Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.

CCCTC-binding factor (CTCF) is an insulator protein that binds to a highly conserved DNA motif and facilitates regulation of three-dimensional (3D) nuclear architecture and transcription. CTCF binding sites (CTCF-BSs) reside in non-coding DNA and are frequently mutated in cancer. Our previous study identified a small subclass of CTCF-BSs that are resistant to CTCF knock down, termed persistent CTCF binding sites (P-CTCF-BSs). P-CTCF-BSs show high binding conservation and potentially regulate cell-type constitutive 3D chromatin architecture. Here, using ICGC sequencing data we made the striking observation that P-CTCF-BSs display a highly elevated mutation rate in breast and prostate cancer when compared to all CTCF-BSs. To address whether P-CTCF-BS mutations are also enriched in other cell-types, we developed CTCF-INSITE-a tool utilising machine learning to predict persistence based on genetic and epigenetic features of experimentally-determined P-CTCF-BSs. Notably, predicted P-CTCF-BSs also show a significantly elevated mutational burden in all 12 cancer-types tested. Enrichment was even stronger for P-CTCF-BS mutations with predicted functional impact to CTCF binding and chromatin looping. Using in vitro binding assays we validated that P-CTCF-BS cancer mutations, predicted to be disruptive, indeed reduced CTCF binding. Together this study reveals a new subclass of cancer specific CTCF-BS DNA mutations and provides insights into their importance in genome organization in a pan-cancer setting.

The H2A.Z-nuclesome code in mammals: emerging functions.

H2A.Z is a histone variant that provides specific structural and docking-side properties to the nucleosome, resulting in diverse and specialised molecular and cellular functions. In this review, we discuss the latest studies uncovering new functional aspects of mammalian H2A.Z in gene transcription, including pausing and elongation of RNA polymerase II (RNAPII) and enhancer activity; DNA repair; DNA replication; and 3D chromatin structure. We also review the recently described role of H2A.Z in embryonic development, cell differentiation, neurodevelopment, and brain function. In conclusion, our cumulative knowledge of H2A.Z over the past 40 years, in combination with the implementation of novel molecular technologies, is unravelling an unexpected and complex role of histone variants in gene regulation and disease.

Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma.

Phyllodes tumours (PTs) are rare fibroepithelial lesions of the breast that are classified as benign, borderline, or malignant. As little is known about the molecular underpinnings of PTs, current diagnosis relies on histological examination. However, accurate classification is often difficult, particularly for distinguishing borderline from malignant PTs. Furthermore, PTs can be misdiagnosed as other tumour types with shared histological features, such as fibroadenoma and metaplastic breast cancers. As DNA methylation is a recognised hallmark of many cancers, we hypothesised that DNA methylation could provide novel biomarkers for diagnosis and tumour stratification in PTs, whilst also allowing insight into the molecular aetiology of this otherwise understudied tumour. We generated whole-genome methylation data using the Illumina EPIC microarray in a novel PT cohort (n = 33) and curated methylation microarray data from published datasets including PTs and other potentially histopathologically similar tumours (total n = 817 samples). Analyses revealed that PTs have a unique methylome compared to normal breast tissue and to potentially histopathologically similar tumours (metaplastic breast cancer, fibroadenoma and sarcomas), with PT-specific methylation changes enriched in gene sets involved in KRAS signalling and epithelial-mesenchymal transition. Next, we identified 53 differentially methylated regions (DMRs) (false discovery rate < 0.05) that specifically delineated malignant from non-malignant PTs. The top DMR in both discovery and validation cohorts was hypermethylation at the HSD17B8 CpG island promoter. Matched PT single-cell expression data showed that HSD17B8 had minimal expression in fibroblast (putative tumour) cells. Finally, we created a methylation classifier to distinguish PTs from metaplastic breast cancer samples, where we revealed a likely misdiagnosis for two TCGA metaplastic breast cancer samples. In conclusion, DNA methylation alterations are associated with PT histopathology and hold the potential to improve our understanding of PT molecular aetiology, diagnostics, and risk stratification. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.

