Sequence Alterations Research Articles

Epigenetics and its essence in understanding human growth, development and disease

Epigenetics is a scientific discipline encompassing the genetic and non-genetic related perspectives of heritable phenotypic modifications of whose aetiologies include behavioural, anthropogenic, environmental, metabolic and spatiotemporal variables. Behavioral epigenetics examines how epigenetics shapes animal and human behaviour to explicate how nurture moulds nature; nature prefers to biological heredity and nurture prefers to occurrrences in the environment and hereditary during the lifespan of all individuals. Behavioural epigenetics features how experiences and the environment produce individual disparities in behaviour, cognition, personality, and mental health influence gene expression. Epigenetic gene regulation relates to modification of DNA sequence and histones as well as DNA methylation. These epigenetic alterations effect the growth of neurons in the developing brain and functional modification of neurons in the developed brain, with resultant significant alterations in neuron morphology. Epigenetic changes occur in the developing fetus and throughout the lifespan of an individual, with alterations in individual traits and transgenerational inheritance. Epigenetics is associated with heritable changes in gene actions and these are not due to DNA sequence alterations. Epigenetics may be termed sustained, long-run changes in the transcription veracity of a heritable or non-heritable cell. DNA methylation and histone alteration are mechanisms which modify gene expression without changing the underlying DNA sequence. Gene expression is driven by repressor protein actions which bind to DNA silencer regions.DNA methylation turns a gene ''off'' culminating in genetic information impairment to be read from DNA, but extricating the methyl tag can turn ''on'' the gene. Histone alteration defines the packaging of DNA into the chromosomes; and.these changes influence gene expression. This review provides the latitude to examine the extant information in the universal characterizations of epigenetic formulations, such as ageing, susceptibility to pollutant and irritant exposure.

Epigenetic Dysregulation in Autoimmune and Inflammatory Skin Diseases.

Epigenetics is the study of heritable, reversible gene expression patterns that do not originate from alterations in the DNA sequence. Epigenetic modifications influence gene expression patterns and include DNA methylation, histone modifications, and gene regulation via non-coding RNAs. While the study of epigenetics has been most broadly applied to neoplastic diseases, the role of the epigenome in a wide range of disease processes including autoimmune, allergic, and inflammatory processes is increasingly being recognized. Recent advances in the study of the epigenome have led to novel insights into the pathogenesis and potential therapeutic targets of various pathologic entities including inflammatory diseases. In this review, we examine the nature of epigenetic modifications in several well-studied autoimmune, allergic, and/or inflammatory disorders of the skin including systemic lupus erythematosus, vitiligo, systemic sclerosis, alopecia areata, pemphigus, psoriasis, atopic dermatitis, keloidal scarring, and hidradenitis suppurativa with the aim to determine how such epigenetic changes may be targeted for therapeutic benefit.

Intron-encoded cistronic transcripts for minimally invasive monitoring of coding and non-coding RNAs

Despite their fundamental role in assessing (patho)physiological cell states, conventional gene reporters can follow gene expression but leave scars on the proteins or substantially alter the mature messenger RNA. Multi-time-point measurements of non-coding RNAs are currently impossible without modifying their nucleotide sequence, which can alter their native function, half-life and localization. Thus, we developed the intron-encoded scarless programmable extranuclear cistronic transcript (INSPECT) as a minimally invasive transcriptional reporter embedded within an intron of a gene of interest. Post-transcriptional excision of INSPECT results in the mature endogenous RNA without sequence alterations and an additional engineered transcript that leaves the nucleus by hijacking the nuclear export machinery for subsequent translation into a reporter or effector protein. We showcase its use in monitoring interleukin-2 (IL2) after T cell activation and tracking the transcriptional dynamics of the long non-coding RNA (lncRNA) NEAT1 during CRISPR interference-mediated perturbation. INSPECT is a method for monitoring gene transcription without altering the mature lncRNA or messenger RNA of the target of interest.

Epigenetic-related Effects of COVID-19 on Human Cells.

