Biochemical Genetics[JOURNAL]
Sun
200 papers
Exploring the Integrated Gut-Brain Metabolic Model for ADHD.
Tas E, Ulgen KO
Biochem Genet · 2026 Jun · PMID 40885796 · Publisher ↗
Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental condition marked by hyperactivity, impulsivity, and inattentiveness that are disproportionate to the patient's developmental stage. Individuals with...
Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental condition marked by hyperactivity, impulsivity, and inattentiveness that are disproportionate to the patient's developmental stage. Individuals with ADHD often experience gastrointestinal (GI) issues, indicating a potential link with the gut microbiome. This study aims to explore how various parameters influence the production and consumption of metabolites in the brain by developing an integrated gut-brain metabolic model, examining the impact of gut microbiota-derived metabolites on the human brain. Genome-scale metabolic models (GEMs), which consider gene-protein-reaction relationships, are utilized to simulate metabolic processes in gut microorganisms. A comprehensive genome-scale metabolic model of the human brain, comprising 812 metabolites, 994 reactions, 671 genes, and 71 metabolic pathways, serves as the healthy brain reference. To mimic an ADHD brain, the gene NOS1 is removed from the healthy model. An integrated gut-brain model is created using a three-compartment approach (gut, blood, and brain). This modeling technique, which accounts for microbial genome-environment interactions and their metabolite interactions with other human organs, helps identify the GI mechanisms underlying ADHD toward enhancing the quality of life for affected individuals. Moreover, understanding the relationship between ADHD, age, gender, and diet can help in developing more effective, personalized approaches to managing ADHD.
Knockoff-Based Fine Mapping of MS-Associated SNPs in Sardinian Trios.
Baldrighi GN, Nova A, Ekstrøm CT … +4 more , Piras ML, Saddi MV, Bernardinelli L, Fazia T
Biochem Genet · 2026 Jun · PMID 40884622 · Full text
Genetic predisposition plays a key role in autoimmune and complex diseases such as multiple sclerosis (MS). However, identifying the specific variants or genomic regions responsible for disease susceptibility remains a s...
Genetic predisposition plays a key role in autoimmune and complex diseases such as multiple sclerosis (MS). However, identifying the specific variants or genomic regions responsible for disease susceptibility remains a significant challenge. In this study a family-based fine mapping approach was applied to analyze 142 trios, aiming to identify associated genetic variants linked to MS. The targeted genomic region resides within the 17:30,820,506-32,483,270 bp (Ch37/hg19), which includes the protein-coding gene ASIC2, previously implicated in MS and other neurological conditions, with surrounding genes comprising strongly correlated genetic variants to capture the broader signal from the region. Given the high prevalence of MS in Sardinia and the unique genetic characteristics of the Sardinian population, including reduced heterogeneity and extended linkage disequilibrium, we designed our study specifically within this population and focused on family-based data to enhance the power for detecting genetic signals, avoiding false discoveries. Genotype imputation found 2537 variants, which were then analyzed using the knockoff Trio method to identify loci associated with MS susceptibility. We found rs756787 (3'UTR of MYO1D) increased disease risk (OR 1.57, 95% CI [1.07-2.29], p = 0.02), while rs56175840 (intronic ASIC2) showed a protective effect (OR 0.17, 95% CI [0.04-0.74], p = 0.02), demonstrating the power of knockoff-based fine mapping in family datasets. Integrating LD-based expression and trait analyses helped reveal how rs756787 correlates with variants affecting genes involved in neurodegeneration and the immune response to Epstein-Barr virus, a known environmental factor implicated in MS pathogenesis. Our study highlights the effectiveness of knockoff-based fine mapping combined with expression-trait integration to identify genetic variants influencing MS risk in the Sardinian population.
Influence of Genotypes and Contrasting Production Environments on Curcuminoids and its Stability in Turmeric (Curcuma longa L.).
Silaru R, Sounderarajan A, Kotha Madduri Y … +1 more , Duraisamy P
Biochem Genet · 2026 Jun · PMID 40884621 · Publisher ↗
Understanding the genotype × environment interaction (GEI) on the performance and stability of curcuminoids among turmeric genotypes across production environments is essential for selecting suitable genotypes for differ...
