Drug Sensitivity Testing Research Articles

High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond.

In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact. This includes the need to assess complex biomarkers, for example microsatellite instability, tumour mutation burden and homologous recombination deficiency, to identify patients suitable for specific therapies, including immunotherapy. Furthermore, the crucial role of biomarker analysis and multidisciplinary molecular tumour boards in selecting patients for trial inclusion is discussed in relation to various trial concepts, including drug repurposing. Recognising that today's exploratory techniques will evolve into tomorrow's routine diagnostics and clinical study inclusion assays, the importance of emerging technologies for multimodal diagnostics, such as proteomics and in vivo drug sensitivity testing, is also discussed. In addition, key regulatory aspects and the importance of patient engagement in all phases of a clinical trial are described. Finally, we propose a set of recommendations for consideration when planning a new precision cancer medicine trial.

Cyclin-dependent kinase 12 deficiency reprogrammes cellular metabolism to alleviate ferroptosis potential and promote the progression of castration-resistant prostate cancer.

Cyclin-dependent kinase 12 (CDK12)-deficient prostate cancer defines a subtype of castration-resistant prostate cancer (CRPC) with a poor prognosis. Current therapy, including PARP inhibitors, shows minimal treatment efficacy for this subtype of CRPC, and the underlying mechanism remains elusive. Based on bioinformatics analysis, we evaluated the relationship between CDK12 deficiency and prostate cancer patient's prognosis and treatment resistance. Furthermore, we used CRISPR-Cas9 technology and mass spectrometry-based metabolomic profiling to reveal the metabolic characteristics of CDK12-deficient CRPC. To elucidate the specific mechanisms of CDK12 deficiency-mediated CRPC metabolic reprogramming, we utilized cell RNA-seq profiling and other molecular biology techniques, including cellular reactive oxygen species probes, mitochondrial function assays, ChIP-qPCR and RNA stability analyses, to clarify the role of CDK12 in regulating mitochondrial function and its contribution to ferroptosis. Finally, through in vitro drug sensitivity testing and in vivo experiments in mice, we identified the therapeutic effects of the electron transport chain (ETC) inhibitor IACS-010759 on CDK12-deficient CRPC. CDK12-deficient prostate cancers reprogramme cellular energy metabolism to support their aggressive progression. In particular, CDK12 deficiency enhanced the mitochondrial respiratory chain for electronic transfer and ATP synthesis to create a ferroptosis potential in CRPC cells. However, CDK12 deficiency downregulated ACSL4 expression, which counteracts the lipid oxidation stress, leading to the escape of CRPC cells from ferroptosis. Furthermore, targeting the ETC substantially inhibited the proliferation of CDK12-deficient CRPC cells in vitro and in vivo, suggesting a potential new target for the therapy of CDK12-deficient prostate cancer. Our findings show that energy and lipid metabolism in CDK12-deficient CRPC work together to drive CRPC progression and provide a metabolic insight into the worse prognosis of CDK12-deficient prostate cancer patients. CDK12 deficiency promotes castration-resistant prostate cancer (CRPC) progression by reprogramming cellular metabolism. CDK12 deficiency in CRPC leads to a more active mitochondrial electron transport chain (ETC), ensuring efficient cell energy supply. CDK12 phosphorylates RNA Pol II to ensure the transcription of ACSL4 to regulate ferroptosis. Mitochondrial ETC inhibitors exhibit better selectivity for CDK12-deficient CRPC cells, offering a promising new therapeutic approach for this subtype of CRPC patients.

Patient tissue-derived FGFR4-variant and wild-type colorectal cancer organoid development and anticancer drug sensitivity testing

