Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma DOI Creative Commons
Benjamin Ziman, Qian Yang, Yueyuan Zheng

и другие.

Cell Death and Disease, Год журнала: 2024, Номер 15(2)

Опубликована: Фев. 19, 2024

Unlike most cancer types, the incidence of esophageal adenocarcinoma (EAC) has rapidly escalated in western world over recent decades. Using whole genome bisulfite sequencing (WGBS), we identify transcription factor (TF) FOXM1 as an important epigenetic regulator EAC. plays a critical role cellular proliferation and tumor growth EAC patient-derived organoids cell line models. We ERBB2 upstream expression transcriptional activity FOXM1. Unexpectedly, gene set enrichment analysis (GSEA) unbiased screen reveals prominent anti-correlation between immune response pathways. Indeed, syngeneic mouse models show that inhibits infiltration CD8

Язык: Английский

Towards artificial intelligence to multi-omics characterization of tumor heterogeneity in esophageal cancer DOI
Junyu Li, Lin Li,

Peimeng You

и другие.

Seminars in Cancer Biology, Год журнала: 2023, Номер 91, С. 35 - 49

Опубликована: Март 1, 2023

Язык: Английский

Процитировано

30
A Roadmap for the Human Gut Cell Atlas DOI
Matthias Zilbauer, Kylie R. James, Mandeep Kaur

и другие.

Nature Reviews Gastroenterology & Hepatology, Год журнала: 2023, Номер 20(9), С. 597 - 614

Опубликована: Май 31, 2023

Язык: Английский

Процитировано

29
FINDER: A Fluidly Confined CRISPR‐Based DNA Reporter on Living Cell Membranes for Rapid and Sensitive Cancer Cell Identification DOI
Yao Yin, Wei Xie, Mengyi Xiong

и другие.

Angewandte Chemie International Edition, Год журнала: 2023, Номер 62(44)

Опубликована: Сен. 15, 2023

The accurate, rapid, and sensitive identification of cancer cells in complex physiological environments is significant biological studies, personalized medicine, biomedical engineering. Inspired by the naturally confined enzymes on fluid cell membranes, a fluidly CRISPR-based DNA reporter (FINDER) was developed living which successfully applied for rapid clinical blood samples. Benefiting from spatial confinement effect improved local concentration, membrane fluidity higher collision efficiency, activity CRISPR-Cas12a was, first time, found to be significantly enhanced membranes. This new phenomenon then combined with multiple aptamer-based logic gate recognition, thus FINDER system capable constructed. rapidly identified target only 20 min, achieved over 80 % recognition efficiency 0.1 presented samples, indicating its potential application

Язык: Английский

Процитировано

28
Gastric intestinal metaplasia: progress and remaining challenges DOI

Qi-Yue Tong,

Min-Jiao Pang,

Xiao-Hai Hu

и другие.

Journal of Gastroenterology, Год журнала: 2024, Номер 59(4), С. 285 - 301

Опубликована: Янв. 19, 2024

Язык: Английский

Процитировано

11
Origins of cancer: ain’t it just mature cells misbehaving? DOI

Charles J. Cho,

Jeffrey W. Brown, Jason C. Mills

и другие.

The EMBO Journal, Год журнала: 2024, Номер 43(13), С. 2530 - 2551

Опубликована: Май 21, 2024

Язык: Английский

Процитировано

9
Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer DOI Creative Commons
Piyali Ganguli, Celia De Los Angeles Colomina Basanta, Amelia Acha‐Sagredo

и другие.

Nature Cancer, Год журнала: 2025, Номер unknown

Опубликована: Янв. 3, 2025

Abstract CDKN2A is a tumor suppressor located in chromosome 9p21 and frequently lost Barrett’s esophagus (BE) esophageal adenocarcinoma (EAC). How other gene co-deletions affect EAC evolution remains understudied. We explored the effects of loss EACs cancer progressor non-progressor BEs with matched genomic, transcriptomic clinical data. Despite its driver role, BE prevents initiation by counterselecting subsequent TP53 alterations. predict poor patient survival but not through context-dependent on cell cycle, oxidative phosphorylation interferon response. Immune quantifications using bulk transcriptome, RNAscope high-dimensional tissue imaging showed that IFNE reduces immune infiltration BE, EAC. Mechanistically, suppresses maintenance squamous epithelium, contributing to more aggressive phenotype. Our study demonstrates roles genes during disease evolution, consequences for detection management.

