Executive functioning following surgery near the frontal aslant tract in low-grade glioma patients: A patient-specific tractography study

BACKGROUND

The Frontal Aslant Tract (FAT) has been associated with executive functions (EF), but it remains unclear what role the FAT plays in EF, and whether preoperative dysfunction of the FAT is associated to long-lasting postsurgical executive impairments.

METHODS

In this study, we examined the course of EF from pre-surgery (n = 75) to 3 (n = 61) and 12 (n = 25) months after surgery in patients with frontal and parietal low-grade gliomas (LGGs), to establish the degree to which long-term EF deficits exist. Secondly, we used patient-specific tractography to investigate the extent to which overlap of the tumor with the FAT, as well as integrity of the FAT, presurgery were related to EF on the short and longer term after surgery.

RESULTS

LGG patients performed worse than healthy controls on all EF tests before and 3 months postsurgery. Whereas performances on three out of the four tests had normalized 1 year postsurgery (n = 26), performance on the cognitive flexibility test remained significantly worse than in healthy controls. Patients in whom the tumor overlapped with the core of the right FAT performed worse presurgery on three of the EF tests compared to those in whom the tumor did not overlap with the right FAT. Presurgical right FAT integrity was not related to presurgical EF, but only to postsurgical EF (from pre-to 3 months postsurgery). Longitudinal analyses demonstrated that patients with right (but not left) FAT core overlap performed on average worse over the pre- and postsurgical timepoints on the cognitive flexibility test.

CONCLUSIONS

We emphasized that LGG patients perform worse than healthy controls on the EF tests, which normalizes 1-year postsurgery except for cognitive flexibility. Importantly, in patients with right hemispheric tumors, tumor involvement of the FAT was associated with worse pre- and 3- months postsurgical performance, specifically concerning cognitive flexibility.

P11.56.A Shared and personalized decision-making in pre-surgical consultations of brain tumor patients and neurosurgeons

Background

In order to assess whether the oncological benefits outweigh the functional risks of treatment for an individual patient, it is important that physicians involve patients in decision-making and personalize the process. This is especially important for brain tumor patients considering the limited treatment options available. The aim of this study is to evaluate shared decision-making and the personalization of the decision-making process during consultations of brain tumor patients and their neurosurgeons.

Material and Methods

For this observational study we collected 66 audio-recordings of pre-surgical consultations of adult brain tumor patients (glioma, meningioma) and their neurosurgeons. A preliminary analysis based on a shared decision-making template was conducted on 14/66 transcribed audio-recordings to assess in how many consultations the following key elements of shared decision-making were present, namely 1) offering a choice to the patient and emphasizing that the patient’s perspective is important in making the decision, 2) discussing treatment options with benefits and risks and 3) asking about treatment preferences and personal goals. Next, thematic analysis will be performed by two independent researchers until data saturation is reached to gain insight into personalization of the decision-making process as an integral part of shared decision-making.

Results

Preliminary findings show that 1) offering the patient a choice and emphasizing that the perspective of the patient is important in decisions was done in 12/14 consultations; 2) discussing treatment options with benefits and risks was present in every consultation (14/14); and 3) in 12/14 consultations the neurosurgeon asked the patient about his or her treatment preference. However, explicitly asking the patient about personal goals occurred only in 3/14 consultations. By the time of the conference, we expect to have explored the decision-making process more in-depth and will be able to share the themes we have identified related to personalization of the decision-making process.

Conclusion

Key elements of shared decision-making were present in most pre-surgical consultations, except for asking patients about their personal goals. Discussing personal goals that patients have concerning daily life may facilitate personalization of the decision-making process.

P18.08.B Fully automatic meningioma segmentation using T1-weighted contrast-enhanced MR images only

Background

Manual segmentation of brain tumors requires expertise, is time-consuming, and is subject to inter-rater variability. Fully automatic brain tumor segmentation is possible for glioma and meningioma when volumetric T1, T1 contrast-enhanced (T1c), T2, and Fluid-attenuated inversion recovery (FLAIR) MRIs are available. In clinical care of meningiomas, however, often only volumetric T1c scans are available. In this work, we trained a deep learning network to segment meningiomas using only T1c scans for use in clinical research.

Material and Methods

NnU-Net, a deep learning model that is optimized for medical image segmentation, was trained to segment meningiomas from T1c images. This was performed on a large clinically collected meningioma dataset (n=374) of T1c scans with semi-automatically generated enhancing tumor masks and additional data from the BraTS2020 glioma dataset. Model performance was compared against inter-rater reliability, between different models, between anatomical tumor locations, and against models using multiple MRI modalities.

Results

The best performing model obtained a Dice score of 0.90. This performance was 0.03 points lower when compared to inter-rater reliability (Dice=0.93) and almost equal to models using multiple MRI modalities. Model performance split over anatomical tumor locations was between 0.90 and 0.97 (Dice).

Conclusion

Fully automatic meningioma segmentation using only T1c images is possible with an accuracy that is similar to inter-rater reliability and models using multiple imaging modalities.

P08.07.A Long-term multidimensional assessment of fatigue and fatigue as predictor of survival in patients with brain metastases after Gamma Knife radiosurgery

Background

The aim of this study was to assess long-term multidimensional fatigue and (change in) fatigue as predictor for survival in patients with brain metastases (BM) up to 21 months after Gamma Knife radiosurgery (GKRS).

