A robust clustering strategy for stratification unveils unique patient subgroups in acutely decompensated cirrhosis.

BACKGROUND: Patient heterogeneity poses significant challenges for managing individuals and designing clinical trials, especially in complex diseases. Existing classifications rely on outcome-predicting scores, potentially overlooking crucial elements contributing to heterogeneity without necessarily impacting prognosis. METHODS: To address patient heterogeneity, we developed ClustALL, a computational pipeline that simultaneously faces diverse clinical data challenges like mixed types, missing values, and collinearity. ClustALL enables the unsupervised identification of patient stratifications while filtering for stratifications that are robust against minor variations in the population (population-based) and against limited adjustments in the algorithm's parameters (parameter-based). RESULTS: Applied to a European cohort of patients with acutely decompensated cirrhosis (n = 766), ClustALL identified five robust stratifications, using only data at hospital admission. All stratifications included markers of impaired liver function and number of organ dysfunction or failure, and most included precipitating events. When focusing on one of these stratifications, patients were categorized into three clusters characterized by typical clinical features; notably, the 3-cluster stratification showed a prognostic value. Re-assessment of patient stratification during follow-up delineated patients' outcomes, with further improvement of the prognostic value of the stratification. We validated these findings in an independent prospective multicentre cohort of patients from Latin America (n = 580). CONCLUSIONS: By applying ClustALL to patients with acutely decompensated cirrhosis, we identified three patient clusters. Following these clusters over time offers insights that could guide future clinical trial design. ClustALL is a novel and robust stratification method capable of addressing the multiple challenges of patient stratification in most complex diseases.

Signature-driven repurposing of Midostaurin for combination with MEK1/2 and KRASG12C inhibitors in lung cancer.

Drug combinations are key to circumvent resistance mechanisms compromising response to single anti-cancer targeted therapies. The implementation of combinatorial approaches involving MEK1/2 or KRASG12C inhibitors in the context of KRAS-mutated lung cancers focuses fundamentally on targeting KRAS proximal activators or effectors. However, the antitumor effect is highly determined by compensatory mechanisms arising in defined cell types or tumor subgroups. A potential strategy to find drug combinations targeting a larger fraction of KRAS-mutated lung cancers may capitalize on the common, distal gene expression output elicited by oncogenic KRAS. By integrating a signature-driven drug repurposing approach with a pairwise pharmacological screen, here we show synergistic drug combinations consisting of multi-tyrosine kinase PKC inhibitors together with MEK1/2 or KRASG12C inhibitors. Such combinations elicit a cytotoxic response in both in vitro and in vivo models, which in part involves inhibition of the PKC inhibitor target AURKB. Proteome profiling links dysregulation of MYC expression to the effect of both PKC inhibitor-based drug combinations. Furthermore, MYC overexpression appears as a resistance mechanism to MEK1/2 and KRASG12C inhibitors. Our study provides a rational framework for selecting drugs entering combinatorial strategies and unveils MEK1/2- and KRASG12C-based therapies for lung cancer.

Lipidomic signatures from physically frail and robust older adults at hospital admission.

Identifying serum biomarkers that can predict physical frailty in older adults would have tremendous clinical value for primary care, as this condition is inherently related to poor quality of life and premature mortality. We compared the serum lipid profile of physically frail and robust older adults to identify specific lipid biomarkers that could be used to assess physical frailty in older patients at hospital admission. Forty-three older adults (58.1% male), mean (range) age 86.4 (78-100 years) years, were classified as physically frail (n = 18) or robust (n = 25) based on scores from the Short Physical Performance Battery (≤ 6 points). Non-targeted metabolomic study by ultra-high performance liquid chromatography coupled to mass spectrometry (UHPLC-MS) analysis with later bioinformatics data analysis. Once the significantly different metabolites were identified, the KEGG database was used on them to establish which were the metabolic pathways mainly involved. Area under receiver-operating curve (AUROC) analysis was used to test the discriminatory ability of lipid biomarkers for frailty based on the Short Physical Performance Battery. We identified a panel of five metabolites including ceramides Cer (40:2), Cer (d18:1/20:0), Cer (d18:1/23:0), cholesterol, and phosphatidylcholine (PC) (14:0/20:4) that were significantly increased in physically frail older adults compared with robust older adults at hospital admission. The most interesting in the physically frail metabolome study found with the KEGG database were the metabolic pathways, vitamin digestion and absorption, AGE-RAGE signaling pathway in diabetic complications, and insulin resistance. In addition, Cer (40:2) (AUROC 0.747), Cer (d18:1/23:0) (AUROC 0.720), and cholesterol (AUROC 0.784) were identified as higher values of physically frail at hospital admission. The non-targeted metabolomic study can open a wide view of the physically frail features changes at the plasma level, which would be linked to the physical frailty phenotype at hospital admission. Also, we propose that metabolome analysis will have a suitable niche in personalized medicine for physically frail older adults.

