Analysis of rare fusions in NSCLC: Genomic architecture and clinical implications

OBJECTIVES

Molecular diagnosis for targeted therapies has been improved significantly in non-small-cell lung cancer (NSCLC) patients in recent years. Here we report on the prevalence of rare fusions in NSCLC and dissect their genomic architecture and potential clinical implications.

MATERIALS AND METHODS

Overall, n = 5554 NSCLC patients underwent next-generation sequencing (NGS) for combined detection of oncogenic mutations and fusions either at primary diagnosis (n = 5246) or after therapy resistance (n = 308). Panels of different sizes were employed with closed amplicon-based, or open assays, i.e. anchored multiplex PCR (AMP) and hybrid capture-based, for detection of translocations, including "rare" fusions, defined as those beyond ALK, ROS1, RET and <0.5 % frequency in NSCLC.

RESULTS

Rare fusions involving EGFR, MET, HER2, BRAF and other potentially actionable oncogenes were detected in 0.5% (n = 26) of therapy-naive and 2% (n = 6) TKI-treated tumors. Detection was increased using open assays and/or larger panels, especially those covering >25 genes, by approximately 1-2% (p = 0.001 for both). Patient characteristics (age, gender, smoking, TP53 co-mutations (56%), or mean tumor mutational burden (TMB) (4.8 mut/Mb)) showed no association with presence of rare fusions. Non-functional alterations, i.e. out-of-frame or lacking kinase domains, comprised one-third of detected rare fusions and were significantly associated with simultaneous presence of classical oncogenic drivers, e.g. EGFR or KRAS mutations (p < 0.001), or use of larger panels (frequency of non-functional among the detected rare fusions 57% for 25+ gene- vs. 12% for smaller panels, p < 0.001). As many rare fusions were identified before availability of targeted therapy, mean survival for therapy-naïve patients was 23.8 months, comparable with wild-type tumors.

CONCLUSION

Approximately 1-2% of advanced NSCLC harbor rare fusions, which are potentially actionable and may support diagnosis. Routine adoption of broad NGS assays capable to identify exact fusion points and potentially retained protein domains can increase the yield of therapeutically relevant molecular information in advanced NSCLC.

Spatial profiling of the microenvironment reveals low intratumoral heterogeneity and STK11-associated immune evasion in therapy-naïve lung adenocarcinomas

OBJECTIVE

Intratumoral heterogeneity was found to be a significant factor causing resistance to lung cancer therapies, including immune checkpoint blockade. Lesser is known about spatial heterogeneity of the tumor microenvironment (TME) and its association with genetic properties of the tumor, which is of particular interest in the therapy-naïve setting.

MATERIALS AND METHODS

We performed multi-region sampling (2-4 samples per tumor; total of 55 samples) from a cohort of 19 untreated stage IA-IIIB lung adenocarcinomas (n = 11 KRAS mutant, n = 1 ERBB2 mutant, n = 7 KRAS wildtype). For each sample the expression of 770 immunooncology-related genes was analyzed using the nCounter platform, while the mutational status was determined by hybrid capture-based next-generation sequencing (NGS) using a large panel covering more than 500 genes.

RESULTS

Global unsupervised analyses revealed clustering of the samples into two groups corresponding to a 'hot' or 'cold' immunologic tumor contexture based on the abundance of immune cell infiltrates. All analyzed specific immune cell signatures (ICsig) showed a significantly higher intertumoral than intratumoral heterogeneity (p < 0.02), as most of the analyzed cases (14/19) showed a very homogenous spatial immune cell profile. PD-L1 exhibited a significantly higher intertumoral than intratumoral heterogeneity (p = 1.03e-13). We found a specific association with 'cold' TME for STK11 (11/14, p < 0.07), but not KRAS, TP53, LRP1B, MTOR, U2AF1 co-mutations, and validated this finding using The Cancer Genome Atlas (TCGA) data.

CONCLUSION

Early-stage lung adenocarcinomas show considerable intertumoral, but limited intratumoral heterogeneity, which is clinically highly relevant as assessment before neoadjuvant treatment is based on small biopsies. STK11 mutations are specifically associated with a 'cold' TME, which could affect the efficacy of perioperative immunotherapy.

Deciphering the immunosuppressive tumor microenvironment in ALK- and EGFR-positive lung adenocarcinoma

Introduction

The advent of immune checkpoint blockade (ICB) has led to significantly improved disease outcome in lung adenocarcinoma (ADC), but response of ALK/EGFR-positive tumors to immune therapy is limited. The underlying immune biology is incompletely understood.

