Prof. Dr. Julio Vera González

I am a physicist working in systems and precision medicine applied to cancer and autoimmune diseases. I lead an interdisciplinary team that combines computational modeling, bioinformatics, multi-criteria decision algorithms, and network biology to cancer diagnostics and therapy.

Research projects

Molecular data-driven engineering of immunotherapy
Omics, network and machine learning-based classification of skin and prostate cancer patients
Multi-layered data-based drug repurposing in therapy-resistant cancer patients

ProDia - Protease Aktivität in Plasma-Vesikeln für die prädiktive Diagnostik von Tumorerkrankungen

(Third Party Funds Single)

Term: 1. November 2023 - 30. April 2026
Funding source: Bayerisches Staatsministerium für Wirtschaft, Landesentwicklung und Energie (StMWi) (seit 2018)

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E034: How neural stem cells shape their regulatory environment in the adult CNS

(FAU Funds)

Term: 1. July 2023 - 31. March 2026
Funding source: Mittelgeber / Förderprogramme

Abstract

An adverse local environment ("niche") impairs the activity of neural stem cells (NSCs) in the adult brain. We investigate the new hypothesis that NSCs play an active role in generating favorable and adverse niche conditions. Specifically, we will investigate how dysfunctional NSCs generate adverse niche conditions focusing i) on the composition and the biomechanical properties of the extracellular matrix and ii) on NSC-derived exosomes and their composition.

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E033: Deubiquitinase Otud7b in oligodendrocyte differentiation and CNS myelination

(FAU Funds)

Term: 1. July 2023 - 31. December 2025

Abstract

Specific regulation of protein degradation by the ubiquitin-proteasome system plays important roles in myelination, remyelination and neurodegenerative diseases. I want to analyse the functions of the deubiquitinase Otud7b in oligodendrocytes in vitro and in vivo in an oligodendrocyte-specific Otud7b knockout mouse model and identify functional targets of Otud7b in oligodendrocytes to deepen the understanding of posttranscriptional regulatory events during OL differentiation and CNS myelination.

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M5-IZFK-D043: Mechanisms controlling functionality and persistence of CD19.CAR T-cells

(FAU Funds)

Term: 16. March 2023 - 15. September 2025

Abstract

CD19-directed chimeric antigen receptor (CAR) T-cells have shown high efficacy in the treatment of B-cell malignancies and are now emerging as a standard approach for patients with relapsed and refractory disease. Despite this progress, a significant portion of patients still experience resistance to treatment. We aim to understand the intrinsic mechanisms controlling persistence and effector functions of CAR T-cells and therefore identify strategies to overcome treatment failure.

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E037: CtBP1 in oligodendroglial development and myelination

(FAU Funds)

Term: 1. February 2023 - 30. November 2025

Abstract

Mutations in transcriptional corepressor CtBP1 cause the neurodevelopmental disorder HADDTS. Functional CtBP1 studies in the central nervous system so far focused on neurons. We recently found that CtBP1 is also important in oligodendrocytes. Here we will characterize the oligodendroglial functions of CtBP1 and the underlying cellular and molecular mechanisms in mice and a human ES cell-derived cellular disease model to show that defects in oligodendrogenesis and myelination contribute to HADDTS

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Systems medicine of melanoma and autoimmunity in the context of immunotherapy

(Third Party Funds Single)

Term: 1. October 2019 - 31. January 2025
Funding source: Bundesministerium für Bildung und Forschung (BMBF)
URL: https://www.melautim.net

Abstract

Immune-checkpointinhibitors have shown clinical activity in advanced melanoma, withsignificant survival benefit and response rates for anti-CTLA-4(19%), anti-PD-1 (36-44%) and combined therapy (58-61%). Whileresponses can be durable, a significant proportion of patients showautoimmune side effects, including autoimmune colitis, hepatitis andmusculoskeletal side effects. Inabout one third of cases patients exhibit side effects in more thanone organ system. In a fraction of the patients autoimmunity ispresent prior the therapy and may exacerbate. To be able to predictthe risk of appearance of these severe autoimmuneside effectswould enable physicians to personalize the anticancer treatment tothe patient and understanding mechanisms of these autoimmunereactions could improve therapy.

