RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and ...comprehensive approach, termed “interactome capture,” to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.
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► Interactome capture identifies hundreds of RBPs previously unknown to bind RNA ► Some globular and disordered regions represent unorthodox binding architectures ► Many RNA binders are linked to Mendelian disease ► Metabolic enzymes moonlighting as RBPs
Interactome capture identifies the landscape of mRNA-binding proteins in mammalian cells, revealing new roles for metabolic enzymes and a propensity for globular and unstructured regions to associate with messages.
Abstract
STUDY QUESTION
What is the success rate in terms of ovarian activity (menstrual cycles) as well as pregnancy and delivery rates 1 year after orthotopic ovarian transplantations conducted in ...a three-country network?
SUMMARY ANSWER
In 49 women with a follow-up >1 year after transplantation, the ovaries were active in 67% of cases and the pregnancy and delivery rates were 33 and 25%, respectively.
WHAT IS KNOWN ALREADY
Cryopreservation of ovarian tissue in advance of cytotoxic therapies and later transplantation of the tissue is being performed increasingly often, and the total success rates in terms of pregnancy and delivery have been described in case series. However, published case series have not allowed either a more detailed analysis of patients with premature ovarian insufficiency (POI) or calculation of success rates based on the parameter ‘tissue activity’.
STUDY DESIGN, SIZE, DURATION
Retrospective analysis of 95 orthotopic transplantations in 74 patients who had been treated for cancer, performed in the FertiPROTEKT network from 2008 to June 2015. Of those 95 transplantations, a first subgroup (Subgroup 1) was defined for further analysis, including 49 women with a follow-up period >1 year after transplantation. Of those 49 women, a second subgroup (Subgroup 5) was further analysed, including 40 women who were transplanted for the first time and who were diagnosed with POI before transplantation.
PARTICIPANTS/MATERIALS, SETTING, METHODS
Transplantation was performed in 16 centres and data were transferred to the FertiPROTEKT registry. The transplantations were carried out after oncological treatment had been completed and after a remission period of at least 2 years. Tissue was transplanted orthotopically, either into or onto the residual ovaries or into a pelvic peritoneal pocket. The success rates were defined as tissue activity (menstrual cycles) after 1 year (primary outcome) and as pregnancies and deliveries achieved.
MAIN RESULTS AND THE ROLE OF CHANCE
The average age of all transplanted 74 women was 31 ± 5.9 years at the time of cryopreservation and 35 ± 5.2 at the time of transplantation. Twenty-one pregnancies and 17 deliveries were recorded. In Subgroup 1, tissue was cryopreserved at the age of 30 ± 5.6 and transplanted at 34 ± 4.9 years. Ovaries remained active 1 year after transplantation in 67% of cases (n = 33/49), the pregnancy rate was 33% (n = 16/49) and the delivery rate was 25% (n = 12/49). In Subgroup 5, tissue was cryopreserved at the age 30 ± 5.9 years and transplanted at 34 ± 5.2 years. Ovaries remained active 1 year after transplantation in 63% of cases (n = 25/40), the pregnancy rate was 28% (n = 11/40) and the delivery rate was 23% (n = 9/40). The success rates were age dependant with higher success in women who cryopreserved at a younger age. In Subgroup 5, tissue was exclusively transplanted into the ovary in 10% (n = 4/40) of women and into a peritoneal pocket in 75% (n = 30/40), resulting in spontaneous conceptions in 91% of patients (n = 10/11).
LIMITATIONS, REASONS FOR CAUTION
The data were drawn from a retrospective analysis. The cryopreservation and transplantation techniques used have changed during the study period. The tissue was stored in many tissue banks and many surgeons were involved, leading to heterogeneity of the procedures. However, this does reflect the realistic situation in many countries. Although patients with POI were evaluated before transplantation to allow specific analysis of the transplanted tissue itself, the possibility cannot be excluded that residual ovarian tissue was also reactivated.
WIDER IMPLICATIONS OF THE FINDINGS
This is the largest case series worldwide to date and it confirms that cryopreservation and transplantation of ovarian tissue can be a successful option for preserving fertility. Persistent tissue activity 12 months after transplantation suggests that the pregnancy and delivery rates may increase further in the future. As transplantation into the peritoneum results in a high success rate, this approach may be an alternative to transplantation into the ovary. However, in order to establish the best transplantation site, a randomized study is required.
STUDY FUNDING/COMPETING INTEREST
This study was in part funded from the Deutsche Forschungsgemeinschaft (# DI 1525) and the Wilhelm Sander Foundation (2012.127.1) and did not receive any funding from a commercial company. No competing interests.
TRIAL REGISTRATION NUMBER
None.
