Early stage gastric adenocarcinoma: clinical and molecular landscapes.

Gastric adenocarcinoma, even when diagnosed at an early (localized) disease stage, poses a major health-care burden with cure rates that remain unsatisfactorily low, particularly in Western countries. This lack of progress reflects, among other aspects, the impracticality of early diagnosis, considerable variations in therapeutic approaches that is partly based on regional preferences, and the ingrained heterogeneity of gastric adenocarcinoma cells and their associated tumour microenvironment (TME). Clinical trials have long applied empirical interventions with the assumption that all early stage gastric adenocarcinomas are alike. Despite certain successes, the shortcomings of these approaches can potentially be overcome by targeting the specific molecular subsets of gastric adenocarcinomas identified by genomic and/or multi-omics analyses, including microsatellite instability-high, Epstein-Barr virus-induced, DNA damage repair-deficient, HER2-positive and PD-L1-high subtypes. Future approaches, including the availability of sophisticated vaccines, novel antibody technologies, agents targeting TME components (including fibroblasts, macrophages, cytokines or chemokines, and T cells) and novel immune checkpoint inhibitors, supported by improved tissue-based and blood-based diagnostic assays, seem promising. In this Review, we highlight current knowledge of the molecular and cellular biology of gastric adenocarcinomas, summarize the current approaches to clinical management of the disease, and consider the role of novel management and/or treatment strategies.

APOBEC mutagenesis is a common process in normal human small intestine.

APOBEC mutational signatures SBS2 and SBS13 are common in many human cancer types. However, there is an incomplete understanding of its stimulus, when it occurs in the progression from normal to cancer cell and the APOBEC enzymes responsible. Here we whole-genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals and found that SBS2/SBS13 mutations were present in 17% of crypts, more frequent than most other normal tissues. Crypts with SBS2/SBS13 often had immediate crypt neighbors without SBS2/SBS13, suggesting that the underlying cause of SBS2/SBS13 is cell-intrinsic. APOBEC mutagenesis occurred in an episodic manner throughout the human lifespan, including in young children. APOBEC1 mRNA levels were very high in the small intestine epithelium, but low in the large intestine epithelium and other tissues. The results suggest that the high levels of SBS2/SBS13 in the small intestine are collateral damage from APOBEC1 fulfilling its physiological function of editing APOB mRNA.

Low-cost and clinically applicable copy number profiling using repeat DNA.

BACKGROUND: Somatic copy number alterations (SCNAs) are an important class of genomic alteration in cancer. They are frequently observed in cancer samples, with studies showing that, on average, SCNAs affect 34% of a cancer cell's genome. Furthermore, SCNAs have been shown to be major drivers of tumour development and have been associated with response to therapy and prognosis. Large-scale cancer genome studies suggest that tumours are driven by somatic copy number alterations (SCNAs) or single-nucleotide variants (SNVs). Despite the frequency of SCNAs and their clinical relevance, the use of genomics assays in the clinic is biased towards targeted gene panels, which identify SNVs but provide limited scope to detect SCNAs throughout the genome. There is a need for a comparably low-cost and simple method for high-resolution SCNA profiling. RESULTS: We present conliga, a fully probabilistic method that infers SCNA profiles from a low-cost, simple, and clinically-relevant assay (FAST-SeqS). When applied to 11 high-purity oesophageal adenocarcinoma samples, we obtain good agreement (Spearman's rank correlation coefficient, rs=0.94) between conliga's inferred SCNA profiles using FAST-SeqS data (approximately £14 per sample) and those inferred by ASCAT using high-coverage WGS (gold-standard). We find that conliga outperforms CNVkit (rs=0.89), also applied to FAST-SeqS data, and is comparable to QDNAseq (rs=0.96) applied to low-coverage WGS, which is approximately four-fold more expensive, more laborious and less clinically-relevant. By performing an in silico dilution series experiment, we find that conliga is particularly suited to detecting SCNAs in low tumour purity samples. At two million reads per sample, conliga is able to detect SCNAs in all nine samples at 3% tumour purity and as low as 0.5% purity in one sample. Crucially, we show that conliga's hidden state information can be used to decide when a sample is abnormal or normal, whereas CNVkit and QDNAseq cannot provide this critical information. CONCLUSIONS: We show that conliga provides high-resolution SCNA profiles using a convenient, low-cost assay. We believe conliga makes FAST-SeqS a more clinically valuable assay as well as a useful research tool, enabling inexpensive and fast copy number profiling of pre-malignant and cancer samples.

