Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR.

NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the ß-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the ß-subunit from solution.

Sedimentation of large, soluble proteins up to 140 kDa for 1H-detected MAS NMR and 13C DNP NMR - practical aspects.

Solution NMR is typically applied to biological systems with molecular weights < 40 kDa whereas magic-angle-spinning (MAS) solid-state NMR traditionally targets very large, oligomeric proteins and complexes exceeding 500 kDa in mass, including fibrils and crystalline protein preparations. Here, we propose that the gap between these size regimes can be filled by the approach presented that enables investigation of large, soluble and fully protonated proteins in the range of 40-140 kDa. As a key step, ultracentrifugation produces a highly concentrated, gel-like state, resembling a dense phase in spontaneous liquid-liquid phase separation (LLPS). By means of three examples, a Sulfolobus acidocaldarius bifurcating electron transfer flavoprotein (SaETF), tryptophan synthases from Salmonella typhimurium (StTS) and their dimeric ß-subunits from Pyrococcus furiosus (PfTrpB), we show that such samples yield well-resolved proton-detected 2D and 3D NMR spectra at 100 kHz MAS without heterogeneous broadening, similar to diluted liquids. Herein, we provide practical guidance on centrifugation conditions and tools, sample behavior, and line widths expected. We demonstrate that the observed chemical shifts correspond to those obtained from µM/low mM solutions or crystalline samples, indicating structural integrity. Nitrogen line widths as low as 20-30 Hz are observed. The presented approach is advantageous for proteins or nucleic acids that cannot be deuterated due to the expression system used, or where relevant protons cannot be re-incorporated after expression in deuterated medium, and it circumvents crystallization. Importantly, it allows the use of low-glycerol buffers in dynamic nuclear polarization (DNP) NMR of proteins as demonstrated with the cyanobacterial phytochrome Cph1.

The Effect of chemo- and radiotherapy on tumor necrosis in soft tissue sarcoma- does it influence prognosis?

BACKGROUND: Soft tissue sarcomas (STSs) are a heterogeneous group of tumors. Wide surgical resection is standard, often combined with neoadjuvant chemotherapy, radiotherapy, or both. Studies have shown the predictive value of tumor necrosis in bone sarcoma (BS); however, the role of necrosis in STS after neoadjuvant therapies is still unclear. This study aimed to investigate the role of chemo- and radiotherapy in the formation of tumor necrosis and to evaluate the influence of tumor necrosis on overall survival and local recurrence-free survival. Data from BS patients and patients who did not receive neoadjuvant therapy were compared. METHODS: A total of 779 patients with STS or BS were treated surgically. In all patients, tumor-specific factors such as type, size, or grading and the type of adjuvant therapy were documented. Local recurrence (LR), the diagnosis of metastatic disease, and survival during follow-up were evaluated. RESULTS: A total of 565 patients with STS and 214 with BS were investigated. In STS, 24.1% G1 lesions, 34.1% G2 lesions, and 41.8% G3 lesions were observed. Two hundred twenty-four of the patients with STS and neoadjuvant therapy had either radiotherapy (RTx) (n = 80), chemotherapy (CTx) (n = 93), or both (n = 51). Three hundred forty-one had no neoadjuvant therapy at all. In STS, tumor necrosis after neoadjuvant treatment was significantly higher (53.5%) than in patients without neoadjuvant therapy (15.7%) (p < 0.001). Patients with combined neoadjuvant chemo-/radiotherapy had substantially higher tumor necrosis than those with radiotherapy alone (p = 0.032). There was no difference in tumor necrosis in patients with combined chemo-/radiotherapy and chemotherapy alone (p = 0.4). The mean overall survival for patients with STS was 34.7 months. Tumor necrosis did not influence survival in a subgroup of G2/3 patients. In STS with no neoadjuvant therapy and grading of G2/3, the correlation between necrosis and overall survival was significant (p = 0.0248). There was no significant correlation between local recurrence (LR) and necrosis. CONCLUSION: STS shows a broad spectrum of necrosis even without neoadjuvant chemo- or radiotherapy. After CTx or/and RTx necrosis is enhanced and is significantly pronounced with a combination of both. There is a trend toward higher necrosis with CTx than with RTx. Grading substantially influences the necrosis rate, but necrosis in soft-tissue sarcoma following neoadjuvant therapy does not correlate with better survival or a lower local recurrence rate, as in bone sarcomas.

5D solid-state NMR spectroscopy for facilitated resonance assignment.

1H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS.

Impact of Dynamic Contrast Enhanced and Diffusion-Weighted MR Imaging on Detection of Early Local Recurrence of Soft Tissue Sarcoma.