BACKGROUND: The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples. RESULTS: We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding. CONCLUSIONS: Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.

Transient exposure to miR-203 enhances the differentiation capacity of established pluripotent stem cells.

Full differentiation potential along with self-renewal capacity is a major property of pluripotent stem cells (PSCs). However, the differentiation capacity frequently decreases during expansion of PSCs in vitro. We show here that transient exposure to a single microRNA, expressed at early stages during normal development, improves the differentiation capacity of already-established murine and human PSCs. Short exposure to miR-203 in PSCs (miPSCs) induces a transient expression of 2C markers that later results in expanded differentiation potency to multiple lineages, as well as improved efficiency in tetraploid complementation and human-mouse interspecies chimerism assays. Mechanistically, these effects are at least partially mediated by direct repression of de novo DNA methyltransferases Dnmt3a and Dnmt3b, leading to transient and reversible erasure of DNA methylation. These data support the use of transient exposure to miR-203 as a versatile method to reset the epigenetic memory in PSCs, and improve their effectiveness in regenerative medicine.

Taxonomy of fibroblasts and progenitors in the synovial joint at single-cell resolution.

OBJECTIVES: Fibroblasts in synovium include fibroblast-like synoviocytes (FLS) in the lining and Thy1+ connective-tissue fibroblasts in the sublining. We aimed to investigate their developmental origin and relationship with adult progenitors. METHODS: To discriminate between Gdf5-lineage cells deriving from the embryonic joint interzone and other Pdgfrα-expressing fibroblasts and progenitors, adult Gdf5-Cre;Tom;Pdgfrα-H2BGFP mice were used and cartilage injury was induced to activate progenitors. Cells were isolated from knees, fibroblasts and progenitors were sorted by fluorescence-activated cell-sorting based on developmental origin, and analysed by single-cell RNA-sequencing. Flow cytometry and immunohistochemistry were used for validation. Clonal-lineage mapping was performed using Gdf5-Cre;Confetti mice. RESULTS: In steady state, Thy1+ sublining fibroblasts were of mixed ontogeny. In contrast, Thy1-Prg4+ lining fibroblasts predominantly derived from the embryonic joint interzone and included Prg4-expressing progenitors distinct from molecularly defined FLS. Clonal-lineage tracing revealed compartmentalisation of Gdf5-lineage fibroblasts between lining and sublining. Following injury, lining hyperplasia resulted from proliferation and differentiation of Prg4-expressing progenitors, with additional recruitment of non-Gdf5-lineage cells, into FLS. Consistent with this, a second population of proliferating cells, enriched near blood vessels in the sublining, supplied activated multipotent cells predicted to give rise to Thy1+ fibroblasts, and to feed into the FLS differentiation trajectory. Transcriptional programmes regulating fibroblast differentiation trajectories were uncovered, identifying Sox5 and Foxo1 as key FLS transcription factors in mice and humans. CONCLUSIONS: Our findings blueprint a cell atlas of mouse synovial fibroblasts and progenitors in healthy and injured knees, and provide novel insights into the cellular and molecular principles governing the organisation and maintenance of adult synovial joints.

Long-term outcomes of pouch surveillance and risk of neoplasia in familial adenomatous polyposis.

