Gene Amplification Research Articles

Identification of Genes Encoded Toxin-Antitoxin System in Mycobacterium Tuberculosis Strains from Clinical Sample.

The toxin-antitoxin system is a genetic element that is highly present in Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis. The toxin-antitoxin system comprises toxin protein and antitoxin protein or non-encoded RNA interacting with each other and inhibiting toxin activity. M. Tuberculosis has more classes of TA loci than non-tubercle bacilli and other microbes, including VapBC, HigBA, MazEF, ParDE, RelBE, MbcTA, PemIK, DarTG, MenTA, one tripartite type II TAC chaperone system, and hypothetical proteins. The study aims to demonstrate the genes encoded toxin-antitoxin system in mycobacterium tuberculosis strains from clinical samples. The pulmonary and extra-pulmonary tuberculosis clinical samples were collected, and smear microscopy (Ziehl-Neelsen staining) was performed for the detection of high bacilli (3+) count, followed by nucleic acid amplification assay. Bacterial culture and growth assay, genomic DNA extraction, and polymerase chain reaction were also carried out. The positive PTB and EPTB samples were determined by 3+ in microscopy smear and the total count of tubercle bacilli determined by NAAT assay was 8.0×1005 in sputum and 1.3×1004 CFU/ml in tissue abscess. Moreover, the genomic DNA was extracted from culture, and the amplification of Rv1044 and Rv1045 genes in 624 and 412 base pairs (between 600-700 and 400-500 in ladder), respectively, in the H37Rv and clinical samples was observed. It has been found that Rv1044 and Rv1045 are hypothetical proteins with 624 and 882 base pairs belonging to the AbiEi/AbiEii family of toxin-antitoxin loci. Moreover, the significant identification of TA-encoded loci genes may allow for the investigation of multidrugresistant and extensively drug-resistant tuberculosis.

A novel Zobellella endophytica W14 strain for nitrogen removal from hypersaline wastewater through simultaneous nitrification and denitrification.

To address the challenges associated with biological treatment of high-salinity wastewater, a novel salt-tolerant strain, Zobellella endophytica W14, was isolated. This strain exhibited heterotrophic nitrification-aerobic denitrification (HN-AD) capabilities. Strain W14 could grow and remove ammonium in high-salinity environments with salinity levels ranging from 0 to 11% (w/v). At 5% salinity, strain W14 demonstrated high removal efficiencies for nitrite, ammonium, and nitrate (100%, 99.58%, and 98.85%, respectively), when these compounds were provided as the single source of nitrogen. In cases of mixed nitrogen sources, total nitrogen removal efficiency of strain reached 95.22%. The nitrogen balance analysis confirmed the utilization of nitrogen sources by strain W14 through both assimilation and dissimilation. Through the amplification of functional genes involved in nitrogen metabolism (i.e., hao, napA, nirS, and nosZ), the nitrogen metabolism pathway of strain W14 was predicted to be: NH₄⁺ → NH₂OH → NO₂⁻ → NO₃⁻ → NO₂⁻ → NO → N₂O → N₂. The study reveals that the novel W14 strain can efficiently remove total nitrogen from high-salinity wastewater and has significant potential for biological treatment of such wastewater.

Protein kinase A and local signaling in cancer.

Protein kinase A (PKA) is a basophilic kinase implicated in the modulation of many cell-signaling and physiological processes. PKA also contributes to cancer-relevant events such as growth factor action, cell cycle control, cell migration and tumor metabolism. Germline and somatic mutations in PKA, gene amplifications, and chromosome rearrangements that encode kinase fusions, are linked to a growing number of malignant neoplasms. Mislocalization of PKA by exclusion from A-Kinase Anchoring Protein (AKAP) signaling islands further underlies cancer progression. This article highlights the influence of AKAP signaling and local kinase action in selected hallmarks of cancer. We also feature the utility of kinase inhibitor drugs as frontline and future anti-cancer therapies.

Evaluation of different inflammatory markers during the infection of domestic cats (Felis catus) by Cystoisospora felis (Coccidia: Apicomplexa).