Material and Methods

Patients with 1 to 10 BM, expected survival >3 months, and Karnofsky Performance Status ≥70 were included. Fatigue was measured with the Multidimensional Fatigue Inventory (MFI). Linear mixed models were used to evaluate fatigue up to 21 months after GKRS. Fatigue before GKRS and changes in fatigue in the first three months after GKRS were evaluated as predictors for survival duration.

Results

Patients with BM experienced significantly higher levels of fatigue on all subscales prior to GKRS (n=92) compared to Dutch controls (n=104), all p’s≤.001. Over 21 months, levels of physical fatigue increased significantly (p=.001), and levels of mental fatigue decreased significantly (p=.004). Between pre-GKRS and 3 months, there was a significant increase in levels of general (p<.001) and physical fatigue (p<.001), followed by stable fatigue scores between 3 (n=67) and 6 (n=53) months, 6 and 12 (n=34) months and 12 and 21 (n=21) months. Minimal clinically important (MCI) increases in general (p=.023, time ratio=0.61) and in physical fatigue (p=.008, time ratio=0.56) from pre-GKRS to 3 months thereafter were independent negative predictors of survival time (i.e., an MCI increase in these domains predicted a reduction of 39% and 44% respectively in survival time compared to stable or decreased fatigue).

Conclusion

Results indicate that up to 21 months after GKRS fatigue is a persistent problem in patients with BM. Except for an increase in general and physical fatigue up to 3 months after treatment, fatigue remained stable up to 21 months after GKRS. In addition, an MCI increase in general or physical fatigue within three months after GKRS may be related to worse survival outcome.

P01.03.B A quantitative comparison of cognitive performance and patient-reported symptoms in preoperative lower-grade glioma patients from two Dutch Hospitals

Background

Protocols for assessment of (neuro)psychological outcomes in lower-grade glioma patients vary between hospitals. This potentially complicates generalization of these outcomes. We compared standardized scores on tests of two frequently impaired cognitive domains (attention and executive functioning (EF)), and two relevant patient-reported outcomes (PROs; depression and fatigue) of two neuro-oncological hospitals that use different measurement instruments.

Material and Methods

Data were used from preoperative assessments of patients with (IDH-mut) WHO grade II/III glioma tested between 2007 and 2021 at Amsterdam UMC (AMS) or at Elisabeth-Tweesteden Hospital Tilburg (ETZ). AMS patients were referred for (neuro)psychological assessment based on physician and patient preference (paper and pencil tests), whereas all ETZ patients routinely undergo screening (computerized tests). To compare scores of the different attention and EF tests we converted patients’ performances to z-scores based on normative data. For cognitive performance, we compared scores of different cognitive flexibility tests (CST vs SAT), processing speed tests (SDC vs LDMT), and Stroop tests (Stroop I and Stroop III). PROs included the CES-D vs HADS-D and the CIS-fatigue vs MVI-general fatigue (AMS vs ETZ, resp.). Differences were tested using Fisher's, χ 2, and Mann-Whitney U tests.

Results

Assessments were done median 4 weeks (AMS, n=97, range 19-0 weeks) and 1 day (ETZ, n=106; range 14-0 days) preoperatively. Age, sex, tumor location and histology were comparable between cohorts (p>0.05), but the AMS cohort showed significantly more grade III tumors (36% vs 16%) and more awake surgeries (84% vs 46%). Z-scores measuring attention and EF (n=94 and n=95, AMS vs ETZ) were not significantly different (CST vs SAT, percentage with a disorder (z <-1.5SD) 15% vs 13%; SDC vs LDMT 13% vs 14%; Stroop I 11% vs 18%; Stroop III 13% vs 16% at AMS and ETZ, resp.). Percentages of patients with possible depression (CES-D≥16, n=88 and HADS-D≥8, n=106) did not differ significantly between hospitals (28% vs 26%), nor did percentages of patients with severe fatigue (CIS-fatigue≥35, n=88 and MVI-general fatigue (z <-1.5SD), n=38, 42% vs 24% at AMS and ETZ, resp.).

Conclusion

Standardized scores of glioma patients on cognitive domains (attention and EF) and PROs (depression and fatigue) did not differ between two centers with slightly different samples using different testing protocols. This cautiously suggests that study findings on cognitive functioning and symptoms could be generalized. For research purposes, conjoint use of pooled populations for outcome evaluation could be explored with different samples from other centers using different instruments.

Implementation study of the 2021 German guideline for diagnosis and treatment of multiple sclerosis

BACKGROUND

In May 2021, a new guideline on the diagnosis and treatment of multiple sclerosis and related disorders was released in Germany. Since the success of a guideline depends on how it integrates into everyday clinical practice, the German Society for Neurology (DGN) has launched a multimethod implementation project. Here we report on the results based on the consultation version of the guideline.

METHODS

We used qualitative and quantitative data analyses to capture the nature and extent of barriers and facilitating factors to the implementation. We centered on the guideline's chapter A on diagnosis, relapse therapy, and immunotherapy of multiple sclerosis. We performed nine online focus group discussions and a web-based survey and analyzed emails and letters with comments from stakeholders and independent parties that were sent spontaneously or by invitation.

RESULTS

94 neurologists answered the survey, and ≥70% agreed with the recommendations of the guideline on each major content topic. Barriers to implementation were detected in group discussions and written input. The most controversial issues of the guideline were "early treatment", "criteria for starting or switching therapy", "stepwise escalation versus early aggressive treatment", "classification of drugs into three categories of efficacy" and the scenarios on "treatment cessation". Some appreciated the highly structured recommendations, but others felt that the guideline restricts the free choice of therapy, or they were afraid of recourse claims. Some considered the guideline as too cautious regarding treatment initiation, possibly delaying necessary therapies. Others appreciated that conflicts of interests of the guideline's authoring group were minimized and thought that the new guideline is clearer, more extensive and practical.

