Gene Profiling Research Articles

Characterization of NOD-like receptor-based molecular heterogeneity in glioma and its association with immune micro-environment and metabolism reprogramming

Background and purposeThe characteristics and role of NOD-like receptor (NLR) signaling pathway in high-grade gliomas were still unclear. This study aimed to reveal the association of NLR with clinical heterogeneity of glioblastoma (GBM) patients, and to explore the role of NLR pathway hub genes in the occurrence and development of GBM.MethodsTranscriptomic data from 496 GBM patients with complete prognostic information were obtained from the TCGA, GEO, and CGGA databases. Using the NMF clustering algorithm and the expression profiles of NLR genes, these 496 GBM patients were classified into different clinical subtypes. The pathway activity of NLR and the immune micro-environment characteristics were then compared between these subtypes. A novel and accurate NLR expression profile-based prognostic marker for GBM was developed using LASSO and COX regression analysis.ResultsBased on the NLR gene expression profile, GBM patients were accurately divided into two clinical subtypes (C1 and C2) with different clinical outcomes. The two groups of patients showed different immune microenvironment characteristics and metabolic characteristics, which might be the potential reason for the difference in prognosis. Differential expression and enrichment analyzes revealed intrinsic gene signature differences between C1 and C2 subtypes. Based on the differential expression profiles of C1 and C2, prognostic molecular markers related to NLR were developed. The AUC value of the 3-year ROC curve ranged from 0.601 to 0.846, suggesting its potential clinical significance. Single-cell sequencing analysis showed that the NLR gene was mainly active in myeloid cells within GBM. The random forest algorithm identified the crucial role of TRIP6 gene in NLR pathway. Molecular biology experiments confirmed that TRIP6 was abnormally overexpressed in GBM. Knockdown of TRIP6 gene can significantly inhibit the proliferation and migration ability of GBM cells.ConclusionThe NLR signaling pathway plays a critical role in regulating immune microenvironment and metabolism reprogramming of GBM. TRIP6 is a potential hub gene within the NLR pathway and affects the malignant biological behavior of GBM cells.

Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores

Sesame products such as tahini (tahin) or halva (halwa or helva), originating from Arabic cuisine, are becoming increasingly popular in Switzerland. Pathogens, such as Salmonella, can contaminate sesame products, as evidenced by various product recalls. In this study, the occurrence of Salmonella and Bacillus cereus group members was investigated in 100 sesame products (25 sesame seeds, 16 halva, 19 different sesame pastes, 7 sesame bars, 25 hummus, and 8 other products containing sesame) collected from Swiss retail stores. None of the products were positive for Salmonella, whereas B. cereus group members could be detected with bacterial counts between 1×102 and 9×102 CFU/g in 11 out of 100 (11%) products. The 11 isolates identified by matrix-assisted laser desorption ionization-time of flight were whole-genome sequenced with Illumina technology to confirm the identity of the pathogen, determine its toxin gene profile, and perform panC typing. Most of the isolates harbored genes encoding the enterotoxins Nhe, Hbl, and CytK. The isolates were assigned to diverse B. cereus group members, including one identified as B. cytotoxicus. In addition, one of the isolates matched genetically with the Thurigiensis strain used in biopesticide products. In conclusion, none of the investigated sesame products contained significant levels of Salmonella or B. cereus group members. However, as B. cereus with pathogenic potential was detected in multiple samples, proper storage is crucial to prevent its growth and ensure consumer safety, especially for products with high water activity such as hummus.