Cystoisospora felis or Isospora felis is a ubiquitous apicomplexan protozoon parasite infecting domestic cats worldwide. this study aims to identify the causative agent of diarrhea in cats by determining several elevating stressors caused by these coccidian protozoans with molecular characterization. So, from January 2023 to April 2023, a total of 370 domestic cats were hospitalized at various clinics in the Cairo and Giza Governorates. Fecal samples were taken from these animals and examined by concentration floatation techniques using a saturated salt solution. The positive samples were sporulated to identify the collected oocyst. Venous blood was taken from the infected cats to evaluate the associated oxidative stress marker (lipid peroxidation products (MDA). Out of 370 examined domestic cats, 27(7.29%) were positive for C. felis. The MDA levels increased with age, and females were higher than males. DNA was extracted from fecal samples for amplification of the ITS1 gene, followed by sequencing. The ITS1 gene was amplified and showed bands at 224bp. The partial nucleotide sequence of the ITS1 gene was aligned with the reference sequences. C. felis increases the free radicals, which in turn means the animals have stress and need a schedule to treat these animals with new, safe protocol drugs that give no resistance and are highly efficient.

Clinical advances and challenges in targeting FGF/FGFR signaling in lung cancer.

Fibroblast growth factors (FGFs) and their receptors regulate numerous cellular processes, such as metabolism and signal transduction, but can also drive tumorigenesis. Specifically, in lung cancer, the overexpression of FGFs, as well as the amplification, mutation and fusion of FGFR genes, are closely linked to the initiation, progression and resistance of the disease, suggesting that targeting FGF/FGFR is an attractive therapeutic strategy for lung cancer treatment. Nintedanib, a multitarget tyrosine kinase inhibitor (TKI) used in combination with docetaxel, has shown some success as a second-line therapy for lung cancer. However, clinical trials evaluating other FGFR inhibitors have yielded mixed results, indicating substantial complexity in targeting aberrant FGF/FGFR signaling. In this review, we describe the aberrations in FGF/FGFR signaling in lung cancer and summarize the clinical efficacy of FGFR inhibitors, such as multitarget TKIs, selective FGFR-TKIs and biological agents. We also discuss various challenges associated with FGFR targeting in lung cancer, including precision patient selection, toxicity and resistance. Finally, we provide perspectives on future directions, namely, developing novel FGFR-targeting drugs, such as FGFR degraders and more specific FGFR-TKIs, adopting combination therapy and targeting FGFs.

Cytogenetic characterization of EPSPS gene amplification in glyphosate-resistant Hordeum glaucum and Bromus diandrus from Australia.

As a result of extensive selection, two polyploid grass weeds, Hordeum glaucum (northern barley grass; 2n = 4x = 28) and Bromus diandrus (ripgut brome; 2n = 8x = 56), have evolved resistance to glyphosate, in Australia. Previous research suggested amplification of 5-enolpyruvylshikimate-3-Phosphate synthase (EPSPS) gene confers resistance in these two weed species. The objective of this research was to investigate the genomic organization of the EPSPS gene in these two species through molecular cytogenetic analyses of fluorescence in situ hybridization (FISH) to understand possible mechanism of amplification of this gene. EPSPS copy number of H. glaucum and B. diandrus plants was estimated via quantitative polymerase chain reaction. The susceptible plants of both species had one copy of EPSPS, whereas the resistant plants of H. glaucum and B. diandrus had 14-17 and 16-32 copies, respectively. FISH analysis of glyphosate-susceptible (Hg-RWS) H. glaucum, revealed four faint signals of the EPSPS gene in two pairs of homologous chromosomes, at the telomeric region. The glyphosate-resistant H. glaucum (Hg-YP1) also showed amplification of EPSPS gene at telomeric regions in two pairs of homologous chromosomes, but the signals were brighter and appeared as cluster of EPSPS genes. Similarly, the glyphosate-susceptible B. diandrus (Bd-S) plants showed faint signals of EPSPS gene on two homologous chromosomes, at the telomeric position. However, samples of two glyphosate-resistant, B. diandrus, Bd-SA988 and Bd-Vic showed much brighter hybridization signals of EPSPS gene, located at the telomere on two homologous chromosomes, suggesting an increase in EPSPS gene copies at this position. Overall, unequal crossover during meiosis may have triggered the initial EPSPS gene duplication sparking the evolution of glyphosate resistance.

