Search Results (14,332)

Epitranscriptomics is the study of modifications of RNA molecules by small molecular residues, such as the methyl (-CH₃) group. These modifications are inheritable and reversible. A specific group of enzymes called “writers” introduces the change to the RNA; “erasers” delete it, while “readers” stimulate a downstream effect. Epitranscriptomic changes are present in every type of organism from single-celled ones to plants and animals and are a key to normal development as well as pathologic processes. Oncology is a fast-paced field, where a better understanding of tumor biology and (epi)genetics is necessary to provide new therapeutic targets and better clinical outcomes. Recently, changes to the epitranscriptome have been shown to be drivers of tumorigenesis, biomarkers, and means of predicting outcomes, as well as potential therapeutic targets. In this review, we aimed to give a concise overview of epitranscriptomics in the context of neoplastic disease with a focus on N¹-methyladenosine (m¹A) modification, in layman’s terms, to bring closer this omics to clinicians and their future clinical practice. Full article

The cestode family Gymnorhynchidae (Trypanorhyncha) comprises three genera and six valid species that, as adults, are all intestinal parasites of large pelagic sharks. Their life cycle has not been elucidated yet, but it has been proposed that copepods serve as first, pelagic euphausiids or schooling fish as second, and larger predatory fishes as third intermediate hosts. Molidae fish have been proposed as intermediate hosts for at least two gymnorhynchid species (i.e., Molicola horridus and M. uncinatus). During a parasitological survey of fish from the coast of Kerala (India), some individuals of a gymnorhynchid species were found in a sharptail mola Masturus lanceolatus. Parasites were located on the subcapsular tissue of liver showing a serpiginous route. Based on 28S rDNA molecular and phylogenetic analysis, parasites were identified as Gymnorhynchus isuri, which resulted genetically identical to G. isuri obtained from the liver of a sun fish Mola mola in the Mediterranean Sea. Full article

Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species’ adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products. Full article

Retroviruses integrate into the genomes of infected host cells to form proviruses, a genetic platform for stable viral gene expression. Epigenetic silencing can, however, hamper proviral transcriptional activity. As gammaretroviruses (γRVs) preferentially integrate into active promoter and enhancer sites, the high transcriptional activity of γRVs can be attributed to this integration preference. In addition, long terminal repeats (LTRs) of some γRVs were shown to act as potent promoters by themselves. Here, we investigate the capacity of different γRV LTRs to drive stable expression within a non-preferred epigenomic environment in the context of diverse retroviral vectors. We demonstrate that different γRV LTRs are either rapidly silenced or remain active for long periods of time with a predominantly active proviral population under normal and retargeted integration. As an alternative to the established γRV systems, the feline leukemia virus and koala retrovirus LTRs are able to drive stable, albeit intensity-diverse, transgene expression. Overall, we show that despite the occurrence of rapid silencing events, most γRV LTRs can drive stable expression outside of their preferred chromatin landscape after retrovirus integrations. Full article

Prostate cancer remains a significant health challenge, being the most prevalent non-cutaneous cancer in men worldwide. This review discusses the critical advancements in biomarker discovery using single-omics and multi-omics approaches. Multi-omics, integrating genomic, transcriptomic, proteomic, metabolomic, and epigenomic data, offers a comprehensive understanding of the molecular heterogeneity of prostate cancer, leading to the identification of novel biomarkers and therapeutic targets. This holistic approach not only enhances the specificity and sensitivity of prostate cancer detection but also supports the development of personalized treatment strategies. Key studies highlighted include the identification of novel genes, genetic mutations, peptides, metabolites, and potential biomarkers through multi-omics analyses, which have shown promise in improving prostate cancer management. The integration of multi-omics in clinical practice can potentially revolutionize prostate cancer prognosis and treatment, paving the way for precision medicine. This review underscores the importance of continued research and the application of multi-omics to overcome current challenges in prostate cancer diagnosis and therapy. Full article

Endometrial carcinoma is a heterogeneous group of malignancies characterized by distinct histopathological features and genetic underpinnings. The 2020 WHO classification has provided a comprehensive framework for the categorization of endometrial carcinoma. However, it has not fully addressed the spectrum of uncommon entities that are currently not recognized by the 2020 WHO and have only been described in the form of small case series and case reports. These neoplasms represent a real diagnostic challenge for pathologists; furthermore, their therapeutic management still remains controversial and information regarding tumor prognosis is very limited. This review aims to elucidate these lesser-known variants of endometrial carcinoma. We discuss the challenges of identifying these rare subtypes and the molecular alterations associated with them. Furthermore, we propose the need for expanded classification systems that include these variants to enhance clinical outcomes and research efforts. We believe that a better histological typing characterization of these entities may lead to more reproducible and accurate diagnoses and more personalized treatments. By raising awareness of these rare entities, we also hope to encourage further investigation and integration into clinical practice to improve patient care in endometrial carcinoma. Full article

