bims-meglyc 2023-04-09 papers

on Metabolic disorders affecting glycosylation

Issue of 2023–04–09
fourteen papers selected by
Silvia Radenkovic, Frontiers in Congenital Disorders of Glycosylation Consortium

Thrombosis risk with estrogen use for puberty induction in congenital disorders of glycosylation.
Orphan medical devices have come a long way.
Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch.
Unlocking the potential of induced pluripotent stem cells for neonatal disease modeling and drug development.
Glutamate shall not pass: a mechanistic role for astrocytic O-GlcNAc transferase in stress and depression.
Need and Challenges in Establishing Newborn Screening Programs for Inherited Metabolic Disorders in Developing Countries.
Novel DPAGT1 Gene Mutation in Two Twins with Congenital Myasthenic Syndrome and a Review of the Literature.
Dataset from dried blood spot acylcarnitine for detection of Carnitine-Acylcarnitine Translocase (CACT) deficiency and Carnitine Palmitoyl Transferase 2 (CPT2) deficiency.
A novel integrative multi-omics approach to unravel the genetic determinants of rare diseases with application in sinusoidal obstruction syndrome.
Cerebral Glucose Metabolism and Potential Effects on Endoplasmic Reticulum Stress in Stroke.
Congenital abnormalities of heart and kidney.
Epigenetics in cardiovascular health and disease.
The Effects of N-Linked Glycosylation on SLC6 Transporters.
Brain-specific glycosylation of protein tyrosine phosphatase receptor type Z (PTPRZ) marks a demyelination-associated astrocyte subtype.

Mol Genet Metab. 2023 Mar 30. pii: S1096-7192(23)00192-0. [Epub ahead of print]138(4): 107562

Thrombosis risk with estrogen use for puberty induction in congenital disorders of glycosylation.

Erik A Eklund, Bradley S Miller, Alexander A Boucher.

  Congenital disorders of glycosylation are a group of rare related disorders causing multisystem dysfunction, including ovarian failure in females that requires early estrogen replacement. Glycosylation defects also disrupt normal synthesis of several coagulation factors, increasing thrombotic risks and complicating hormone replacement. This series describes four females with different types of CDG who developed venous thromboses while on transdermal estrogen replacement. The authors highlight the knowledge gaps around anticoagulation for this population and propose further investigations.

Keywords:  Anticoagulation; Congenital disorders of glycosylation; Delayed puberty; Estrogen replacement; Gonadal failure; Thrombosis

DOI:  https://doi.org/10.1016/j.ymgme.2023.107562
Orphanet J Rare Dis. 2023 Apr 05. 18(1): 71

Orphan medical devices have come a long way.

M Dooms.

   BACKGROUND: In many countries worldwide orphan drug regulations are installed but only the United States of America and Japan have an orphan device regulation. For many years surgeons have used off-label or self-assembled medical devices for the prevention, diagnosis or treatment of rare disorders. Four examples are given: an external cardiac pacemaker, a metal brace for clubfoot in newborns, a transcutaneous nerve stimulator and a cystic fibrosis mist tent.
CONCLUSION: In this article we argue that we need authorized medical devices as well as medicinal products to prevent, diagnose and treat patients with life-threatening or chronically debilitating disorders with a low prevalence/incidence. Several arguments are given to support this statement.

Keywords:  Custom-made medical device; History of medicine; Humanitarian-use device; Medtech; Rare diseases; Repurposing

DOI:  https://doi.org/10.1186/s13023-023-02685-7
Stem Cell Res Ther. 2023 Apr 03. 14(1): 63

Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch.

Jingran Zhang, Guang Shi, Junjie Pang, Xing Zhu, Qingcai Feng, Jie Na, Wenbin Ma, Dan Liu, Zhou Songyang.