Effects of Different Doses of Exercise on Inflammation Markers Among Adolescents With Overweight/Obesity: HEPAFIT Study.

PROPOSE: Obesity-related metabolic risk factors in adolescents who are overweight/obese may be associated with systemic low-grade inflammation; therefore, we investigated whether 6 months of exercise training altered markers of inflammation. METHODS: Secondary analyses of a randomized controlled exercise-based intervention trial (September 2017-December 2018). Adolescents aged 11 to 17 years (Tanner stage II-V), 70% girls, with a body mass index z-score at or above the 85th percentile, and/or with excess of adiposity (body fat ≥ 30%). The participants were randomly assigned to the following 4 groups for 6 months: (1) standard physical education lessons, as a control (CTRL); (2) high-intensity physical education class (HIPE); (3) low-to-moderate intensity physical education class (LIPE); (4) a combined group (PLUS). Inflammatory markers and immune molecules including chemokines, cytokines, and growth factors (n = 65 biomarkers) were determined by cytokine antibody array. RESULTS: Of the 120 randomly assigned participants, 95 were included in the analysis. Considering these 22 proteins, the LIPE group shows statistical significance in 9 proteins with log-fold change (logFC) and P < 0.05 (in BLC, eotaxin, fibroblast growth factor-6 [FGF-6], GCP-2, I-309, IGFBP-4, MCP-4, NAP-2, and PARC), followed by the PLUS group in 9 proteins (BLC, pro-epidermal growth factor, eotaxin, FGF-6, MCP-4, NAP-2, osteopontin, PARC, and RANTES), the HIPE group in 7 proteins (FGF-4, FGF-7, GCP-2, IGF-1, IGFBP-1, IGFBP-4, and MIP-1 delta), and the CTRL group in 6 proteins (FGF-4, IP-10, Leptin, MCP-1, MIG, and MIP-1 delta). However, subanalysis performed to detect differentially expressed proteins at baseline and after intervention, with significance at an adjusted P value ≤ 0.05 and absolute log fold-change (logFC) ≥ 1.0, showed 3 downregulated proteins in the LIPE group (BLC(logFC) = 1.27, eotaxin(logFC) = 1.18, and MCP-4(logFC) = 1.14), and 4 proteins in the HIPE group (BLC(logFC) = 1.45, FGF-6(logFC) = 1.20, MCP-4(logFC) = 1.50, and PARC(logFC) = 1.33), supporting that the changes we observed in the exercise groups were not time-related changes but occurred in response to exercise. CONCLUSIONS: Implementing a 6-month physical exercise program in overweight/obese adolescents, based on LIPE and PLUS groups, significantly change several circulating inflammatory levels. Interventions involving supervised physical exercise may reduce the associated effects of systemic low-grade inflammation, thus preventing the development of obesity-related metabolic diseases in adolescents with overweight/obesity.

Exercise dose on hepatic fat and cardiovascular health in adolescents with excess of adiposity.

OBJECTIVE: The HEPAFIT study was aimed at examining the impact of a 6-month physical education intervention, considering various levels of exercise intensity, on hepatic fat and cardiometabolic health outcomes in adolescents with excess adiposity. METHODS: Adolescents (n = 120), 11-17 years with excess adiposity by body fat >30%, were randomly assigned to one of the following 4 groups for 6 months: (1) standard physical education lessons, control (CTRL); (2) high-intensity physical education (HIPE); (3) low-to-moderate intensity physical education (LIPE) and (4) combined HIPE and LIPE (PLUS). The primary outcome was hepatic fat content measured by vibration-controlled transient elastography (controlled attenuation parameter [CAP]). Secondary outcomes were traditional cardiovascular health markers (body composition, serum lipids, aminotransferases and health-related physical fitness components). RESULTS: Adjusted mixed effects linear models revealed a significant decrease in CAP levels in HIPE (-20.02 dB/m, p < 0.0001) (p = 0.001 vs. CTRL group) and PLUS (-16.25 dB/m, p = 0.005) groups. Body fat decreased in the HIPE (-2.88%, p < 0.001) (p = 0.001 vs. CTRL group) and LIPE (-1.26%, p = 0.022) groups. The physical fitness components were increased in the HIPE and PLUS group relative to the baseline (p < 0.05), and the HIPE group showed a reduction in the total cholesterol and low-density lipoprotein cholesterol (LDL-C) levels (p < 0.05). CONCLUSIONS: Implementation of a 6-month physical education exercise program, particularly high-intensity or combined high and low-intensity, improves hepatic fat storage and significantly reduces cardiometabolic markers in adolescents with excess of adiposity. Interventions involving supervised physical exercise may help to improve metabolism and fat deposition at the hepatic level, thus preventing the development of non-alcoholic fatty liver disease in adolescents.

