Neural networks have been extensively used in the proteomics field and their role on improving identifications is rapidly becoming more relevant. DeepiRT is a neural network designed to predict Indexed Retention Time (iRT) (Escher, 2012) for a given precursor based on its modified sequence.
Our collaborator, GreyWolf Therapeutics, has uncovered the effect of aminopeptidase ERAP2 inhibition for generating the de novo antitumor T-cell responses, thereby overcoming the resistance mechanism for current immune-oncology therapy.
Learn more about leveraging our TrueDiscovery® immunopeptidomics CRO services to overcome the challenges in immune-oncology.
Disclaimer: The contact information provided for poster download will also be shared with GreyWolf Therapeutics
This poster delves into the ULTRA-DEEP EXPLORATION OF HUMAN TISSUE PROTEOMES, where 20025 protein groups were identified across all 22 tissue samples (19 healthy and 3 cancer). The poster concludes that the qualitative human tissue digital proteome serves as a rich resource that can be mined for various applications such as basal protein expression, different proteoforms, PTMs etc.
Veronica G. Anania, Kebing Yu, Francesco Pingitore, Qingling Li, Christopher M. Rose, Peter Liu, Wendy Sandoval, Ann E. Herman, Jennie R. Lill, and W. Rodney Mathews. Journal of Proteome Research.
Lupus nephritis (LN) is a severe clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Assessment of severity and activity of renal involvement in SLE requires a kidney biopsy, an invasive procedure with limited prognostic value. Noninvasive biomarkers are needed to inform treatment decisions and to monitor disease activity. Proteinuria is associated with disease progression in LN; however, the composition of the LN urinary proteome remains incompletely characterized. To address this, we profiled LN urine samples using complementary mass spectrometry-based methods: protein gel fractionation, chemical labeling using tandem mass tags, and data-independent acquisition. Combining results from these approaches yielded quantitative information on 2573 unique proteins in urine from LN patients. A multiple-reaction monitoring (MRM) method was established to confirm eight proteins in an independent cohort of LN patients, and seven proteins (transferrin, α-2-macroglobulin, haptoglobin, afamin, α-1-antitrypsin, vimentin, and ceruloplasmin) were confirmed to be elevated in LN urine compared to healthy controls. In this study, we demonstrate that deep mass spectrometry profiling of a small number of patient samples can identify high-quality biomarkers that replicate in an independent LN disease cohort. These biomarkers are being used to inform clinical biomarker strategies to support longitudinal and interventional studies focused on evaluating disease progression and treatment efficacy of novel LN therapeutics.
Presenter: Amaury Lachaud
Date: Wednesday, Sep 20, 2023, 11:45 AM – 1:00 PM
Session: PP05
Presenter: Roland Bruderer
Date: November 7
Alterations in biofluid proteomes are powerful molecular biosignatures for the screening and diagnosis of bladder and kidney-related diseases. At HUPO 2022, Roland Bruderer presented a poster on how we identified actionable biomarkers for bladder cancer and chronic kidney disease in urine with our TrueDiscovery™ platform for deep unbiased mass-spectrometry-based proteomics.
From the total of 12,617 proteins identified in the urine samples, we revealed changes in proteins involved in programmed cell death, telomerase organization, keratinocyte, and epidermal cell differentiation, as well as inflammation markers and previously described markers such as urokinase plasminogen activator surface receptor (UPAR). Of the altered proteins analyzed, 23 significantly differentiated the pathophysiological conditions. Download the poster to discover more.
E-Poster 1374/5 presented at AACR 2022
Presenter: Marco Tognetti
Session: PO.IM01.05 – Tumor Antigens, Antigen Presentation, and Tumor Immunity
Date: April 11
Poster 1267/14 presented at AACR 2022
Presenter: Jakob Vowinckel
Session: PO.CL11.07 Biomarkers Predictive of Therapeutic Benefit 2
Date: April 11
Endoplasmic reticulum aminopeptidase 1 (ERAP1) plays a central role in the modulation of the immunopeptidome
in all human cells and in N-terminal trimming of immunopeptides to 9-10mers in the endoplasmic reticulum
(ER) for loading and presentation via major histocompatibility-1 (MHC-1).
Therapeutic inhibition of ERAP1 provides a mechanism to increase the visibility of previously hidden neoantigens and
the visibility of the tumor to the immune system.
Discover how our TrueDiscovery Immunopeptidome Profiling services enabled Grey Wolf to assess immunomodulation following ERAP inhibition.
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