Genotoxin-producing Salmonella enterica induces tissue-specific types of DNA damage and DNA damage response outcomes

Telomemore enables single-cell analysis of cell cycle and chromatin condensation

Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.

Lyophilized and Oven-Dried Manilkara zapota Extracts: Characterization and In Vitro, In Vivo, and In Silico Analyses

In this work, extracts from the pulp, peel, and seed of Manilkara zapota were obtained via lyophilization and oven drying. Bromatological analyses were performed to investigate variabilities in the nutritional content of fruits after nine post-harvest days. The phytochemical content of fruits was assessed by gas chromatography flame ionization detector (GC-FID), and their biological performance was studied using in vitro antibacterial and antioxidant assays (DPPH and ABTS) and in vivo toxicity models. Molecular docking was implemented to evaluate the interaction between polar compounds from chicozapote fruits with receptors involved in the pathogenesis of bacterial strains. Results revealed that water or soluble solids content did not vary after post-harvest. It was demonstrated that lyophilization or oven-drying approaches influenced the insoluble, total dietary fiber and digestible carbohydrates among samples. According to GC-FID analysis, it was observed that lyophilization and oven-drying methods also altered the content of myristic and pentadecanoic acids among the obtained extracts. It was noted that the antibacterial and antioxidant activities of extracts were weak due to their MIC (>1000 μg/mL) and IC50 (>2000 μg/mL) values. Still, the toxicity of extracts was poor against Artemia salina nauplii. In silico evaluation unveiled that polar compounds in M. zapota fruits possess a high binding affinity towards the DNA gyrase B of the cultured strains. This study expands the scientific evidence regarding the influence of distinct extraction methods on the nutritional and nutraceutical content of native fruits and the importance of considering additional approaches to enhance their bioactivities.

Combined In Situ Transcriptomic and Immunofluorescence to Assess the Effects on DNA Damage and Innate Immune Responses Induced by Bacterial Genotoxin in In Vivo Models

Understanding complex pathophysiological processes involves studying intercellular responses and phenotypes within the organ microenvironment, preserving the spatial tissue architecture. This chapter explores a practical and cost-effective method for combining techniques such as in situ immunostaining and transcriptomics analysis. These protocols are adaptable to various mRNA targets, antibodies, tissue types, and tissue fixation appealing to a wide scientific community. We demonstrate their application in studying the host response to infection with a Salmonella enterica strain producing a toxin that induces DNA breaks. Specifically, we assessed the: (i) innate immune response to DNA breaks; (ii) co-detection of Salmonella mRNA fljB with the DNA damage marker γH2AX; (iii) co-detection of mRNAs for the cell cycle arrest marker p16INK4A and the proinflammatory and anti-inflammatory cytokines, Il6 and Il10, respectively. Considering that DNA damage is one of the leading causes of oncogene- and stress-induced-senescence, these protocols can be suitable to assess the cytokine profile associated with cellular phenotype and types of DNA damage of senescent cells in situ.

Targeted therapy with polymeric nanoparticles in PBRM1-mutant biliary tract cancers: Harnessing DNA damage repair mechanisms

Biliary tract cancers (BTCs) are aggressive malignancies with a dismal prognosis that require intensive targeted therapy. Approximately 10 % of BTCs have PBRM1 mutations, which impede DNA damage repair pathways and make cancer cells more susceptible to DNA-damaging chemicals. This review focus on development of poly(lactic-co-glycolic acid) (PLGA)-based nanoparticles targeting delivery system to selectively deliver chemotherapy into PBRM1-deficient BTC cells. These nanoparticles improve therapy efficacy by increasing medication targeting and retention at tumour locations. In preclinical studies, pharmacokinetic profile of this nanoparticle was encouraging and supported its ability to achieve extended circulation time with high drug accumulation in tumor. The review also highlights potential of Pou3F3:I54N to expedite bioassays for patient selection in BTC targeted therapies.

Isolation and Characterization of a Bacteriophage with Potential for the Control of Multidrug-Resistant Salmonella Strains Encoding Virulence Factors Associated with the Promotion of Precancerous Lesions

BACKGROUND

Antimicrobial-resistant bacteria represent a serious threat to public health. Among these bacteria, Salmonella is of high priority because of its morbidity levels and its ability to induce different types of cancer.

AIM

This study aimed to identify Salmonella strains encoding genes linked to the promotion of precancerous lesions and to isolate a bacteriophage to evaluate its preclinical potential against these bacteria.

METHODOLOGY

An epidemiological approach based on wastewater analysis was employed to isolate Salmonella strains and detect genes associated with the induction of precancerous lesions. Antimicrobial susceptibility was assessed by the disk diffusion method. A bacteriophage was isolated via the double agar technique, and its morphological characteristics, stability, host range, replication dynamics, and ability to control Salmonella under different conditions were evaluated. The bacteriophage genome was sequenced and analyzed using bioinformatics tools.

RESULTS

Thirty-seven Salmonella strains were isolated, seventeen of which contained the five genes associated with precancerous lesions' induction. These strains exhibited resistance to multiple antimicrobials, including fluoroquinolones. A bacteriophage from the Autographiviridae family with lytic activity against 21 bacterial strains was isolated. This phage exhibited a 20 min replication cycle, releasing 52 ± 3 virions per infected cell. It demonstrated stability and efficacy in reducing the Salmonella concentration in simulated gastrointestinal conditions, and its genome lacked genes that represent a biosafety risk.

CONCLUSION

This bacteriophage shows promising preclinical potential as a biotherapeutic agent against Salmonella.