bims-meglyc 2023-05-14 papers

on Metabolic disorders affecting glycosylation

Issue of 2023–05–14
eight papers selected by
Silvia Radenkovic, Frontiers in Congenital Disorders of Glycosylation Consortium

Glycosylation and behavioral symptoms in neurological disorders.
Identification and characterization of a new variation in DPM2 gene in two Chinese siblings with mild intellectual impairment.
CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions.
FDA approval, clinical trial evidence, efficacy, epidemiology, and price for non-orphan and ultra-rare, rare, and common orphan cancer drug indications: cross sectional analysis.
Perspectives of Rare Disease Experts on Newborn Genome Sequencing.
Chemically Defined Production of Tri-Lineage Human iPSC-Derived Cardiac Spheroids.
Bi-allelic variants of FILIP1 cause congenital myopathy, dysmorphism and neurological defects.
Emerging roles of O-glycosylation in regulating protein aggregation, phase separation, and functions.

Transl Psychiatry. 2023 May 08. 13(1): 154

Glycosylation and behavioral symptoms in neurological disorders.

Prajitha Pradeep, Hyeyeon Kang, Boyoung Lee.

Glycosylation, the addition of glycans or carbohydrates to proteins, lipids, or other glycans, is a complex post-translational modification that plays a crucial role in cellular function. It is estimated that at least half of all mammalian proteins undergo glycosylation, underscoring its importance in the functioning of cells. This is reflected in the fact that a significant portion of the human genome, around 2%, is devoted to encoding enzymes involved in glycosylation. Changes in glycosylation have been linked to various neurological disorders, including Alzheimer's disease, Parkinson's disease, autism spectrum disorder, and schizophrenia. Despite its widespread occurrence, the role of glycosylation in the central nervous system remains largely unknown, particularly with regard to its impact on behavioral abnormalities in brain diseases. This review focuses on examining the role of three types of glycosylation: N-glycosylation, O-glycosylation, and O-GlcNAcylation, in the manifestation of behavioral and neurological symptoms in neurodevelopmental, neurodegenerative, and neuropsychiatric disorders.

DOI: https://doi.org/10.1038/s41398-023-02446-x
Front Genet. 2023 ;14 930692

Identification and characterization of a new variation in DPM2 gene in two Chinese siblings with mild intellectual impairment.

Peiwei Zhao, Yanqiu Hu, Juan Hu, Cheng Li, Yufeng Huang, Lei Zhang, Sukun Luo, Hongmin Zhu, Jun Jiang, Xuelian He.

  Introduction: Congenital disorders of glycosylation (CDGs) are a genetically heterogeneous group of metabolic disorders caused by abnormal protein or lpid glycosylation. DPM2 is one subunit of a heterotrimeric complex for dolichol-phosphatemannose synthase (DPMS), a key enzyme in glycosylation, and only four patients with DPM2-CDG have been reported. Methods: Whole-exome sequencing (WES) was performed in a Chinese family having two siblings with a mild form of DPM2-CDG with developmental delay, mild intellectual disability, hypotonia, and increased serum creatine kinase. Sanger sequencing was used to validate the variants identified in the siblings and their parents. In vitro functional study was performed. Results: A homozygous mutation, c.197G>A (p.Gly66Glu) in exon 4 of DPM2 (NM_003863) was identified by whole exome sequencing (WES). In vitro functional analysis demonstrated that this variant increased the expression level of DPM2 protein and western blot revealed a significant decrease in ICAM1, a universal biomarker for hypoglycosylation in patients with CDG, suggesting abnormal N-linked glycosylation. We also reviewed the 4 previously reported patients carrying homozygous or compound heterozygous variants of DMP2 gene, and found that patients with variants within the region encoding the first domain had more severe clinical symptoms than those with variants within the second domain. However, the actual genotype-phenotype relationship needs more study. Discussion: Overall, our study broadens the variant spectrum of DPM2 gene, attempts to explain the different phenotypes in patients with different DPM2 variants, and emphasizes the need of further functional studies to understand the underlying pathophysiology of the phenotypic heterogeneity.

Keywords:  DPM2; congenital disorders of glycosylation; correlation of genotype–phenotype; mutation; whole-exome sequencing

DOI:  https://doi.org/10.3389/fgene.2023.930692
bioRxiv. 2023 Apr 27. pii: 2023.04.26.538498. [Epub ahead of print]

CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions.

Emmy Li, Camila Benitez, Steven C Boggess, Mark Koontz, Indigo V L Rose, Nina Draeger, Olivia M Teter, Avi J Samelson, Erik M Ullian, Martin Kampmann.