Survival outcomes for HER2-low breast cancer: Danish national data.

We investigated the prognosis of breast cancer (BC) with low expression of human epidermal growth factor receptor 2 (HER2), as previous studies have found varying impacts on survival of HER2-low BC compared with HER2 0 BC (HER2 IHC score of 0). HER2-low is defined as a score of 1+ or 2+ in an immunohistochemical (IHC) assay without HER2 gene amplification. Patients with HER2 0 or HER2-low BC from the national Danish Breast Cancer Group database were examined by multivariable survival analysis in a retrospective noninterventional investigation. Patients were grouped as either HER2 0 or HER2-low. The primary endpoint was time to recurrence (TR), and the secondary endpoints were overall survival (OS) and distant recurrence-free interval (DRFI). 41,610 patients were included (12,981 with HER2 0 BC and 28,629 with HER2-low BC). HER2-low BC was associated with a lower risk of recurrence (hazard ratio [HR]: 0.92, p = 0.03). Regarding secondary endpoints, HER2-low disease was linked to improved overall OS (HR: 0.94, p = 0.02). No statistically significant effect of HER2-low was found for DRFI, along with no differential effect of HER2-low according to estrogen receptor (ER) status. HER2-low BC was found to show an improved HR for OS and DRFI compared with HER2 0 BC; however, further studies are need to establish whether it represents a separate biological entity.

Characteristics of soil microbial community assembly patterns in fields with serious occurrence of tobacco Fusarium wilt disease

IntroductionFusarium wilt disease (FWD) of tobacco is a destructive disease caused by Fusarium spp. in tobacco-growing regions worldwide. The Fusarium spp. infection may alter the composition and structure of the tobacco root microbial community; however, the relationship between these factors under large-scale geographical conditions in China remains underexplored.MethodsIn the context of this investigation, soil samples from the rhizosphere of tobacco plants were procured from fields afflicted with FWD and those devoid of the disease in the Hanzhong region of Shaanxi province, as well as in the Sanmenxia and Nanyang regions of Henan province. These regions are recognized for the commercial cultivation of tobacco. The examination focused on discerning the influence of tobacco FWD on the composition and configuration of the rhizosphere microbial community, along with their co-occurrence patterns. This scrutiny was underpinned by targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of the 16S rRNA gene and the ITS1 region.ResultsThe amplicon data analyses showed that FWD influenced the microbial structure and composition of the tobacco rhizosphere soil. FWD had a greater impact on the microbiome of the tobacco fungal community than on the microbiome of the bacterial community. Healthy plants had the ability to recruit potential beneficial bacteria. Diseased plants were more susceptible to colonization by other pathogenic fungi, but they still had the capacity to recruit potential beneficial bacteria. The analysis of microbial intra- and inter-kingdom networks further indicated that FWD destabilized microbial networks. In the overall microbial interaction, microorganisms primarily interacted within their boundaries, but FWD increased the proportion of interactions occurring across boundaries. In addition, FWD could disrupt the interactions within microbial network modules.DiscussionThis study provides evidence that FWD can cause changes in the composition and network of microbial communities, affecting the interactions among various microorganisms, including bacteria and fungi. These findings contribute to our understanding of how plant microbiomes change due to disease. Furthermore, they add to our knowledge of the mechanisms that govern the assembly and interactions of microbial communities under the influence of FWD.

Contrasting patterns of Asaia association with Plasmodium falciparum between field-collected Anopheles gambiae and Anopheles coluzzii from Cameroon.