Epigenetics is related to the various pathways that show long-term impacts on the gene expression patterns without alterations in nucleotide sequences. Over the last decade, epigenetics advanced significantly in the science of biology, oncology, innate immunity as well as pathogens and infectious diseases. In the present paper, we aimed to review the relationships between COVID-19 and epigenetic alterations of the infected cells. Coronavirus is one of the known infectious diseases that causes respiratory infection, such as pneumonia and coughing, while in animals, it causes diarrhea and upper respiratory disorders. This virus could be transmitted human to human or human to an animal through droplets. It translocates via membrane ACE-2 exopeptidase into the host cells. In conclusion, hypomethylation of angiotensin II converting enzyme (ACE II) possibly upregulates its expression, enhancing the possibility of SARS-CoV-2 infection.

Integrated metabolomic and transcriptomic analysis of the anthocyanin and proanthocyanidin regulatory networks in red walnut natural hybrid progeny leaves.

BackgroundWalnuts are among the most important dry fruit crops worldwide, typically exhibiting green leaves and yellow–brown or gray–yellow seed coats. A specific walnut accession with red leaves and seed coats, ‘RW-1’, was selected for study because of its high anthocyanin and proanthocyanidin (PA) contents. Anthocyanins and PAs are important secondary metabolites and play key roles in plant responses to biotic and abiotic stresses. However, few studies have focused on the molecular mechanism of anthocyanin biosynthesis in walnuts.MethodsIn this study, we determined the anthocyanin and PA components and their contents in different color leaves of ‘RW-1’ natural hybrid progenies at various developmental stages. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). We also performed conjoint analyses on DEGs and DAMs to ascertain the degree pathways, and explore the regulation of anthocyanin and PA biosynthesis.ResultsThe results of widely targeted metabolome profiling and anthocyanin detection revealed 395 substances, including four PAs and 26 anthocyanins, in red (SR) and green leaves (SG) of ‘RW-1’ natural hybrid progenies. From the research, the contents of all anthocyanin components in SR were higher than that in SG. Among them, the contents of delphinidin 3-O-galactoside, cyanidin 3-O-galactoside, delphinidin 3-O-arabinoside and cyanidin 3-O-glucoside were significantly higher than others, and they were considered as the main types of anthocyanins. However, nine anthocyanins were detected only in SR. For PAs, the content of procyanidin C1 was higher in SR compared with SG, while procyanidin B1 and procyanidin B3 were higher in SR-1 and SR-3 but downregulated in SR-2 compared with the controls. Furthermore, transcriptome analysis revealed that the expressions of structural genes (C4H, F3H, F3′5′H, UFGT, LAR and ANR), three MYBs predicted as the activators of anthocyanin and PA biosynthesis, two MYBs predicted as the repressors of anthocyanin biosynthesis, and five WD40s in the anthocyanin and PA biosynthetic pathways were significantly higher in the SR walnuts. Gene-metabolite correlation analyses revealed a core set of 31 genes that were strongly correlated with four anthocyanins and one PA metabolites. The alteration of gene coding sequence altered the binding or regulation of regulatory factors to structural genes in different color leaves, resulting in the effective increase of anthocyanins and PAs accumulation in red walnut.ConclusionsThis study provides valuable information on anthocyanin and PA metabolites and candidate genes for anthocyanin and PA biosynthesis, yielding new insights into anthocyanin and PA biosynthesis in walnuts.

Fine Mapping and Candidate-Gene Analysis of an open glume multi-pistil 3 (mp3) in Rice (Oryza sativa L.)