CONCLUSION

In contrast to the survey, feedback in the focus group discussions and from individuals was diverse and sometimes more critical. Based on the overall feedback rate of about 250 people in relation to the number of 6500 board-certified neurologists in Germany, the overall appreciation of the guideline can only be considered as an indicator and not proof of acceptance. Results of this analysis were incorporated into several adjustments to the final guideline of 2021. Since the guideline is to be updated regularly under the auspices of a "living guideline", active interaction with users will continue to matter and help to improve it.

AB0067 RHEUMATOID ARTHRITIS IS DRIVEN NOT ONLY BY INFLAMMATION BUT ALSO BY FIBROGENESIS

Background:

Rheumatoid arthritis (RA) is a chronic, autoimmune disease characterized by inflammation of the synovium, cartilage and bone leading to joint swelling, tenderness, and dysfunction. The destruction of the joint tissue involves degradation of the extracellular matrix (ECM). The ECM consist of collagens and other connective proteins1. Studies have shown that elevated levels of collagen metabolites, such as those of type I, II, III and VI, are highly elevated in RA, correlated to disease activity and modulated in response to, for example tocilizumab2, baricitinib3 and methotrexate4. However, little is known about the formation of collagen, fibroblast activity, the fibrotic component of RA and how this influence likelihood of response to treatment.

Objectives:

We investigated the level of active fibrogenesis in a population of moderate to severe RA patients (in contrast healthy controls) by assessing blood-levels of PRO-C3 and PRO-C6 (type III and VI collagen formation markers), which have been reported to be associated with the degree and extent of fibrosis5.

Methods:

PRO-C3 and PRO-C6 was measured in serum of 166 RA patients (age; 54 (20-82), 83 % females, 91% white) at baseline and week 16 after treatment with an anti-IL6 receptor antibody in combination with MTX, as well as in serum of 77 donors (age; 42 (20-69), 51 % females, 66% white). Marker data was LN transformed. A general linear model was used when comparing groups.

Results:

The serum fibrogenesis marker PRO-C3, but not PRO-C6, was significantly elevated in RA compared to donors (2.1 vs. 2.4 ≈ 30% difference, p<0.0001, fig. 1A). None of the markers were correlated with disease measures such as DAS28, CRP, VASpain. None of the markers were modulated significantly in response to treatment. Interestingly, PRO-C3 levels were significantly higher at in non-responders (resp.) at week 16 compared to resp. (2.8 vs. 2.4 ≈ 40% difference, p=0.0018, fig. 1C). Similar trend was observed for PRO-C6 (2.2 vs. 2.0 ≈ 20% difference, p=0.061 fig. 1D).

Conclusion:

Active fibrosis, with activated fibroblasts, may play an unseen role in RA. Patients will elevated levels of the fibrosis markers PRO-C3 and PRO-C6 were less likely to respond to an anti-IL6R. This may also give clue why such treatment are less efficacious in diseases with a clear fibrotic component.

References:

[1]Karsdal et al. Rheumatoid arthritis: A case for personalized health care? ACR 2014; 66: 1273–80.

[2]Bay-Jensen et al. Effect of tocilizumab combined with methotrexate on circulating biomarkers of synovium, cartilage, and bone in the LITHE study. SAR 2014; 43: 470–8.

[3]Thudium et al. The Janus kinase 1/2 inhibitor baricitinib reduces biomarkers of joint destruction in moderate to severe rheumatoid arthritis. ART 2020; 22.

[4]Drobinski et al. Connective tissue remodeling is differently modulated by tocilizumab versus methotrexate monotherapy in patients with early rheumatoid arthritis: the AMBITION study. ART 2021; 23.

[5]Karsdal et al. Profiling and targeting connective tissue remodeling in autoimmunity - A novel paradigm for diagnosing and treating chronic diseases. AutoRev 2021; 20.

Disclosure of Interests:

None declared

Sorting Beef Subprimals by Ribeye Size at the Packer Level to Maximize Utility and Product Uniformity in Foodservice and Retail Sectors

ObjectivesTo determine the impact of sorting beef carcasses at the packer level by ribeye area, instead of sorting subprimals by weight, to provide more consistent products for the end user via foodservice and retail channelsMaterials and MethodsInstrument grading technology was used to select 100 USDA Choice, yield grade 2 or 3 sides, and 100 USDA Select, yield grade 2 or 3 sides. Carcass sides were sorted into one of five ribeye area (REA) categories, as outlined in Tabsle 6.USDA Choice carcass sides were fabricated to remove beef rib, ribeye, lip-on (IMPS 112A) and beef loin, strip loin, boneless (IMPS 180) from each USDA Choice. Beef loin, tenderloin, full, side muscle on, partially defatted (IMPS 189B) subprimals were procured from each USDA Select side. Subprimals were weighed, trimmed to specification, and passed through a 3-D visual analysis portioning machine and to obtain scan data for a variety of portioning outcomes generated by simulation software.ResultsBased on input from our foodservice collaborators, 1.25 inches (3.18 cm) was identified, for ribeye and strip loin steaks, as the targeted optimal thickness to meet consumer expectations. After evaluation of multiple portioning outcomes, it was determined that a 14.00-ounce (396.89 g) portion, for each REA category, most consistently delivered the preferred steak thickness identified previously. REA categories 1 and 2 most frequently produced desirable thickness and portion weight outcomes in ribeye and strip loin steaks. Statistical analysis of number of portions per subprimal stratified by portion weight and portion thickness revealed differences (P < 0.05) across all REA area categories in both ribeyes and strip loins. As portion weight and thickness increased, steak portion number tended to decrease. In tenderloins, an optimal steak thickness of 1.75 to 2.00 in (4.45 to 5.08 cm) was identified as optimal. Most frequently, 8, 9, and 10-ounce (226.80, 255.15, and 283.50 g) portions met the targets for optimal portion weight and thickness parameters. For tenderloins, number of portions by portion weight showed significant differences (P < 0.05) in all ribeye area categories with the exception of 7-ounces (198.45 g) and showed no differences when stratified by portion thickness. In this investigation, USDA Choice carcasses (r = 0.76) and USDA Select carcasses (r = 0.56) expressed moderate correlation between REA area and hot carcass weight.ConclusionResults of the present study suggest strip loin, ribeye, and tenderloin subprimals from carcasses possessing a ribeye area ranging from 74.8 cm2 to 87.1 cm2 offered the greatest level of utility when portioned for use in foodservice and retail sectors. Further research is warranted to continue examining the merit of sorting carcasses by ribeye area at the packer level, but results of this study suggest that there is potential for improved consistency and utility of subprimals in the foodservice and retail sectors.Table 6.Ribeye area (REA) categories and associated acceptable REA ranges.