Methods

We performed comparative mRNA expression profiling of 31 ALK-positive, 40 EGFR-positive and 43 ALK/EGFR-negative lung ADC focused on immune gene expression. The presence and levels of tumor infiltration lymphocytes (TILs) as well as fourteen specific immune cell populations were estimated from the gene expression profiles.

Results

While total TILs were not lower in ALK-positive and EGFR-positive tumors compared to ALK/EGFR-negative tumors, specific immunosuppressive characteristics were detected in both subgroups: In ALK-positive tumors, regulatory T cells were significantly higher compared to EGFR-positive (fold change: FC = 1.9, p = 0.0013) and ALK/EGFR-negative tumors (FC = 2.1, p = 0.00047). In EGFR-positive tumors, cytotoxic cells were significantly lower compared to ALK-positive (FC =  − 1.7, p = 0.016) and to ALK/EGFR-negative tumors (FC =  − 2.1, p = 2.0E-05). A total number of 289 genes, 40 part of cytokine–cytokine receptor signaling, were differentially expressed between the three subgroups. Among the latter, five genes were differently expressed in both ALK-positive and EGFR-positive tumors, while twelve genes showed differential expression solely in ALK-positive tumors and eleven genes solely in EGFR-positive tumors.

Conclusion

Targeted gene expression profiling is a promising tool to read out tumor microenvironment characteristics from routine diagnostic lung cancer biopsies. Significant immune reactivity including specific immunosuppressive characteristics in ALK- and EGFR-positive lung ADC, but not a total absence of immune infiltration supports further clinical evaluation of immune-modulators as partners of ICB in such tumors.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00262-021-02981-w.

Photon-counting detectors in computed tomography: from quantum physics to clinical practice

Over the last decade, a fundamentally new type of computed tomography (CT) detectors has proved its superior capabilities in both physical and preclinical evaluations and is now approaching the stage of clinical practice. These detectors are able to discriminate single photons and quantify their energy and are hence called photon-counting detectors. Among the promising benefits of this technology are improved radiation dose efficiency, increased contrast-to-noise ratio, reduced metal artifacts, improved spatial resolution, simultaneous multi-energy acquisitions, and the prospect of multi-phase imaging within a single acquisition using multiple contrast agents. Taking the conventional energy-integrating detectors as a reference, the authors demonstrate the technical principles of this new technology and provide phantom and patient images acquired by a whole-body photon-counting CT. These images serve as a basis for discussing the potential future of clinical CT.

A gene expression signature associated with B cells predicts benefit from immune checkpoint blockade in lung adenocarcinoma

Immune checkpoint blockade (ICB) expands the therapeutic options for metastatic lung cancer nowadays representing a standard frontline strategy as monotherapy or combination therapy, as well as an option in oncogene-addicted NSCLC after exhaustion of targeted therapies. Predictive markers are urgently needed, since only a minority of patients benefits from ICB, while serious adverse effects of immunotoxicity may occur. The study cohort included 43 ICB-treated metastatic lung adenocarcinoma showing long-term response (n = 16), rapid progression (n = 21) or intermediate patterns of response (n = 6). Lung biopsies acquired before initiation of ICB were analyzed by targeted mRNA expression profiling of 770 genes. Level and proportions of 14 immune cell types were estimated using characteristic gene expression signatures. Abundance of B cells (HR = 0.66, p = .00074), CD45+ cells (HR = 0.61, p = .01) and total TILs (HR = 0.62, p = .025) was associated with prolonged progression-free survival after ICB treatment. In a ROC analysis, B cells (AUC = 0.77, p = .0055) and CD45+ cells (AUC = 0.73, p = .019) predicted benefit of ICB, which was not the case for PD-L1 mRNA (AUC = 0.54, p = .72) and PD-L1 protein expression (AUC = 0.68, p = .082). Clustering of 79 candidate predictive markers identified among 770 investigated genes revealed two distinct predictive clusters which included cytotoxic cell or macrophage markers, respectively. In summary, targeted gene expression profiling was feasible using routine diagnostics biopsies. This study proposes B cells and total TILs as complementary predictors of ICB benefit in NSCLC. While further preferably prospective validation is required, gene expression profiling could be integrated in the routine diagnostic work-up complementing existing NGS protocols.

