Artificial intelligence for predictive biomarker discovery in immuno-oncology: a systematic review

BACKGROUND

The widespread use of immune checkpoint inhibitors (ICIs) has revolutionised treatment of multiple cancer types. However, selecting patients who may benefit from ICI remains challenging. Artificial intelligence (AI) approaches allow exploitation of high-dimension oncological data in research and development of precision immuno-oncology.

MATERIALS AND METHODS

We conducted a systematic literature review of peer-reviewed original articles studying the ICI efficacy prediction in cancer patients across five data modalities: genomics (including genomics, transcriptomics, and epigenomics), radiomics, digital pathology (pathomics), and real-world and multimodality data.

RESULTS

A total of 90 studies were included in this systematic review, with 80% published in 2021-2022. Among them, 37 studies included genomic, 20 radiomic, 8 pathomic, 20 real-world, and 5 multimodal data. Standard machine learning (ML) methods were used in 72% of studies, deep learning (DL) methods in 22%, and both in 6%. The most frequently studied cancer type was non-small-cell lung cancer (36%), followed by melanoma (16%), while 25% included pan-cancer studies. No prospective study design incorporated AI-based methodologies from the outset; rather, all implemented AI as a post hoc analysis. Novel biomarkers for ICI in radiomics and pathomics were identified using AI approaches, and molecular biomarkers have expanded past genomics into transcriptomics and epigenomics. Finally, complex algorithms and new types of AI-based markers, such as meta-biomarkers, are emerging by integrating multimodal/multi-omics data.

CONCLUSION

AI-based methods have expanded the horizon for biomarker discovery, demonstrating the power of integrating multimodal data from existing datasets to discover new meta-biomarkers. While most of the included studies showed promise for AI-based prediction of benefit from immunotherapy, none provided high-level evidence for immediate practice change. A priori planned prospective trial designs are needed to cover all lifecycle steps of these software biomarkers, from development and validation to integration into clinical practice.

STYLE (NCT03449173) a phase II Trial of Sunitinib in patients with type B3 Thymoma or Thymic Carcinoma in second and further lines

BACKGROUND

Thymic malignancies are rare tumors with few therapeutic options. The STYLE trial was aimed to evaluate activity and safety of sunitinib in advanced/recurrent type B3 thymoma (T) and thymic carcinoma (TC).

METHODS

In this multicenter Simon 2 stages phase II trial, patients with pretreated T/TC were enrolled in two cohorts and assessed separately. Sunitinib was administered 50mg daily for 4-weeks, followed by a 2-week rest period (schedule 4/2), until disease progression or unacceptable toxicity. The primary endpoint was objectives response rate (ORR). Progression free survival (PFS), overall survival (OS), disease control rate (DCR) and safety were secondary endpoints.

RESULTS

From 03/2017 to 01/2022, 12 T and 32 TC patients were enrolled. At stage 1 ORR was 0% (90%CI 0.0-22.1) in T and 16.7% (90%CI 3.1-43.8) in TC, so T cohort was closed. At stage 2, the primary endpoint was met for TC with ORR of 21.7% (90%CI 9.0%-40.4%). In the ITT analysis DCR was 91.7% (95%CI 61.5%-99.8%) in Ts and 89.3% (95%CI 71.8%-97.7%) in TCs. mPFS was 7.7 months (95%CI 2.4-45.5) in Ts, 8.8 (95%CI 5.3-11.1) in TCs; mOS was 47.9 months (95%CI 4.5-not reached) in Ts, and 27.8 (95%CI 13.2-53.2) in TCs. Adverse events (AEs) occurred in 91.7% T and 93.5% TCs. Grade ≥3 treatment-related AEs were reported in 25.0% T and 51.6% TC.

CONCLUSIONS

This trial confirms the activity of sunitinib in TC patients, supporting its use as second line treatment.

PEOPLE (NCT03447678), a first-line phase II pembrolizumab trial, in negative and low PD-L1 advanced NSCLC: clinical outcomes and association with circulating immune biomarkers

BACKGROUND

The PEOPLE trial aimed to identify new immune biomarkers in negative and low programmed death-ligand 1 (PD-L1) (0%-49%) advanced non-small-cell lung cancer (aNSCLC) patients treated with first-line pembrolizumab. Here we report the main outcomes and the circulating immune biomarkers analysis.

