RNA N6-methyladenosine: a new player in autophagy-mediated anti-cancer drug resistance.

Dysregulation of N6-methyladenosine (m6A) modification is associated with cancer development and progression. The m6A modification plays a crucial role in autophagy regulation precipitating anti-cancer drug resistance. In line with this fact, this commentary discusses m6A modification interfering with autophagy machinery as a major contributing factor for drug resistance in cancer.

Prevalence of carbapenem-hydrolyzing OXA-type ß-lactamases among Acinetobacter baumannii in patients with severe urinary tract infection.

Acinetobacter baumannii produces carbapenemase-hydrolyzing class D ß-lactamases (CHDLs) as one of the major drug resistance mechanisms. This investigation is thus aimed to assess the prevalence and to characterize the CHDL-producing strains of A. baumannii by both phenotypic assays and genotypic characterization. A total of 73 isolates of A. baumannii were phenotypically and genotypically characterized from patients (N = 1,000) with severe urinary tract infection. Tested strains were subjected to double disk synergy testing by Kirby-Bauer disk diffusion method with modified Hodge test (MHT) for carbapenemase production. Plasmid DNA was molecularly screened for CHDL-encoding blaoxa-51, blaoxa-23, and blaoxa-143 genes by polymerase chain reaction. Carbapenem-resistant profile showed 100%, 61.64%, and 67.12% resistance by Kirby-Bauer disk diffusion method that correlated with MHT positivity for 100% (n = 73), 80% (n = 36), and 78% (n = 38) of the isolates against imipenem, doripenem, and meropenem, respectively. The blaoxa-51 and blaoxa-23 were observed in 41.09% (n = 30) and 35.61% (n = 26) with co-occurrence in 4.10% (n = 3) of the isolates. MHT-positive isolates showed 100%, 91.66%, and 71.4% for blaoxa-51 and 91.78%, 51.11%, and 34.69% for blaoxa-23 with imipenem, doripenem, and meropenem resistance, respectively. None of the strains yielded blaoxa-143 gene. The findings of this study showed prevalence of carbapenem resistance and high frequency of blaoxa-51 and blaoxa-23 among A. baumannii.

Emerging Role of RNA m5C Modification in Cardiovascular Diseases.

Epitranscriptomics is the emerging field of research that comprises the study of epigenetics changes in RNAs. Progressing development in the field of epigenetics has helped to manage and comprehend human diseases. RNA methylation regulates all aspects of RNA functions, which are involved in the pathogenesis of human diseases. Interestingly, RNA m5C methylation is significantly linked to various types of human disease, including cardiovascular diseases (CVD). The m5C methylation is controlled by m5C regulatory proteins, which act as methyltransferase, demethyltransferase, and RNA-binding protein. Dysregulated expression in m5C regulatory proteins is significantly associated with cardiovascular disease, and these regulatory proteins have crucial roles in biological and cellular functions. This review is mainly focused on the role of RNA m5C modification in CVD and mitochondrial dysfunction. Thus, m5C will contribute to discovering the new diagnostic marker and therapeutic target for CVD.

Genomic and transcriptomic alterations in m6A regulatory genes are associated with tumorigenesis and poor prognosis in head and neck squamous cell carcinoma.

Genetic alterations in N6-methyladenosine (m6A) regulatory genes are observed in many cancers. Recent studies have shown that newly identified m6A regulatory gene family (IGF2BPs; IGF2BP1, IGF2BP2, and IGF2BP3) were highly expressed in various types of cancer that stabilize and promote translation of multiple oncogenes, resulting in tumor development, survival and drug resistance. However, the oncogenic roles and prognostic values of IGF2BPs in head and neck squamous cell carcinoma (HNSCC) remain largely unknown. In this study, we examined the m6A regulatory genes alteration, their mRNAs expression and the prognostic values in HNSCC. We also analyzed the interaction network and functional enrichment of m6A regulators. Our results showed that m6A regulatory genes were altered in 41% (205/504) of HNSCC patients, of which IGF2BP2 was amplified in 20% (101/504) of HNSCC patents and positively correlated with its mRNA expression. Importantly, we have validated the expression of IGF2BP2 in HNSCC and normal tissue samples. Interestingly, we also found that the IGF2BP2 was frequently co-amplified with the most common oncogenes in HNSCC patients. In addition, this study found that other m6A regulatory genes such as METTL3, METTL14, WTAP, KIAA1429, ZC3H13, RBM15, ALKBH5, FTO, YTHDF1, YTHDF2, YTHDF3, YTHDC1, IGF2BP1, and IGF2BP3 were significantly upregulated in HNSCC samples. Moreover, patients with high expression of IGF2BP1, IGF2BP2, and IGF2BP3 had poor overall survival (OS) than those with low expression. Therefore, it is evident that IGF2BP family plays a key role in the oncogenesis of HNSCC and might serve as novel prognostic biomarkers and potential therapeutic targets in HNSCC.

