Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis DOI Creative Commons
Yingjie Li, Cankun Wang, Anjun Ma

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Авг. 14, 2023

Human Papillomaviruses (HPVs) are associated with around 5-10% of human cancer, notably nearly 99% cervical cancer. The mechanisms HPV interacts stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study gene host cell differentiation-associated heterogeneity HPV-positive cancer tissue. We examined HPV16 genes - E1, E6, E7, found they expressed differently across nine epithelial clusters. that three clusters had highest proportion cells (33.6%, 37.5%, 32.4%, respectively), while two exhibited lowest proportions (7.21% 5.63%, respectively). Notably, cluster most deviated significantly from normal layer markers, exhibiting functional altered structuring, indicating significant molecular existed in tissues these unique/different signatures compared cells. These cells, HPV-negative, showed different expressions related extracellular matrix, adhesion, proliferation, apoptosis. Further, oncogenes E6 E7 appeared modify function via distinct pathways, thus contributing progression. investigated transcripts a novel viewpoint focusing on heterogeneity. Our results indicated varied expression oncogenes, biological insights critical field study.

Язык: Английский

Untangling the web of intratumor microbiota in lung cancer DOI Open Access
Weici Liu, Jingtong Xu, Zheshun Pi

и другие.

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, Год журнала: 2023, Номер 1878(6), С. 189025 - 189025

Опубликована: Ноя. 1, 2023

Язык: Английский

Процитировано

9
Unraveling the potential of bioengineered microbiome-based strategies to enhance cancer immunotherapy DOI
Muhammad Hamza, Shuai Wang, Yike Liu

и другие.

Microbiological Research, Год журнала: 2025, Номер unknown, С. 128156 - 128156

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Host–microbiota interaction during cancer progression from bulk to single‐cell level DOI Creative Commons

Yongjing Ma,

Run‐Ze Zhu,

Ning‐Ning Liu

и другие.

Clinical and Translational Discovery, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 28, 2024

Abstract Background Cancer, a global threat to human health, refers large crowd of lethal diseases that can start in almost all tissues or organs our body when abnormal cells grow uncontrollably and beyond their usual boundaries, followed by invading adjacent normal spreading distant organs. Recently, substantial evidence has demonstrated polymorphic microbiome as an emerging cancer characteristic present variety tumour types. By releasing metabolites other signalling molecules, microbiota affect immune cell differentiation activity, including both innate adaptive immunological responses, well the growth multiplication cells. It was now employed biomarker predict patients’ survival rate degree progression. Main To investigate underlying mechanism technology development how influence microenvironment subsequently progression, we have carried out systematic literature review about from bulk single‐cell level. Conclusions Here, provide overview current advancements host–microbiota interactions during progression level discuss challenges opportunities future, looking forward ascertain specific activity different somatic types with without existence various multi‐kingdom by‐products supply holistic elaborate investigation host‐microbiota interaction cancer.

Язык: Английский

Процитировано

2
An Explainable Graph Neural Framework to Identify Cancer‐Associated Intratumoral Microbial Communities DOI Creative Commons
Zhaoqian Liu, Yuhan Sun, Yingjie Li

и другие.

Advanced Science, Год журнала: 2024, Номер unknown

Опубликована: Сен. 3, 2024

Abstract Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis treatment responses. However, the underlying relationships between intratumoral microbes tumors remain poorly understood. Here, a MIcrobial Cancer‐association Analysis using Heterogeneous graph transformer (MICAH) to identify cancer‐associated microbial communities is presented. MICAH integrates metabolic phylogenetic into heterogeneous representation. It uses holistically capture tissues, which improves explainability of associations identified cancers. applied bacterial data across 5 types fungi datasets, its generalizability reproducibility demonstrated. After experimentally testing representative observation mouse model tumor‐microbe‐immune interactions, result consistent with MICAH's relationship observed. Source tracking analysis reveals that primary known contributor community organs affected by type cancer. Overall, this neural network framework refines number can be used for follow‐up experimental validation from thousands tens, thereby helping accelerate understanding microbiomes.

