Colorectal cancer is initiated by loss of APC, which drives expansion of LGR5+ intestinal stem cell (ISC) populations. Whilst LGR5 + ISC expansion is a critical step for tumour initiation and progression, its regulation is poorly understood. Emerging evidence suggests post-transcriptional RNA modifications play a key role in cancer biology, but their role in CRC initiation has not been explored. Here, we identify the m5C methyltransferase NSUN2 as a key regulator of ISC expansion and intestinal tumourigenesis. NSUN2 is upregulated in multiple CRC mouse models and human tumours, and its depletion impairs ISC expansion and hyperproliferation, leading to reduced tumour initiation. Transcriptome-wide bisulfite sequencing revealed that NSUN2 mediates m5C methylation on mRNAs encoding key ISC regulators and components of the MAPK/ERK pathway. Mechanistically, loss of NSUN2 reduces ERK phosphorylation in Apc-deficient models, and oncogenic KrasG12D expression is sufficient to restore ERK signalling and rescue ISC expansion. Together, this establishes a novel role for NSUN2 as a key regulator of ISC-driven CRC initiation and describes a critical molecular mechanism linking m5C methylation to MAPK-driven stem cell transformation.

Bone marrow adipose tissue is a distinct adipose subtype comprising more than 10% of fat mass in healthy humans. However, the functions and pathophysiological correlates of this tissue are unclear, and its genetic determinants remain unknown. Here, we use deep learning to measure bone marrow adiposity in the femoral head, total hip, femoral diaphysis, and spine from MRI scans of approximately 47,000 UK Biobank participants, including over 41,000 white and over 6300 non-white participants. We then establish the heritability and genome-wide significant associations for bone marrow adiposity at each site. Our meta-GWAS in the white population finds 67, 147, 134, and 174 independent significant single nucleotide polymorphisms, which map to 54, 90, 43, and 100 genes for the femoral head, total hip, femoral diaphysis, and spine, respectively. Transcriptome-wide association studies, colocalization analyses, and sex-stratified meta-GWASes in the white participants further resolve functional and sex-specific genes associated with bone marrow adiposity at each site. Finally, we perform a multi-ancestry meta-GWAS to identify genes associated with bone marrow adiposity across the different bone regions and across ancestry groups. Our findings provide insights into BMAT formation and function and provide a basis to study the impact of BMAT on human health and disease.

By integrating findings from large-scale omics analyses with experimental tests, this study aims to decipher susceptibility genes and the underlying biological mechanisms involved in the development of colorectal cancer (CRC). We first conducted a trans-ancestry transcriptome-wide association study (TWAS) among 57,402 CRC cases and 119,110 controls, aiming to examine how altered gene expression influences CRC risk in European and Asian populations. Then, functional experiments in (i) CRC cell lines and (ii) tumor xenografts were conducted to examine potential underlying mechanisms involved in colorectal carcinogenesis. Further, a drug sensitivity test was employed to explore possible clinical implications for CRC treatment. The TWAS identified 67 genes highly associated with CRC risk, 23 of which were novel findings. Functional annotation of variants within TWAS-identified loci revealed that the majority (93.6%) showed evidence of transcriptional regulatory mechanisms via proximal promoter or distal enhancer-promoter interactions. Among the identified susceptibility genes, splicing factor 3a subunit 3 (SF3A3) may act as an oncogene on the basis that overexpression of this gene was significantly associated with increased risk of CRC (P = 5.75 × 10−11). Further cell and animal experiments confirmed that SF3A3 plays an oncogenic role in CRC development, and the underlying biological mechanism is likely to be related to its anti-apoptosis effect. The drug sensitivity test suggested that phenethyl isothiocyanate (PEITC) targeting SF3A3 can inhibit CRC progression. This study identified novel CRC susceptibility genes and potential biological mechanisms of SF3A3 involved in CRC development, providing important insight into the etiology and potential leads to the treatment of CRC.

Table S5 shows the SNPs for adenoma and polyps.

Table S3 shows the SNPs that associated with six gut microbial metabolites.