Deciphering the genetic alterations in matrix metallo-proteinase gene family and its putative association with head and neck squamous cell carcinoma.

Matrix metallo-proteinases (MMPs) a group of zinc-dependent proteolytic enzymes which play a key role in tumorigenesis by degrading almost all extracellular matrix (ECM) components. MMPs are associated with tumour progression including invasion, angiogenesis, metastasis and poor prognosis. Genetic alterations such as single nucleotide variations and other gross chromosomal abnormalities have been found to drive the process of malignant transformation. In line with the above facts, the present study aims to analyse the genetic alterations, associated gene expression patterns and survival probability of HNSCC patients upon differential expression of the crucial members of the MMP family. The observational study utilised several computational tools. The cBioportal database was used as the primary source of identification of genetic alterations in the MMP family of genes. The Cancer Gene Atlas dataset (Firehose Legacy) was used for the investigations. The highest frequency of alteration was identified in the MMP20 gene (8%). The common gene alterations were amplifications, deep deletions, mis-sense and truncating mutations. Interestingly, amplification and deep deletion followed the same pattern in about 31 patients, in genes MMP1, 3, 7, 8, 10, 12, 20, and 27. The MMP20 gene expression analysis showed a significant difference between the normal subjects and the patients with primary tumors (6.95 x 10-4). The Kaplan-Meier survival curve analysis identified that female patients with high-level expression of the MMP20 gene had a low survival probability when compared to male HNSC patients. Taken together, the present study provides preliminary information about the involvement of the MMP20 gene of the MMP family with HNSCC. Further experimental analysis is required to derive a strong association between the gene alterations observed with HNSCC.

Repurposing calcium channel blockers as antiviral drugs.

The current pandemic caused by the SARS-CoV-2 has claimed over a half a million lives within a very short span of time. A therapeutic drug which could prevent the entry and propagation of the virus is the need of the hour. Several lines of evidence collected from experimental studies older than three decades have pointed out the fact that inhibiting calcium entry into cells can affect vital steps in the lifecycle of viruses. Hence, calcium channel blockers may be considered as an effective measure in the containment of the viruses. This commentary throws light two scientific papers although with divergent facts converging at a point by suggesting a promising treatment option for CoVID-19 (Fang et al. Lancet Respir Med 8:e21, 2020; Straus et al. J Virol 94:e00426, 2020).

The m6A readers YTHDF1 and YTHDF3 aberrations associated with metastasis and predict poor prognosis in breast cancer patients.

N6-Methyladenosine (m6A) is the most common RNA modification in eukaryotic mRNAs and growing evidence suggests the crucial roles of m6A and its regulators in human tumorigenesis. Recent studies have shown that the m6A regulators promote tumorigenesis of various types of cancer. However, the underlying molecular mechanisms of m6A regulators in breast cancer remain largely unknown. We therefore assessed the genetic alterations, expression and prognostic role of m6A regulators in breast cancer using openly available data from The Cancer Genome Atlas (TCGA). Analysis of TCGA data revealed that m6A regulators including KIAA1429, YTHDF1, and YTHDF3 were upregulated in breast cancer tissues, and the expression level significantly correlated with intrinsic subclasses and nodal metastasis. Importantly, we found for the first time that YTHDF1 and YTHDF3 were frequently amplified which contribute to the overexpression of YTHDF1 and YTHDF3 transcripts, thereby promoting breast cancer progression. Moreover, overexpression of YTHDF1 and YTHDF3 were associated with poor prognosis of breast cancer patients. Therefore, YTHDF1 and YTHDF3 serve a crucial role in the pathogenesis of breast cancer, which are potentially useful for prognosis stratification and therapeutic target for breast cancer.

Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta.

Amelogenin gene (AMEL-X) encodes an enamel protein called amelogenin, which plays a vital role in tooth development. Any mutations in this gene or the associated pathway lead to developmental abnormalities of the tooth. The present study aims to analyze functional missense mutations in AMEL-X genes and derive an association with amelogenesis imperfecta. The information on missense mutations of human AMEL-X gene was collected from Ensembl database (https://asia.ensembl.org). Three different computational tools viz., SIFT, PolyPhen and PROVEAN were used to identify the deleterious or pathogenic forms of mutations in the gene studied. I-Mutant Suit was used to identify the stability of the proteins identified as deleterious by the three tools. Further, MutPred analysis revealed the pathogenicity of these mutations. Among 96 missense variants reported in AMEL-X gene, 18 were found to be deleterious using the three prediction tools (SIFT, PolyPhen and PROVEAN). When these variants were subjected to protein stability analysis, about 14 missense variants showed decreased stability whereas the other 8 variants showed increased stability. Further, these variants were analyzed using MutPred which identified 9 variants to be highly pathogenic. ExAC database revealed that all the pathogenic mutations had a minor allele frequency less than 0.01. The in silico analysis revealed highly pathogenic mutations in amelogenin gene which could have a putative association with amelogenesis imperfecta. These mutations should be screened in patients for early diagnosis of susceptibility to AI.

