Markkanen Publications

ZORA Publication List

Publications

• 2025

  • Yundung, Y., Pelisek, J., Maccio, U., Varga, Z., Ech-Cherif, H., Markkanen, E., Rössler, F., Ouda, A., Dzemali, O., Zimmermann, A., & Reutersberg, B. (2025). Identification of putative baroreceptors in human aortic arch by histological and omics analyses Hypertension Research, 48, 2083–2094. https://doi.org/10.1038/s41440-025-02217-9
  • Beebe, E., Krudewig, C., Motamed, Z., Malbon, A., & Markkanen, E. (2025). Stromal Expression Profiling Reveals Immune‐Driven Adaption to Malignancy in Canine Melanoma Subtypes Veterinary and Comparative Oncology, 23, 20–29. https://doi.org/10.1111/vco.13021
  • Inglebert, M., Dettwiler, M., He, C., Markkanen, E., Opitz, L., Naguleswaran, A., & Rottenberg, S. (2025). Individualized Pooled CRISPR/Cas9 Screenings Identify CDK2 as a Druggable Vulnerability in a Canine Mammary Carcinoma Patient Veterinary Sciences, 12, 183. https://doi.org/10.3390/vetsci12020183
  • Beer, P., Grest, P., Krudewig, C., Staudinger, C., Ohlerth, S., Rohrer Bley, C., Jarosch, A., Ech-Cherif, H., Markkanen, E., Park, B., & Nolff, M. C. (2025). Evaluation of a targeted anti-α$_{v}$β$_{3}$ integrin near-infrared fluorescent dye for fluorescence-guided resection of naturally occurring soft tissue sarcomas in dogs European Journal of Nuclear Medicine and Molecular Imaging, 52, 1137–1148. https://doi.org/10.1007/s00259-024-06953-x
  • Weber, M., Fuchs, D., Pöschel, A., Beebe, E., Garajova, Z., Jarosch, A., Kunz, L., Wolski, W., Opitz, L., Guscetti, F., Nolff, M. C., & Markkanen, E. (2025). Transcriptomic and proteomic profiling identifies feline fibrosarcoma as clinically amenable model for aggressive sarcoma subtypes Neoplasia, 60, 101104. https://doi.org/10.1016/j.neo.2024.101104

• 2024

  • Leblond, A.-L., Helmchen, B., Ankavay, M., Lenggenhager, D., Jetzer, J., Helmchen, F., Yurtsever, H., Parrotta, R., Healy, M. E., Pöschel, A., Markkanen, E., Semmo, N., Ferrié, M., Cocquerel, L., Seeger, H., Hopfer, H., Müllhaupt, B., Gouttenoire, J., Moradpour, D., … Weber, A. (2024). HEV ORF2 protein-antibody complex deposits are associated with glomerulonephritis in hepatitis E with reduced immune status Nature Communications, 15, 8849. https://doi.org/10.1038/s41467-024-53072-0

• 2023

  • Ettlin, J., Bauer, A., Opitz, L., Malbon, A., & Markkanen, E. (2023). Deciphering Stromal Changes between Metastatic and Non-metastatic Canine Mammary Carcinomas Journal of Mammary Gland Biology and Neoplasia, 28, 14. https://doi.org/10.1007/s10911-023-09542-0
  • Banik, I., Ghosh, A., Beebe, E., Burja, B., Bertoncelj, M. F., Dooley, C. M., Markkanen, E., Dummer, R., Busch-Nentwich, E. M., & Levesque, M. P. (2023). P38 Mediates Tumor Suppression through Reduced Autophagy and Actin Cytoskeleton Changes in NRAS-Mutant Melanoma Cancers, 15, 877. https://doi.org/10.3390/cancers15030877
  • Beer, P., Pauli, C., Haberecker, M., Grest, P., Beebe, E., Fuchs, D., Markkanen, E., Krudewig, C., & Nolff, M. C. (2023). Cross-species evaluation of fibroblast activation protein alpha as potential imaging target for soft tissue sarcoma: a comparative immunohistochemical study in humans, dogs, and cats Frontiers in Oncology, 13, 1210004. https://doi.org/10.3389/fonc.2023.1210004
  • Beebe, E., Pöschel, A., Kunz, L., Wolski, W., Motamed, Z., Meier, D., Guscetti, F., Nolff, M. C., & Markkanen, E. (2023). Proteomic profiling of canine fibrosarcoma and adjacent peritumoral tissue Neoplasia, 35, 100858. https://doi.org/10.1016/j.neo.2022.100858

• 2022

  • Beebe, E., Motamed, Z., Opitz, L., Cheng, P. F., Levesque, M. P., Markkanen, E., & Feldmeyer, L. (2022). Defining the Molecular Landscape of Cancer-Associated Stroma in Cutaneous Squamous Cell Carcinoma Journal of Investigative Dermatology, 142, 3304-3312.e5. https://doi.org/10.1016/j.jid.2022.06.017
  • Mueller, F. S., Amport, R., Notter, T., Schalbetter, S. M., Lin, H.-Y., Garajova, Z., Amini, P., Weber-Stadlbauer, U., & Markkanen, E. (2022). Deficient DNA base-excision repair in the forebrain leads to a sex-specific anxiety-like phenotype in mice BMC Biology, 20, 170. https://doi.org/10.1186/s12915-022-01377-1