The mutational landscape of human somatic and germline cells.

Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.

Extensive phylogenies of human development inferred from somatic mutations.

Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.

Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma.

The poor outcomes in esophageal adenocarcinoma (EAC) prompted us to interrogate the pattern and timing of metastatic spread. Whole-genome sequencing and phylogenetic analysis of 388 samples across 18 individuals with EAC showed, in 90% of patients, that multiple subclones from the primary tumor spread very rapidly from the primary site to form multiple metastases, including lymph nodes and distant tissues-a mode of dissemination that we term 'clonal diaspora'. Metastatic subclones at autopsy were present in tissue and blood samples from earlier time points. These findings have implications for our understanding and clinical evaluation of EAC.

The landscape of somatic mutation in normal colorectal epithelial cells.

The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer1. However, our understanding of the earliest phases of colorectal neoplastic changes-which may occur in morphologically normal tissue-is comparatively limited, as for most cancer types. Here we use whole-genome sequencing to analyse hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed; some of these were ubiquitous and continuous, whereas others were only found in some individuals, in some crypts or during certain periods of life. Probable driver mutations were present in around 1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. Colorectal cancers exhibit substantially increased mutational burdens relative to normal cells. Sequencing normal colorectal cells provides quantitative insights into the genomic and clonal evolution of cancer.

Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics.

Esophageal adenocarcinoma (EAC) incidence is increasing while 5-year survival rates remain less than 15%. A lack of experimental models has hampered progress. We have generated clinically annotated EAC organoid cultures that recapitulate the morphology, genomic, and transcriptomic landscape of the primary tumor including point mutations, copy number alterations, and mutational signatures. Karyotyping of organoid cultures has confirmed polyclonality reflecting the clonal architecture of the primary tumor. Furthermore, subclones underwent clonal selection associated with driver gene status. Medium throughput drug sensitivity testing demonstrates the potential of targeting receptor tyrosine kinases and downstream mediators. EAC organoid cultures provide a pre-clinical tool for studies of clonal evolution and precision therapeutics.

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status. Inclusion of samples collected post-chemotherapy increased the proportion of late-stage tumors. When comparing matched pre- and post-chemotherapy samples from 10 cases, the mutational signatures, copy number, and SNV mutational profiles reflect the expected heterogeneity in this disease. Analysis of SNVs in relation to allele-specific copy-number changes pinpoints the common ancestor to a point prior to chemotherapy. For cases in which pre- and post-chemotherapy samples do show substantial differences, the timing of the divergence is near-synchronous with endoreduplication. Comparison across a large prospective cohort (62 treatment-naive, 58 chemotherapy-treated samples) reveals no significant differences in the overall mutation rate, mutation signatures, specific recurrent point mutations, or copy-number events in respect to chemotherapy status. In conclusion, whole-genome sequencing of samples obtained following neoadjuvant chemotherapy is representative of the genomic landscape of esophageal adenocarcinoma. Excluding these samples reduces the material available for cataloging and introduces a bias toward the earlier stages of cancer.

Assessment of Renal Injury in Patients Undergoing Elective EVAR Using Urinary Neutrophil Gelatin-Associated Lipocalin, Interleukin 18, and Retinol-Binding Protein.