HER2 is one of the predominant therapeutic targets in breast cancer. The metastatic selection process may lead to discrepancies between the HER2 status of the primary tumor and circulating tumor ...cells (CTCs). This study analyzed the HER2 status of CTCs in patients with HER2-positive primary breast cancer at the time of diagnosis. Aim of the study was to assess potential discordance of HER2 status between primary tumor and CTCs, as this may have important implications for the use of HER2-targeted therapy.
The number and HER2 status of CTCs out of 30ml peripheral blood were assessed in 642 patients using the CellSearch System (Janssen Diagnostics, USA). The cutoff for CTC positivity was the presence of at least 1 CTC, and the cutoff for HER2 positivity of CTCs was the presence of at least 1 CTC with a strong HER2 staining.
258 (40.2%) of the 642 patients were positive for CTCs (median 2; range 1-1,689). 149 (57.8%) of these 258 patients had at least 1 CTC with strong HER2 staining. The presence of HER2-positive CTCs was not associated with tumor size (p = 0.335), histopathological grading (p = 0.976), hormone receptor status (ER: p = 0.626, PR: p = 0.263) or axillary lymph node involvement (p = 0.430). Overall, 83 (32.2%) of the CTC-positive patients exclusively had CTCs with strong HER2 staining, whereas 31 (12.0%) had only CTCs with negative HER2 staining. Within-sample variation in the HER2 status of CTCs was found in 86 (57.8%) of the 149 patients with more than 1 CTC.
This study demonstrated that discordance between the HER2 expression of CTCs and that of the primary tumor frequently occurs in early breast cancer. Future follow-up evaluation will assess whether this discrepancy may contribute to trastuzumab resistance.
Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ...ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (
RNA-determined RNPs
) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.
Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing ...proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). We have developed the Phenol Toluol extraction (PTex) protocol that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a global RNA-bound proteome of human HEK293 cells and the bacterium Salmonella Typhimurium.
RNA-protein complexes play pivotal roles in many central biological processes. Although methods based on high-throughput sequencing have advanced our ability to identify the specific RNAs bound by a ...particular protein, there is a need for precise and systematic ways to identify RNA interaction sites on proteins. We have developed an experimental and computational workflow combining photo-induced cross-linking, high-resolution mass spectrometry and automated analysis of the resulting mass spectra for the identification of cross-linked peptides, cross-linking sites and the cross-linked RNA oligonucleotide moieties of such RNA-binding proteins. The workflow can be applied to any RNA-protein complex of interest or to whole proteomes. We applied the approach to human and yeast mRNA-protein complexes in vitro and in vivo, demonstrating its powerful utility by identifying 257 cross-linking sites on 124 distinct RNA-binding proteins. The open-source software pipeline developed for this purpose, RNP(xl), is available as part of the OpenMS project.
Objective
To compare clinical outcomes following induction of labour (IOL) using a balloon catheter and going home, versus prostaglandin (PG) as an inpatient.
Design
Randomised controlled trial.
...Setting
Eight Australian maternity hospitals.
Population
Women with uncomplicated term singleton pregnancies undergoing IOL for low‐risk indications including post‐term, advanced maternal age and ‘social’ reasons.
Methods
Between September 2015 and October 2018, 347 women were randomised to a balloon outpatient group and 348 to a PG inpatient group. The PG group received Dinoprostone, either 2 mg gel or 10 mg controlled‐release tape. The balloon group had a double‐balloon catheter inserted and went home.
Main outcome measures
The primary outcome was a composite neonatal measure comprising nursery admission, intubation/cardiac compressions, acidaemia, hypoxic ischaemic encephalopathy, seizure, infection, pulmonary hypertension, stillbirth or death. Clinical and process outcomes are reported.
Results
There were no statistically significant differences in the primary outcome comparing balloon with PG (18.6% versus 25.8%; relative risk = 0.77, 95% CI 0.51–1.02; P = 0.070), cord arterial pH <7.10 (3.5% versus 9.2%; P = 0.072), nursery admissions (12.6% versus 15.5%; P = 0.379), neonatal antibiotic use (12.1% versus 17.6%; P = 0.103), or mode of birth. Nulliparous women in the balloon group had lower rates of the primary outcome (20.4% versus 31.0%;P = 0.032); Parous women were less likely to have an unassisted vaginal birth (77.6% versus 92.3%; P = 0.045).
Conclusions
Balloon catheters may be a superior method of cervical priming for nulliparous women, whereas this may not be the case for parous women. It is feasible that nulliparous women go home after commencing balloon catheter IOL, and the likelihood of adverse outcomes is low.
Tweetable
Multicentre trial shows outpatient induction using balloon catheter is safe and feasible for nulliparous women.
Tweetable
Multicentre trial shows outpatient induction using balloon catheter is safe and feasible for nulliparous women.
To compare clinical outcomes following induction of labour (IOL) using a balloon catheter and going home, versus prostaglandin (PG) as an inpatient.