Язык: Английский

Процитировано

1
Single Cell Transcriptomics Reveals the Hidden Microbiomes of Human Tissues DOI Open Access
Gita Mahmoudabadi,

Sheela Crasta,

Stephen R. Quake

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Окт. 12, 2022

Abstract The human microbiome has been studied extensively across those sites in the body that are readily accessible to sampling. Internal organs and tissues, however, have remained largely unexplored and, absence of infectious disease, widely assumed be free microorganisms. Using single-cell transcriptomic data from Tabula Sapiens spanning 11 organ donors, 19 tissue types, 400,000+ annotated cells, 100+ cell ∼70 billion sequences, we created an atlas with type resolution three domains life which refer as Microbiome. Together 8 additional donors derived a different set experimental techniques for validation, identified sequences numerous bacterial, viral fungal species tissues. We mapped likely microbial flow routes external-facing microbiomes natural environments internal tissues tumors, demonstrating existence several unexpected routes. In case tumor microbiomes, find considerable number bacterial genera found tumors detectable tumor-free suggesting part sourced adjacent normal even distant sites. Finally, by increasing sampling quantified load diversity types reveal network host microbe associations. For example, traces both latent active Epstein Barr Virus infections various such splenic plasma cells. Broad exploration may provide insights ultimately clinical importance.

Язык: Английский

Процитировано

6
Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single‐cell transcriptomic analysis DOI Creative Commons
Yingjie Li, Cankun Wang, Anjun Ma

и другие.

Journal of Medical Virology, Год журнала: 2023, Номер 95(8)

Опубликована: Авг. 1, 2023

Human Papillomaviruses (HPVs) are associated with around 5%-10% of human cancer, notably nearly 99% cervical cancer. The mechanisms HPV interacts stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study gene host cell differentiation-associated heterogeneity HPV-positive cancer tissue. We examined HPV16 genes-E1, E6, E7, found they expressed differently across nine epithelial clusters. that three clusters had highest proportion cells (33.6%, 37.5%, 32.4%, respectively), while two exhibited lowest proportions (7.21% 5.63%, respectively). Notably, cluster most deviated significantly from normal layer markers, exhibiting functional altered structuring, indicating significant molecular existed in tissues these unique/different signatures compared cells. These cells, HPV-negative, showed different expressions related extracellular matrix, adhesion, proliferation, apoptosis. Further, oncogenes E6 E7 appeared modify function via distinct pathways, thus contributing progression. investigated transcripts a novel viewpoint focusing on heterogeneity. Our results indicated varied expression oncogenes, biological insights critical field study.

Язык: Английский

Процитировано

3
An explainable graph neural framework to identify cancer-associated intratumoral microbial communities DOI Creative Commons
Zhaoqian Liu, Yuhan Sun, Anjun Ma

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Апрель 18, 2023

ABSTRACT Microbes are extensively present among various cancer tissues and play a vital role in prevention treatment responses. However, the underlying relationships between intratumoral microbes tumors still not well understood. Here, we developed MIcrobial Cancer-association Analysis using Heterogeneous graph transformer (MICAH) to identify cancer-associated microbial communities. MICAH integrates metabolic phylogenetic into heterogeneous representation. It uses attention holistically capture tissues, which improves explainability of association identified communities cancer. We applied microbiome data across five types demonstrated its good generalizability reproducibility. believe this neural network framework can provide novel insights pathogenesis associated with microbiome.

Язык: Английский

Процитировано

2
Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis DOI Creative Commons
Yingjie Li, Cankun Wang, Anjun Ma

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Авг. 14, 2023

Human Papillomaviruses (HPVs) are associated with around 5-10% of human cancer, notably nearly 99% cervical cancer. The mechanisms HPV interacts stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study gene host cell differentiation-associated heterogeneity HPV-positive cancer tissue. We examined HPV16 genes - E1, E6, E7, found they expressed differently across nine epithelial clusters. that three clusters had highest proportion cells (33.6%, 37.5%, 32.4%, respectively), while two exhibited lowest proportions (7.21% 5.63%, respectively). Notably, cluster most deviated significantly from normal layer markers, exhibiting functional altered structuring, indicating significant molecular existed in tissues these unique/different signatures compared cells. These cells, HPV-negative, showed different expressions related extracellular matrix, adhesion, proliferation, apoptosis. Further, oncogenes E6 E7 appeared modify function via distinct pathways, thus contributing progression. investigated transcripts a novel viewpoint focusing on heterogeneity. Our results indicated varied expression oncogenes, biological insights critical field study.

Язык: Английский

Процитировано

0