Acute kidney injury (AKI) is a recognized complication post-endovascular aneurysm repair (EVAR). Neutrophil gelatin-associated lipocalin (NGAL), interleukin 18 (IL-18), and retinol-binding protein are emerging urinary biomarkers that have shown promise in detecting subclinical and clinical renal impairment. In this study, we assessed changes in these urinary biomarkers as well as serum creatinine (SCr) in patients undergoing EVAR. Urine samples were collected prospectively at 5 time points for each recruited patient: pre-EVAR (baseline) and 6, 12, 24, and 48 hours after the procedure for serial assessment of urinary biomarkers. Serum creatinine was quantified preoperatively and at 24 and 48 hours postoperatively. Serial changes of urinary biomarkers and SCr were assessed. A significant increase in NGAL and IL-18 from baseline was observed ( P < .05), as early as 6 hours for NGAL. A significant rise in levels of NGAL and IL-18 precedes the significant rise in SCr. These findings highlight the potential of emerging urinary biomarkers in detecting early AKI following EVAR.

Amplification of TRIM44: pairing a prognostic target with potential therapeutic strategy.

BACKGROUND: Many prognostic biomarkers have been proposed recently. However, there is a lack of therapeutic strategies exploiting novel prognostic biomarkers. We aimed to propose therapeutic options in patients with overexpression of TRIM44, a recently identified prognostic gene. METHODS: Genomic and transcriptomic data of epithelial cancers (n = 1932), breast cancers (BCs; n = 1980) and esophago-gastric cancers (EGCs; n = 163) were used to identify genomic aberrations driving TRIM44 overexpression. The driver gene status of TRIM44 was determined using a small interfering RNA (siRNA) screen of the 11p13 amplicon. Integrative analysis was applied across multiple datasets to identify pathway activation and potential therapeutic strategies. Validation of the in silico findings were performed using in vitro assays, xenografts, and patient samples (n = 160). RESULTS: TRIM44 overexpression results from genomic amplification in 16.1% of epithelial cancers, including 8.1% of EGCs and 6.1% of BCs. This was confirmed using fluorescent in situ hybridization. The siRNA screen confirmed TRIM44 to be a driver of the amplicon. In silico analysis revealed an association between TRIM44 and mTOR signalling, supported by a decrease in mTOR signalling after siRNA knockdown of TRIM44 in cell lines and colocalization of TRIM44 and p-mTOR in patient samples. In vitro inhibition studies using an mTOR inhibitor (everolimus) decreased cell viability in two TRIM44-amplified cells lines by 88% and 70% compared with 35% in the control cell line. These findings were recapitulated in xenograft models. CONCLUSIONS: Genomic amplification drives TRIM44 overexpression in EGCs and BCs. Targeting the mTOR pathway provides a potential therapeutic option for TRIM44-amplified tumors.

Perioperative fluid restriction in major abdominal surgery: systematic review and meta-analysis of randomized, clinical trials.

BACKGROUND: Fluid management is a fundamental component of surgical care. Recently, there has been considerable interest in perioperative fluid restriction as a method of facilitating recovery following elective major surgery. A number of randomized trials have addressed the issue in various surgical specialities, and a recent meta-analysis proposed uniform definitions regarding fluid amount as well as examining fluid restriction in patients undergoing colonic resection. METHODS: Medline, Embase, trial registries, conference proceedings, and article reference lists were searched to identify randomized, controlled trials of perioperative fluid restriction versus "standard" perioperative fluid management, as per definitions formulated previously. All of the studies involved patients undergoing colonic resection. The primary outcome measure was postoperative morbidity. Secondary endpoints included mortality, renal failure, time to first flatus, and length of hospital stay. A random effects model was applied. RESULTS: Seven randomized, controlled trials with a total of 856 patients investigating standard versus restrictive fluid regimes, as denoted by the definitions, were included. Perioperative fluid restriction had no effect on the risk of postoperative complications (OR 0.49 (95 % confidence interval (CI) 0.2-1.18; P = 0.101). There was no detectable effect on death and fluid restriction did not reduce hospital stay (Pooled weighted mean difference -0.25; 95 % CI 0.72-0.21; P = 0.29). CONCLUSIONS: Perioperative fluid restriction does not significantly reduce the risk of complications following major abdominal surgery. Furthermore, it does not appear to reduce length of hospital stay.

Cost-effectiveness analysis of endovascular versus open surgical repair of acute abdominal aortic aneurysms based on worldwide experience.