Frequency of and predictors for withholding patient safety concerns among oncology staff: a survey study

Speaking up about patient safety is vital to avoid errors reaching the patient and to improve a culture of safety. This study investigated the prevalence of non-speaking up despite concerns for safety and aimed to identify predictors for withholding voice among healthcare professionals (HCPs) in oncology. A self-administered questionnaire assessed safety concerns, speaking up beliefs and behaviours among nurses and doctors from nine oncology departments. Multiple regression analysis was used to identify predictors for withholding safety concerns. A total of 1013 HCPs returned the completed survey (response rate 65%). Safety concerns were common among responders. Fifty-four per cent reported to recognise their colleagues making potentially harmful errors at least sometimes. A majority of responders reported at least some episodes of withholding concerns about patient safety. Thirty-seven per cent said they remained silent at least once when they had information that might have helped prevent an incident. Respondents believed that a high level of interpersonal, communication and coping skills are necessary to speak up about patient safety issues at their workplace. Higher levels of perceived advocacy for patient safety and psychological safety significantly decreased the frequency of withholding voice. Remaining silent about safety concerns is a common phenomenon in oncology. Improved strategies are needed to support staff in effective communication and make cancer care safer.

'Saying it without words': a qualitative study of oncology staff's experiences with speaking up about safety concerns

OBJECTIVES

To explore the experiences of oncology staff with communicating safety concerns and to examine situational factors and motivations surrounding the decision whether and how to speak up using semistructured interviews.

SETTING

7 oncology departments of six hospitals in Switzerland.

PARTICIPANTS

Diverse sample of 32 experienced oncology healthcare professionals.

RESULTS

Nurses and doctors commonly experience situations which raise their concerns and require questioning, clarifying and correcting. Participants often used non-verbal communication to signal safety concerns. Speaking-up behaviour was strongly related to a clinical safety issue. Most episodes of 'silence' were connected to hygiene, isolation and invasive procedures. In contrast, there seemed to exist a strong culture to communicate questions, doubts and concerns relating to medication. Nearly all interviewees were concerned with 'how' to say it and in particular those of lower hierarchical status reflected on deliberate 'voicing tactics'.

CONCLUSIONS

Our results indicate a widely accepted culture to discuss any concerns relating to medication safety while other issues are more difficult to voice. Clinicians devote considerable efforts to evaluate the situation and sensitively decide whether and how to speak up. Our results can serve as a starting point to develop a shared understanding of risks and appropriate communication of safety concerns among staff in oncology.

[Patient safety in outpatient care - study of Swiss primary care offices]

Knowledge of the most frequent and relevant safety problems is necessary in order to identify areas of risk in patient safety and to specify need for action. For Switzerland, there was no data available that systematically describes the type and frequency of critical incidents in outpatient care. Due to differences in primary care systems world wide, the transfer of international data to the Swiss context is of limited validity. For this reason the Patient Safety Foundation conducted a research project in cooperation with partners from primary care practice. We analysed the frequency and severity of patient safety risks in primary care offices as well as the safety climate in those practices. Results of the survey show the following areas of risk are of high relevance: medication, triage by nurse at initial contact (by phone), diagnosis as well as failures to monitor patients in the office. In addition, errors in tests and therapeutic interventions should be prioritized for future action. Several differences between professional groups could be identified regarding the perception and estimation of critical incidents as with respect to the safety climate. In conclusion, physicians and nurses should be involved when analysing risks and developing measures in order to insure high quality standards in patient care.

A randomized trial on the efficacy of methylphenidate and modafinil for improving cognitive functioning and symptoms in patients with a primary brain tumor

Limited research is available regarding the efficacy of psychostimulants in treating cognitive function in primary brain tumor patients. An open-label, randomized, pilot trial examined both the general and differential efficacy of 4 weeks of methylphenidate (MPH) and modafinil (MOD) in 24 brain tumor patients. Participants completed cognitive tests and self-report measures of fatigue, sleep disturbance, mood and quality of life at baseline and after 4 weeks.Following stimulant treatment, there was evidence of a beneficial effect on test performance in speed of processing and executive function requiring divided attention. Patients with the greatest deficit in executive function at baseline appeared to derive the greatest benefit following stimulant therapy. Inconsistent, differential effects were found on a measure of attention in favor of MPH and on a measure of processing speed in favor of MOD. There was also evidence of a general beneficial effect on patient-reported measures of fatigue, mood, and quality of life, with no statistically significant differences between treatment arms in these measures over time. The results from this small pilot study should be interpreted with caution, but appear to warrant additional research, in larger study samples, targeting fatigue, processing speed and executive function, and exploring different doses of stimulants. Future studies may also wish to explore the specific patient factors that may be associated with responsiveness to psychostimulant treatment.