ObjectivesFGFR4-variant and wild-type colorectal cancer (CRC) organoids were developed to investigate the effects of FGFR4-targeted drugs, including FGFR4-IN and erdafitinib, on CRC and their possible molecular mechanism. MethodsClinical CRC tissues were collected, seven CRC organoids were developed, and whole exome sequencing (WES) was performed. CRC organoids were cultured and organoid drug sensitivity studies were conducted. Finally, an FGFR4-variant (no wild-type) CRC patient-derived orthotopic xenograft mouse model was developed. Western blot measured ERK/AKT/STAT3 pathway-related protein levels. ResultsWES results revealed the presence of FGFR4-variants in 5 of the 7 CRC organoids. The structural organization and integrity of organoids were significantly altered under the influence of targeted drugs (FGFR4-IN-1 and erdafitinib). The effects of FGFR4 targeted drugs were not selective for FGFR4 genotypes. FGFR4-IN-1 and erdafitinib significantly reduced the growth, diameter, and Adenosine Triphosphate (ATP) activity of organoids. Furthermore, chemotherapeutic drugs, including 5-fluorouracil and cisplatin, inhibited FGFR4-variant and wild-type CRC organoid activity. Moreover, the tumor volume of mice was significantly reduced at week 6, and p-ERK1/2, p-AKT, and p-STAT3 levels were down-regulated following FGFR4-IN-1 and erdafitinib treatment. ConclusionsFGFR4-targeted and chemotherapeutic drugs inhibited the activity of FGFR4-variant and wild-type CRC organoids, and targeted drugs were more effective than chemotherapeutic drugs at the same concentration. Additionally, FGFR4 inhibitors hindered tumorigenesis in FGFR4-variant CRC organoids through ERK1/2, AKT, and STAT3 pathways. However, no wild-type control was tested in this experiment, which need further confirmation in the next study.

Characterization of Escherichia coli pathogenicity and drug resistance in yolk peritonitis

Yolk Peritonitis can lead to a rapid decline in egg production, which seriously affects the health of laying hens and the profitability of chicken farms. Escherichia coli (E. coli) is the most common cause of yolk peritonitis in laying hens. In this study, bacterial samples were collected from the ovaries and fallopian tubes of laying hens with suspected yolk peritonitis from a laying farm in Jiangsu Province, and their pathogenicity and drug resistance were investigated. Initially, morphological and biochemical detection methods were employed to isolate and identify the pathogenic bacteria. The results showed that a total of 16 strains of E. coli were isolated from laying hens with yolk peritonitis. Subsequently, the drug resistance and pathogenicity of a randomly selected E. coli strain were analyzed and predicted by genome sequencing technology, and the drug resistance of E. coli was verified by drug sensitivity test and PCR. Finally, the virulence was verified by infection experiment in mice. The study revealed that the egg-yolk peritonitis in laying hens was caused by E. coli infection, and the genome sequencing analysis revealed that the bacteria had multidrug resistance and high virulence. The drug susceptibility testing indicates that E. coli exhibited resistance to aminoglycosides, β-lactam, macrolides, fluoroquinolones, and sulfonamides. In this study, resistance genes including KdpE, aadA5, APH(3 ")-ID, APH(6)-ID, and TEM-1 were identified, and their expression levels varied across different stages of bacterial growth. The results of virulence analysis indicated a mortality rate of 50% in mice infected with E. coli at a concentration of 2.985 × 107 CFU/mL. E. coli infection resulted in damage to various tissues and organs in mice, with the intestinal tissue structure being the most severely affected. This study provides a reference for the study of drug resistance mechanisms in E. coli and provides valuable insights into the selection of drugs for the treatment of vitelline peritonitis.

Investigation of folate-modified EGCG-loaded thermosensitive nanospheres inducing immunogenic cell death and damage-associated molecular patterns in hepatocellular carcinoma

BackgroundThe systemic treatment of advanced hepatocellular carcinoma is currently facing a bottleneck. EGCG, the primary active compound in green tea, exhibits anti-tumor effects through various pathways. However, there is a lack of study on EGCG-induced immunogenic cell death (ICD) in hepatocellular carcinoma. MethodsIn a previous study, we successfully synthesized folate-modified thermosensitive nano-materials, encapsulated EGCG within nanoparticles using a hydration method, and established the EGCG nano-drug delivery system. The viability of HepG2 cells post-EGCG treatment was assessed via the MTT and EdU assays. Cell migration and invasion were evaluated through wound healing experiments, Transwell assays, and Annexin V-FITC/PI assay for apoptosis detection. Additionally, the expression levels of damage-associated molecular patterns (DAMPs) were determined using immunofluorescence, ATP measurement, RT-qPCR, and Western Blot. ResultsThe drug sensitivity test revealed an IC50 value of 96.94 μg/mL for EGCG in HepG2 cells after 48 h. EGCG at a low concentration (50 μg/mL) significantly impeded the migration and invasion of HepG2 cells, showing a clear dose-dependent response. Moreover, medium to high EGCG concentrations induced cell apoptosis in a dose-dependent manner and upregulated DAMPs expression. Immunofluorescence analysis demonstrated a notable increase in CRT expression following low-concentration EGCG treatment. As EGCG concentration increased, cell viability decreased, leading to CRT exposure on the cell membrane. EGCG also notably elevated ATP levels. RT-qPCR and Western Blot analyses indicated elevated expression levels of HGMB1, HSP70, and HSP90 following EGCG intervention. ConclusionEGCG not only hinders the proliferation, migration, and invasion of hepatocellular carcinoma cells and induces apoptosis, but also holds significant clinical promise in the treatment of malignant tumors by promoting ICD and DAMPs secretion.