PURPOSE: To present an economic evaluation of endovascular versus open surgical repair of ruptured abdominal aortic aneurysms (AAA). METHODS: Endovascular aneurysm repair (EVAR) is currently being appraised by the National Institute for Clinical Excellence. To aid in this appraisal, a health economic model developed to demonstrate the cost-effectiveness of EVAR for elective treatment of non-ruptured AAAs versus OSR was used for an analysis in the emergency setting. The base case data on 730 patients undergoing EVAR was extracted from our recently published 22-study meta-analysis of 7040 patients presenting with acute AAA (ruptured or symptomatic) treated with either emergency EVAR or OSR. These data reflected a patient population with an average age of 70 years. The base case model, which assumed a time horizon of 30 years and applied all-cause mortality rates, was subjected to a number of 1-way sensitivity analyses. A multivariate analysis was undertaken using 10,000 Monte-Carlo simulations. RESULTS: EVAR dominated OSR in the base case analysis, with a mean cumulative cost/patient of pound17,422 ($26,133) for EVAR and pound18,930 ($28,395) for OSR [- pound1508 ($2262) difference]. The mean quality-adjusted life years (QALYs)/patient was 3.09 for EVAR versus 2.49 for OSR (0.64 difference). EVAR was cost-effective compared with OSR at a threshold value of pound20,000 to pound30,000 ($30,000-$45,000)/QALY. In no single combination tested did open surgical repair provide the patient with more QALYs than EVAR. Sensitivity analyses demonstrated that the results were most sensitive to length of hospital and intensive care stays, use of blood products, and the cost of the evar device, which were the main cost drivers. CONCLUSION: While the UK's National Institute for Clinical Excellence does not set an absolute limit at which treatments would not be funded, pound30,000 ($45,000) is generally regarded as the upper limit of acceptability. At this level, there is almost a 100% probability that EVAR is a cost-effective treatment for ruptured AAA.

Cerebral hemodynamic changes following carotid endarterectomy: 'cerebral hyperperfusion syndrome'.

Carotid endarterectomy is associated with significant changes in cerebral hemodynamics. In the chronically ischemic brain of patients with carotid stenosis, this can result in postoperative development of 'cerebral hyperperfusion syndrome'. This can cause severe cerebral edema, intracerebral hemorrhage and death. Impaired autoregulation as a result of endothelial dysfunction mediated by the generation of free oxygen radicals is implicated in the pathogenesis of cerebral hyperperfusion syndrome. Intensive blood pressure monitoring and control forms the backbone of treatment. Complete recovery occurs in mild cases, but disability and death can occur in more severe cases. This review concentrates on the mechanism, current management and identification of risk factors that can predispose to this rare but potentially life threatening complication.

Comparison of aortomonoiliac endovascular aneurysm repair versus a bifurcated stent-graft: analysis of perioperative morbidity and mortality.

PURPOSE: To compare the perioperative morbidity and mortality following endovascular aneurysm repair (EVAR) with a bifurcated stent-graft versus an aortomonoiliac stent-graft combined with a femorofemoral crossover graft. METHODS: A prospectively maintained database of patients undergoing EVAR over a 7-year period (January 2001 to June 2008) was interrogated retrospectively to identify all patients receiving either a bifurcated or an aortomonoiliac stent-graft. Patients undergoing emergency treatment or renal/mesenteric fenestrated or iliac branched EVAR were excluded. Data retrieval found 210 patients (194 men; mean age 75 years) who had been treated with 41 aortomonoiliac stent-grafts and 169 bifurcated devices. The impact of preoperative and intraoperative variables on postoperative morbidity was assessed by means of univariate and multivariate logistic regression analysis. RESULTS: Significant postoperative complications occurred in 41% (17/41) of aortomonoiliac stent-graft patients compared to 14% (23/169) of bifurcated stent-graft patients (p = 0.0001). Univariate logistic regression analyses identified patient age, operating time, and implantation of an aortomonoiliac stent-graft as significant predictors of postoperative complications. In a multivariate logistic regression model, only implantation of an aortomonoiliac stent-graft was independently associated with postoperative complications (p = 0.003). CONCLUSION: Compared to EVAR with a bifurcated device, the implantation of an aortomonoiliac stent-graft and crossover bypass is associated with higher patient morbidity similar to rates reported after open repair. These patients comprise a high-risk endovascular group and require careful postoperative management in order to minimize complications.