The widespread prevalence of Asaia in mosquitoes makes it a potential candidate for paratrangenic control in Anopheles. To better understand whether this bacterium could be used for malaria control, we quantified Asaia in An. gambiae s.l populations in malaria endemic regions examining co-infection with Plasmodium falciparum. Adult Anopheles mosquitoes were collected across two different eco-geographical localities in Cameroon, during both the dry and wet seasons. DNA was extracted from whole individual mosquitoes, and real time-qPCR amplification of the 16S ribosomal RNA was used to quantify Asaia in both An. gambiae and An. coluzzii samples. We also detected and quantified P. falciparum infection in the same mosquitoes. The density of Asaia was successfully quantified in a total of 864 field mosquitoes, comprising of 439 An. gambiae from Bankeng and 424 An. coluzii collected from Gounougou. Interestingly, a higher prevalence of Asaia in An. gambiae (88.3%) compared to An. coluzzii (80.9%) was observed. Moreover, the density of Asaia in both species was significantly affected by seasonal changes in the two localities. Furthermore, a significant difference between the infection densities of Asaia and the Plasmodium infection status in the two species was recorded. However, no correlation was observed between the number of Asaia and P. falciparum infections. This study provides evidence that naturally occurring Asaia infection is not correlated to P. falciparum development within An. gambiae and An. coluzzii. Nevertheless, further studies incorporating experimental infections are required to better investigate the correlation between Anopheles mosquitoes, Asaia, and Plasmodium.IMPORTANCEThe symbiont Asaia has emerged as a promising candidate for paratransgenic control of malaria, but further analysis of its biology and genetics across Africa is necessary. In this study, we investigated and quantified the influence of Asaia in naturally infected An. gambiae s.l. populations with the malaria parasite Plasmodium falciparum. Genomic DNA was extracted from whole individual mosquitoes collected from two localities, and Asaia was quantified using real-time qPCR by amplification of the 16S ribosomal RNA gene. We also detected and quantified Plasmodium falciparum infection in the same mosquitoes and established the correlation between Asaia and Plasmodium coinfection. This study provides evidence that naturally occurring Asaia infection is not correlated with P. falciparum development within An. gambiae and An. coluzzii mosquitoes.

Use of 3′ Rapid Amplification of cDNA Ends (3′ RACE)-Based Targeted RNA Sequencing for Profiling of Druggable Genetic Alterations in Urothelial Carcinomas

Targeted treatment of advanced or metastatic urothelial carcinomas (UCs) requires the identification of druggable mutations. This study describes the development of a 3′ Rapid Amplification of cDNA Ends (3′ RACE)-based targeted RNA sequencing panel which accounts for the status of all genes relevant to UC treatment, namely, FGFR1-4, KRAS, NRAS, BRAF, ERBB2 (HER2), CD274 (PD-L1) and PIK3CA. FGFR2/3-activating point mutations or fusions were found in 54/233 (23.2%) tumors. FGFR3 rearrangements were identified in 11 patients, with eight of them being undetectable by commonly used PCR kits. In addition, one tumor contained a high-copy FGFR2 gene amplification accompanied by strong overexpression of the gene. Mutations in RAS/RAF genes were present in 30/233 (12.9%) UCs and were mutually exclusive with alterations affecting FGFR2/3 genes. On the contrary, activating events in the HER2 oncogene (point mutations and overexpression), as well as PIK3CA mutations, which were relatively common, occurred with similar frequencies in RAS/RAF- or FGFR2/3-positive vs. negative samples. High PD-L1 mRNA expression was associated with advanced disease stage and was not observed in tumors with increased HER2 mRNA expression or in UCs with evidence for FGFR2/3 activation. Three of the studied carcinomas had high-level microsatellite instability (MSI). Overall, more than half of the UCs had potentially druggable genetic alterations. The proposed NGS panel permits comprehensive and cost-efficient analysis of UC-specific molecular targets and may be considered in clinical routine.

Impact of TiO2, ZnO, and Ag nanoparticles on anammox activity in enriched river Nile sediment cultures: unveiling differential effects and environmental implications.