The rice mutant mp3 was derived from an indica–japonica cross between Rejing35 and XieqingzaoB, producing an inconstant number of pistils ranging from one to four pistils in a floret at heading stage, which also developed an open-glume with one or two seeds and twin seedlings at mature and seedling stage. Several altered characteristics, including filling grain panicle–1 (62.90), grain-setting rate (60.48%) and grain yield plant–1 (13.42 g), decreased but an increase in 1000-grain weight (36.87 g) was observed. Genetic analysis revealed that the mp3 mutant phenotype was controlled by a single recessive gene. Using a chromosome walking strategy in the F2 population of 02428/mp3, the mp3 gene was fine mapped between L3-135 and RM7576, with a physical distance of 30.617 kb on rice chromosome 3. Four candidate genes were found in this region referred to the rice genome annotations. LOC_Os03g11614/OsMADS1 corresponded with the mutant mp3 phenotype. Sequencing showed no sequence alterations in the coding and promoter sequence of the LOC_Os03g11614/OsMADS1 of mp3. The mp3 gene may be an allelic gene with three previously reported genes but controlled different mutant floral organ phenotypes in rice. Therefore, this mp3 gene provided a novel perspective on the biological function of OsMADS1 in the development of rice floral organ.

Experimental temperatures shape host microbiome diversity and composition.

Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms-especially in marine habitats-experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.

NOTCH1 Signalling: A key pathway for the development of high-risk chronic lymphocytic leukaemia.

NOTCH1 is a cell surface receptor that releases its intracellular domain as transcription factor upon activation. With the advent of next-generation sequencing, the NOTCH1 gene was found recurrently mutated in chronic lymphocytic leukaemia (CLL). Here, virtually all NOTCH1 mutations affect the protein’s PEST-domain and impair inactivation and degradation of the released transcription factor, thus increasing NOTCH1 signalling strength. Besides sequence alterations directly affecting the NOTCH1 gene, multiple other genomic and non-genomic alterations have by now been identified in CLL cells that could promote an abnormally strong NOTCH1 signalling strength. This renders NOTCH1 one of the key signalling pathways in CLL pathophysiology. The frequency of genomic alterations affecting NOTCH1 signalling is rising over the CLL disease course culminating in the observation that besides TP53 loss, 8q gain and CDKN2A/B loss, NOTCH1 mutation is a hallmark genomic alteration associated with transformation of CLL into an aggressive lymphoma (Richter transformation). Both findings associate de-regulated NOTCH1 signalling with the development of high-risk CLL. This narrative review provides data on the role of NOTCH1 mutation for CLL development and progression, discusses the impact of NOTCH1 mutation on treatment response, gives insight into potential modes of NOTCH1 pathway activation and regulation, summarises alterations that have been discussed to contribute to a de-regulation of NOTCH1 signalling in CLL cells and provides a perspective on how to assess NOTCH1 signalling in CLL samples.

ECFS standards of care on CFTR-related disorders: Diagnostic criteria of CFTR dysfunction

The spectrum of disorders involving CFTR (cystic fibrosis transmembrane conductance regulator) dysfunction correlates with a continuous gradient of CFTR function defined by the combination of two allelic CFTR variants. CFTR-related disorders are clinical entities with features of cystic fibrosis (CF) and evidence for presence of CFTR dysfunction but not meeting criteria for diagnosis of CF. Individuals with CFTR-RDs demonstrate a wide range of CFTR activity and are still under-recognized or misclassified. The level of CFTR dysfunction may be measured in vivo (sweat testing, nasal potential difference measurements) and/or by ex vivo tests (intestinal current measurement), or indirectly indicated by CFTR variants, as alteration in sequence of the CFTR gene translates into CFTR dysfunction. CFTR bioassays can aid in the diagnosis of individuals with CF, but we lack parameters to differentiate CF from CFTR-RD. In the era of the CFTR modulators and their potential clinical benefit, it is of utmost importance to diagnose CFTR-RD as unambiguously as possible. We therefore propose the following to define compatible CFTR dysfunction in a person with a suspected diagnosis of CFTR-RD :(1) evidence of CFTR dysfunction in vivo or ex vivo in at least two different CFTR functional test types, or(2) One CFTR variant known to reduce CFTR function and evidence of CFTR dysfunction in vivo or ex vivo in at least two different CFTR functional test types, or(3) Two CFTR variants shown to reduce CFTR function, with at most one CF-causing variant.

Modular, programmable RNA sensing using ADAR editing in living cells.