The future of EVAR in the management of ruptured AAAs.

Endovascular repair of ruptured abdominal aortic aneurysms is an evolving technique. Data from nonrandomized series suggest that it may be beneficial in selected patients. In the next few years, a number of large randomized clinical trials will clarify its role. Issues regarding anatomical suitability, techniques, perioperative care, and service provision need to be addressed in order to optimize outcomes.

Neurological complications after left subclavian artery coverage during thoracic endovascular aortic repair: a systematic review and meta-analysis.

INTRODUCTION: Recent studies suggest an increased risk of neurologic complications after coverage of the left subclavian artery (LSA) during thoracic endovascular aortic repair (TEVAR). The preventative role of preoperative revascularization of the LSA using carotid-subclavian bypass or transposition remains controversial. We assessed this increased risk and the role of revascularization by undertaking a systematic review and meta-analysis of the literature. METHODS: In the absence of any randomized controlled trials, the Pubmed and Embase databases were searched to identify all series reporting TEVAR without LSA coverage compared with LSA coverage with and without revascularization. The incidence of neurologic complications, namely cerebrovascular accident (CVA) and spinal cord ischemia (SCI), were recorded for each group. Pooled odds ratios (POR) were then calculated for postoperative CVA and SCI. RESULTS: Compared with patients without LSA coverage, the risk of CVA was increased both in patients with LSA coverage alone (4.7% vs 2.7%; POR, 2.28; 95% confidence interval [CI], 1.28-4.09; P = .005) and in those with LSA coverage after revascularization (4.1% vs 2.6%; POR, 3.18; 95% CI, 1.17-8.65; P = .02). The risk of SCI was also increased in patients requiring LSA coverage (2.8% vs 2.3%; POR, 2.39; 95% CI, 1.30-4.39; P = .005) but not for LSA coverage after revascularization (0.8% vs 2.7%; POR, 1.69; 95% CI, 0.56-5.15; P = .35). CONCLUSION: The risk of neurologic complications is increased after coverage of the LSA during TEVAR. Preemptive revascularization offers no protection against CVA, perhaps indicating a heterogeneous etiology. Revascularization may reduce the risk of SCI, although limited data tempers this conclusion. Improved or perhaps compulsory reporting to registries of a minimum data set may help further assess the exact etiology of these complications and identify a higher-risk subset of patients in whom revascularization might prove protective.

Atrial fibrillation following elective open abdominal aortic aneurysm repair.

BACKGROUND: Atrial fibrillation is a common complication following major vascular surgery. It is often considered to be relatively benign but may represent the first sign of cardiac and non-cardiac complications. We conducted a retrospective study to determine the incidence and clinical associations of atrial fibrillation following open elective abdominal aortic aneurysm repair as well as its effect on prognosis. METHODS: The case-notes of 200 consecutive patients undergoing open aneurysm repair were reviewed. Known pre-operative and intra-operative risk factors and potential post-operative associations with new-onset AF were recorded. Significant univariate correlates with AF were entered into a forward stepwise logistic regression model to test for independence. The effect of new-onset AF on long-term prognosis was assessed. RESULTS: AF developed in 20 patients (10%) post-operatively. Previous cerebrovascular disease, aneurysm size and post-operative cardiac failure were associated with post-operative AF in univariate analyses. Cerebrovascular disease and post-operative cardiac failure were independently associated with new-onset AF. AF patients had a longer hospital stay. There was no difference in survival between those patients with and without new-onset AF. CONCLUSION: New-onset AF is a common complication of open abdominal aortic aneurysm surgery and may indicate an underlying myocardial infarction. It is associated with a longer hospital stay and an increased risk of cardiac failure. Assessed and treated appropriately, it appears to have no effect on long-term prognosis.