The increasing use of nanoparticles (NPs) necessitates investigation of their impact on wastewater treatment processes, particularly anammox, a critical biological nitrogen removal pathway. This study explored the effects of short-term exposure to TiO2, ZnO, and Ag-NPs on anammox activity in enriched cultures derived from River Nile sediments. Anammox bacteria were identified and enriched, with activity confirmed through 16S rRNA and hydrazine oxidoreductase (hzo) gene amplification and sequencing. Activity assays demonstrated efficient ammonium removal by the enriched culture. Subsequently, the impact of different sized and concentrated NPs on anammox activity was assessed. XRD analysis confirmed NP behavior within the microcosms: TiO2 transformed, ZnO partially dissolved, and Ag remained ionic. hzo gene expression served as a biomarker for anammox bacterial activity. Interestingly, 100nm TiO2-NPs up-regulated hzo expression, potentially indicating a non-inhibitory transformed phase. Conversely, ZnO and Ag-NPs across all sizes and concentrations significantly down-regulated hzo expression, suggesting detrimental effects. Ag-NPs amended microcosms showed a significant reduction (79%) in hzo gene expression and a detrimental effect on bacterial populations. Overall, anammox activity mirrored hzo expression patterns, with TiO2 (21 and 25nm, respectively) exhibiting the least inhibition, followed by ZnO and Ag-NPs. This study highlights the differential effects of NPs on anammox, with the order of impact being Ag > ZnO > TiO2. These findings provide valuable insights into the potential environmental risks of NPs on anammox-mediated nitrogen cycling in freshwater ecosystems.

BIOM-05. FUSION TRANSCRIPTOME LANDSCAPE IN GLIOBLASTOMA

Abstract BACKGROUND For most patients with glioblastoma (GBM), no truly effective salvage therapies exist. However, there are compelling examples in oncology where gene fusions lead to functioning oncoproteins that are highly effective targets (ie BCR-ABL1 in CML). Using a large genomic database, we sought to determine the prevalence of fusion transcripts in GBMs. METHODS A total of 4392 GBMs were tested at Caris Life Sciences (Phoenix, AZ). Mutations were detected by NextGen sequencing of DNA (592-gene panel or whole exome sequencing); gene fusions were detected by Whole Transcriptome Sequencing. All tumors were wild type for IDH1/2. Significance was tested by Fisher-Exact and ChiSquare and adjusted by Benjamini-Hochberg (q <0.05). RESULTS Overall, pathogenic fusions were found in 428 (9.7%). The most prevalent were FGFR3 [N=159 (37%), highest FGFR3:TACC3, N=134], MET [N=92 (21%), highest PTPRZ1:Met, N=31; ST7:MET N=25; CAPZA2: MET, N=23), EGFR [N=87(20%), highest EGFR:SETP14, N=21 and SEC61G: EGFR, N=19], NTRK2 (N=27), PDGFRA (N=23), ROS1 (N=14) and BRAF (N=10). Other actionable fusions including ALK (N=3), NTRK3 (N=3), RAF1(N=3), RET (N=3), NTRK1(N=2) were seen. Tumors with fusions were more likely to have pathogenic gene amplifications including: MET (7.5% vs. 0.7%), FGFR3 (5% vs. 0.2%), CDK4 (17% vs. 11%) and MDM2 (12% and 7.5%) but less frequent EGFR mutation (6.1% vs. 18%), amplification (6.1% vs. 18%) and EGFRvIII mutation (11.9% vs. 22.5%), RB1 (2.9% vs. 11.5%) and TP53mutation (22% vs. 30%) (all q<0.05). EGFR fusions are enriched with EGFR amplification (92%) and EGFRvIII mutation (51%); cMET fusion with MET amplification (40%). CONCLUSIONS Comprehensive molecular profiling reveals that approximately 10% of IDH WT GBMs carry oncogenic fusions that may be therapeutic targets. Broad spectrum of observed fusions underscores the need for novel clinical trial designs to allow efficient enrollment for prospective testing of potential targeted agents.

Coexistence of the blaZ gene and selected virulence determinants in multidrug-resistant Staphylococcus aureus: insights from three Nigerian tertiary hospitals.