Population characteristics of pathogenic Escherichia coli in puerperal metritis of dairy cows in Ningxia region of China: a systemic taxa distribution of virulence factors and drug resistance genes.

Escherichia coli (E. coli) is closely associated with the occurrence of puerperal metritis in dairy cows. E. coli carries some the virulence and multi-drug resistant genes, which pose a serious threat to the health of postpartum cows. In this study, E. coli was isolated and identified from the uterine contents of postpartum cows with puerperal metritis in the Ningxia region of China, and its phylogenetic subgroups were determined. Meanwhile, virulence and drug resistance genes carried by E. coli and drug sensitivity were detected, and the characteristics of virulence and drug resistance genes distribution in E. coli phylogroups were further analyzed. The results showed that the isolation rate of E. coli in puerperal metritis samples was 95.2%. E. coli was mainly divided into phylogroups B2 and D, followed by groups A and B1, and was more connected to O157:H7, O169:H4, and ECC-1470 type strains. The virulence genes were mainly dominated by ompF (100%), traT (100%), fimH (97%), papC (96%), csgA (95%), Ang43 (93.9%), and ompC (93%), and the resistance genes were dominated by TEM (99%), tetA (71.7%), aac(3)II (66.7%), and cmlA (53.5%). Additionally, it was observed that the virulence and resistance gene phenotypes could be divided into two subgroups, with subgroup B2 and D having the highest distributions. Drug sensitivity tests also revealed that the E. coli was most sensitive to the fluoroquinolones enrofloxacin, followed by macrolides, aminoglycosides, tetracyclines, β-lactams, peptides and sulfonamides, and least sensitive to lincosamides. These results imply that pathogenic E. coli, which induces puerperal metritis of dairy cows in the Ningxia region of China, primarily belongs to the group B2 and D, contains multiple virulence and drug resistance genes, Moreover, E. coli has evolved resistance to several drugs including penicillin, lincomycin, cotrimoxazole, and streptomycin. It will offer specific guidelines reference for the prevention and treatment of puerperal metritis in dairy cows with E. coli infections in the Ningxia region of China.

Singular value thresholding two-stage matrix completion for drug sensitivity discovery

Incomplete data presents significant challenges in drug sensitivity analysis, especially in critical areas like oncology, where precision is paramount. Our study introduces an innovative imputation method designed specifically for low-rank matrices, addressing the crucial challenge of data completion in anticancer drug sensitivity testing. Our method unfolds in two main stages: Initially, the singular value thresholding algorithm is employed for preliminary matrix completion, establishing a solid foundation for subsequent steps. Then, the matrix rows are segmented into distinct blocks based on hierarchical clustering of correlation coefficients, applying singular value thresholding to the largest block, which has been proved to possess the largest entropy. This is followed by a refined data restoration process, where the reconstructed largest block is integrated into the initial matrix completion to achieve the final matrix completion. Compared to other methods, our approach not only improves the accuracy of data restoration but also ensures the integrity and reliability of the imputed values, establishing it as a robust tool for future drug sensitivity analysis.

Biological characteristics and pathogenicity comparison of Nocardia seriolae isolated from Micropterus salmoides and Channa argus.

Nocardia seriolae is the primary pathogen causing nocardiosis in various fish species, leads to significant economic losses in the aquaculture industry. In this study, 10 bacterial strains isolated from Micropterus salmoides and Channa argus infected with nocardiosis, were identified as N. seriolae by physiological and biochemical identification, as well as 16S rDNA sequencing. Moreover, the key virulence-related genes such as ESX-1, T7SS-2, T7SS-3, EspG1, sodC, sod2 and ESAT6 were all positive, and showing high homology among different strains. Pathogenicity testing revealed mortality rates ranging from 70 to 100%, accompanied by the presence of white nodules in the viscera of deceased fish. The drug sensitivity test demonstrated that LY21811, the most lethal strain, exhibited high sensitivity to nine types of antibiotics, including azithromycin, doxycycline, florfenicol and compound sulfamethoxazole, yet showed complete resistance to β-lactam antibiotics. Additionally, the tannic acid also demonstrated potent inhibitory effects against LY21811, with a minimum inhibitory concentration of 0.0625 mg/mL. These results showed that N. seriolae originated from M. salmoides and C. argus in Zhejiang Province were highly conserved, demonstrating a high homogeneity in genetic characteristics, pathogenicity and antimicrobial susceptibilities. These results provide a foundation for further research on the pathogenic characteristics and disease prevention of N. seriolae infections.

