Supporting the decision to perform molecular profiling for cancer patients based on routinely collected data through the use of machine learning

BACKGROUND

Personalized medicine offers targeted therapy options for cancer treatment. However, the decision whether to include a patient into next-generation sequencing (NGS) testing is not standardized. This may result in some patients receiving unnecessary testing while others who could benefit from it are not tested. Typically, patients who have exhausted conventional treatment options are of interest for consideration in molecularly targeted therapy. To assist clinicians in decision-making, we developed a decision support tool using routine data from a precision oncology program.

METHODS

We trained a machine learning model on clinical data to determine whether molecular profiling should be performed for a patient. To validate the model, the model's predictions were compared with decisions made by a molecular tumor board (MTB) using multiple patient case vignettes with their characteristics.

RESULTS

The prediction model included 440 patients with molecular profiling and 13,587 patients without testing. High area under the curve (AUC) scores indicated the importance of engineered features in deciding on molecular profiling. Patient age, physical condition, tumor type, metastases, and previous therapies were the most important features. During the validation MTB experts made the same decision of recommending a patient for molecular profiling only in 10 out of 15 of their previous cases but there was agreement between the experts and the model in 9 out of 15 cases.

CONCLUSION

Based on a historical cohort, our predictive model has the potential to assist clinicians in deciding whether to perform molecular profiling.

How can current oncological datasets be adjusted to support the automated patient recruitment in clinical trials?

OBJECTIVES

This study aims to identify necessary adjustments required in existing oncological datasets to effectively support automated patient recruitment.

METHODS

We extracted and categorized the inclusion and exclusion criteria from 115 oncological trials registered on ClinicalTrials.gov in 2022. These criteria were then compared with the content of the oBDS (Oncological Base Dataset version 3.0), Germany's legally mandated oncological data standard.

RESULTS

The analysis revealed that 42.9% of generalized inclusion and exclusion criteria are typically present as data fields in the oBDS. On average, 54.6% of all criteria per trial were covered. Notably, certain criteria such as comorbidities, pregnancy status, and laboratory values frequently appeared in trial protocols but were absent in the oBDS.

CONCLUSION

The omission of criteria, notably comorbidities, within the oBDS restricts its functionality to support trial recruitment. Addressing this limitation would enhance its overall effectiveness. Furthermore, the implications of these findings extend beyond Germany, suggesting potential relevance and applicability to oncological datasets globally.

Early clinical trial unit tumor board: a real-world experience in a national cancer network

PURPOSE

Early clinical trials are the first step into clinical therapies for new drugs. Within the six Bavarian university-based hospitals (Augsburg, Erlangen, Regensburg, Munich (LMU and TU), Würzburg) we have enrolled a virtual network platform for patient discussion.

METHODS

The virtual Early Clinical Trial Unit Tumor Board (ECTU Tumor Board) is a secured web-based meeting to evaluate early clinical trial options for patients, where representatives from local ECTUs participate. We retrospectively analyzed patient cases discussed between November 2021 and November 2022.

RESULTS

From November 2021 to November 2022, a total of 43 patients were discussed in the ECTU Tumor Board. Median age at diagnosis was 44.6 years (range 10-76 years). The median number of previous lines of therapies was 3.7 (range 1-9 therapies) including systemic treatment, surgery, and radiation therapy. A total of 27 different tumor entities were presented and 83.7% (36/43) patients received at least one trial recommendation. In total, 21 different active or shortly recruiting clinical trials were recommended: ten antibody trials, four BiTE (bispecific T cell engager) trials, six CAR (chimeric antigen receptor) T-cell trials, and one chemotherapy trial. Only six trials (28.6%) were recommended on the basis of the previously performed comprehensive genetic profiling (CGP).

CONCLUSION

The ECTU Tumor Board is a feasible and successful network, highlighting the force of virtual patient discussions for improving patient care as well as trial recruitment in advanced diseases. It can provide further treatment options after local MTB presentation, aiming to close the gap to access clinical trials.