Язык: Английский

Процитировано

1
inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples DOI Creative Commons
Simonas Juzėnas, Karolis Goda, Vaidotas Kiseliovas

и другие.

Nucleic Acids Research, Год журнала: 2025, Номер 53(2)

Опубликована: Янв. 11, 2025

Abstract The expansion of single-cell analytical techniques has empowered the exploration diverse biological questions at individual cells. Droplet-based RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems contributed widespread adoption droplet-based scRNA-seq, relatively high cost limits ability profile large numbers cells samples. Moreover, as scale continues expand, accommodating workflows cost-effective multi-biospecimen profiling becomes more critical. Herein, we present inDrops-2, an open-source scRNA-seq technology designed live or preserved with a sensitivity matching that state-of-the-art but 6-fold lower cost. We demonstrate flexibility by implementing two prominent protocols, based on exponential linear amplification barcoded-complementary DNA, provide useful insights into advantages disadvantages inherent each approach. applied inDrops-2 simultaneously multiple human lung carcinoma samples had subjected cell preservation, long-term storage multiplexing obtain multiregional cellular tumor microenvironment. scalability, efficiency make stand out among other methods, ideal for large-scale studies rare molecular signatures.

Язык: Английский

Процитировано

1
Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium DOI Creative Commons

Mohammad Faujul Kabir,

Adam Karami,

Ricardo Cruz‐Acuña

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Апрель 20, 2022

Abstract Although morphologic progression coupled with expression of specific molecular markers has been characterized along the esophageal squamous differentiation gradient, heterogeneity within cell types this trajectory yet to be classified at single level. To address knowledge gap, we perform RNA-sequencing 44,679 murine epithelial, identify 11 distinct populations as well pathways alterations basal-superficial axis and in each individual population. We evaluate impact aging upon epithelial demonstrate age-associated mitochondrial dysfunction. compare transcriptomic profiles 3D organoids human biopsies that epithelium. Finally, employ pseudotemporal analysis develop a working model fate determination These studies provide comprehensive perspective on cellular epithelium context homeostasis aging.

Язык: Английский

Процитировано

35
The single cell transcriptional landscape of esophageal adenocarcinoma and its modulation by neoadjuvant chemotherapy DOI Creative Commons
Wayne Croft,

Richard Evans,

Hayden Pearce

и другие.

Molecular Cancer, Год журнала: 2022, Номер 21(1)

Опубликована: Окт. 17, 2022

Abstract Immune checkpoint blockade has recently proven effective in subsets of patients with esophageal adenocarcinoma (EAC) but little is known regarding the EAC immune microenvironment. We determined single cell transcriptional profile 8 who were treatment-naive ( n = 4) or had received neoadjuvant chemotherapy 4). Analysis 52,387 cells revealed 10 major tumor, and stromal cells. Prior to tumors heavy infiltrated by T regulatory exhausted effector whilst plasmacytoid dendritic markedly expanded. Two dominant cancer-associated fibroblast populations also observed endothelial suppressed. Pathological remission following associated broad reversal abnormalities together transition an increase a chemoresistant epithelial stem population correlated poor response. These findings reveal features that underlie limit response current immunotherapy identify range novel opportunities for targeted therapy.

Язык: Английский

Процитировано

35
Applications of human organoids in the personalized treatment for digestive diseases DOI Creative Commons
Qinying Wang,

Fanying Guo,

Yutao Jin

и другие.

Signal Transduction and Targeted Therapy, Год журнала: 2022, Номер 7(1)

Опубликована: Сен. 27, 2022

Abstract Digestive system diseases arise primarily through the interplay of genetic and environmental influences; there is an urgent need in elucidating pathogenic mechanisms these deploy personalized treatments. Traditional long-established model systems rarely reproduce either tissue complexity or human physiology faithfully; shortcomings underscore for better models. Organoids represent a promising research model, helping us gain more profound understanding digestive organs; this can also be used to provide patients with precise individualized treatment build rapid vitro test models drug screening gene/cell therapy, linking basic clinical treatment. Over past few decades, use organoids has led advanced composition each organ facilitated disease modeling, chemotherapy dose prediction, CRISPR-Cas9 intervention, high-throughput screening, identification SARS-CoV-2 targets, infection. However, existing mainly include epithelial system. In order reveal mechanism diseases, it necessary establish completer physiological organoid model. Combining techniques treatments different formulations approach that requires further exploration. This review highlights advancements field technology from perspectives modeling therapy.

Язык: Английский

Процитировано

33