BACKGROUND: Long-term pouch surveillance outcomes for familial adenomatous polyposis (FAP) are unknown. We aimed to quantify surveillance outcomes and to determine which of selected possible predictive factors are associated with pouch dysplasia. METHODS: Retrospective analysis of collected data on 249 patients was performed, analyzing potential risk factors for the development of adenomas or advanced lesions ( ≥ 10 mm/high grade dysplasia (HGD)/cancer) in the pouch body and cuff using Cox proportional hazards models. Kaplan-Meier analyses included landmark time-point analyses at 10 years after surgery to predict the future risk of advanced lesions. RESULTS: Of 249 patients, 76 % developed at least one pouch body adenoma, with 16 % developing an advanced pouch body lesion; 18 % developed an advanced cuff lesion. Kaplan-Meier analysis showed a 10-year lag before most advanced lesions developed; cumulative incidence of 2.8 % and 6.4 % at 10 years in the pouch body and cuff, respectively. Landmark analysis suggested the presence of adenomas prior to the 10-year point was associated with subsequent development of advanced lesions in the pouch body (hazard ratio [HR] 4.8, 95 %CI 1.6-14.1; P = 0.004) and cuff (HR 6.8, 95 %CI 2.5-18.3; P < 0.001). There were two HGD and four cancer cases in the cuff and one pouch body cancer; all cases of cancer/HGD that had prior surveillance were preceded by ≥ 10-mm adenomas. CONCLUSIONS: Pouch adenoma progression is slow and most advanced lesions occur after 10 years. HGD and cancer were rare events. Pouch phenotype in the first decade is associated with the future risk of developing advanced lesions and may guide personalized surveillance beyond 10 years.

Tracking Chinese newspaper coverage of elephant ivory through topic modeling.

Mass media worldwide has contributed to increasing awareness of the illegal wildlife trade and its significant impact on wildlife conservation. We used mass media coverage as a proxy for macro-level public opinion to analyze the media framing of elephant ivory in 6394 Chinese newspaper articles published from 2000 to 2021 and thus determine the effects of wildlife policies on public opinion. We focused on 2 events: the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) approval of China as a trading partner in the purchase and import of ivory stockpiles from Africa in July 2008 and the Chinese government's announcement of a domestic ivory ban in December 2016. Using latent Dirichlet allocation topic modeling, we identified 8 topics about elephant ivory and grouped them into 3 frames: ivory arts and culture, ivory crimes, and elephant conservation. Over the last 2 decades, topics related to ivory crimes remained the most prevalent in news articles. Topics about ivory arts and culture showed a significant shift in media salience before and after the 2 events (from 0.44 to 0.19 and from 0.08 to 0.15, respectively, p < 0.05), whereas the other 2 frames did not change significantly. Contrary to popular belief, our results indicated that Chinese macro-level public opinion on ivory had become more negative following the CITES approval of ivory importation and less negative after the ivory ban announcement, at least for certain periods. The relationship between mass media, public opinion, and wildlife trade policies is complex and requires further examination of the sociopolitical dynamics that influence media narratives. Our results showed the value of topic modeling in monitoring and assessing media representations of wildlife issues in the era of big data. Conservationists should remain vigilant of mass media coverage and collaborate with media practitioners to produce comprehensive narratives on wildlife issues if resources permit.

Los medios masivos han contribuido a una mayor conciencia mundial del mercado ilegal de fauna y el impacto significativo que tiene sobre la conservación. Usamos la cobertura de los medios masivos como sustituto de la opinión pública a nivel macro para analizar el encuadre mediático que le dan al marfil 6,394 artículos publicados en periódicos chinos entre el 2000 y 2021 para así determinar los efectos que tienen las políticas de fauna sobre la opinión pública. Nos enfocamos en dos eventos: la autorización que dio la Convención sobre el Comercio Internacional de Especies Amenazadas (CITES) a China como socio comercial en la compra e importación de reservas de marfil desde África en julio de 2008 y la prohibición doméstica de marfil anunciada por el gobierno chino en diciembre de 2016. Usamos el modelado de asignación latente de Dirichlet para identificar ocho temas sobre el marfil y los agrupamos en tres encuadres: arte y cultura del marfil, crimen del marfil y conservación de elefantes. Durante las últimas dos décadas, los temas relacionados con los crímenes del marfil fueron los más prevalentes en los artículos periodísticos. Los temas relacionados al arte y cultura del marfil mostraron un cambio significativo en la relevancia mediática antes y después de los dos eventos (de 0.44 a 0.19 y de 0.08 a 0.15, respectivamente, p<0.05), mientras que los otros dos encuadres no cambiaron significativamente. Contrario a las creencias populares, nuestros resultados indicaron que la opinión pública a nivel macro sobre el marfil en China se ha vuelto más negativa después de la autorización de CITES y menos negativa después de la prohibición del marfil, al menos durante ciertos periodos. La relación entre los medios masivos, la opinión pública y las políticas del comercio de fauna es compleja y requiere un análisis más profundo de las dinámicas sociopolíticas que influyen sobre las narrativas mediáticas. Nuestros resultados muestran el valor del modelado de temas en el monitoreo y evaluación de la representación en medios de los temas sobre fauna en tiempos de los macrodatos. Los conservacionistas deberían permanecer atentos a la cobertura de los medios masivos y colaborar con los profesionales de los medios para producir narraciones completas sobre la fauna si los recursos lo permiten.

Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate.

Whole genome bisulphite sequencing (WGBS) permits the genome-wide study of single molecule methylation patterns. One of the key goals of mammalian cell-type identity studies, in both normal differentiation and disease, is to locate differential methylation patterns across the genome. We discuss the most desirable characteristics for DML (differentially methylated locus) and DMR (differentially methylated region) detection tools in a genome-wide context and choose a set of statistical methods that fully or partially satisfy these considerations to compare for benchmarking. Our data simulation strategy is both biologically informed-employing distribution parameters derived from large-scale consortium datasets-and thorough. We report DML detection ability with respect to coverage, group methylation difference, sample size, variability and covariate size, both marginally and jointly, and exhaustively with respect to parameter combination. We also benchmark these methods on FDR control and computational time. We use this result to backend and introduce an expanded version of DMRcate: an existing DMR detection tool for microarray data that we have extended to now call DMRs from WGBS data. We compare DMRcate to a set of alternative DMR callers using a similarly realistic simulation strategy. We find DMRcate and RADmeth are the best predictors of DMRs, and conclusively find DMRcate the fastest.

ELF5 modulates the estrogen receptor cistrome in breast cancer.

Acquired resistance to endocrine therapy is responsible for half of the therapeutic failures in the treatment of breast cancer. Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight into the mechanisms by which ELF5 modulates estrogen sensitivity. Using chromatin immunoprecipitation sequencing we found that ELF5 binding overlapped with FOXA1 and ER at super enhancers, enhancers and promoters, and when elevated, caused FOXA1 and ER to bind to new regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy. RNA sequencing demonstrated that these changes altered estrogen-driven patterns of gene expression, the expression of ER transcription-complex members, and 6 genes known to be involved in driving the acquisition of endocrine resistance. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, and proximity ligation assays, we found that ELF5 interacted physically with members of the ER transcription complex, such as DNA-PKcs. We found 2 cases of endocrine-resistant brain metastases where ELF5 levels were greatly increased and ELF5 patterns of gene expression were enriched, compared to the matched primary tumour. Thus ELF5 alters ER-driven gene expression by modulating the ER/FOXA1 cistrome, by interacting with it, and by modulating the expression of members of the ER transcriptional complex, providing multiple mechanisms by which ELF5 can drive endocrine resistance.

MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection.

SUMMARY: DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of an epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualization and remotely sharing data with collaborators and clinicians. AVAILABILITYAND IMPLEMENTATION: MethPanel is freely available at https://github.com/thinhong/MethPanel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Targeting the IL-6-Yap-Snail signalling axis in synovial fibroblasts ameliorates inflammatory arthritis.

