Cancer Informatics最新文献

Background: Cancer development and progression involve a complex network of pathways among which certain pathways play a pivotal role in promoting tumor growth and survival. An important pathway in this context is the PI3K/AKT pathway, which regulates crucial cellular processes including proliferation, viability, and metabolic regulation. Dysregulation of this pathway has been strongly linked to the development of various types of cancers. Consequently, it is imperative to identify the key proteins within this pathway as potential targets for impeding cancer cell proliferation and survival.

Results: One of the key findings of this study was the identification of signaling proteins that dominate various forms of PI3K/Akt pathway. Furthermore, proteins play critical roles in cancer networks, acting as oncogenes that promote cancer development or as tumor suppressor genes that inhibit tumor growth. This study identified several genes, including KIT, ERBB2, PDGFRA, MET, FGFR2, and FGFR3, which are involved in various types of the PI3K/Akt pathways. Additionally, this study identified 55 proteins that are commonly found in various forms of PI3K/Akt, and these proteins play crucial roles in regulating various biological functions.

Conclusions: This study highlights the importance of identifying key proteins involved in the PI3K/AKT pathway. In this study, we identified several genes involved in different pathways that play essential roles in the activation, signaling, and regulation of the pathway. Understanding the proteins participating in the PI3K/AKT pathway is vital for the development of targeted therapies, not only for cancer but also for other related diseases. By elucidating their roles and functions, this study contributes to the advancement of knowledge in the field and paves the way for the development of effective treatments targeting this pathway.

User measurement bias during subcutaneous tumor measurement is a source of variation in preclinical in vivo studies. We investigated whether this user variability could impact efficacy study outcomes, in the form of the false negative result rate when comparing treated and control groups. Two tumor measurement methods were compared; calipers which rely on manual measurement, and an automatic 3D and thermal imaging device. Tumor growth curve data were used to create an in silico efficacy study with control and treated groups. Before applying user variability, treatment group tumor volumes were statistically different to the control group. Utilizing data collected from 15 different users across 9 in vivo studies, user measurement variability was computed for both methods and simulation was used to investigate its impact on the in silico study outcome. User variability produced a false negative result in 0.7% to 18.5% of simulated studies when using calipers, depending on treatment efficacy. When using an imaging device with lower user variability this was reduced to 0.0% to 2.6%, demonstrating that user variability impacts study outcomes and the ability to detect treatment effect. Reducing variability in efficacy studies can increase confidence in efficacy study outcomes without altering group sizes. By using a measurement device with lower user variability, the chance of missing a therapeutic effect can be reduced and time and resources spent pursuing false results could be saved. This improvement in data quality is of particular interest in discovery and dosing studies, where being able to detect small differences between groups is crucial.

The CRISPR/Cas9 system offers a new approach to genome editing and cancer treatment. This approach is able to detect drug targets and genomic analysis of cancer. The use of artificial intelligence (AI) capacity to edit genomes through CRISPR/Cas9 enables modification of gene mutations, molecular simulation. AI approaches include knowledge discovery approaches, antigen and epitope prediction approaches, and agent based-model approaches. These methods in combination with CRISPR/Cas9 can be used in vaccine design.

Patient-derived tumor xenograft (PDX) models were used to evaluate the effectiveness of preclinical anticancer agents. A design using 1 mouse per patient per drug (1 × 1 × 1) was considered practical for large-scale drug efficacy studies. We evaluated modifiable parameters that could increase the statistical power of this design based on our consolidated PDX experiments. Real studies were used as a reference to investigate the relationship between statistical power with treatment effect size, inter-mouse variation, and tumor measurement frequencies. Our results showed that large effect sizes could be detected at a significance level of .2 or .05 under a 1 × 1 × 1 design. We found that the minimum number of mice required to achieve 80% power at an alpha level of .05 under all situations explored was 21 mice per group for a small effect size and 5 mice per group for a medium effect size.