PATIENTS AND METHODS

The primary endpoint of this phase II trial was the identification of immune biomarkers associated with progression-free survival (PFS). Overall survival (OS), objective response rate (ORR), disease control rate (DCR), duration of response (DoR) and safety were secondary endpoints. Absolute cell counts for 36 subsets belonging to innate and adaptive immunity were determined by multiparametric flow cytometry in peripheral blood at baseline and at first radiologic evaluation. An orthoblique principal components-based clustering approach and multivariable Cox regression model adjusted for clinical variables were used to analyze immune variables and their correlation with clinical endpoints.

RESULTS

From May 2018 to October 2020, 65 patients were enrolled. After a median follow-up of 26.4 months, the median PFS was 2.9 months [95% confidence interval (CI) 1.8-5.6 months] and median OS was 12.1 months (95% CI 8.7-17.1 months). The ORR was 21.5%, DCR was 47.7% and median DoR was 14.5 months (95% CI 6.4-24.9 months). Drug-related grade 3-4 adverse events were 9.2%. Higher T cell and natural killer (NK) cell count at baseline and at the first radiologic evaluation were associated with improved PFS, DCR and OS. On the contrary, higher myeloid cell count at baseline or at the first radiologic evaluation was significantly associated with worse OS and DCR.

CONCLUSIONS

Circulating immune biomarkers can contribute to predict outcomes in negative and low PD-L1 aNSCLC patients treated with first-line single-agent pembrolizumab.

Choosing wisely first line immunotherapy in non-small cell lung cancer (NSCLC): what to add and what to leave out

Immunotherapy has dramatically changed the therapeutic scenario in treatment naïve advanced non-small cell lung cancer (NSCLC). While single agent pembrolizumab has become the standard therapy in patients with PD-L1 expression on tumor cells ≥ 50%, the combination of pembrolizumab or atezolizumab and platinum-based chemotherapy has emerged as an effective first line treatment regardless of PD-L1 expression both in squamous and non-squamous NSCLC without oncogenic drivers. Furthermore, double immune checkpoint inhibition has shown promising results in treatment naïve patients with high tumor mutational burden (TMB). Of note, the presence of both negative PD-L1 expression and low TMB may identify a subgroup of patients who has little benefit from immunotherapy combinations and for whom the best treatment option may still be platinum-based chemotherapy. To date, first-line single agent immune checkpoint blockade has demonstrated limited activity in EGFR mutated NSCLC and the combination of immunotherapy and targeted agents has raised safety concerns in both EGFR and ALK positive NSCLC patients. Finally, in EGFR mutated or ALK rearranged NSCLC, atezolizumab in combination with platinum-based chemotherapy and bevacizumab is emerging as a potential treatment option upon progression to first line tyrosine kinase inhibitors.

Implementation of cardiovascular secondary prevention guidelines in clinical practice: a nationwide survey in Italy

AIMS

To report the implementation of cardiovascular secondary prevention guidelines following a cardiovascular event in Italy.

METHODS AND RESULTS

Data were collected from 878 consecutive patients, who had suffered a cardiovascular event requiring hospitalisation in the preceding 12-24 months and who presented at 49 outpatient clinics across Italy. Cardiovascular risk markers were assessed through clinical examination, interview and reviewing of patients' charts; in addition, we collected information on changes in prevalence of selected risk factors that occurred since the time of index event. At the time of evaluation, increased body mass index (BMI) was observed in 35% of patients, with 20% being obese; 26% had diabetes and 21% uncontrolled hypertension. Although 91% of patients were on statins, no measurement of low-density lipoprotein (LDL)-cholesterol was available in the previous 6 months in 27% of patients and 16% had no knowledge of any lipid parameter in the same period. In the remaining patients, LDL was <100 mg dl(-1) in 57% and <70 mg dl(-1) in 20% of them. From the time of index event to interview, prevalence of uncontrolled hypertension remained stable, from 24% to 21% of patients; according to the patients' self-reporting, smoking had declined from 32% to 13% of patients and physical inactivity from 43% to 33% of patients.

CONCLUSIONS

This survey shows, in a large national cohort, a suboptimal implementation of lifestyle changes and inadequate lipid control in patients at high cardiovascular risk after a cardiovascular event. Reinforcement of patients and physicians, implementation and adherence to guidelines is needed to reduce the burden of cardiovascular disease.