   BACKGROUND: Post-translational modifications of proteins are crucial to the regulation of their activity and function. As a newly discovered acylation modification, crotonylation of non-histone proteins remains largely unexplored, particularly in human embryonic stem cells (hESCs).
METHODS: We investigated the role of crotonylation in hESC differentiation by introduce crotonate into the culture medium of GFP tagged LTR7 primed H9 cell and extended pluripotent stem cell lines. RNA-seq assay was used to determine the hESC transcriptional features. Through morphological changes, qPCR of pluripotent and germ layer-specific gene markers and flow cytometry analysis, we determined that the induced crotonylation resulted in hESC differentiating into the endodermal lineage. We performed targeted metabolomic analysis and seahorse metabolic measurement to investigate the metabolism features after crotonate induction. Then high-resolution tandem mass spectrometry (LC-MS/MS) revealed the target proteins in hESCs. In addition, the role of crotonylated glycolytic enzymes (GAPDH and ENOA) was evaluated by in vitro crotonylation and enzymatic activity assays. Finally, we used knocked-down hESCs by shRNA, wild GAPDH and GAPDH mutants to explore potential role of GAPDH crotonylation in regulating human embryonic stem cell differentiation and metabolic switch.
RESULT: We found that induced crotonylation in hESCs resulted in hESCs of different pluripotency states differentiating into the endodermal lineage. Increased protein crotonylation in hESCs was accompanied by transcriptomic shifts and decreased glycolysis. Large-scale crotonylation profiling of non-histone proteins revealed that metabolic enzymes were major targets of inducible crotonylation in hESCs. We further discovered GAPDH as a key glycolytic enzyme regulated by crotonylation during endodermal differentiation from hESCs.
CONCLUSIONS: Crotonylation of GAPDH decreased its enzymatic activity thereby leading to reduced glycolysis during endodermal differentiation from hESCs.

Keywords:  Crotonylation; Embryonic stem cell; Endodermal differentiation; GAPDH; Metabolic switch

DOI:  https://doi.org/10.1186/s13287-023-03290-y
Semin Perinatol. 2023 Mar 11. pii: S0146-0005(23)00032-0. [Epub ahead of print] 151729

Unlocking the potential of induced pluripotent stem cells for neonatal disease modeling and drug development.

Ziyi Liu, Bonny Lami, Laertis Ikonomou, Mingxia Gu.

  Neonatal lung and heart diseases, albeit rare, can result in poor quality of life, often require long-term management and/or organ transplantation. For example, Congenital Heart Disease (CHD) is one of the most common type of congenital disabilities, affecting nearly 1% of the newborns, and has complex and multifactorial causes, including genetic predisposition and environmental influences. To develop new strategies for heart and lung regeneration in CHD and neonatal lung disease, human induced pluripotent stem cells (hiPSCs) provide a unique and personalized platform for future cell replacement therapy and high-throughput drug screening. Additionally, given the differentiation potential of iPSCs, cardiac cell types such as cardiomyocytes, endothelial cells, and fibroblasts and lung cell types such Type II alveolar epithelial cells can be derived in a dish to study the fundamental pathology during disease progression. In this review, we discuss the applications of hiPSCs in understanding the molecular mechanisms and cellular phenotypes of CHD (e.g., structural heart defect, congenital valve disease, and congenital channelopathies) and congenital lung diseases, such as surfactant deficiencies and Brain-Lung-Thyroid syndrome. We also provide future directions for generating mature cell types from iPSCs, and more complex hiPSC-based systems using three-dimensional (3D) organoids and tissue-engineering. With these potential advancements, the promise that hiPSCs will deliver new CHD and neonatal lung disease treatments may soon be fulfilled.

Keywords:  Congenital heart disease; Congenital lung disorder; Disease modeling; Drug development; Human induced pluripotent stem cells

DOI:  https://doi.org/10.1016/j.semperi.2023.151729
J Clin Invest. 2023 Apr 03. pii: e168662. [Epub ahead of print]133(7):

Glutamate shall not pass: a mechanistic role for astrocytic O-GlcNAc transferase in stress and depression.

Sam Ej Paton, Caroline Menard.