Correction to: Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.

The article "Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures".

Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.

Epitranscriptomic systems enable post-transcriptional modifications of cellular RNA that are essential for regulating gene expression. Of the ~ 170 known RNA chemical modifications, methylation is among the most common. Loss of function mutations in NSUN3, encoding the 5-methylcytosine (m5C) methyltransferase NSun3, have been linked to multisystem mitochondrial disease associated with combined oxidative phosphorylation deficiency. Here, we report a patient with early-onset mitochondrial encephalomyopathy and seizures in whom the novel biallelic NSUN3 missense variants c.421G>C (p.A141P) and c.454T>A (p.C152S) were detected. Segregation studies and in silico functional analysis confirmed the likely pathogenic effects of both variants. These findings expand the molecular and phenotypic spectrum of NSUN3-related mitochondrial disease.

Homozygous R627W mutations in POLG cause mitochondrial DNA depletion leading to encephalopathy, seizures and stroke-like episodes.

Mutations in the mitochondrial DNA maintenance gene POLG (DNA Polymerase Gamma, Catalytic Subunit), encoding mitochondrial DNA polymerase gamma (pol γ), are associated with an extremely broad phenotypic spectrum. We identified homozygous POLG c.1879C>T; p.R627W mutations in two siblings from a consanguineous South Asian family following targeted resequencing of 75 nuclear-encoded mitochondrial genes. Both patients presented with encephalopathy, seizures and stroke-like episodes, and mitochondrial DNA depletion was confirmed in the proband's muscle tissue. Subsequent Sanger sequencing of POLG in a further 275 unrelated probands with genetically unconfirmed mitochondrial disease revealed a third unrelated proband with a similar phenotype harboring homozygous c.1879C>T; p.R627W mutations and a fourth patient, with a milder clinical disorder, harboring compound heterozygous POLG c.1879C>T; p.R627W and c.2341G>A; p.A781T mutations. Given endogamous practices in the Indian subcontinent, homozygous POLG c.1879C>T; p.R627W mutations should be excluded in South Asian patients presenting with encephalopathy, seizures and stroke-like episodes.

Outcome of epilepsy in patients with mitochondrial disorders: Phenotype genotype and magnetic resonance imaging correlations.

OBJECTIVES: Studies exploring the outcome of epilepsy in patients with mitochondrial disorders are limited. This study examined the outcome of epilepsy in patients with mitochondrial disorders and its relation with the clinical phenotype, genotype and magnetic resonance imaging findings. PATIENTS AND METHODS: The cohort was derived from the database of 67 patients with definite genetic diagnosis of mitochondrial disorders evaluated over a period of 11years (2006-2016). Among this, 27 had epilepsy and were included in final analysis. Data were analyzed with special reference to clinical phenotypes, genotypes, epilepsy characteristics, EEG findings, anti epileptic drugs used, therapeutic response, and magnetic resonance imaging findings. Patients were divided into three groups according to the seizure frequency at the time of last follow up: Group I- Seizure free; Group II- Infrequent seizures; Group III- uncontrolled seizures. For each group the clinical phenotype, genotype, magnetic resonance imaging and duration of epilepsy were compared. RESULTS: The phenotypes & genotypes included Mitochondrial Encephalopathy Lactic Acidosis and Stroke like episodes (MELAS) & m.3243A>G mutation (n = 10), Myoclonic Epilepsy Ragged Red Fiber syndrome (MERRF) & m.8344A>G mutation (n = 4), Chronic Progressive External Ophthalmoplegia plus &POLG1 mutation (CPEO, n = 6), episodic neuroregression due to nuclear mutations (n = 6; NDUFV1 (n = 3), NDUFA1, NDUFS2, MPV17-1 one each), and one patient with infantile basal ganglia stroke syndrome, mineralizing angiopathy &MT-ND5 mutations. Seven patients (25.9%) were seizure free; seven had infrequent seizures (25.9%), while thirteen (48.1%) had frequent uncontrolled seizures. Majority of the subjects in seizure free group had episodic neuroregression & leukoencephalopathy due to nuclear mutations (85.7%). Patients in group II with infrequent seizures had CPEO, POLG1 mutation and a normal MRI (71%) while 62% of the subjects in group III had MELAS, m.3243A>G mutation and stroke like lesions on MRI. CONCLUSIONS: A fair correlation exists between the outcome of epilepsy, clinical phenotypes, genotypes and magnetic resonance imaging findings in patients with mitochondrial disorders. The recognition of these patterns is important clinically because of the therapeutic and prognostic implications.