Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach

CONTEXT.—

The neurotrophic tropomyosin receptor kinase (NTRK) family gene rearrangements have been recently incorporated as predictive biomarkers in a "tumor-agnostic" manner. However, the identification of these patients is extremely challenging because the overall frequency of NTRK fusions is below 1%. Academic groups and professional organizations have released recommendations on the algorithms to detect NTRK fusions. The European Society for Medical Oncology proposal encourages the use of next-generation sequencing (NGS) if available, or alternatively immunohistochemistry (IHC) could be used for screening with NGS confirmation of all positive IHC results. Other academic groups have included histologic and genomic information in the testing algorithm.

OBJECTIVE.—

To apply some of these triaging strategies for a more efficient identification of NTRK fusions within a single institution, so pathologists can gain practical insight on how to start looking for NTRK fusions.

DESIGN.—

A multiparametric strategy combining histologic (secretory carcinomas of the breast and salivary gland; papillary thyroid carcinomas; infantile fibrosarcoma) and genomic (driver-negative non-small cell lung carcinomas, microsatellite instability-high colorectal adenocarcinomas, and wild-type gastrointestinal stromal tumors) triaging was put forward.

RESULTS.—

Samples from 323 tumors were stained with the VENTANA pan-TRK EPR17341 Assay as a screening method. All positive IHC cases were simultaneously studied by 2 NGS tests, Oncomine Comprehensive Assay v3 and FoundationOne CDx. With this approach, the detection rate of NTRK fusions was 20 times higher (5.57%) by only screening 323 patients than the largest cohort in the literature (0.30%) comprising several hundred thousand patients.

CONCLUSIONS.—

Based on our findings, we propose a multiparametric strategy (ie, "supervised tumor-agnostic approach") when pathologists start searching for NTRK fusions.

Fgf signalling triggers an intrinsic mesodermal timer that determines the duration of limb patterning

Complex signalling between the apical ectodermal ridge (AER - a thickening of the distal epithelium) and the mesoderm controls limb patterning along the proximo-distal axis (humerus to digits). However, the essential in vivo requirement for AER-Fgf signalling makes it difficult to understand the exact roles that it fulfils. To overcome this barrier, we developed an amenable ex vivo chick wing tissue explant system that faithfully replicates in vivo parameters. Using inhibition experiments and RNA-sequencing, we identify a transient role for Fgfs in triggering the distal patterning phase. Fgfs are then dispensable for the maintenance of an intrinsic mesodermal transcriptome, which controls proliferation/differentiation timing and the duration of patterning. We also uncover additional roles for Fgf signalling in maintaining AER-related gene expression and in suppressing myogenesis. We describe a simple logic for limb patterning duration, which is potentially applicable to other systems, including the main body axis.

Cell-free KRAS in pancreatic cancer as a rapid prognostic marker

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Background: KRAS mutations are present over 90% of patients with pancreatic cancer (PC). Liquid biopsies provide the opportunity to genotype alterations in a less invasive way and offer a possibility to monitor the molecular characteristics of a cancer through the course of treatment. We aim to establish an association between the mutational levels of KRAS detected in plasma with patient stage and evolution. Methods: Plasma samples were collected from patients with newly diagnosed PC, before any treatment and during one year. Diagnosis of any previous cancer was an exclusion criterion. Samples were frozen (-80ºC) until analysis of KRAS mutations in cell free DNA (cfDNA) by real time PCR. Specifically, Idylla TM technology was used due to the rapid capacity to report up to 21 KRAS mutations in exon 2, 3, and 4 (LOD = < 5%), without necessity of cfDNA isolation. Mutation was considered present (categorical measurement), taking into account cycle quantification values (Cq) established by the commercial test. Cut-off values for Cq were studied by the ROC curve (receiver operating characteristic) with the Youden's J statistic. Paired tissue samples were analyzed when available. Results: A total of 23 patients were enrolled, median age 65 years old, 57% male, 100% adenocarcinoma, 18 (70%) metastatic. Sixteen patients could also be tested in tissue, being 15 (93.8%) positive for KRAS mutation. Plasma basal mutations were detected in 10 patients (43.5%), all in stage IV (p = 0.046), and interestingly, all with liver involvement (p = 0.003). Moreover, these patients also had metastasis in another organ apart from the liver. The most frequent mutation was G12V (5), followed by G12D (4) and G12R (1). Patients with basal KRAS mutations detected in plasma had a survival of 6.1 months (CI 95%, 3.7-8.5), and non-mutated 11.2 months (95% CI, 7.8-14.7) (p = 0.041). The presence of these cell-free KRAS mutations was more informative for survival than stage IV disease vs III (p = 0.054). Paying attention to KRAS wild type detection in plasma samples used as an internal control of the PCR, we could establish a Cq value cut-off of < 21 Cq for mutant samples, with a sensitivity of 100% (95% CI, 75%-100%) and specificity of 50% (95% CI, 19%-81%), area under ROC curve 0.823 (95% CI, 0.649-0.997). Conclusions: Measurement of cell-free KRAS in plasma samples at diagnosis could be used to quickly predict metastasis and survival in patients with pancreatic adenocarcinoma.