OBJECTIVE: We aimed to understand the role of the transcriptional co-factor Yes-associated protein (Yap) in the molecular pathway underpinning the pathogenic transformation of synovial fibroblasts (SF) in rheumatoid arthritis (RA) to become invasive and cause joint destruction. METHODS: Synovium from patients with RA and mice with antigen-induced arthritis (AIA) was analysed by immunostaining and qRT-PCR. SF were targeted using Pdgfrα-CreER and Gdf5-Cre mice, crossed with fluorescent reporters for cell tracing and Yap-flox mice for conditional Yap ablation. Fibroblast phenotypes were analysed by flow cytometry, and arthritis severity was assessed by histology. Yap activation was detected using Yap-Tead reporter cells and Yap-Snail interaction by proximity ligation assay. SF invasiveness was analysed using matrigel-coated transwells. RESULTS: Yap, its binding partner Snail and downstream target connective tissue growth factor were upregulated in hyperplastic human RA and in mouse AIA synovium, with Yap detected in SF but not macrophages. Lineage tracing showed polyclonal expansion of Pdgfrα-expressing SF during AIA, with predominant expansion of the Gdf5-lineage SF subpopulation descending from the embryonic joint interzone. Gdf5-lineage SF showed increased expression of Yap and adopted an erosive phenotype (podoplanin+Thy-1 cell surface antigen-), invading cartilage and bone. Conditional ablation of Yap in Gdf5-lineage cells or Pdgfrα-expressing fibroblasts ameliorated AIA. Interleukin (IL)-6, but not tumour necrosis factor alpha (TNF-α) or IL-1ß, Jak-dependently activated Yap and induced Yap-Snail interaction. SF invasiveness induced by IL-6 stimulation or Snail overexpression was prevented by Yap knockdown, showing a critical role for Yap in SF transformation in RA. CONCLUSIONS: Our findings uncover the IL-6-Yap-Snail signalling axis in pathogenic SF in inflammatory arthritis.

Attenuated Familial Adenomatous Polyposis: A Phenotypic Diagnosis but Obsolete Term?

BACKGROUND: Attenuated familial adenomatous polyposis is characterised by low number (≤100) and delayed development of colorectal adenomas. Various definitions have been used, and genotype-phenotype correlations have been suggested. OBJECTIVE: We aimed to evaluate phenotypic and genotypic correlation in patients with presumed attenuated familial adenomatous polyposis and assess familial variability. DESIGN: This is a retrospective study. SETTINGS: This study was conducted at a tertiary polyposis registry. PATIENTS: Individuals with attenuated familial adenomatous polyposis were identified. Phenotypic group was defined as 100 or fewer adenomas at age 25 years and genotypic group was defined as a variant in the adenomatous polyposis coli region associated with attenuated familial adenomatous polyposis. Pathology polyp count was used for patients who had undergone surgery and endoscopic polyp count for those with intact colon. MAIN OUTCOME MEASURES: We evaluated phenotypic and genotypic correlation in patients with presumed attenuated familial adenomatous polyposis and familial variability. RESULTS: A total of 69 patients were identified in the phenotypic group, of whom 54 (78%) had a pathogenic variant in the attenuated regions of the adenomatous polyposis coli gene. Forty-eight (70%) had intact colon (median age at last colonoscopy 43 [25-73] years; median endoscopic polyp count 20 [0-100]) and 21 (30%) had undergone colectomy (median age at surgery 45 [25-54] years; median pathology polyp count 43 [3-100]). Eighty-three patients were identified in the genotypic group of which 54 (65%) had attenuated phenotype. Inter- and intrafamilial variability were observed. LIMITATIONS: This study was limited by its retrospective nature and single-center experience. CONCLUSION: Phenotype in familial adenomatous polyposis lies on a spectrum and is determined in part by genotype and age at adenoma count. Diagnosis of attenuated familial adenomatous polyposis should be based on phenotype; genotype is not a reliable indicator. Management should be personalized according to the phenotype of each individual. See Video Abstract at http://links.lww.com/DCR/B775. POLIPOSIS ADENOMATOSA FAMILIAR ATENUADA UN DIAGNSTICO FENOTPICO PERO TRMINO OBSOLETO: ANTECEDENTES:La poliposis adenomatosa familiar atenuada se caracteriza por un número bajo (≤100) y desarrollo retardado de adenomas colorrectales. Se han utilizado varias definiciones y se han sugerido correlaciones genotipo-fenotipo.OBJETIVO:Nuestro objetivo es evaluar la correlación fenotípica y genotípica en pacientes con presunta poliposis adenomatosa familiar atenuada y evaluar la variabilidad familiar.DISEÑO:Este es un estudio retrospectivo.AJUSTE:Este estudio se realizó en un registro terciario de poliposis.PACIENTES:Se identificaron individuos con poliposis adenomatosa familiar atenuada. El grupo fenotípico se definió como ≤100 adenomas a la edad de 25 años y el grupo genotípico se definió como una variante en la región de poliposis coli adenomatosa asociada con poliposis adenomatosa familiar atenuada. Se utilizó el recuento de pólipos en patología para los pacientes que se habían sometido a cirugía y el recuento de pólipos endoscópico para los que tenían el colon intacto.PRINCIPALES MEDIDAS DE RESULTADO:Evaluamos la correlación fenotípica y genotípica en pacientes con presunta poliposis adenomatosa familiar atenuada y variabilidad familiar.RESULTADOS:Un total de 69 pacientes se identificaron en el grupo fenotípico de los cuales 54 (78%) tenían una variante patogénica en las regiones atenuadas del gen de la poliposis coli adenomatosa. Cuarenta y ocho (70%) tenían colon intacto (edad media en la última colonoscopia 43 [25-73] años; mediana del recuento de pólipos endoscópicos 20 [0-100]) y 21 (30%) se habían sometido a colectomía (edad edia en el momento de la cirugía 45 [25-54] años; mediana del recuento de pólipos patológicos 43 [3-100]). Se identificaron 83 pacientes en el grupo genotípico de los cuales 54 (65%) tenían fenotipo atenuado. Se observó variabilidad inter e intrafamiliar.LIMITACIONES:Este estudio estuvo limitado por su naturaleza retrospectiva y la experiencia de un solo centro.CONCLUSIÓNES:El fenotipo en la poliposis adenomatosa familiar se encuentra en un espectro, determinado en parte por el genotipo y la edad en el momento del recuento de adenomas. El diagnóstico de poliposis adenomatosa familiar atenuada debe basarse en el fenotipo; el genotipo no es un indicador confiable. El manejo debe personalizarse según el fenotipo de cada individuo. Consulte Video Resumen en http://links.lww.com/DCR/B775.

