New tricks for an old dog: Brf2-dependent RNA Polymerase III transcription in oxidative stress and cancer

Targeting BRF2: insights from in silico screening and molecular dynamic simulations

The Transcription factor II B (TFIIB)‑related factor 2 (BRF2) containing TFIIIB complex recruits RNA polymerase III multi-subunit complex to selective gene promoters that altogether are responsible for synthesizing a variety of small non-coding RNAs, including a special type of selenocysteine tRNA (tRNASec), micro-RNA (miRNA), and other regulatory RNAs. BRF2 has been identified as a potential oncogene that promotes cancer cell survival under oxidative stress through its genetic activation. The structure of the BRF2 protein was modeled using the Robetta server, refined, and validated using the Ramachandran plot. A virtual approach utilizing molecular docking was used to screen a natural compound library to determine potential compounds that can interact with the molecular pin motif of the BRF2 protein using Maestro (Schrodinger). Subsequent molecular dynamics simulation studies of the top four ligands that exhibited low glide scores were performed using GROMACS. The findings derived from the simulations, in conjunction with the exploration of hydrogen bonding patterns, evaluation of the free energy landscape, and thorough analysis of residue decomposition, collectively converged to emphasize the robust interaction characteristics exhibited by Ligand 366 (Deacetyl lanatoside C) and ligand 336 (Neogitogenin)-with the BRF2 protein. These natural compounds may be potential inhibitors of BRF2, which could modulate the regulation of selenoprotein synthesis in cancer cells. Targeting BRF2 using these promising compounds may offer a new therapeutic approach to sensitize cancer cells to ferroptosis and apoptosis.Communicated by Ramaswamy H. Sarma.

RNA Polymerase III Subunit Mutations in Genetic Diseases

RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.

Nrf2 in Cancer, Detoxifying Enzymes and Cell Death Programs

Reactive oxygen species (ROS) play an important role in cell proliferation and differentiation. They are also by-products of aerobic living conditions. Their inherent reactivity poses a threat for all cellular components. Cells have, therefore, evolved complex pathways to sense and maintain the redox balance. Among them, Nrf2 (Nuclear factor erythroid 2-related factor 2) plays a crucial role: it is activated under oxidative conditions and is responsible for the expression of the detoxification machinery and antiapoptotic factors. It is, however, a double edge sword: whilst it prevents tumorigenesis in healthy cells, its constitutive activation in cancer promotes tumour growth and metastasis. In addition, recent data have highlighted the importance of Nrf2 in evading programmed cell death. In this review, we will focus on the activation of the Nrf2 pathway in the cytoplasm, the molecular basis underlying Nrf2 binding to the DNA, and the dysregulation of this pathway in cancer, before discussing how Nrf2 contributes to the prevention of apoptosis and ferroptosis in cancer and how it is likely to be linked to detoxifying enzymes containing selenium.

Amplification of 8p11.23 in cancers and the role of amplicon genes

Copy number alterations are widespread in cancer genomes and are part of the genomic instability underlying the pathogenesis of neoplastic diseases. Recurrent copy number alterations of specific chromosomal loci may result in gains of oncogenes or losses of tumor suppressor genes and become entrenched in the genomic framework of certain types of cancers. The locus at chromosome 8p11.23 presents recurrent amplifications most commonly in squamous lung carcinomas, breast cancers, squamous esophageal carcinomas, and urothelial carcinomas. Amplification is rare in other cancers. The amplified segment involves several described oncogenes that may promote cancer cell survival and proliferation, as well as less well characterized genes that could also contribute to neoplastic processes. Genes proposed to be "drivers" in 8p11.23 amplifications include ZNF703, FGFR1 and PLPP5. Additional genes in the locus that could be functionally important in neoplastic networks include co-chaperone BAG4, lysine methyltransferase NSD3, ASH2L, a member of another methyltransferase complex, MLL and the mRNA processing and translation regulators LSM1 and EIF4EBP1. In this paper, genes located in the amplified segment of 8p11.23 will be examined for their role in cancer and data arguing for their importance for cancers with the amplification will be presented.

8p11.23 Amplification in Breast Cancer: Molecular Characteristics, Prognosis and Targeted Therapy

BACKGROUND

Amplification of the locus 8p11.23 has been observed in cancer and genes of this locus, including ZNF703 (Zinc finger protein 703), NSD3 (Nuclear receptor binding SET domain protein 3) and FGFR1 (Fibroblast growth factor receptor 1), have been put forward as dominant oncogenes conferring pathophysiologic benefit in cancers with amplifications. However, there is no consensus on the importance of each of them or any other genes of the amplicon or even a consensus on which genes are part of the amplicon.

