Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics.

Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.

ABCG2 Gene Polymorphisms May Affect the Bleeding Risk in Patients on Apixaban and Rivaroxaban.

Purpose: Direct oral anticoagulants (DOACs) are widely used for stroke prevention in atrial fibrillation. However, they have a bleeding complication. Breast cancer resistance protein, encoded by ABCG2, is known to be an efflux transporter of apixaban and rivaroxaban among DOACs. This study aimed to investigate the association between gene variants and bleeding complications during treatment with ABCG2 substrates (apixaban and rivaroxaban). Patients and Methods: Patients treated with apixaban and rivaroxaban were enrolled from June 2018 to December 2021. Five single nucleotide polymorphisms (SNPs) of ABCG2 were selected. Previously studied genes (ABCB1, CYP3A4, and CYP3A5) were further analyzed as possible confounders. Finally, a total of 16 SNPs were examined in this case-control study. The outcome was defined as major bleeding and clinically relevant non-major bleeding. Two models were constructed using the multivariable analysis. Results: Among 293 patients, 64 were cases. The mean age of the patients was 68.8 years, and males comprised 62.5% of the study population. Model I revealed that a history of bleeding, concurrent use of proton pump inhibitor (PPI), ABCG2 rs3114018, and ABCB1 rs1045642 were significantly associated with bleeding complications; the AORs (95% CI) were 6.209 (2.210-17.442), 2.385 (1.064-5.349), 2.188 (1.156-4.142), and 3.243 (1.371-7.671), respectively. Model II showed that modified HAS-BLED score, concurrent use of PPI, ABCG2 rs3114018, and ABCB1 rs1045642 were significantly associated with bleeding complications. Conclusion: The modified HAS-BLED score, a history of bleeding, concurrent use of PPI, ABCG2 rs3114018, and ABCB1 rs1045642 were significantly associated with the risk of bleeding complications in patients on apixaban and rivaroxaban, after adjusting for other confounders. These findings can be used to develop individualized treatment strategies for patients taking apixaban and rivaroxaban.

Beneficial, safety, and antioxidant properties of lactic acid bacteria: A next step in their evaluation as potential probiotics.

The role of lactic acid bacteria (LAB) as probiotics as health promoting factors for human or veterinary practice has gained increasing interest during the last three decades. This is reflected in screening approaches of LAB strains in line with minimal requirements for a "probiotic" with regard to safety and functionality. The latter might also include natural antioxidant properties, thereby constituting an additional benefit in substituting synthetic antioxidants. The in vitro antioxidant assays conducted in this study included the scavenging of the 2,2-diphenyl-1-picrylhydrazil (DPPH) free radical, metal (Fe+2) ion chelation, determining the scavenging properties of the hydroxyl and superoxide radicals, and anti-lipid peroxidation. Analysis of DPPH free radical scavenging property for the microorganisms included in current study, showed Streptococcus salivarius ST59HK to exhibit the highest activity at a level of 85.24%. The greatest Fe+2 chelation activity with 98.2% was recorded for Str. salivarius ST62HK while the lowest was recorded for Str. salivarius ST48HK at 71.5%. The greatest and minimal hydroxyl radical scavenging levels were detected for Str. salivarius ST59HK (98.6%) and Lactiplantibacillus plantarum ST63HK (35.60%), respectively. Superoxide anion radical scavenging activity was highly exhibited by Str. salivarius ST61HK (54.62%) and the least exhibited by Enterococcus faecium ST651ea (18.7%). Lastly, the strains Lactobacillus gasseri ST16HK and E. faecium ST7319ea showed the highest and lowest anti-lipid peroxidation levels with 69.43% and 26.15%, respectively. Anti-oxidative properties appear to be strain specific and thus some of these strains could be potentially applied as natural antioxidants in fermented food products.