Assessment of typing methods, virulence genes profile and antimicrobial susceptibility for clinical isolates of Proteus mirabilis

Proteus mirabilis (P. mirabilis) is one of the most important causative pathogens associated with complicated urinary tract infections with a 20% incidence. For epidemiological determinations, several phenotypic and molecular typing methods have been implicated. Sixty P. mirabilis isolated undergo antibiotic susceptibility test by standard Kirby Bauer method. They showed high resistance to nitrofurantoin and trimethoprim/sulfamethoxazole that appear mainly in 3rd age group. The 2nd age group comprised most of the resistant isolates to the tested antibiotics. A total of 73.33% of isolates were classified as multi drug resistance (MDR) and 78.3% of isolates were distributed in several antibiotypes with MAR index over 0.2. Twenty-one isolates were strong biofilm-producers and they were significantly related to MDR. Different virulence factors as protease, urease and hemolysin production are detected. Detection of several virulence genes by PCR; zapA and ureC were harbored by all isolates, followed by rsbA (95%), ureA and flaA (93%), hpmA (91.7%) and mrpA (73.3%). Determination of genetic diversity between isolates was performed by different methods (RAPD, ISSR, ERIC, BOX-AIR and REP-PCR) by using several parameters as typeability and discriminatory power indicating that ERIC-PCR was the best method followed by REP-PCR 1R. Rand’s & Wallace coefficients were used for calculating the congruence among typing methods. Conclusions: The results obtained from both conventional and molecular typing methods indicated that molecular methods are superior to conventional methods in the discrimination of isolates. ERIC-PCR and Rep-PCR provide high discrimination ability among P. mirabilis clinical isolates contributing to epidemiological studies.

Antimicrobial Resistance Gene Profiles in Communities Selected with Novel and Previously Encountered Antibiotics

Antibiotics are extensively employed worldwide for therapeutic purposes, often leading to overuse, which constitutes a contributing factor to the emergence of antibiotic resistance (ABR). This phenomenon arises from diminished effectiveness of antibiotics in treating bacterial infections due to resistance development. However, limitations in experimental conditions and equipment making it challenging to pinpoint the precise sources of antibiotic resistance, consequently constraining the breadth of research on ABR. Genomic analysis of antibiotic-resistant bacteria assists in unveiling the origins and pathways of resistance dissemination. This study employs Nanopore-based metagenomic sequencing, enabling direct sequencing of microbial DNA within macrogenomic samples, thereby yielding comprehensive sequence data. Coupled with qPCR and 16S rRNA gene datasets, this approach facilitates the exploration of antibiotic resistance gene distribution and prevalence within microbial communities across different environments Focusing on microbial communities within Scottish farmlands, isolated colonies were exposed to antibiotics (sulfamonomethoxine and erythromycin) for several weeks. By comparing them to untreated control group microorganisms, the identification of antibiotic resistance genes (ABRGs), along with their variations in prevalence and abundance, aims to analyse the impact of these two antibiotics on these species.

Digestive and absorptive capacity and digesta microbiota throughout the gastrointestinal tract of nursery pigs from parents with divergent estimated breeding value for feed conversion ratio

This study investigated digestive and absorptive function changes and microbiota adaptations during weaning in nursery pigs from parents with divergent estimated breeding values for feed conversion ratio (EBV_FCR). The research aimed to investigate whether these changes differed between two groups: pigs from high EBV_FCR (low efficiency, LE) parents and pigs from low EBV_FCR (high efficiency, HE) parents. Furthermore, digesta samples from duodenum, jejunum, ileum, colon, and cecum were collected from 56-day-old post-weaned pigs and subjected to microbiota analysis using 16S rRNA gene profiling. Enzyme activity kinetics and gene expression analyses of nutrient transporters in various segments of the digestive tract showed no significant differences between the two groups. Tight junction proteins gene expression also showed no significant differences in the jejunum between the two groups. Microbiota analysis revealed consistent dominance of Firmicutes in the jejunum and ileum, with Firmicutes and Bacteroidetes prevalent in the cecum and colon across both groups. However, significant differences were observed at the genus level. Lactobacillus was predominant in the small intestine of HE pigs, while the large intestine of LE pigs harbored higher levels of Prevotella, Streptococcus, and Blautia compared to HE pigs. These differences suggest potential functional differences that warrant further investigation.