Major depressive disorder, characterized by aberrant glutamatergic signaling in the prefrontal cortex (PFC), is a leading cause of disability worldwide. Depression is highly comorbid with metabolic disorders, but a mechanistic link is elusive. In this issue of the JCI, Fan and coauthors report that elevated posttranslational modification with the glucose metabolite N-acetylglucosamine (GlcNAc) by O-GlcNAc transferase (OGT) contributed to stress-induced establishment of depression-like behaviors in mice. This effect was specific to medial PFC (mPFC) astrocytes, with glutamate transporter-1 (GLT-1) identified as an OGT target. Specifically, O-GlcNAcylation of GLT-1 resulted in diminished glutamate clearance from excitatory synapses. Further, astrocytic OGT knockdown restored stress-induced deficits in glutamatergic signaling, promoting resilience. These findings provide a mechanistic link between metabolism and depression and have relevance for antidepressant targets.

DOI: https://doi.org/10.1172/JCI168662
Adv Biol (Weinh). 2023 Apr 05. e2200318

Need and Challenges in Establishing Newborn Screening Programs for Inherited Metabolic Disorders in Developing Countries.

Muhammad Wasim, Haq Nawaz Khan, Hina Ayesha, Fazli Rabbi Awan.

  Even in this post genomic era, no national level newborn screening (NBS) programs for inborn errors of metabolism (IEMs) are yet available in several developing countries including Pakistan. Through NBS, various IEMs can be screened using minute quantities of biofluids. Targeted metabolomics and genomic techniques are the main approaches used for NBS. However, lack of technical expertise and such high-end "omics" based analytical facilities, and meager funding for healthcare in developing countries are the major reasons for unavailability of NBS programs. As it is reflected by only a handful reports about IEMs from Pakistan with population of ≈220 million and consanguinity rate of about 70%, which suggests an unmet need for an NBS program owing to reasonably high prevalence of inherited diseases. Around 200 IEMs are potentially treatable if diagnosed at an earlier stage through biochemical marker and genetic screening, so such patients can get benefit from the NBS program. This overview will help to persuade the stakeholders to setup NBS programs in developing countries including Pakistan, due to multitude of benefits for IEMs; timely diagnosis and early treatment can help the patients to live a nearly healthy life, reduced suffering of the family and minimal burden on society or national healthcare system.

Keywords:  gas chromatography-mass spectrometry; inborn errors of metabolism; liquid chromatography - mass spectrometry; metabolomics; newborn screening

DOI:  https://doi.org/10.1002/adbi.202200318
J Neuromuscul Dis. 2023 Mar 28.

Novel DPAGT1 Gene Mutation in Two Twins with Congenital Myasthenic Syndrome and a Review of the Literature.

Marta Cheli, Raffaella Brugnoni, Sara Gibertini, Renato Mantegazza, Lorenzo Maggi.

  Congenital myasthenic syndromes (CMS) are rare diseases caused by mutation in genes coding for proteins involved in neuromuscular junction structure and function. DPAGT1 gene mutations are a rare cause of CMS whose clinical evolution and pathophysiological mechanisms have not been clarified completely. We present the case of two twins displaying an infancy-onset predominant limb-girdle phenotype and carrying a novel DPAGT1 mutation associated with unusual histological and clinical findings. CMS can mimic paediatric and adult limb-girdle phenotype, hence neurophysiology plays a fundamental role in the differential diagnosis.

Keywords:  Keywords:

DOI:  https://doi.org/10.3233/JND-221675
Data Brief. 2023 Jun;48 109090

Dataset from dried blood spot acylcarnitine for detection of Carnitine-Acylcarnitine Translocase (CACT) deficiency and Carnitine Palmitoyl Transferase 2 (CPT2) deficiency.

Anasufiza Habib, Muhammad Irfan Bukhari Ahmad Nazri, Salina Abdul Rahman.