Table S9 shows the reverse MR analyses of colorectal cancer, adenoma and polyps with the abundance of nine gut microbiota.

Table S2 shows the SNPs that associated with nine microbiota taxa (P<1×10-5).

Table S8 shows the forward MR analyses of the six gut microbial metabolites with the risk of colorectal cancer.

Table S1 shows the SNPs that associated with 24 microbiota taxa in MiBioGen (P<5×10-8).

Table S7 shows the forward MR analyses of nine gut microbiota with the risk of colorectal cancer.

Table S4 shows the SNPs for colorectal cancer.

BACKGROUND:Colorectal (CRC) cancer is becoming a disease of the elderly. Ageing is the most significant risk factor for presenting CRC. Early diagnosis of CRC and management is the best way in achieving good outcomes and longer survival but patients aged ≥75 years are usually not screened for CRC. This group of patients is often required to be managed when they are symptomatic in the emergency setting with high morbidity and mortality rates. Our main aim is to provide clinical data about the management of elderly patients presenting complicated colorectal cancer who required emergency surgical management to improve their care.METHODS:The management of complicated COlorectal cancer in OLDER patients (CO-OLDER; ClinicalTrials.gov ID: NCT05788224; evaluated by the local ethical committee CPP EST III-France with the national number 2023-A01094-41) in the emergency setting project provides carrying out an observational multicenter international cohort study aimed to collect data about patients aged ≥75 years to assess modifiable risk factors for negative outcomes and mortality correlated to the emergency surgical management of this group of patients at risk admitted with a complicated (obstructed and perforated) CRC. The CO-OLDER protocol was approved by Institutional Review Board and released. Each CO-OLDER collaborator is asked to enroll ≥25 patients over a study period from 1st January 2018 to 30th October 2023. Data will be analyzed comparing two periods of study: before and after the COVID-19 pandemic. A sample size of 240 prospectively enrolled patients with obstructed colorectal cancer in a 5-month period was calculated. The secured database for entering anonymized data will be available for the period necessary to achieve the highest possible participation.RESULTS:One hundred eighty hospitals asked to be a CO-OLDER collaborator, with 36 potentially involved countries over the world.CONCLUSIONS:The CO-OLDER project aims to improve the management of elderly people presenting with a complicated colorectal cancer in the emergency setting. Our observational global study can provide valuable data on the effectiveness of different management strategies in improving primary assessment, management and outcomes for elderly patients with obstructed or perforated colorectal cancer in the emergency setting, guiding clinical decision-making. This information can help healthcare providers make informed decisions about the best course of action for these patients.

Variation in outcomes definitions and reporting limit the utility of clinical trial results. The Core Outcome Research Measures in Anal Cancer (CORMAC) project developed a core outcome set (COS) for chemoradiotherapy trials for anal squamous cell carcinoma (ASCC) through an international healthcare professional and patient consensus process. The CORMAC-COS comprises 19 outcomes across 4 domains (disease activity, survival, toxicity, life impact). In CORMAC-2 we have established standardised definitions for the 11 disease activity and survival outcomes in the CORMAC COS. Definitions were agreed through a 3 step process, initially identifying existing definitions through systematic review (registered with PROSPERO, CRD42016036540), using these to populate a two-round Delphi questionnaire completed by 51 experts from 13 countries, and finally ratification through an online consensus meeting. Standardising the definitions for these core outcomes facilitates real world utilisation of the CORMAC-COS, thereby increasing the quality of data available for clinical decision-making and ultimately enhancing patient care.

