PUBLICATIONS

2024

  1. Pawlicka K, Henek T, Uhrik L, Hernychova L, Padariya M, Faktor J, Makowiec S, Vojtesek B,  Goodlett D, Hupp T, Kalathiya U, Misincorporations of amino acids in p53 in human cells at artificially constructed termination codons in the presence of the aminoglycoside Gentamicin, Frontiers in Genetics, Volume 15 – 2024, 05 November 2024, (https://doi.org/10.3389/fgene.2024.1407375).
  2. Karakostis K, Padariya M, Thermou A, Fåhraeus R, Kalathiya U, Vollrath F, Thermal stress, p53 structures and learning from elephants, Cell Death Discovery, Volume 10, Article number: 353, 07 August 2024 (https://www.nature.com/articles/s41420-024-02109-w).
  3. Daniels A, Padariya M, Fletcher S, Ball K, Singh A, Carragher N, Hupp T, Tait-Burkard C,  Kalathiya U, Molecules targeting a novel homotrimer cavity of Spike protein attenuate replication of SARS-CoV-2, Antiviral Research, Volume 228, 26 June 2024, 105949 (https://doi.org/10.1016/j.antiviral.2024.105949).
  4. Faktor J, Henek T, Hernychova L, Singh A, Vojtesek B, Polom J, Bhatia R, Polom K, Cuschieri K, Cruickshank M, Gurumurthy M, Goodlett DR, Al Shboul S, Kumar Samal S, Hupp T, Kalampokas E, Kote S, Metaproteomic analysis from cervical biopsies and cytologies identifies proteinaceous biomarkers representing both human and microbial species, Talanta, Volume 278, 22 June 2024. (https://doi.org/10.1016/j.talanta.2024.126460).
  5. Faktor J, Kote S, Bienkowski M, Hupp T, Marek-Trzonkowska N, Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker, Commun Biol 7, 708, 8 June 2024. (https://doi.org/10.1038/s42003-024-06354-8).
  6. Faria D, Eugénio P, Contreiras Silva M, Balbi L, Bedran B, Kallor AA, Nunes S, Palkowski A, Waleron M, Alfaro JA, Pesquita C. The Immunopeptidomics Ontology (ImPO), Database, Volume 2024, 10 June 2024 (https://doi.org/10.1093/database/baae014)
  7. Kocikowski M, Dziubek K, Węgrzyn K, Hrabal V, Zavadil-Kokas F, Vojtesek B, Alfaro JA, Hupp T, Parys M, Comparative characterization of two monoclonal antibodies targeting canine PD-1, 08 May 2024, Sec. Comparative Immunology, Volume 15 – 2024, (https://doi.org/10.3389/fimmu.2024.1382576)
  8. Padariya M, Kalathiya U, Single Ferritin Nanocages Expressing SARS-CoV-2 Spike Variants to Receptor and Antibodies, 23 April 2024, Vaccines 2024, Volume 12 (https://doi.org/10.3390/vaccines12050446)
  9. O’Neill JR, Yébenes Mayordomo M, Mitulović G, Al Shboul S, Bedran G, Faktor J,  Hernychova L, Uhrik L, Gomez Herranz M, Kocikowski M, Save V, Vojtěšek B, Arends M, OCCAMS consortium, Hupp T, Alfaro JA, 8 April 2024, Multi-omic analysis of Esophageal Adenocarcinoma uncovers candidate therapeutic targets and cancer-selective post-transcriptional regulation, Molecular & Cellular Proteomics 2024, (https://doi.org/10.1016/j.mcpro.2024.100764)
  10. Kobiela A, Hewelt-Belka W, E. Frąckowiak N, Kordulewska N, Hovhannisyan L, Bogucka A, Etherington R, Piróg A, Dapic I, Gabrielsson S, J. Brown S, S. Ogg G, Gutowska-Owsiak D, Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency, 22 March 2024, Frontiers in Immunology, Sec. Immunological Tolerance and Regulation, Volume 15 – 2024 (https://doi.org/10.3389/fimmu.2024.1369238)
  11. C. T. Sng C, Kallor AA, S. Simpson B, Bedran G, Alfaro JA, Litchfield K. Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy., 15 March 2024, Sec. Cancer Immunity and Immunotherapy, Volume 15- 2024 (https://doi.org/10.3389/fimmu.2024.1347542)
  12. Padariya M, Vojtesek B, Hupp T, Kalathiya U, In Vitro Cross-Linking MS Reveals SMG1–UPF2–SMG7 Assembly as Molecular Partners within the NMD Surveillance. 10 March 2024, International Journal of Molecular Sciences, (https://doi.org/10.3390/ijms25063182)
  13. Bedran D, Bedran G, Kote S, A Comprehensive Review of Neurodegenerative Manifestations of SARS-CoV-2, Vaccines12, no. 3: 222, 21 February 2024. (https://doi.org/10.3390/vaccines12030222).
  14. Nirmala S, Kayani K, Gliwiński M, Yueyuan, H, Iwaszkiewicz-Grześ D, Piotrowska-Mieczkowska M, Sakowska J, Tomaszewicz M, Marin Morales JM, Lakshmi K, Marek-Trzonkowska N, Trzonkowski P, Htun Oo Y, Fuchs A. Beyond FOXP3: A 20-year journey unravelling human regulatory T-cell heterogeneity. Front. Immunol., 12 January 2024, Sec. T Cell Biology, Vol.14 – 2023  (doi.org/10.3389/fimmu.2023.1321228)