True morels (Morchella spp.) are highly valuable and medicinal mushrooms. Saprophytic morels have been cultivated, especially in China and some Western countries, over the last few decades. Türkiye has a rich potential in terms of wild morel diversity, with nearly 40 Morchella species in its genetic pool, though only 22 of these have been identified molecularly. It has high economic value worldwide, and Türkiye exports morels worth approximately 2 million $ annually. There is also significant interest in morel mushroom cultivation in Türkiye. In this study, 40 Morchella strains were collected and isolated from different regions of Türkiye and analyzed based on the Internal Transcribed Spacer (ITS) of the nuclear ribosomal DNA (rDNA) region. A phylogenetic dendrogram was drawn. The isolates of M. importuna, M. exima, M. exuberans, M. dunali, M. tridentina, M. crassipes, and M. esculenta were identified based on the ITS rDNA region. However, the identification of isolates 849-Kg027 and 966-Kg142 could not be determined clearly, and the isolates of M. vulgarius and M. spongiola were not distinct based on the ITS analysis. The macro-morphological features of the mycelia were investigated. Mycelia colors ranged from off-white to pale gray in the juvenile stage, orange to pale brown during early pigmentation, and pale brown to dark brown in the senescence stage. M. crassipes, M. exuberans, and 966-Kg142 formed lighter-colored mycelia, whereas M. dunali and M. vulgarius exhibited the darkest mycelial pigments. Sclerotia formation was compact, pale yellow to yellow, and abundant. In conclusion, molecular identification of Turkish morel cultures was performed, and cultural characteristics along with morphological differences were examined. The cultures have been deposited for further study in the Mushroom Gene Bank at the Atatürk Central Horticultural Research Institute. Full article

Background: Prader–Willi syndrome (PWS) is a rare genetic disorder characterized by distinctive physical, cognitive, and behavioral manifestations, coupled with profound alterations in appetite regulation, leading to severe obesity and metabolic dysregulation. These clinical features arise from disruptions in neurodevelopment and neuroendocrine regulation, yet the molecular intricacies of PWS remain incompletely understood. Methods: This study aimed to comprehensively profile circulating neuromodulatory factors in the serum of 53 subjects with PWS and 34 patients with non-syndromic obesity, utilizing a proximity extension assay with the Olink Target 96 neuro-exploratory and neurology panels. The ANOVA p-values were adjusted for multiple testing using the Benjamani–Hochberg method. Protein–protein interaction networks were generated in STRING V.12. Corrplots were calculated with R4.2.2 by using the Hmisc, Performance Analytics, and Corrplot packages Results: Our investigation explored the potential genetic underpinnings of the circulating protein signature observed in PWS, revealing intricate connections between genes in the PWS critical region and the identified circulating proteins associated with impaired oxytocin, NAD metabolism, and sex-related neuromuscular impairment involving, CD38, KYNU, NPM1, NMNAT1, WFIKKN1, and GDF-8/MSTN. The downregulation of CD38 in individuals with PWS (p < 0.01) indicates dysregulation of oxytocin release, implicating pathways associated with NAD metabolism in which KYNU and NMNAT1 are involved and significantly downregulated in PWS (p < 0.01 and p < 0.05, respectively). Sex-related differences in the circulatory levels of WFIKKN1 and GDF-8/MSTN (p < 0.05) were also observed. Conclusions: This study highlights potential circulating protein biomarkers associated with impaired oxytocin, NAD metabolism, and sex-related neuromuscular impairment in PWS individuals with potential clinical implications. Full article

Human epidermal growth factor receptor 2 (HER2) is a major driver of disease progression, treatment resistance, and worse survival for patients with various types of cancers, including prostate cancer. However, key bench studies and clinical trials have failed to evaluate the role of HER2 in prostate cancer using racially diverse experimental designs and protocols. This lack of diversity represents what has been the status quo of cancer research in the United States for decades. In the case of prostate cancer, homogenic study designs are problematic as Black men are much more likely to be diagnosed and die from aggressive and incurable forms of the disease. Therefore, the strategic inclusion of biospecimens collected from Black patients as well as the recruitment and enrollment of Black men into prostate cancer clinical trials is necessary to comprehensively evaluate genetic and molecular factors that contribute to variable outcomes in this high-risk population. Additionally, a higher prevalence of HER2 expression in Black men was recently reported in a small cohort of prostate cancer patients and may contribute to worsened prognosis. In this review, we carefully consider the role of HER2 in prostate cancer while, for the first time, taking into account the influences of race and genetic ancestry. Full article