The sheer complexity of the brain has complicated our ability to understand its cellular mechanisms in health and disease. Genome-wide association studies have uncovered genetic variants associated with specific neurological phenotypes and diseases. In addition, single-cell transcriptomics have provided molecular descriptions of specific brain cell types and the changes they undergo during disease. Although these approaches provide a giant leap forward towards understanding how genetic variation can lead to functional changes in the brain, they do not establish molecular mechanisms. To address this need, we developed a 3D co-culture system termed iAssembloids (induced multi-lineage assembloids) that enables the rapid generation of homogenous neuron-glia spheroids. We characterize these iAssembloids with immunohistochemistry and single-cell transcriptomics and combine them with large-scale CRISPRi-based screens. In our first application, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response in the presence of reactive oxygen species elicited by high neuronal activity, which was not previously found in 2D monoculture neuron screens. We also apply the platform to investigate the role of APOE-χ4, a risk variant for Alzheimer's Disease, in its effect on neuronal survival. This platform expands the toolbox for the unbiased identification of mechanisms of cell-cell interactions in brain health and disease.

DOI: https://doi.org/10.1101/2023.04.26.538498
BMJ. 2023 05 09. 381 e073242

FDA approval, clinical trial evidence, efficacy, epidemiology, and price for non-orphan and ultra-rare, rare, and common orphan cancer drug indications: cross sectional analysis.

Thomas Michaeli, Hendrik Jürges, Daniel Tobias Michaeli.

OBJECTIVE: To analyze the US Food and Drug Administration (FDA) approval, trials, unmet needs, benefit, and pricing of ultra-rare (<6600 affected US citizens), rare (6600-200 000 citizens), and common (>200 000 citizens) orphan cancer drug indications and non-orphan cancer drug indications.
DESIGN: Cross sectional analysis.
SETTING: Data from Drugs@FDA, FDA labels, Global Burden of Disease study, and Medicare and Medicaid.
POPULATION: 170 FDA approved drugs across 455 cancer indications between 2000 and 2022.
MAIN OUTCOME MEASURES: Comparison of non-orphan and ultra-rare, rare, and common orphan indications regarding regulatory approval, trials, epidemiology, and price. Hazard ratios for overall survival and progression-free survival were meta-analyzed.
RESULTS: 161 non-orphan and 294 orphan cancer drug indications were identified, of which 25 were approved for ultra-rare diseases, 205 for rare diseases, and 64 for common diseases. Drugs for ultra-rare orphan indications were more frequently first in class (76% v 48% v 38% v 42%; P<0.001), monotherapies (88% v 69% v 72% v 55%; P=0.001), for hematologic cancers (76% v 66% v 0% v 0%; P<0.001), and supported by smaller trials (median 85 v 199 v 286 v 521 patients; P<0.001), of single arm (84% v 44% v 28% v 21%; P<0.001) phase 1/2 design (88% v 45% v 45% v 27%; P<0.001) compared with rare and common orphan indications and non-orphan indications. Drugs for common orphan indications were more often biomarker directed (69% v 26% v 12%; P<0.001), first line (77% v 39% v 20%; P<0.001), small molecules (80% v 62% v 48%; P<0.001) benefiting from quicker time to first FDA approval (median 5.7 v 7.1 v 8.9 years; P=0.02) than those for rare and ultra-rare orphan indications. Drugs for ultra-rare, rare, and common orphan indications offered a significantly greater progression-free survival benefit (hazard ratio 0.53 v 0.51 v 0.49 v 0.64; P<0.001), but not overall survival benefit (0.50 v 0.73 v 0.71 v 0.74; P=0.06), than non-orphans. In single arm trials, tumor response rates were greater for drugs for ultra-rare orphan indications than for rare or common orphan indications and non-orphan indications (objective response rate 57% v 48% v 55% v 33%; P<0.001). Disease incidence/prevalence, five year survival, and the number of available treatments were lower, whereas disability adjusted life years per patient were higher, for ultra-rare orphan indications compared with rare or common indications and non-orphan indications. For 147 on-patent drugs with available data in 2023, monthly prices were higher for ultra-rare orphan indications than for rare or common orphan indications and non-orphan indications ($70 128 (£55 971; €63 370) v $33 313 v $16 484 v $14 508; P<0.001). For 48 on-patent drugs with available longitudinal data from 2005 to 2023, prices increased by 94% for drugs for orphan indications and 50% for drugs for non-orphan indications on average.
CONCLUSIONS: The Orphan Drug Act of 1983 incentivizes development of drugs not only for rare diseases but also for ultra-rare diseases and subsets of common diseases. These orphan indications fill significant unmet needs, yet their approval is based on small, non-robust trials that could overestimate efficacy outcomes. A distinct ultra-orphan designation with greater financial incentives could encourage and expedite drug development for ultra-rare diseases.