Unraveling Effects of miRNAs Associated with APR Leaf Rust Resistance Genes in Hybrid Forms of Common Wheat (Triticum aestivum L.)

The fungus Puccinia triticina Eriks (Pt) is the cause of leaf rust, one of the most damaging diseases, which significantly reduces common wheat yields. In Pt-resistant adult plants, an APR-type resistance is observed, which protects the plant against multiple pathogen races and is distinguished by its persistence under production conditions. With a more complete understanding of the molecular mechanisms underlying the function of APR genes, it will be possible to develop new strategies for resistance breeding in wheat. Currently, mainly APR genes, such as Lr34, Lr46, and Lr67, are principally involved in resistance breeding as they confer durable resistance to multiple fungal races occurring under different climatic and environmental conditions. However, the mechanisms underlying the defence against pathogens mediated by APR genes remain largely unknown. Our research aimed to shed light on the molecular mechanisms related to resistance genes and miRNAs expression, underlying APR resistance to leaf rust caused by Pt. Furthermore, the present study aimed to identify and functionally characterize the investigated miRNAs and their target genes in wheat in response to leaf rust inoculation. The plant material included hybrid forms of wheat from the F2 and BC1F1 generations, obtained by crossing the resistance cultivar Glenlea (CItr 17272) with agriculturally important Polish wheat cultivars. Biotic stress was induced in adult plants via inoculation with Pt fungal spores under controlled conditions. The RT-qPCR method was used to analyze the expression profiles of selected APR genes at five time points (0, 6, 12, 24, and 48 hpi). The results presented here demonstrate the differential expression of APR genes and miRNAs at stages of leaf rust development at selected timepoints after inoculation. We analyzed the expression of three leaf rust resistance genes, using different genetic backgrounds in F2 and BC1F1 segregation materials, in leaf tissues after Pt infection. Our goal was to investigate potential differences resulting from the genetic background found in different generations of hybrid forms of the same parental forms. Gene ontology analysis predicted 190 target genes for tae-miR5384-3p and 167 target genes for tae-miR9653b. Our findings revealed distinct expression profiles for genes, with the highest expression levels observed mainly at 6, 24, and 48 hpi. The candidate gene Lr46-Glu2 displayed an upregulation, suggesting its potential involvement in the immune response against Pt infection.

Asymptomatic HyperCKemia in the Pediatric Population: A Prospective Study Utilizing Next-Generation Sequencing and Ancillary Tests.

Persistent elevation of serum creatine kinase levels (hyperCKemia) as an isolated manifestation presents a diagnostic challenge. Genetic myopathies are frequently involved; however, studies using next-generation sequencing (NGS) in pediatric patients are lacking, and the significance of genetic aberrations remains poorly understood. This study, therefore, aimed to investigate the relevance of NGS and the support of contemporary diagnostic tools in the diagnosis of pediatric asymptomatic hyperCKemia. This was a prospective cohort study enrolling pediatric (0-18 years old) patients meeting the predefined criteria for asymptomatic/paucisymptomatic hyperCKemia, excluding DMD gene deletion/duplication, recruited from a referral center. NGS, muscle MRI, EMG, and muscle biopsies with immunolabeling and inflammatory markers were performed according to a prespecified protocol. Data analysis was performed using descriptive/univariate statistics and Bayesian logistic regression. The series comprised 65 patients (78% male). NGS diagnosis was achieved in 55% of the cohort, with 70% of the pathogenic variants involving 7 genes (DMD, CAPN3, ANO5, DYSF, RYR1, GAA, and CAV3). The diagnostic rate was similar across all age groups; however, the gene profiles varied between the childhood and juvenile groups. EMG yielded myopathic features in 48% of the investigated cases, being predictive for diagnosis (p < 0.05; odds ratio [OR] 13.484, 95% CI 1.358-705.297). MRI showed normal (64%), focal fatty change (26%), or short-tau inversion recovery hyperintensity (10%) profiles, which were not predictive of diagnosis but supported muscle biopsy indications. Muscle biopsy provided a significant diagnostic effect (p < 0.05; OR 0.028, 95% CI 0.001-0.238), contributing to myopathologic features clarifying the variant pathogenicity and identifying inflammatory myopathies. The diagnoses remained inconclusive and unresolved in 14% and 29% of the cohorts, respectively. The diagnostic rate for patients with CK levels below the threshold of 3× was 42%. In multivariate analysis, NGS was the only variable achieving a significant diagnostic effect (β = 9.85, 95% CI 4.65-16.09). NGS, as the primary diagnostic tool for investigating hyperCKemia in the pediatric population, yielded a higher diagnostic rate. However, muscle biopsies are necessary to define variants of uncertain pathogenicity and aid in identifying inflammatory myopathies. EMG and MRI may play a role in hyperCKemia characterization, guiding the decision to perform muscle biopsy. The primary limitation of this study was that not all ancillary tests were performed in all recruited patients owing to ethical restrictions, which lowered the power of the predictive analysis.