2023

  1. Bedran, G, Polasky, DA, Hsiao, Y, Yu F, da Veiga Leprevost, F, Alfaro, JA, Cieslik, M, Nesvizhskii, Alexey I. Unraveling the glycosylated immunopeptidome with HLA-Glyco. Nature Communications 14, 3461 (2023). https://doi.org/10.1038/s41467-023-39270-2
  2. Canel M, Sławińska AD, Lonergan DW, Kallor AA, Upstill-Goddart R, Davidson C, von Kriegsheim A, Biankin AV, Byron A, Alfaro JA, Serrels A. FAK suppresses antigen processing and presentation to promote immune evasion in pancreatic cancer. Gut Published Online First: 28 March 2023. doi: 10.1136/gutjnl-2022-327927.
  3. Bedran G, Gasser HC, Weke K, Wang T, Bedran D, Laird A, Battail C, Zanzotto FM, Pesquita C, Axelson H, Rajan A, Harrison DJ, Palkowski A, Pawlik M, Parys M, O’Neill JR, Brennan PM, Symeonides SN, Goodlett DR, Litchfield K, Fahraeus R, Hupp TR, Kote S, Alfaro JA; The immunopeptidome from a genomic perspective: Establishing the non-canonical landscape of MHC class I–associated peptides, Cancer Immunololgy Research 2023, doi: 10.1158/2326-6066.CIR-22-0621
  4. MacCoss, MJ., Alfaro, JA, Faivre, DA. et al. Sampling the proteome by emerging single-molecule and mass spectrometry methods. Nature Methods 20, 339–346 (2023),  doi: 10.1038/s41592-023-01802-5.
  5. Sroka E, Lavigne M, Pla M, Daskalogianni C, Tovar Fernandez M, Prado Martins R, Manoury B, Darrasse-Jéze G, Nascimento M, Apcher S, Fahraeus R,  Major histocompatibility class I antigenic peptides derived from translation of pre-mRNAs generate immune tolerance, Proceedings of the National Academy of Sciences of the United States of America, 2023, vol. 120 (7) e2208509120, doi: 10.1073/pnas.2208509120.
  6. Gomez-Herranz M, Taylor J, Sloan RD, IFITM proteins: Understanding their diverse roles in viral infection, cancer, and immunity, Journal of Biological Chemistry, Vol. 299, Issue 1, Jan 2023, 102741, doi: 10.1016/j.jbc.2022.102741.
  7. Katarzyna Stefańska K, Kurkowiak M, Piekarska K, Chruściel E, Zamkowska D, Jassem-Bobowicz J, Adamski P, Świątkowska-Stodulska R, Abacjew-Chmyłko A, Leszczyńska K, Zieliński M, Preis K, Zielińska H, Tymoniuk B, Trzonkowski P, Marek-Trzonkowska  N. High maternal-fetal HLA eplet compatibility is associated with severe manifestation of preeclampsia.Front. Immunol., 03 November 2023. Sec. Immunological Tolerance and Regulation. Vol. 14-2023 (doi.org/10.3389/fimmu.2023.1272021)
  8. Kurkowiak M, Fletcher S, Daniels Alison, Mozolewski P, Silvestris D, Król E, Marek-Trzonkowska N, Hupp TR, Tait-Burkard C. Differential RNA editing landscapes in host cell versus the SARS-CoV-2 genome. iScience 2023, 26(11): 108031 (doi: 10.1016/j.isci.2023.108031)
  9. Brankiewicz W, Kalathiya U, Padariya M, Węgrzyn K, Prusinowski M, Zebrowska J, Zylicz-Stachula A, Skowron P, Drab M, Szajewski M, Ciesielski M, Gawrońska M, Kallingal A, Makowski M, Bagiński M, , 29, e202300970. Modified peptide molecules as potential modulators of shelterin protein functions; TRF1. Chem. Eur. J. 2023 (doi: 10.1002/chem.202300970 )

2022

  1. Lisowska M, Lickiss F, Gil-Mir M, Huart A-S, Trybala Z, Way L, Hernychova L, Krejci A, Muller P, Krejcir R, Zhukow I, Jurczak P, Rodziewicz-Motowidło S, Ball K, Vojtesek B, Hupp T, Kalathiya U. Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit the in vitro ubiquitin transfer cascade, Frontiers in Microbiology, Vol. 13, 2022, doi: 10.3389/fmicb.2022.875556.
  2. Minoli, L.; Licenziato, L.; Kocikowski, M.; Cino, M.; Dziubek, K.; Iussich, S.; Fanelli, A.; Morello, E.; Martano, M.; Hupp, T.; et al. Development of Monoclonal Antibodies Targeting Canine PD-L1 and PD-1 and Their Clinical Relevance in Canine Apocrine Gland Anal Sac Adenocarcinoma. Cancers 2022, 14, 6188. doi: 10.3390/cancers14246188
  3. Padariya M, Kalathiya U,  The Binding Specificity of PAB1 with Poly(A) mRNA, Regulated by Its Structural Folding. Biomedicines 2022, 10, 2981, doi: 10.3390/biomedicines10112981.
  4. Padariya M, Baginski M, Babak Minofar, Kalathiya U, Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme, Biophysical Chemistry, Vol. 291, 2022, 106909, doi: 10.1016/j.bpc.2022.106909.
  5. Singh A, Padariya M, Faktor J, Kote S, Mikac S, Dziadosz A, Lam TW, Brydon J, Wear MA, Ball KL, Hupp T, Sznarkowska A, Vojtesek B, Kalathiya U,  Identification of novel interferon responsive protein partners of human leukocyte antigen A (HLA-A) using cross-linking mass spectrometry (CLMS) approach. Scientific Reports 12, 19422 (2022)., doi: 10.1038/s41598-022-21393-z.