DOI: https://doi.org/10.1136/bmj-2022-073242
JAMA Netw Open. 2023 05 01. 6(5): e2312231

Perspectives of Rare Disease Experts on Newborn Genome Sequencing.

Nina B Gold, Sophia M Adelson, Nidhi Shah, Shardae Williams, Sarah L Bick, Emilie S Zoltick, Jessica I Gold, Alanna Strong, Rebecca Ganetzky, Amy E Roberts, Melissa Walker, Alexander M Holtz, Vijay G Sankaran, Ottavia Delmonte, Weizhen Tan, Ingrid A Holm, Jay R Thiagarajah, Junne Kamihara, Jason Comander, Emily Place, Janey Wiggs, Robert C Green.

Importance: Newborn genome sequencing (NBSeq) can detect infants at risk for treatable disorders currently undetected by conventional newborn screening. Despite broad stakeholder support for NBSeq, the perspectives of rare disease experts regarding which diseases should be screened have not been ascertained.
Objective: To query rare disease experts about their perspectives on NBSeq and which gene-disease pairs they consider appropriate to evaluate in apparently healthy newborns.
Design, Setting, and Participants: This survey study, designed between November 2, 2021, and February 11, 2022, assessed experts' perspectives on 6 statements related to NBSeq. Experts were also asked to indicate whether they would recommend including each of 649 gene-disease pairs associated with potentially treatable conditions in NBSeq. The survey was administered between February 11 and September 23, 2022, to 386 experts, including all 144 directors of accredited medical and laboratory genetics training programs in the US.
Exposures: Expert perspectives on newborn screening using genome sequencing.
Main Outcomes and Measures: The proportion of experts indicating agreement or disagreement with each survey statement and those who selected inclusion of each gene-disease pair were tabulated. Exploratory analyses of responses by gender and age were conducted using t and χ2 tests.
Results: Of 386 experts invited, 238 (61.7%) responded (mean [SD] age, 52.6 [12.8] years [range 27-93 years]; 126 [52.9%] women and 112 [47.1%] men). Among the experts who responded, 161 (87.9%) agreed that NBSeq for monogenic treatable disorders should be made available to all newborns; 107 (58.5%) agreed that NBSeq should include genes associated with treatable disorders, even if those conditions were low penetrance; 68 (37.2%) agreed that actionable adult-onset conditions should be sequenced in newborns to facilitate cascade testing in parents, and 51 (27.9%) agreed that NBSeq should include screening for conditions with no established therapies or management guidelines. The following 25 genes were recommended by 85% or more of the experts: OTC, G6PC, SLC37A4, CYP11B1, ARSB, F8, F9, SLC2A1, CYP17A1, RB1, IDS, GUSB, DMD, GLUD1, CYP11A1, GALNS, CPS1, PLPBP, ALDH7A1, SLC26A3, SLC25A15, SMPD1, GATM, SLC7A7, and NAGS. Including these, 42 gene-disease pairs were endorsed by at least 80% of experts, and 432 genes were endorsed by at least 50% of experts.
Conclusions and Relevance: In this survey study, rare disease experts broadly supported NBSeq for treatable conditions and demonstrated substantial concordance regarding the inclusion of a specific subset of genes in NBSeq.

DOI: https://doi.org/10.1001/jamanetworkopen.2023.12231
Curr Protoc. 2023 May;3(5): e767

Chemically Defined Production of Tri-Lineage Human iPSC-Derived Cardiac Spheroids.

Madelyn Arzt, Stephany Pohlman, Maedeh Mozneb, Arun Sharma.

  Cardiac spheroids derived from human induced pluripotent stem cells (hiPSC-cardiac spheroids) represent a powerful three-dimensional (3D) model for examining cardiac physiology and for drug toxicity screening. Recent advances with self-organizing, multicellular cardiac organoids highlight the capability of directed stem cell differentiation approaches to recapitulate the composition of the human heart in vitro. Using hiPSC-derived cardiomyocytes (hiPSC-CMs), hiPSC-derived endothelial cells (hiPSC-ECs), and hiPSC-derived cardiac fibroblasts (hiPSC-CFs) is advantageous for enabling tri-cellular crosstalk within a multilineage system and for generating patient-specific models. Chemically defined medium containing factors needed to simultaneously maintain hiPSC-CMs, hiPSC-ECs, and hiPSC-CFs is used to produce the spheroid system. In this article, we present protocols to illustrate the methods for conducting small-molecule-mediated differentiations of hiPSCs into cardiomyocytes, endothelial cells, and cardiac fibroblasts, as well as to assemble the fully integrated cardiac spheroids. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Maintenance and expansion of hiPSCs Basic Protocol 2: Differentiation of hiPSCs into cardiomyocytes Basic Protocol 3: Differentiation of hiPSCs into vascular endothelial cells Basic Protocol 4: Differentiation of hiPSCs into cardiac fibroblasts Basic Protocol 5: Production of hiPSC-derived cardiac spheroids.