The effect of LARP7 on gene expression during osteogenesis.

La-related protein 7 (LARP7) is a key regulator of RNA metabolism and is thought to play a role in various cellular processes. LARP7 gene autosomal recessive mutations are the cause of Alazami syndrome, which presents with skeletal abnormalities, intellectual disabilities, and facial dysmorphisms. This study aimed to determine the role of LARP7 in modulating gene expression dynamics during osteogenesis. First, the temporal expression profile of the LARP7 gene during various stages of osteogenesis was examined. Then, RNA interference-mediated knockdown of LARP7 was implemented and high-throughput RNA-seq analysis was performed in order to identify global gene expression changes associated with knockdown of LARP7. The findings show there were significant alterations in the overall gene expression profile. The observed down-regulation in extracellular matrix (ECM) component genes suggests that it might lead to impairments in the structure and function of the bone matrix. Additionally, modulation of alternative splicing events were observed, especially in the RUNX2 and SPP1, indicating the potential contribution of LARP7 to the phenotypic features observed in Alazami syndrome. Overall, the findings clarify the regulatory mechanisms of LARP7 in osteogenic differentiation and illuminate potential avenues for therapeutic interventions in patients with skeletal disorders.

Effects of NK cell-related lncRNA on the immune microenvironment and molecular subtyping for pancreatic ductal adenocarcinoma

BackgroundPatients with pancreatic ductal adenocarcinoma (PDAC) face a highly unfavorable outcome and have a poor response to standard treatments. Immunotherapy, especially therapy based on natural killer (NK) cells, presents a promising avenue for the treatment of PDAC.AimsThis research endeavor seeks to formulate a predictive tool specifically designed for PDAC based on NK cell-related long non-coding RNA (lncRNA), revealing new molecular subtypes of PDAC to promote personalized and precision treatment.MethodsUtilizing the Tumor Immune Single-cell Hub 2 platform, we discovered genes associated with NK cells in PDAC. We employed the TCGA-PAAD dataset to ascertain the expression profiles of these NK cell-related genes and to screen for lncRNAs correlated with NK cells. Subsequently, we utilized Cox regression analysis for hazard ratios and LASSO regression analysis to identify three NK cell-related lncRNAs that were used to develop a prognostic assessment model. The forecasting accuracy of this model was appraised using the ROC curve and validated using a test set and the complete dataset.ResultsSuccessful construction of a prognostic model comprising three lncRNAs was achieved, demonstrating good predictive efficiency in the training set, validation dataset, and the entire dataset. NK cells display robust interactions with malignant cells, CD8 T cells, and fibroblasts in the PDAC tumor microenvironment and participate in the transport of various signaling molecules and following immune responses in PDAC. According to the expression patterns of NK cell-related lncRNA, we labeled PDAC patients as four molecular subtypes, exhibiting significant differences in immune cell infiltration, drug sensitivity, and other aspects.ConclusionThis study Uncovered the activity of NK cells within PDAC, proposed an NK cell-related lncRNA model, and delineated new molecular subtypes, thereby providing targets for personalized therapy.