Infections caused by β-lactamase-producing strains of Staphylococcus aureus have become increasingly difficult to treat due to the expression of multiple virulence factors. This has heightened concerns about managing S. aureus-related infections. This study was conducted to characterize the blaZ gene and selected virulence determinants in β-lactam resistant S. aureus from human sources in three Nigerian tertiary hospitals. Three hundred and sixty samples were collected for the study. S. aureus was isolated and characterized following standard microbiological protocols and nuc gene amplification. Antibiotic susceptibility and minimum inhibitory concentration tests were performed using the disk diffusion method and E-tests, respectively. Biofilm formation and β-lactamase production were assessed using Congo red agar and nitrocefin kits, while the blaZ gene was examined using conventional PCR. Capsular polysaccharide genotyping, accessory gene regulator (agr) detection, Panton-valentine leucocidin (PVL), and PVL proteins were performed using PCR and Western blotting. S. aureus was recovered from 145 samples, 50 (34.5%) of these isolates exhibited multidrug resistance, with MICs ranging from 0.125 to 1.00µg/mL, and showed significant resistance to aminoglycosides, fluoroquinolones, and β-lactams. Of these, 31 strains produced β-lactamases, 30 of which carried the blaZ gene in combination with cap8 (80%) or cap5 (20%). Biofilm formation and PVL gene were observed in 85% of the 20 randomly selected blaZ-positive multidrug-resistant (MDR) strains. The agr2 allele was predominant, found in 70% of the selected MDR strains. No significant difference in the occurrence of the blaZ gene was found among the three clinical sources (p ≤ α0.05). The co-occurrence of the blaZ gene with PVL, capsular polysaccharide genes, and agr alleles is associated with biofilm formation, indicating a high risk of β-lactam-resistant S. aureus infections. Our findings highlight the need for continuous molecular surveillance to enhance infection management, treatment options, and patient outcomes in the study locality. A limitation of this study is the random selection of MDR isolates, which may affect the comprehensiveness of the analyses.

CTNI-48. A PHASE 1 STUDY OF ERAS-801, A POTENT, SELECTIVE, AND CENTRAL NERVOUS SYSTEM (CNS)-PENETRANT EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR) INHIBITOR, FOR PATIENTS WITH RECURRENT GLIOBLASTOMA MULTIFORME (GBM)

Abstract EGFR is among the most common targets for genetic alterations in GBM. Changes in EGFR gene amplification and the extracellular domain result in receptor overexpression or constitutive activation, and enhanced oncogenic signaling. ERAS-801 is a potent, selective, and highly CNS-penetrant EGFR inhibitor being developed for the treatment of GBM, with a focus on tumors harboring EGFR genetic alterations. THUNDERBBOLT-1 is the first-in-human phase 1 dose escalation and expansion trial evaluating ERAS-801 monotherapy for patients with recurrent GBM. ERAS-801 is administered orally once daily for continuous 28-day cycles. As of April 10, 2024, a total of 52 patients were treated across 7 dose cohorts: 20 mg (n=3), 40 mg (n=5), 80 mg (n=3), 160 mg (n=6), 240 mg (n=25), 280 mg (n=4), or 320 mg (n=6). Key patient characteristics were median age of 60 years, 67% male, mostly one prior therapy, and 81% tumors with alterations. The MTD was 240 mg. Dose-limiting toxicities were observed at 320 mg (n=2, Grade 2 QT prolongation, Grade 3 rash and Grade 3 dermatitis acneiform), 280 mg (n=3, Grade 3 QT prolongation), and 240 mg (n=1, Grade 3 QT prolongation) doses. The most common treatment related adverse events (TRAEs), in >10% of patients, were dermatitis acneiform, diarrhea, and nausea. Electrocardiogram QT prolongation occurred in 11.5% of patients and was not associated with clinical findings. ERAS-801 showed rapid absorption; peak plasma concentration was generally achieved within 6 hours post dose. PK exposure increased in a dose-dependent manner over the doses evaluated. Across all doses there was a confirmed partial response (using mRANO) in 1 patient and 6 patients achieved a PFS of 6 months. ERAS-801 shows well behaved PK with substantial CNS penetration, preliminary safety, and tolerability in patients with recurrent GBM. The TRAEs were reversible, manageable, and consistent with known toxicities of EGFR inhibitors.