Understanding the genotype × environment interaction (GEI) on the performance and stability of curcuminoids among turmeric genotypes across production environments is essential for selecting suitable genotypes for different production environments. In the present investigation, 21 turmeric genotypes of various geographical locations in India were assessed for curcuminoids (CUR-curcumin, DMC-demethoxycurcumin, and BDMC-bis demethoxycurcumin) under three environmental conditions viz, green house, vertical structures and open field. The analysis of variance indicated significant GEI effects on curcuminoids, underscoring the importance of GEI on genotype performance. In vertical structures, IISR Pragati and Waigon Turmeric were found to be superior for all three curcuminoids. In greenhouse conditions, CIM Pitambar, CO 3, and Acc. 1545 were superior for BDMC, while CIM Pitambar, IISR Prathiba, and IISR Pragati excelled for DMC, and Acc. 1545 for CUR. Under field conditions, Waigon Turmeric recorded higher BDMC and DMC, while Roma, Acc. 1545, and IISR Prathiba had the highest CUR. Our findings revealed that the curcuminoids relative ratio among the genotypes, which grouped into four patterns, was primarily influenced by genotype rather than environment. The promising genotypes for curcuminoids across the production environments were Waigon Turmeric, Rajendra Sonali, Roma, IISR Prathiba, Acc. 1545, NDH 8, IISR Pragati, and CIM Pitambar. Additionally, IISR Pragati for BDMC, Acc. 69/22/5/I3 for DMC, and Rajendra Sonali for CUR exhibited both superior performance and greater stability compared to other genotypes. In the present study, Field conditions, followed by greenhouse conditions, were found to be the best for all three curcuminoid across three production environments. These findings are crucial for extraction industries and farmers to choose the best genotypes and suitable production environments for targeted production of higher curcuminoids in turmeric.
Suggestive Contribution of Sequence Signal Gene Variants of TGF-β1 in Development of Type 1 Diabetes, Diabetic Neuropathy, and Modulation of Lipid Profile.
Mihoubi E, Bouldjennet F, Amroun H … +3 more , Azzouz M, Touil-Boukoffa C, Raache R
Biochem Genet · 2026 Jun · PMID 40879861 · Publisher ↗
Type 1 diabetes mellitus (T1DM) and its associated complications result from the interplay between genetic and environmental factors, with inflammation playing a central role in their pathogenesis. This study aimed to as...
Type 1 diabetes mellitus (T1DM) and its associated complications result from the interplay between genetic and environmental factors, with inflammation playing a central role in their pathogenesis. This study aimed to assess the association between TGF-β1 gene variants and T1DM, as well as its neuropathy, in the Algerian population. A case-control study was conducted, analyzing 344 blood samples. The TGF-β1 rs1800470 and rs1800471 were genotyped using the PCR-SSP method. Genotype and allele frequencies were compared among participants, and phenotype-genotype interactions were determined.The results revealed that the TGF-β1 rs1800470 CC genotype was significantly more frequent in patients (OR = 2.08, p = 0.016), while the GC genotype was significantly more frequent in controls (OR = 0.49, p = 0.001). The C allele (OR = 2.97, p < 0.0001) and the GC genotype (OR = 2.93, p = 0.0003) of the TGF-β1 rs1800471 were significantly more frequent in T1DM patients, while the G allele (OR = 0.34, p < 0.0001) and GG genotype (OR = 0.32, p < 0.0001) were more frequent in controls. Furthermore, the GG genotype of rs1800471 was associated with diabetic neuropathy (OR = 3.30, p = 0.03), and carrying at least one copy of the minor C allele was linked to higher levels of total cholesterol (p = 0.0096) and triglycerides (p = 0.001). Based on these data, we suggest an association between the TGF-β1 variants rs1800470 and rs1800471 and susceptibility to T1DM. Furthermore, the rs1800471 variant may be involved in the development of diabetic neuropathy with a possible impact on lipid profiles.
Genetic Variants and Alteration in Transcription Factor 7-Like 2 (TCF7L2) mRNA Level in Ischemic Stroke Patients Among Bengali and Gujarati Population from India.
Sadhukhan D, Roy A, Nath S … +12 more , Basu E, Mukherjee J, Ghosh KC, Banerjee TK, Krishnan P, Chatterjee SK, Desai S, Patel VA, Ray D, Hui SP, Gupta S, Biswas A
Biochem Genet · 2026 Jun · PMID 40864349 · Publisher ↗
Diabetes and Hyperlipidemia are major risk factors for stroke across the world population. TCF7L2, a key regulator of the WNT signaling pathway shows genetic association with these metabolic disorders in ethnicity depend...
Diabetes and Hyperlipidemia are major risk factors for stroke across the world population. TCF7L2, a key regulator of the WNT signaling pathway shows genetic association with these metabolic disorders in ethnicity dependant manner. However, its role in stroke pathogenesis (if any) is not well characterized. Here, we aim to (a) investigate and correlate dysregulation of TCF7L2 expression with diabetes or hyperlipidemia-associated Ischemic Stroke (b) identify genetic risk variants in the TCF7L2 gene, and (c) establish correlations between TCF7L2 mRNA levels and biochemical parameters. Based on radiological findings for Ischemic Stroke, a total of 50 unrelated subjects were recruited with diverse biochemical parameters for TCF7L2 mRNA expression study in PBMC, followed by correlation with fasting blood sugar and lipid profile. Furthermore, mutation screening (31 Cases and 30 Controls) and genetic association studies (rs7901695 & rs7903146) were performed among 326 cases and 258 controls from two different ethnic population of India. In our study, a significant downregulation of TCF7L2 transcript was observed between stroke cases and controls as major finding. Furthermore, stratification of stroke cases, according to their blood lipid and glucose level revealed a lower quantity of TCF7L2 transcript in hyperlipidemia stroke cases than non-hyperlipidemia subjects. However, no such association against diabetic status was observed. A simultaneous finding showing negative correlation of gene expression with total blood cholesterol level (P = 0.0187; r = - 0.4012) but not for diabetes, thus suggests TCF7L2 mediated altered lipid metabolism as a risk for stroke pathogenesis. On the other hand, allelic (P = 0.0207) and genotypic (P = 0.0002) association of functional variants like rs7901695 variants [P = 0.0207] among the majorly Bengali population of Kolkata and rs7903146 [P = 0.0164] among the Gujarati cohort was observed, respectively. Thus, on basis of our findings, genotyping of TCF7L2 variants or quantification of transcript, consumption of low-fat diet may be recommended to hyperlipidemia individuals for risk prediction and preventive treatment regimen, respectively.