Closing the cancer care gap with a patient-reported nutrition screening: A retrospective analysis of a quality improvement project on an oncology ward (CCC study)

BACKGROUND & AIMS

Early identification of patients at risk for malnutrition followed by individualized nutrition interventions is a central step to the provision of appropriate nutrition care. However, a health care professional (HCP)-based nutrition screening is not always consistently integrated into routine care. Patient-reported (PR) nutrition screening could thus potentially alleviate the burden on the HCPs and contribute to a greater number of patients who are identified and treated for malnutrition.

METHODS

In 2021 a Quality Improvement Project (QIP) at our out-patient oncology clinic was undertaken to implement the change from a HCP-based nutrition screening to a PR-screening. This was followed by a retrospective analysis in which the primary outcome measure was the rate of nutrition consultations initiated for patients undergoing cancer therapy.

RESULTS

In total n = 1657 patient data sets derived from comparable time periods before and after the QIP were analyzed and compared. Both groups had a comparable mean age and gender distribution. The most common diagnosis in both groups was gastrointestinal tumors. The change in routine care from a HCP-based nutrition screening to a PR-screening led to a significant increase in nutrition consultation rates (RD = 19%; p < 0.001; 95% CI 14.4%-23.5%) and screening rates (RD = 30.5%; p < 0.001; 95% CI 26.2%-34.7%).

CONCLUSIONS

The change to PR-screening potentially facilitates an increase in nutrition screening rates. This in turn leads to an increased rate of patients identified at risk for malnutrition and thus referrals for nutrition consultations. Our findings indicate that a PR nutrition screening tool could play a role in closing the care gap and contribute to reducing rates of malnutrition among this population where screening is not consistently integrated into routine care.

Optimizing the Analytical Value of Oncology-Related Data Based on an In-Memory Analysis Layer: Development and Assessment of the Munich Online Comprehensive Cancer Analysis Platform

Background

Many comprehensive cancer centers incorporate tumor documentation software supplying structured information from the associated centers’ oncology patients for internal and external audit purposes. However, much of the documentation data included in these systems often remain unused and unknown by most of the clinicians at the sites.

Objective

To improve access to such data for analytical purposes, a prerollout of an analysis layer based on the business intelligence software QlikView was implemented. This software allows for the real-time analysis and inspection of oncology-related data. The system is meant to increase access to the data while simultaneously providing tools for user-friendly real-time analytics.

Methods

The system combines in-memory capabilities (based on QlikView software) with innovative techniques that compress the complexity of the data, consequently improving its readability as well as its accessibility for designated end users. Aside from the technical and conceptual components, the software’s implementation necessitated a complex system of permission and governance.

Results

A continuously running system including daily updates with a user-friendly Web interface and real-time usage was established. This paper introduces its main components and major design ideas. A commented video summarizing and presenting the work can be found within the Multimedia Appendix.

Conclusions

The system has been well-received by a focus group of physicians within an initial prerollout. Aside from improving data transparency, the system’s main benefits are its quality and process control capabilities, knowledge discovery, and hypothesis generation. Limitations such as run time, governance, or misinterpretation of data are considered.

Dynamic Survival Analysis Using In-Memory Technology

In the field of oncology, survival analysis is one of the most important tools in terms of measuring therapy success, evaluating risk or prognostic factors. Within this work, a variety of common survival analyses were embedded into a real-time analysis platform based on a comprehensive oncological dataset. The analysis platform utilizes an in-memory database, therefore allowing spontaneous adjustments of the survival curves to selections and stratifications. In contrast to classical statistics, where individual scripts have to be formulated for every possible request, the running system allows the deduction of instantaneous results.

Knockout of mitochondrial thioredoxin reductase stabilizes prolyl hydroxylase 2 and inhibits tumor growth and tumor-derived angiogenesis

AIMS

Mitochondrial thioredoxin reductase (Txnrd2) is a central player in the control of mitochondrial hydrogen peroxide (H2O2) abundance by serving as a direct electron donor to the thioredoxin-peroxiredoxin axis. In this study, we investigated the impact of targeted disruption of Txnrd2 on tumor growth.

RESULTS

Tumor cells with a Txnrd2 deficiency failed to activate hypoxia-inducible factor-1α (Hif-1α) signaling; it rather caused PHD2 accumulation, Hif-1α degradation and decreased vascular endothelial growth factor (VEGF) levels, ultimately leading to reduced tumor growth and tumor vascularization. Increased c-Jun NH2-terminal Kinase (JNK) activation proved to be the molecular link between the loss of Txnrd2, an altered mitochondrial redox balance with compensatory upregulation of glutaredoxin-2, and elevated PHD2 expression.