  Clinical diagnosis of inborn errors of metabolism in the suspected patients is usually guided by the initial general investigations in the laboratory such as the concentration of ammonia, blood gases status, blood glucose and ketones. The establishment of a biochemical diagnosis in patients with inborn errors of metabolism depends on the detection of the specific metabolites in the abnormal metabolic pathway which can appear in any of the body fluids but are most commonly tested in blood and urine samples. Acylcarnitine and/or acylcarnitine ratio in patients with carnitine acylcarnitine translocase and carnitine palmitoyl transferase deficiency showed an abnormal profile regardless of the metabolic status of patients. The acylcarnitine was derived from the analysis of dried blood spot using multiple reaction monitoring (MRM) which was performed using quadrupole mass spectrometry. The dataset presented in this article was generated from analysis of acylcarnitines in the 17,121 dried blood spots from symptomatic Malaysian patients less than fifty years old who exhibited symptoms suggestive of inborn errors of metabolism, but had a normal acylcarnitine profile. A precursor or ion scan of m/z 85 was selected for the analysis. Quantification of each analyte was obtained using the signal intensity ratio of the acylcarnitine to its internal standard. The acylcarnitines analyzed included C0, C2, C3, C3DC, C4, C5, C5:1, C5DC, C5OH, C6, C8, C10, C12, C14, C16, C18, C18:1, C16OH, C18OH and C18:1OH and was analyzed using Neolynx V4.0 software. We decided to choose the 1st and 99th percentiles as the minimum and maximum cut-offs. The filtered part of data in this article was used in the article Novel mutations associated with Carnitine-Acylcarnitine Translocase and Carnitine Palmitoyl Transferase 2 deficiencies in Malaysia. This dataset is intended to enable the scientific communities to get access to the raw dataset for future translational research use in inborn errors of metabolism as very few acylcarnitine data was developed and published for the symptomatic patients suspected of inborn errors of metabolism especially in the Asian population.

Keywords:  Acylcarnitine; Carnitine palmitoyl transferase 2 deficiency; Carnitine-acylcarnitine translocase deficiency; Inborn errors of metabolism; tandem mass spectrometry

DOI:  https://doi.org/10.1016/j.dib.2023.109090
PLoS One. 2023 ;18(4): e0281892

A novel integrative multi-omics approach to unravel the genetic determinants of rare diseases with application in sinusoidal obstruction syndrome.

Nicolas Waespe, Simona Jurkovic Mlakar, Isabelle Dupanloup, Mohamed Aziz Rezgui, Henrique Bittencourt, Maja Krajinovic, Claudia E Kuehni, Tiago Nava, Marc Ansari.

BACKGROUND: Genotype-phenotype analyses of rare diseases often suffer from a lack of power, due to small sample size, which makes identifying significant associations difficult. Sinusoidal obstruction syndrome (SOS) of the liver is a rare but life-threatening complication of hematopoietic stem cell transplantation (HSCT). The alkylating agent busulfan is commonly used in HSCT and known to trigger SOS. We developed a novel pipeline to identify genetic determinants in rare diseases by combining in vitro information with clinical whole-exome sequencing (WES) data and applied it in SOS patients and controls.
METHODS: First, we analysed differential gene expression in six lymphoblastoid cell lines (LCLs) before and after incubation with busulfan. Second, we used WES data from 87 HSCT patients and estimated the association with SOS at the SNP and the gene levels. We then combined the results of the expression and the association analyses into an association statistic at the gene level. We used an over-representation analysis to functionally characterize the genes that were associated with a significant combined test statistic.
RESULTS: After treatment of LCLs with busulfan, 1708 genes were significantly up-, and 1385 down-regulated. The combination of the expression experiment and the association analysis of WES data into a single test statistic revealed 35 genes associated with the outcome. These genes are involved in various biological functions and processes, such as "Cell growth and death", "Signalling molecules and interaction", "Cancer", and "Infectious disease".
CONCLUSIONS: This novel data analysis pipeline integrates two independent omics datasets and increases statistical power for identifying genotype-phenotype associations. The analysis of the transcriptomics profile of cell lines treated with busulfan and WES data from HSCT patients allowed us to identify potential genetic contributors to SOS. Our pipeline could be useful for identifying genetic contributors to other rare diseases where limited power renders genome-wide analyses unpromising.
TRIAL REGISTRATION: For the clinical dataset: Clinicaltrials.gov: NCT01257854. https://clinicaltrials.gov/ct2/history/NCT01257854.