Obesity alters the fitness of peritumoral adipose tissue, exacerbating tumor invasiveness in renal cancer through the induction of ADAM12 and CYP1B1.

Obesity exacerbates the risk and aggressiveness of many types of cancer. Adipose tissue (AT) represents a prevalent component of the tumor microenvironment (TME) and contributes to cancer development and progression. Reciprocal communication between cancer and adipose cells leads to the generation of cancer-associated adipocytes (CAAs), which in turn foster tumor invasiveness by producing paracrine metabolites, adipocytokines, and growth factors. Interfering with the crosstalk between CAAs and cancer cells is of key relevance in the prevention of tumor progression. The present study aimed to analyze the contribution of peritumoral AT in renal cell carcinoma (RCC) progression in lean versus overweight or obese patients. By isolating human adipose-derived stromal/stem cells from the three groups of patients and performing conditioned medium studies with RCC cells along with in vivo xenograft experiments, we found that peritumoral adipocytes from the three groups show a distinct expression profile of genes. In particular, ADAM metallopeptidase domain 12 (ADAM12) and cytochrome P450 family 1 subfamily B member 1 (CYP1B1) were found to be upregulated in obesity and their silencing reduced RCC cell invasiveness. In conclusion, high ADAM12 and CYP1B1 expressions in the peritumoral adipocytes boost tumor invasiveness and may serve as an indicator of poor prognosis in RCC.

NtLPA1 overexpression regulates the growth of tobacco and enhances resistance to blight.

The involvement of Loose Plant Architecture 1 (LPA1) in regulating plant growth and leaf angle has been previously demonstrated. However, the fundamental genetic background remains unidentified. To further understand the tissue expression profile of the NtLPA1 gene, an overexpression vector (pBI121-NtLPA1) was developed and employed to modify tobacco using the leaf disc method genetically. Validation confirmed the generation of transgenic tobacco plants with NtLPA1 overexpression. The findings indicated that increased NtLPA1 overexpression substantially decreased plant auxin sensitivity and modulated signal transduction and polar transport, significantly reducing leaf angle, diminished leaf area during early and late growth stages, and shortened root length. In summary, NtLPA1 augmented tobacco resistance to severe shin disease by modulating the expression of disease-associated genes PBZ1, PR1b, and the growth regulator auxin polar transport factor PIN1.

Genetic Underpinnings of Oligoasthenoteratozoospermia.

Oligoasthenoteratozoospermia (OAT) is a frequent but severe type of male infertility. As one of the most multifaceted male infertility resulting from sperm problems, its genetic etiology remains unknown in most cases. In this review, we systematically sort out the latest literature on clinical reports and animal models leading to OAT, summarise the expression profiles of causative genes for OAT, and highlight the important role of the protein transport system during spermiogenesis, spermatid cell-specific genes, Golgi and acrosome-related genes, manchette-related genes, HTCA-related genes, and axoneme-related genes in OAT development. These causative genes would be instrumental in genetic etiological screening, genetic counseling, and pre-implantation genetic testing of patients with clinical OAT.

Profiling of antimicrobial resistance genes from Staphylococcus pseudintermedius isolated from dogs with pyoderma using whole genome sequencing.

