within the bone marrow microenvironment, leukemia cells can hijack regulatory intercellular communication routes usually employed by benign hematopoietic cells and establish a microenvironment permissive for (chemo-)therapy-evasive growth. An important means of transmitting signals by leukemia cells is the release of extracellular vesicles (EVs). Large oncosomes (LO) are a distinct population of EVs known to contribute to aggressive growth in solid tumors. Here, we show that BCR-ABL1+ B-cell acute lymphoblastic leukemia (B-ALL) cells release LO capable of reprogramming primary mesenchymal stromal cells (MSC) towards a tumor growth-supportive phenotype. Transcriptome analysis combined with targeted secretome profiling of MSC revealed that BCR-ABL1+ B-ALL cells use LO to modulate pathways previously shown to regulate the availability of insulin-like growth factor (IGF) 1 in the bone marrow microenvironment. Specifically, LO-conditioned MSC secrete less inhibitory IGF binding proteins (IGFBPs) and show altered expression of extracellular matrix-degrading fibrinolytic proteins. Furthermore, LO metabolically reprogram MSC and prime MSC towards differentiation into adipocytes capable of sustaining B-ALL cell growth. Thus, LO-educated MSC, and the adipocytes derived from them, support B-ALL cells by distinct mechanisms, and targeting of LO-mediated communication pathways to prevent B-ALL progression has potential for the development of novel adjuvant treatment strategies.

Glucagon-like peptide-1 (GLP-1) and glucose-induced insulinotropic polypeptide (GIP) receptor agonists have revolutionized obesity therapy, but causes of obesity-associated dysregulation of endogenous incretin production remain incompletely understood. Here we show that intestinal transmembrane serine protease 2 (TMPRSS2) plays a pivotal role in deregulating anti-diabetic GLP-1 production in obesity. TMPRSS2 is widely coexpressed in intestinal epithelial cells along with its signaling target protease-activated receptor 2 (PAR2). In addition to its role in regulating coagulation protease–mediated adipose tissue inflammation, PAR2 signaling in the gut controls postprandial GIP secretion. TMPRSS2, but not the epithelial cell–expressed proteases FXa or matriptase, activates PAR2 and thereby promotes postprandial GIP release. Accordingly, a PAR2-mutant mouse resistant to TMPRSS2 cleavage is protected from GIP upregulation and diet-induced obesity. In the context of obesity, TMPRSS2 also attenuates bioavailability of the ghrelin pathway and thereby suppresses GLP-1–mediated control of glucose homeostasis. Pharmacological inhibition or genetic deletion of TMPRSS2 restores ghrelin signaling–dependent GLP-1 secretion and GLP-1’s anti-diabetic effects on nutritional glucose homeostasis. Thus, epithelial cell–expressed TMPRSS2, which critically contributes to the lung pathology in SARS-CoV-2 infection, emerges as an intestinal incretin regulator and a potential link between infection and chronic cardiometabolic diseases. GLP-1 based therapeutics revolutionized anti-diabetic and anti-obesity treatments. The current study identifies epithelial TMPRSS2 as a critical regulator of GLP-1 in obesity induced diabetes.

Malignancies increase the risk for thrombosis and metastasis dependent on complex interactions of innate immune cells, platelets, and the coagulation system. Immunosuppressive functions of platelets and macrophage-derived coagulation factors in the tumor microenvironment (TME) drive tumor growth. Here we show that patients with malignancies and tumor-bearing mice have increased levels of coagulation factor (F) X expressing circulating monocytes engaged in platelet aggregate formation. This interaction and resulting thrombin generation on platelets interferes with monocyte differentiation and antigen uptake of antigen-presenting cells (APCs). Myeloid cell-specific deletion of FX or abrogated FXa signaling via protease activated receptor 2 (PAR2) averts the suppressive activity of platelets on tumor cell debris uptake and promotes the immune stimulatory activity of APCs in the TME. Myeloid cell FXa-PAR2 signaling deficiency specifically enhances activation of the cGAS-STING-IFN-I pathway with a resulting expansion of antigen experienced progenitor exhausted CD8⁺ T cells. Pharmacological blockade of FXa with direct oral anticoagulants expands T cell priming-competent immune cells in the TME and synergizes with the reactivation of exhausted CD8+ T cells by immune checkpoint inhibitors for improved anti-tumor responses. These data provide mechanistic insights into the emerging clinical evidence demonstrating the translational potential of FXa inhibition to synergize with immunotherapy.