A description of a cognitive rehabilitation programme evaluated in brain tumour patients with mild to moderate cognitive deficits

This series of articles for rehabilitation in practice aims to cover a knowledge element of the rehabilitation medicine curriculum. Nevertheless they are intended to be of interest to a multidisciplinary audience. The competency addressed in this article is cognitive rehabilitation.

BACKGROUND

There is a paucity of literature on the rationale, design, and content of successful cognitive rehabilitation programmes. In the current paper, we describe in detail a cognitive rehabilitation programme that has previously proven effective in a randomized controlled trial in patients with primary brain tumours. The programme's content may be of practical interest to those working with populations of cognitively impaired patients. Programme: The programme consists of six weekly, individual, 2-hour sessions plus homework, and incorporates both strategy training and attention retraining. The elements were taken from two of the few programmes that are evidence-based. It's design consists of psycho-education, teaching of strategies to compensate for problems in attention, memory and executive functioning in daily life. The retraining was based on the assumption that a target process can be improved by frequently practising exercises. It is focused on attention as intact attention may also be necessary for adequate functioning of other cognitive domains. The hierarchically organized exercises, embedded in a game-like computer program, were tailored to the needs of the individual patient.

EVALUATION

Mean total training time was estimated to be 35 hours in seven weeks. Adherence to the programme was high. The majority of the participants found the programme to be (very) useful. However, older participants found the programme more burdensome than younger patients.

DISCUSSION

Splitting up and spreading out sessions may increase the feasibility and usefulness of the programme for older participants. Further suggestions for improvements and future studies on this programme are also provided.

ERp57 and PDI: multifunctional protein disulfide isomerases with similar domain architectures but differing substrate–partner associationsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease

Secretory proteins become folded and acquire stabilizing disulfide bonds in the endoplasmic reticulum (ER). Correct disulfide bond formation is a key step in ER quality control (ERQC). Proteins with incorrect disulfide bonds are recognized by the quality control machinery and are retrotranslocated into the cytosol where they are degraded by the proteasome. The mammalian ER contains 17 disulfide isomerases and at least one of them, ERp57, works in conjunction with the ER lectin-like chaperones calnexin and calreticulin. The targeting of ERp57 to calnexin–calreticulin is mediated by its noncatalytic b′ domain, and analogous domains in other disulfide isomerases likely determine their substrate and partner preferences. This review discusses some explanations for the multiplicity of disulfide isomerases and highlights structural differences in the b′ domains of PDI and ERp57 as an example of how noncatalytic domains define specialized roles in oxidative folding.

Molecular mechanisms in clathrin-mediated membrane budding revealed through subcellular proteomics

Subcellular proteomics is a powerful new approach that combines subcellular fractionation and MS (mass spectrometry) to identify the protein complement of cellular compartments. The approach has been applied to isolated organelles and major suborganellar structures and each study has identified known proteins not previously understood to associate with the compartment and novel proteins that had been described only as predicted open-reading frames from genome sequencing data. We have utilized subcellular proteomics to analyse the protein components of CCVs (clathrin-coated vesicles) isolated from adult brain. Accounting for identified fragmented peptides allows for a quantitative assessment of protein complexes associated with CCVs, and the identification of many of the known components of post-fusion synaptic vesicles demonstrates that a main function for brain CCVs is to recycle synaptic vesicles. In addition, we have identified a number of novel proteins that participate in CCV formation and function at the trans-Golgi network and the plasma membrane. Characterization of two of these proteins, NECAP1 and NECAP2, has led to the identification of a new consensus motif that mediates protein interactions with the clathrin adaptor protein 2. These studies highlight the ability of proteomics to reveal new insights into the mechanisms and functional roles of subcellular compartments.

Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids

Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a 'rigid' O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 +/- 0.5 A, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.

NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes

The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.

Structure and function of the C-terminal PABC domain of human poly(A)-binding protein

We have determined the solution structure of the C-terminal quarter of human poly(A)-binding protein (hPABP). The protein fragment contains a protein domain, PABC [for poly(A)-binding protein C-terminal domain], which is also found associated with the HECT family of ubiquitin ligases. By using peptides derived from PABP interacting protein (Paip) 1, Paip2, and eRF3, we show that PABC functions as a peptide binding domain. We use chemical shift perturbation analysis to identify the peptide binding site in PABC and the major elements involved in peptide recognition. From comparative sequence analysis of PABC-binding peptides, we formulate a preliminary PABC consensus sequence and identify human ataxin-2, the protein responsible for type 2 spinocerebellar ataxia (SCA2), as a potential PABC ligand.

Properties of arabinonucleic acids (ANA & 20'F-ANA): implications for the design of antisense therapeutics that invoke RNase H cleavage of RNA

Inversion of configuration of the C2' position of RNA leads to a very unique nucleic acid structure: arabinonucleic acid (ANA). ANA, and its 2'-fluoro derivative (2'F-ANA) from hybrids with RNA that are capable of activating RNase H, resulting in cleavage of the RNA strand. In this paper, we review the properties of duplexes formed between ANA (or 2'F-ANA) and its RNA complement. These studies support the notion that RNase H is sensitive to the minor groove dimensions of the hybrid substrate.

