Evidence map›Paper›PMID 40091688›Full record

ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025

Enhancer Profiling Reveals a Protective Role of RXRα Against Calcium Oxalate-Induced Crystal Deposition and Kidney Injury.

Yu Yang, Xudan Dou, Yongzhan Sun, Mengyao Wang, Jing Wang, Xinyi Cao, Haijie Xie, Linguo Xie, Weiping Tian, Jing Nie and 3 more

Abstract read
In one paragraph

Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Time-Restricted Feeding With High-Fat Diet Slows Weight Gain and Reduces Renal Calcium Oxalate Crystal Formation Without Reducing Energy Intake.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026
    Article
  2. Review
  3. Article
  4. 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

13 authors.

Yu YangDepartment of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
Xudan DouThe Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
Yongzhan SunJiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
Mengyao WangThe Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
Jing WangResearch Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
Xinyi CaoTianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
Haijie XieDepartment of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
Linguo XieDepartment of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
Weiping TianResearch Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
Jing NieBiobank of Peking University First Hospital, Beijing, 100034, China.
Yupeng ChenDepartment of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
Chunyu LiuDepartment of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
Lirong ZhangThe Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.ORCID https://orcid.org/0000-0001-7466-1029

Funding

China Postdoctoral Science Foundation 2022M722380Innovative Research Group Project of the National Natural Science Foundation of China 82300785National Natural Science Foundation of China 32070634National Natural Science Foundation of China 32241018National Natural Science Foundation of China 82070689National Natural Science Foundation of China 82090023National Natural Science Foundation of China 82300785National Natural Science Foundation of China 82371869National Natural Science Foundation of China 92068113Natural Science Foundation of Tianjin 21JCJQJC00100Tianjin Health Science and Technology Project TJWJ2022QN019Tianjin Health Science and Technology Project TJWJ2022ZD004Tianjin Municipal Education Commission 2022ZD054
6 · The paper itself

Abstract

During the formation of kidney stones, the interaction between crystals and tubular epithelial cells (TECs) leads to tubular injury and dysfunction, which in turn promote stone formation. However, the molecular mechanisms underlying these changes in TECs remain elusive. Drug screening revealed that JQ1 inhibited the adhesion of calcium oxalate (CaOx) crystals to TECs. Its therapeutic effect is further confirmed in a glyoxylic acid-induced CaOx crystal deposition mouse model. Utilizing epigenomic and transcriptomic profiling, dynamic enhancer landscape and gene expression program associated with nephrolithiasis are charted. Bioinformatic analysis pinpointing the RXRα as a central transcription factor (TF) modulating enhancer activity. Importantly, the animal studies revealed that RXRα deletion promoted the CaOx crystal deposition, while its activation by Bexarotene (Bex), an FDA-approved drug, mitigated this progression. Mechanistically, under normal circumstances, RXRα inhibited nephrolithiasis-promoting genes by recruiting the HDAC3/SMART complex to repress enhancer activity. Yet, with the progression of CaOx crystal deposition, RXRα expression decreased, leading to enhancer activation and subsequent upregulation of nephrolithiasis-promoting genes. In summary, the work illustrates an epigenetic mechanism underlying TECs fate transition during CaOx crystal deposition and highlights the therapeutic potential of JQ1 and Bex in managing kidney stone diseases.

Indexed as

Calcium OxalateKidney CalculiRetinoid X Receptor alphaAnimalsBexaroteneDisease Models, AnimalEpithelial CellsHumansKidneyMaleMiceMice, Inbred C57BLBexaroteneCalcium OxalateRetinoid X Receptor alphaenhancerepigeneticsJQ1nephrolithiasisRXRα

Identifiers

PMID40091688
PMCPMC12140378

What OpenQuestion holds

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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.