Theaim of the project is to improve our understanding of the molecularand cellular mechanisms underlying the interplay between autoimmunityand cancer, with an interest on the role of predisposing factors inthe appearance or exacerbation of autoimmunity under immunotherapy.The project uses melanoma, inflammatory bowel and rheumatoid diseasesas models. Under the systems medicine paradigm, we will generate invivo/patientdata-based molecular networks and multi-level models accounting forthe mechanisms behind the immune activation involved in theautoimmunity-cancer-immunotherapy axis. Combining data and networkanalysis, computer simulations and model experimentation, we willgenerate molecular and phenotypic signatures accounting for theemergence or enhancement of autoimmunity under checkpointinhibitor therapy, and will correlate these signatures with publishedand denovopatient data. We expect the project to pavethe way towards the translation into clinical practice of systemsmedicine-based methods for monitoring autoimmunity in melanomapatients receiving immunotherapy and establish a basis for rationaletreatment approaches for autoimmunity in cancer patients.

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2025

Rivera Monroy, L., Rist, L., Ostalecki, C., Bauer, A., Vera González, J., Breininger, K., & Maier, A. (2025). Graph Neural Networks in Multi-Stained Pathological Imaging: Extended Comparative Analysis of Radiomic Features. (Unpublished, Submitted).

2024

Kramer, N., Müller, G., Zierold, S., Röckel, M., Fröhlich, W., Schefzyk, M.,... Heinzerling, L. (2024). Checkpoint inhibitor-induced bullous pemphigoid differs from spontaneous bullous pemphigoid. Journal of the European Academy of Dermatology and Venereology. https://doi.org/10.1111/jdv.19860
Lischer, C., Eberhardt, M., Flamann, C., Berges, J., Güse, E., Wessely, A.,... Vera, J. (2024). Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy. Journal for ImmunoTherapy of Cancer, 12(5). https://doi.org/10.1136/jitc-2023-008104
Meier-Schiesser, B., Zecha, C., Zierold, S., Kolm, I., Röckel, M., Fröhlich, W.,... Heinzerling, L. (2024). Checkpoint inhibitor–induced lichen planus differs from spontaneous lichen planus on the clinical, histological, and gene expression level. Journal of the American Academy of Dermatology, 15, 157-164. https://doi.org/10.1016/j.jdin.2023.11.013
Rivera Monroy, L., Rist, L., Eberhardt, M., Ostalecki, C., Bauer, A., Vera, J.,... Maier, A. (2024). Comparative Analysis of Radiomic Features and Gene Expression Profiles in Histopathology Data using Graph Neural Networks. In Andreas Maier, Thomas M. Deserno, Heinz Handels, Klaus Maier-Hein, Christoph Palm, Thomas Tolxdorff (Eds.), Proceedings of the Bildverarbeitung für die Medizin 2024 (pp. 160-165). Erlangen, DE: Springer Link.
Rivera Monroy, L., Rist, L., Ostalecki, C., Bauer, A., Vera, J., Breininger, K., & Maier, A. (2024). Graph neural networks in multi-stained pathological imaging: extended comparative analysis of Radiomic features. International Journal of Computer Assisted Radiology and Surgery. https://doi.org/10.1007/s11548-024-03277-x
Rivera Monroy, L., Rist, L., Wilm, F., Ostalecki, C., Baur, A., Vera González, J.,... Maier, A. (2024). Multi-level cancer profiling through joint cell-graph representations. Smart Health, 32, 100470. https://doi.org/10.1016/j.smhl.2024.100470
Wang, Y., Ertl, C., Schmitt, C., Hammann, L., Kramer, R., Grabmaier, U.,... Heinzerling, L. (2024). Stringent monitoring can decrease mortality of immune checkpoint inhibitor induced cardiotoxicity. Frontiers in Cardiovascular Medicine, 11. https://doi.org/10.3389/fcvm.2024.1408586
Wessely, A., Koch, E., Vera, J., Berking, C., & Heppt, M. (2024). Identifizierung von Biomarkern und neuen therapeutischen Zielen beim Aderhautmelanom. Journal der Deutschen Dermatologischen Gesellschaft, 22(1), 29-33. https://doi.org/10.1111/ddg.15225_g
Winter, S., Schneider, M., Oelschlaegel, U., Maggioni, G., Riva, E., Raddi, M.G.,... Kordasti, S. (2024). Mutations in the splicing factor SF3B1 are linked to frequent emergence of HLA-DRlow/neg monocytes in lower-risk myelodysplastic neoplasms. Leukemia. https://doi.org/10.1038/s41375-024-02249-z