Structural proteomics of an archaeon

A set of 424 nonmembrane proteins from Methanobacterium thermoautotrophicum were cloned, expressed and purified for structural studies. Of these, approximately 20% were found to be suitable candidates for X-ray crystallographic or NMR spectroscopic analysis without further optimization of conditions, providing an estimate of the number of the most accessible structural targets in the proteome. A retrospective analysis of the experimental behavior of these proteins suggested some simple relations between sequence and solubility, implying that data bases of protein properties will be useful in optimizing high throughput strategies. Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods. This demonstrates that structural proteomics is feasible and can play a central role in functional genomics.

Design and solution structure of functional peptide mimetics of nerve growth factor

The C-D loop in nerve growth factor (NGF) is involved in binding to the NGF receptor, TrkA. It is flexible and adopts several different types conformations in different NGF crystal forms. We have previously shown that a small cyclic peptide derived from the C-D loop of NGF binds to the TrkA receptor by mimicking the structure of this loop. To understand structure-function relationships in NGF C-D loop mimetics, we have produced a series of peptides predicted to form different types of beta-turns. The peptides were tested for their ability to promote cell survival in serum-free medium and to induce TrkA tyrosine phosphorylation. NMR structural studies were used to determined the backbone conformation and the spatial orientation of side chains involved in binding to the TrkA receptor. Peptides that form type I or type gammaL-alphaR beta-turns were the most active. The variety of active loop conformations suggests that the mimetics (and NGF) accommodate the binding site on TrkA by an 'induced fit' mechanism. In agreement with this hypothesis, NMR relaxation measurements detected both fast and slow motion in the peptides. We also characterized a retro-inverso peptide derived from the NGF C-D loop. This D-amino acid cyclic peptide did not adopt a conformation homologous to the NGF C-D loop and was inactive. This may be representative of difficulties in producing structural and functional mimetics by retro-inverso schemes.

Determination of sex from femora

The determination of sex from bones or bone fragments considerably contributes to identifying unknown bodies or skeletal remains. Due to temporal change and regional differences anthropometric standards have to be constantly renewed. The present study provides measurements of femoral dimensions in a contemporary German population and analyses sexual dimorphism by discriminant analysis. Maximum length (male: 46.4+/-2.4 cm, female: 43.4+/-2.4 cm), maximum midshaft diameter (male: 3.1+/-0.2 cm, female: 2.8+/-0.2 cm), condylar width (male: 8.4+/-1.0 cm, female: 7.7+/-0.5 cm), vertical head diameter (male: 4.9+/-0.3 cm, female: 4.4+/-0.3 cm), head circumference (male: 15.7+/-0.8 cm, female: 13.8+/-1.0 cm) and transverse head diameter (male: 4.9+/-0.3 cm, female: 4.3+/-0.3 cm) were measured in 170 femora, 100 from male (age: 16-92 years, mean: 60.8 years; body height: 153-190 cm, mean: 171 cm) and 70 from female (age: 20-96 years, mean: 72 years; body height: 146-175 cm, mean: 161 cm) individuals. In the discriminant analysis (leave-one-out-method) 67.7% of cases could be grouped correctly with the maximum length alone, 72.4% with the maximum midshaft diameter, 81.4% with the condylar width, 86.8% with the vertical head diameter, 87.7% with the head circumference and 89.6% with the transverse head diameter. The stepwise procedure with all head measurements showed that the results for the transverse head diameter could not be improved. With all measurements subjected to stepwise procedure 91.7% of cases could be classified correctly combining midshaft diameter and head circumference (D=3.012xmidshaft diameter in cm+0.780xhead circumference in cm 20.569).

Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides

PBX is a member of the three amino acid loop extension (TALE) class of homeodomains. PBX binds DNA cooperatively with HOX homeodomain proteins that contain a conserved YPWM motif. The amino acids immediately C-terminal to the PBX homeodomain increase the affinity of the homeodomain for its DNA site and HOX proteins. We have determined the structure of the free PBX homeodomain using NMR spectroscopy. Both the PBX homeodomain and the extended PBX homeodomain make identical contacts with a 5'-TGAT-3' DNA site and a YPWM peptide. A fourth alpha-helix, which forms upon binding to DNA, stabilizes the extended PBX structure. Variations in DNA sequence selectivity of heterodimeric PBX-HOX complexes depend on the HOX partner; however, a comparison of five different HOX-derived YPWM peptides showed that each bound to PBX in the same way, differing only in the strength of the association.

Rapid fold and structure determination of the archaeal translation elongation factor 1beta from Methanobacterium thermoautotrophicum

The tertiary fold of the elongation factor, aEF-1beta, from Methanobacterium thermoautotrophicum was determined in a high-throughput fashion using a minimal set of NMR experiments. NMR secondary structure prediction, deuterium exchange experiments and the analysis of chemical shift perturbations were combined to identify the protein fold as an alpha-beta sandwich typical of many RNA binding proteins including EF-G. Following resolution of the tertiary fold, a high resolution structure of aEF-1beta was determined using heteronuclear and homonuclear NMR experiments and a semi-automated NOESY assignment strategy. Analysis of the aEF-1beta structure revealed close similarity to its human analogue, eEF-1beta. In agreement with studies on EF-Ts and human EF-1beta, a functional mechanism for nucleotide exchange is proposed wherein Phe46 on an exposed loop acts as a lever to eject GDP from the associated elongation factor G-protein, aEF-1alpha. aEF-1beta was also found to bind calcium in the groove between helix alpha2 and strand beta4. This novel feature was not observed previously and may serve a structural function related to protein stability or may play a functional role in archaeal protein translation.