Research on the toxicological prognostic significance of age-related genes in endometrial cancer unveiling key factors in patient prognosis.

This study investigates the influence of aging-related genes on endometrial cancer, a prominent gynecological malignancy with rising incidence and mortality. By analyzing gene expression differences between cancerous and normal endometrial tissues, 42 aging-related genes were identified as differentially expressed. Utilizing the TCGA-UCEC sample, consensus clustering divided the samples into two molecular subgroups, Aging low and Aging high, based on their expression profiles. These subgroups showed distinct prognoses and survival rates, with the Aging high group associated with DNA repair and cell cycle pathways, and the Aging low group showing suppressed metabolic pathways and increased immune cell infiltration, suggesting a potential for better immunotherapy outcomes. Mutation analysis did not find significant differences in mutation frequencies between the groups, but a high Tumor Mutation Burden (TMB) correlated with better prognosis. A risk score model was also developed, showcasing significant prognostic power. Further analysis of the SIX1 gene revealed its overexpression in cancer cells. Drug sensitivity tests indicated that the low-risk group might respond better to chemotherapy. This research underscores the significance of aging-related genes in endometrial cancer, offering insights into their prognostic value and therapeutic potential, which could lead to personalized treatment approaches and enhanced patient management.

An original aneuploidy-related gene model for predicting lung adenocarcinoma survival and guiding therapy.

Aneuploidy is a hallmark of cancers, but the role of aneuploidy-related genes in lung adenocarcinoma (LUAD) and their prognostic value remain elusive. Gene expression and copy number variation (CNV) data were enrolled from TCGA and GEO database. Consistency clustering analysis was performed for molecular cluster. Tumor microenvironment was assessed by the xCell and ESTIMATE algorithm. Limma package was used for selecting differentially expressed genes (DEGs). LASSO and stepwise multivariate Cox regression analysis were used to establish an aneuploidy-related riskscore (ARS) signature. GDSC database was conducted to predict drug sensitivity. A nomogram was designed by rms R package. TCGA-LUAD patients were stratified into 3 clusters based on CNV data. The C1 cluster displayed the optimal survival advantage and highest inflammatory infiltration. Based on integrated intersecting DEGs, we constructed a 6-gene ARS model, which showed effective prediction for patient's survival. Drug sensitivity test predicted possible sensitive drugs in two risk groups. Additionally, the nomogram exhibited great predictive clinical treatment benefits. We established a 6-gene aneuploidy-related signature that could effectively predict the survival and therapy for LUAD patients. Additionally, the ARS model and nomogram could offer guidance for the preoperative estimation and postoperative therapy of LUAD.

Performance of the BD MAX MDR-TB assay in a clinical setting and its impact on the clinical course of patients with pulmonary tuberculosis: a retrospective before-after study.

Missing isoniazid (INH) resistance during tuberculosis (TB) diagnosis can worsen the outcomes of INH-resistant TB. The BD MAX MDR-TB assay (BD MAX) facilitates the rapid detection of TB and INH and rifampin (RIF) resistance; however, data related to its performance in clinical setting remain limited. Moreover, its effect on treatment outcomes has not yet been studied. We compared the performance of BD MAX for the detection of INH/RIF resistances to that of the line probe assay (LPA) in patients with pulmonary TB (PTB), using the results of a phenotypic drug sensitivity test as a reference standard. The treatment outcomes of patients who used BD MAX were compared with those of patients who did not. Of the 83 patients included in the study, the BD MAX was used for an initial PTB diagnosis in 39 patients. The sensitivity of BD MAX for detecting PTB was 79.5%. The sensitivity and specificity of BD MAX for INH resistance were both 100%, whereas these were 50.0% and 95.8%, respectively, for RIF resistance. The sensitivity and specificity of BD MAX were comparable to those of LPA. The BD MAX group had a shorter time interval from specimen request to the initiation of anti-TB drugs (2.0 days vs. 5.5 days, p=0.001). BD MAX showed comparable performance to conventional tests for detecting PTB and INH/RIF resistances. The implementation of BD MAX as a diagnostic tool for PTB resulted in a shorter turnaround time for the initiation of PTB treatment.