2023

Petzold, A., Steeb, T., Wessely, A., Koch, E., Vera, J., Berking, C., & Heppt, M. (2023). Is tebentafusp superior to combined immune checkpoint blockade and other systemic treatments in metastatic uveal melanoma? A comparative efficacy analysis with population adjustment. Cancer Treatment Reviews, 115. https://doi.org/10.1016/j.ctrv.2023.102543
Reimann, H., Kremer, A., Blumenberg, V., Schmidt, K., Aigner, M., Jacobs, B.,... Völkl, S. (2023). Cellular and humoral immune responses to SARS-CoV-2 vaccination in patients after CD19.CAR T-cell therapy. Blood Advances, 7(10), 2066-2069. https://doi.org/10.1182/bloodadvances.2022007806
Retzlaff, J., Lai, X., Berking, C., & Vera, J. (2023). Integration of transcriptomics data into agent-based models of solid tumor metastasis. Computational and Structural Biotechnology Journal, 21, 1930-1941. https://doi.org/10.1016/j.csbj.2023.02.014
Rivera Monroy, L., Rist, L., Eberhardt, M., Ostalecki, C., Baur, A., Vera, J.,... Maier, A. (2023). Employing Graph Representations for Cell-Level Characterization of Melanoma MELC Samples. In IEEE (Eds.), 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI). Cartagena, CO.
Schmitt, C., Hoefsmit, E.P., Fangmeier, T., Kramer, N., Kabakci, C., Vera González, J.,... Heinzerling, L.M. (2023). Immune checkpoint inhibitor-induced neurotoxicity is not associated with seroprevalence of neurotropic infections. Cancer Immunology, Immunotherapy. https://doi.org/10.1007/s00262-023-03498-0
Singh, N., Khan, F.M., Bala, L., Vera, J., Wolkenhauer, O., Pützer, B.,... Gupta, S.K. (2023). Logic-based modeling and drug repurposing for the prediction of novel therapeutic targets and combination regimens against E2F1-driven melanoma progression. BMC Chemistry, 17(1). https://doi.org/10.1186/s13065-023-01082-2
Wessely, A., Koch, E., Vera, J., Berking, C., & Heppt, M. (2023). Identifying biomarkers and novel therapeutic targets in uveal melanoma. Journal der Deutschen Dermatologischen Gesellschaft. https://doi.org/10.1111/ddg.15225
Zhang, L., Fan, S., Vera, J., & Lai, X. (2023). A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer. Computational and Structural Biotechnology Journal, 21, 34-45. https://doi.org/10.1016/j.csbj.2022.11.037