  6. Zheng AJ, Thermou A, Daskalogianni C, Malbert-Colas L, Karakostis K, Le S R, Dinh VT, Tovar Fernandez M, Chen S, Fahraeus R, The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA, Nucleic Acids Research, 2022 Sep 23;50(17):10110-10122, doi: 10.1093/nar/gkac751.

  7. Gomez-Herranz M, Faktor J, Mayordomo MY, Pilch M, Nekulova M, Hernychova L, Ball KL, Vojtesek B, Hupp T, Kote S, Emergent Role of IFITM1/3 towards Splicing Factor (SRSF1) and Antigen-Presenting Molecule (HLA-B) in Cervical Cancer, Biomolecules, 8 August 2022, doi: 10.3390/biom12081090.

  8. Padariya M, Jooste M-L, Hupp T, Fahraeus R, Vojtesek B, Vollrath F, Kalathiya U, Karakostis K, The Elephant Evolved p53 Isoforms that Escape MDM2 – Mediated Repression and Cancer, Molecular Biology and Evolution, 6 July 2022, doi: 10.1093/molbev/msac149.

  9. Papak I, Chruściel E, Dziubek K, Kurkowiak M, Urban-Wójciuk Z, Marjański T, Rzyman W, Marek-Trzonkowska N, What Inhibits Natural Killers’ Performance in Tumour, International Journal of Molecular Science, 24 June 2022, doi: 10.3390/ijms23137030,

  10. Mayordomo MY, Al Shboul S, Gomez-Herranz M, Azfer A, Meynert A, Salter D, Hayward L, Oniscu A, Patton JT, Hupp T, Arends MJ, Alfaro JA, Gorham-Stout case report: a multi-omic analysis reveals recurrent fusion as new potential drivers of the disease, BMC Medical Genomics, 6 June 2022, doi: 10.1186/s12920-022-01277-x.

  11. Padariya M, Daniels A, Tait-Burkard C, Hupp T, Kalathiya U, Self-derived peptides from the SARS-CoV-2 spike glycoprotein disrupting shaping and stability of the homotrimer unit, Biomedicine & Pharmacotherapy, 25 May 2022, doi: 10.1016/j.biopha.2022.113190.

  12. Sakowska J, Arcimowicz Ł, Jankowiak M, Papak I, Markiewicz A, Dziubek K, Kurkowiak M, Kote S, Kaźmierczak-Siedlecka K, Połom K, Marek-Trzonkowska N, Trzonkowski P, Autoimmunity and Cancer – Two Sides of the Same Coin, Frontiers in Immunology, 13 May 2022, doi: 10.3389/fimmu.2022.793234.

  13. Weke K, Kote S, Faktor J, Shboul S, Uwugiaren N, Brennan PM, Goodlett D, Hupp T, Dapic I, DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues, Analytica Chimica Acta, 29 April 2022, doi: 10.1016/j.aca.2022.339695.

  14. Tovar-Fernanadez M, Sroka E, Lavigne M, Thermou A, Daskalogianni C, Manoury B, Prado Martins R, Fahraeus R, Substrate-specific presentation of MHC class I-restricted antigens via autophagy pathway, Cellular Immunology, 17 February 2022, doi: 10.1016/j.cellimm.2022.104484.

  15. Piekarska K, Urban-Wójciuk Z, Kurkowiak M, Pelikant-Małecka I, Schumacher A, Sakowska J, Spodnik JH, Arcimowicz Ł, Zielińska H, Tymoniuk B, Renkielska A, Siebert J, Słomińska E, Trzonkowski P, Hupp T & Marek-Trzonkowska N, Mesenchymal stem cells stransfer mitochondria to allogeneic Tregs in an HLA-dependent manner improving their immunosuppressive activity, Nature Communications, 14 February 2022, doi: 10.1038/s41467-022-28338-0.

  16. Dapic I, Uwugiaren N, Kers J, Mohammed Y, Goodlett D, Corthals G,  Evaluation of Fast and Sensitive Proteome Profiling of FF and FFPE Kidney Patient Tissues, Molecules, 8 February 2022, doi: 10.3390/molecules27031137.

  17. Gomez-Herranz M, Faktor J, Pilch M, Vojtesek B, Hupp T, Kote S, SRSF1 as a novel interacting partner for IFIT1/3 unravels the emergent role of IFITM1/3 mediating protein expression, BioRxiv, 3 February 2022, doi: 10.1101/2022.02.02.478792.