UTRN as a potential biomarker in breast cancer: a comprehensive bioinformatics and in vitro study

Utrophin (UTRN), known as a tumor suppressor, potentially regulates tumor development and the immune microenvironment. However, its impact on breast cancer’s development and treatment remains unstudied. We conducted a thorough examination of UTRN using both bioinformatic and in vitro experiments in this study. We discovered UTRN expression decreased in breast cancer compared to standard samples. High UTRN expression correlated with better prognosis. Drug sensitivity tests and RT-qPCR assays revealed UTRN’s pivotal role in tamoxifen resistance. Furthermore, the Kruskal–Wallis rank test indicated UTRN’s potential as a valuable diagnostic biomarker for breast cancer and its utility in detecting T stage of breast cancer. Additionally, our results demonstrated UTRN’s close association with immune cells, inhibitors, stimulators, receptors, and chemokines in breast cancer (BRCA). This research provides a novel perspective on UTRN’s role in breast cancer’s prognostic and therapeutic value. Low UTRN expression may contribute to tamoxifen resistance and a poor prognosis. Specifically, UTRN can improve clinical decision-making and raise the diagnosis accuracy of breast cancer.

Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers

Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376.

A radiogenomic multimodal and whole-transcriptome sequencing for preoperative prediction of axillary lymph node metastasis and drug therapeutic response in breast cancer: a retrospective, machine learning and international multicohort study.

Axillary lymph nodes (ALN) status serves as a crucial prognostic indicator in breast cancer (BC). The aim of this study was to construct a radiogenomic multimodal model, based on machine learning and whole-transcriptome sequencing (WTS), to accurately evaluate the risk of ALN metastasis (ALNM), drug therapeutic response and avoid unnecessary axillary surgery in BC patients. In this study, conducted a retrospective analysis of 1078 BC patients from The Cancer Genome Atlas (TCGA), The Cancer Imaging Archive (TCIA), and Foshan cohort. These patients were divided into the TCIA cohort ( N =103), TCIA validation cohort ( N =51), Duke cohort ( N =138), Foshan cohort ( N =106), and TCGA cohort ( N =680). Radiological features were extracted from BC radiological images and differentially expressed gene expression was calibrated using technology. A support vector machine model was employed to screen radiological and genetic features, and a multimodal model was established based on radiogenomic and clinical pathological features to predict ALNM. The accuracy of the model predictions was assessed using the area under the curve (AUC) and the clinical benefit was measured using decision curve analysis. Risk stratification analysis of BC patients was performed by gene set enrichment analysis, differential comparison of immune checkpoint gene expression, and drug sensitivity testing. For the prediction of ALNM, rad-score was able to significantly differentiate between ALN- and ALN+ patients in both the Duke and Foshan cohorts ( P <0.05). Similarly, the gene-score was able to significantly differentiate between ALN- and ALN+ patients in the TCGA cohort ( P <0.05). The radiogenomic multimodal nomogram demonstrated satisfactory performance in the TCIA cohort (AUC 0.82, 95% CI: 0.74-0.91) and the TCIA validation cohort (AUC 0.77, 95% CI: 0.63-0.91). In the risk sub-stratification analysis, there were significant differences in gene pathway enrichment between high and low-risk groups ( P <0.05). Additionally, different risk groups may exhibit varying treatment responses ( P <0.05). Overall, the radiogenomic multimodal model employs multimodal data, including radiological images, genetic, and clinicopathological typing. The radiogenomic multimodal nomogram can precisely predict ALNM and drug therapeutic response in BC patients.