2022

Choudhari, J.K., Eberhardt, M., Chatterjee, T., Hohberger, B., & Vera, J. (2022). Glaucoma-TrEl: A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma. BMC Research Notes, 15(1). https://doi.org/10.1186/s13104-022-06210-0
Hoang, Y., Gryzik, S., Hoppe, I., Rybak, A., Schaedlich, M., Kadner, I.,... Baumgrass, R. (2022). PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.849329
Lai, X., Keller, C., Santos Rosales, G., Schaft, N., Dörrie, J., & Vera, J. (2022). Multi-Level Computational Modeling of Anti-Cancer Dendritic Cell Vaccination Utilized to Select Molecular Targets for Therapy Optimization. Frontiers in Cell and Developmental Biology, 9. https://doi.org/10.3389/fcell.2021.746359
Lai, X., Schmitz, U., & Vera, J. (2022). The Role of MicroRNAs in Cancer Biology and Therapy from a Systems Biology Perspective. In (pp. 1-22). Springer.
Lee, J.H., Ostalecki, C., Oberstein, T., Schierer, S., Zinser, E., Eberhardt, M.,... Baur, A. (2022). Alzheimer's disease protease-containing plasma extracellular vesicles transfer to the hippocampus via the choroid plexus. EBioMedicine, 77. https://doi.org/10.1016/j.ebiom.2022.103903
Lischer, C., Eisenhauer, N., Aigner, M., Jacobs, B., Schletter, M., Gebhard, C.,... Völkl, S. (2022). Single-cell Transcriptome Analysis and clonal Kinetics in a Patient after CD19.CAR-T Cell Therapy. In ONCOLOGY RESEARCH AND TREATMENT (pp. 125-125). BASEL: KARGER.
Mohr, E., Hinnenthal, T., Gryzik, S., Hoang, Y., Lischke, T., Retzlaff, J.,... Baumgrass, R. (2022). Bin-based visualization of cytokine-co-expression patterns of IL-10-producing CD4 T cell subsets. European Journal of Immunology. https://doi.org/10.1002/eji.202249829
Nikolov, S.G., Wolkenhauer, O., Nenov, M., & Vera González, J. (2022). Detection and Analysis of Critical Dynamic Properties of Oligodendrocyte Differentiation. Mathematics, 10(16). https://doi.org/10.3390/math10162928
Rivera Monroy, L., Eberhardt, M., Ostalecki, C., Baur, A., Vera, J., & Maier, A. (2022). Melanoma Segmentation and Classification Employing Imaging and Graph Encodings. In Proceedings - 2022 IEEE/ACM International Conference on Connected Health: Applications, Systems and Engineering Technologies, CHASE 2022 (pp. 144-145). Washington, DC, US: Institute of Electrical and Electronics Engineers Inc..
Sauerer, T., Lischer, C., Berking, C., Vera González, J., & Dörrie, J. (2022). Dissecting the IFN gamma-mediated transcriptomic alterations in Merkel cell carcinoma cell lines using Nanopore sequencing. In EXPERIMENTAL DERMATOLOGY (pp. E94-E94). HOBOKEN: WILEY.
Vera, J., Lai, X., Baur, A., Erdmann, M., Gupta, S., Gutta, C.,... Berking, C. (2022). Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbac433
Wessely, A., Kammerbauer, C., Lischer, C., Weich, A., Vera, J., Berking, C., & Heppt, M. (2022). SOX10-based drug repurposing identifies novel therapeutic targets in uveal melanoma. In JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT (pp. 82-82). HOBOKEN: WILEY.
You, Y., Lai, X., Pan, Y., Zheng, H., Vera, J., Liu, S.,... Zhang, L. (2022). Artificial intelligence in cancer target identification and drug discovery. Signal Transduction and Targeted Therapy, 7(1). https://doi.org/10.1038/s41392-022-00994-0

