Journal of Applied Genetics最新文献

Background: Colorectal cancer (CRC) is a major global health concern with increasing incidence. Current treatments, though improved, require novel biomarkers for better diagnosis and management. Disulfidptosis, a recently characterized form of cell death, may play a critical role in CRC progression.

Methods: Utilizing summary-data-based Mendelian randomization (SMR), we identified RNH1 as a gene linked to CRC and disulfidptosis. The expression and intercellular communication of RNH1 in CRC were analyzed using single-cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing (stRNA-seq). A prognostic model was built using a Deep Learning Survival Neural Network (DeepSurv). Additionally, we performed RNA sequencing (RNA-seq) analysis to analyze the function of RNH1. Validation was performed through qPCR on CRC and normal tissue samples.

Results: RNH1 was identified as a gene linked to disulfidptosis and positively correlated with CRC risk. scRNA-seq analysis revealed that RNH1 + malignant cells showed distinct metabolic pathways and greater cell interactions. stRNA-seq analysis confirmed these interactions, especially with endothelial cells. DeepSurv analysis produced a prognostic model, showing different survival outcomes between high-risk and low-risk groups. RNA-seq analysis showed that the RNH1 + high expression group had higher immune cell abundance scores and tumor microenvironment scores, and RNH1 was positively correlated with most immune checkpoints. Drug sensitivity analysis suggested that CRC patients with high RNH1 expression were more sensitive to certain therapeutic agents. qPCR showed that the expression level of RNH1 in cancer tissues of CRC patients was significantly higher than that in normal tissues.

Conclusion: RNH1 acts as a biomarker for CRC, influencing tumor growth via disulfidptosis, tumor microenvironment alterations, and metabolic pathways. Its high expression correlates with immune escape. This study suggests RNH1 as a potential therapeutic target for CRC, warranting further exploration of its mechanistic roles and treatment potential.

Cohen syndrome (CS) is a rare autosomal recessive disorder caused by biallelic pathogenic variants in the VPS13B gene. It is characterized by early-onset multisystemic symptoms, including chorioretinal dystrophy, progressive high myopia, developmental delay, hypotonia, abnormal fat distribution, short stature, microcephaly, facial dysmorphism, and leukopenia. However, the condition exhibits extensive phenotypic and allelic heterogeneity. Here, we report a 24-year-old male presenting with atypical retinitis pigmentosa, myopia, leukopenia, abnormal fat distribution, and minor facial dysmorphic features. The patient showed neither neurologic symptoms nor other commonly observed CS traits. Multigene next-generation sequencing (NGS) panel testing revealed two novel VPS13B variants - an intragenic deletion encompassing exon 5 and a donor splice site variant c.11392 + 2dup in a compound heterozygous state. Furthermore, we conducted a literature review and summarized the phenotypic and genetic heterogeneity of CS, with an additional emphasis on individuals exhibiting mild manifestations. The present study introduces two novel VPS13B variants associated with mild CS and highlights the possibility that biallelic VPS13B mutations may lead to a less severe clinical presentation without developmental delay, which is widely considered an inherent part of the syndrome clinical picture.

15q26 deletion syndrome is a rare genetic condition caused by the deletion of terminal end of the long arm of chromosome 15 (Drayer's syndrome). Clinical presentation usually implies intrauterine growth restriction, postnatal growth failure, varying degrees of intellectual disability, developmental delay, typical facial appearance, brachydactyly and diaphragmatic hernia. Lymphangioleiomiomatosis (LAM) is a rare genetic disease affecting multiple organs, which almost exclusively afflicts women. Typical presentation of LAM disease is pulmonary LAM, characterized by cyst-like destruction of pulmonary tissue, which leads to loss of pulmonary function, and if progresses further can lead to recurring pneumothoraxes. Co-existence of these two rare diseases hasn't been reported so far. Here we report a case of the simultaneous presence of 15q26 deletion syndrome and LAM disease in a 38-year-old female. She presented with short statue, brachydactyly, pes equinovarus, microcephaly and signs of intellectual disability manifesting from birth and early childhood. At the age of 23 she starts to suffer of recurring pneumothoraxes with gradual loss of pulmonary function. CT and pathohistological findings revealed the presence of pulmonary LAM and genetic testing revealed 15q26.2 microdeletion characteristic for 15q26 deletion syndrome. Successful treatment of LAM using mTOR inhibitor Sirolimus resulted in clinical and functional improvement.