Aldehyde dehydrogenases (ALDHs) constitute a diverse superfamily of NAD(P)⁺-dependent enzymes pivotal in oxidizing endogenous and exogenous aldehydes to carboxylic acids. Beyond metabolic roles, ALDHs participate in essential biological processes, including differentiation, embryogenesis and the DNA damage response, while also serving as markers for cancer stem cells (CSCs). Aldehyde dehydrogenase 1B1 (ALDH1B1) is a mitochondrial enzyme involved in the detoxification of lipid peroxidation by-products and metabolism of various aldehyde substrates. This study examines the potential role of ALDH1B1 in human lung adenocarcinoma and its association with the CSC phenotype. To this end, we utilized the lung adenocarcinoma cell line A549, engineered to stably express the human ALDH1B1 protein tagged with green fluorescent protein (GFP). Overexpression of ALDH1B1 led to notable changes in cell morphology, proliferation rate and clonogenic efficiency. Furthermore, ALDH1B1-overexpressing A549 cells exhibited enhanced resistance to the chemotherapeutic agents etoposide and cisplatin. Additionally, ALDH1B1 overexpression correlated with increased migratory potential and epithelial–mesenchymal transition (EMT), mediated by the upregulation of transcription factors such as SNAI2, ZEB2 and TWIST1, alongside the downregulation of E-cadherin. Moreover, Spearman’s rank correlation coefficient analysis using data from 507 publicly available lung adenocarcinoma clinical samples revealed a significant correlation between ALDH1B1 and various molecules implicated in CSC-related signaling pathways, including Wnt, Notch, hypoxia, Hedgehog, retinoic acid, Hippo, NF-κΒ, TGF-β, PI3K/PTEN-AKT and glycolysis/gluconeogenesis. These findings provide insights into the role of ALDH1B1 in lung tumor progression and its relation to the lung CSC phenotype, thereby offering potential therapeutic targets in the clinical management of lung adenocarcinoma. Full article

Pancreatic ductal adenocarcinoma (PDAC), a leading cause of cancer mortality in the United States, presents significant treatment challenges due to its late diagnosis and poor prognosis. Despite advances, the five-year survival rates remain dismally low, with only a fraction of patients eligible for potentially curative surgical interventions. This review aims to comprehensively examine the current landscape of targeted therapies in PDAC, focusing on recent developments in precision medicine approaches. We explore various molecular targets, including KRAS mutations, DNA damage repair deficiencies, mismatch repair pathway alterations, and rare genetic fusions. The review discusses emerging therapies, such as PARP inhibitors, immune checkpoint inhibitors, and novel targeted agents, like RET and NTRK inhibitors. We analyze the results of key clinical trials and highlight the potential of these targeted approaches in specific patient subgroups. Recent developments in PDAC research have emphasized precision oncology, facilitated by next-generation sequencing and the identification of genetic and epigenetic alterations. This approach tailors treatments to individual genetic profiles, improving outcomes and reducing side effects. Significant strides have been made in classifying PDAC into various subtypes, enhancing therapeutic precision. The identification of specific mutations in genes like KRAS, along with advancements in targeted therapies, including small molecule inhibitors, offers new hope. Furthermore, emerging therapies targeting DNA repair pathways and immunotherapeutic strategies also show promising results. As research evolves, integrating these targeted therapies with conventional treatments might improve survival rates and quality of life for PDAC patients, underscoring the shift towards a more personalized treatment paradigm. Full article

Background: The role of microRNAs (miRNAs) in the pathogenesis of rare genetic disorders has been gradually discovered. MiRNAs, a class of small non-coding RNAs, regulate gene expression by silencing target messenger RNAs (mRNAs). Their biogenesis involves transcription into primary miRNA (pri-miRNA), processing by the DROSHA–DGCR8 (DiGeorge syndrome critical region 8) complex, exportation to the cytoplasm, and further processing by DICER to generate mature miRNAs. These mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), where they modulate gene expression. Methods/Results: The dysregulation of miRNAs is implicated in various Mendelian disorders and familial diseases, including DICER1 syndrome, neurodevelopmental disorders (NDDs), and conditions linked to mutations in miRNA-binding sites. We summarized a few mechanisms how miRNA processing and regulation abnormalities lead to rare genetic disorders. Examples of such genetic diseases include hearing loss associated with MIR96 mutations, eye disorders linked to MIR184 mutations, and skeletal dysplasia involving MIR140 mutations. Conclusions: Understanding these molecular mechanisms is crucial, as miRNA dysregulation is a key factor in the pathogenesis of these conditions, offering significant potential for the diagnosis and potential therapeutic intervention. Full article

