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When colorectal cancer (CRC) metastasizes, this is mostly to the liver via the portal circulation. In addition, 10-25 % of CRC patients eventually show metastases in the peritoneum. A selection of these patients is treated with cytoreductive surgery (CRS) and hyperthermic intra-peritoneal chemotherapy (HIPEC). However, several clinical needs still exist in which biomarkers could play an important role. Relatively little is known about the biology of peritoneal spread of CRC. The development of peritoneal metastases (PM) involves several steps, including: detachment of malignant cells; anoikis evasion; attachment to and invasion of the peritoneal surface ultimately ending in a colonization phase in which the malignant cells thrive in the newly formed niche. In this paper, we provide an overview of molecules associated with peritoneal dissemination and explore the clinical possibilities of these candidate biomarkers. A literature search was conducted using the PubMed database of the U.S. National Library of Medicine and Medline to identify studies on the biological behaviour of PM of CRC. In a series of over 100 studies on PM published between 1990 and 2010, IGF-1, HIF1α, VEGF, EGFR and ITGB1 emerge as the most interesting candidates for possible clinical application. Even though these promising candidate biomarkers have been identified, all of these require extensive further validation prior to clinical application. Yet, the pace of the omics revolution makes that the question is not if, but when biomarkers will be introduced to improve diagnosis and ultimately outcome of patients with PM due to CRC. [ABSTRACT FROM AUTHOR]

RATIONALE: Autofluorescence bronchoscopy (AFB) is a valid strategy for detecting premalignant endobronchial lesions. However, no biomarker can reliably predict lung cancer risk of subjects with AFB-visualized premalignant lesions. OBJECTIVES: The present study set out to identify AFB-visualized squamous metaplastic (SqM) lesions with malignant potential by DNA copy number profiling. METHODS: Regular AFB examinations in 474 subjects at risk of lung cancer identified six subjects with SqM lesions at baseline, and carcinoma in situ or carcinoma (carcinoma in situ or greater) at the initial SqM site at follow-up bronchoscopy. These progressive SqM lesions were compared for immunostaining pattern and array comparative genomic hybridization-based chromosomal profiles with 23 SqM lesions of subjects who remained cancer-free. Specific DNA copy number alterations (CNAs) linked to cancer risk were identified and accuracy of CNAs to predict endobronchial cancer in this series was determined. MEASUREMENTS AND MAIN RESULTS: At baseline, p53, p63, and Ki-67 immunostaining were not predictive for a differential clinical outcome of SqM lesions. The mean number of CNAs in baseline SqM of cases was significantly higher compared with control subjects (P < 0.01). Chromosomal regions significantly more frequently altered in SqM of cases were 3p26.3-p11.1, 3q26.2-q29, 9p13.3-p13.2, and 17p13.3-p11.2 (family-wise error rate <0.10). CNAs were specifically detected at the site of future cancer. In cases, baseline-detected CNAs persisted in subsequent biopsies taken from the initial site, and levels increased toward cancer progression. In this series, a model based on CNAs at 3p26.3-p11.1, 3q26.2-29, and 6p25.3-24.3 predicted cancer with 97% accuracy. CONCLUSIONS: The data suggest that the presence of specific CNAs in SqM lesions predict endobronchial cancer. [ABSTRACT FROM AUTHOR]