Gilles de la Tourette syndrome (GTS) and other tic disorders (TDs) have a substantial genetic component with their heritability estimated at between 60 and 80%. Here we propose an oligogenic risk score of TDs using whole-genome sequencing (WGS) data from a group of Polish GTS patients, their families, and control samples (n = 278). In this study, we first reviewed the literature to obtain a preliminary list of 84 GTS/TD candidate genes. From this list, 10 final risk score genes were selected based on single-gene burden tests (SKAT p < 0.05) between unrelated GTS cases (n = 37) and synthetic control samples based on a database of local allele frequencies. These 10 genes were CHADL, DRD2, MAOA, PCDH10, HTR2A, SLITRK5, SORCS3, KCNQ5, CDH9, and CHD8. Variants in and in the vicinity (± 20 kbp) of the ten risk genes (n = 7654) with a median minor allele frequency in the non-Finnish European population of 0.02 were integrated into an additive classifier. This risk score was then applied to healthy and GTS-affected individuals from 23 families and 100 unrelated healthy samples from the Polish population (AUC-ROC = 0.62, p = 0.02). Application of the algorithm to a group of patients with other tic disorders revealed a continuous increase of the oligogenic score with healthy individuals with the lowest mean, then patients with other tic disorders, then GTS patients, and finally with severe GTS cases with the highest oligogenic score. We have further compared our WGS results with the summary statistics of the Psychiatric Genomics Consortium genome-wide association study (PGC GWAS) of TDs and found no signal overlap except for the CHADL gene locus. Polygenic risk scores from common variants of GTS GWAS show no difference between patient and control groups, except for the comparison between patients with non-GTS TDs and patients with severe GTS. Overall, we leveraged WGS data to construct a GTS/TD risk score based on variants that may cooperatively contribute to the aetiology of these disorders. This study provides evidence that typical and severe adult GTS as well as other tic disorders may exist on a single spectrum in terms of their genetic background.

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins are the most promising toolkit of synthetic biology for genetic engineering applications across species. Essentially, the Type II CRISPR system, featuring Cas9 nuclease from Streptococcus pyogenes complexed with sgRNA, introduces targeted DNA cleavage, enabling modifications with exceptional precision. This technology can be utilized for not only editing but also modulating gene expressions, thereby finding widespread utility in various biotechnological applications. Here we discuss strategies to construct a consolidated platform aiming at developing a CRISPR-based gene editing system in microbial hosts such as yeast. Employing the well-known gene editing enzymes, i.e., Cpf1 and dCas9, two independent strategies to develop a one-pot plasmid system have been proposed. Furthermore, approaches to reduce off-target cleavages introduced by non-specific targeting of CRISPR complex have been discussed. Finally, an overarching discussion on advanced strategies to design robust CRISPR components is provided for streamlining future genome editing applications.

Recessive opaque2 (o2) and opaque16 (o16) genes enhance lysine and tryptophan in maize kernels. Though few o2, o16-, and o2o16-based maize genotypes have been developed, the transition of quality attributes and seed morphology through different stages of kernel development has not been studied yet. To understand the role of o2 and o16 genes in the regulation of essential amino acids and kernel opaqueness in maize, we analyzed the accumulation pattern of lysine and tryptophan, and the occurrence of opaqueness in the developing kernels at 15, 30, and 45 days after pollination (DAP) among a set of o2-, o16-, and o2o16-based inbreds. Genotypes with o2o16 possessed significantly higher lysine (0.64%) and tryptophan (0.25%) over o2 (lysine, 0.48%; tryptophan, 0.18%) and o16 (lysine, 0.46%; tryptophan, 0.17%) alone across kernel development stages. A decreasing trend of amino acid accumulation in o2-, o16-, and o2o16-based genotypes was observed through 15-, 30-, and 45-DAP. Kernel opaqueness also showed a similar decreasing trend among o2-, o16-, and o2o16-based inbreds during kernel development. A positive association was observed between lysine and tryptophan (r = 0.95), tryptophan and opaqueness (r = 0.60), and lysine and opaqueness (r = 0.60) across DAPs. Hard endosperm in wild types and o16 genotypes was due to compact starch-granule structures packed with more proteinaceous matrix compared to o2 and o2o16. This is the first report on nutritional quality and opaqueness at different stages of kernel development in o2-, o16-, and o2o16-based genotypes.

Adenosine deaminase acting on RNA 1 (ADAR1) plays an essential role in the development of malignancies by modifying the expression of different oncogenes. ADAR1 presents three distinct activities: adenosine-to-inosine RNA editing, modulating IFN pathways, and response to cellular stress factors. Following stressors such as heat shock, ADAR1p110 isoform relocates from the nucleus to the cytoplasm, where it suppresses RNA degradation which leads to the arrest of apoptosis and cell survival. In this study, we assessed the expression of ADAR1 across different cancer cell lines. We revealed that the presence of ADAR1 varies between cells of different origins and that a high transcript level does not reflect protein abundance. Additionally, we subjected cells to a heat shock in order to evaluate how cellular stress factors affect the expression of ADAR1. Our results indicate that ADAR1 transcript and protein levels are relatively stable and do not change under heat shock in examined cell lines. This research lays a groundwork for future directions on ADAR1-related studies suggesting in which types of cancer ADAR1 may be a promising target for novel therapeutic approaches.

