Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state.

Esophageal adenocarcinoma (EAC) is one of the most frequent causes of cancer death, and yet compared to other common cancers, we know relatively little about the molecular composition of this tumor type. To further our understanding of this cancer, we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in EAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centered on HNF4A and GATA6. These transcription factors work together to control the EAC transcriptome. We show that this network is activated in Barrett's esophagus, the putative precursor state to EAC, thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone is sufficient to drive chromatin opening and activation of a Barrett's-like chromatin signature when expressed in normal human epithelial cells. Collectively, these data provide a new way to categorize EAC at a genome scale and implicate HNF4A activation as a potential pivotal event in its malignant transition from healthy cells.

Classifying cells with Scasat, a single-cell ATAC-seq analysis tool.

ATAC-seq is a recently developed method to identify the areas of open chromatin in a cell. These regions usually correspond to active regulatory elements and their location profile is unique to a given cell type. When done at single-cell resolution, ATAC-seq provides an insight into the cell-to-cell variability that emerges from otherwise identical DNA sequences by identifying the variability in the genomic location of open chromatin sites in each of the cells. This paper presents Scasat (single-cell ATAC-seq analysis tool), a complete pipeline to process scATAC-seq data with simple steps. Scasat treats the data as binary and applies statistical methods that are especially suitable for binary data. The pipeline is developed in a Jupyter notebook environment that holds the executable code along with the necessary description and results. It is robust, flexible, interactive and easy to extend. Within Scasat we developed a novel differential accessibility analysis method based on information gain to identify the peaks that are unique to a cell. The results from Scasat showed that open chromatin locations corresponding to potential regulatory elements can account for cellular heterogeneity and can identify regulatory regions that separates cells from a complex population.

Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma.

Oesophageal adenocarcinoma (OAC) is one of the ten most prevalent forms of cancer and is showing a rapid increase in incidence and yet exhibits poor survival rates. Compared to many other common cancers, the molecular changes that occur in this disease are relatively poorly understood. However, genes encoding chromatin remodeling enzymes are frequently mutated in OAC. This is consistent with the emerging concept that cancer cells exhibit reprogramming of their chromatin environment which leads to subsequent changes in their transcriptional profile. Here, we have used ATAC-seq to interrogate the chromatin changes that occur in OAC using both cell lines and patient-derived material. We demonstrate that there are substantial changes in the regulatory chromatin environment in the cancer cells and using this data we have uncovered an important role for ETS and AP1 transcription factors in driving the changes in gene expression found in OAC cells.

Trailblazers in cancer research: the next generation - the British Association of Cancer Research early-career conference.

The inaugural 'British Association of Cancer Research (BACR) Early Career Conference, Trailblazers in Cancer Research 2023', was a 2-day meeting held in Manchester, UK. Recognising the disruption caused by the COVID-19 pandemic to early-career researchers (ECRs), the BACR executive committee organised an in-person conference to address the lack of network and training opportunities during this time. The conference brought together PhD students and post-doctoral researchers from across the UK and beyond, who shared their outstanding contributions to cancer research. The meeting incorporated several cutting-edge cancer themes, including 'Cancer Cell Signalling and The Tumour Microenvironment'; 'Emerging Approaches in Cancer Treatment'; 'Cancer Omics and Lifestyle', and 'Nutrition and Cancer'. Alongside showcasing world-class cancer research, the meeting included a career-focused session which allowed industrial and non-academic speakers to provide vital insight into alternative career paths aside from the familiar 'academic' route. Importantly, the conference also introduced delegates to Patient Public Involvement in cancer research, an area of limited experience for many. Overall, the BACR Trailblazers Conference was hugely successful and presented an excellent platform for collaboration and networking among ECRs in cancer research.

FOXA2 controls the anti-oxidant response in FH-deficient cells.

Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a cancer syndrome caused by inactivating germline mutations in fumarate hydratase (FH) and subsequent accumulation of fumarate. Fumarate accumulation leads to profound epigenetic changes and the activation of an anti-oxidant response via nuclear translocation of the transcription factor NRF2. The extent to which chromatin remodeling shapes this anti-oxidant response is currently unknown. Here, we explored the effects of FH loss on the chromatin landscape to identify transcription factor networks involved in the remodeled chromatin landscape of FH-deficient cells. We identify FOXA2 as a key transcription factor that regulates anti-oxidant response genes and subsequent metabolic rewiring cooperating without direct interaction with the anti-oxidant regulator NRF2. The identification of FOXA2 as an anti-oxidant regulator provides additional insights into the molecular mechanisms behind cell responses to fumarate accumulation and potentially provides further avenues for therapeutic intervention for HLRCC.

