Structural view on 60S ribosome biogenesis

Eukaryotic ribosomes undergo a complex maturation process through which the ribosomal RNA (rRNA) must bind to ribosomal proteins (r-proteins) and fold into its native state. This requires numerous auxiliary factors responsible of rRNA processing, remodeling, intracellular transport and quality control checkpoints. Impairments in the process of ribosome production can lead to different diseases known as ribosomopathies. However, little is known about which defects in the ribosome biogenesis pathway can escape all quality checkpoints and what targets these faulty ribosomes and their putative products for degradation. The first part of this thesis constitutes a first attempt to address these questions, focusing on a specific impairment of the 60S biogenesis pathway that leads to the production of structurally deficient 80S ribosomes. Here, using cryo-EM and biochemical analysis, it is shown that large structural defects in the ribosome may bypass all quality control mechanisms in the nucleus, but are recognized in the cytoplasm after faulty ribosomes engage in translation. Then, the resulting proteins are targeted for degradation by the ribosome quality-control complex (RQC) after subunit splitting is carried out. The second part of this thesis focuses on a nucleoplasmic step of 60S ribosome biogenesis in which both the Rix1 complex and the dynein related AAA+ ATPase Rea1 bind to maturing pre-60S particles. Rea1 is required for the ATP-dependent dissociation of the assembly factor Rsa4 and may be involved in rearranging the Central Protuberance (CP). Several cryo-electron microscopy (cryo-EM) structures of native pre-60S particles bound to the Rix1-Rea1 machinery are presented in this thesis. Overall, the Rix1-Rea1 particle is similar to the earlier intermediate, the socalled Arx1 particle. However, a 180° rotation of the CP required to reach the final conformation of the 60S, has already happened in the Rix1-Rea1 state, constituting the largest remodeling step at the end of the maturation pathway. By performing cryo-EM analysis on two similar particles that were mutated on either Rix1 or Rea1 and by comparing the structures of the Arx1 and Rix1-Rea1 particles, a mechanistic model for the transition between the two intermediates is provided

Structural view on 60S ribosome biogenesis

Eukaryotic ribosomes undergo a complex maturation process through which the ribosomal RNA (rRNA) must bind to ribosomal proteins (r-proteins) and fold into its native state. This requires numerous auxiliary factors responsible of rRNA processing, remodeling, intracellular transport and quality control checkpoints. Impairments in the process of ribosome production can lead to different diseases known as ribosomopathies. However, little is known about which defects in the ribosome biogenesis pathway can escape all quality checkpoints and what targets these faulty ribosomes and their putative products for degradation. The first part of this thesis constitutes a first attempt to address these questions, focusing on a specific impairment of the 60S biogenesis pathway that leads to the production of structurally deficient 80S ribosomes. Here, using cryo-EM and biochemical analysis, it is shown that large structural defects in the ribosome may bypass all quality control mechanisms in the nucleus, but are recognized in the cytoplasm after faulty ribosomes engage in translation. Then, the resulting proteins are targeted for degradation by the ribosome quality-control complex (RQC) after subunit splitting is carried out. The second part of this thesis focuses on a nucleoplasmic step of 60S ribosome biogenesis in which both the Rix1 complex and the dynein related AAA+ ATPase Rea1 bind to maturing pre-60S particles. Rea1 is required for the ATP-dependent dissociation of the assembly factor Rsa4 and may be involved in rearranging the Central Protuberance (CP). Several cryo-electron microscopy (cryo-EM) structures of native pre-60S particles bound to the Rix1-Rea1 machinery are presented in this thesis. Overall, the Rix1-Rea1 particle is similar to the earlier intermediate, the socalled Arx1 particle. However, a 180° rotation of the CP required to reach the final conformation of the 60S, has already happened in the Rix1-Rea1 state, constituting the largest remodeling step at the end of the maturation pathway. By performing cryo-EM analysis on two similar particles that were mutated on either Rix1 or Rea1 and by comparing the structures of the Arx1 and Rix1-Rea1 particles, a mechanistic model for the transition between the two intermediates is provided

Aged Human Dermal Extracellular Matrix as an Innovative Scaffold for Aging on Chip Model

Currently, there is a growing demand for developing innovative biomaterials that represent skin microenvironment more realistically. Here, we present an optimised protocol to extract and characterize an innovative human adult dermal extracellular matrix scaffold to represent the dermal layer in advanced 3D skin models

IKZF1/3 and CRL4-CRBN E3 ubiquitin ligase mutations and IMiD resistance in multiple myeloma