Laboratory tests and analysis of drug resistance in non-tuberculous mycobacteria

BackgroundThis study analyzed the laboratory diagnosis results and drug resistance of patients infected with non-tuberculous mycobacterium (NTM). MethodsWe collected information on patients with positive indicators of NTM infection at the Henan Provincial Chest Hospital from 2020 to 2022. Acid-fast smear, mycobacterium culture, QB-SPOT assay, GeneXpert MTB/RIF assay, immunoglobulin E test, tuberculosis antibody test, and microplate method for drug sensitivity test were analyzed using strain identification as the gold standard. ResultsThe 242 cases of NTM infection were predominantly detected with slow-growing mycobacteria (a detection rate of 87.19%), among which Mycobacterium intracellulare (66.53%), Mycobacterium avium (15.70%), and Mycobacterium chelonei/abscessus complex (11.16%) ranked the top three in terms of the isolation rate. Males patients accounted for a higher proportion (58.26%) than females (41.74%), and the majority of them were over 60 years (50.83%). Among laboratory tests for patients with NTM infection, mycobacterium culture showed a highest detected rate (87.20%) among laboratory tests. The results of the drug sensitivity test demonstrated that the resistance rate of NTM was generally high. Moreover, the Mycobacterium avium complex with the highest isolation rate showed 100% resistant to doxycycline and minocycline, but exhibited relatively high sensitivity to moxifloxacin (a resistance rate of 7.89%) and rifabutin (a resistance rate of 13.16%). The Mycobacterium chelonei/abscessus complex was 100% resistant to doxycycline and relatively sensitive to cefoxitin (29.17%) and clarithromycin (37.50%). ConclusionThe NTM species isolated by the Henan Provincial Chest Hospital is dominated by Mycobacterium intracellulare and the highest positive rate is detected by mycobacterium culture among laboratory tests. NTM infection generally exhibits a high rate of drug resistance. Accordingly, the accurate diagnosis of NTM diseases requires enhanced drug sensitivity testing to provide patients with targeted combination drug treatment.

Establishment of patient-derived organoids for guiding personalized therapies in breast cancer patients.

Breast cancer has become the most commonly diagnosed cancer. The intra- and interpatient heterogeneity induced a considerable variation in treatment efficacy. There is an urgent requirement for preclinical models to anticipate the effectiveness of individualized drug responses. Patient-derived organoids (PDOs) can accurately recapitulate the architecture and biological characteristics of the origin tumor, making them a promising model that can overtake many limitations of cell lines and PDXs. However, it is still unclear whether PDOs-based drug testing can benefit breast cancer patients, particularly those with tumor recurrence or treatment resistance. Fresh tumor samples were surgically resected for organoid culture. Primary tumor samples and PDOs were subsequently subjected to H&E staining, immunohistochemical (IHC) analysis, and whole-exome sequencing (WES) to make comparisons. Drug sensitivity tests were performed to evaluate the feasibility of this model for predicting patient drug response in clinical practice. We established 75 patient-derived breast cancer organoid models. The results of H&E staining, IHC, and WES revealed that PDOs inherited the histologic and genetic characteristics of their parental tumor tissues. The PDOs successfully predicted the patient's drug response, and most cases exhibited consistency between PDOs' drug susceptibility test results and the clinical response of the matched patient. We conclude that the breast cancer organoids platform can be a potential preclinical tool used for the selection of effective drugs and guided personalized therapies for patients with advanced breast cancer.

Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli in Animal Farms in Hunan Province, China.

Multi-drug resistance of bacteria producing extended-spectrum β-lactamase (ESBL) is a public health challenge. Thus, this study aimed to investigate the antimicrobial susceptibility of ESBL-producing Escherichia coli (ESBL-EC) in Hunan Province, China. A total of 1366 fecal samples were collected from pig, chicken, and cattle farms over a six-year period, which were assessed using strain isolation, 16S rRNA identification, polymerase chain reaction, drug sensitivity testing, whole-genome sequencing, and bioinformatics analysis. The results showed an overall prevalence of 6.66% for ESBL-EC strains, with ESBL positivity extents for pigs, chickens, and cattle isolates at 6.77%, 6.54%, and 12.5%, respectively. Most ESBL-EC isolates were resistant to cefotaxime, tetracycline, and trimethoprim-sulfamethoxazole; however, all the isolates were susceptible to meropenem, with relatively low resistance to amikacin and tigecycline. Various multi-locus sequence types with different origins and similar affinities were identified, with ST155 (n = 16) being the most common subtype. Several types of resistance genes were identified among the 91 positive strains, with beta-lactamase blaCTX-M-55 being the most common ESBL genotype. IncFIB was the predominant plasmid type. Widespread use of antibiotics in animal farming may increase antibiotic resistance, posing a serious threat to the health of farmed animals and, thus, to human food security and health.