Parasporin PS2Aa1, recently renamed Mpp46Aa1, is an anti-cancer protein known for its selectivity against various human cancer cell lines. We genetically modified native PS2Aa1 to create a library of approximately 100 mutants. From this library, we selected promising mutants based on their half-maximal inhibitory concentration (IC₅₀) and sequence variations. In this study, Variant 3–35, with the G257V substitution, demonstrated increased cytotoxicity and selectivity against the colon cancer cell line SW480. Conversely, Variant N65, featuring substitutions N92D, K175R, and S218G, yielded the most favorable results against the cancer cell lines SW-620, MOLT-4, and Jurkat. The caspase 3/7 and 9, Annexin V-Cy3 and 6-GFDA activities, and, most notably, mitochondrial membrane permeabilization assays confirmed the apoptotic marker elevation. These findings indicate that residues 92, 175, 218, and 257 may play a critical role in the cytotoxic activity and selectivity. We successfully obtained genetically improved variants with substitutions at these key amino acid positions. Additionally, we conducted molecular dynamic simulations to explore the potential interactions between PS2Aa1 and the CD59 GPI-anchored protein. The simulation results revealed that residues 57, 92, and 101 were consistently present, suggesting their possible significance in the interactions between parasporin and the CD59 protein. Full article

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and is associated with high morbidity and mortality. One of the main challenges in the management of HCC is late clinical presentation and thus diagnosis of the disease, which results in poor survival. The pathogenesis of HCC is complex and involves chronic liver injury and genetic alterations. Diagnosis of HCC can be made either by biopsy or imaging; however, conventional tissue-based biopsy methods and serological biomarkers such as AFP have limited clinical applications. While hepatocellular carcinoma is associated with a range of molecular alterations, including the activation of oncogenic signaling pathways, such as Wnt-TGFβ, PI3K-AKT-mTOR, RAS-MAPK, MET, IGF, and Wnt-β-catenin and TP53 and TERT promoter mutations, microfluidic applications have been limited. Early diagnosis is crucial for advancing treatments that would address the heterogeneity of HCC. In this context, microfluidic droplet-based methods are crucial, as they enable comprehensive analysis of the genome and transcriptome of individual cells. Single-cell RNA sequencing (scRNA-seq) allows the examination of individual cell transcriptomes, identifying their heterogeneity and cellular evolutionary relationships. Other microfluidic methods, such as Drop-seq, InDrop, and ATAC-seq, are also employed for single-cell analysis. Here, we examine and compare these microfluidic droplet-based methods, exploring their advantages and limitations in liver cancer research. These technologies provide new opportunities to understand liver cancer biology, diagnosis, treatment, and prognosis, contributing to scientific efforts in combating this challenging disease. Full article

Purple Pak-choi is rich in anthocyanins, which have both ornamental and edible health functions, and has been used more and more widely in facility cultivation. In order to further clarify the molecular mechanism of purple Pak-choi, two Pak-choi inbred lines (‘PQC’ and ‘HYYTC’) were selected for the determination of pigment content and transcriptome analysis, and the key genes controlling the formation of purple character in leaves of Pak-choi were discovered. The results of pigment determination showed that the anthocyanin content of ‘PQC’ was 0.29 mg/g, which was about 100 times than ‘HYYTC’; The chlorophyll content of ‘HYYTC’ was 2.25 mg/g, while ‘PQC’ only contained 1.05 mg/g. A total of 20 structural genes related to anthocyanin biosynthesis and 28 transcriptional regulatory genes were identified by transcriptome analysis. Weighted gene co-expression network analysis (WGCNA) was used to construct the weight network analysis map of 14 genes. The results showed that the cinnamate hydroxylase gene (BraA04002213, BrC4H3), flavanone-3- hydroxylase (BraA09004531, BrF3H1), and chalcone synthetase (BraA10002265, BrCHS1) were the core genes involved in the anthocyanin synthesis pathway of purple Pak-choi. The results identified the key genes controlling the formation of purple leaf traits, which laid a foundation for further analysis of the molecular mechanism of anthocyanin accumulation in purple Pak-choi and provided a theoretical basis for leaf color regulation. Full article