[Epidemiology, Diagnosis and Treatment of Adult Patients with Nosocomial Pneumonia - Update 2017 - S3 Guideline of the German Society for Anaesthesiology and Intensive Care Medicine, the German Society for Infectious Diseases, the German Society for Hygiene and Microbiology, the German Respiratory Society and the Paul-Ehrlich-Society for Chemotherapy, the German Radiological Society and the Society for Virology]

Nosocomial pneumonia (HAP) is a frequent complication of hospital care. Most data are available on ventilator-associated pneumonia. However, infections on general wards are increasing. A central issue are infections with multidrug resistant (MDR) pathogens which are difficult to treat in the empirical setting potentially leading to inappropriate use of antimicrobial therapy.This guideline update was compiled by an interdisciplinary group on the basis of a systematic literature review. Recommendations are made according to GRADE giving guidance for the diagnosis and treatment of HAP on the basis of quality of evidence and benefit/risk ratio.This guideline has two parts. First an update on epidemiology, spectrum of pathogens and antimicrobials is provided. In the second part recommendations for the management of diagnosis and treatment are given. New recommendations with respect to imaging, diagnosis of nosocomial viral pneumonia and prolonged infusion of antibacterial drugs have been added. The statements to risk factors for infections with MDR pathogens and recommendations for monotherapy vs combination therapy have been actualised. The importance of structured deescalation concepts and limitation of treatment duration is emphasized.

[Tracheobronchoplasty for Severe Diffuse Tracheomalacia]

Patients with diffuse airway instability due to tracheobronchomalacia or excessive dynamic airway collapse are typically highly symptomatic, with marked dyspnoea, recurrent bronchopulmonary infections and excruciating intractable cough. Silicone stents achieve immediate symptom control, but are - due to the typical complications associated with stent treatment - usually not an option for long-term treatment. The aim of surgical intervention is definitive stabilisation of the trachea and of both main bronchi by posterior splinting of the Paries membranaceus with a polypropylene mesh. This operation is an appropriate treatment option for patients with documented severe tracheobronchomalacia or excessive dynamic airway collapse and is ultimately the only therapy that can achieve permanent symptom control. The success of the operation, however, depends on many factors and requires close interdisciplinary collaboration.

Identification of invasive fungal diseases in immunocompromised patients by combining an Aspergillus specific PCR with a multifungal DNA-microarray from primary clinical samples

The increasing incidence of invasive fungal diseases (IFD), most of all invasive aspergillosis (IA) in immunocompromised patients emphasises the need to improve the diagnostic tools for detection of fungal pathogens. We investigated the diagnostic performance of a multifungal DNA-microarray detecting 15 different fungi [Aspergillus, Candida, Fusarium, Mucor, Rhizopus, Scedosporium and Trichosporon species (spp.)] in addition to an Aspergillus specific polymerase chain reaction (PCR) assay. Biopsies, bronchoalveolar lavage and peripheral blood samples of 133 immunocompromised patients (pts) were investigated by a multifungal DNA-microarray as well as a nested Aspergillus specific PCR assay. Patients had proven (n = 18), probable (n = 29), possible (n = 48) and no IFD (n = 38) and were mostly under antifungal therapy at the time of sampling. The results were compared to culture, histopathology, imaging and serology, respectively. For the non-Aspergillus IFD the microarray analysis yielded in all samples a sensitivity of 64% and a specificity of 80%. Best results for the detection of all IFD were achieved by combining DNA-microarray and Aspergillus specific PCR in biopsy samples (sensitivity 79%; specificity 71%). The molecular assays in combination identify genomic DNA of fungal pathogens and may improve identification of causative pathogens of IFD and help overcoming the diagnostic uncertainty of culture and/or histopathology findings, even during antifungal therapy.

Treatment and outcome of lung cancer in idiopathic interstitial pneumonias

BACKGROUND

Idiopathic interstitial pneumonias (IIP) are associated with an increased lung cancer (LC) risk. However, data on the prognostic and therapeutic impact are limited. We therefore aimed to analyze the outcome of IIP patients with LC under different treatment modalities.

METHODS

Patients with IIPs diagnosed in a tertiary interstitial lung diseases (ILD) center were reviewed for LC diagnosis.

RESULTS

Of 265 patients with idiopathic pulmonary fibrosis (IPF), 142 with non-specific interstitial pneumonia (NSIP), and 71 with cryptogenic organizing pneumonia (COP), 16%, 4%, and 6% were affected byLC, respectively. Patient characteristics were: IPF: 93% male, median age 67 years, forced vital capacity (FVC) 82%, diffusion capacity for Carbon monoxide (DLCO) 41%, mean survival 20 months. NSIP: 67% male, median age 70 years, FVC 72%, DLCO 43%, mean survival 35 months. COP: 50% male, median age 66 years, FVC 93%, DLCO 77%, mean survival 88 months. Significant treatment-related toxicities occurred in 55% IPF, 20% NSIP und 0% COP patients. 30-days postoperative mortality was 25% in IPF, and 0% in NSIP/COP while rate of radiation pneumonitis was 24% in IPF.

CONCLUSIONS

LC is a frequent comorbidity in IIP, with a higher incidence and reduced survival in IPF compared to other IIPs. LC treatment is associated with significant toxicity, specifically in IPF. Interdisciplinary evaluation of therapeutic options in IIP patients diagnosed with LC is therefore mandatory.

CT-morphological characterization of respiratory syncytial virus (RSV) pneumonia in immune-compromised adults

PURPOSE

Characterization and follow-up evaluation of chest CT of RSV pneumonia in immune-compromised adults during a seasonal epidemic.

MATERIALS AND METHODS

Retrospective analysis of 132 chest CT examinations of 51 adult immune-compromised patients (29 m/22f, Ø58 years) with clinical signs of pneumonia and positive RSV test in winter 2011/2012. Two experienced chest radiologists evaluated the morphology (bronchial wall thickening, tree-in-bud, nodules, halo, ground-glass opacities, consolidations, pleural fluid) of the CT scans by consensus.

RESULTS

Pathological findings were in 86 % of the chest CT scans: Areas of ground-glass attenuation in 64 %, consolidations in 56 %, nodules in 55 % (Ø 8 mm in maximal diameter, with halo in 71 %), pleural fluid in 44 % (Ø 2 cm), tree-in-bud in 36 %, bronchial wall thickening in 27 % and more than one morphological finding in 72 %. There were no pathological CT findings in 14 % of patients with clinical symptoms of pneumonia because these patients did not undergo follow-up. Radiological progression was found in 45 % of patients and regression in 33 % in follow-up examinations. In 37 % an additional examination of the paranasal sinuses was performed and showed sinusitis in 63 % of cases. 90 % of the patients had sinusitis as well as pneumonia. In addition to RSV, a further pathogenic agent was found in bronchoalveolar lavage of five patients (Aspergillus spec., herpes simplex virus, Pseudomonas aeruginosa).

CONCLUSION

The most characteristic signs in chest CT scans were at the beginning of pneumonia with nodules and tree-in-bud often combined with bronchial wall thickening. The following CT scans showed characteristic but not pathognomonic chest CT findings of RSV pneumonia. These morphological findings should be recognized seasonally (winter) especially at the beginning of the case of pneumonia. RSV-associated additional sinusitis is probably common and should be noticed.

[Chronic obstructive pulmonary disease, periorbital and subconjunctival swelling]

A 70-year-old man with a history of chronic obstructive pulmonary disease (COPD) and dilative cardiomyopathy was referred due to acute dyspnea and chest pain. After spontaneous pneumothorax was confirmed by chest radiography, a chest tube was inserted into the right side. Persistent air bubbles escaping through the water seal of the drainage in synchrony with respiration indicated a bronchopleural fistula. A physical examination revealed orbital and subconjunctival emphysemas. Skull and chest computed tomography (CT) scans showed further massive cervical, thoracic and pulmonary subcutaneous emphysemas which are increased subcutaneous amounts of gas which can disperse along the fasciae. Cardinal sign is the sensation of air under the skin known as subcutaneous crepitation (similiar to touching rice crispies). Conditions causing subcutaneous emphysemas are trauma, medical treatment and intracutaneous gas production by bacteria. In this case, large amounts of air leaked out of the pleural space through the incision made for the chest tube into the subcutaneous tissue, mediastinum and retroperitoneum causing subcutaneous emphysemas. From there, ascending air spread along the fascial planes of the mediastinum and cervical area through the inferior orbital fissure to the orbits and eyelids causing orbital and subconjunctival emphysemas. On the basis of the progressive emphysemas and persistent pneumothorax, a second chest tube was inserted. Subsequently, the signs and symptoms disappeared completely.

[Dyspnea, fatigue and subpulmonary mass]

A 52-year-old man was referred for progressive dyspnea and fatigue. The medical history was unremarkable and there were no signs of late infections or previous tumorous diseases. Physical examination revealed diminished breath sounds and a dull tone over the right lower side. Routine blood tests, arterial blood gas and body plethysmography were all within normal ranges. Chest X-ray and thorax computed tomography (CT) showed the presence of a homogeneous subpulmonary mass with a diameter of 10 cm which had a water-like density of approximately 1 Hounsfield unit (HU). The presence of an extraordinary large pericardial cyst compromising the right lower lobe and therefore causing dyspnea was confirmed by video-assisted thoracoscopic surgery (VATS). Pericardial cysts are rare congenital mediastinal masses. They are usually asymptomatic and are usually found incidentally during routine chest X-ray, CT, magnetic resonance imaging (MRI) or echocardiography. Most pericardial cysts are situated at the right cardiophrenic angle. When reaching a relevant size they can cause symptoms such as dyspnea, coughing, chest pain and fatigue. The imaging studies most useful for diagnosis are CT, MRI and echocardiography. Differential diagnoses are diaphragmatic hernia, trapped pleural effusion or other pleural or mediastinal tumors.