Evidence map›Paper›PMID 40749681›Full record

ArticleCell reports. Medicine2025

Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer.

Matthew V Holt, Yongchao Dou, Meggie N Young, Alexander B Saltzman, Meenakshi Anurag, Jonathan T Lei, Antrix Jain, Mei Leng, Beom-Jun Kim, Lacey E Dobrolecki and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports. Medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Article
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

25 authors.

Matthew V HoltLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Yongchao DouLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Meggie N YoungLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Alexander B SaltzmanAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA.
Meenakshi AnuragLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Jonathan T LeiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Antrix JainAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA.
Mei LengAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA.
Beom-Jun KimLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Lacey E DobroleckiAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA.
Stefanie F FaucherAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA.
Sara SavageLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Chenwei WangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Zhiao ShiLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Hugo VillanuevaAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA; Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX 77030, USA.
Karoline KremersScott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Kyle D DrinnonScott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Patricia D CastroAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA.
Michael M IttmannAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA.
Mehak Mehboob KhataniScott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Sung Han KimScott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Matthew J EllisLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
Bing ZhangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Anna MalovannayaAdvanced Technology Core Facilities, Baylor College of Medicine, Houston, TX 77030, USA.
Seth P LernerScott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: slerner@bcm.edu.

Funding

Tumor BiologyP30CA125123 · NCI · BAYLOR COLLEGE OF MEDICINE · PI Suzanne AW Fuqua · 2007 to 2026
$73.9M
MICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALSU01CA214125 · NCI · BAYLOR COLLEGE OF MEDICINE · PI ANURAG, MEENAKSHI, CARR, STEVEN A · 2017 to 2021
$7.0M
THERMO SCIENTIFIC Q EXACTIVE HF-X HYBRID QUADRUPOLE-ORBITRAP MASS SPECTROMETERS10OD026804 · OD · BAYLOR COLLEGE OF MEDICINE · PI MALOVANNAYA, ANNA · 2019 to 2019
$717k
NCI NIH HHS P30 CA125123NCI NIH HHS U01 CA214125NIH HHS S10 OD026804
6 · The paper itself

Abstract

To explore potential chemoresistance mechanisms and identify therapeutic opportunities in muscle-invasive bladder cancer (MIBC), we conduct comprehensive proteogenomic characterization of 46 pre- and 14 post-treatment MIBC tumors incorporating genomics, transcriptomics, proteomics, and phosphoproteomics. Multi-omics clustering not only recapitulated established molecular subtypes but also revealed subtypes associated with chemotherapy sensitivity. Protein isoform level analysis identifies protein abundance of a short isoform of ATAD1 and RAF family proteins as biomarkers of chemosensitivity. Integration of proteomic and phosphoproteomic data reveals Wnt signaling via GSK3B-S9 phosphorylation and the JAK/STAT pathway as potential targets to overcome chemoresistance. Correlations between PD-L1 and TROP-2/NECTIN-4 indicate an additive benefit of combination therapy targeting these proteins. Overall, this study serves as a valuable resource for researchers and clinicians aiming to better understand and treat chemoresistant MIBC.

Indexed as

Biomarkers, TumorDrug Resistance, NeoplasmProteogenomicsUrinary Bladder NeoplasmsAgedATPases Associated with Diverse Cellular ActivitiesCell Adhesion MoleculesFemaleHumansMaleMiddle AgedNeoplasm InvasivenessProteomicsSignal TransductionATPases Associated with Diverse Cellular ActivitiesBiomarkers, TumorCell Adhesion MoleculesbiomarkerschemoresistanceGSK3Bmuscle-invasive bladder cancerproteogenomicsRAF familySTAT3

Identifiers

PMID40749681
PMCPMC12432383

What OpenQuestion holds

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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.