With the increasing availability of single-cell transcriptomes, RNA signatures offer a promising basis for targeting living cells. Molecular RNA sensors would enable the study of and therapeutic interventions for specific cell types/states in diverse contexts, particularly in human patients and non-model organisms. Here we describe a modular, programmable system for live RNA sensing using adenosine deaminases acting on RNA (RADAR). We validate, and then expand, our basic design, characterize its performance, and analyze its compatibility with human and mouse transcriptomes. We identify strategies to boost output levels and improve the dynamic range. Additionally, we show that RADAR enables compact AND logic. In addition to responding to transcript levels, RADAR can distinguish disease-relevant sequence alterations of transcript identities, such as point mutations and fusions. Finally, we demonstrate that RADAR is a self-contained system with the potential to function in diverse organisms.

Novel POU3F4 variants identified in patients with inner ear malformations exhibit aberrant cellular distribution and lack of SLC6A20 transcriptional upregulation.

Hearing loss (HL) is the most common sensory defect and affects 450 million people worldwide in a disabling form. Pathogenic sequence alterations in the POU3F4 gene, which encodes a transcription factor, are causative of the most common type of X-linked deafness (X-linked deafness type 3, DFN3, DFNX2). POU3F4-related deafness is characterized by a typical inner ear malformation, namely an incomplete partition of the cochlea type 3 (IP3), with or without an enlargement of the vestibular aqueduct (EVA). The pathomechanism underlying POU3F4-related deafness and the corresponding transcriptional targets are largely uncharacterized. Two male patients belonging to a Caucasian cohort with HL and EVA who presented with an IP3 were submitted to genetic analysis. Two novel sequence variants in POU3F4 were identified by Sanger sequencing. In cell-based assays, the corresponding protein variants (p.S74Afs*8 and p.C327*) showed an aberrant expression and subcellular distribution and lack of transcriptional activity. These two protein variants failed to upregulate the transcript levels of the amino acid transporter gene SLC6A20, which was identified as a novel transcriptional target of POU3F4 by RNA sequencing and RT-qPCR. Accordingly, POU3F4 silencing by siRNA resulted in downregulation of SLC6A20 in mouse embryonic fibroblasts. Moreover, we showed for the first time that SLC6A20 is expressed in the mouse cochlea, and co-localized with POU3F4 in the spiral ligament. The findings presented here point to a novel role of amino acid transporters in the inner ear and pave the way for mechanistic studies of POU3F4-related HL.

Sequence alterations affect the antidiabetic attributes of hazelnut peptide fractions during the industrial manufacture and simulated digestion of hazelnut paste.

The online version contains supplementary material available at 10.1007/s13197-022-05601-2.

Nudging Finnish Adults into Replacing Red Meat with Plant-Based Protein via Presenting Foods as Dish of the Day and Altering the Dish Sequence

This study investigated whether Finnish working-aged omnivores (n = 163) could be nudged into replacing red meat with a fava-bean-based protein source via “Dish of the Day” (DoD) and main dish sequence alteration (SA) strategies in a controlled real-world Finnish self-service buffet restaurant with smart scales (Flavoria® Multidisciplinary Research Platform). A further aim was to study whether the effectiveness of the strategies differed by gender, age, and body mass index. The participants were assigned one of four experimental treatments: standard menu (T1), DoD (T2), standard menu + SA (T3), or DoD + SA (T4). The participants could choose any amount or combination of salad components and casseroles with minced meat or fava bean protein. Being subjected to a DoD menu and/or SA had no effect on main dish choice or the share of the meat-based dish in the meal weight. Men were more likely to choose a meat-based main dish and had a higher share of the meat dish in the meal weight compared to women, but no differences were observed between those aged 18–29, 30–44, or 45–65 years or those who were normal weight, overweight, or obese. Future studies should have a larger sample size and investigate food choice motives such as price or environmental awareness.

