Bassani lab
Our main goal is to identify clinically relevant cancer specific Human Leukocyte Antigen (HLA) ligands that will guide the development of personalized cancer immunotherapy using state of the art proteogenomics and mass-spectrometry (MS) approaches. In the clinic, we aim to integrate, for the first time, mass-spectrometry-based immunopeptidomics into the innovative translational clinical strategy of personalized immunotherapy within the Department of Oncology. ...
Research projects
Immunopeptidomics
- We develop proteogenomics and MS-based immunopeptidomics analytical and computational approaches to identify HLA ligands derived from tumor-associated proteins, mutated neoantigens, non-canonical ORFs and post translationally modified peptides.
- We have initiated fundamental discovery work to elucidate how tumor cells present antigens and what are the bases of tumor immunogenicity in mouse and human.
- We are investigating the differences between T cell inflamed and non-inflamed tumors in terms of antigen presentation and the antigenic landscape and how drugs modulate the immunopeptidome.
- We have established a continuous bioinformatics pipeline called NeoDisc enabling direct and personalized identification and prediction of neoantigens by combining genomic information derived from exome-seq analysis and transcriptomics data with measured immunopeptidomics data.
- We apply our discovery pipeline in the context of phase I clinical vaccine and adoptive T cell therapy trials at the CHUV to identify personalized neoantigens from patient tumor samples.
Latest publications
Multifactorial Remodeling of the Cancer Immunopeptidome by IFNγ.
Newey A, Yu L, Barber LJ, (...), Choudhary JS, Bassani-Sternberg M, Gerlinger M
Cancer research communications – 2023 Nov 17
Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.
Zhang B, Bassani-Sternberg M
Journal for immunotherapy of cancer – 2023 Oct 6
Machine learning methods and harmonized datasets improve immunogenic neoantigen prediction.
Müller M, Huber F, Arnaud M, (...), Coukos G, Harari A, Bassani-Sternberg M
Immunity – 2023 Oct 4
A phase 1 trial of adoptive transfer of vaccine-primed autologous circulating T cells in ovarian cancer.
Bobisse S, Bianchi V, Tanyi JL, (...), Kandalaft LE, Harari A, Coukos G
Nature Cancer – 2023 Sep 21
What can Ribo-seq, immunopeptidomics, and proteomics tell us about the non-canonical proteome?
Prensner JR, Abelin JG, Kok LW, (...), Moritz RL, Deutsch EW, van Heesch S
Molecular & cellular proteomics : MCP – 2023 Aug 10
Restoring tumor immunogenicity with dendritic cell reprogramming.
Zimmermannova O, Ferreira AG, Ascic E, (...), Bassani-Sternberg M, Svane IM, Pereira CF
Science immunology – 2023 Jul 7
Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors.
Schmidt J, Chiffelle J, Perez MAS, (...), Zoete V, Coukos G, Harari A
Nature communications – 2023 Jun 6
A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics.
Li X, Pak HS, Huber F, (...), Taillandier-Coindard M, Altimiras ER, Bassani-Sternberg M
Cell reports methods – 2023 May 19
What can Ribo-seq and proteomics tell us about the non-canonical proteome?
Prensner JR, Abelin JG, Kok LW, (...), Bassani-Sternberg M, Deutsch EW, van Heesch S
bioRxiv : the preprint server for biology – 2023 May 18
The immunopeptidome landscape associated with T cell infiltration, inflammation and immune editing in lung cancer.
Kraemer AI, Chong C, Huber F, (...), Coukos G, Tissot S, Bassani-Sternberg M
Nature cancer – 2023 May 1
Team
Michal Bassani-Sternberg
Tenure Track Assistant Professor, Group leader Human integrated tumor immunology discovery engine (Hi-TIDe), Department of Oncology, Head of clinical mass spectrometry unit, Center of experimental therapeutics UNIL & CHUV, Ludwig Institute for Cancer Research Lausanne
michal.bassani@chuv.ch BassaniLabOther members
Selected Publications
Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes.
Racle J, Guillaume P, Schmidt J, (...), Bassani-Sternberg M, Harari A, Gfeller D
Immunity – 2023 Mar 30
Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma.
Mohsen MO, Speiser DE, Michaux J, (...), Coukos G, Bassani-Sternberg M, Bachmann MF
Journal for immunotherapy of cancer – 2022 Jan
Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope.
Ebrahimi-Nik H, Moussa M, Englander RP, (...), Mandoiu II, Bassani-Sternberg M, Srivastava PK
Nature communications – 2021 Nov 5
Identification of tumor antigens with immunopeptidomics.
Chong C, Coukos G, Bassani-Sternberg M
Nature biotechnology – 2021 Oct 11
Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction.
Pak H, Michaux J, Huber F, (...), Müller M, Coukos G, Bassani-Sternberg M
Molecular & cellular proteomics : MCP – 2021 Apr 9
CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens.
Forlani G, Michaux J, Pak H, (...), Linnebacher M, Accolla RS, Bassani-Sternberg M
Molecular & cellular proteomics : MCP – 2021 Jan 6
Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference.
Marino F, Semilietof A, Michaux J, (...), Coukos G, Müller M, Bassani-Sternberg M
Frontiers in immunology – 2020 Aug 28
Deciphering the Mechanisms of Improved Immunogenicity of Hypochlorous Acid-Treated Antigens in Anti-Cancer Dendritic Cell-Based Vaccines.
Graciotti M, Marino F, Pak H, (...), Harari A, Bassani-Sternberg M, Kandalaft LE
Vaccines – 2020 Jun 2
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Chong C, Müller M, Pak H, (...), Ohler U, Coukos G, Bassani-Sternberg M
Nature communications – 2020 Mar 10
Editorial: Novel Strategies for Anti-Tumor Vaccines.
Accolla RS, Buonaguro L, Melief C, Rammensee HG, Bassani-Sternberg M
Frontiers in immunology – 2020 Jan 17
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.
Solleder M, Guillaume P, Racle J, (...), Coukos G, Bassani-Sternberg M, Gfeller D
Molecular & cellular proteomics : MCP – 2019 Dec 17
A Phase I/II trial comparing autologous dendritic cell vaccine pulsed either with personalized peptides (PEP-DC) or with tumor lysate (OC-DC) in patients with advanced high-grade ovarian serous carcinoma.
Sarivalasis A, Boudousquié C, Balint K, (...), Harari A, Bassani-Sternberg M, Kandalaft LE
Journal of translational medicine – 2019 Nov 26
Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment.
Newey A, Griffiths B, Michaux J, (...), Cunningham D, Bassani-Sternberg M, Gerlinger M
Journal for immunotherapy of cancer – 2019 Nov 18
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes.
Racle J, Michaux J, Rockinger GA, (...), Jandus C, Bassani-Sternberg M, Gfeller D
Nature biotechnology – 2019 Oct 14
A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma-A Proof of Antigen Discovery Feasibility in Three Patients.
Bassani-Sternberg M, Digklia A, Huber F, (...), Harari A, Demartines N, Kandalaft LE
Frontiers in immunology – 2019 Aug 8
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