A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning

The identification of biomarker signatures is important for cancer diagnosis and prognosis. However, the detection of clinical reliable signatures is influenced by limited data availability, which may restrict statistical power. Moreover, methods for integration of large sample cohorts and signature identification are limited. We present a step-by-step computational protocol for functional gene expression analysis and the identification of diagnostic and prognostic signatures by combining meta-analysis with machine learning and survival analysis. The novelty of the toolbox lies in its all-in-one functionality, generic design, and modularity. It is exemplified for lung cancer, including a comprehensive evaluation using different validation strategies. However, the protocol is not restricted to specific disease types and can therefore be used by a broad community. The accompanying R package vignette runs in ~1 h and describes the workflow in detail for use by researchers with limited bioinformatics training

Is neoadjuvant chemotherapy followed by surgery the appropriate treatment for esophagogastric signet ring cell carcinomas? A systematic review and meta-analysis

BackgroundThe impact of neoadjuvant chemotherapy (nCTX) on survival and tumor response in patients with esophagogastric signet ring cell carcinoma (SRCC) is still controversial.MethodsTwo independent reviewers performed a systematic literature search in Medline, CENTRAL, and Web of Science including prospective and retrospective two-arm non-randomized and randomized controlled studies (RCTs). Data was extracted on overall survival (OS) and tumor regression in resected esophagogastric SRCC patients with or without nCTX. Survival data was analyzed using published hazard ratios (HR) if available or determined it from other survival data or survival curves. OS and histopathological response rates by type of tumor (SRCC vs. non-SRCC) were also investigated.ResultsOut of 559 studies, ten (1 RCT, 9 non-RCTs) were included in this meta-analysis (PROSPERO CRD42022298743) investigating 3,653 patients in total. The four studies investigating survival in SRCC patients treated with nCTX + surgery vs. surgery alone showed no survival benefit for neither intervention, but heterogeneity was considerable (HR, 1.01; 95% CI, 0.61–1.67; p = 0.98; I2 = 89%). In patients treated by nCTX + surgery SRCC patients showed worse survival (HR, 1.45; 95% CI, 1.21–1.74; p < 0.01) and lower rate of major histopathological response than non-SRCC patients (OR, 2.47; 95% CI, 1.78–3.44; p < 0.01).ConclusionThe current meta-analysis could not demonstrate beneficial effects of nCTX for SRCC patients. Histopathological response to and survival benefits of non-taxane-based nCTX seem to be lower in comparison to non-SRC esophagogastric cancer. However, certainty of evidence is low due to the scarcity of high-quality trials. Further research is necessary to determine optimal treatment for SRCC patients.Systematic Review Registrationhttps://www.crd.york.ac.uk/, PROSPERO (CRD42022298743)

Prognosis of light chain amyloidosis: a multivariable analysis for survival prediction in patients with cardiac involvement proven by endomyocardial biopsy

Background Cardiac involvement is a main determinant of mortality in light chain (AL) amyloidosis but data on survival of patients with cardiac AL amyloidosis proven by endomyocardial biopsy (EMB) are sparse.Methods This study analysed clinical, laboratory, electrocardiography and echocardiographic parameters for their prognostic value in the assessment of patients with AL amyloidosis and cardiac involvement. Patients with AL amyloidosis who had their first visit to the amyloidosis centre at the University Hospital Heidelberg between 2006 and 2017 (n=1628) were filtered for cardiac involvement proven by EMB. In the final cohort, mortality-associated markers were analysed by univariate and multivariable Cox regression. Cut-off values for each parameter were calculated using the survival time.Results One-hundred and seventy-four patients could be identified. Median overall survival time was 1.5 years and median follow-up time was 5.2 years. At the end of the investigation period, 115 patients had died. In multivariable analysis, New York Heart Association-functional class >II (HR 1.65; 95% CI 1.09 to 2.50; p=0.019), left ventricular global longitudinal strain (HR 1.12; 95% CI 1.03 to 1.22; p=0.007), left ventricular end-systolic volume (HR 1.02; 95% CI 1.01 to 1.03; p=0.001), systolic pulmonary artery pressure (HR 0.98; 95% CI 0.96 to 0.99; p=0.027), N-terminal pro-B-type natriuretic peptide (HR 1.57; 95% CI 1.17 to 2.11; p=0.003) and difference in free light chains (HR 1.30; 95% CI 1.05 to 1.62; p=0.017) were independently predictive.Conclusion Among all patients with AL amyloidosis those with cardiac involvement represent a high-risk population with limited therapy options. Therefore, accurate risk stratification is necessary to identify cardiac amyloidosis patients with favourable prognosis. Incorporation of modern imaging techniques into existing or newly developed scoring systems is a promising option that might enable the implementation of risk-adapted therapeutic strategies