Staphylococcus pseudintermedius is considered as a most common cause of canine pyoderma. Antimicrobial resistance is considered as a global public health concern. The main aim of the study was to evaluate the distribution of Antimicrobial resistance genes in S. pseudintermedius isolates using whole genome sequencing. In the current work, Antimicrobial susceptibility testing and Whole genome sequencing was performed on Five S. pseudintermedius isolates recovered from canine pyoderma cases presented at Veterinary Clinical Complex, Navsari. Bioinformatics analysis of sequencing data was performed to detect Antimicrobial resistance genes, plasmids and mobile genetic elements in S. pseudintermedius isolates. All S. pseudintermedius isolates shows resistance towards amikacin, ampicillin, cefpodoxime, cephalexin, erythromycin and trimethoprim. Higher sensitivity was observed against clindamycin (4/5, 80 %). A total 15 AMR genes, one plasmid (repUS43), two insertion sequences (ISLgar5 and IS256) and one Integrative Conjugative Element (Tn6009) were detected using whole genome sequencing analysis. This study aids us to know about relationship between antimicrobial resistance and presence of AMR genes, plasmids and mobile genetic elements.

Genomic insights into fibrinogen-related proteins and expression analysis in the Pacific white shrimp, Litopenaeusvannamei.

Fibrinogen-related domain (FReD) containing proteins are an evolutionarily conserved immune gene family characterized by the C-terminal fibrinogen (FBG) and diverse N-terminal domains. To understand the complexity of this family in crustaceans, we performed genome screening and identified 43 full-length FReDs encoding genes in Litopenaeus vannamei. Structural classification analysis revealed these putative FReDs could be divided into six types, including two reported types (LvFReDI and II) and four new types (LvFReDIII-VI). Sequence and phylogenetic analysis showed that FBG domains were highly conserved throughout and phylogeny clusters correlated strongly with gene type. We analyzed the temporal and spatial expression patterns of LvFReD genes based on the transcriptomes of developmental stages, adult tissues or pathogen infected tissues of L. vannamei. Most LvFReDs were expressed from larval in membrane stage, and exhibited tissue-specific expression patterns and immune-responsive transcription after challenge with bacteria or virus. Further time-course expression analysis suggested that LvFReDII genes with additional coiled-coil region were more sensitive to pathogens than LvFReDI genes. Our findings provided comprehensive gene sequence resources and expression profiles of FReD genes in shrimp, which give insights into clarifying the diversity and function of these genes in crustaceans.

Expression profiling of antimicrobial peptides and immune-related genes in Nile tilapia following Pseudomonas putida infection and nano-titanium dioxide gel exposure.

Pseudomonas putida is a virulent bacterium that prompts major losses in fish. Recently, there has been a noticeable direction for utilizing nanomaterials in the aquaculture industry for sustaining fish health and performance. Hence, the present study is the first trial to investigate the antibacterial influence of nano titanium dioxide gel (NTG) as a watery addition for combating P. putida infection in Nile tilapia (Oreochromis niloticus). Further, antioxidant-immune capacity, and gene expression in the spleen including antimicrobial peptides and immune-related genes are assessed. Fish (n=200; 47.50±1.32g of body weight) were assigned into four groups for 10 days [control, NTG (0.9mg/L), P. putida, and NTG+P. putida]. Findings demonstrated that the infection by P. putida induced a decline in antioxidant immune indicators including catalase, glutathione peroxidase, and nitric oxide. Furthermore, a noteworthy rise in lipid peroxide (malondialdehyde), tumor necrosis factor-alpha (TNF-α), and stress indicator (glucose) levels was noticed. P. putida infection induced remarkable alterations in the expression of antimicrobial peptides genes [tilapia piscidin (TP3 and TP4), colony-stimulating factor 1 receptor, hepcidin-2, beta-defensin1, and neutrophil cytosolic factor 4] and immune-relevant genes [transforming growth factor beta, tumor necrosis factor receptor-associated factor 6, TNF-α, interleukins (IL-10 and IL-11)]. Notably, applying NTG regenerated all the negative consequences of P. putida infection. Inclusive, this study underscores the crucial role of NTG as a potent antibacterial and immune-antioxidant agent, highlighting its potential in protecting O. niloticus from P. putida infection and improving immune-antioxidant response.