Although most gastric cancers occur in elderly patients, a substantial number of cases of this common disease occur in young patients. Gastric cancer is a heterogeneous disease at the genomic level and different patterns of DNA copy number alterations are associated with different clinical behaviour. The aim of the present study was to explore differences in DNA copy number alterations in relation to age of onset of gastric cancer. DNA isolated from 46 paraffin-embedded gastric cancer tissue samples from 17 patients less than 50 years of age [median 43 (21-49) years] and 29 patients greater than or equal to 70 years of age [median 75 (70-83) years] was analysed by genome-wide microarray comparative genomic hybridization (array CGH) using an array of 5000 BAC clones. Patterns of DNA copy number aberrations were analysed by hierarchical cluster analysis of the mode-normalized and smoothed log2 ratios of tumour to normal reference fluorescence signal intensities using TMEV software, after which cluster membership was correlated with age group. In addition, supervised analysis was performed using CGH Multi-array. Hierarchical cluster analysis of the array CGH data revealed three clusters with different genomic profiles that correlated significantly with age ( p = 0.006). Cluster 1 mainly contained young patients, while elderly patients were divided over clusters 2 and 3. Chromosome regions 11q23.3 and 19p13.3 contributed most to age-related differences in tumour profiles. Gastric cancers of young and old patients belong to groups with different genomic profiles, which likely reflect different pathogenic mechanisms of the disease. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The carry-over of contaminants from feed to animal food products is an important aspect of the animal production chain. For a proper containment, limits for feed as well food products are fixed for a series of chemicals, e.g. dioxins and dioxin-like PCBs, lead, cadmium, some chlorinated pesticides, and aflatoxin B1 (and its metabolite M1 in milk). The relationship between feed and food limits is an important issue. An ideal goal is to assure that compliance to a feed limits automatically results in compliance to food limits. In order to collect information about this relationship, several simulation models and a large database on transfer factors have been developed. An optimal choice between either a model or an application of data from the Transfer Database is based on both the knowledge level, and on the circumstances of the specific situation. To reach and validate such an optimal choice an Expert System Carry-Over is currently in development, containing four different modules: 1) the different calculation models and the Transfer Database, 2) a decision tree for choosing the optimal strategy, 3) data tables indicating knowledge levels of compound/animal/product parameters, and 4) supporting databases containing information on consumption and composition of daily diets, animal parameters, and amounts of (daily) production. Calculations indicate that for dioxins compliance to feed levels does not necessarily mean that food limits are complied as well. Besides an estimation of the compliance to limits, the expert system is a tool for feed related risk assessments, and for planning of future research.

Ovarian cancer is a leading cause of death for women worldwide in part due to ineffective screening methods. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome and protein biomarker (CA-125 and HE4) analyses to evaluate 591 women with ovarian cancer, benign adnexal masses, or without ovarian lesions. Using a machine learning model with the combined features, we detected ovarian cancer with specificity >99% and sensitivity of 72%, 69%, 87%, and 100% for stages I-IV, respectively. At the same specificity, CA-125 alone detected 34%, 62%, 63%, and 100% of ovarian cancers for stages I-IV. Our approach differentiated benign masses from ovarian cancers with high accuracy (AUC=0.88, 95% CI=0.83-0.92). These results were validated in an independent population. These findings show that integrated cfDNA fragmentome and protein analyses detect ovarian cancers with high performance, enabling a new accessible approach for noninvasive ovarian cancer screening and diagnostic evaluation.

Structural variants (SVs) caused by chromosomal rearrangements in common fragile sites or long interspersed nuclear element (LINE) retrotranspositions are highly prevalent in colorectal cancer. However, methodology for the targeted detection of these SVs is lacking. This article reports the use of formalin-fixed paraffin-embedded targeted-locus capture (FFPE-TLC) sequencing as a novel technology for the targeted detection of tumor-specific SVs. Analysis of 29 FFPE colorectal tumor samples and 8 matched normal samples revealed tumor-specific SVs in 24 patients (83%), with a median of 2 SVs per patient (range, 1 to 21). A total of 104 SVs were found in the common fragile site-associated genes MACROD2, PRKN, FHIT, and WWOX in 18 patients (62%), and 39 SVs caused by three LINE transposable elements were found in 15 patients (52%). Tumor specificity of SVs was independently verified by Droplet Digital PCR of tumor tissue DNA, and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. It was concluded that FFPE-TLC sequencing enables the detection of tumor-specific SVs caused by chromosomal rearrangements and LINE retrotranspositions in FFPE tissue. Therefore, FFPE-TLC sequencing facilitates the investigation of the biological and clinical effects of SVs using FFPE material from (retrospective) cohorts of cancer patients and has potential clinical applicability in the detection of SV biomarkers in the routine molecular diagnostics setting., Competing Interests: Disclosure Statement C.R.-A. declares nonfinancial support from Personal Genome Diagnostics and Cergentis BV. E.S., J.S., and H.F. are employees of Cergentis BV (a Solvias company), the inventor and owner of the patents on FFPE-TLC technology. S.L. reports nonfinancial support from Cergentis BV and a patent pending. E.J.v.B. reports nonfinancial support from Cergentis BV. D.v.d.B. has provided lectures, expert testimony, and advisory board presence to Roche Diagnostics, all outside the submitted work and all financial supports transferred to institute. G.A.M. is co-founder and board member (CSO) of CRCbioscreen BV; has had research collaboration with CZ Health Insurances (cash matching to ZonMW grant); has had research collaborations with Exact Sciences, Sysmex, Sentinel Ch SpA, Personal Genome Diagnostics, DELFi, and HMF (these companies provide materials, equipment and/or sample/genomic analyses); and has several patents pending/issued. S.A. reports public–private partnership consortia grants in collaboration with Cergentis BV, Olink Proteomics AB, and Quanterix Corporation and has a patent pending. R.J.A.F. reports public–private partnership consortia grants in collaboration with Cergentis BV; reports public–private partnership consortia grants and nonfinancial support in collaboration with Personal Genome Diagnostics, Delfi, Natera, and Merck BV outside the submitted work; and has several patents pending., (Copyright © 2024. Published by Elsevier Inc.)