Triple Negative Breast Cancer: Experience of the Obstetrics and Gynecology Department 2 Over A Period of 3 Years about 105 Cases at the Hassan II University Hospital in Fes

Introduction: Breast cancer is the second leading cause of death worldwide and the leading cancer in women. It is both the most common and the leading cause of death in women from cancer, thus posing a real public health problem. It presents tumor heterogeneity on the histological and molecular levels, explaining the diversity of presentations, responses to treatments, and prognosis. Triple-negative breast cancer is defined by the absence of expression of hormone receptors: estrogen receptors (ER), progesterone receptors (PR) and by the absence of overexpression or amplification of genes encoding HER2 receptors (Human epidermal growth factor receptor 2) and representing only a minority of breast cancers (10-20%). The therapeutic choices for this type of breast cancer are limited because patients do not benefit from hormonal therapy or targeted therapies, which poses a real problem in therapeutic management. Our objective is to describe the epidemiological, clinical, anatomo-pathological characteristics, as well as the evolutionary profile after adequate management of triple-negative breast cancer through the analysis of a series of cases of triple-negative breast cancer collected at the gynecology-obstetrics department 2 at the Hassan II University Hospital in Fez. Method: This is a retrospective study of a series of triple negative breast cancer cases collected in the gynecology-obstetrics department II at the Hassan II University Hospital in Fez during the period between January 2020 and December 2023. Inclusion criteria: Histologically confirmed triple negative infiltrating breast cancer treated in the gynecology-obstetrics department 2 of the Hassan II University Hospital in Fez. IHC = ER = 0% RP = 0% HER2 negative Exclusion criteria: male sex and presence of distant metastases. Results: On the epidemio-clinical level: a peak in frequency between 31 and 42 years old, and 45.7% of patients still in genital activity. On the anatomo-pathological level: ...

Research progress on the role of bypass activation mechanisms in resistance to tyrosine kinase inhibitors in non-small cell lung cancer

The clinical application of small molecule tyrosine kinase inhibitors (TKIs) has significantly improved the quality of life and prognosis of patients with non-small cell lung cancer (NSCLC) carrying driver genes. However, resistance to TKI treatment is inevitable. Bypass signal activation is one of the important reasons for TKI resistance. Although TKI drugs inhibit downstream signaling pathways of driver genes, key signaling pathways within tumor cells can still be persistently activated through bypass routes such as MET gene amplification, EGFR gene amplification, and AXL activation. This continuous activation maintains tumor cell growth and proliferation, leading to TKI resistance. The fundamental strategy to treat TKI resistance mediated by bypass activation involves simultaneously inhibiting the activated bypass signals and the original driver gene signaling pathways. Some clinical trials based on this combined treatment approach have yielded promising preliminary results, offering more treatment options for NSCLC patients with TKI resistance. Additionally, early identification of resistance mechanisms through liquid biopsy, personalized targeted therapy against these mechanisms, and preemptive targeting of drug-tolerant persistent cells may provide NSCLC patients with more sustained and effective treatment.

Isolation and selection of spore-forming bacilli with potential for self-healing of concrete

The self-healing of concrete through the use of bacteria is an ecological, sustainable, and environmentally friendly method that can replace time-consuming and costly repairs. The aim of this research was to isolate and select spore-forming bacilli with potential for concrete self-healing. Soil samples from the limestone mines of Simbal, Trujillo, La Libertad, Peru were used. These samples were processed to primarily isolate spore-forming bacteria. The self-healing potential of these bacteria was evaluated through their ability to produce the urease enzyme, grow at an alkaline pH, and produce calcium carbonate crystals in a culture medium with urea and CaCl2 at pH 8.0. The produced crystals were visualized with scanning electron microscopy and their calcium content was confirmed through EDS analysis. The isolated bacteria were identified by 16 S rRNA gene amplification by PCR as Bacillus sp and Streptomyces sp. It was observed that Bacillus sp. produces CaCO3 crystals with vaterite morphology, while Streptomyces sp. produces rhombohedral calcite crystals. It is concluded that the isolated bacteria have the potential to be used in concrete self-healing processes.

Design and Optimization of Isothermal Gene Amplification for Generation of High-Gain Oligonucleotide Products by MicroRNAs

Design and Optimization of Isothermal Gene Amplification for Generation of High-Gain Oligonucleotide Products by MicroRNAs

Differentiating HER2-low and HER2-zero tumors with 21-gene multigene assay in 2,295h + HER2- breast cancer: a retrospective analysis.

