Evidence map›Paper›PMID 37662211›Full record

ArticlebioRxiv : the preprint server for biology2023

Design of Cytotoxic T Cell Epitopes by Machine Learning of Human Degrons.

Nicholas L Truex, Somesh Mohapatra, Mariane Melo, Jacob Rodriguez, Na Li, Wuhbet Abraham, Deborah Sementa, Faycal Touti, Derin B Keskin, Catherine J Wu and 3 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Nicholas L TruexDepartment of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Somesh MohapatraDepartment of Materials Science and Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Mariane MeloThe Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA.
Jacob RodriguezDepartment of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Na LiThe Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA.
Wuhbet AbrahamThe Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA.
Deborah SementaDepartment of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Faycal ToutiDepartment of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Derin B KeskinDepartment of Medical Oncology, Dana-Farber Cancer Institute; Boston, Massachusetts, 02215, USA.
Catherine J WuDepartment of Medical Oncology, Dana-Farber Cancer Institute; Boston, Massachusetts, 02215, USA.
Darrell J IrvineDepartment of Materials Science and Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Rafael Gómez-BombarelliDepartment of Materials Science and Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Bradley L PenteluteDepartment of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

Funding

Treatments for Nipah Virus InfectionU54AI057159 · NIAID · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI KIRCHHAUSEN, TOMAS · 2003 to 2013
$113.7M
VIRUS PRODUCTION COREP30CA014051 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Paula T Hammond · 1985 to 2026
$93.9M
Targeting NMDA Receptors and Brain Estradiol to Rescue Memory in Aging FemalesP20GM109091 · NIGMS · UNIVERSITY OF SOUTH CAROLINA AT COLUMBIA · PI KIARIS, HIPPOKRATIS, RONINSON, IGOR B · 2014 to 2024
$25.2M
Systematic identification of minor histocompatibility antigens to address GVHDR01HL157174 · NHLBI · DANA-FARBER CANCER INST · PI HO, VINCENT TRIEN-VINH, KESKIN, DERIN B · 2022 to 2025
$3.0M
Cytosolic Delivery of Tumor Antigens into Dendritic CellsF32CA239362 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI TRUEX, NICHOLAS L · 2020 to 2022
$179k
NCI NIH HHS F32 CA239362NCI NIH HHS P30 CA014051NHLBI NIH HHS R01 HL157174NIAID NIH HHS U54 AI057159NIGMS NIH HHS P20 GM109091
6 · The paper itself

Abstract

Antigen processing is critical for producing epitope peptides that are presented by HLA molecules for T cell recognition. Therapeutic vaccines aim to harness these epitopes for priming cytotoxic T cell responses against cancer and pathogens, but insufficient processing often reduces vaccine efficacy through limiting the quantity of epitopes released. Here, we set out to improve antigen processing by harnessing protein degradation signals called degrons from the ubiquitin-proteasome system. We used machine learning to generate a computational model that ascribes a proteasomal degradation score between 0 and 100. Epitope peptides with varying degron activities were synthesized and translocated into cells using nontoxic anthrax proteins: protective antigen (PA) and the N-terminus of lethal factor (LF

Identifiers

PMID37662211
PMCPMC10473641

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.