Robustness of cancer microbiome signals over a broad range of methodological variation

Oncogene, Год журнала: 2024, Номер 43(15), С. 1127 - 1148

Опубликована: Фев. 23, 2024

Abstract In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2–12]. Given this impact, carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested comparing raw Voom-SNM-corrected data per-batch, finding predictive equivalence significantly similar features. found consistent results a modern microbiome-specific method (ConQuR [14]), when restricting to taxa an independent, highly-decontaminated cohort. (2) Using Conterminator [15], low levels human original databases (~1% genomes). demonstrated increased detection reads was due using newer genome reference. (3) developed Exhaustive, twice as sensitive Conterminator, clean RefSeq. comprehensively host-deplete TCGA many (pan)genome references. repeated all analyses pipeline, These extensive re-analyses updated methods validate conclusion signatures exist TCGA, show they are robust methodology.

Язык: Английский

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Development of tumor-evolution-targeted anticancer therapeutic nanomedicineEVT

Chem, Год журнала: 2024, Номер 10(5), С. 1337 - 1356

Опубликована: Янв. 25, 2024

Язык: Английский

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Aggregation-Induced Emission Luminogen: Role in Biopsy for Precision Medicine

Chemical Reviews, Год журнала: 2024, Номер 124(20), С. 11242 - 11347

Опубликована: Окт. 9, 2024

Biopsy, including tissue and liquid biopsy, offers comprehensive real-time physiological pathological information for disease detection, diagnosis, monitoring. Fluorescent probes are frequently selected to obtain adequate on processes in a rapid minimally invasive manner based their advantages biopsy. However, conventional fluorescent have been found show aggregation-caused quenching (ACQ) properties, impeding greater progresses this area. Since the discovery of aggregation-induced emission luminogen (AIEgen) promoted advancements molecular bionanomaterials owing unique high quantum yield (QY) signal-to-noise ratio (SNR),

Язык: Английский

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Microbiome Integrity Enhances the Efficacy and Safety of Anticancer Drug

Biomedicines, Год журнала: 2025, Номер 13(2), С. 422 - 422

Опубликована: Фев. 10, 2025

The intricate relationship between anticancer drugs and the gut microbiome influences cancer treatment outcomes. This review paper focuses on role of integrity in enhancing efficacy safety drug therapy, emphasizing pharmacokinetic interactions microbiota. It explores how disruptions to composition, or dysbiosis, can alter metabolism, immune responses, side effects. By examining mechanisms disruption caused by drugs, this highlights specific case studies like cyclophosphamide, 5-fluorouracil, irinotecan, their impact microbial diversity clinical also discusses microbiome-targeted strategies, including prebiotics, probiotics, postbiotics, fecal microbiota transplantation (FMT), as promising interventions enhance treatment. Furthermore, potential profiling personalizing therapy integrating these into practice is explored. Finally, proposes future research directions, developing novel biomarkers a deeper comprehension drug-microbiome interactions, respond current gaps knowledge improve patient outcomes care.

Язык: Английский

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Methanogenic archaea in the human gastrointestinal tract

Nature Reviews Gastroenterology & Hepatology, Год журнала: 2022, Номер 19(12), С. 805 - 813

Опубликована: Сен. 1, 2022

Язык: Английский

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