Evidence map›Paper›PMID 36098856›Full record

ArticleJournal of cancer research and clinical oncology2023

Delineation of a T-cell receptor CDR3-cancer mutanome aromaticity factor, assessable via blood samples, that facilitates the establishment of survival distinctions in bladder cancer.

Jacqueline Wahura Waweru, Kennedy Wanjau Mwangi, Vayda R Barker, Etienne C Gozlan, Michelle Yeagley, George Blanck, Francis W Makokha

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of cancer research and clinical oncology, 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, top 88% of its field
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, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 4 institutions in 2 countries.

Jacqueline Wahura WaweruDepartment of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya.
Kennedy Wanjau MwangiDepartment of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya.
Vayda R BarkerDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA.
Etienne C GozlanDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA.
Michelle YeagleyDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA.
George BlanckDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA. gblanck@usf.edu.
Francis W MakokhaDirectorate of Research and Innovation, Mount Kenya University, Thika, 342-01000, Kenya.
University of South Florida · USJomo Kenyatta University of Agriculture and Technology · KEMoffitt Cancer Center · USMount Kenya University · KE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

purposeA very large and still expanding collection of adaptive immune receptor (IR) recombination reads, representing many diseases, is becoming available for downstream analyses. Among the most productive approaches has been to establish risk stratification parameters via the chemical features of the IR complementarity determining region-3 (CDR3) amino acid (AA) sequences, particularly for large datasets where clinical information is available. Because the IR CDR3 AA sequences often play a large role in antigen binding, the chemistry of these AAs has the likelihood of representing a disease-related fingerprint as well as providing pre-screening information for candidate antigens. To approach this issue in a novel manner, we developed a bladder cancer, case evaluation approach based on CDR3 aromaticity.

methodsWe developed and applied a simple and efficient algorithm for assessing aromatic, chemical complementarity between T-cell receptor (TCR) CDR3 AA sequences and the cancer specimen mutanome.

resultsResults indicated a survival distinction for aromatic CDR3-aromatic mutanome complementary, versus non-complementary, bladder cancer case sets. This result applied to both tumor resident and blood TCR CDR3 AA sequences and was supported by CDR3 AA sequences represented by both exome and RNAseq files.

conclusionThe described aromaticity factor algorithm has the potential of assisting in prognostic assessments and guiding immunotherapies for bladder cancer.

Indexed as

Complementarity Determining RegionsUrinary Bladder NeoplasmsAmino Acid SequenceHumansReceptors, Antigen, T-CellReceptors, Antigen, T-Cell, alpha-betaComplementarity Determining RegionsReceptors, Antigen, T-CellReceptors, Antigen, T-Cell, alpha-betaAdaptive immune receptorsBladder cancerCDR3 aromaticityRisk stratificationSurvival distinctions

Identifiers

PMID36098856
PMCPMC11797305
OpenAlexW4295441688

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.