  18. Gomez-Herranz M, Pilch M, Hupp T, Kote S, Interferon Gamma, MHC Class I Regulation and Immunotherapy, Journal of Cellular Signaling, 21 January 2022.

  19. Bedran G, Wang T, Pankanin D, Weke K, Laird A, Battail C, Zanzotto FM, Hupp T, Kote S, Alfaro J, A comprehensive library of canonical and non-canonical MHC class I antigens for cancer vaccine development, BioRxiv, 20 January 2022, doi: 10.1101/2022.01.13.475872.
  20. Magdalena Bojko, Katarzyna Węgrzyn, Emilia Sikorska, Mikołaj Kocikowski, Maciej Parys, Claire Battin, Peter Steinberger, Małgorzata M Kogut, Michał Winnicki, Adam K Sieradzan, Marta Spodzieja, Sylwia Rodziewicz-Motowidło, Design, synthesis and biological evaluation of PD-1 derived peptides as inhibitors of PD-1/PD-L1 complex formation for cancer therapy, Bioorganic Chemistry, November 2022, doi: 10.1016/j.bioorg.2022.106047

2021

  1. Apcher S, Tovar-Fernandez M, Ducellier S, Thermou A, Nascimento M, Sroka E, Fahraeus R, mRNA translation from an antigen presentation perspective: A tribute to the works of Nilabh Shastri, Molecular Immunology, 15 December, 2021, doi: 10.1016/j.molimm.2021.12.010.

  2. Padariya M, Fahraeus R, Hupp T, Kalathiya U, Molecular Determinants and Specificity of mRNA with Alternatively-Spliced UPF1 Isoforms, Influenced by an Insertion in the ‘Regulatory Loop’, International Journal of Molecular Sciences, 25 November 2021, doi: 10.3390/ijms222312744.

  3. Zheng A, Thermou A, Gallardo PG, Malbert-Colas Laurence, Daskalogianni C, Vaudiau N, Brohagen P, Granzhan A, Blondel M, Teulade-Fichou MP, Prado Martins R, Fahraeus R, The different activities of RNA G-quadruplex structures are controlled by flanking sequences, Life Science Alliance, 16 November 2021, doi: 10.26508/lsa.202101232.

  4. Shboul S, Curran OE, Alfaro JA, Lickiss F, Nita E, Kowalski J, Naji F, Nenutil R, Ball KL, Krejcir R, Vojtesek B, Hupp TR, Brennan PM, Kinomics platform using GBM tissue identifies BTK as being associated with higher patient survival, Life Science Alliance, 13 October 2021, doi: 10.26508/lsa.202101054.

  5. Jassem J, Marek-Trzonkowska N, Smiatacz T, Arcimowicz Ł, Papak I, Jassem E, Zaucha JM, Successful Treatment of Persistent SARS-CoV-2 Infection in a B-Cell Depleted Patient with Activated Cytotoxic T and NK Cells: A Case Report, International Journal of Molecular Sciences, 10 October 2021, doi: 10.3390/ijms222010934.

  6. Bibi N, Farid A, Gul S, Ali J, Amin F, Kalathiya U, Hupp T, Drug repositioning against COVID-19: a first line treatment, Journal of Biomolecular Structure and Dynamics, 14 September 2021, doi: 10.1080/07391102.2021.1977698.

  7. Padariya M, Kote S, Mayordomo M, Dapic I, Alfaro J, Hupp T, Fahraeus R, Kalathiya U, Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations, Computational and Structural Biotechnology Journal, 9 September 2021, doi: 10.1016/j.csbj.2021.09.006.

  8. Daskalogianni C, Zeng A, Tovar-Fernandez M, Thermou K, Sroka E, Mikac S, Oumata N, Galons H, Fahraeus R, Targeting Viral mRNA Translation Control as a New Concept for Anti-Virus Therapeutic Strategies, Infectious Diseases and Therapeutics, 16 August 2021, doi: 10.31038/IDT.2021221.

  9. Białobrzeska W, Dziąbowska K, Lisowska M, Mohtar MA, Muller P, Vojtesek B, Krejcir R, O’Neill R, Hupp TR, Malinowska N, Bięga E, Bigus D, Cebula Z, Pala K, Czaczyk E, Żołędowska S, Nidzworski D, An Ultrasensitive Biosensor for Detection of Femtogram Levels of the Cancer Antigen AGR2 Using Monoclonal Antibody Modified Screen-Printed Gold Electrodes, Biosensors, 7 June 2021, doi: 10.3390/bios11060184.

  10. Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M Yin P, Meller A, Joo C, The emerging landscape of single-molecule protein sequencing technologies, Nature Methods, 7 June 2021, doi: 10.1038/s41592-021-01143-1.

  11. Kurkowiak M, Grasso G, Faktor J, Scheiblecker, Winniczuk M, Mayordomo M, O’Neill JR, Oster B, Vojtesek B, Al-Saadi A, Marek-Trzonkowska N, Hupp TR, An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus, RNA Biology, 30 June 2021, doi: 10.1080/15476286.2021.1932345.