HER2-positivity is an essential marker for therapeutic decisions, while HER2 expression is heterogenous. In recent years, there has been increasing recognition of a subgroup of breast cancer patients who have low levels of HER2 expression, also known as HER2-low because trastuzumab deruxtecan offers clinical benefit for patients with HER2-low metastatic breast cancer. Despite the growing interest in HER2-low breast cancer, there is limited research on how multigene assays can help differentiate between HER2-low and HER2-negative breast cancer. Among HR + HER2- breast cancer, we compared genomic characteristics between HER2-low and HER2-zero using the 21-gene assay. A retrospective review of clinical records was performed in 2,295 patients who underwent Oncotype DX® test in two hospitals between 2013 and 2020. Patients were classified into two groups as the HER2-zero and HER2-low based on HER2 immunohistochemistry. In cases with HER2 2+, no amplification of HER2 gene was confirmed by silver in situ hybridization. High genomic risk was defined as cases with 21-gene recurrence score (RS) > 25. Multivariable binary logistic-regression analysis was performed. Of these, 944 (41.1%) patients were assigned to the HER2-zero group, while 1351 (58.9%) patients were assigned to the HER2-low group. The average Recurrence Score (RS) was found to be 17.802 in the HER2-zero breast cancer group and 18.503 in the HER2-low group, respectively (p-value < 0.005). When comparing the proportion of high RS between the two groups, the HER2-zero group had a high RS rate of 12.4% (117 out of 944), while the HER2-low group had a high RS rate of 17.0% (230 out of 1351) (p = 0.002). The HER2 score identified by qRT-PCR was 8.912 in the HER2-zero group and 9.337 in the HER2-low group (p < 0.005). In multivariable analysis, HER2-low status was found to be an independent factor for high RS, with an odds ratio of 1.517 (1.172-1.964), independent of ER, PR, and Ki67. Within the subgroup of patients with invasive ductal carcinoma, the high RS rates were 19% in the HER2-low group and 14% in the HER2-zero group. However, when considering all patients, there were no significant differences observed in recurrence-free survival and overall survival between the HER2-low and HER2-zero groups. Within HR + HER2- breast cancer, HER2-low tumors are associated with high RS, especially for histologically invasive ductal carcinoma. A prognostic influence of HER2-low expression among HR + HER2- breast cancer remains as an area that requires further study.

YgiV promoter mutations cause resistance to cystobactamids and reduced virulence factor expression in Escherichia coli

Antimicrobial resistance is one of the major health threats of the modern world. Thus, new structural classes of antimicrobial compounds are needed in order to overcome existing resistance. Cystobactamids represent one such new compound class that inhibit the well-established target bacterial type II topoisomerases while exhibiting superior antibacterial and resistance-breaking properties. Understanding potential mechanisms of emerging resistances is crucial in the development of novel antibiotics as they directly impact the future therapeutic application and market success. Therefore, the frequency and molecular basis of cystobactamid resistance in Escherichia coli was analyzed. High-level resistant E. coli mutants were selected and found to harbor single nucleotide polymorphisms in the promotor region of the ygiV gene, causing an upregulation of the respective protein. These stable mutations are contrary to what was observed as a resistance genotype in the structurally related albicidins, where ygiV gene amplifications were identified as causing resistance. Overexpression of YgiV in the mutants was additionally amplified upon cystobactamid exposition, showing further adaptation to this compound class under treatment. YgiV binds cystobactamids with high binding affinity, thereby preventing their interaction with the antimicrobial targets topoisomerase IV and DNA gyrase. In addition, we observed a substantial impact of YgiV on in vitro gyrase activity by leading to increased DNA cleavage and concurrent reduction in the efficacy of cystobactamids in inhibiting gyrase supercoiling activity. Furthermore, we identified co-upregulation of membrane-modifying proteins, such as EptC, and the transcriptional regulator QseB. This presumably contributes to the observed reduced motility and fimbrial protein expression in resistant mutants, resulting in a reduced expression of virulence factors and potentially pathogenicity, associated with ygiV promotor mutations.