Investigating Drug Interactions And Antibacterial Activity Of Vitamin C On Pathogenic Factors Of Escherichia Coli Clinical Isolates

Today, the phenomenon of multi-drug resistance has become a major cause of concern, and insufficient achievements have been made in the development of new antibiotics for the treatment of bacterial infections. Therefore, there is an unmet need for new auxiliary search. Vitamin C is one such promising supplement. The current study was conducted with the aim of explaining the antibacterial interaction effect of vitamin C in different concentrations (5-20 mg/ml) and drugs effective on Escherichia coli bacteria. In order to collect clinical samples during the months of September to November 2022, clinical samples were collected from 100 patients suspected of urinary tract infection who referred to medical centers. For identification, biochemical tests and gram staining and culture in IMViC and EMB environments were used to see metallic green polish. Then antimicrobial sensitivity test And the effect of antibiotic on biofilm formation, the effect of antibiotic and ascorbic acid on biofilm formation, biofilm inhibition rate was done for the single and combined effects of both antimicrobial substances. Finally, in order to investigate and identify the virulence gene of the isolated strains, DNA extraction was performed by PCR method. 45 samples of urinary infection culture were identified from the total of 100 samples collected, in 45 (45%) of them colonies with metallic polish were observed. 45% were men and 55% were women, and of these, a total of 45 positive E. coli cases were found in women and 17 positive cases were seen in men. Less than one year, teenagers, young and old were divided. 2 cases (2%) were in the age group of less than one year, 3 cases (3%) were teenagers, 63 cases (63%) were young and 32 cases (32%) were in the age group of middle-aged people. In a situation where the ability to form biofilm under vitamin C (ascorbic acid) treatment was not very effective and did not differ much from normal conditions, antibiotic treatment (under MBC gentamicin treatment) was somewhat successful in inhibiting biofilm formation, finally with the combination of antibiotic and Ascorbic acid was completely isolated in many resistant strains, the inability to form biofilm was evident, and this indicated the synergistic effects in the investigated composition. As the results showed, the ability to produce biofilm in the samples that had the target genes in this study was not much different from the other samples. Considering the increasing resistance to some antibiotics and wide changes in the effective spectrum of drugs and preventing the increase of drug-resistant cases, the necessity of conducting drug sensitivity tests seems very necessary. The high prevalence of E. coli antibiotic resistance and the high percentage of resistance genes in patients suffering from infections caused by this bacterium can indicate the excessive use of antibiotics. Finally, the prevalence of antibiotic resistance is a useful marker for investigating resistance genes and can be useful in ecological investigations. Also, with clear inhibitory effects, the selected antibiotic in this study along with ascorbic acid, this vitamin can be used as a supplement in some infections caused by E. coli bacteria.

Abstract 941: Patient-derived model systems of endometrial cancers for disease modeling and drug sensitivity testing

Abstract Background: Endometrial cancer (EC) is the most common gynecological cancer in the US, with increasing incidence and mortality rates. The survival rate lags behind four decades ago (81% vs 87%), underscoring the critical need for more effective treatment strategies. The heterogeneous nature of EC contributes to varied outcomes with current treatments. This project aims to establish reliable EC models for characterizing each individual tumor, distinguish optimal drug treatment, and determine specific drug effect mechanisms for personalized therapy. Methods: Freshly collected tumors were used for patient-derived xenograft models (PDXs) and patient-derived primary cancer cells (PDCs). Immunohistochemistry (IHC) staining was used to confirm the tumors grown in mice faithfully replicate the characteristics of patient tumor tissues. FDA-approved anticancer drugs were used to screen the optimal drugs to inhibit tumor cell proliferation and further utilized to inhibit tumor growth using PDXs. Results: We have collected 26 EC tumors and characterize them by DNA mutation and RNA-seq analysis. We implanted them in NSG mice, and 16 tumor samples have successfully grown in mice with a success rate of 61%. Most PDXs can be faithfully passaged to three generations. From the 16 PDXs, we created six novel PDCs. Using 2D and 3D spheroid cell culture, we screened 133 FDA-approved oncology drugs in the EC-PDC models. The drug screening results clearly highlighted several standout drugs, including CUDC-907 (a dual PI3K/HDAC inhibitor), two histone deacetylase (HDAC) inhibitors including romidepsin and panobinostat, four topoisomerase II (TOP II) inhibitors including mitoxantrone, daunorubicin, doxorubicin, and epirubicin, two proteasome inhibitors including carfilzomib and bortezomib, 2 DNA-directed RNA synthesis inhibitor dactinomycin and plicamycin, omacetaxine mepesuccinate (protein synthesis inhibitor), and valrubicin (DNA synthesis inhibitor). These drugs have demonstrated a significant capacity to inhibit tumor cell proliferation. Our pilot studies using single drugs, CUDC-907, romidepsin and mitoxantrone, achieved moderate drug effects. Combine mitoxantrone with romidepsin or CUDC-907 show surprisingly synergistic effects in multiple PDC models. The combination strategy will be tested in PDXs in the near future. Conclusion: Our unique PDXs and PDCs are excellent models for representing various characteristics of EC and testing novel therapeutics. This current study presents a promising direction for developing personalized therapy options for EC patients and provides a platform for further investigation of drug mechanisms and tumor development. Future studies will also involve etiology, such as chronic psychological stress, DNAm age and intratumoral microbiome. This information will help with endometrial cancer prevention, diagnosis, and prognosis. Citation Format: Tianyue Li, Xiaohao Huang, Riley Rosenmeyer, Samuel Robinson, Kazi Salsabil, Yiqin Xiong, Xiangbing Meng, Shujie Yang. Patient-derived model systems of endometrial cancers for disease modeling and drug sensitivity testing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 941.