• 2021

  • Clementi, E., Garajova, Z., & Markkanen, E. (2021). Measurement of DNA Damage Using the Neutral Comet Assay in Cultured Cells Bio-Protocol, 11, e4226. https://doi.org/10.21769/BioProtoc.4226
  • Clementi, E., Garajova, Z., & Markkanen, E. (2021). Measuring DNA Damage Using the Alkaline Comet Assay in Cultured Cells Bio-Protocol, 11, e4119. https://doi.org/10.21769/BioProtoc.4119
  • Pöschel, A., Beebe, E., Kunz, L., Amini, P., Guscetti, F., Malbon, A., & Markkanen, E. (2021). Identification of disease-promoting stromal components by comparative proteomic and transcriptomic profiling of canine mammary tumors using laser-capture microdissected FFPE tissue Neoplasia, 23, 400–412. https://doi.org/10.1016/j.neo.2021.03.001
  • Pantelyushin, S., Ranninger, E., Guerrera, D., Hutter, G., Maake, C., Markkanen, E., Bettschart-Wolfensberger, R., Rohrer Bley, C., Läubli, H., & vom Berg, J. (2021). Cross-reactivity and functionality of approved human immune checkpoint blockers in dogs Cancers, 13, 785. https://doi.org/10.3390/cancers13040785

• 2020

  • Guscetti, F., Nassiri, S., Beebe, E., Rito Brandao, I., Graf, R., & Markkanen, E. (2020). Molecular homology between canine spontaneous oral squamous cell carcinomas and human head-and-neck squamous cell carcinomas reveals disease drivers and therapeutic vulnerabilities Neoplasia, 22, 778–788. https://doi.org/10.1016/j.neo.2020.10.003
  • Clementi, E., Inglin, L., Beebe, E., Gsell, C., Garajova, Z., & Markkanen, E. (2020). Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction BMC Biology, 18, 36. https://doi.org/10.1186/s12915-020-00771-x
  • Amini, P., Nassiri, S., Malbon, A., & Markkanen, E. (2020). Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components Scientific Reports, 10, 5506. https://doi.org/10.1038/s41598-020-62354-8
  • Markkanen, E. (2020). Remodelling of cancer-associated stroma (Habilitation, University of Zurich)

• 2019

  • Markkanen, E. (2019). Know thy model: charting molecular homology in stromal reprogramming between canine and human mammary tumors Frontiers in Cell and Developmental Biology, 7, 348. https://doi.org/10.3389/fcell.2019.00348
  • Amini, P., Nassiri, S., Ettlin, J., Malbon, A., & Markkanen, E. (2019). Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma Disease Models & Mechanisms, 12, dmm.040444. https://doi.org/10.1242/dmm.040444

• 2018

  • Labouesse, M. A., Polesel, M., Clementi, E., Müller, F., Markkanen, E., Mouttet, F., Cattaneo, A., & Richetto, J. (2018). MicroRNA expression profiling in the prefrontal cortex: putative mechanisms for the cognitive effects of adolescent high fat feeding Scientific Reports, 8, 8344. https://doi.org/10.1038/s41598-018-26631-x

• 2017

  • Markkanen, E. (2017). Not breathing is not an option: how to deal with oxidative DNA damage DNA Repair, 59, 82–105. https://doi.org/10.1016/j.dnarep.2017.09.007
  • Amini, P., Ettlin, J., Opitz, L., Clementi, E., Malbon, A., & Markkanen, E. (2017). An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing BMC Molecular Biology, 18:22. https://doi.org/10.1186/s12867-017-0099-7
  • Ettlin, J., Clementi, E., Amini, P., Malbon, A., & Markkanen, E. (2017). Analysis of gene expression signatures in cancer-associated stroma from canine mammary tumours reveals molecular homology to human breast carcinomas International Journal of Molecular Sciences, 18, E1101. https://doi.org/10.3390/ijms18051101

• 2016

  • Markkanen, E., Meyer, U., & Dianov, G. L. (2016). DNA damage and repair in schizophrenia and autism: implications for cancer comorbidity and beyond International Journal of Molecular Sciences, 17, E856. https://doi.org/10.3390/ijms17060856
  • Zimmer, J., Tacconi, E. M. C., Folio, C., Badie, S., Porru, M., Klare, K., Tumiati, M., Markkanen, E., Halder, S., Ryan, A., Jackson, S. P., Ramadan, K., Kuznetsov, S. G., Biroccio, A., Sale, J. E., & Tarsounas, M. (2016). Targeting BRCA1 and BRCA2 deficiencies with G-Quadruplex-interacting compounds Molecular Cell, 61, 449–460. https://doi.org/10.1016/j.molcel.2015.12.004

• 2015

  • Pfister, S. X., Markkanen, E., Jiang, Y., Sarkar, S., Woodcock, M., Orlando, G., Mavrommati, I., Pai, C.-C., Zalmas, L.-P., Drobnitzky, N., Dianov, G. L., Verrill, C., Macaulay, V. M., Ying, S., La Thangue, N. B., D’Angiolella, V., Ryan, A. J., & Humphrey, T. C. (2015). Inhibiting WEE1 selectively kills histone H3K36me3-deficient cancers by dNTP starvation Cancer Cell, 28, 557–568. https://doi.org/10.1016/j.ccell.2015.09.015
  • Markkanen, E., Fischer, R., Ledentcova, M., Kessler, B. M., & Dianov, G. L. (2015). Cells deficient in base-excision repair reveal cancer hallmarks originating from adjustments to genetic instability Nucleic Acids Research, 43, 3667–3679. https://doi.org/10.1093/nar/gkv222