BACKGROUND:To investigate the association between circulating 25-hydroxyvitamin D (25-OHD) and colorectal cancer (CRC) survival outcomes. METHODS:We conducted analyses among the Study of Colorectal Cancer in Scotland (SOCCS) and the UK Biobank (UKBB). Both cancer-specific survival (CSS) and overall survival (OS) outcomes were examined. The 25-OHD levels were categorised into three groups, and multi-variable Cox-proportional hazard models were applied to estimate hazard ratios (HRs). We performed individual-level Mendelian randomisation (MR) through the generated polygenic risk scores (PRS) of 25-OHD and summary-level MR using the inverse-variance weighted (IVW) method. RESULTS:We observed significantly poorer CSS (HR = 0.65,95%CI = 0.55-0.76,P = 1.03 × 10-7) and OS (HR = 0.66,95%CI = 0.58-0.75,P = 8.15 × 10-11) in patients with the lowest compared to those with the highest 25-OHD after adjusting for covariates. These associations remained across patients with varied tumour sites and stages. However, we found no significant association between 25-OHD PRS and either CSS (HR = 0.98,95%CI = 0.80-1.19,P = 0.83) or OS (HR = 1.07,95%CI = 0.91-1.25,P = 0.42). Furthermore, we found no evidence for causal effects by conducting summary-level MR analysis for either CSS (IVW:HR = 1.04,95%CI = 0.85-1.28,P = 0.70) or OS (IVW:HR = 1.10,95%CI = 0.93-1.31,P = 0.25). CONCLUSION:This study supports the observed association between lower circulating 25-OHD and poorer survival outcomes for CRC patients. Whilst the genotype-specific association between better outcomes and higher 25-OHD is intriguing, we found no support for causality using MR approaches.

BACKGROUND:We aimed to identify plasma and urinary metabolites related to colorectal cancer (CRC) risk and elucidate their mediator role in the associations between modifiable risk factors and CRC. METHODS:Metabolite quantitative trait loci were derived from 2 published metabolomics genome-wide association studies, and summary-level data were extracted for 651 plasma metabolites and 208 urinary metabolites. Genetic associations with CRC were obtained from a large-scale genome-wide association study meta-analysis (100 204 cases, 154 587 controls) and the FinnGen cohort (4957 cases, 304 197 controls). Mendelian randomization and colocalization analyses were performed to evaluate the causal roles of metabolites in CRC. Druggability evaluation was employed to prioritize potential therapeutic targets. Multivariable Mendelian randomization and mediation estimation were conducted to elucidate the mediating effects of metabolites on the associations between modifiable risk factors and CRC. RESULTS:The study identified 30 plasma metabolites and 4 urinary metabolites for CRC. Plasma sphingomyelin and urinary lactose, which were positively associated with CRC risk, could be modulated by drug interventions (ie, olipudase alfa, tilactase). Thirteen modifiable risk factors were associated with 9 metabolites, and 8 of these modifiable risk factors were associated with CRC risk. These 9 metabolites mediated the effect of modifiable risk factors (Actinobacteria, body mass index, waist to hip ratio, fasting insulin, smoking initiation) on CRC. CONCLUSION:This study identified key metabolite biomarkers associated with CRC and elucidated their mediator roles in the associations between modifiable risk factors and CRC. These findings provide new insights into the etiology and potential therapeutic targets for CRC and the etiological pathways of modifiable environmental factors with CRC.

BackgroundCommon genetic variation at 11q23.1 is associated with colorectal cancer (CRC) risk, exerting local expression quantitative trait locus (cis-eQTL) effects onPOU2AF2,COLCA1andPOU2AF3genes. However, complex linkage disequilibrium and correlated expression has hindered elucidation of the mechanisms by which genetic variants impart underlying CRC risk.ObjectiveUndertake an interdisciplinary approach to understand how variation at 11q23.1 locus imparts CRC risk.DesignWe employ analysis of RNA sequencing, single-cell RNA sequencing, chromatin immunoprecipitation sequencing and single-cell ATAC sequencing data to identify, prioritise and characterise the genes that contribute to CRC risk. We further validate these findings using mouse models and demonstrate parallel effects in human colonic mucosa.ResultsWe establish rs3087967 as a prime eQTL variant at 11q23.1, colocalising with CRC risk. Furthermore, rs3087967 influences expression of 21 distant genes, thereby acting as a trans-eQTL hub for a gene-set highly enriched for tuft cell markers. Epigenomic analysis implicates POU2AF2 as controlling the tuft cell-specific trans-genes, through POU2F3-correlated genomic regulation. Immunofluorescence confirms rs3087967 risk genotype (T) to be associated with a tuft cell deficit in the human colon. CRISPR-mediated deletion of the 11q23.1 risk locus genes in the mouse germline exacerbated theApcMin/+mouse phenotype on abrogation ofPou2af2expression specifically.ConclusionWe demonstrate that genotype at rs3087967 controls a portfolio of genes through misregulation ofPOU2AF2. POU2AF2is the primary transcriptional activator of tuft cells with a tumour suppressive role in mouse models. We therefore implicate tuft cells as having a key tumour-protective role in the large bowel epithelium.