DOI: https://doi.org/10.1371/journal.pone.0281892
Aging Dis. 2023 Apr 01. 14(2): 450-467

Cerebral Glucose Metabolism and Potential Effects on Endoplasmic Reticulum Stress in Stroke.

Sichao Guo, Alexandra Wehbe, Shabber Syed, Melissa Wills, Longfei Guan, Shuyu Lv, Fengwu Li, Xiaokun Geng, Yuchuan Ding.

  Ischemic stroke is an extremely common pathology with strikingly high morbidity and mortality rates. The endoplasmic reticulum (ER) is the primary organelle responsible for conducting protein synthesis and trafficking as well as preserving intracellular Ca2+ homeostasis. Mounting evidence shows that ER stress contributes to stroke pathophysiology. Moreover, insufficient circulation to the brain after stroke causes suppression of ATP production. Glucose metabolism disorder is an important pathological process after stroke. Here, we discuss the relationship between ER stress and stroke and treatment and intervention of ER stress after stroke. We also discuss the role of glucose metabolism, particularly glycolysis and gluconeogenesis, post-stroke. Based on recent studies, we speculate about the potential relationship and crosstalk between glucose metabolism and ER stress. In conclusion, we describe ER stress, glycolysis, and gluconeogenesis in the context of stroke and explore how the interplay between ER stress and glucose metabolism contributes to the pathophysiology of stroke.

Keywords:  endoplasmic reticulum stress; gluconeogenesis; glycolysis; stroke

DOI:  https://doi.org/10.14336/AD.2022.0905
Clin Case Rep. 2023 Apr;11(4): e7158

Congenital abnormalities of heart and kidney.

Hiroya Takafuji, Nahoko Kato, Yuta Azumi, Kotaro Obunai.

  Patients with congenital anomalies of the kidney and urinary tract (CAKUT) may be at risk for congenital cardiac defects or cardiomyopathies as comorbidities. It is crucial to recognize the coexistence of cardiac abnormalities and CAKUT and recommend screening for cardiac involvement in CAKUT patients using echocardiography.

Keywords:  atrial septal defect; autosomal dominant polycystic kidney disease; hemodialysis; left ventricular hypertrophy

DOI:  https://doi.org/10.1002/ccr3.7158
Prog Mol Biol Transl Sci. 2023 ;pii: S1877-1173(23)00002-9. [Epub ahead of print]197 105-134

Epigenetics in cardiovascular health and disease.

Nicholas W S Chew, Shaun S E Loong, Roger Foo.

  Conrad Waddington's epigenetics landscape has provided a metaphorical framework for how cells progress from undifferentiated states to one of several discrete, distinct, differentiated cell fates. The understanding of epigenetics has evolved over time, with DNA methylation being the most studied epigenetic modification, followed by histone modifications and non-coding RNA. Cardiovascular diseases (CVD) are leading contributors to death worldwide, with the prevalence of CVDs increasing across the last couple of decades. Significant amount of resources being poured into researching key mechanisms and underpinnings of the various CVDs. These molecular studies looked at the genetics, epigenetics as well as the transcriptomics of various cardiovascular conditions, aiming to provide mechanistic insights. It has paved the way for therapeutics to be developed and in recent years, epi-drugs for the treatment of CVDs. This chapter aims to cover the various roles of epigenetics in the context of cardiovascular health and disease. The following will be examined in detail: the developments in basic experimental techniques used to study epigenetics, the role of epigenetics in various CVDs (hypertension, atrial fibrillation, atherosclerosis, and heart failure), and current advances in epi-therapeutics, providing a holistic view of the current concerted efforts in advancing the field of epigenetics in CVDs.

Keywords:  Cardiovascular diseases; Epigenetics; Health; Molecular biology

DOI:  https://doi.org/10.1016/bs.pmbts.2023.01.002
J Chem Inf Model. 2023 Apr 07.