Predictive Value of circ_0020850 for Functional Outcomes After Acute Ischemic Stroke in Hospitalized Convalescent Patients.
Qin S, Li Z, Yan Z … +1 more , Zhou W
Biochem Genet · 2026 Jun · PMID 40856974 · Publisher ↗
Acute ischemic stroke (AIS) is the primary reason for death. CircRNAs have become a hotspot of stroke research. The study aimed to detect the concentration of circ_0020850 and elucidate its prognostic roles. Differently...
Acute ischemic stroke (AIS) is the primary reason for death. CircRNAs have become a hotspot of stroke research. The study aimed to detect the concentration of circ_0020850 and elucidate its prognostic roles. Differently expressed circRNAs and miRNAs were identified based on the GEO database. Serum samples were collected from AIS and healthy persons to assess the levels of circ_0020850 and miR-629 before and after rehabilitation. Their interrelationships with MMSE scores were evaluated using the Spearman method. The targeted connection was verified by luciferase reporter assay. ROC and logistic regression further revealed the prognostic roles of circ_0020850 and miR-629. GO, KEGG, PPI methods were applied for potential functional and pathway analysis of targets of miR-629. The upregulation of circ_0020850 and downregulation of miR-629 were detected in AIS patients. After rehabilitation, both circ_0020850 and miR-629 expression were maintained normal. Circ_0020850 and miR-629 were correlated with MMSE scores and could predict the prognosis of AIS patients. Further analysis indicated that the targets of miR-629 were enriched in the Wnt signaling pathway, ficolin-1-rich granule, and pathways of neurodegeneration or multiple diseases. Circ_0020850 and miR-629 were related to patients' recovery, they are promising prognostic markers of AIS patients.
lncRNA EBLN3P Promotes Proliferation, Metastasis and Stemness of Gastric Cancer Cells via miR-141-3p/HMGCS1.
Zong Y, Shen J, Wang L … +5 more , Wang L, Chen Y, Ge C, Gu J, Hu Q
Biochem Genet · 2026 Jun · PMID 40855016 · Publisher ↗
Long non-coding RNAs (lncRNAs) have become an essential factor in gastric cancer (GC) initiation and metastasis. This study is aimed to uncover the functional significance of EBLN3P in GC. In GC, EBLN3P and HMGCS1 was si...
Long non-coding RNAs (lncRNAs) have become an essential factor in gastric cancer (GC) initiation and metastasis. This study is aimed to uncover the functional significance of EBLN3P in GC. In GC, EBLN3P and HMGCS1 was significantly increased. In contrast, miR-141-3p was decreased. Localization assay revealed that EBLN3P primarily localized in the cytoplasm rather than the nucleus. In MKN28 and SGC7901 cells, EBLN3P knockdown suppressed cell proliferation, metastasis and stemness. On the contrary, overexpression of EBLN3P facilitated these cellular processes. The EBLN3P/miR-141-3p/HMGCS1 axis was identified to play crucial functions in GC progression.
BRI3 Orchestrates Lipid Metabolism and Autophagy in Glioblastoma: Implications for Tumor Cell Resilience.
Chen J, Zuo P, Kuang S … +3 more , Li P, Li X, Zhan D
Biochem Genet · 2026 Jun · PMID 40855015 · Publisher ↗
Glioblastoma multiforme (GBM) is an aggressive brain tumor characterized by metabolic plasticity and resistance to therapy. Understanding the mechanisms underlying GBM's adaptability to metabolic stress is crucial for de...