BACKGROUND: Diagnosis of residual or recurrent tumor in soft-tissue sarcomas (STS) is a differential diagnostic challenge since post-therapeutic changes impede diagnosis. PURPOSE: To evaluate the diagnostic accuracy of quantitative dynamic contrast enhanced (DCE)-MRI and diffusion-weighted imaging (DWI) to detect local recurrence of STS of the limb. STUDY TYPE: Prospective. POPULATION: A totalof 64 consecutive patients with primary STS of the limbs were prospectively included 3-6 months after surgery between January 2016 and July 2021. FIELD STRENGTH/SEQUENCE: A 1.5 T; axial DWI echo-planar imaging sequences and DCE-MRI using a 3D T1-weighted spoiled gradient-echo sequence. ASSESSMENT: The quantitative DCE-MRI parameters relative plasma flow (rPF) and relative mean transit time (rMTT) were calculated and ADC mapping was used to quantify diffusion restriction. Regions of interest of tumor growth and postoperative changes were drawn in consensus by two experts for diffusion and perfusion analysis. An additional morphological assessment was done by three independent and blinded radiologists. STATISTICAL TEST: Unpaired t-test, ROC-analysis, and a logistic regression model were applied. Interobserver reliability was calculated using Fleiss kappa statistics. A P value of 0.05 was considered statistically significant. RESULTS: A total of 11 patients turned out to have local recurrence. rPF was significantly higher in cases of local recurrence when compared to cases without local recurrence (61.1-4.5) while rMTT was slightly and significantly lower in local recurrence. ROC-analysis showed an area under the curve (AUC) of 0.95 (SEM ± 0.05) for rPF while a three-factor multivariate logistic regression model showed a high diagnostic accuracy of rPF (R2  = 0.71). Compared with morphological assessment, rPF had a distinct higher specificity and true positive value in detection of LR. DATA CONCLUSION: DCE-MRI is a promising additional method to differentiate local recurrence from benign postoperative changes in STS of the limb. Especially specificity in detection of LR is increased compared to morphological assessment. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 2.

Impact of postoperative baseline MRI on diagnostic confidence and performance in detecting local recurrence of soft-tissue sarcoma of the limb.

OBJECTIVE: To evaluate the impact of a postoperative baseline (PB) MRI on diagnostic confidence and performance in detecting local recurrence (LR) of soft-tissue sarcoma (STS) of the limb. MATERIALS AND METHODS: A total of 72 patients (8 with LR, 64 without LR) with primary STS of the limb were included. Routine follow-up MRI (1.5 T) at 6 and approximately 36 months (meanLR: 39.7 months; meanno LR: 34.9 months) after multimodal therapy or at time of LR were assessed by three independent readers using a 5-point Likert scale. Furthermore, the following imaging parameters were evaluated: presence of a mass, signal characteristics at T2- and T1-weighted imaging, contrast enhancement (CE), and in some of the cases signal intensity on the apparent diffusion coefficient (ADC). U-test, McNemar test, and ROC-analysis were applied. Interobserver reliability was calculated using Fleiss kappa statistics. A p value of 0.05 was considered statistically significant. RESULTS: The presence of a PB MRI significantly improved diagnostic confidence in detecting LR of STS (p < 0.001) and slightly increased specificity (mean specificity without PE 74.1% and with presence of PB MRI 81.2%); however, not to a significant level. The presence of a mass showed highest diagnostic performance and highest interreader agreement (AUC [%]; κ: 73.1-83.6; 0.34) followed by T2-hyperintensity (50.8-66.7; 0.08), CE (52.4-62.5; 0.13), and T1-hypointensity (54.7-77.3; 0.23). ADC showed an AUC of 65.6-96.6% and a κ of 0.55. CONCLUSION: The presence of a PB MRI increases diagnostic confidence in detecting LR of STS of the limb.

Sarcomas of the extremities and the pelvis: comparing local recurrence after incisional and after core-needle biopsy.

BACKGROUND: The degree of contamination of healthy tissue with tumor cells during a biopsy in bone or soft tissue sarcomas is clearly dependant on the type of biopsy. Some studies have confirmed a clinically relevant contamination of the biopsy tract after incisional biopsies, as opposed to core-needle biopsies. The aim of our prospective study was to evaluate the risk of local recurrence depending on the biopsy type in extremity and pelvis sarcomas. METHODS: We included 162 patients with a minimum follow-up of 6 months after wide resection of extremity sarcomas. All diagnostic and therapeutic procedures were performed at a single, dedicated sarcoma center. The excision of the biopsy tract after an incisional biopsy was performed as a standard with all tumor resections. All patients received their follow-up after the conclusion of therapy at our center by means of regional MRI studies and, at a minimum, CT of the thorax to rule out pulmonary metastatic disease. The aim of the study was the evaluation of the influence of the biopsy type and of several other clinical factors on the rate of local recurrence and on the time of local recurrence-free survival. RESULTS: One hundred sixty-two patients with bone or soft tissue tumors of the extremities and the pelvis underwent either an incisional or a core-needle biopsy of their tumor, with 70 sarcomas (43.2%) being located in the bone. 84.6% of all biopsies were performed as core-needle biopsies. The median follow-up time was 55.6 months, and 22 patients (13.6%) developed a local recurrence after a median time of 22.4 months. There were no significant differences between incisional and core-needle biopsy regarding the risk of local recurrence in our subgroup analysis with differentiation by kind of tissue, grading of the sarcoma, and perioperative multimodal therapy. CONCLUSIONS: In a large and homogenous cohort of extremity and pelvic sarcomas, we did not find significant differences between the groups of incisional and core-needle biopsy regarding the risk of local recurrence. The excision of the biopsy tract after incisional biopsy in the context of the definitive tumor resection seems to be the decisive factor for this result.