  12. Piróg A, Faktor J, Urban-Wójciuk Z, Kote S, Chruściel E, Arcimowicz Ł, Marek-Trzonkowska N, Vojtesek B, Hupp TR, Al Shboul S, Brennan PM, Smoleński RT, Goodlett DR, Dapic I, Comparison of different digestion methods for proteomic analysis of isolated cells and FFPE tissue samples, Talanta, 28 May 2021, doi: 10.1016/j.talanta.2021.122568.

  13. Mikac S, Rychłowski M, Dziadosz A, Szabelska-Beresewicz A, Fahraeus R, Hupp TR, Sznarkowska A, Identification of a Stable, Non-Canonically Regulated Nrf2 Form in Lung Cancer Cells, Antioxidants, 15 May 2021, doi: 10.3390/antiox10050786.

  14. Padariya M, Sznarkowska A, Kote S, Gomez-Herranz M, Mikac C, Pilch M, Alfaro JA, Fahraeus R, Hupp TR, Kalathiya U, Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes, Biomolecules, 22 April 2021, doi: 10.3390/biom11050622.

  15. Salomao N, Karakostis K, Hupp TR, Vollrath F, Vojtesek B, Fahraeus R, What do we need to know and understand about p53 to improve its clinical value?, The Journal of Pathology, 7 April 2021, doi: 10.1002/path.5677.

  16. Padariya M, Kalathiya U, Mikac S, Dziubek K, Tovar Fernandez MC, Sroka E, Fahraeus R, Sznarkowska A, Viruses, cancer and non-self recognition, Open Biology, 31 March 2021, doi: 10.1098/rsob.200348.

  17. Iwaszkiewicz-Grzes D, Piotrowska M, Gliwinski M, Urban-Wójciuk Z, Trzonkowski P, Antigenic Challenge Influences Epigenetic Changes in Antigen-Specific T Regulatory Cells, Frontiers in Immunology, 23.03.2021, doi: 10.3389/fimmu.2021.642678.

  18. Faktor J, Goodlett DR, Dapic I, Trends in Sample Preparation for Proteome Analysis, Intech Open, 16 March 2021, doi: 10.5772/intechopen.95962.

  19. Gauthier AE, Chandler CE, Poli V, Gardner FM, Tekiau A, Smith R, Bonham KS, Cordes EE, Shank TM, Zanoni I, Goodlett DR, Biller SJ, Ernst RK, Rotjan RD, Kagan JC, Deep-sea microbes as tools to refine the rules of innate immune pattern recognition, Science Immunology, 12 March, 2021, doi: 10.1126/sciimmunol.abe0531.

  20. Bhowmick P, Roome S, Borchers CH, Goodlett DR, Mohammed Y, An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community, Journal of Proteome Research, 8 March 2021, doi: 10.1021/acs.jproteome.0c00961.

  21. Kalathiya U, Padariya M,  Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR, Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS), Biomolecules, 4 March 2021, doi: 10.3390/biom11030382.

  22. Kurkowiak M, Arcimowicz Ł, Chruściel E, Urban-Wójciuk Z, Papak I, Keegan L, O’Connell M, Kowalski J, Hupp TR, Marek-Trzonkowska N, The effects of RNA editing in cancer tissue at different stages in carcinogenesis, RNA Biology, 17 February 2021, doi: 10.1080/15476286.2021.1877024.

  23. Sicari D, Centonze FG, Pineau R, Le Reste PJ, Negroni L, Chat S, Mohtar MA, Thomas D, Gillet R, Hupp TR, Chevet E, Igbaria A, Reflux of Endoplasmic Reticulum proteins to the cytosol in Cytosol Inactivates Tumor Suppressors, Embo Reports, 17 February 2021, doi: 10.15252/embr.202051412.

  24. Kalathiya U, Padariya M,  Chakraborti S, Fahraeus R, Hupp TR, Multivalent Display of SARS-CoV-2 Spike (RBD Domain) of COVID-19 to Nanomaterial, Protein, Ferritin Nanocages, Biomolecules, 17 February 2021, doi: 10.3390/biom11020297.

  25. Weke K, Singh A, Uwugiaren N, Alfaro JA, Wang T, Hupp TR, O’Neill JR, Vojtesek B, Goodlett DR, Williams SM, Zhou M, Kelly RT, Zhu Y, Dapic I, MicroPOTS Analysis of Barrett’s Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress, Journal of Proteome Research, 25 January 2021, doi: 10.1021/acs.jproteome.0c00629.