Glioblastoma multiforme (GBM) is an aggressive brain tumor characterized by metabolic plasticity and resistance to therapy. Understanding the mechanisms underlying GBM's adaptability to metabolic stress is crucial for developing effective treatments. This study investigates the role of Brain Protein I3 (BRI3) in regulating lipid metabolism and autophagy in GBM, and its potential as a therapeutic target. We performed integrative bioinformatics analysis using TCGA-GBM and CGGA datasets to identify lipophagy-related gene signatures. BRI3's function was examined through in vitro studies using GBM cell lines and patient-derived samples. Lipid metabolism and autophagy were assessed under normal and oxygen-glucose deprivation (OGD) conditions in BRI3-knockdown and control GBM cells. Bioinformatics analysis revealed a lipophagy-related gene signature associated with poor prognosis in GBM. BRI3 emerged as a key upregulated gene in GBM, correlating with altered lipid homeostasis and enhanced autophagy. In vitro studies demonstrated that BRI3 knockdown led to lipid accumulation, impaired autophagy, reduced proliferation, and increased apoptosis in GBM cells. Under OGD conditions mimicking the tumor microenvironment, BRI3-depleted cells showed compromised lipid mobilization, autophagy induction, and cell survival compared to controls. Our findings suggest BRI3 as a critical regulator of lipophagy in GBM, enhancing tumor cell resilience to metabolic stress. This study provides insights into GBM's metabolic adaptability and identifies BRI3 as a potential therapeutic target for modulating tumor cell survival in the challenging glioblastoma microenvironment.
HTSNPedia: A Molecular Perspective and Risk Estimator Database for Hypertension-Associated Genes.
Sankar J, Arumugam A, Prakash AA … +2 more , Wong LS, Muthusamy K
Biochem Genet · 2026 Jun · PMID 40853437 · Publisher ↗
Hypertension is a major public health concern, affecting more than one billion adults worldwide. The etiology of hypertension is associated with various genetic and epigenetic interactions. The candidate genes from vario...
Hypertension is a major public health concern, affecting more than one billion adults worldwide. The etiology of hypertension is associated with various genetic and epigenetic interactions. The candidate genes from various signaling pathways, such as RAAS, KKS and endothelin system, play a significant role in the progression of hypertension. The research aimed to develop a comprehensive knowledge base pertaining to hypertension, which would facilitate the integration of information related to SNPs associated with hypertension, pertinent biological pathways, risk assessment factors, molecular mechanisms, pharmacogenomic aspects of hypertension, a blood pressure calculator, and the existing literature on hypertension. This database has been implemented using HTML and Java programming languages. The deployment of the HTSNPedia database is expected to enhance the efficiency of identifying novel pharmacological drug candidates for the treatment of hypertension. A comprehensive understanding of the interrelationships among signaling pathways, molecular mechanisms, and risk-associated SNPs related to hypertension may significantly contribute to advancements in human health, particularly for individuals affected by this condition. The HTSNPedia is an openly accessible database, available at the following URL: https://www.generisk.in/HTSNPedia/main.html.
Targeted Gene Editing in Honey Bees Using Liposome-Based CRISPR-Cas9.
Yıldız Bİ, Karabağ K
Biochem Genet · 2026 Jun · PMID 40853436 · Publisher ↗
Genome editing technologies have revolutionized molecular biology, enabling precise manipulation of gene functions across diverse organisms. In this study, we introduce a novel liposome-mediated delivery system for CRISP...
Genome editing technologies have revolutionized molecular biology, enabling precise manipulation of gene functions across diverse organisms. In this study, we introduce a novel liposome-mediated delivery system for CRISPR-Cas9 components targeting the Juvenile Hormone Acid Methyltransferase (JHAMT) gene in honey bees (Apis mellifera anatoliaca). This approach leverages drone sperm cells as vectors for CRISPR-Cas9 transfection, overcoming the technical challenges of embryo microinjection in honey bees, such as low survival rates and labor-intensive procedures. The study involved artificial insemination of queen bees with transfected sperm and subsequent evaluation of gene-editing efficiency across generations.Our findings demonstrate the successful generation of both heterozygous and homozygous mutants, with gene-editing efficiencies reaching approximately 43%. This innovative method highlights the potential of liposome-mediated delivery systems for non-invasive, efficient, and scalable genome editing in eusocial insects. The results pave the way for broader applications in honey bee genetic research, offering a viable alternative to traditional methods. Furthermore, this study underscores the importance of genetic tools in advancing apiculture and addressing ecological challenges linked to pollinator health.
RASEL: An Ensemble Model for Selection of Core SNPs and Its Application for Identification and Classification of Cattle Breeds.
Kanaka KK, Ganguly I, Singh S … +4 more , Kuralkar SV, Dixit S, Sukhija N, Goli RC
Biochem Genet · 2026 Jun · PMID 40844696 · Publisher ↗
Identifying and classifying different cattle populations as per their breed and utility holds immense practical importance in effective breeding management. For accurate identification and classification of cattle breeds...
