scholarly journals ALG1-CDG Caused by Non-functional Alternative Splicing Involving a Novel Pathogenic Complex Allele

2021 ◽  
Vol 12 ◽  
Author(s):  
Carlos Alberto González-Domínguez ◽  
Moisés O. Fiesco-Roa ◽  
Samuel Gómez-Carmona ◽  
Anke Paula Ingrid Kleinert-Altamirano ◽  
Miao He ◽  
...  
Keyword(s):  
Latin America ◽  
Alternative Splicing ◽  
Exome Sequencing ◽  
The Other ◽  
Neurological Involvement ◽  
Serum Transferrin ◽  
Type I ◽  
Mexican Mestizo ◽  
Clinical Exome Sequencing ◽  
Encoding Gene

This study reports on a Mexican mestizo patient with a multi-systemic syndrome including neurological involvement and a type I serum transferrin profile. Clinical exome sequencing revealed complex alleles in ALG1, the encoding gene for the chitobiosyldiphosphodolichol beta-mannosyltransferase that participates in the formation of the dolichol-pyrophosphate-GlcNAc2Man5, a lipid-linked glycan intermediate during N-glycan synthesis. The identified complex alleles were NM_019109.5(ALG1): c.[208 + 16_208 + 19dup; 208 + 25G > T] and NM_019109.5(ALG1): c.[208 + 16_208 + 19dup; 1312C > T]. Although both alleles carried the benign variant c.208 + 16_208 + 19dup, one allele carried a known ALG1 pathogenic variant (c.1312C > T), while the other carried a new uncharacterized variant (c.208 + 25G > T) causing non-functional alternative splicing that, in conjunction with the benign variant, defines the pathogenic protein effect (p.N70S_S71ins9). The presence in the patient’s serum of the pathognomonic N-linked mannose-deprived tetrasaccharide marker for ALG1-CDG (Neu5Acα2,6Galβ1,4-GlcNAcβ1,4GlcNAc) further supported this diagnosis. This is the first report of an ALG1-CDG patient from Latin America.

An audit and insights from clinical exome sequencing in psychiatry: genotype-phenotype correlation

2020 ◽  
Author(s):  
Jayant Mahadevan ◽  
Reeteka Sud ◽  
Ravi Kumar Nadella ◽  
Vani P ◽  
Anand G Subramaniam ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Psychiatric Symptoms ◽  
Pathogenic Variant ◽  
Clinical Exome Sequencing ◽  
Mapt Gene ◽  
Nf1 Gene ◽  
Novel Variant ◽  
History Of ◽  
Atypical Presentations ◽  
Minor Physical Anomalies

BACKGROUND:Psychiatric syndromes have polymorphic symptomatology, and are known to be heritable. Psychiatric symptoms (and even syndromes) often occur as part of the clinical presentation in rare Mendelian syndromes. Clinical exome sequencing reports may help with refining diagnosis and influence treatment decisions, in addition to providing a window into the biology of brain and behaviour. We describe a clinical audit of 12 individuals who sought treatment at our hospital, and for whom targeted sequencing was ordered. Three cases are discussed in detail to demonstrate correlations between genotype and phenotype in the clinic.METHODS:Targeted Next-Generation Sequencing (NGS) was done using Clinical Exome Panel (TruSight One, Illumina) covering coding exons and flanking intronic sequences of 4811 genes associated with known inherited diseases. Variants detected were classified according to the American College for Medical Genetics (ACMG) recommendation for standards of interpretation and reporting of sequence variations.RESULTS:Ten out of twelve cases had at least one pathogenic variant. In one of these cases, we detected a known pathogenic variant in MAPT gene in a suspected FTD case, which helped us to confirm the diagnosis. In another case, we detected a novel variant predicted to be deleterious in NF1 gene. Identification of this mutation suggested a change in treatment for the patient, that was of benefit. The same patient also harboured a novel variant in the TRIO gene. This gene may be involved in biological processes that underlie the patient’s psychiatric illness.CONCLUSIONS:The cases discussed here exemplify different scenarios under which targeted exome sequencing can find meaningful application in the clinic: confirming diagnosis (MAPT variant), or modifying treatment (NF1). We suggest that clinical exome sequencing can be a helpful addition to a clinician’s toolkit when there are expediting factors to consider— such as early-onset, strong family history of mental illness, complex/atypical presentations and minor physical anomalies or neurocutaneous markers.

scholarly journals Charged Residues Flanking the Transmembrane Domain of Two Related Toxin–Antitoxin System Toxins Affect Host Response

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 329
Author(s):  
Andrew Holmes ◽  
Jessie Sadlon ◽  
Keith Weaver
Keyword(s):  
Amino Acid ◽  
Enterococcus Faecalis ◽  
Host Response ◽  
Cytoplasmic Membrane ◽  
Transmembrane Domain ◽  
The Other ◽  
Type I ◽  
Transcriptomic Response ◽  
Specific Amino Acid ◽  
Transporter Protein