A Novel Rolling Circle Amplification-Based Detection of SARS-CoV-2 with Multi-Region Padlock Hybridization

SARS-CoV-2 has remained a global health burden, primarily due to the continuous evolution of different mutant strains. These mutations present challenges to the detection of the virus, as the target genes of qPCR, the standard diagnostic method, may possess sequence alterations. In this study, we develop an isothermal one-step detection method using rolling circle amplification (RCA) for SARS-CoV-2. This novel strategy utilizes a multi-padlock (MP-RCA) approach to detect viral-RNA via a simplified procedure with the reliable detection of mutated strains over other procedures. We designed 40 padlock-based probes to target different sequences across the SARS-CoV-2 genome. We established an optimal one-step isothermal reaction protocol utilizing a fluorescent output detected via a plate reader to test a variety of padlock combinations. This method was tested on RNA samples collected from nasal swabs and validated via PCR. S-gene target failure (SGTF)-mutated strains of SARS-CoV-2 were included. We demonstrated that the sensitivity of our assay was linearly proportional to the number of padlock probes used. With the 40-padlock combination the MP-RCA assay was able to correctly detect 45 out 55 positive samples (81.8% efficiency). This included 10 samples with SGTF mutations which we were able to detect as positive with 100% efficiency. We found that the MP-RCA approach improves the sensitivity of the MP-RCA assay, and critically, allows for the detection of SARS-CoV-2 variants with SGTF. Our method offers the simplicity of the reaction and requires basic equipment compared to standard qPCR. This method provides an alternative approach to overcome the challenges of detecting SARS-CoV-2 and other rapidly mutating viruses.

Recent Developments in Autism Genetic Research: A Scientometric Review from 2018 to 2022.

Genetic research in Autism Spectrum Disorder (ASD) has progressed tremendously in recent decades. Dozens of genetic loci and hundreds of alterations in the genetic sequence, expression, epigenetic transformation, and interactions with other physiological and environmental systems have been found to increase the likelihood of developing ASD. There is therefore a need to represent this wide-ranging yet voluminous body of literature in a systematic manner so that this information can be synthesised and understood at a macro level. Therefore, this study made use of scientometric methods, particularly document co-citation analysis (DCA), to systematically review literature on ASD genetic research from 2018 to 2022. A total of 14,818 articles were extracted from Scopus and analyzed with CiteSpace. An optimized DCA analysis revealed that recent literature on ASD genetic research can be broadly organised into 12 major clusters representing various sub-topics. These clusters are briefly described in the manuscript and potential applications of this study are discussed.

Biochemical characterization of a disease-causing human osteoprotegerin variant

Recently, a human mutation of OPG was identified to be associated with familial forms of osteoarthritis. This missense mutation (c.1205A = > T; p.Stop402Leu) occurs on the stop codon of OPG, which results in a 19-residue appendage to the C-terminus (OPG+19). The biochemical consequence of this unusual sequence alteration remains unknown. Here we expressed OPG+19 in 293 cells and the mutant OPG was purified to homogeneity by heparin affinity chromatography and size exclusion chromatography. We found that in sharp contrast to wildtype OPG, which mainly exists in dimeric form, OPG+19 had a strong tendency to form higher-order oligomers. To our surprise, the hyper-oligomerization of OPG+19 had no impact on how it binds cell surface heparan sulfate, how it inhibits RANKL-induced osteoclastogenesis and TRAIL-induced chondrocytes apoptosis. Our data suggest that in biological contexts where OPG is known to play a role, OPG+19 functions equivalently as wildtype OPG. The disease-causing mechanism of OPG+19 likely involves an unknown function of OPG in cartilage homeostasis and mineralization. By demonstrating the biochemical nature of this disease-causing OPG mutant, our study will likely help elucidating the biological roles of OPG in cartilage biology.

EP16.04-018 DNA Mismatch Repair in Lung Adenocarcinoma in Morocco

Microsatellite Instability (MSI) refers to the hypermutable state of cells as a consequence of DNA mismatch repair (MMR) deficiency. Identification of hypermutable tumors is clinically valuable for selecting patients suitable for immunotherapy treatment. These alterations in microsatellite sequences characterize hereditary nonpolyposis colorectal cancer, but they have been reported in other cancers. This study aims to evaluate the status of primary lung adenocarcinoma in Morocco.