Identifying and classifying different cattle populations as per their breed and utility holds immense practical importance in effective breeding management. For accurate identification and classification of cattle breeds, a reference panel of 10 breeds, 657 identified ancestry informative markers and different machine learning classifiers were employed. To boost the accuracy of breed identification, three distinct machine learning classification models: logistic regression, XGBoost, and random forest, each one having an accuracy of > 95%, were ensembled achieving an accuracy of > 98% with just 207 markers [breed informative markers (BIMs)]. Further, for classification of dairy and draft purpose cattle, the breed informative markers along with those in selection signatures specific to dairy and draft utility were explored, and 17 utility informative markers (UIMs) including 12 BIMs and 5 markers in selection signatures were identified based on an ensemble approach. The accuracy of classification of cattle based on the utility (dairy or draft) was > 96%. To demonstrate the application of UIMs, these markers were used to identify the utility of non-descript cattle of Maharashtra, India and found that many of these cattle were draft purpose and were aligning with their production performance. This information can further be used for taking breeding decisions for their grading up to dairy or draft cattle. Here, a novel pipeline which utilized [R-] reference panel, [A-] ancestry informative markers, [S-] selection signatures and the power of [EL-] ensemble machine learning for identifying and classifying the cattle, breed- and utility-wise, was developed, and we called it as RASEL (available at: https://github.com/kkokay07/RASEL ).
DNA Sequence Perplexity Reveals Evolutionarily Conserved Patterns in cis-Regulatory Regions Across Diverse Species.
Gummadi ASC, Yella VR
Biochem Genet · 2026 Jun · PMID 40841702 · Publisher ↗
Deciphering cis-regulatory regions in genomes is essential for understanding various physiological processes and pathological mechanisms. Regulatory signatures, namely promoter motifs, transcription factor binding sites,...
Deciphering cis-regulatory regions in genomes is essential for understanding various physiological processes and pathological mechanisms. Regulatory signatures, namely promoter motifs, transcription factor binding sites, enhancers, GC content, CpG islands, DNA structural motifs, and other cis-regulatory features, are well-established for their roles in transcriptional regulation. However, these features often exhibit species-specific variations, challenging the identification of conserved regulatory principles across different genomes. In this study, we introduce DNA sequence perplexity as an innovative and efficient information-theoretic metric for characterizing cis-regulatory regions. Derived from information theory and natural language processing, perplexity quantifies the complexity and predictability of sequence, offering a motif-independent framework for DNA analysis. By examining transcription and translation start site regions across 1180 species spanning diverse taxa, we demonstrate that cis-regulatory regions consistently exhibit lower perplexity compared to adjacent flanking regions. This trend persists irrespective of taxonomic classification, establishing perplexity as an evolutionarily conserved pattern of regulatory DNA. Additionally, we observe an inverse correlation between perplexity and promoter strength in yeast datasets, suggesting that higher transcriptional outputs are associated with markedly reduced sequence perplexity. Our findings reveal that perplexity may hold valuable insights into the generalizable aspects of cis-regulatory DNA architecture. Integrating this abstraction-based strategy with motif-based approaches and high-throughput functional datasets could enhance its applicability in predictive applications across comparative and functional genomics.
Extracellular Vesicle-Associated MicroRNA-25-3p Derived from Pancreatic Cancer Cells Promotes Hepatic Stellate Cell Activation and Enhances Cancer Progression.
Wu X, Shen R, Yang Z … +3 more , Tang Y, Huang J, Yao W
Biochem Genet · 2026 Jun · PMID 40839193 · Publisher ↗
Pancreatic cancer is a highly aggressive malignancy with a poor prognosis, mainly due to late diagnosis and early metastatic spread. The underlying mechanisms of pancreatic cancer metastasis, particularly the role of hep...
Pancreatic cancer is a highly aggressive malignancy with a poor prognosis, mainly due to late diagnosis and early metastatic spread. The underlying mechanisms of pancreatic cancer metastasis, particularly the role of hepatic stellate cell (HSC) activation, are not fully understood. This study tried to find potential biomarkers for pancreatic cancer progression and prognosis by analyzing extracellular vesicle (EV)-associated miRNA profiles in plasma from pancreatic cancer patients and non-cancer controls. Functional assays, including transfection, western blotting, immunofluorescence, and enzyme-linked immunosorbent assay (ELISA), were used to assess the ability of the identified miRNA to activate HSCs and promote cancer progression. Our findings revealed that miR-25-3p was significantly upregulated in EVs derived from pancreatic cancer patients, correlating with increased metastasis and worse survival outcomes. EV-associated miR-25-3p from metastatic pancreatic cancer cells activated HSCs by regulating the expression of Krüppel-like factor 4 (KLF4). Additionally, activated HSCs secreted vascular endothelial growth factor (VEGF), further driving pancreatic cancer metastasis and progression. These results suggest that miR-25-3p could serve as a novel biomarker for pancreatic cancer progression and a potential therapeutic target to improve patient outcomes.
Integrated Analysis of Bulk and Single-Cell Transcriptomics Identifies Prognostic Biomarkers in Breast Cancer Metastasis.
Wu QQ, Liu K, Xu JF … +12 more , Zhang Y, Jiang JR, Wang HL, Wang LF, Zhou JN, Liu J, Lin X, Chen H, Guan YY, Yang P, Sun J, Wu WX
Biochem Genet · 2026 Jun · PMID 40828203 · Full text
Breast cancer (BC) remains one of the leading causes of cancer-related mortality among women worldwide, with distant metastasis being the primary contributor to poor prognosis. However, the molecular mechanisms driving B...