Regular endoscopic surveillance and polypectomy is effective in managing rectal adenoma progression following colectomy and ileorectal anastomosis in patients with familial adenomatous polyposis.

AIM: Total colectomy with ileorectal anastomosis (TC-IRA) is a surgical option for patients with familial adenomatous polyposis (FAP). Regular endoscopic surveillance of the rectum is recommended to prevent rectal cancer. We aimed to document polyp progression in the rectum following TC-IRA and evaluate the role of polypectomy during surveillance. METHOD: Patients with FAP who underwent TC-IRA between 1990 and 2017 were identified. Demographic, endoscopic and genetic data were retrieved. Cumulative rectal adenoma (polyp) counts were obtained, whilst accounting for any polypectomies during the study period. The rate of polyp progression and factors influencing secondary proctectomy were evaluated. RESULTS: One hundred and ninety-nine patients fulfilled our inclusion criteria, of which 44% were male. The median age at colectomy was 19 (range 11-70) years and median preoperative rectal polyp count was 7 (range 0-50). All patients had an APC pathogenic variant, of which 151 (79%) were 5' of the mutation cluster region (MCR), 19 (10%) in the MCR, six (3%) were 3' of the MCR and 15 (8%) had a gross deletion. After a median follow-up of 8.6 (range1-27) years and a median of 11 (range 2-37) flexible sigmoidoscopies per patient, the median rate of polyp progression was 5.5 polyps/year (range 0-70.2). There was no evidence of polyp regression. Eight (4%) patients underwent secondary proctectomy for neoplasia, of which one (0.5%) had rectal adenocarcinoma. A total of 13,527 polyps were removed, a median of 35 polyps/patient (range 0-829). The rate of polyp progression was not significantly associated with genotypic or phenotypic factors. CONCLUSION: Progression of rectal adenoma burden following TC-IRA appears to be slow and dependent on the length of follow-up. In the modern era of stringent endoscopic surveillance and therapeutic procedures such as cold snare polypectomy, the rate of secondary proctectomy and the risk of rectal cancer after TC-IRA are very low. These findings are important when counselling patients with regard to the choice of surgery for FAP and implementing endoscopic surveillance.