Abstract Introduction Approximately 20,000 people in the UK undergo stoma formation annually(1), with 20% being emergency procedures(2). The reversal rate for these stomas is widely variable, with restoration of continuity being reported in 33-70% of patients(3). Previous research in the elective setting has demonstrated that delayed reversal leads to increased complications and reduced quality of life, but there is a lack of evidence in the emergency cohort. Aim To describe post-operative outcomes of stoma reversal after emergency formation, and to determine whether those reversed within a ‘standard’ timeframe have better outcomes than those with ‘delayed’ reversal. Methods A retrospective review of a prospectively maintained national emergency laparotomy database (ELLSA) from 4 hospitals over a 3-year period (Dec ’19 - ’22) was performed in Dec ’23. All patients undergoing stoma reversal by time of follow-up were included. Those reversed within 18 months of index procedure were classified as ‘standard’. Results 455 patients were identified (Median follow-up 31 months), 95 of whom had died and 34 had a pre-existing permanent stoma. Of the remaining 326, 34.4% underwent reversal (Median age 59; median time to reversal 458 days; 55% ileostomies). 56% of those underwent ‘standard’ reversal (62% ileostomies, p=0.08), and had reduced length of stay (6 days v 7 days, p=0.041) and reduced post-operative ileus rates (23.8% v 44.9%,p=0.019) than those undergoing ‘delayed’ reversal. Conclusion The majority of stomas formed in the emergency setting remain permanent. Prompt reversal of an emergency stoma should be undertaken to reduce complication profile and length of stay. Further work to identify risk factors associated with non-reversal should be undertaken.

Abstract Aims This study aimed to deepen understanding of the psychosocial impacts of adverse events on general surgical trainees and evaluate the experiences of current support mechanisms. Methods The study was conducted in two parts: a scoping review and a qualitative focus group study. The scoping review was conducted in accordance with the PRISMA-ScR guidelines and JBI methodology. These themes were taken forward for extended discussion as part of a focus group study of general surgical trainees (n = 10; split in two discrete groups of five participants). Reflexive thematic analysis using anonymised transcripts and contemporary field notes were used to analyse the data. Results The scoping review identified six themes related to the impact of adverse events on surgeons' well-being and professional performance. These were clarified and elaborated on through qualitative analysis of focus group data, developing three key themes with associated subthemes: (1) Support structures and external factors influencing responses to adverse events, (2) impact on clinical practice and professional development and (3) methods of learning from adverse events. Surgical trainees experience significant emotional and professional repercussions in the aftermath of adverse events, often exacerbated by insufficient formal support and a prevalent blame culture within hospital environments. Conclusions Substantial deficiencies exist in the support structures available to surgical trainees dealing with adverse events. It is evident that the existing systems fail to adequately address the complex needs of trainees, leading to significant emotional distress and professional insecurity. System changes are necessary for surgical trainees, including the establishment of mentorship and peer support networks.