Human saliva contains extracellular vesicles (EVs). These EVs expose extrinsic tenase complexes of tissue factor (TF) and activated factor VII (FVIIa), and trigger blood coagulation. Here, we show that EVs exposing extrinsic tenase complexes are also present in saliva of persons with severe hemophilia A, that is, persons with FVIII deficiency. Addition of these salivary EVs to autologous FVIII-deficient blood results in FXa generation, thereby compensating for the lack of FXa generation via intrinsic tenase (FVIIIa/FIXa) complexes. Consistently, in our retrospective analysis of persons with severe hemophilia A who do not receive prophylactic FVIII substitution, oropharyngeal mucosal bleedings are infrequent and self-limited. Conversely, in saliva of persons with severe FVII deficiency, in whom oropharyngeal bleedings are prevalent, functional extrinsic tenase complexes are absent, because EVs lack FVII. Saliva of persons with severe FVII deficiency is unable to restore blood coagulation, which is because of the absence of FVII in both their saliva and blood. Picomolar levels of recombinant FVIIa can restore the coagulant potential of saliva of persons with FVII deficiency. Taken together, our findings may explain the paucity of oropharyngeal bleedings in persons with hemophilia A as well as the occurrence of such bleedings in persons with severe FVII deficiency.

Fibrinolysis influences the mobilization of hematopoietic stem cells from their bone marrow microenvironment (BMM). Here we show that activation of plasmin, a key fibrinolytic agent, by annexin A2 (ANXA2) distinctly impacts progression of BCR-ABL1⁺ B-cell acute lymphoblastic leukemia (B-ALL) via modulation of the extracellular matrix (ECM) in the BMM. The dense ECM in a BMM with decreased plasmin activity entraps insulin-like growth factor (IGF) 1 and reduces mTORC2-dependent signaling and proliferation of B-ALL cells. Conversely, B-ALL conditions the BMM to induce hepatic generation of plasminogen, the plasmin precursor. Treatment with ε-aminocaproic acid (EACA), which inhibits plasmin activation, reduces tumor burden and prolongs survival, including in xenogeneic models via increased fibronectin in the BMM. Human data confirm that IGF1 and fibronectin staining in trephine biopsies are correlated. Our studies suggest that fibrinolysis-mediated ECM remodeling and subsequent growth factor release influence B-ALL progression and inhibition of this process by EACA may be beneficial as adjunct therapy.

Aims: Epidemiology links noise to increased risk of metabolic diseases like diabetes and obesity. Translational studies in humans and experimental animals showed that noise causes reactive oxygen species (ROS)–mediated cardiovascular damage. The interaction between noise and diabetes, specifically potential additive adverse effects, remains to be determined. Methods and results: C57BL/6 mice were treated with streptozotocin (i.p. injections, 50 mg/kg/day for 5 days) to induce type 1 diabetes mellitus, with S961 (subcutaneous osmotic mini-pumps, 0.57 mg/kg/day for 7 days) or fed a high-fat diet (HFD, 20 weeks) to induce type 2 diabetes mellitus. Control and diabetic mice were exposed to aircraft noise to an average sound pressure level of 72 dB(A) for 4 days. While body weight was unaffected, noise reduced insulin production in all diabetes models. The oral glucose tolerance test showed only an additive aggravation by noise in the HFD model. Noise increased blood pressure and aggravated diabetes-induced aortic, mesenteric, and cerebral arterioles’ endothelial dysfunction. ROS formation in cerebral arterioles, the aorta, the heart, and isolated mitochondria was consistently increased by noise in all models of diabetes. Mitochondrial respiration was impaired by diabetes and noise, however without additive effects. Noise increased ROS and caused inflammation in adipose tissue in the HFD model. RNA-sequencing data and alteration of gene pathway clusters also supported additive damage by noise in the setting of diabetes. Conclusion: In all three models of diabetes, aircraft noise exacerbates oxidative stress, inflammation, and endothelial dysfunction in mice with pre-existing diabetes. Thus, noise may potentiate the already increased cardiovascular risk in diabetic patients.