Abstract 6890: 2D Tumor cell culture based Ex vivo drug sensitivity screening platform for South African patient samples (leukemia, multiple myeloma, ovarian and uterine cancer) demonstrate potential for targeted cancer therapies

Abstract Resistance to standard chemotherapy is a major challenge with Leukemia (Leuk), Multiple Myeloma (MM), Ovarian Cancer (OvCa) and Uterine Cancer (UtCa) treatments, which ultimately leads to relapse. Our study objective is to establish a robust drug sensitivity screening platform that can identify drugs and drug combinations that are effective in precision medicine for individual South African patient samples (Leuk, MM, OvCa and UtCa). Given that resistance to chemotherapy treatment accounts for high mortality and morbidity, we focus on the hypothesis that several drug combinations will be required for patients to achieve better response for drug regimens beyond first line of chemotherapy. Therefore, our defined objectives were to 1) establish 2D ex vivo tumour cell culturing using South African patient samples; 2) develop a drug sensitivity screening platform through which selected single and drug combinations will be identified; 3) to provide South African cancer (OvCa, Ut Ca, CLL, MM) patients with individualized treatment options with effective drug combinations for targeted therapies. Through collaboration with, Steve Biko Hospital Pretoria, Chris Hani Baragwanath Hospital and Wits Donald Gordon Medical Centre, Johannesburg, South Africa, we performed 100 patient sample collections including Acute myeloid leukaemia (AML) (n=7), Chronic lymphocytic leukaemia (CLL) (n=4), Chronic myeloid leukaemia (CML) (n= 30), MM (n=40), OvCa (n=10), UtCa (n=4) and healthy donors (n=5). Culture setting for all patient-derived tumor cells were established through the 2D cancer cell culturing in 96 well plates. This was followed by functional drug sensitivity testing using a panel of FDA approved chemotherapy drugs. The average turnaround time from biopsy to drug sensitivity test results is currently at 14 days. We have completed ex vivo drug sensitivity screening to perform analysis on patient samples (n=80) using 30 drugs with a concentration range of 1-1000 nm. Our preliminary drug sensitivity screening studies show good response to proteosome inhibitors, melphalan, doxorubicin and kinase inhibitors. We have established a wound healing assay for OvCa and UtCa samples and demonstrated sustained cell growth for the period of 2 weeks with tumor cells growing faster than twin normal tissue. We are now at stage of performing drug sensitivity screening for OvCa and UtCa patient samples for both twin normal and tumor tissues. We have established a drug sensitivity screening platform and wound healing assay with primary patient derived cells that utilizes South African Patient samples to select effective drugs for monotherapy and also drug combinations. Citation Format: Mutsa Takundwa, Vanelle Kenmogne, Thudzelani Malise, Bernice Monchusi, Phumuzile Dube, Ekene Nweke, June Fabian, Heather Maher, Justin du Toit, Vinitha Philip-Cherian, Pascaline Fru, Adekunle Sajo, Arnold (Arrie) Mouton, Matthys C. van Aardt, Cathy Visser, Greta Dreyer, Deepak Govindaraj. 2D Tumor cell culture based Ex vivo drug sensitivity screening platform for South African patient samples (leukemia, multiple myeloma, ovarian and uterine cancer) demonstrate potential for targeted cancer therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6890.