2021

Faas, M., Ipseiz, N., Ackermann, J., Culemann, S., Grüneboom, A., Schröder, F.,... Krönke, G. (2021). IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation. Immunity, 54(11), 2531-2546.e5. https://doi.org/10.1016/j.immuni.2021.09.010
Hofbauer, D., Mougiakakos, D., Broggini, L., Zaiss, M., Büttner-Herold, M., Bach, C.,... Bruns, H. (2021). β2-microglobulin triggers NLRP3 inflammasome activation in tumor-associated macrophages to promote multiple myeloma progression. Immunity, 54(8), 1772-1787.e9. https://doi.org/10.1016/j.immuni.2021.07.002
Koch, E., Petzold, A., Wessely, A., Dippel, E., Erdmann, M., Heinzerling, L.,... Heppt, M. (2021). Clinical determinants of long-term survival in metastatic uveal melanoma. Cancer Immunology, Immunotherapy. https://doi.org/10.1007/s00262-021-03090-4
Koch, E., Petzold, A., Wessely, A., Dippel, E., Erdmann, M., Heinzerling, L.,... Heppt, M. (2021). Clinical Prognostic Factors in metastatic Choroidal Melanoma. In JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT (pp. 82-83). HOBOKEN: WILEY.
Lai, X., Dreyer, F., Cantone, M., Eberhardt, M., Gerer, K.F., Jaitly, T.,... Vera, J. (2021). Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy. Theranostics, 11(3), 1412-1428. https://doi.org/10.7150/thno.53092
Lai, X., Zhou, J., Wessely, A., Heppt, M., Maier, A., Berking, C.,... Zhang, L. (2021). A disease network-based deep learning approach for characterizing melanoma. International Journal of Cancer. https://doi.org/10.1002/ijc.33860
Lischer, C., & Vera González, J. (2021). The Road to Effective Cancer Immunotherapy—A Computational Perspective on Tumor Epitopes in Anti-Cancer Immunotherapy. In Systems Medicine. (pp. 593-607).
Mougiakakos, D., Bach, C., Böttcher, M., Beier, F., Röhner, L., Stoll, A.,... Völkl, S. (2021). The IKZF1–IRF4/IRF5 axis controls polarization of myeloma-associated macrophages. Cancer Immunology Research, 9(3), 265-278. https://doi.org/10.1158/2326-6066.CIR-20-0555
Nikolov, S.G., Nenov, M., & Vera, J. (2021). Investigation of a kinetic model reproducing the mechanisms of oligodendrocytes differentiation. Series on Biomechanics, 35(2), 51-57.
Sauerer, T., Lischer, C., Weich, A., Berking, C., Vera, J., & Dörrie, J. (2021). Single-Molecule RNA Sequencing Reveals IFN gamma-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.785662
Vera, J., Lischer, C., Nenov, M., Nikolov, S., Lai, X., & Eberhardt, M. (2021). Mathematical modelling in biomedicine: A primer for the curious and the skeptic. International Journal of Molecular Sciences, 22(2), 1-16. https://doi.org/10.3390/ijms22020547
Wagner, N., Eberhardt, M., Vera, J., Cuomo, F., Blume, K., Galster, S.,... Baur, A. (2021). Plasma-derived extracellular vesicles discriminate type-1 allergy subjects from non-allergic controls. World Allergy Organization Journal, 14(9). https://doi.org/10.1016/j.waojou.2021.100583
Wessely, A., Kammerbauer, C., Lischer, C., Vera González, J., Berking, C., & Heppt, M. (2021). Inhibiting the neural crest transcription factor SOX10 leads to cell cycle arrest and apoptosis in uveal melanoma cells. In EXPERIMENTAL DERMATOLOGY (pp. E95-E95). HOBOKEN: WILEY.