Breast cancer (BC) remains one of the leading causes of cancer-related mortality among women worldwide, with distant metastasis being the primary contributor to poor prognosis. However, the molecular mechanisms driving BC metastasis are not yet fully understood. We integrated three public microarray datasets (GSE14776, GSE103357, and GSE32489) to identify the differentially expressed genes (DEGs) associated with breast cancer metastasis. Functional enrichment analysis, protein-protein interaction (PPI) network construction, and hub gene identification were performed using bioinformatics tools including DAVID, STRING, Cytoscape, and R. The prognostic significance of hub genes was assessed using Kaplan-Meier plotter and GEPIA. Expression validation was conducted through UALCAN, immunohistochemistry (IHC), and single-cell RNA sequencing (scRNA-seq) analysis from the GSE180286 dataset. A total of 295 co-DEGs were identified across the three datasets, enriched in pathways such as MAPK signaling, Rap1 signaling, and cell adhesion molecules. Twenty hub genes were identified from the PPI network, with eight showing strong prognostic value. Among them, PRC1 and POLR3H emerged as potential novel biomarkers. IHC confirmed the differential protein expression of PRC1, CDCA8, KIF14, and POLR3H. scRNA-seq analysis revealed that these hub genes were predominantly expressed in malignant epithelial and EMT (epithelial-mesenchymal transition) cells, particularly those from metastatic lymph node sites. This integrative analysis combining bulk and single-cell transcriptomic data identified key metastasis-associated genes in breast cancer. PRC1 and POLR3H, in particular, may serve as novel prognostic biomarkers and potential therapeutic targets.
Bioinformatics and Experimental Validation of Diagnostic Marker Genes for Myocardial Infarction and Analysis of Their Immune Cell Infiltration.
Wu S, Wang R, Cui J … +2 more , Huo H, Yao Z
Biochem Genet · 2026 Jun · PMID 40828202 · Publisher ↗
This study aimed to identify diagnostic marker genes for myocardial infarction (MI) and analyzed the key genes pertaining to immune cell infiltration. The MI expression microarrays GSE48060 and GSE66360 were retrieved an...
This study aimed to identify diagnostic marker genes for myocardial infarction (MI) and analyzed the key genes pertaining to immune cell infiltration. The MI expression microarrays GSE48060 and GSE66360 were retrieved and downloaded from the GEO database. The merged expression data were subjected to Weighted Gene Co-expression Network Analysis (WGCNA). Subsequently, differentially expressed genes (DEGs) were analyzed in MI. Primary rat cardiomyocytes (NRVMs) were isolated for an oxygen-glucose deprivation/reoxygenation (OGD/R) model, in which the effect of ICAM1, NFIL3, TULP2, and ZFP36 on cell phenotype experiments was detected. Gene differential expression analysis identified 96 significant DEGs, and the intersection of these genes with the module genes obtained from WGCNA analysis yielded 81 candidate genes. LASSO regression and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) algorithms identified 7 candidate diagnostic genes. ICAM1, NFIL3, TULP2, and ZFP36 exhibited good diagnostic potential in both experimental and validation datasets, showing significant correlations with immune cells, including Neutrophils. ICAM1, NFIL3, TULP2, and ZFP36 were markedly up-regulated in OGD/R-treated NRVMs, while ICAM1 knockdown suppressed NRVM damage triggered by OGD/R. ICAM1, NFIL3, TULP2, and ZFP36 can serve as candidate diagnostic genes for MI, and ICAM1 silencing can ameliorate OGD/R-elicited myocardial cell damage.
Unraveling the Chloroplast Genome of Stellaria media: Comprehensive Analysis, Taxonomic Implications, and Evolutionary Perspectives.
Kadam SK, Tamboli AS, Youn JS … +2 more , Pak JH, Choo YS
Biochem Genet · 2026 Jun · PMID 40828201 · Publisher ↗
The chloroplast (Cp) genome offers valuable perceptions into plant evolution, systematics, and phylogenetics. Here we are reporting complete chloroplast genome of Stellaria media (L.) Vill. collected from Dokdo Island, S...
The chloroplast (Cp) genome offers valuable perceptions into plant evolution, systematics, and phylogenetics. Here we are reporting complete chloroplast genome of Stellaria media (L.) Vill. collected from Dokdo Island, South Korea. The genome, assembled at 6340 × coverage, is 147,329 bp with a typical quadripartite structure, covering two inverted repeat (IR) regions of 25,600 bp and one single copy of large (79,366 bp) and small region (16,763 bp) each. Genome annotation identified 129 genes, including 84 protein-coding genes, 8 rRNA and 37 tRNA genes. In the IR region, ycf3 and clpP1 each contain two introns, while 17 genes, including rpl2, trnL-CAA, ycf2, and ndhB are present in duplicate, whereas rps19 is present as a single copy, reflecting structural conservation and evolutionary mechanisms such as intron retention and gene duplication. Comparative genomic analysis revealed substantial variations both among Stellaria species and in the formerly classified Stellaria dichotoma var. lanceolata. Codon usage showed a biasness toward codons ending with A/U, with leucine being most frequently encoded amino acid. Phylogenetic reconstruction based on complete chloroplast genomes positioned S. media within the Alsineae tribe and highlighted monophyletic relationships in the genus. Sliding window analysis identified hypervariable regions, including ycf1, ndhF-rpl32, and trnK-rps16 as potential molecular markers. This study provides crucial perceptions into chloroplast genome evolution, comparative genomics, and phylogeny within Caryophyllaceae, contributing essential data for taxonomic and conservation research. Additionally, multiple lines of evidence, including comparative chloroplast genomics, analyses of long and short repeat sequences, codon usage patterns, and phylogenetic relationships, support the taxonomic revision of inclusion of the genus Myosoton within Stellaria, and the exclusion of Stellaria dichotoma var. lanceolata from the genus Stellaria.
