Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer.

OBJECTIVES: Mutational signatures (MS) are gaining traction for deriving therapeutic insights for immune checkpoint inhibition (ICI). We asked if MS attributions from comprehensive targeted sequencing assays are reliable enough for predicting ICI efficacy in non-small cell lung cancer (NSCLC). METHODS: Somatic mutations of m = 126 patients were assayed using panel-based sequencing of 523 cancer-related genes. In silico simulations of MS attributions for various panels were performed on a separate dataset of m = 101 whole genome sequenced patients. Non-synonymous mutations were deconvoluted using COSMIC v3.3 signatures and used to test a previously published machine learning classifier. RESULTS: The ICI efficacy predictor performed poorly with an accuracy of 0.51-0.09+0.09, average precision of 0.52-0.11+0.11, and an area under the receiver operating characteristic curve of 0.50-0.09+0.10. Theoretical arguments, experimental data, and in silico simulations pointed to false negative rates (FNR) related to panel size. A secondary effect was observed, where deconvolution of small ensembles of point mutations lead to reconstruction errors and misattributions. CONCLUSION: MS attributions from current targeted panel sequencing are not reliable enough to predict ICI efficacy. We suggest that, for downstream classification tasks in NSCLC, signature attributions be based on whole exome or genome sequencing instead.

Using genomic scars to select immunotherapy beneficiaries in advanced non-small cell lung cancer.

In advanced non-small cell lung cancer (NSCLC), response to immunotherapy is difficult to predict from pre-treatment information. Given the toxicity of immunotherapy and its financial burden on the healthcare system, we set out to identify patients for whom treatment is effective. To this end, we used mutational signatures from DNA mutations in pre-treatment tissue. Single base substitutions, doublet base substitutions, indels, and copy number alteration signatures were analysed in [Formula: see text] patients (the discovery set). We found that tobacco smoking signature (SBS4) and thiopurine chemotherapy exposure-associated signature (SBS87) were linked to durable benefit. Combining both signatures in a machine learning model separated patients with a progression-free survival hazard ratio of 0.40[Formula: see text] on the cross-validated discovery set and 0.24[Formula: see text] on an independent external validation set ([Formula: see text]). This paper demonstrates that the fingerprints of mutagenesis, codified through mutational signatures, select advanced NSCLC patients who may benefit from immunotherapy, thus potentially reducing unnecessary patient burden.

Cell water balance of white button mushrooms (Agaricus bisporus) during its post-harvest lifetime studied by quantitative magnetic resonance imaging.

A combination of quantitative water density and T2 MRI and changes therein observed after infiltration with 'invisible' Gd-DTPA solution was used to study cell water balances, cell water potentials and cell integrity. This method was applied to reveal the evolution and mechanism of redistribution of water in harvested mushrooms. Even when mushrooms did not lose water during the storage period, a redistribution of water was observed from stipe to cap and gills. When the storage condition resulted in a net loss of water, the stipe lost more water than the cap. The water density in the gill increased, probably due to development of spores. Deterioration effects (i.e. leakage of cells, decrease in osmotic water potential) were found in the outer stipe. They were not found in the cap, even at prolonged storage at 293 K and R.H.=70%. The changes in osmotic potential were partly accounted for by changes in the mannitol concentration. Changes in membrane permeability were also indicated. Cells in the cap had a constant low membrane (water) permeability. They developed a decreasing osmotic potential (more negative), whereas the osmotic potential in the outer stipe increased, together with the permeability of cells.

Quantitative 1H-NMR imaging of water in white button mushrooms (Agaricus bisporus).

MRI represents a valuable tool for studying the amount and physical status of water in plants and agricultural products, for example, mushrooms (Agaricus bisporus). Contrast in NMR images originates from the mixed influence of the fundamental NMR parameters, amongst others, spin-density, T2- and T1 relaxation processes. Maps of these parameters contain valuable anatomical and physiological information. They can, however, be severely distorted, depending on the combination of parameter settings and anatomy of the object under study. The influence of the tissue structure of mushrooms, for example, tissue density (susceptibility inhomogeneity) and cell shape on the amplitude, T2, and T1 images is analyzed. This is achieved by vacuum infiltration of the cavities in the mushroom's spongy structure with Gd-DTPA solutions and acquiring Saturation Recovery-Multispin Echo images. It is demonstrated that the intrinsic long T2 values in the cap and outer stipe tissue strongly relate to the size and geometry of the highly vacuolated cells in these spongy tissues. All observed T2 values are strongly affected by susceptibility effects. The T2 of gill tissue is shorter than T2 of the cap and outer stipe, probably because these cells are less vacuolized and smaller in size. The calculated amplitude images are not directly influenced by susceptibility inhomogeneities as long as the observed relaxation times remained sufficient long. They reflect the water distribution in mushrooms best if short echo times are applied in a multispin echo imaging sequence at low magnetic field strength.

NMR imaging of white button mushroom (Agaricus bisporis) at various magnetic fields.

Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) have been applied to visualize physiological phenomena in plants and agricultural crops. Imaging sequences that result in contrast of a combination of parameters (e.g., proton density, T1, T2, T2*) cannot be used for a correct and unique interpretation of the results. In this study multiecho imaging together with monoexponential T2 decay fitting was applied to determine reliable proton density and T2 distributions over a mushroom. This was done at three magnetic field strengths (9.4, 4.7, and 0.47 T) because susceptibility inhomogeneities were suspected to influence the T2 relaxation times negatively, and because the influences of susceptibility inhomogeneities increase with a rise in magnetic field strength. Electron microscopy was used to understand the different T2's for the various tissue types in mushrooms. Large influences of the tissue ultrastructure on the observed T2 relaxation times were found and explained. Based on the results, it is concluded that imaging mushrooms at low fields (around or below 0.47 T) and short echo times has strong advantages over its high-field counterpart, especially with respect to quantitative imaging of the water balance of mushrooms. These conclusions indicate general validity whenever NMR imaging contrast is influenced by susceptibility inhomogeneities.