The work was supported by the Deutsche Forschungsgemeinschaft (KFO216), the IZKF, the BTHA and the CDW Stiftung (KMK). UM was supported by a grant of the German Excellence Initiative to the Graduate School of Life Sciences, University of Würzburg.S

Urine NMR-based TB metabolic fingerprinting for the diagnosis of TB in children

Tuberculosis (TB) is a major cause of morbidity and mortality in children, and early diagnosis and treatment are crucial to reduce long-term morbidity and mortality. In this study, we explore whether urine nuclear magnetic resonance (NMR)-based metabolomics could be used to identify differences in the metabolic response of children with different diagnostic certainty of TB. We included 62 children with signs and symptoms of TB and 55 apparently healthy children. Six of the children with presumptive TB had bacteriologically confirmed TB, 52 children with unconfirmed TB, and 4 children with unlikely TB. Urine metabolic fingerprints were identified using high- and low-field proton NMR platforms and assessed with pattern recognition techniques such as principal components analysis and partial least squares discriminant analysis. We observed differences in the metabolic fingerprint of children with bacteriologically confirmed and unconfirmed TB compared to children with unlikely TB (p = 0.041 and p = 0.013, respectively). Moreover, children with unconfirmed TB with X-rays compatible with TB showed differences in the metabolic fingerprint compared to children with non-pathological X-rays (p = 0.009). Differences in the metabolic fingerprint in children with different diagnostic certainty of TB could contribute to a more accurate characterisation of TB in the paediatric population. The use of metabolomics could be useful to improve the prediction of TB progression and diagnosis in children

A comparison of Covid-19 early detection between convolutional neural networks and radiologists

[EN] Background The role of chest radiography in COVID-19 disease has changed since the beginning of the pandemic from a diagnostic tool when microbiological resources were scarce to a different one focused on detecting and monitoring COVID-19 lung involvement. Using chest radiographs, early detection of the disease is still helpful in resource-poor environments. However, the sensitivity of a chest radiograph for diagnosing COVID-19 is modest, even for expert radiologists. In this paper, the performance of a deep learning algorithm on the first clinical encounter is evaluated and compared with a group of radiologists with different years of experience. Methods The algorithm uses an ensemble of four deep convolutional networks, Ensemble4Covid, trained to detect COVID-19 on frontal chest radiographs. The algorithm was tested using images from the first clinical encounter of positive and negative cases. Its performance was compared with five radiologists on a smaller test subset of patients. The algorithm's performance was also validated using the public dataset COVIDx. Results Compared to the consensus of five radiologists, the Ensemble4Covid model achieved an AUC of 0.85, whereas the radiologists achieved an AUC of 0.71. Compared with other state-of-the-art models, the performance of a single model of our ensemble achieved nonsignificant differences in the public dataset COVIDx. Conclusion The results show that the use of images from the first clinical encounter significantly drops the detection performance of COVID-19. The performance of our Ensemble4Covid under these challenging conditions is considerably higher compared to a consensus of five radiologists. Artificial intelligence can be used for the fast diagnosis of COVID-19.Project Chest screening for patients with COVID 19 (COV2000750 Special COVID19 resolution) funded by Instituto de Salud Carlos III. Project DIRAC (INNVA1/2020/42) funded by the Agencia Valenciana de la Innovacion, Generalitat Valenciana.Albiol Colomer, A.; Albiol, F.; Paredes Palacios, R.; Plasencia-Martínez, JM.; Blanco Barrio, A.; García Santos, JM.; Tortajada, S.... (2022). A comparison of Covid-19 early detection between convolutional neural networks and radiologists. Insights into Imaging. 13(1):1-12. https://doi.org/10.1186/s13244-022-01250-311213

The syndrome of central hypothyroidism and macroorchidism: IGSF1 controls TRHR and FSHB expression by differential modulation of pituitary TGFβ and Activin pathways

IGSF1 (Immunoglobulin Superfamily 1) gene defects cause central hypothyroidism and macroorchidism. However, the pathogenic mechanisms of the disease remain unclear. Based on a patient with a full deletion of IGSF1 clinically followed from neonate to adulthood, we investigated a common pituitary origin for hypothyroidism and macroorchidism, and the role of IGSF1 as regulator of pituitary hormone secretion. The patient showed congenital central hypothyroidism with reduced TSH biopotency, over-secretion of FSH at neonatal minipuberty and macroorchidism from 3 years of age. His markedly elevated inhibin B was unable to inhibit FSH secretion, indicating a status of pituitary inhibin B resistance. We show here that IGSF1 is expressed both in thyrotropes and gonadotropes of the pituitary and in Leydig and germ cells in the testes, but at very low levels in Sertoli cells. Furthermore, IGSF1 stimulates transcription of the thyrotropin-releasing hormone receptor (TRHR) by negative modulation of the TGFβ1-Smad signaling pathway, and enhances the synthesis and biopotency of TSH, the hormone secreted by thyrotropes. By contrast, IGSF1 strongly down-regulates the activin-Smad pathway, leading to reduced expression of FSHB, the hormone secreted by gonadotropes. In conclusion, two relevant molecular mechanisms linked to central hypothyroidism and macroorchidism in IGSF1 deficiency are identified, revealing IGSF1 as an important regulator of TGFβ/Activin pathways in the pituitary