Genuine monovalent ligands of TrkA nerve growth factor receptors reveal a novel pharmacological mechanism of action

Developing small molecule agonistic ligands for tyrosine kinase receptors has been difficult, and it is generally thought that such ligands require bivalency. Moreover, multisubunit receptors are difficult to target, because each subunit contributes to ligand affinity, and each subunit may have distinct and sometimes opposing functions. Here, the nerve growth factor receptor subunits p75 and the tyrosine kinase TrkA were studied using artificial ligands that bind specifically to their extracellular domain. Bivalent TrkA ligands afford robust signals. However, genuine monomeric and monovalent TrkA ligands afford partial agonism, activate the tyrosine kinase activity, cause receptor internalization, and induce survival and differentiation in cell lines and primary neurons. Monomeric and monovalent TrkA ligands can synergize with ligands that bind the p75 subunit. However, the p75 ligands used in this study must be bivalent, and monovalent p75 ligands have no effect. These findings will be useful in designing and developing screens of small molecules selective for tyrosine kinase receptors and indicate that strategies for designing agonists of multisubunit receptors require consideration of the role of each subunit. Last, the strategy of using anti-receptor mAbs and small molecule hormone mimics as receptor ligands could be applied to the study of many other heteromeric cell surface receptors.

Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor

The solution structure of the second PDZ domain (PDZ2) from human phosphatase hPTP1E has been determined using 2D and 3D heteronuclear NMR experiments. The binding of peptides derived from the C-terminus of the Fas receptor to PDZ2 was studied via changes in backbone peptide and protein resonances. The structure is based on a total of 1387 nonredundant experimental NMR restraints including 1261 interproton distance restraints, 45 backbone hydrogen bonds, and 81 torsion angle restraints. Analysis of 30 lowest-energy structures resulted in rmsd values of 0.41 +/- 0.09 A for backbone atoms (N, Calpha, C') and 1.08 +/- 0.10 A for all heavy atoms, excluding the disordered N- and C-termini. The hPTP1E PDZ2 structure is similar to known PDZ domain structures but contains two unique structural features. In the peptide binding domain, the first glycine of the GLGF motif is replaced by a serine. This serine appears to replace a bound water observed in PDZ crystal structures that hydrogen bonds to the bound peptide's C-terminus. The hPTP1E PDZ2 structure also contains an unusually large loop following strand beta2 and proximal to the peptide binding site. This well-ordered loop folds back against the PDZ domain and contains several residues that undergo large amide chemical shift changes upon peptide binding. Direct observation of peptide resonances demonstrates that as many as six Fas peptide residues interact with the PDZ2 domain.

Development of pharmacological agents for targeting neurotrophins and their receptors

Neurotrophins comprise a family of protein growth factors that control the survival, growth, and/or differentiation of neurons and several other cell populations derived from the neuroectoderm. Neurotrophins and their receptors are important targets for the therapy of human disease, with potential applications ranging from the treatment of chronic or acute neurodegeneration to pain and cancer. Neurotrophins have been used clinically but are poor pharmacological agents. Consequently, approaches to develop pharmacological agents that target neurotrophins, their receptors or neurotrophin signaling pathways have been attempted.

An NMR study of ligand binding by maltodextrin binding protein

Proton NMR spectra of maltodextrin binding protein from Escherichia coli were used to monitor conformational changes that accompany ligand binding. Chemical shift changes associated with the binding of different maltodextrins to maltodextrin binding protein were studied using one-dimensional difference spectra. Line-shape analysis of an isolated upfield methyl resonance was used to measure the kinetics of maltose binding at several temperatures. Maltose and linear maltodextrins caused similar changes to the upfield protein spectrum with no detectable differences between alpha and beta sugar anomers. Binding of a cyclic ligand, beta-cyclodextrin, caused smaller chemical shift changes than binding of linear maltodextrins. Two maltodextrin derivatives were also studied. Both maltohexaitol and maltohexanoic acid gave one-dimensional difference spectra that were intermediate between those of linear maltodextrins and beta-cyclodextrin. The methyl resonances at -1 and -0.35 ppm were assigned to leucine 160 on the basis of homonuclear COSY and TOCSY experiments and theoretical chemical shift calculations using the X-ray crystal structure of maltodextrin binding protein.

Effect of peptide binding on amide proton exchange rates in the PDZ2 domain from human phosphatase hPTP1E

Amide hydrogen-deuterium exchange rates were measured in the PDZ2 domain from human phosphatase hPTPIE by 1H-15N heteronuclear NMR spectroscopy. Protection factors were calculated for the slowly exchanging hydrogens in both the free PDZ2 domain and its complex with an octapeptide peptide, R-N-E-I-Q-S-L-V, derived from the C-terminus of the Fas receptor. Aside from a short alpha-helical region alpha1 (amino acids A-45 to D-49), the pattern of highly protected amides correlated well with the presence of hydrogen bonds in elements of the secondary structure. Hydrogen-bonded amides showed relatively fast exchange rates with half-lives of less than 9 h at pD 7.6 and 8 degrees C. Protection factors, calculated as the ratio of theoretical (denatured) and observed exchange rates, showed less dispersion in maximal values than did the actual exchange rates. This behavior and the large pH dependence of the exchange rates suggest that amide exchange is close to the EX2 limit. In this limit, exchange of the most protected amides occurs through a global unfolding mechanism. The free energy of the unfolding calculated from the largest protection factors is 4.8 +/- 0.4 kcal/mol (1 cal = 4.184 J). This deltaG(o) closely matches the value measured by experiments with guanidine hydrochloride and fluorescence emission spectroscopy. Peptide binding to PDZ2 resulted in mostly global effects and stabilized the folded domain by 1.4 kcal/mol.