Tumor mutational burden (TMB), a surrogate for tumor neoepitope burden, is used as a pan-tumor biomarker to identify patients who may benefit from anti-program cell death 1 (PD1) immunotherapy, but it is an imperfect biomarker. Multiple additional genomic characteristics are associated with anti-PD1 responses, but the combined predictive value of these features and the added informativeness of each respective feature remains unknown. We evaluated whether machine learning (ML) approaches using proposed determinants of anti-PD1 response derived from whole exome sequencing (WES) could improve prediction of anti-PD1 responders over TMB alone. Random forest classifiers were trained on publicly available anti-PD1 data (n = 104), and subsequently tested on an independent anti-PD1 cohort (n = 69). Both the training and test datasets included a range of cancer types such as non-small cell lung cancer (NSCLC), head and neck squamous cell carcinoma (HNSCC), melanoma, and smaller numbers of patients from other tumor types. Features used include summaries such as TMB and number of frameshift mutations, as well as more gene-level features such as counts of mutations associated with immune checkpoint response and resistance. Both ML algorithms demonstrated area under the receiver-operator curves (AUC) that exceeded TMB alone (AUC 0.63 "human-guided," 0.64 "cluster," and 0.58 TMB alone). Mutations within oncogenes disproportionately modulate anti-PD1 responses relative to their overall contribution to tumor neoepitope burden. The use of a ML algorithm evaluating multiple proposed genomic determinants of anti-PD1 responses modestly improves performance over TMB alone, highlighting the need to integrate other biomarkers to further improve model performance.

Context: Models for predicting individual risks of surgical complications are advantageous for operative decision making and the nature of postoperative management procedures.

Objective: Validate the "ACS NSQIP^® Risk Calculator" in the prediction of postoperative complications during colorectal cancer surgery, operated during the years 2015 to 2019.

Methods: this is a prognostic validation study of the "ACS NSQIP^®" applied retrospectively to patients operated on for colorectal cancer in the surgical department of Farhat Hached hospital, during the 2015 and 2019 5-year term. Three levels of adjustment. Discrimination and calibration were carried out mainly by ROC curves (AUC ⩾ 0.8).

Results: In this study, 129 patients were included with a sex ratio of 1.22 and a median age of 62 years. The most common operative procedure was low segmental colectomy with colorectal anastomosis. Thirty-seven patients (28.7%) had at least one postoperative complication. The prediction and cuts-off points values of mortality (AUC = 0.858; CI_95% [0.570-0.960]; Cuts-off points = 1.8%), cardiac complications (AUC = 0.824; CI_95% [0.658-0.990]; Cuts-off points = 1.8%), thromboembolic complications (AUC = 0.802; CI_95% [0.617-0.987]; Cuts-off point = 3.1%), and renal insufficiency (AUC = 0.802; CI_95% [ 0.623-0.981]; Cuts-off point = 1.2%) were adjusted according to level 1 of the calculator.

Conclusion: This work contextualized the prediction of postoperative complications in colorectal surgery in the university general surgery department of Farhat Hached in Sousse (Tunisia), making it possible to improve the quality and safety of surgical care. The application of the Tunisian mini calculator is recommended as well as the generalization of validation following the development of a generic calculator for all operating procedures.

Background: Our objective was to describe the hospital-based systemic treatment sequences in early stage HER2+ breast cancer patients treated with trastuzumab in France in 2016.

Methods: This retrospective observational study was based on the national hospital discharge database (PMSI). Patients hospitalized for breast cancer in 2016 and administration of trastuzumab between 6 months prior and 1 year after surgery were included. The following treatments were identified: (1) trastuzumab ± chemotherapy; (2) chemotherapy alone; (3) q3w trastuzumab weekly chemotherapy. Hospital admissions for cardiac events before and after the surgery were investigated. An unsupervised machine learning technic called TAK (Time-sequence Analysis through K-clustering) was used to identify and visualize typical systemic treatment sequences.