Exploration Biomarkers for Recurrence of Hepatocellular Carcinoma After Liver Transplantation Based on Bioinformatics Analysis.
Zhu G, Li S, Luo Z … +6 more , Wen N, Li H, Fu Y, Li W, Wu J, Sun X
Biochem Genet · 2026 Jun · PMID 40826252 · Full text
This study aimed to explore thrombin-related prognostic biomarkers for hepatocellular carcinoma (HCC) recurrence after liver transplantation (LT). Bioinformatics analyses were conducted using TCGA-LIHC and GEO datasets....
This study aimed to explore thrombin-related prognostic biomarkers for hepatocellular carcinoma (HCC) recurrence after liver transplantation (LT). Bioinformatics analyses were conducted using TCGA-LIHC and GEO datasets. LASSO Cox regression screened thrombin-related genes (TRGs). Differential expression analysis, GSEA, and protein-protein interaction (PPI) network analysis were performed to identify key pathways and hub genes. Clinical validation included immunohistochemistry (IHC) on 78 post-LT HCC tissues. In vitro assays (CCK-8, Transwell, Colony formation) assessed MMP1/SPP1 roles in HCC cell proliferation and migration. Nine TRGs were prognostic in HCC, with MMP1 and SPP1 emerging as core regulators linked to EMT. Both genes were significantly upregulated in recurrent HCC tissues (1-year recurrence group vs. non-recurrence, P < 0.05) and correlated with reduced overall survival (OS) and recurrence-free survival (RFS). GSEA revealed EMT as a key enriched pathway. PPI network analysis highlighted MMP1/SPP1 centrality in ECM remodeling and cell adhesion. Clinical samples confirmed MMP1 association with vascular invasion (P = 0.023) and poor differentiation. In vitro, MMP1/SPP1 overexpression enhanced HCC cell proliferation, migration, and colony formation. Multivariate analysis identified MMP1 expression and tumor differentiation as independent recurrence risk factors. MMP1 and SPP1 are potential biomarkers for predicting post-LT HCC recurrence, likely driving metastasis via EMT activation. Their overexpression correlates with aggressive tumor behavior and adverse outcomes, offering prognostic utility and therapeutic targets to improve transplant outcomes.
Genetic Heterogeneity of Autism Spectrum Disorder: Identification of Five Novel Mutations (RIMS2, FOXG1, AUTS2, ZCCHC17, and SPTBN5) in Iranian Families via Whole-Exome and Whole-Genome Sequencing.
Mirahmadi M, Kahani SM, Sharifi-Zarchi A … +3 more , Firouzabadi SG, Behjati F, Garshasbi M
Biochem Genet · 2026 Jun · PMID 40819013 · Publisher ↗
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by abnormal social interactions, verbal communication difficulties, and restricted repetitive behaviors. Identifying the underlying genetic fa...
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by abnormal social interactions, verbal communication difficulties, and restricted repetitive behaviors. Identifying the underlying genetic factors is crucial because of the complex genetic and environmental etiology. In this study, we performed whole-exome sequencing (WES), whole-genome sequencing (WGS), and array comparative genomic hybridization (aCGH) of four Iranian families with ASD-related conditions to identify novel genomic alterations. Five previously undescribed mutations were identified in these families. Family 1: A homozygous 290.7 kb deletion CNV (chr8:103,652,204-103942926; hg38) encompassing exons 2-16 of RIMS2 (NM_001348484), confirmed in a 7-year-old male proband with developmental delay and cone-rod synaptic disorder. Family 2: A heterozygous nonsense mutation in FOXG1 (NM_005249.5:c.839C > A; p.Ser280Ter) in a 6-year-old female with Rett-like features, resulting in a truncated protein lacking corepressor domains. Family 3: A splice donor site mutation in AUTS2 (NM_015570.4:c.742 + 1G > C) in a 10-year-old female with ASD and Attention-deficit/hyperactivity disorder, generating a frameshift and premature stop codon affecting mRNA-binding functionality. Family 4: A heterozygous nonsense mutation in ZCCHC17 (NM_016505.4:c.220C > T; p.Arg74Ter) and a splicing variant in SPTBN5 (NM_016642.4:c.3470 + 2T > A) in two male siblings with ASD were predicted to result in truncated proteins and aberrant splicing. Pathogenicity was supported through in silico analyses and structural modeling using I-TASSER, and segregation was confirmed using Sanger sequencing. This study highlights the genetic diversity of ASD and underscores the importance of advanced sequencing technologies in identifying novel mutations. Our findings contribute to the growing body of knowledge regarding the genetic basis of ASD, paving the way for personalized treatment strategies and early diagnosis.