Macrophage development and activation involve coordinated intron retention in key inflammatory regulators.

Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response.

Enduring epigenetic landmarks define the cancer microenvironment.

The growth and progression of solid tumors involves dynamic cross-talk between cancer epithelium and the surrounding microenvironment. To date, molecular profiling has largely been restricted to the epithelial component of tumors; therefore, features underpinning the persistent protumorigenic phenotype of the tumor microenvironment are unknown. Using whole-genome bisulfite sequencing, we show for the first time that cancer-associated fibroblasts (CAFs) from localized prostate cancer display remarkably distinct and enduring genome-wide changes in DNA methylation, significantly at enhancers and promoters, compared to nonmalignant prostate fibroblasts (NPFs). Differentially methylated regions associated with changes in gene expression have cancer-related functions and accurately distinguish CAFs from NPFs. Remarkably, a subset of changes is shared with prostate cancer epithelial cells, revealing the new concept of tumor-specific epigenome modifications in the tumor and its microenvironment. The distinct methylome of CAFs provides a novel epigenetic hallmark of the cancer microenvironment and promises new biomarkers to improve interpretation of diagnostic samples.

Gastric adenomas and their management in familial adenomatous polyposis.

BACKGROUND: Patients with familial adenomatous polyposis (FAP) are at increased risk of developing gastric adenomas. There is limited understanding of their clinical course and no consensus on management. We reviewed the management of gastric adenomas in patients with FAP from two centers. METHODS: Patients with FAP and histologically confirmed gastric adenomas were identified between 1997 and 2018. Patient demographics, adenoma characteristics, and management/surveillance outcomes were collected. RESULTS: Of 726 patients with FAP, 104 (14 %; 49 female) were diagnosed with gastric adenomas at a median age of 47 years (range 19 - 80). The median size of gastric adenomas was 6 mm (range 1.5 - 50); 64 (62 %) patients had adenomas located distally to the incisura. Five patients (5 %) had gastric adenomas demonstrating high-grade dysplasia (HGD) on initial diagnosis, distributed equally within the stomach. The risk of HGD was associated with adenoma size (P = 0.04). Of adenomas > 20 mm, 33 % contained HGD. Two patients had gastric cancer at initial gastric adenoma diagnosis. A total of 63 patients (61 %) underwent endoscopic therapy for gastric adenomas. Complications occurred in three patients (5 %) and two (3 %) had recurrence, all following piecemeal resection of large (30 - 50 mm) lesions. Three patients were diagnosed with gastric cancer at median follow-up of 66 months (range 66 - 115) after initial diagnosis. CONCLUSIONS: We observed gastric adenomas in 14 % of patients with FAP. Of these, 5 % contained HGD; risk of HGD correlated with adenoma size. Endoscopic resection was feasible, with few complications and low recurrence rates, but did not completely eliminate the cancer risk.

Implications for the colorectal surgeon following the 100 000 Genomes Project.