PPAB001, a novel bispecific antibody against CD47 and CD24, enhances anti-PD-L1 efficacy in triple-negative breast cancer via reprogramming tumor-associated macrophages towards M1 phenotype

Triple-negative breast cancer (TNBC) is a biologically aggressive tumor with a strong association with a high recurrence rate and poor prognosis. Although anti-PD-L1 antibody, Tecentriq has been approved by FDA for treating TNBC, the overall response rate (ORR) is still generally less than 20 %. PPAB001 is a novel bispecific antibody simultaneously targeting CD47 and CD24. In the present study, we firstly evaluated the activity of PPAB001 on promoting the phagocytosis of TNBC cell lines. And the efficacy by combination of PPAB001 and Tecentriq was also assessed in TNBC 4T-1 mouse model. Moreover, the expression profiling of macrophage-associated genes and surface markers were evaluated upon the combinatorial treatment by flow cytometry, Western blot and IHC analysis. Cell signaling involved in M1 macrophage polarization was further identified via the analysis of RNA-seq, Western blot and immunofluorescnece. Our results demonstrated that PPAB001 effectively promotes phagocytosis of macrophages against human TNBC cell lines and significantly delayed TNBC tumor growth, especially when combined with Tecentriq treatment which may be attributed to the mechanism that simultaneous blockade of CD47 and CD24 signaling maximized the polarization toward M1 phenotype polarization. Especially, RNA-seq analysis and Western blotting further revealed that CXCL9/10-CXCR3 axis was markedly up-regulated and JAK/STAT1 pathway was activated upon treatment with PPAB001 plus Tecentriq. Overall, our results underscore that simultaneous blockade of CD47 and CD24 is a potential therapeutic option to improve the efficacy of anti-PD-L1 therapy mainly by resetting tumor-associated macrophages toward M1 phenotype.

Relationship of biofilm formation with antibiotic resistance, virulence determinants and genetic diversity in clinically isolated Acinetobacter baumannii strains in Karachi, Pakistan.

Multi-drug resistant (MDR) Acinetobacter baumannii causes nosocomial infections due to a plethora of virulence determinants like biofilm formation which are pivotal to its survival and pathogenicity. Hence, investigation of these mechanisms in currently circulating strains is required for effective infection control and drug development. This study investigates the prevalence of antibiotic resistance and virulence factors and their relationship with biofilm formation in Acinetobacter baumannii strains in Karachi, Pakistan. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR) was used for observing genetic variations. The results revealed that 100% A. baumannii strains were MDR and 74.4% had multiple antibiotic resistance index (MARi) of 0.875-1. There were 27 biofilm forming strains with a moderate correlation between biofilm formation and MARi. A high prevalence of abaI (86.04%), bfmR (95.3%), bfmS (97.6%), csuE (90.69%), ompA (74.4%), and pgaA virulence genes (95.3%) and resistance genes adeF (53.4%), adeJ (74.4%), ampC (51.1%), tem-1 (51.1%), and vim (65.1%)) were observed in these strains. ERIC PCR revealed that 5 of 22 genetic types had strong biofilm form strains with similar virulence genes profiles. Conclusively, the study shows escalated resistance and virulence in clinical strains which warrants consistent epidemiological studies to prevent infections spread and future outbreaks.

Development and validation of a one-step SMN assay for genetic testing in spinal muscular atrophy via MALDI-TOF MS.