Results: Overall, 3531 patients were included: 2619 adjuvant cohort patients (74.2%) and 912 neoadjuvant cohort patients (25.8%). The mean age was 56.4 years (±12.3), 99.7% patients were female. Treatment initiation occurred within 6 weeks of the surgery in 58% and 92% of patients, and trastuzumab treatment lasted 12 months (±1 month) in 75% and 66% of patients in the adjuvant and neoadjuvant cohorts, respectively. Nevertheless, 12% and 22% of patients were treated with trastuzumab for <11 months in the adjuvant and neoadjuvant cohorts, respectively. There was not one standard sequence of treatments per cohort, but 4 and 3 typical treatment sequences in the adjuvant and the neoadjuvant cohorts, respectively, plus 2 treatment sequences with an early treatment withdrawal. The frequency of patients with ⩾1 hospital stay with a cardiac event was higher among patients with an early treatment withdrawal.

Conclusions: The treatment sequences of most patients were in line with the recommendations in force. The machine learning approach provided a telling visual display of the results, thereby allowing healthcare professionals, health authorities, patients, and care givers to see the whole picture of the hospital-administered drug strategies.

Background: Though the development of targeted cancer drugs continues to accelerate, doctors still lack reliable methods for predicting patient response to standard-of-care therapies for most cancers. DNA methylation has been implicated in tumor drug response and is a promising source of predictive biomarkers of drug efficacy, yet the relationship between drug efficacy and DNA methylation remains largely unexplored.

Method: In this analysis, we performed log-rank survival analyses on patients grouped by cancer and drug exposure to find CpG sites where binary methylation status is associated with differential survival in patients treated with a specific drug but not in patients with the same cancer who were not exposed to that drug. We also clustered these drug-specific CpG sites based on co-methylation among patients to identify broader methylation patterns that may be related to drug efficacy, which we investigated for transcription factor binding site enrichment using gene set enrichment analysis.

Results: We identified CpG sites that were drug-specific predictors of survival in 38 cancer-drug patient groups across 15 cancers and 20 drugs. These included 11 CpG sites with similar drug-specific survival effects in multiple cancers. We also identified 76 clusters of CpG sites with stronger associations with patient drug response, many of which contained CpG sites in gene promoters containing transcription factor binding sites.

Conclusion: These findings are promising biomarkers of drug response for a variety of drugs and contribute to our understanding of drug-methylation interactions in cancer. Investigation and validation of these results could lead to the development of targeted co-therapies aimed at manipulating methylation in order to improve efficacy of commonly used therapies and could improve patient survival and quality of life by furthering the effort toward drug response prediction.

Motivation: Prediction of cancer outcome is a major challenge in oncology and is essential for treatment planning. Repositories such as The Cancer Genome Atlas (TCGA) contain vast amounts of data for many types of cancers. Our goal was to create reliable prediction models using TCGA data and validate them using an external dataset.

Results: For 16 TCGA cancer type cohorts we have optimized a Random Forest prediction model using parameter grid search followed by a backward feature elimination loop for dimensions reduction. For each feature that was removed, the model was retrained and the area under the curve of the receiver operating characteristic (AUC-ROC) was calculated using test data. Five prediction models gave AUC-ROC bigger than 80%. We used Clinical Proteomic Tumor Analysis Consortium v3 (CPTAC3) data for validation. The most enriched pathways for the top models were those involved in basic functions related to tumorigenesis and organ development. Enrichment for 2 prediction models of the TCGA-KIRP cohort was explored, one with 42 genes (AUC-ROC = 0.86) the other is composed of 300 genes (AUC-ROC = 0.85). The most enriched networks for both models share only 5 network nodes: DMBT1, IL11, HOXB6, TRIB3, PIM1. These genes play a significant role in renal cancer and might be used for prognosis prediction and as candidate therapeutic targets.

Availability and implementation: The prediction models were created and tested using Python SciKit-Learn package. They are freely accessible via a friendly web interface we called surviveAI at https://tinyurl.com/surviveai.