Keywords:  cardiac fibroblasts; cardiac spheroids; cardiomyocytes; endothelial cells; iPSCs

DOI:  https://doi.org/10.1002/cpz1.767
Brain. 2023 May 10. pii: awad152. [Epub ahead of print]

Bi-allelic variants of FILIP1 cause congenital myopathy, dysmorphism and neurological defects.

Andreas Roos, Peter F M van der Ven, Hadil Alrohaif, Heike Kölbel, Lorena Heil, Adela Della Marina, Joachim Weis, Marvin Aßent, Stefanie Beck-Wödl, Rita Barresi, Ana Töpf, Kaela O'Connor, Albert Sickmann, Nicolai Kohlschmidt, Magdeldin El Gizouli, Nancy Meyer, Nassam Daya, Valentina Grande, Karin Bois, Frank J Kaiser, Matthias Vorgerd, Christopher Schröder, Ulrike Schara-Schmidt, Andrea Gangfuss, Teresinha Evangelista, Luisa Röbisch, Andreas Hentschel, Anika Grüneboom, Dieter O Fuerst, Alma Kuechler, Andreas Tzschach, Christel Depienne, Hanns Lochmüller.

  Filamin-A-interacting protein 1 (FILIP1) is a structural protein that is involved in neuronal and muscle function and integrity and interacts with FLNa and FLNc. Pathogenic variants in filamin-encoding genes have been linked to neurological disorders (FLNA) and muscle diseases characterized by myofibrillar perturbations (FLNC), but human diseases associated with FILIP1 variants have not yet been described. Here, we report on five patients from four unrelated consanguineous families with homozygous FILIP1 variants (two nonsense and two missense). Functional studies indicated altered stability of the FILIP1 protein carrying the p.[Pro1133Leu] variant. Patients exhibit a broad spectrum of neurological symptoms including brain malformations, neurodevelopmental delay, muscle weakness and pathology, and dysmorphic features. Electron and immunofluorescence microscopy on the muscle biopsy derived from the patient harbouring the homozygous p.[Pro1133Leu] missense variant revealed core-like zones of myofibrillar disintegration, autophagic vacuoles and accumulation of FLNc. Proteomic studies on the fibroblasts derived from the same patient showed dysregulation of a variety of proteins including FLNc and alpha-B-crystallin, a finding (confirmed by immunofluorescence) which is in line with the manifestation of symptoms associated with the syndromic phenotype of FILIP1opathy. The combined findings of this study show that the loss of functional FILIP1 leads to a recessive disorder characterized by neurological and muscular manifestations as well as dysmorphic features accompanied by perturbed proteostasis and myopathology.

Keywords:  FLNA; FLNC; MFM/myofibrillar myopathy; protein aggregate myopathy; vacuolar myopathy

DOI:  https://doi.org/10.1093/brain/awad152
Curr Opin Chem Biol. 2023 May 06. pii: S1367-5931(23)00052-2. [Epub ahead of print]75 102314

Emerging roles of O-glycosylation in regulating protein aggregation, phase separation, and functions.

Xiang Li, Pinou Lv, Yifei Du, Xing Chen, Cong Liu.

Protein O-glycosylation is widely identified in various proteins involved in diverse biological processes. Recent studies have demonstrated that O-glycosylation plays crucial and multifaceted roles in modulating protein amyloid aggregation and liquid-liquid phase separation (LLPS) under physiological conditions. Dysregulation of these processes is closely associated with human diseases such as neurodegenerative diseases (NDs) and cancers. In this review, we first summarize the distinct roles of O-glycosylation in regulating pathological aggregation of different amyloid proteins related to NDs and elaborate the underlying mechanisms of how O-glycosylation modulates protein aggregation kinetics, induces new aggregated structures, and mediates the pathogenesis of amyloid aggregates under diseased conditions. Furthermore, we introduce recent discoveries on O-GlcNAc-mediated regulation of synaptic LLPS and phase separation potency of low-complexity domain-enriched proteins. Finally, we identify challenges in future research and highlight the potential for developing new therapeutic strategies of NDs by targeting protein O-glycosylation.

DOI: https://doi.org/10.1016/j.cbpa.2023.102314