Spinal muscular atrophy (SMA) is a fatal neuromuscular disorder primarily attributed to the homozygous deletion of the survival motor neuron 1 (SMN1) gene, with disease severity closely correlated to the copy number variations (CNV) of SMN2. Conventional methodologies, however, fail to provide a comprehensive gene overview of SMN and are often both time-intensive and costly. In this study, we present a novel one-step MALDI-TOF MS assay for SMA gene testing. To accurately quantify CNV, we incorporated RPPH1 as an internal control alongside normal samples and competing templates targeting SMN1, SMN2, and RPPH1 for multiple corrections. The CNV assay enables precise quantification of exons 7/8 in both SMN1 and SMN2 genes, achieving a kappa value of 0.935 (P < 0.001) when compared with multiple ligation-dependent probe amplification (MLPA) during its development phase. This accuracy was further corroborated in a cohort comprising 78 individuals. To identify patients harboring compound heterozygous mutations or silent carriers, prevalent pathogenic variants along with sequence variants of SMN1 were integrated into our analysis framework; plasmids were constructed for methodological validation purposes. Utilizing these combinatorial assays for SMN detection, we identified one patient exhibiting a compound heterozygous mutation characterized by genotype [0 + 1d] and another subject presenting genotype [2 + 1], who harbored simultaneous variants of g.27134T > G and g.27706_27707delAT. The CNV assessment combined with pathogenic variants analysis developed through MALDI-TOF MS provides a comprehensive gene profile of SMN within a single analytical run. Given its unparalleled cost-effectiveness and time efficiency, this approach holds significant promise for further application in clinical diagnosis as well as newborn screening for SMA.

Study of the genomics and transcriptomics profiles of male-infertility genes in human prostate cancer: an in silico analysis

The World Health Organization has considered the infertility as an international public health problem. Infertility affect nearly 1 in 7 couples and male component contributes to 50% of infertility cases. There is a clear link between male infertility and some cancers such as testicular germ cell, prostate and colon cancers. Two possibilities support this finding: 1) Cancer treatments can affect the fertility factors 2) Genetic profile of infertility genes have been altered in cancer patients. Although the previously published researches have mostly focused on the first factor, no article has yet confirmed the role of genetic factors. In this in silico study, we collected the large number of genes (n = 17703) involved in infertility. These genes were collected from NGS panel tests of male infertility and comprehensive literature review or online data base. The Prostate Adenocarcinoma genomic and transcriptomics raw data were downloaded from the cBioPortal Cancer dataset. This included with 494 patients of Prostate Cancer with 494 mutation data, 489 with CNA and 493 with RNA seqV2 data. TCGA RNA-Seq raw data was extracted in R using the cgdsr extension package with a threshold of ±2 relative to normal samples. The observed data showed that male infertility genes have been distributed through the human genome. Among the 17703 analyzed genes of this study, the genomic profile of three genes including OR9Q1, H4C6 and PSG7 were changed approximately in 100% of (n = 493) patients. In most of patients (>98%), genetic alteration was related to change in gene expression. In conclusion, this study showed that the genomic and transcriptomics patterns of some male-infertility genes are notably altered in patients of prostate cancer and suggested a possible role of genetic factors in occurrence of infertility in cancer patients. Our information can be used as a source for the design of genetic database of male-infertility.

Human miR-1 Stimulates Metabolic and Thermogenic-Related Genes in Adipocytes.

MicroRNAs play a pivotal role in the regulation of adipose tissue function and have emerged as promising therapeutic candidates for the management of obesity and associated comorbidities. Among them, miR-1 could be a potential biomarker for metabolic diseases and contribute to metabolic homeostasis. However, thorough research is required to fully elucidate the impact of miR-1 on human adipocyte thermogenesis and metabolism. This study aimed to explore the effect of miR-1 on human adipocyte browning, a process whose activation has been linked to obesity protection and counteraction. Human multipotent adipose-derived stem cells, hMADS cells, were differentiated into white and brown-like adipocytes and transfected with miR-1 mimics for gene expression and western blotting analyses. miR-1 inhibited the expression of its previously validated target PTK9/TWF1 and modulated the expression profile of key genes involved in thermogenesis and adipocyte browning (increased UCP1 at mRNA and protein level, increased CPT1M, decreased HIF3A), adipocyte differentiation and metabolism (decreased PLIN1, FASN, RXRA, PPARG, FABP4, MAPKAPK2), as well as genes related to the cytoskeleton (decreased ACTB) and extracellular matrix (decreased COL1A1). These findings suggest that miR-1 can modulate the expression of adipocyte human genes associated with thermogenesis and metabolism, which could hold value for eventual therapeutic potential in obesity.