Functional results after oncological scapula resections.

INTRODUCTION: Tumors of the scapula are rare representing only 1.6%-2.8% of all skeletal tumor localizations. Wide resection of these tumors is often necessary, and their anatomic location is the most decisive factor for the extent of the resection. Because of the importance of the shoulder girdle for all daily activities, such resections can have major functional consequences. However, only few reports with small numbers of cases are found in the literature. PATIENTS AND METHODS: We retrospectively evaluated 31 consecutive patients with scapular tumors treated surgically for aggressive benign or malignant tumors of the scapula. Patients who had received curettage only were excluded. Four of these 31 patients were lost to follow-up. In 7 of the remaining 27 patients, a total scapulectomy had to be performed, whereas all others received a partial resection. In 1 case, a partial resection and replantation after irradiation was performed. Musculoskeletal Tumor Society Scoring System (MSTS) and Toronto Extremity Salvage Score (TESS) scores were evaluated postoperatively at the time of their follow-up. RESULTS: In 16 men and 11 women, the median age was 46.2 years and the tumor entities were heterogeneous. The median follow-up time was 71 months. Three patients died during follow-up due to their tumor and 1 due to cardiac disease. We found significantly better functional results in the group with incomplete scapula resections as opposed to the scapulectomy group. We did not see a significant functional difference between the patients with benign and those with malignant lesions. Both the MSTS score with median 83.3% (range between 23% and 100%) and the TESS score with 81.6% (ranging from 20.4% to 100%) were at a satisfactory level. The preservation of the supraspinatus muscle was shown to be advantageous for better shoulder function, and younger patients also tended to have better postoperative results. CONCLUSION: The resection of scapular tumors may lead to a significant functional disability of the shoulder girdle and the affected arm in many cases. However, this is represented neither in the MSTS or TESS score nor in the overall acceptance of the patients. Only 1 patient, an artisan, had to change his job. In total, the clinical results are quite good in short- and long-term follow-up. The score results were comparable to other studies.

Considerations in genetic counseling of transgender patients: Cultural competencies and altered disease risk profiles.

Transgender people are a growing population with specific healthcare needs, barriers to care, and disease risk factors. Cultural competencies for working with transgender people in healthcare settings are essential to reduce barriers to care and combat the associated health disparities. Genetic counselors support their patients to understand and manage medically and personally complex life events and decisions. A genetic counselor caring for a transgender patient or a patient with a transgender relative will therefore require specific cultural competencies and medical knowledge that may not have been covered in their training. Transgender health is also a relatively young field in which new insights may quickly become fundamental. The present paper therefore provides an overview of current best practices for culturally sensitive working with transgender patients, and an introduction to the additional considerations for assessment of disease risk in transgender people. Guidance on how to ensure communication with patients and other stakeholders is inclusive and affirming of transgender identities, is offered. Medical interventions used for gender transitions are described, and their (potential) effects on cancer and cardiovascular disease risk are discussed. Furthermore, the effects of sociocultural risk factors such as minority stress are outlined. In sum, we invite the reader to consider the specific biological, psychological, and social context of the consultation. Finally, we explore culturally competent approaches to pedigree charting and physical examinations with transgender people and provide recommendations for practice.

Primary stability of the Activ L® intervertebral disc prosthesis in cadaver bone and comparison of the keel and spike anchoring concept.

BACKGROUND: High primary stability is the key prerequisite for safe osseointegration of cementless intervertebral disc prostheses. The aim of our study was to determine the primary stability of intervertebral disc prostheses with two different anchoring concepts - keel and spike anchoring. METHODS: Ten ActivL intervertebral disc prostheses (5 x keel anchoring, 5 x spike anchoring) implanted in human cadaver lumbar spine specimens were tested in a spine movement simulator. Axial load flexion, extension, left and right bending and axial rotation motions were applied on the lumbar spine specimens through a defined three-dimensional movement program following ISO 2631 and ISO/CD 18192-1.3 standards. Tri-dimensional micromotions of the implants were measured for both anchor types and compared using Student's T-test for significance after calculating 95 % confidence intervals. RESULTS: In the transverse axis, the keel anchoring concept showed statistically significant (p < 0.05) lower mean values of micromotions compared to the spike anchoring concept. The highest micromotion values for both types were observed in the longitudinal axis. In no case the threshold of 200 micrometers was exceeded. CONCLUSIONS: Both fixation systems fulfill the required criteria of primary stability. Independent of the selected anchorage type an immediate postoperative active mobilization doesn't compromise the stability of the prostheses.