Serum leptin as a mediator of the influence of insulin resistance on hepatic steatosis in youths with excess adiposity.

BACKGROUND AND AIMS: The relationship between insulin resistance (IR) and hepatic steatosis (fatty liver) is well known; however, the extent to which the satiety hormone leptin acts as a confounder or mediator in this relationship is uncertain. We examined whether the association between IR and hepatic steatosis is mediated by leptin in Colombian adolescents with excess adiposity. METHODS AND RESULTS: A total of 122 adolescents (mean age: 13.4 years; 68% girls) participated in the study. We assessed body composition, hepatic steatosis (as defined by the controlled attenuation parameter [CAP]), cardiometabolic risk factors (body mass index, waist circumference, body composition), biochemical variables (leptin, insulin, glucose, lipid profile, cardiometabolic Z-score, transaminases, etc.), and physical fitness (cardiorespiratory fitness and grip strength). Partial correlation, regression, and mediation analyses were conducted using the Barron and Kenny framework. RESULTS: Ninety-two youths (75.4%) had IR. Mediation analysis revealed a positive relationship between Homeostasis Model Assessment-IR (HOMA-IR) and CAP (ßdir = 3.414, 95% confidence interval [CI]: 1.012 to 5.816, p < 0.001), which was attenuated when leptin was included in the model, thus indicating that leptin mediates this relationship (ßind = 1.074, 95% CI: 0.349 to 2.686, p < 0.001). The percentage of the total effect mediated by leptin was 21%. Regarding sex, the mediation effect of leptin remains significant among boys (ßind = 0.962, 95% CI: 0.009 to 2.615, p < 0.001), but not in girls (ßind = 0.991, 95% CI: 1.263 to 5.483, p = 0.477). CONCLUSIONS: The findings are clinically relevant to consider leptin levels as a surrogate marker of insulin sensitivity when assessing youths with excess adiposity and/or suspected Nonalcoholic hepatic steatosis or nonalcoholic fatty liver disease (NAFLD).

Strategy for identification of a potential inherited leukemia predisposition in a 299 patient's cohort with tumor-only sequencing data.

Myeloid neoplasms (MN) are usually sporadic late-onset cancers; nevertheless, growing evidence suggests that ∼5% of the cases could emerge as a consequence of inherited predisposition. Distinguishing somatic from germline variants is of vital importance, in order to establish an appropriate individualized management and counsel the patients and their relatives. Since many of the genes associated with myeloid neoplasm germline predisposition (MNGP) are also affected in sporadic MN, we intended to design a strategy to identify potentially inherited variants in a tumor only NGS panel in a cohort of 299 patients with a variety of MN. We considered as indicative of potential inherited origin, variants detected in BM sample at a ∼50% VAF classified as pathogenic, likely pathogenic or of unknown significance detected in MNGP-related genes. A total of 104 suspicious variants from 90 patients were filtered-in in tumor samples. Mutational patterns, follow-up data, and sequencing of a range of non-myeloid tissues were used for narrowing down the list of suspicious variants, and ultimately discriminate their nature. Our data supports the importance of considering variants found upon tumor-only sequencing as potentially of germline origin, and we offer a pipeline to define the nature of the variants.

Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design.

The diagnosis of myeloid neoplasms (MN) has significantly evolved through the last few decades. Next Generation Sequencing (NGS) is gradually becoming an essential tool to help clinicians with disease management. To this end, most specialized genetic laboratories have implemented NGS panels targeting a number of different genes relevant to MN. The aim of the present study is to evaluate the performance of four different targeted NGS gene panels based on their technical features and clinical utility. A total of 32 patient bone marrow samples were accrued and sequenced with 3 commercially available panels and 1 custom panel. Variants were classified by two geneticists based on their clinical relevance in MN. There was a difference in panel's depth of coverage. We found 11 discordant clinically relevant variants between panels, with a trend to miss long insertions. Our data show that there is a high risk of finding different mutations depending on the panel of choice, due both to the panel design and the data analysis method. Of note, CEBPA, CALR and FLT3 genes, remains challenging the use of NGS for diagnosis of MN in compliance with current guidelines. Therefore, conventional molecular testing might need to be kept in place for the correct diagnosis of MN for now.