2020

  1. Sorensen M, Chandler CE, Gardner FM, Ramadan S, Khot PD, Leung LM, Farrance CE, Goodlett DR, Ernst RK, Nilsson E, Rapid microbial identification and colistin resistance detection via MALDI-TOF MS using a novel on-target extraction of membrane lipids, Scientific Reports, 9 December 2020, doi: 10.1038/s41598-020-78401-3.
  2. Uhrik L, Hernychova L, Muller P, Kalathiya U, Lisowska MM, Kocikowski M, Parys M, Faktor J, Nekulova M, Nortcliffe C, Zatloukalova P, Ruetgen B, Fahraeus R, Ball KL, Argyle DJ, Vojtesek B, Hupp TR, Hydrogen Deuterium Exchange Mass Spectrometry identifies the dominant paratope in CD20 antigen binding to the NCD1.2 monoclonal antibody, Biochemical Journal, 7 December 2020, doi: 10.1042/BCJ20200674.
  3. Chandler CE, Harberts EM, Pelletier MR, Thaipisuttikul I, Jones JW, Hajjar AM, Sahl JW, Goodlett DR, Pride AC, Rasko DA, Trent MS, Bishop RE, Ernst RK, Early evolutionary loss of the lipid A modifying enzyme PagP resulting in innate immune evasion in Yersinia pestis, PNAS, 15 September 2020, doi: 10.1073/pnas.1917504117.
  4. Yang H, Jackson SN, Woods AS, Goodlett DR, Ernst RK, Scott AJ, Streamlined Analysis of Cardiolipins in Prokaryotic and Eukaryotic Samples Using a Norharmane Matrix by MALDI-MSI, Journal of the American Society for Mass Spectrometry, 14 September 2020, doi: 10.1021/jasms.0c00201.
  5. Yang H, Chandler CE, Jackson SN, Woods AS, Goodlett DR, Ernst RK, Scott AJ, On-Tissue Derivatization of Lipopolysaccharide for Detection of Lipid A Using MALDI-MSI, Analytical Chemistry, 9 September 2020, doi: 10.1021/acs.analchem.0c02566.
  6. Li R, Zatloukalova P, Muller P, Gil-Mir M, Kote S, Wilkinson S, Kemp AJ, Hernychova L, Wang Y, Ball KL, Tao K, Hupp TR, Vojtesek B, The MDM2 ligand Nutlin-3 differentially alters expression of the immune blockade receptors PD-L1 and CD276, Cellular & Molecular Biology Letters, 25, 41(2020), 31 August 2020, doi: 10.1186/s11658-020-00233-w.
  7. Faktor J, Grasso G, Kokas FZ, Kurkowiak M, Mayordomo MY, Kote S, Singh A, Li R, O’Neill JR, Mulle P, Goodlett DR, Vojtesek B, Hupp TR, The effects of p53 gene inactivation on mutant proteome expression in a human melanoma cell model, Biochimica et Biophysica Acta (BBA) – General Subjects, 1864 (2020) 129722, 29 August 2020, doi: 10.1016/j.bbagen.2020.129722.
  8. Iwaszkiewicz-Grzes D, Gliwinski M, Eugster A, Piotrowska M, Dahl A, Marek-Trzonkowska N, Trzonkowski P, Antigen-reactive regulatory T cells can be expanded in vitro with monocytes and anti-CD28 and anti-CD154 antibodies, Cytotherapy, 7 August 2020, doi: 10.1016/j.jcyt.2020.07.001.
  9. Sun D, Böhringer KF, Sorensen M, Nilsson E, Edgar JS, Goodlett DR, Droplet delivery and nebulization system using surface acoustic wave for mass spectrometry, Lab on a Chip, 24 July 2020, doi: 10.1039/d0lc00495b.
  10. Ryu SY, Wendt GA, Ernst RK, Goodlett DR, MGMS2: Membrane glycolipid mass spectrum simulator for polymicrobial samples, Rapid Communications in Mass Spectrometry, 16 July 2020, doi: 10.1002/rcm.8824.
  11. Sivakumar VG, Malbert-Colas L, Chen S, Fusee L, Daskalogianni C, Fahraeus R, MDM2’s dual mRNA binding domains co-ordinate its oncogenic and tumour suppressor activities, 9 July 2020, doi: 10.1093/nar/gkaa431.
  12. Kalathiya U, Padariya M, Mayordomo M, Lisowska M, Nicholson J, Singh A, Baginski M, Fahraeus R, Carragher N, Ball K, Haas J, Daniels A, Hupp TR, Alfaro JA, Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site, Journal of Clinical Medicine 2020, 9(5), 1473, 14 May 2020, doi: 10.3390/jcm905147.