This study aimed to improve the restorer line IR 42266-29-3R (A42) for multiple stress tolerance using integrated marker-assisted backcross breeding (MABB) and the doubled haploid (DH) approach. The primary objective was to introduce the abiotic stress tolerant QTL (qDTY1.1 and qHTSF4.1) into the background IR 42266-29-3R, which already harbors three bacterial blight (BB) resistance genes (xa5, xa13, and Xa21). The BC₁F₁ population was derived from crosses between IR 42266-29-3R and N22, leading to the development of 113 true DHs. Efficient callus induction (29.64%) was achieved using N6 medium supplemented with 2.0 mg/l 2,4-D, 0.5 mg/l BAP, and 3% maltose. Green plant regeneration rates were notably high on the MS medium supplemented with 0.5 mg/l NAA, 0.5 mg/l Kn, 2.0 mg/l BAP, and 3% sucrose, reaching 68.6% and 61.9% on the 2nd and 7th days, respectively. From the 113 DHs, 24 were selected based on superior morpho-agronomic traits and maximum gene combinations. These DHs underwent phenotypic evaluation during the reproductive stage for drought and heat stress responses, alongside assessment for BB resistance. Among them, CS65 showed a genetic profile encompassing xa13, Xa21, qDTY1.1, and qHTSF4.1, while six others exhibited xa5, Xa21, qDTY1.1, and qHTSF4.1. Notably, CS1, CS3, CS37, CS64, and CS65 demonstrated low susceptibility to heat and drought stresses, coupled with yields comparable to the recurrent parent and moderate to high resistance against bacterial blight. CS65 emerged as the most promising genotype due to its robust tolerance to multiple stresses and improved yield potential. Moreover, eight out of the 24 DHs tested positive for both Rf3 and Rf4 genes, displaying spikelet fertility rates exceeding 75%. These selected restorer lines will serve as foundational material for developing superior hybrid rice lines, while the non-restorer lines will contribute to the broader pool of rice varieties in future breeding programs.

Infertility remains a significant global health challenge. With up to one in seven couples affected worldwide, the inability to conceive has become a major concern for reproductive health. Many causes of infertility are linked to genetic variants that are disruptive for germ cell homeostasis. Using causative variants to model human infertility can improve our understanding of the molecular pathways that regulate germ cell development. One notable example is the germ cell morphogen NANOS, which is highly conserved across species. Variants of NANOS are associated with infertility in various animal models, from Drosophila to humans. Here, we examine how modelling human infertility based on NANOS variants can offer insights into the molecular processes underlying germ cell development. Ultimately, uncovering the molecular basis of human infertility through this approach is vital for developing advanced diagnostic methods and therapeutic options in the future.

Drought stress can damage crop growth and lead to a decline in yield, thereby affecting food security, especially in regions vulnerable to climate change. SNAC1 (stress-responsive NAC1), the NAC transcription factor family member, plays a crucial role in stomatal movement regulation. Effective regulation of stomatal movement is essential for protecting plants from water loss during adverse conditions. Our hypothesis revolves around altering HvSNAC1 activity by introducing a point mutation in its encoding gene, thereby influencing stomatal dynamics in barley. Two TILLING mutants, each harboring missense mutations in the NAC domain, exhibited higher stomatal density after drought stress compared to the parent cultivar 'Sebastian'. These mutants also demonstrated distinct patterns of ABA-induced stomatal movement compared to the wild-type (WT). To delve deeper, we conducted a comprehensive analysis of the transcriptomes of these mutants and the parent cultivar 'Sebastian' under both optimal watering conditions and 10 days of drought stress treatment. We identified differentially expressed genes (DEGs) between the mutants and WT plants under control and drought conditions. Furthermore, we pinpointed DEGs specifically expressed in both mutants under drought conditions. Our experiments revealed that the cis-regulatory motif CACG, previously identified in Arabidopsis and rice, is recognized by HvSNAC1 in vitro. Enrichment analysis led to the identification of the cell wall organization category and potential target genes, such as HvEXPA8 (expansin 8), HvXTH (xyloglucan endotransglucosylase/hydrolase), and HvPAE9 (pectin acetylesterase 9), suggesting their regulation by HvSNAC1. These findings suggest that HvSNAC1 may play a role in regulating genes associated with stomatal density, size and reopening.