Motivation: Genomic instability is a hallmark of cancer, leading to many somatic alterations. Identifying which alterations have a system-wide impact is a challenging task. Nevertheless, this is an essential first step for prioritizing potential biomarkers. We developed CIBRA (Computational Identification of Biologically Relevant Alterations), a method that determines the system-wide impact of genomic alterations on tumor biology by integrating two distinct omics data types: one indicating genomic alterations (e.g. genomics), and another defining a system-wide expression response (e.g. transcriptomics). CIBRA was evaluated with genome-wide screens in 33 cancer types using primary and metastatic cancer data from the Cancer Genome Atlas and Hartwig Medical Foundation., Results: We demonstrate the capability of CIBRA by successfully confirming the impact of point mutations in experimentally validated oncogenes and tumor suppressor genes (0.79 AUC). Surprisingly, many genes affected by structural variants were identified to have a strong system-wide impact (30.3%), suggesting that their role in cancer development has thus far been largely under-reported. Additionally, CIBRA can identify impact with only 10 cases and controls, providing a novel way to prioritize genomic alterations with a prominent role in cancer biology. Our findings demonstrate that CIBRA can identify cancer drivers by combining genomics and transcriptomics data. Moreover, our work shows an unexpected substantial system-wide impact of structural variants in cancer. Hence, CIBRA has the potential to preselect and refine current definitions of genomic alterations to derive more nuanced biomarkers for diagnostics, disease progression, and treatment response., Availability and Implementation: The R package CIBRA is available at https://github.com/AIT4LIFE-UU/CIBRA., (© The Author(s) 2024. Published by Oxford University Press.)

Background & Aims: Colonoscopy-based surveillance to prevent colorectal cancer (CRC) causes substantial burden for patients and health care. Stool tests may help to reduce surveillance colonoscopies by limiting colonoscopies to individuals at increased risk of advanced neoplasia., Methods: This cross-sectional observational study included individuals aged 50-75 years with surveillance indication. Before bowel preparation, participants collected samples for a multitarget stool DNA test and 2 fecal immunochemical tests (FITs). Test accuracy was calculated for all surveillance indications. For the post-polypectomy indication only, which is the most common and is associated with a relatively low CRC risk, long-term impact of stool-based surveillance was evaluated with the Adenoma and Serrated Pathway to Colorectal Cancer model. Stool-based strategies were simulated to tune each test's positivity threshold to obtain strategies at least as effective as colonoscopy surveillance., Results: There were 3453 individuals with results for all stool tests and colonoscopy; 2226 had previous polypectomy, 1003 had previous CRC, and 224 had a familial risk. Areas under the receiver operating characteristic curve for advanced neoplasia were 0.72 (95% CI, 0.69-0.75) for the multitarget stool DNA test, 0.61 (95% CI, 0.58-0.64) for the FIT OC-SENSOR (Eiken Chemical Co, Tokyo, Japan) and 0.59 (95% CI, 0.56-0.61) for the FIT FOB-Gold (Sentinel, Milan, Italy). Stool-based post-polypectomy surveillance strategies at least as effective as colonoscopy surveillance reduced the number of colonoscopies by 15%-41% and required 5.6-9.5 stool tests over a person's lifetime. Multitarget stool DNA-based surveillance was more costly than colonoscopy surveillance, whereas FIT-based surveillance saved costs., Conclusions: This study found that stool-based post-polypectomy surveillance strategies can be safe and cost-effective, with potential to reduce the number of colonoscopies by up to 41%., Clinicaltrials: gov, Number: NCT02715141., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)