2020

Bertrams, W., Griss, K., Han, M., Eberhardt, M., Seidel, K., Klemmer, A.,... Schmeck, B. (2020). Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation. In PNEUMOLOGIE (pp. S20-S21). STUTTGART: GEORG THIEME VERLAG KG.
Bertrams, W., Griss, K., Han, M., Seidel, K., Klemmer, A., Sittka-Stark, A.,... Schmeck, B. (2020). Transcriptional Analysis identifies long non-coding RNAs as potential biomarkers in pneumonia and COPD exacerbation. In PNEUMOLOGIE (pp. S21-S21). STUTTGART: GEORG THIEME VERLAG KG.
Bertrams, W., Griss, K., Han, M., Seidel, K., Klemmer, A., Sittka-Stark, A.,... Schmeck, B. (2020). Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-019-57108-0
Huber, A., Killy, B., Grummel, N., Bodendorfer, B., Paul, S., Wiesmann, V.,... Lang, R. (2020). Mycobacterial Cord Factor Reprograms the Macrophage Response to IFN-γ towards Enhanced Inflammation yet Impaired Antigen Presentation and Expression of GBP1. Journal of Immunology, 205(6), 1580-1592. https://doi.org/10.4049/jimmunol.2000337
Jaitly, T., Gupta, S.K., Wolkenhauer, O., Schuler, G., & Vera, J. (2020). Envisioning the application of systems biology in cancer immunology. In Nima Rezaei (Eds.), Cancer Immunology: A Translational Medicine Context. (pp. 599-624). Springer International Publishing.
Lee, J.H., Eberhardt, M., Blume, K., Vera, J., & Baur, A. (2020). Evidence for liver and peripheral immune cells secreting tumor-suppressive extracellular vesicles in melanoma patients. EBioMedicine, 62. https://doi.org/10.1016/j.ebiom.2020.103119
Lindner, P., Paul, S., Eckstein, M., Hampel, C., Muenzner, J.K., Erlenbach-Wuensch, K.,... Schneider-Stock, R. (2020). EMT transcription factor ZEB1 alters the epigenetic landscape of colorectal cancer cells. Cell Death & Disease, 11(2). https://doi.org/10.1038/s41419-020-2340-4
Nikolov, S., Wolkenhauer, O., Vera, J., & Nenov, M. (2020). The role of cooperativity in a p53-miR34 dynamical mathematical model. Journal of Theoretical Biology, 495. https://doi.org/10.1016/j.jtbi.2020.110252
Santos, G., & Vera, J. (2020). The role of age, neutrophil infiltration and antibiotics timing in the severity of streptococcus pneumoniae pneumonia. Insights from a multi-level mathematical model approach. International Journal of Molecular Sciences, 21(22), 1-16. https://doi.org/10.3390/ijms21228428
Singh, N., Eberhardt, M., Wolkenhauer, O., Vera, J., & Gupta, S.K. (2020). An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. BMC Bioinformatics, 21(1), 329-. https://doi.org/10.1186/s12859-020-03656-6
Wach, S., Taubert, H., Weigelt, K., Hase, N., Köhn, M., Misiak, D.,... Lai, X. (2020). RNA sequencing of collecting duct renal cell carcinoma suggests an interaction between miRNA and target genes and a predominance of deregulated solute carrier genes. Cancers, 12(1). https://doi.org/10.3390/cancers12010064
Wessely, A., Steeb, T., Erdmann, M., Heinzerling, L., Vera, J., Schlaak, M.,... Heppt, M. (2020). The role of immune checkpoint blockade in uveal melanoma. International Journal of Molecular Sciences, 21(3). https://doi.org/10.3390/ijms21030879

Related Research Fields

Digital Health

Research projects

Current projects

ProDia - Protease Aktivität in Plasma-Vesikeln für die prädiktive Diagnostik von Tumorerkrankungen

E034: How neural stem cells shape their regulatory environment in the adult CNS

E033: Deubiquitinase Otud7b in oligodendrocyte differentiation and CNS myelination

M5-IZFK-D043: Mechanisms controlling functionality and persistence of CD19.CAR T-cells

E037: CtBP1 in oligodendroglial development and myelination

Systems medicine of melanoma and autoimmunity in the context of immunotherapy

Recent publications