AIM: The 100 000 Genomes Project was completed in 2019 with the objective of integrating genomic medicine into routine National Health Service (NHS) clinical pathways. This project and genomic research will revolutionize the way we practice colorectal surgery in the 21st century. This paper aims to provide an overview of genomic medicine and its implications for the colorectal surgeon. RESULTS: Within NHS England, consolidation has created seven regional Genomic Laboratory Hubs. DNA from solid tumours, including colorectal cancers, will be assessed using 500-gene panels, results will be fed back to Genome Tumour Advisory Boards. Identifying variants from biopsies earlier in the clinical pathway may alter surgical and other treatment options for patients. However, there is an important distinction between somatic variants within a tumour biopsy and germline variants that may suggest a heritable condition such as Lynch syndrome. Novel drugs, for example immunotherapy, will increase treatment options including downstaging cancers and changing the surgical approach. The use of circulating tumour DNA (liquid biopsies) will have applications in diagnosis, treatment and surveillance of cancer. There are many exciting potential future applications of this technology for offering personalized medicine that will require multidisciplinary working and the colorectal community. CONCLUSION: There are many challenges but also exciting opportunities to embed new 'omic' technologies and innovation into 21st century colorectal surgery. The next phase for the colorectal community is how we engage with this change, with questions around training, identification of genomic multidisciplinary team (MDT) champions and how we collaborate with the core members of the MDT, clinical geneticists and national genomic testing.

MRI-enema for the assessment of pelvic intestinal anastomotic integrity.

AIM: Anastomotic leak causes significant morbidity for patients undergoing pelvic intestinal surgery. Fluoroscopic assessment of anastomotic integrity using water-soluble contrast enema (WSCE) is of questionable benefit over examination alone. We hypothesized that MRI-enema may be more accurate. The aim of this study was to compare MRI-enema with fluoroscopic WSCE. METHOD: Patients referred for WSCE with pelvic intestinal anastomosis and defunctioning ileostomy (including patients with suspected or known leaks) were invited to participate. WSCE and MRI-enema were undertaken within 48 h of each other. MRI sequences were performed before, during and immediately after the introduction of 400 ml of 1% gadolinium contrast solution per anus. MRI examinations were reported to protocol by two blinded gastrointestinal radiologists. A Likert-scale patient questionnaire was administered to compare patient experience. Follow-up was >12 months after ileostomy reversal. Anastomotic leak was determined by unblinded consensus of examination and radiological findings. RESULTS: Sixteen patients were recruited, with a median age of 39 years (range 22-69). Ten were men, 11 had ileoanal pouch formation and five had low anterior resection. Five patients had anastomotic leak identified by MRI and four by WSCE. The radial location of the anastomotic defect was identified in all five patients by MRI versus two on WSCE. MRI revealed additional information including contents of a widened presacral space. Patient experience was equivalent. Eleven patients eventually had ileostomy reversal without complications. CONCLUSION: MRI-enema is a feasible and tolerable alternative to WSCE and offers greater anatomical detail in the context of pelvic intestinal anastomotic leak. Larger prospective studies are required to define its potential role in the UK National Health Service.

The pouch behaving badly: management of morbidity after ileal pouch-anal anastomosis.

AIM: Ileal pouch-anal anastomosis (IPAA), or a 'pouch', allows restoration of intestinal continuity after proctocolectomy for ulcerative colitis or familial adenomatous polyposis. Most patients have a good long-term outcome after IPAA, but in a significant proportion the functional outcome and quality of life are unsatisfactory. We term this outcome 'the pouch behaving badly'. Managing this, especially one is when unfamiliar with the possible underlying pathologies, is a challenge for both patient and clinician. We aim to outline the clinical approach to the pouch behaving badly, highlighting key aspects of investigation and management. METHOD: This is a narrative review of the literature covering the investigation and management of postoperative complications and morbidity after IPAA. RESULTS: Management of the pouch behaving badly requires a careful clinical assessment. The patient may present with multiple symptoms and a clear picture of the symptomatology and past history should be constructed before thorough examination and specialist investigation. We divide the pathology that underlies this clinical scenario into surgical, inflammatory, mechanical, functional and dysplastic causes and outline the investigation and management of each one. CONCLUSION: The pouch behaving badly is a challenging problem for both patient and clinician. A detailed clinical assessment with careful specialist investigation is key to diagnosing the underlying pathology. We stress the importance of patient-centred care - the aim is to improve quality of life.