A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation

The following corrections appear in the attached pdf labelled "Correction to Version of Record". The authors inadvertently omitted Woonghee Lee from the list of authors. The corrected author list and affiliations are noted. Revised acknowledgment paragraphs including Woonghee Lee’s funding source and contribution also appear in the correction. In addition, the authors noted the omission of details of NMR structure calculation from the Materials and Methods section. The relevant paragraph and the references associated with it are appended.Eukaryotic ribosome biogenesis involves ∼200 assembly factors, but how these contribute to ribosome maturation is poorly understood. Here, we identify a network of factors on the nascent 60S subunit that actively remodels preribosome structure. At its hub is Rsa4, a direct substrate of the force-generating ATPase Rea1. We show that Rsa4 is connected to the central protuberance by binding to Rpl5 and to ribosomal RNA (rRNA) helix 89 of the nascent peptidyl transferase center (PTC) through Nsa2. Importantly, Nsa2 binds to helix 89 before relocation of helix 89 to the PTC. Structure-based mutations of these factors reveal the functional importance of their interactions for ribosome assembly. Thus, Rsa4 is held tightly in the preribosome and can serve as a “distribution box,” transmitting remodeling energy from Rea1 into the developing ribosome. We suggest that a relay-like factor network coupled to a mechano-enzyme is strategically positioned to relocate rRNA elements during ribosome maturation

Urine NMR-based TB metabolic fingerprinting for the diagnosis of TB in children

Tuberculosis (TB) is a major cause of morbidity and mortality in children, and early diagnosis and treatment are crucial to reduce long-term morbidity and mortality. In this study, we explore whether urine nuclear magnetic resonance (NMR)-based metabolomics could be used to identify differences in the metabolic response of children with different diagnostic certainty of TB. We included 62 children with signs and symptoms of TB and 55 apparently healthy children. Six of the children with presumptive TB had bacteriologically confirmed TB, 52 children with unconfirmed TB, and 4 children with unlikely TB. Urine metabolic fingerprints were identified using high- and low-field proton NMR platforms and assessed with pattern recognition techniques such as principal components analysis and partial least squares discriminant analysis. We observed differences in the metabolic fingerprint of children with bacteriologically confirmed and unconfirmed TB compared to children with unlikely TB (p = 0.041 and p = 0.013, respectively). Moreover, children with unconfirmed TB with X-rays compatible with TB showed differences in the metabolic fingerprint compared to children with non-pathological X-rays (p = 0.009). Differences in the metabolic fingerprint in children with different diagnostic certainty of TB could contribute to a more accurate characterisation of TB in the paediatric population. The use of metabolomics could be useful to improve the prediction of TB progression and diagnosis in children

Urine NMR-based TB metabolic fingerprinting for the diagnosis of TB in children

Tuberculosis (TB) is a major cause of morbidity and mortality in children, and early diagnosis and treatment are crucial to reduce long-term morbidity and mortality. In this study, we explore whether urine nuclear magnetic resonance (NMR)-based metabolomics could be used to identify differences in the metabolic response of children with different diagnostic certainty of TB. We included 62 children with signs and symptoms of TB and 55 apparently healthy children. Six of the children with presumptive TB had bacteriologically confirmed TB, 52 children with unconfirmed TB, and 4 children with unlikely TB. Urine metabolic fingerprints were identified using high- and low-field proton NMR platforms and assessed with pattern recognition techniques such as principal components analysis and partial least squares discriminant analysis. We observed differences in the metabolic fingerprint of children with bacteriologically confirmed and unconfirmed TB compared to children with unlikely TB (p = 0.041 and p = 0.013, respectively). Moreover, children with unconfirmed TB with X-rays compatible with TB showed differences in the metabolic fingerprint compared to children with non-pathological X-rays (p = 0.009). Differences in the metabolic fingerprint in children with different diagnostic certainty of TB could contribute to a more accurate characterisation of TB in the paediatric population. The use of metabolomics could be useful to improve the prediction of TB progression and diagnosis in children