The Effects of N-Linked Glycosylation on SLC6 Transporters.

Matthew C Chan, Diwakar Shukla.

Membrane transporters of the solute carrier 6 (SLC6) family mediate various physiological processes by facilitating the translocation of amino acids, neurotransmitters, and other metabolites. In the body, the activity of these transporters is tightly controlled through various post-translational modifications with implications on protein expression, stability, membrane trafficking, and dynamics. While N-linked glycosylation is a universal regulatory mechanism among eukaryotes, a consistent mechanism of how glycosylation affects the SLC6 transporter family remains elusive. It is generally believed that glycans influence transporter stability and membrane trafficking; however, the role of glycosylation on transporter dynamics remains disputable, with differing conclusions among individual transporters across the SLC6 family. In this study, we collected over 1 ms of aggregated all-atom molecular dynamics (MD) simulation data to systematically identify the impact of N-glycans on SLC6 transporter dynamics. We modeled four human SLC6 transporters, the serotonin, dopamine, glycine, and B0AT1 transporters, by first simulating all possible combinations of a glycan attached to each glycosylation site followed by investigating the effect of larger, oligo-N-linked glycans to each transporter. The simulations reveal that glycosylation does not significantly affect the transporter structure but alters the dynamics of the glycosylated extracellular loop and surrounding regions. The structural consequences of glycosylation on the loop dynamics are further emphasized with larger glycan molecules attached. However, no apparent differences in ligand stability or movement of the gating helices were observed, and as such, the simulations suggest that glycosylation does not have a profound effect on conformational dynamics associated with substrate transport.

DOI: https://doi.org/10.1021/acs.jcim.2c00940
J Neurochem. 2023 Apr 02.

Brain-specific glycosylation of protein tyrosine phosphatase receptor type Z (PTPRZ) marks a demyelination-associated astrocyte subtype.

Kazuto Takahashi, Kenji Kanekiyo, Kanoko Sakuda, Yui Muto, Masahiro Iguchi, Nozomu Matsuda, Yuko Hashimoto, Kazuaki Kanai, Haruko Ogawa, Hajime Hirase, Akiyoshi Kakita, Norihisa Bizen, Hirohide Takebayashi, Yasushi Kawaguchi, Miwa Uzuki, Shinobu Kitazume.

Astrocytes are the most abundant glial cell type in the brain, where they participate in various homeostatic functions. Transcriptomically diverse astrocyte subpopulations play distinct roles during development and disease progression. However, the biochemical identification of astrocyte subtypes, especially by membrane surface protein glycosylation, remains poorly investigated. Protein tyrosine phosphatase receptor type zeta (PTPRZ) is a highly expressed membrane protein in CNS glia cells that can be modified with diverse glycosylation, including the unique HNK-1 capped O-mannosyl (O-Man) core M2 glycan mediated by brain-specific branching enzyme GnT-IX. Although PTPRZ modified with HNK-1 capped O-Man glycans (HNK-1-O-Man+ PTPRZ) is increased in reactive astrocytes of demyelination model mice, whether such astrocytes emerge in a broad range of disease-associated conditions or are limited to conditions associated with demyelination remains unclear. Here, we show that HNK-1-O-Man+ PTPRZ localizes in hypertrophic astrocytes of damaged brain areas in patients with multiple sclerosis. Furthermore, we show that astrocytes expressing HNK-1-O-Man+ PTPRZ are present in two demyelination mouse models (cuprizone-fed mice and a vanishing white matter disease model), while traumatic brain injury does not induce glycosylation. Administration of cuprizone to Aldh1l1-eGFP and Olig2KICreER/+ ;Rosa26eGFP mice revealed that cells expressing HNK-1-O-Man+ PTPRZ are derived from cells in the astrocyte lineage. Notably, GnT-IX but not PTPRZ mRNA was upregulated in astrocytes isolated from the corpus callosum of cuprizone-model mice. These results suggest that the unique PTPRZ glycosylation plays a key role in the patterning of demyelination-associated astrocytes.

DOI: https://doi.org/10.1111/jnc.15820