Evidence map›Paper›PMID 34980126›Full record

ArticleBMC medical genomics2022

A genomic mutation spectrum of collecting duct carcinoma in the Chinese population.

Huaru Zhang, Xiaojun Lu, Gang Huang, Meimian Hua, Wenhui Zhang, Tao Wang, Liqun Huang, Ziwei Wang, Qing Chen, Jing Li and 2 more

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

Article in BMC medical genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
3.1field-weighted citation impact, top 9% 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

6 citing papers in PubMed, 15 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Review
  6. 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

12 authors at 5 institutions in 1 country.

Huaru Zhang *The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China.
Xiaojun Lu *Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China.
Gang Huang *Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
Meimian Hua *Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China.
Wenhui ZhangDepartment of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China.
Tao WangDepartment of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
Liqun HuangDepartment of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
Ziwei WangDepartment of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China.
Qing ChenDepartment of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China.
Jing LiDepartment of Bioinformatics, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China. ljing@smmu.edu.cn.
Qing YangDepartment of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China. dryangq@gmail.com.
Guosheng YangThe Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China. 2008yangguosheng@sina.com.
Second Military Medical University · CNShanghai East Hospital · CNFirst Affiliated Hospital of Zhengzhou University · CNShanghai Ninth People's Hospital · CNSouthern Medical University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundRenal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In this study, we aimed to identify the genomic mutation spectrum of CDC in the Chinese population.

methodsWhole-exome sequencing was performed using the Illumina Novaseq™ 6000 platform. MuTect2 detects single-nucleotide variants (SNVs) and small scale insertions/deletions (INDELs). The identified mutations were annotated with ANNOVAR and validated by Sanger sequencing. Control-FREEC was used to detect copy number variation (CNV), and GISTIC was applied to detect frequently mutated altered regions. These data were compared with associated The Cancer Genome Atlas cohorts.

resultsTen normal-matched CDC patients were included. The mean tumour mutation burden was 1.37 Mut/Mb. Six new recurrent somatic mutated genes were identified, including RBM14, MTUS1, GAK, DST, RNF213 and XIRP2 (20% and 2 of 10, respectively), and validated by Sanger sequencing. In terms of common mutated genes, SETD2 was altered in both CDC and other RCC subtypes but not in bladder urothelial carcinoma (BLCA); CDKN2A was a driver gene in both CDC (SNV: 10%, 1 of 10) and BLCA but not in other RCC subtypes. Next, 29 amplifications and 6 deletions of recurrent focal somatic CNVs were identified by GISTIC2.0, which displayed differences from kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP) and BLCA cohorts. Of note, CDKN2A (CNV alteration: 30%, 3 of 10) and CDKN2A-AS1 were the only overlapping genes of these four cohorts. Importantly, the CDKN2A mutation in our cohort differed from previous studies in urinary carcinomas. Moreover, CDKN2A-altered cases had significantly worse overall survival than wild-type cases in both KIRC and KIRP cohorts. In addition, the most frequently altered genomic pathway of our CDC cohort was the CDKN2A-mediated p53/RB1 pathway.

conclusionsOur study offers the first genomic spectrum of the Chinese population with CDC, which differs from that of the Western population. The altered CDKN2A-mediated p53/RB1 pathway might provide new insight into potential therapeutic targets for CDC patients.

Indexed as

Carcinoma, Renal CellCarcinoma, Transitional CellKidney NeoplasmsUrinary Bladder NeoplasmsAdenosine TriphosphatasesChinaDNA Copy Number VariationsHumansMutationTumor Suppressor ProteinsUbiquitin-Protein LigasesAdenosine TriphosphatasesMTUS1 protein, humanRNF213 protein, humanTumor Suppressor ProteinsUbiquitin-Protein LigasesCDKN2ACollecting duct carcinomaCopy number variantsSomatic mutations

Identifiers

PMID34980126
PMCPMC8722201
OpenAlexW4205937727

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.