Genes Located on 18q23 Are Epigenetic Markers and Have Prognostic Significance for Patients with Head and Neck Cancer

Misawa, Kiyoshi; Kanazawa, Takemichi; Mochizuki, Daiki; Imai, Atsushi; Mima, Masato; Yamada, Satoshi; Morita, K.; Misawa, Yuki; Shinmura, Kazuya; Mineta, Hiroyuki

doi:10.3390/cancers11030401

Cited by 7 publications

(13 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It was detected in HepG2 and LNCaT cell lines by Professor Mann’s group 32 using the deep proteome coverage (8–12 thousand protein groups in the identification list) with original SPIDER technology of low-loss digest mixture separation. Information has been published about the involvement of this gene in the development head and neck cancer 40 , pancreas adenocarcinomas 41 . HSBP1L1 is involved in chemical hepatocyte injury 42 , prioritizing this target to investigate the genetic aspects of liver diseases.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Human Chr18: “Stakhanovite” Genes, Missing and uPE1 Proteins in Liver Tissue and HepG2 Cells

Krasnov

Лисица

Ponomarenko

et al. 2020

Preprint

View full text Add to dashboard Cite

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets has changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors compared with the HepG2 cell line. The data mining of Expression Atlas (EMBL-EBI) and the profiling of our biospecimens using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except for selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of Russian C-HPP Consortia. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and analytical platform. Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation. The dependence on the choice of bioinformatics analysis pipeline was also noticeable but significantly less. Furthermore, the combination of Illumina HiSeq and ONT MinION sequencing to validate proteotypic peptides of missing and uPE1 proteins was performed for the heat-shock factor binding protein HSBP1L1 (missing protein, recently transferred to PE1 category) and uncharacterized protein C18orf21 (uPE1). We observed that a nonsynonymous SNP led to the loss of the site of trypsinolysis in HSBP1L1. The modified version of HSBP1L1 was included in the sequence database and searched against the MS/MS dataset from Kulak, Geyer & Mann (2017), but delivered no significant identification. Thus, HSBP1L1 is still missing for the MS-pillar of C-HPP, although its existence at the protein level has been confirmed.

show abstract

Section: Resultsmentioning

confidence: 99%

“…The use of the EMBL-EBI's gene ExpressionAtlas 38 40 , pancreas adenocarcinomas 41 . HSBP1L1 is involved in chemical hepatocyte injury 42 , prioritizing this target to investigate the genetic aspects of liver diseases.…”

Section: Overview Of Chr18-coded Missing and Upe1 Proteinsmentioning

confidence: 99%

Human Chr18: “Stakhanovite” Genes, Missing and uPE1 Proteins in Liver Tissue and HepG2 Cells

Krasnov

Лисица

Ponomarenko

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, the expression of GALR1 could be recovered by treatment with the histone deacetylase inhibitor, trichostatin A, and the methyltransferase inhibitor, 5-azacytodine [ 11 ]. The status of GALR1 methylation may be an important site-specific biomarker for predicting clinical outcomes in HNSCC patients, and assessing methylation of its promoter can play a role in risk stratification for individualized treatment [ 12 , 13 ]. GALR1 has also been used in the formation of a risk model to diagnose non-small-cell lung cancer (NSCLC) [ 14 ].…”

Section: Discussionmentioning

confidence: 99%

A Three Protein-Coding Gene Prognostic Model Predicts Overall Survival in Bladder Cancer Patients

Ning

Wang

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

Bladder cancer (BLCA) is the most common urinary tract tumor and is the 11th most malignant cancer worldwide. With the development of in-depth multisystem sequencing, an increasing number of prognostic molecular markers have been identified. In this study, we focused on the role of protein-coding gene methylation in the prognosis of BLCA. We downloaded BLCA clinical and methylation data from The Cancer Genome Atlas (TCGA) database and used this information to identify differentially methylated genes and construct a survival model using lasso regression. We assessed 365 cases, with complete information regarding survival status, survival time longer than 30 days, age, gender, and tumor characteristics (grade, stage, T, M, N), in our study. We identified 353 differentially methylated genes, including 50 hypomethylated genes and 303 hypermethylated genes. After annotation, a total of 227 genes were differentially expressed. Of these, 165 were protein-coding genes. Three genes (zinc finger protein 382 (ZNF382), galanin receptor 1 (GALR1), and structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1)) were selected for the final risk model. Patients with higher-risk scores represent poorer survival than patients with lower-risk scores in the training set ( HR = 2.37 , 95% CI 1.43-3.94, p = 0.001 ), in the testing group ( HR = 1.85 , 95% CI 1.16-2.94, p = 0.01 ), and in the total cohort ( HR = 2.06 , 95% CI 1.46-2.90, p < 0.001 ). Further univariate and multivariate analyses using the Cox regression method were conducted in these three groups, respectively. All the results indicated that risk score was an independent risk factor for BLCA. Our study screened the different methylation protein-coding genes in the BLCA tissues and constructed a robust risk model for predicting the outcome of BLCA patients. Moreover, these three genes may function in the mechanism of development and progression of BLCA, which should be fully clarified in the future.

show abstract

“…The SALL promoters are also aberrantly methylated in HPV-related cancers. Several studies indicate that the hypermethylation of SALL1 and SALL3 promoters correlates with poor outcomes and recurrence in head and neck squamous cell carcinoma (HNSCC) [ 95 , 96 , 97 ]. However, SALL4 is upregulated in this type of cancer, and its expression correlates with disease recurrence and decreased disease-free survival.…”

Section: Common Regulatory Mechanisms For Sall Proteins In Cancermentioning

confidence: 99%

SALL Proteins; Common and Antagonistic Roles in Cancer

Álvarez

Quiroz

Benítez-Riquelme

et al. 2021

Cancers

View full text Add to dashboard Cite

SALL proteins are a family of four conserved C2H2 zinc finger transcription factors that play critical roles in organogenesis during embryonic development. They regulate cell proliferation, survival, migration, and stemness; consequently, they are involved in various human genetic disorders and cancer. SALL4 is a well-recognized oncogene; however, SALL1–3 play dual roles depending on the cancer context and stage of the disease. Current reviews of SALLs have focused only on SALL2 or SALL4, lacking an integrated view of the SALL family members in cancer. Here, we update the recent advances of the SALL members in tumor development, cancer progression, and therapy, highlighting the synergistic and/or antagonistic functions they perform in similar cancer contexts. We identified common regulatory mechanisms, targets, and signaling pathways in breast, brain, liver, colon, blood, and HPV-related cancers. In addition, we discuss the potential of the SALL family members as cancer biomarkers and in the cancer cells’ response to therapies. Understanding SALL proteins’ function and relationship will open new cancer biology, clinical research, and therapy perspectives.

show abstract

Genes Located on 18q23 Are Epigenetic Markers and Have Prognostic Significance for Patients with Head and Neck Cancer

Cited by 7 publications

References 34 publications

Human Chr18: “Stakhanovite” Genes, Missing and uPE1 Proteins in Liver Tissue and HepG2 Cells

Human Chr18: “Stakhanovite” Genes, Missing and uPE1 Proteins in Liver Tissue and HepG2 Cells

A Three Protein-Coding Gene Prognostic Model Predicts Overall Survival in Bladder Cancer Patients

SALL Proteins; Common and Antagonistic Roles in Cancer

Contact Info

Product

Resources

About