An intrinsic cell cycle timer terminates limb bud outgrowth

The longstanding view of how proliferative outgrowth terminates following the patterning phase of limb development involves the breakdown of reciprocal extrinsic signalling between the distal mesenchyme and the overlying epithelium (e-m signalling). However, by grafting distal mesenchyme cells from late stage chick wing buds to the epithelial environment of younger wing buds, we show that this mechanism is not required. RNA sequencing reveals that distal mesenchyme cells complete proliferative outgrowth by an intrinsic cell cycle timer in the presence of e-m signalling. In this process, e-m signalling is required permissively to allow the intrinsic cell cycle timer to run its course. We provide evidence that a temporal switch from BMP antagonism to BMP signalling controls the intrinsic cell cycle timer during limb outgrowth. Our findings have general implications for other patterning systems in which extrinsic signals and intrinsic timers are integrated.

Intrinsic properties of limb bud cells can be differentially reset

An intrinsic timing mechanism specifies the positional values of the zeugopod (i.e. radius/ulna) and then autopod (i.e. wrist/digits) segments during limb development. Here, we have addressed whether this timing mechanism ensures that patterning events occur only once by grafting GFP-expressing autopod progenitor cells to the earlier host signalling environment of zeugopod progenitor cells. We show by detecting Hoxa13 expression that early and late autopod progenitors fated for the wrist and phalanges, respectively, both contribute to the entire host autopod, indicating that the autopod positional value is irreversibly determined. We provide evidence that Hoxa13 provides an autopod-specific positional value that correctly allocates cells into the autopod, most likely through the control of cell-surface properties as shown by cell-cell sorting analyses. However, we demonstrate that only the earlier autopod cells can adopt the host proliferation rate to permit normal morphogenesis. Therefore, our findings reveal that the ability of embryonic cells to differentially reset their intrinsic behaviours confers robustness to limb morphogenesis. We speculate that this plasticity could be maintained beyond embryogenesis in limbs with regenerative capacity.

An intrinsic timer specifies distal structures of the vertebrate limb

How the positional values along the proximo-distal axis (stylopod-zeugopod-autopod) of the limb are specified is intensely debated. Early work suggested that cells intrinsically change their proximo-distal positional values by measuring time. Recently, however, it is suggested that instructive extrinsic signals from the trunk and apical ectodermal ridge specify the stylopod and zeugopod/autopod, respectively. Here, we show that the zeugopod and autopod are specified by an intrinsic timing mechanism. By grafting green fluorescent protein-expressing cells from early to late chick wing buds, we demonstrate that distal mesenchyme cells intrinsically time Hoxa13 expression, cell cycle parameters and the duration of the overlying apical ectodermal ridge. In addition, we reveal that cell affinities intrinsically change in the distal mesenchyme, which we suggest results in a gradient of positional values along the proximo-distal axis. We propose a complete model in which a switch from extrinsic signalling to intrinsic timing patterns the vertebrate limb.