Randomised controlled trial.
Eight Australian ...maternity hospitals.
Women with uncomplicated term singleton pregnancies undergoing IOL for low-risk indications including post-term, advanced maternal age and 'social' reasons.
Between September 2015 and October 2018, 347 women were randomised to a balloon outpatient group and 348 to a PG inpatient group. The PG group received Dinoprostone, either 2 mg gel or 10 mg controlled-release tape. The balloon group had a double-balloon catheter inserted and went home.
The primary outcome was a composite neonatal measure comprising nursery admission, intubation/cardiac compressions, acidaemia, hypoxic ischaemic encephalopathy, seizure, infection, pulmonary hypertension, stillbirth or death. Clinical and process outcomes are reported.
There were no statistically significant differences in the primary outcome comparing balloon with PG (18.6% versus 25.8%; relative risk = 0.77, 95% CI 0.51-1.02; P = 0.070), cord arterial pH <7.10 (3.5% versus 9.2%; P = 0.072), nursery admissions (12.6% versus 15.5%; P = 0.379), neonatal antibiotic use (12.1% versus 17.6%; P = 0.103), or mode of birth. Nulliparous women in the balloon group had lower rates of the primary outcome (20.4% versus 31.0%;P = 0.032); Parous women were less likely to have an unassisted vaginal birth (77.6% versus 92.3%; P = 0.045).
Balloon catheters may be a superior method of cervical priming for nulliparous women, whereas this may not be the case for parous women. It is feasible that nulliparous women go home after commencing balloon catheter IOL, and the likelihood of adverse outcomes is low.
Multicentre trial shows outpatient induction using balloon catheter is safe and feasible for nulliparous women.
In order to counteract fatigue, physical activity (PA) is recommended for all stages of cancer. However, only few advanced cancer patients (ACP) are physically active. Quantitative data with high ...numbers of ACP reporting barriers to PA are missing. This study aimed to identify barriers to PA in ACP with tiredness/weakness and investigate their motivation towards it.
Outpatients with metastatic cancer receiving cancer care at a German Cancer Center reporting moderate/severe tiredness/weakness during self-assessment (MIDOS II) were enrolled. We assessed Fatigue-(FACF-F) and Depression (PHQ8) Scores, demographics, cancer-specific parameters, motivation for PA, physical, psychological and social barriers.
141 of 440 eligible patients (32.0%) with different diagnoses agreed to participate. Patients frequently reported "I feel weakened due to my tumor therapy" (n = 108; 76.6%), physical symptoms (tiredness, weakness, dyspnea, joint-problems, pain, nausea n = 107; 75.9%) and fatigue (n = 99; 70.2%) as barriers to PA. However, no significant group differences regarding these barriers were found between physically active and inactive patients. Social barriers were rarely chosen. Motivated patients were 5.6 times more likely to be physically active (p < 0.001), also motivation turned out to be the strongest predictor for a physically active behavior (β = 1.044; p = 0.005). Motivated attitude towards PA was predicted by fatigue (β = - 2.301; p = 0.008), clinically relevant depression (β = - 1.390, p = 0.039), knowledge about PA and quality of life (QoL) (β = 0.929; p = 0.002), PA before diagnosis (β = 0.688; p = 0.005 and Interest in exercise program (β = 0.635; p = 0.008).
"I feel weakened due to my tumor therapy" is the most reported barrier to PA among both, physically and inactive patients. Motivation for PA is the strongest predictor of performing PA. Interest in PA, knowledge about PA/QoL and PA before diagnosis are main predictors of a motivated attitude. Absence/presence of social barriers did not associate with motivation, fatigue and depression proved to be a negative predictor. Programs including information, motivational counseling and individualized training should be offered for ACP to overcome barriers and reduce fatigue.
German Register of Clinical Trials DRKS00012514, registration date: 30.5.2017.
In general, a thin film deposited on a substrate surface exhibits a certain amount of stress that causes a deformation of the substrate. Usually, the deformation is elastic, however, under some ...circumstances, a non-recoverable deformation of the substrate can be observed. Recently, we demonstrated that a large non-recoverable deformation of fused silica substrates can be obtained if on one side a film of substoichiometric silicon oxide is deposited and the film-substrate system is annealed at a temperature in the glass transition range. By laser patterning of the film, specific surface shapes can be obtained. Here, we report on a similar approach for the viscoelastic deformation of plates of borosilicate glass (Schott N-BK7). The substrates are coated by a film of substoichiometric silicon oxide, which is patterned by application of a XeCl-excimer laser. We measured the surface shape of the non-coated side after different annealing durations. Deformation of the samples corresponds to a tensile film stress. But by application of a line pattern, toroid surface shapes with curvatures of different sign can be easily obtained. With further investigation and development, the process might be applied for production of freeform surfaces.
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