METHODS

Publicly available data were used to characterize the locus amplified at 8p11.23 and derive information on each of the genes and roles as oncogenes. The frequency of the amplifications in the locus was examined in the cBioportal platform, and expression levels of the amplicon genes in amplified cases were derived from genomic studies reported in the platform. Examination of the influence of mRNA expressions of each gene of the locus for Recurrence-free survival in breast cancer was performed using K-M plotter.

RESULTS

The 8p11.23 amplicon is present in higher frequency in squamous cell lung carcinomas, breast cancers and bladder carcinomas and is only rarely observed in other cancers. The most frequently amplified genes within the amplicon vary between different types of cancers. In breast cancer, amplified cases are most commonly of the luminal B type. Amplified genes are not always over-expressed and there is a low correlation of amplification with over-expression in amplicon genes with variation between genes. The presence of the amplicon does not influence the aneuploidy score or the tumor mutation burden of breast cancers. Regarding prognosis, the two genes of the amplicon whose mRNA hyper-expression portends adverse relapse-free survival in breast cancer are EIF4EBP1 (Eukaryotic transcription initiation factor 4E binding protein 1) and LSM1 (LSM1 homolog, mRNA degradation associated).

CONCLUSION

Besides the previously proposed genes to play a role as dominant oncogenes in the 8p11.23 cancer amplified locus, other genes may also be important in breast cancer based on the high correlation of their amplification and mRNA expression and adverse prognosis conferred by over-expression, consistent with an oncogenic role.

Anti-RNA polymerase III antibody in lupus patients with proteinuria

BACKGROUND

To investigate the relationship between serum anti-ribonucleic acid polymerase III (anti-RNAP3) autoantibodies (Abs) and proteinuria severity in lupus patients.

METHODS

Serum antibodies reacting with anti-RNAP3 were measured in 49 systemic lupus erythematosus (SLE) patients (29 cases of SLE with proteinuria and 20 cases of SLE without proteinuria) and 10 healthy controls (HCs). For the patients, we recorded demographic data, daily urinary protein loss, serum anti-double strand deoxyribonucleic acid (anti-ds-DNA) antibodies, serum creatinine (Cr), estimated glomerular filtrating rate (eGFR), complement 3 (C3), and C4.

RESULTS

Fewer anti-RNAP3 antibodies were found in the SLE patients than in the HCs (p = 0.061). In the SLE with proteinuria group, positive correlations were observed among anti-RNAP3 antibodies and daily urinary protein loss, serum C3, C4, and eGFR, and negative correlations were observed between anti-RNAP3-Abs and anti-ds-DNA-Abs and serum Cr levels. However, these correlations were nonsignificant (p > 0.05).

CONCLUSION

This study demonstrated the possible role of anti-RNAP3 antibodies in SLE patients with proteinuria, as evidenced by their positive and negative relationships with daily urinary protein loss, eGFR, C3, C4, serum Cr, and anti-ds-DNA-Abs. Although these correlations were nonsignificant, our study builds a foundation for future tailored studies, and more in-depth studies with larger samples are warranted to provide more information.

BRF2 as a promising indicator for radical lymph-node dissection surgery in patients with cN0 squamous cell carcinoma of the middle thoracic esophagus

PURPOSE

Radical lymph-node dissection surgery in patients with cN0 middle thoracic esophageal squamous cell carcinoma (ESCC) remains controversial. We sought a novel biomarker that could be used for decision-making in relation to radical lymph-node dissection.

METHODS

One hundred and nineteen patients with cN0 middle thoracic ESCC undergoing three-field lymph-node dissection (3FLND) or two-field lymph-node dissection (Ivor Lewis) esophagectomy were reviewed. A survival analysis, and Chi-square and parametric tests were performed.

RESULTS

A Cox regression analysis revealed that the expression of BRF2 was an independent prognostic factor for overall survival (P = 0.014) and progression-free survival (P = 0.014). The survival of patients who underwent 3FLND was better than that of patients who underwent Ivor Lewis esophagectomy in the BRF2 overexpression group (P = 0.002), but not in the BRF2 nonoverexpression group (P = 0.386). The risk of lymph-node recurrence and the number of recurrent lymph nodes in patients with the overexpression of BRF2 were increased in the Ivor Lewis group in comparison to the 3FLND group (P = 0.01 and P < 0.001). The risk of cervical and superior mediastinal lymph-node recurrence was positively correlated with the overexpression of BRF2 (P = 0.027). Furthermore, in the Ivor Lewis group, a significant correlation was found between the risk of lymph-node recurrence or the number of recurrent lymph nodes and the expression of BRF2 (P = 0.002 and P = 0.004), but not in the 3FLND group (P = 0.193 and P = 0.694).

CONCLUSIONS

3FLND generated better survival outcomes and reduced the rate of lymph-node recurrence in comparison to Ivor Lewis in patients with the overexpression of BRF2. BRF2 can be used as an indicator for radical lymph-node dissection surgery in cN0 ESCC patients.