Effect of copper and silver ions on sequence and DNA methylation changes in triticale regenerants gained via somatic embryogenesis

Somatic embryogenesis is a plant regeneration method that can be exploited in tissue culture systems for a variety of tasks, such as genetic modification or the selection of somaclones with advantageous characteristics. Therefore, it is crucial to create efficient regeneration procedures and comprehend how medium components affect regeneration effectiveness or the degree of variation created in plant tissue cultures. The level of tissue culture-induced variation in triticale regenerants was examined in the current study in relation to the concentration of copper and silver ions in the induction media as well as the length of time immature zygotic embryo explants were incubated on these media. The high degree of variation (45%) revealed by the methylation-sensitive amplified fragment length polymorphism approach for estimating variation included 38% DNA sequence alterations, 6% DNA demethylation, and 1% de novo DNA methylation. Different levels of variance were found in relation to various DNA sequence settings. The CHG context had the most alterations, whereas CG experienced the fewest; sequence variation predominated in each sequence context. Lower copper ion concentrations showed the most variance. However, it could not be connected to the duration of in vitro culture or the effect of silver ions. Accordingly, we think that altering the concentration of copper ions in the induction medium may throw off the equilibrium of the metabolic processes in which copper is involved, resulting in tissue culture-induced variation.

Site-specific N-terminal PEGylation-based controlled release of biotherapeutics: An application for GLP-1 delivery to improve pharmacokinetics and prolong hypoglycemic effects

PEGylation is a well-established technology for half-life extension in drug delivery. In this study, we aimed to develop a site-specific N-terminal PEGylation for biotherapeutics to achieve controlled release, using GLP-1 as a model. An additional threonine was introduced at N-terminal GLP-1. Followed by periodate oxidation, hydrazide-based PEGylation was achieved in a site-selective manner under reductive condition. Two homogenous monovalent mPEG5k-GLP-1 (peptide 4) and mPEG20k-GLP-1 (peptide 5) were successfully constructed. After PEGylation, the degradation by DPP-IV and rat plasma was obviously reduced. Their pharmacokinetic performances were enhanced at the expense of impaired GLP-1R stimulating potency, and their hypoglycemic effects were improved in different degrees. Compared with conventional strategies, this approach is devoid of the restriction and alteration of native peptide sequences, and can produce utterly homogenous conjugates with excellent selectivity and efficiency. It provides a practical controlled release approach for peptides by site-specific modification to achieve better pharmacological and therapeutic properties.

Serous tubal intra-epithelial carcinoma: what do we really know at this point?

Serous tubal intra-epithelial carcinoma (STIC) is the earliest morphologically recognisable step in the development of invasive high-grade serous carcinoma of the fallopian tube. Lesions occurring prior to STIC within the carcinogenic sequence for the pathogenesis of invasive high-grade serous carcinoma include the p53 signature and secretory cell outgrowth (SCOUT). Variable histological criteria have been used for diagnosing STIC, but a combination of morphology and immunohistochemistry for p53/Ki-67 improves interobserver agreement. Half of all carcinomas identified in risk-reducing salpingo-oophorectomy specimens are in the form of STIC; however, STIC also may be incidentally found on occasion in specimens from women at low or average risk of ovarian/tubal/peritoneal carcinoma. TP53 mutation is the earliest known DNA sequence alteration in STIC and almost all invasive high-grade serous carcinomas of the ovary and peritoneum. Data on the clinical behaviour of STIC are limited. While the short-term follow-up in the prior literature suggests a low risk of malignant progression, a more recent meta-analysis indicates a 10-year risk of 28%. STIC probably should be best regarded as a lesion with uncertain malignant potential at present, and future molecular analysis will help to classify those with higher risk of dissemination. This review provides an update on the current knowledge of STIC and related issues.