INNOVATION

Our data provide compelling evidence for a yet-unrecognized mitochondrial Txnrd-driven, regulatory mechanism that ultimately prevents cellular Hif-1α accumulation. In addition, simultaneous targeting of both the mitochondrial thioredoxin and glutathione systems was used as an efficient therapeutic approach in hindering tumor growth.

CONCLUSION

This work demonstrates an unexpected regulatory link between mitochondrial Txnrd and the JNK-PHD2-Hif-1α axis, which highlights how the loss of Txnrd2 and the resulting altered mitochondrial redox balance impairs tumor growth as well as tumor-related angiogenesis. Furthermore, it opens a new avenue for a therapeutic approach to hinder tumor growth by the simultaneous targeting of both the mitochondrial thioredoxin and glutathione systems.

Using Supercritical Carbon Dioxide for Physical Foaming of Advanced Polymer Materials

Foams from high performance polymers find more and more interest. The processes to generate them can be difficult, however. It is shown how physical foaming with CO2 can be used as a first step to assess the potentials of such materials. For investigations of such kind an autoclave on a laboratory scale which allows pressure variations up to 300 bars and temperatures up to 300°C was set up. The samples are saturated with supercritical carbon dioxide (s.c. CO2) which acts as a foaming agent. Depending on the process and material parameters different foam characteristics and cell morphologies were obtained and characterised. The potential of this method is demonstrated for two different classes of advanced polymer materials, thermoplastic fluoropolymers (FEP), and a silicone resin. In the case of the fluoropolymer, previously prepared films were foamed and the effects of various process parameters on the foam characteristics were investigated. Besides the general potential of foams from fluoropolymers, they are candidates for polymeric piezoelectric materials with a relatively high temperature stability. Silicone polymers possess some properties superior to common organic polymers. First results on the foaming behaviour of a silicone resin are presented.

Silica-supported TEMPO catalysts: synthesis and application in the Anelli oxidation of alcohols

The application of silica-supported TEMPO as a recyclable catalyst in the Anelli oxidation of alcohols is reported. The catalyst is easily obtained in a one-step reductive amination procedure starting from a commercially available aminopropyl-functionalized silica. Details of the synthesis of the supported catalyst and its analysis by MAS NMR are presented. Various alcohol oxidations according to the Anelli protocol have been carried out and the stability of the applied silica-supported TEMPO has been studied.

3,5-Bis(trifluoromethyl)pyrazoles: a novel class of NFAT transcription factor regulator

A series of bis(trifluoromethyl)pyrazoles (BTPs) has been found to be a novel inhibitor of cytokine production. Identified initially as inhibitors of IL-2 synthesis, the BTPs have been optimized in this regard and even inhibit IL-2 production with a 10-fold enhancement over cyclosporine in an ex vivo assay. Additionally, the BTPs show inhibition of IL-4, IL-5, IL-8, and eotaxin production. Unlike the IL-2 inhibitors, cyclosporine and FK506, the BTPs do not directly inhibit the dephosphorylation of NFAT by calcineurin.

[Broadband ultrasound attenuation (BUA) in the diagnosis of osteoporosis]

The measurement of broadband ultrasound attenuation (BUA) of the calcaneus has been introduced as a new technique that provides information about both bone mass and structure without the use of ionizing radiation. BUA measurements of the calcaneus were obtained in 324 patients, 109 of whom had osteoporosis. Two hundred and fifteen patients served as control group. BUA values were compared with dual-energy X-ray absorptiometry (DXA) measurements of the lumbar spine, the neck and the heel. The precision error of BUA was 4.1%. The correlation with spinal bone mineral density was r = 0.49, with DXA of the neck r = 0.52 and of the calcaneus r = 0.56, respectively. Patients with osteoporosis showed a significant decrease in BUA compared with healthy subjects (61.4 dB/MHz vs 74.6 dB/MHz). Roc analysis demonstrated that BUA was inferior to DXA of the lumbar spine in detecting osteoporosis.