  13. Rybicka M, Woziwodzka A, Sznarkowska A, Romanowski T, Stalke P, Dręczewski M, Verrier ER, Baumert TF, Bielawski KP, Genetic variation in IL-10 influences the progression of hepatitis B infection, International Journal of Infectious Diseases, 6 May 2020,  doi: 10.1016/j.ijid.2020.04.079.
  14. Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, Goodlett DR, Dapic I, Paša-Tolić L, Zhu Y, Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform, Analytical Chemistry 2020, 92, 10, 7087–7095, 6 May 2020, doi: 10.1021/acs.analchem.0c00467.
  15. Sznarkowska A, Mikac S, Pilch M, MHC Class I Regulation: The Origin Perspective, Cancers 2020, 12 (5), 1155, 4 May 2020, doi: 10.3390/cancers12051155.
  16. Bajor M, Graczyk-Jarzynka A, Marhelava K, Kurkowiak M, Rahman A, Aura C, Russell C, Zych AO, Firczuk M, Winiarska M, Gallagher WM, Zagozdzon R, Triple Combination of Ascorbate, Menadione and the Inhibition of Peroxiredoxin-1 Produces Synergistic Cytotoxic Effects in Triple-Negative Breast Cancer Cells, Antioxidants 2020, 9(4), 320, 16 April  2020,  https://doi.org/10.3390/antiox9040320.
  17. Kocikowski M, Dziubek K, Parys M, Hyperprogression Under Immune Checkpoint-Based Immunotherapy—Current Understanding, The Role of PD-1/PD-L1 Tumour-Intrinsic Signalling, Future Directions and a Potential Large Animal Model, Cancers 2020, 12(4), 804, 27 March 2020, doi: 10.3390/cancers12040804.
  18. Pawlicka K, Kalathiya U, Alfaro JA, Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics, Cancers 2020, 12(3), 765, 24 March 2020, doi: 10.3390/cancers12030765.
  19. Padariya M, Kalathiya U, Houston DR, Alfaro JA, Recognition Dynamics of Cancer Mutations on the ERp57 – Tapasin Interface, Cancers 2020, 12(3), 737, 20 March 2020, doi: 10.3390/cancers12030737.
  20. Chruściel E, Urban-Wójciuk Z, Arcimowicz Ł, Kurkowiak M, Kowalski J, Gliwiński M, Marjański T, Rzyman W, Biernat W, Dziadziuszko R, Montesano C, Bernardini R, Marek-Trzonkowska N,  Adoptive Cell Therapy—Harnessing Antigen-Specific T Cells to Target Solid Tumours, Cancers 2020, 12(3), 683, 13 March 2020, doi: 10.3390/cancers12030683.
  21. Kote S, Pirog A, Bedran G, Alfaro J, Dapic I, Mass Spectrometry-Based Identification of MHC-Associated Peptides, Cancers 2020, 12(3), 535, 26 February 2020, doi: 10.3390/cancers12030535.
  22. Gliwiński M, Iwaszkiewicz-Grześ D, Wołoszyn-Durkiewicz A, Tarnowska M, Żalińska M, Hennig M, Zielińska H, Dukat-Mazurek A, Zielkowska-Dębska J, Zieliński M, Jaźwińska-Curyłło A, Owczuk R, Jarosz-Chobot P, Bossowski A, Szadkowska A, Młynarski W, Marek-Trzonkowska N, Moszkowska G, Siebert J, Myśliwiec M, Trzonkowski P, Proinsulin-specific T regulatory cells may control immune responses in type 1 diabetes: implications for adoptive therapy, BMJ Open Diabetes Research & Care, 2020, 8(1): e000873, 24 Februrary 2020, doi: 10.1136/bmjdrc-2019-000873.
  23. Fusée LTS, Marín M, Fahraeus R, López I, Alternative Mechanisms of p53 Action During the Unfolded Protein Response, Cancers (Basel), 10 February 2020, doi: 10.3390/cancers12020401.
  24. Harberts E, Liang T, Yoon SH, Opene BN, McFarland MA, Goodlett DR, Ernst RK, TLR4-Independent Effects of LPS Identified Using Longitudinal Serum Proteomics, Journal of Proteome Research, 10 February 2020, doi: 10.1021/acs.jproteome.9b00765.
  25. Piszczek P, Radtke A, Ehlert M, Jędrzejewski T, Sznarkowska A, Sadowska B, Bartmański M, Erdogan YK, Ercan B, Jedrzejczyk W, Comprehensive Evaluation of the Biological Properties of Surface-Modified Titanium Alloy Implants, Journal of Clinical Medicine 2020, 9(2), 342, 25 January 2020, https://doi.org/10.3390/jcm9020342.