HIRA loss transforms FH-deficient cells.

Fumarate hydratase (FH) is a mitochondrial enzyme that catalyzes the reversible hydration of fumarate to malate in the tricarboxylic acid (TCA) cycle. Germline mutations of FH lead to hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a cancer syndrome characterized by a highly aggressive form of renal cancer. Although HLRCC tumors metastasize rapidly, FH-deficient mice develop premalignant cysts in the kidneys, rather than carcinomas. How Fh1-deficient cells overcome these tumor-suppressive events during transformation is unknown. Here, we perform a genome-wide CRISPR-Cas9 screen to identify genes that, when ablated, enhance the proliferation of Fh1-deficient cells. We found that the depletion of the histone cell cycle regulator (HIRA) enhances proliferation and invasion of Fh1-deficient cells in vitro and in vivo. Mechanistically, Hira loss activates MYC and its target genes, increasing nucleotide metabolism specifically in Fh1-deficient cells, independent of its histone chaperone activity. These results are instrumental for understanding mechanisms of tumorigenesis in HLRCC and the development of targeted treatments for patients.

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma.

Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths. Barrett's oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the molecular events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin to directly regulate cell cycle genes specifically in OAC cells. This new KLF5 target gene programme has potential prognostic significance as high levels correlate with poorer patient survival. Thus, the repurposing of KLF5 for novel regulatory activity in OAC provides new insights into the mechanisms behind disease progression.

Acid fluids present in the gut can sometimes 'go up' and damage the oesophagus, the pipe that connects the mouth and the stomach. As a result, a small number of individuals can develop Barrett's oesophagus, a condition where cells in the lining of the lower oesophagus show abnormal shapes. In certain patients, these cells then become cancerous, but exactly how this happens is unknown. This lack of understanding contributes to late diagnoses, limited treatment and low survival rates. Many cancers feature 'signature' mutations in a set of genes that controls how a cell can multiply. Yet, in the case of cancers of the lower oesophagus, known genetic changes have had a limited impact on our understanding of the emergence of the disease. Here, Rogerson et al. focused instead on non-genetic changes and studied transcription factors, the proteins that bind to regulatory regions of the DNA to switch genes on and off. A close inspection of cancer cells in the lower oesophagus revealed that, in that state, a transcription factor called KLF5 controls the abnormal activation of genes involved in cell growth. This is linked to the transcription factor adopting a different pattern of binding onto regulatory regions in diseased cells. Crucially, when the cell growth genes regulated by KLF5 are activated, patients have lower survival rates. Further work is now required to examine whether this finding could help to identify patients who are most at risk from developing cancer. More broadly, the results from the work by Rogerson et al. demonstrate how transcription factors can be repurposed in a disease context.

The RUNX Transcriptional Coregulator, CBFß, Suppresses Migration of ER+ Breast Cancer Cells by Repressing ERα-Mediated Expression of the Migratory Factor TFF1.

Core binding factor ß (CBFß), the essential coregulator of RUNX transcription factors, is one of the most frequently mutated genes in estrogen receptor-positive (ER+) breast cancer. Many of these mutations are nonsense mutations and are predicted to result in loss of function, suggesting a tumor suppressor role for CBFß. However, the impact of missense mutations and the loss of CBFß in ER+ breast cancer cells have not been determined. Here we demonstrate that missense mutations in CBFß accumulate near the Runt domain-binding region. These mutations inhibit the ability of CBFß to form CBFß-Runx-DNA complexes. We further show that deletion of CBFß, using CRISPR-Cas9, in ER+ MCF7 cells results in an increase in cell migration. This increase in migration is dependent on the presence of ERα. Analysis of the potential mechanism revealed that the increase in migration is driven by the coregulation of Trefoil factor 1 (TFF1) by CBFß and ERα. RUNX1-CBFß acts to repress ERα-activated expression of TFF1. TFF1 is a motogen that stimulates migration and we show that knockdown of TFF1 in CBFß-/- cells inhibits the migratory phenotype. Our findings reveal a new mechanism by which RUNX1-CBFß and ERα combine to regulate gene expression and a new role for RUNX1-CBFß in the prevention of cell migration by suppressing the expression of the motogen TFF1. IMPLICATIONS: Mutations in CBFß contribute to the development of breast cancer by inducing a metastatic phenotype that is dependent on ER.

Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper.