Neurotrophic tyrosine receptor kinase gene fusions in adult and pediatric patients with solid tumors: a clinicogenomic biobank and record linkage study of expression frequency and patient characteristics from Finland.

BACKGROUND: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers. Using the Auria Biobank in Finland, we aimed to identify and characterize patients with these gene fusions, and describe their clinical and tumor characteristics, treatments received, and outcomes. MATERIAL AND METHODS: We evaluated pediatrics with any solid tumor type and adults with colorectal cancer (CRC), non-small cell lung cancer (NSCLC), sarcoma, or salivary gland cancer. We determined tropomyosin receptor kinase (TRK) protein expression by pan-TRK immunohistochemistry (IHC) staining of tumor samples from the Auria Biobank, scored by a certified pathologist. NTRK gene fusion was confirmed by next generation sequencing (NGS). All 2,059 patients were followed-up starting 1 year before their cancer diagnosis. RESULTS: Frequency of NTRK gene fusion tumors was 3.1% (4/127) in pediatrics, 0.7% (8/1,151) for CRC, 0.3% (1/288) for NSCLC, 0.9% (1/114) for salivary gland cancer, and 0% (0/379) for sarcoma. Among pediatrics there was one case each of fibrosarcoma (TPM3::NTRK1), Ewing's sarcoma (LPPR1::NTRK2), primitive neuroectodermal tumor (DAB2IP::NTRK2), and papillary thyroid carcinoma (RAD51B::NTRK3). Among CRC patients, six harbored tumors with NTRK1 fusions (three fused with TPM3), one harbored a NTRK3::GABRG1 fusion, and the other a NTRK2::FXN/LPPR1 fusion. Microsatellite instability was higher in CRC patients with NTRK gene fusion tumors versus wild-type tumors (50.0% vs. 4.4%). Other detected fusions were SGCZ::NTRK3 (NSCLC) and ETV6::NTRK3 (salivary gland cancer). Four patients (three CRC, one NSCLC) received chemotherapy; one patient (with CRC) received radiotherapy. CONCLUSION: NTRK gene fusions are rare in adult CRC, NSCLC, salivary tumors, sarcoma, and pediatric solid tumors.

Neurotrophic-tyrosine receptor kinase gene fusion in papillary thyroid cancer: A clinicogenomic biobank and record linkage study from Finland.

Selective tropomyosin receptor kinase (TRK) inhibitors are approved targeted therapies for patients with solid tumors harboring a neurotrophic tyrosine receptor kinase (NTRK) gene fusion. Country-specific estimates of NTRK gene fusion frequency, and knowledge on the characteristics of affected patients, are limited. We identified patients with histologically-confirmed papillary thyroid cancer (PTC) from Finland's Auria Biobank. TRK protein expression was determined by pan-TRK immunohistochemistry. Immuno-stained tumor samples were scored by a certified pathologist. Gene fusions and other co-occurring gene alterations were identified by next generation sequencing. Patient characteristics and vital status were determined from linked hospital electronic health records (EHRs). Patients were followed from 1 year before PTC diagnosis until death. 6/389 (1.5%) PTC patients had an NTRK gene fusion (all NTRK3); mean age 43.8 years (and none had comorbidities) at PTC diagnosis. Gene fusion partners were EML4 (n = 3), ETV6 (n = 2), and RBPMS (n = 1). Of 3/6 patients with complete EHRs, all received radioactive iodine ablation only and were alive at end of follow-up (median observation, 9.12 years). In conclusion, NTRK gene fusion is infrequent in patients with PTC. Linkage of biobank samples to EHRs is feasible in describing the characteristics and outcomes of patients with PTC and potentially other cancer types.

Real-world EGFR testing practices for non-small-cell lung cancer by thoracic pathology laboratories across Europe.

BACKGROUND: Testing for epidermal growth factor receptor (EGFR) mutations is an essential recommendation in guidelines for metastatic non-squamous non-small-cell lung cancer, and is considered mandatory in European countries. However, in practice, challenges are often faced when carrying out routine biomarker testing, including access to testing, inadequate tissue samples and long turnaround times (TATs). MATERIALS AND METHODS: To evaluate the real-world EGFR testing practices of European pathology laboratories, an online survey was set up and validated by the Pulmonary Pathology Working Group of the European Society of Pathology and distributed to 64 expert testing laboratories. The retrospective survey focussed on laboratory organisation and daily EGFR testing practice of pathologists and molecular biologists between 2018 and 2021. RESULTS: TATs varied greatly both between and within countries. These discrepancies may be partly due to reflex testing practices, as 20.8% of laboratories carried out EGFR testing only at the request of the clinician. Many laboratories across Europe still favour single-test sequencing as a primary method of EGFR mutation identification; 32.7% indicated that they only used targeted techniques and 45.1% used single-gene testing followed by next-generation sequencing (NGS), depending on the case. Reported testing rates were consistent over time with no significant decrease in the number of EGFR tests carried out in 2020, despite the increased pressure faced by testing facilities during the COVID-19 pandemic. ISO 15189 accreditation was reported by 42.0% of molecular biology laboratories for single-test sequencing, and by 42.3% for NGS. 92.5% of laboratories indicated they regularly participate in an external quality assessment scheme. CONCLUSIONS: These results highlight the strong heterogeneity of EGFR testing that still occurs within thoracic pathology and molecular biology laboratories across Europe. Even among expert testing facilities there is variability in testing capabilities, TAT, reflex testing practice and laboratory accreditation, stressing the need to harmonise reimbursement technologies and decision-making algorithms in Europe.

Prognosis and oncogenomic profiling of patients with tropomyosin receptor kinase fusion cancer in the 100,000 genomes project.

INTRODUCTION: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. Limited data exist on the overall survival (OS) of patients with tumors with NTRK gene fusions and on the co-occurrence of NTRK fusions with other oncogenic drivers. MATERIALS AND METHODS: This retrospective study included patients enrolled in the Genomics England 100,000 Genomes Project who had linked clinical data from UK databases. Patients who had undergone tumor whole genome sequencing between March 2016 and July 2019 were included. Patients with and without NTRK fusions were matched. OS was analyzed along with oncogenic alterations in ALK, BRAF, EGFR, ERBB2, KRAS, and ROS1, and tumor mutation burden (TMB) and microsatellite instability (MSI). RESULTS: Of 15,223 patients analyzed, 38 (0.25%) had NTRK gene fusions in 11 tumor types, the most common were breast cancer, colorectal cancer (CRC), and sarcoma. Median OS was not reached in both the NTRK gene fusion-positive and -negative groups (hazard ratio 1.47, 95% CI 0.39-5.57, P = 0.572). A KRAS mutation was identified in two (5%) patients with NTRK gene fusions, and both had hepatobiliary cancer. High TMB and MSI were both more common in patients with NTRK gene fusions, due to the CRC subset. While there was a higher risk of death in patients with NTRK gene fusions compared to those without, the difference was not statistically significant. CONCLUSION: This study supports the hypothesis that NTRK gene fusions are primary oncogenic drivers and the co-occurrence of NTRK gene fusions with other oncogenic alterations is rare.

Prognosis of patients with malignant mesothelioma by expression of programmed cell death 1 ligand 1 and mesothelin in a contemporary cohort in Finland.

OBJECTIVES: We aimed to describe mesothelin (MSLN) and programmed cell death 1 ligand 1 (PD-L1) tumour overexpression amongst patients with malignant mesothelioma (MM), and their associations with survival, amongst a cohort of patients with MM in Finland. METHODS: Between 2004 and 2017, 91 adults with histologically confirmed MM were identified from the Auria Biobank in Finland and followed-up using linked data from electronic health records and national statistics. Biomarker content in tumour cell membranes was determined using automated Immunohistochemistry on histological sections. Stained tumour sections were scored for MSLN and PD-L1 intensity. Adjusted associations between MSLN/PD-L1 co-expression and mortality were evaluated by estimating hazard ratios (HRs) with 95% confidence intervals (CIs) using Cox regression. RESULTS: Biomarker overexpression occurred in 52 patients for MSLN and 34 patients for PD-L1 and was associated with tumour histology and certain comorbidities. Fifteen per cent of patients had a tumour that overexpressed both biomarkers; r =-0.244, p-value: 0.02. Compared with MSLN+/PD-L1+ patients, HRs (95% CIs) for death were 4.18 (1.71-10.23) for MSLN-/PD-L1+ patients, 3.03 (1.35-6.77) for MSLN-/PD-L1- patients, and 2.13 (0.97-4.67) for MSLN+/PD-L1- patients. CONCLUSIONS: Both MSLN and PD-L1 markers were independent prognostic indicators in patients with MM. Overexpression of MSLN was associated with longer survival; yet their combined expression gave a better indication of survival. The risk of death was four times higher amongst MSLN-/PD-L1+ patients than in MSLN+/PD-L1+ patients.

The Impact of Cand1 in Prostate Cancer.

Evidence has accumulated asserting the importance of cullin-RING (really interesting new gene) ubiquitin ligases (CRLs) and their regulator Cullin-associated neural-precursor-cell-expressed developmentally down-regulated 8 (NEDD8) dissociated protein 1 (Cand1) in various cancer entities. However, the role of Cand1 in prostate cancer (PCa) has not been intensively investigated so far. Thus, in the present study, we aimed to assess the relevance of Cand1 in the clinical and preclinical setting. Immunohistochemical analyses of radical prostatectomy specimens of PCa patients showed that Cand1 protein levels are elevated in PCa compared to benign areas. In addition, high Cand1 levels were associated with higher Gleason Scores, as well as higher tumor recurrence and decreased overall survival. In line with clinical findings, in vitro experiments in different PCa cell lines revealed that knockdown of Cand1 reduced cell viability and proliferation and increased apoptosis, therefore underlining its role in tumor progression. We also found that the cyclin-dependent kinase inhibitor p21 is significantly upregulated upon downregulation of Cand1. Using bioinformatic tools, we detected genes encoding for proteins linked to mRNA turnover, protein polyubiquitination, and proteasomal degradation to be significantly upregulated in Cand1high tumors. Next generation sequencing of PCa cell lines resistant to the anti-androgen enzalutamide revealed that Cand1 is mutated in enzalutamide-resistant cells, however, with little functional and clinically relevant impact in the process of resistance development. To summarize the present study, we found that high Cand1 levels correlate with PCa aggressiveness.

Hepatocyte Growth Factor Receptor overexpression predicts reduced survival but its targeting is not effective in unselected HNSCC patients.

BACKGROUND: MET has emerged as target in head and neck squamous cell carcinoma (HNSCC). However, clinical data on MET inhibition in HNSCC are limited. METHODS: HNSCC biopsies and cell lines were tested for MET activity. The response of cell lines to BAY-853474 was tested in proliferation assays. The prognostic value of MET expression was also analyzed. RESULTS: HNSCC cell lines do not respond to MET inhibition. MET-dependent gastric cancer cell lines have much higher levels of MET expression and phosphorylation than HNSCC cell lines. Clinical samples of HNSCC contain much less MET than responsive models. CONCLUSIONS: No clinical response to MET inhibitors in monotherapy may be expected in unselected cases of HNSCC. Only selected patients with MET amplifications should be treated with MET inhibitors. Patients with increased MET immunoreactivity have shorter overall survival. MET might be useful as marker for the detection of patients with more aggressive types of HNSCC.

Evidence for an alternative fatty acid desaturation pathway increasing cancer plasticity.

Most tumours have an aberrantly activated lipid metabolism1,2 that enables them to synthesize, elongate and desaturate fatty acids to support proliferation. However, only particular subsets of cancer cells are sensitive to approaches that target fatty acid metabolism and, in particular, fatty acid desaturation3. This suggests that many cancer cells contain an unexplored plasticity in their fatty acid metabolism. Here we show that some cancer cells can exploit an alternative fatty acid desaturation pathway. We identify various cancer cell lines, mouse hepatocellular carcinomas, and primary human liver and lung carcinomas that desaturate palmitate to the unusual fatty acid sapienate to support membrane biosynthesis during proliferation. Accordingly, we found that sapienate biosynthesis enables cancer cells to bypass the known fatty acid desaturation pathway that is dependent on stearoyl-CoA desaturase. Thus, only by targeting both desaturation pathways is the in vitro and in vivo proliferation of cancer cells that synthesize sapienate impaired. Our discovery explains metabolic plasticity in fatty acid desaturation and constitutes an unexplored metabolic rewiring in cancers.

Endometriosis Leads to an Increased Trefoil Factor 3 Concentration in the Peritoneal Cavity but Does Not Alter Systemic Levels.

This study analyzed whether trefoil factor 3 (TFF3) is locally elevated and correlated with common biomarkers and inflammatory processes in endometriosis. Peritoneal fluid (PF) was obtained from 50 women and serum from 124 women with or without endometriosis. Experimental endometriosis was induced in female C57BL/6 mice by syngeneic transplantation of uterine tissue to the abdominal wall. Levels of TFF3 in PF of women with endometriosis were significantly increased ( P < .05) and correlated with local levels of known biomarkers for endometriosis: cancer antigen (CA) 125, CA-19-9, interleukin 8, monocyte chemotactic protein 1, and matrix metalloproteinase 7. Serum levels of TFF3 in women were significantly influenced by the menstrual cycle but were independent from disease state. In mice, local TFF3 levels were significantly elevated in early endometriosis (up to 4 weeks after transplantation, P < .001) and corresponded to increases in spleen weight as marker for systemic inflammation. This study provides the first evidence that TFF3 is locally elevated in the peritoneal cavity in endometriosis and might play a role in disease pathogenesis and its associated inflammatory processes. Furthermore, the results show that TFF3 is regulated through the menstrual cycle. With respect to animal models, syngeneic mouse model does reflect local TFF3 upregulation in the peritoneal cavity affected by endometriosis.

Quadriceps and hamstring muscle activity during cycling as measured with intramuscular electromyography.

PURPOSE: The aim of this study was to describe thigh muscle activation during cycling using intramuscular electromyographic recordings of eight thigh muscles, including the biceps femoris short head (BFS) and the vastus intermedius (Vint). METHODS: Nine experienced cyclists performed an incremental test (start at 170 W and increased by 20 W every 2 min) on a bicycle ergometer either for a maximum of 20 min or to fatigue. Intramuscular electromyography (EMG) of eight muscles and kinematic data of the right lower limb were recorded during the last 20 s in the second workload (190 W). EMG data were normalized to the peak activity occurring during this workload. Statistical significance was assumed at p ≤ 0.05. RESULTS: The vastii showed a greater activation during the 1st quadrant compared to other quadrants. The rectus femoris (RF) showed a similar activation, but with two bursts in the 1st and 4th quadrants in three subjects. This behavior may be explained by the bi-articular function during the cycling movement. Both the BFS and Vint were activated longer than, but in synergy with their respective agonistic superficial muscles. CONCLUSION: Intramuscular EMG was used to verify muscle activation during cycling. The activation pattern of deep muscles (Vint and BFS) could, therefore, be described and compared to that of the more superficial muscles. The complex coordination of quadriceps and hamstring muscles during cycling was described in detail.

Determining in vivo sternoclavicular, acromioclavicular and glenohumeral joint centre locations from skin markers, CT-scans and intracortical pins: A comparison study.

To describe shoulder motion the sternoclavicular, acromioclavicular and glenohumeral joint centres must be accurately located. Within the literature various methods to estimate joint centres of rotation location are proposed, with no agreement of the method best suited to the shoulder. The objective of this study was to determine the most reliable non-invasive method for locating joint centre locations of the shoulder complex. Functional methods using pin mounted markers were compared to anatomical methods, functional methods using skin mounted markers, imaging-based methods using CT-scan data, and regression equations. Three participants took part in the study, that involved insertion of intracortical pins into the clavicle, scapula and humerus, a CT-scan of the shoulder, and finally data collection using a motion analysis system. The various methods to estimate joint centre location did not all agree, however suggestions about the most reliable non-invasive methods could be made. For the sternoclavicular joint, the authors suggest the anatomical method using the most ventral landmark on the sternoclavicular joint, as recommended by the International Society of Biomechanics. For the acromioclavicular joint, the authors suggest the anatomical method using the landmark defined as the most dorsal point on the acromioclavicular joint, as proposed by van der Helm. For the glenohumeral joint, the simple regression equation of Rab is recommended.

Ultrasound-based testing of tendon mechanical properties: a critical evaluation.

In the past 20 years, the use of ultrasound-based methods has become a standard approach to measure tendon mechanical properties in vivo. Yet the multitude of methodological approaches adopted by various research groups probably contribute to the large variability of reported values. The technique of obtaining and relating tendon deformation to tensile force in vivo has been applied differently, depending on practical constraints or scientific points of view. Divergence can be seen in 1) methodological considerations, such as the choice of anatomical features to scan and to track, force measurements, or signal synchronization; and 2) in physiological considerations related to the viscoelastic behavior or length measurements of tendons. Hence, the purpose of the present review is to assess and discuss the physiological and technical aspects connected to in vivo testing of tendon mechanical properties. In doing so, our aim is to provide the reader with a qualitative analysis of ultrasound-based techniques. Finally, a list of recommendations is proposed for a number of selected issues.

[Respiratory epithelial adenomatoid hamartoma of the nose and nasal sinuses : a rare differential diagnosis of nasal polyposis]. / Respiratorische epitheliale adenomatoide Hamartome der Nase und der Nasennebenhöhlen : Seltene Differenzialdiagnose der Polyposis nasi.

INTRODUCTION: Hamartomas are benign tumor-like lesions resulting from incorrectly differentiated germplasm and can manifest in different organ systems. In the nasal cavity and the sinuses these lesions are rare. Only few data on etiology, epidemiology and clinical significance of these tumors exist to date. MATERIALS AND METHODS: In a retrospective study, material from patients treated in the Clinic for Otorhinolaryngology, Head and Neck Surgery of the Ulm Military Hospital was screened on the incidence and clinical courses of respiratory epithelial adenomatoid hamartomas (REAH) of the nose and nasal cavity. Furthermore, for cases of REAH, formalin-fixated paraffin-embedded tissue samples were re-evaluated and examined for human papillomavirus (HPV) DNA by PCR. RESULTS: Tissue samples from 8145 surgical interventions on the nose and nasal sinuses from 2003 to 2012 were included. A total of 22 patients (3 female, 19 male; median age 57.5 years) diagnosed with REAH could be identified. Major complaints were nasal blockage (91 %), sinusitis (82 %), rhinorrhea (36 %) and cephalgia (23 %). Nasal endoscopy showed polyps in 68 % of patients. Native nasal sinus CT scans revealed no indications of REAH. Intraoperatively, hamartomas were found in 12 patients originating from the ethmoid bone, in 8 from the middle meatus or infundibulum and in 2 from the olfactory cleft. Macroscopic and histological examination showed compact lesions sized between 4 and 25 mm in the largest diameter containing homologous tissue, without signs of dysplasia or malignancy. HPV DNA was not identified in any case. CONCLUSION: REAH of the nasal cavity and sinuses are rare benign local tissue lesions, usually without any autonomous proliferation. Clinical signs and findings correspond to those in polypoid pansinusitis. Only with single-sided or olfactory cleft location might CT scans provide indication of a tumorous lesion. For differentiation from true neoplasms, surgical resection and histopathological clarification is indicated. On the basis of current knowledge, complete surgical resection is adequate therapy.

The Research Biobank of the Year Competition of the European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB): aims and achievements.

With the increasing number of research biobanks and the importance of their role in supporting medical and biological research, the development and sharing of biobanking best practices and benchmarking standards has become paramount. To promote outstanding biobank services for research, the Research Biobank of the Year Competition (RBYC) has been inaugurated by the European, Middle-Eastern, and African Society for Biopreservation and Biobanking (ESBB) in October 2013. The procedures for the call and evaluation procedure, including the newly developed scoring system, are presented here. The statistics and evaluation results of the first year's applications, as well as the experiences of the jury are reported here, and improvements for the RBYC in subsequent years are proposed. Beyond offering a unique benchmarking opportunity for biobanks, the RBYC is discussed as a novel tool to enhance biobank quality, transparency, usage, connectivity, innovation, and sustainability.

Cytokeratin-19 as a biomarker in urine and in serum for the diagnosis of endometriosis--a prospective study.

Endometriosis compromises the quality of life of countless women worldwide and is a leading cause of disability. Clinical symptoms of endometriosis can be very heterogeneous leading to a long interval between onset of symptoms and surgical diagnosis. A noninvasive, rapid diagnostic test is urgently needed. In this prospective study, we evaluated the usefulness of Cytokeratin-19 (CK19) as a biomarker for the diagnosis of endometriosis through urine and serum ELISA. 76 reproductive-aged women undergoing laparoscopy for benign conditions were included to this study and divided into two groups by the presence (n = 44) or absence (n = 32) of endometriosis. There was no statistically significant correlation between the concentration of CK19 in urine (p = 0.51) or in serum (p = 0.77) and the diagnosis of endometriosis. Assigning the samples to the proliferative or secretory cycle stage did not sufficiently lower the p values. In this study, the promising data reported in the recent literature about CK19 serving as a sufficient biomarker for endometriosis could not be verified when tested in a larger sample size. Further studies are warranted to explore the usefulness of CK19 in the diagnosis of endometriosis.

Seated double-poling ergometer performance of individuals with spinal cord injury - a new ergometer concept for standardized upper body exercise.

This study aimed to evaluate biomechanics during seated double-poling exercises in individuals with spinal cord injury (SCI) and to compare these with those of able-bodied persons (AB). 26 participants volunteered for the study; 13 with SCI (injury levels C7-T12), and 13 AB. A seated double-poling ergometer (SDPE) was developed. 3-dimensional kinematics was measured and piezoelectric force sensors were used to register force in both poles for calculation of power during incremental intensities. Significantly lower power outputs, (143.2 ± 51.1 vs. 198.3 ± 74.9 W) and pole forces (137.1 ± 43.1 vs. 238.2 ± 81.2 N) were observed during maximal effort in SCI compared to AB. Sagittal upper trunk range of motion increased with intensity and ranged from 6.1-34.8° for SCI, and 6.9-31.3° for AB, with larger peak amplitudes in flexion for AB (31.4 ± 12.9°) compared to SCI (10.0 ± 8.0°). All subjects with SCI were able to exercise on the SDPE. Upper body kinematics, power and force outputs increased with intensity in both groups, but were in general, lower in SCI. In conclusion, the SDPE could be successfully used at low to high work intensities enabling both endurance and strength training for individuals with SCI.