2019

  1. Delom F, Mohtar MA, Hupp TR, Fessart D, The anterior gradient-2 interactome, American Journal of Physiology Cell Physiology, 18 December 2019, doi: 10.1152/ajpcell.00532.2018.
  2. Kalathiya U, Padariya M, Pawlicka K,  Verma CS, Houston D, Hupp TR, Alfaro JA, Insights into the effects of cancer associated mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1, International Journal of Molecular Sciences, 11 November 2019, doi: 10.3390/ijms20225644.
  3. Rybicka M, Woziwodzka A, Romanowski A, Sznarkowska A, Stalke P, Dręczewski M, Bielawski KP, Host genetic background affects the course of infection and treatment response in patients with chronic hepatitis B, Journal of Clinical Virology, Volume 120, November 2019, doi: 10.1016/j.jcv.2019.09.002.
  4. Yewdell JW, Dersh D, Fahraeus R, Peptide Channeling: The Key to MHC Class I Immunosurveillance?, Trends in Cell Biology, 26 October 2019, doi: 10.1016/j.tcb.2019.09.004.
  5. Urban-Wojciuk Z, Khan MM, Oyler BL, Fahraeus R, Marek-Trzonkowska N, Nita-Lazar A, Hupp TR, Goodlett DR, The role of TLRs in anti-cancer immunity and tumor rejection, Frontiers in Immunology, 22 October 2019, doi: 10.3389/fimmu.2019.02388.
  6. Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals G, Proteome analysis of tissues by mass spectrometry, Mass Spectrometry Reviews, 7 August 2019, doi: 10.1002/mas.21598.
  7. Ryu SY, Wendt GA, Chandler CE, Ernst RK, Goodlett DR, Model-based spectral library approach for bacterial identification via membranę glycolipids, Analytical Chemistry 2019, 91, 1 August 2019, doi: 10.1021/acs.analchem.9b03340.
  8. Kote S, Faktor J, Dapic I, Mayordomo MY, Kocikowski M, Kagansky A, Goodlett DR, Vojtesek B, Hupp TR, Wilcockson D, Analysis of venom sac constituents from the solitary, aculeate wasp cerceris rybyensis, Toxicon, Volume 169, 25 July 2019, doi: 10.1016/j.toxicon.2019.07.012.
  9. Kalathiya U, Padariya M, Baginski M, Structural, functional, and stability change predictions in human telomerase upon specific point mutations, Scientific Reports, 18 June 2019, doi: 10.1038/s41598-019-45206-y.
  10. Maurel M, Obac J, Avril T, Ding Y-P, Papadodima O, Treton X, Fanny D, Pilalis E, Hörberg J, Hou W, Beauchamp M-C, Tourneur‐Marsille J, Cazals‐Hatem D, Sommerova L, Samali A, Tavernier J, Hrstka R, Dupont A, Fessart D, Delom F, Fernandez‐Zapico ME, Jansen G, Eriksson LA, Thomas DY, Jerome‐Majewska L, Hupp TR, Chatziioannou A, Chevet E, Ogier‐Denis E, Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostatsis to inflammation, EMBO Molecular Medicine (2019) 11, e10120, Published online 30 April 2019, doi: 10.15252/emmm.201810120.
  11. Gliwiński M, Piotrowska M, Iwaszkiewicz-Grześ D, Urban-Wójciuk Z, Trzonkowski P, Therapy with CD4+CD25+ T regulatory cells – should we be afraid of cancer?, 5 April 2019, doi: 10.5114/wo.2019.84110.
  12. Gómez-Herranz M, Nekulova M, Faktor J, Hernychov L, Kote S, Sinclaira EH, Nenutilb R, Vojtesek B, Ball K, Hupp TR, The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis, Cellular Signalling, 60(2019) 39-56, 2 April 2019, doi: 10.1016/j.cellsig.2019.03.024.
  13. Haronikova L, Olivares-Illana V, Wang L, Karakostis K, Chen S, Fahraeus R, The p53 mRNA: an integral part of the cellular stress response, Nucleic Acids Research Res, 4 March 2019, doi: 10.1093/nar/gkz124.
  14. Coufalova D⁠, Remnant⁠a L⁠,⁠ Hernychova L⁠, Muller P⁠, Healy⁠ A, Kannan S⁠, Vojtesek⁠ B, Westwood N⁠, Verma CS⁠⁠, Hupp TR⁠, Houston DR⁠,⁠ An inter-subunit protein-peptide interface that stabilizes the specific activity and oligomerization of the AAA+ chaperone Reptin, Journal of Proteomics, 9 March 2019, doi:10.1016/j.jprot.2019.02.012.
  15. Khan MM, Chattagul S, Tran BQ, Freiberg JA, Nita-Lazar A, Shirtliff ME, Sermswan RW, Ernst RK, Goodlett DR, Temporal proteomic profiling reveals changes that support Burkholderia biofilms, Pathogens and Disease, 77, 13 February 2019, doi: 10.1093/femspd/ftz005.
  16. Sroka EM, Prado Martins R, Daskalogianni C, Apcher S, Fahraeus R, Origins of neoantigens for the major histocompatibility complex class I pathway, Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival, February 2019, doi: 10.1158/2326-6074.CRICIMTEATIAACR18-B187.
  17. Gonzalez Urionabarrenetxea A, Fahraeus R, Hupp TR, Ball K, Neo-antigen peptide vaccines as emerging cancer therapeutics, The Biochemist Vol. 41 No. 1, 16-21, February 2019 , doi: 10.1042/BIO04101016.
  18. Prado Martins R, Malbert-Colas L, Jose Lista M, Daskalogianni C, Apcher S, Pla M, Findakly S, Blondel M, Fahraeus R, Nuclear processing of nascent transcripts determines synthesis of full-length proteins and antigenic peptides, Nucleic Acids Research, 9 January 2019, doi: 10.1093/nar/gky1296.

2018

  1. Prado Martins R, Findakly S, Fahraeus R, Daskalogianni C, In Cellulo Protein-mRNA Interaction Assay to Determine the Action of G-Quadruplex-Binding Molecules, Molecules, 23(12):3124, 29 November 2018, doi: 10.3390/molecules23123124.
  2. Gnanasundram SV, Fahraeus R, Translation Stress Regulates Ribosome Synthesis and Cell Proliferation, International Journal of Molecular Sciences, 27 November 2018, doi: 10.3390/ijms19123757.
  3. Mohtar MA, Hernychova L, O’Neill R, Lawrence ML, Murray E, Vojtesek B, Hupp TR, The Sequence-specific Peptide-binding Activity of the Protein Sulfide Isomerase AGR2 Directs Its Stable Binding to the Oncogenic Receptor EpCAM, Molecular & Cellular Proteomics, 2018 Apr; 17(4):737-763, epub 16 January 2018,  doi: 10.1074/mcp.RA118.000573.