CircRNA_0001412 and CircRNA_0001566 as Potential Biomarkers for the Diagnosis of Rheumatoid Arthritis.
Li X, Deng A, Wang Z … +4 more , Liao S, Luo K, Hu J, Yang B
Biochem Genet · 2026 Jun · PMID 40810915 · Publisher ↗
Rheumatoid arthritis (RA) is a chronic autoimmune disease with high disability rates, necessitating early diagnosis. This study investigated the potential of circRNAs, specifically CircRNA_0001412 and CircRNA_0001566, as...
Rheumatoid arthritis (RA) is a chronic autoimmune disease with high disability rates, necessitating early diagnosis. This study investigated the potential of circRNAs, specifically CircRNA_0001412 and CircRNA_0001566, as diagnostic biomarkers for RA. High-throughput transcriptome sequencing was performed on peripheral blood mononuclear cells (PBMCs) from RA patients and healthy controls to identify differentially expressed circRNAs. Reverse transcription quantitative PCR (RT-qPCR) was used to validate circRNA expression in an independent cohort of 78 RA patients and 82 healthy controls. Receiver operating characteristic (ROC) curve analysis was performed to assess the diagnostic value of the selected circRNAs. Correlation analyses with clinical markers such as CRP, ESR, CCP, RF, WBC, lymphocyte count, and monocyte count were also conducted. Bioinformatics analyses, including GO and KEGG pathway enrichment, were conducted to explore the functional roles of the identified circRNAs and associated miRNAs. A total of 54 circRNAs were identified as differentially expressed in RA, with 21 circRNAs upregulated and 33 downregulated. Among these, CircRNA_0001412 and CircRNA_0001566 were highly expressed in RA PBMCs and demonstrated good sensitivity and specificity as diagnostic biomarkers (AUC = 0.751 (95%CI 0.673, 0.830) and 0.605(95%CI 0.516, 0.694)). Combined analysis of these circRNAs further improved diagnostic performance (AUC = 0.776 (95%CI 0.702, 0.851)). Notably, CircRNA_0001412 showed a significant correlation with CRP, suggesting its potential as a biomarker for RA disease severity. Bioinformatics analysis predicted that CircRNA_0001412 and CircRNA_0001566 could promote T-cell activation via the PI3K-Akt signaling pathway, contributing to RA pathogenesis. CircRNA_0001412 and CircRNA_0001566 are promising diagnostic biomarkers for RA, with CircRNA_0001412 additionally serving as a potential indicator of inflammatory activity. These findings provide a basis for further research into the diagnostic and prognostic utility of circRNAs in RA.
CBFA2T3 as a Key Prognostic Biomarker in Lung Adenocarcinoma: Insights from Comprehensive Analysis and Validation.
Xiao J, Luo K, Liu M … +4 more , Zhao H, Cai Y, Gui Y, Zhang H
Biochem Genet · 2026 Jun · PMID 40804206 · Publisher ↗
Lung cancer is a common and highly lethal malignancy globally, predominantly comprising non-small cell lung cancer (NSCLC), accounting for 80-85% of lung cancer cases. Lung adenocarcinoma (LUAD) represents the predominan...
Lung cancer is a common and highly lethal malignancy globally, predominantly comprising non-small cell lung cancer (NSCLC), accounting for 80-85% of lung cancer cases. Lung adenocarcinoma (LUAD) represents the predominant subtype of NSCLC and is characterized by challenging early diagnosis and poor prognosis. Studies have implicated CBFA2T3 expression in treatment outcomes and prognosis across various cancers, yet its specific mechanisms remain under investigation. Analysis of TCGA data revealed a negative correlation between CBFA2T3 expression and tumor growth, suggesting that lower CBFA2T3 levels are associated with poorer outcomes in patients with LUAD. Our research identifies CBFA2T3 as a therapeutic target and potential prognostic indicator in LUAD, closely linked to immune cell infiltration and key immune regulatory markers. A model integrating CBFA2T3-regulated immune-related genes was constructed to predict the prognosis and immunotherapy response of patients with LUAD. Our findings were validated using GSE31210 and IMvigor210 datasets. qPCR and WB experiments on clinically collected samples confirmed reduced CBFA2T3 expression in LUAD. Online analysis using the Kaplan‒Meier plotter website confirmed a correlation between reduced CBFA2T3 expression and poorer prognosis in patients with lung cancer. Ultimately, our study identifies CBFA2T3 as a pivotal prognostic biomarker and potential therapeutic target for managing LUAD.
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