H(C)CH-COSY and (H)CCH-COSY experiments for 13C-labeled proteins in H2O solution

We present three experiments which serve to identify carbon and proton sidechain resonances in 13C-labeled proteins. The first is an improvement on the previously published H(C)CH-COSY experiment and comprises the application of gradients for coherence selection and a reduction in the phase cycle. The second experiment is a new (H)CCH-COSY with two carbon dimensions. The (H)CCH-COSY presents several advantages over the H(C)CH-COSY experiment in terms of better sensitivity, improved resolution and easier identification of amino acid spins systems. The third experiment is a 2D proton-edited (H)C(C)H-COSY that allows suppression of methylene resonances. All three HCCH-COSY experiments show good sensitivity and excellent solvent suppression. The 2D version can be acquired in as little as 45 minutes and the 3D versions acquired overnight. The experiments are demonstrated on a 13C-labeled sample of the second PDZ domain from human phosphatase PTP1E in H2O solution.

Solution structure and internal motion of a bioactive peptide derived from nerve growth factor

The conformation and internal dynamics of a bioactive cyclic peptide, N-acetyl-YCTDEKQCY, derived from the C-D loop of beta-nerve growth factor (beta-NGF) were analyzed by solution NMR spectroscopy. NMR experimental data were used to calculate an ensemble of peptide structures. All of the structures had a beta-turn at residues Asp4-Gln7 but could be divided into two families according the presence or absence of a hydrogen bond at Gln7. Comparison of the calculated structures with the corresponding C-D loops from the x-ray structures of the NGF revealed striking similarity. The orientation of Glu5, Lys6, and Gln7 side chains in the NGF mimetic was very similar to the C-D loop of NGF. These residues are known to participate in interactions with the TrkA receptor. Relaxation measurements of the peptidomimetic alpha-carbons at 13C natural abundance and calculated dynamic parameters suggest that the loop region of peptide is well structured but that residues Thr3, Asp4, Glu5, and Lys6 undergo slow conformational exchange. These results suggest that conformational similarity and possibly peptide dynamics are responsible for the bioactivity of the peptide.

Structural conservation in RNA loops III and VI of the internal ribosome entry sites of enteroviruses and rhinoviruses

Alignment of the internal ribosome entry sites (IRES) of members of the Enteroviridae-Rhinoviridae (E/R) family reveals a consensus loop sequence of AANCCA closed by a C.G base pair. The consensus sequence was present in two distinct loops in domains III and VI. Four hairpins corresponding to the most common loop sequences, AAUCCA, AAACCA, GAACCA and AUCCA, were synthesized and studied by UV spectroscopy. Although all four oligomers had similar UV melting points their thermodynamic parameters revealed differing stabilities consistent with their loop size. Comparison of the aromatic proton and H1' chemical shifts for the four loop sequences obtained from this and our previous NMR study revealed strikingly similar trends. The pattern of chemical shifts suggest similar solution structures in spite of differences in sequence and loop size. This common structure provides a structural basis for their sequence conservation in E/R IRESes.

Association of branched oligonucleotides into the i-motif

The unique architecture of branched oligonucleotides mimicking lariat RNA introns [Wallace and Edmons, Proc. Natl. Acad. Sci. USA 80, 950-954 (1983)] was exploited to study compounds that associate as two parallel duplexes with intercalating C/C+ base pairs (i-motif DNA) [Gehring et al. Nature 363, 561-565 (1993)]. The formation of a branched cytosine tetrad was induced by joining the 5'-ends of pair of pentadeoxycytidine strands with a branching riboadenosine (rA) linker. This arrangement causes the orientation of the dC strands to be parallel, and forces the formation of a C/C+ duplex that self-associates into i-DNA. Presence of the i-motif in this structure is supported by thermal denaturation, native gel electrophoresis, CD, and NMR spectroscopy.

NMR structural studies of human cystatin C dimers and monomers

Human cystatin C undergoes dimerization before unfolding. Dimerization leads to a complete loss of its activity as a cysteine proteinase inhibitor. A similar process of dimerization has been observed in cells, and may be related to the amyloid formation seen for the L68Q variant of the protein. Dimerization is barrier controlled, and no dimer/monomer interconversion can be observed at physiological conditions. As a consequence, very stable, "trapped" dimers can be easily separated from monomers. A study of the structural aspects of cystatin C dimer formation was undertaken using NMR spectroscopy. The monomer/dimer model was verified by (pulse field gradient NMR) self-diffusion molecular mass measurements. Complete backbone resonance assignments and secondary structure determination were obtained for the monomer using data from triple resonance experiments performed on 13C/15N doubly labeled protein. A marked similarity of the cystatin C secondary structure to that of chicken cystatin was observed. Using uniformly and amino-acid-specific 15N-enriched protein, backbone NH signals were assigned for cystatin C in its dimeric state. Comparison of 1H -15N correlation NMR spectra of the monomer and dimer shows that the three-dimensional structure remains unchanged in the dimer and that only local perturbations occur. These are localized to the amino acid residues comprising the cysteine proteinase binding site. Such a mode of dimerization readily explains the complete loss of the inhibitory activity in the dimer. The NMR results also demonstrate that the dimer is symmetric.