Background It is known that gene- and disease-specific evidence domains can potentially improve the capability of the ACMG/AMP classification criteria to categorize pathogenicity for variants. We aimed to include gene–disease-specific clinical, predictive, and functional domain specifications to the ACMG/AMP criteria with respect to MMR genes. Methods Starting with the original criteria (InSiGHT criteria) developed by the InSiGHT Variant Interpretation Committee, we systematically addressed specifications to the ACMG/AMP criteria to enable more comprehensive pathogenicity assessment within the ClinGen VCEP framework, resulting in an MMR gene-specific ACMG/AMP criteria. Results A total of 19 criteria were specified, 9 were considered not applicable and there were 35 variations of strength of the evidence. A pilot set of 48 variants was tested using the new MMR gene-specific ACMG/AMP criteria. Most variants remained unaltered, as compared to the previous InSiGHT criteria; however, an additional four variants of uncertain significance were reclassified to P/LP or LB by the MMR gene-specific ACMG/AMP criteria framework. Conclusion The MMR gene-specific ACMG/AMP criteria have proven feasible for implementation, are consistent with the original InSiGHT criteria, and enable additional combinations of evidence for variant classification. This study provides a strong foundation for implementing gene–disease-specific knowledge and experience, and could also hold immense potential in a clinical setting. ### Competing Interest Statement Becky Milewski previously had a role with the pilot variant classification efforts in 2020/2021. She was previously an employee of GeneDx, LLC. Lauren Currie is an employee of GeneDx, LLC Ester Borras is an employee and shareholder of Invitae Corporation. John Paul Plazzer has previously consulted as curator for an external diagnostic testing company. ### Funding Statement JPP was supported by the Alan Watt and Chris Geyer Oncology Fellowship through The Royal Melbourne Hospital Foundation and NIH PA-18-591 Administrative Supplements to Promote Data Sharing in Cancer Epidemiology Studies. ABS was supported by NHMRC Funding (APP1104808). Grant funding for MKC: Cancer Council NSW, RG19-1. In Spain, this study has been partially funded by Ministerio de Ciencia e Innovacion, which is part of Agencia Estatal de Investigacion (AEI), through the Retos Investigacion grant, number PID2019-111254RB-I00, and La Marato de TV3 (202028-30). We also thank CERCA Programme / Generalitat de Catalunya for institutional support. MG was supported by Italian Ministry of Health RC 2022. KA and GY was supported by Japan Agency Medical Research and Development (AMED) under grant JP 18kk0205004, JSPS KAKENHI Grant Number JP18K07339 and JP22K07266. We would like to thank Ms. Lubaina Koti for editing the manuscript for language, structure, and accuracy. We acknowledge Marissa Rose for analysis of an early draft of the criteria. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Data is available in published literature (Pubmed IDs are provided in the databases listed here) or online open-access databases including: ClinVar , LOVD , and InSiGHT classification websites: [https://www.insight-database.org/classifications/mmr\_integrative\_eval.html][1] and Curated evidence will be available on I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Variant classifications are published in ClinVar () and curated evidence is available on the ClinGen Evidence Repository (). * ACMG : American College of Medical Genetics and Genomics AMP : Association for Molecular Pathology B : Benign BA : Benign Stand-Alone BS : Benign Strong BP : Benign Supporting ClinGen : Clinical Genome Resource CMMRD : constitutional mismatch repair deficiency GI : gastrointestinal gnomAD : Genome Aggregation Database FDA : Food and Drug Administration (United States) HCI : Huntsman Cancer Institute HGVS : Human Genome Variation Society IARC : International Agency for Research on Cancer IHC : immunohistochemistry InSiGHT : International Society for Gastrointestinal Hereditary Tumours IVS : intervening sequence (intron) LB : likely benign LP : likely pathogenic LOVD : Leiden Open Variation Database LS : Lynch syndrome MANE : matched annotation from National Center for Biotechnology Information and European Molecular Biology Laboratory and European Bioinformatics Institute MMR : mismatch repair (genes) MSI : microsatellite instability NGS : next generation sequencing NMD : nonsense–mediated mRNA decay P : Pathogenic PVS : Pathogenic Very Strong PS : Pathogenic Strong PM : Pathogenic Moderate PP : Pathogenic Supporting SVI WG : Sequence Variant Interpretation Working Group VCEP : variant curation expert panel VUS : variant of uncertain significance [1]: https://www.insight-database.org/classifications/mmr_integrative_eval.html

Purpose: The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. Methods: Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene -specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. Results: The APC-specific criteria represented gene- and disease -informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). Conclusion: The APC-specific ACMG/AMP criteria preserved the classification of wellcharacterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use. (c) 2023 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY -NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).