A majority of toxins produced by type I toxin–antitoxin (TA-1) systems are small membrane-localized proteins that were initially proposed to kill cells by forming non-specific pores in the cytoplasmic membrane. The examination of the effects of numerous TA-1 systems indicates that this is not the mechanism of action of many of these proteins. Enterococcus faecalis produces two toxins of the Fst/Ldr family, one encoded on pheromone-responsive conjugative plasmids (FstpAD1) and the other on the chromosome, FstEF0409. Previous results demonstrated that overexpression of the toxins produced a differential transcriptomic response in E. faecalis cells. In this report, we identify the specific amino acid differences between the two toxins responsible for the differential response of a gene highly induced by FstpAD1 but not FstEF0409. In addition, we demonstrate that a transporter protein that is genetically linked to the chromosomal version of the TA-1 system functions to limit the toxicity of the protein.

scholarly journals Genetic landscape of recessive diseases in the Vietnamese population from large‐scale clinical exome sequencing

2021 ◽  
Author(s):  
Ngoc Hieu Tran ◽  
Thanh‐Huong Nguyen Thi ◽  
Hung‐Sang Tang ◽  
Le‐Phuc Hoang ◽  
Trung‐Hieu Le Nguyen ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Large Scale ◽  
Clinical Exome Sequencing ◽  
Genetic Landscape ◽  
Vietnamese Population

Fetal pulmonary choristoma: report of first case and literature review

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Anupam Nanda ◽  
Rajinder Nanda ◽  
Seema Thakur ◽  
Tej Prakash Gupta ◽  
Sudhir Jain ◽  
...  
Keyword(s):  
Literature Review ◽  
Exome Sequencing ◽  
Posterior Fossa ◽  
Spinal Column ◽  
Fetal Autopsy ◽  
Case Presentation ◽  
Antenatal Ultrasound ◽  
Clinical Exome Sequencing ◽  
First Case ◽  
Pathologic Findings

AbstractObjectivesLung tissue choristoma is a very rare disorder where mature lung tissues develop in the site not normal to the lung.Case presentationWe hereby report a first case of fetal pulmonary choristoma in a 23–24 weeks fetus where antenatal ultrasound showed a mass in posterior fossa with severe ventriculomegaly. The mass extended inferiorly in cervical spinal column and thereafter extended in the skin over the back of fetus. Fetal autopsy confirmed these findings. Pathologic findings showed mature lung tissues with bronchi, bronchioles, and alveoli. Clinical exome sequencing showed normal results.ConclusionsWe describe the antenatal ultrasound, fetal autopsy and pathologic findings of an intracranial and cutaneous pulmonary choristoma.

scholarly journals Role of Alternative Splicing in Regulating Host Response to Viral Infection

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1720
Author(s):  
Kuo-Chieh Liao ◽  
Mariano A. Garcia-Blanco
Keyword(s):  
Innate Immunity ◽  
Alternative Splicing ◽  
Immune Responses ◽  
Viral Infection ◽  
Rna Splicing ◽  
Type I ◽  
Host Immune Responses ◽  
Transcriptional Regulatory Mechanisms ◽  
Host Virus Interactions

The importance of transcriptional regulation of host genes in innate immunity against viral infection has been widely recognized. More recently, post-transcriptional regulatory mechanisms have gained appreciation as an additional and important layer of regulation to fine-tune host immune responses. Here, we review the functional significance of alternative splicing in innate immune responses to viral infection. We describe how several central components of the Type I and III interferon pathways encode spliced isoforms to regulate IFN activation and function. Additionally, the functional roles of splicing factors and modulators in antiviral immunity are discussed. Lastly, we discuss how cell death pathways are regulated by alternative splicing as well as the potential role of this regulation on host immunity and viral infection. Altogether, these studies highlight the importance of RNA splicing in regulating host–virus interactions and suggest a role in downregulating antiviral innate immunity; this may be critical to prevent pathological inflammation.

scholarly journals Trends and dynamics of material and energy flows in an urban context: a case study of a city with an emerging economy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Clara Inés Pardo Martínez ◽  
William Alfonso Piña ◽  
Angelo Facchini ◽  
Alexander Cotte Poveda
Keyword(s):  
Latin America ◽  
Population Growth ◽  
Construction Materials ◽  
The Other ◽  
Material Flows ◽  
Urban Context ◽  
Rapid Urbanization ◽  
Urban Agglomerations ◽  
Energy Flows ◽  
The City

Abstract Background Currently, most of the world’s population lives in cities, and the rapid urbanization of the population is driving increases in the demand for products, goods and services. To effectively design policies for urban sustainability, it is important to understand the trends of flows in energy and materials as they enter and leave a city. This knowledge is essential for determining the key elements characterizing future urban growth and addressing future supply challenges. Methods This paper presents an analysis of the energy and material flows in the city of Bogotá over the time span from 2001 to 2017. Urban flows are also characterized in terms of their temporal evolution with respect to population growth to compare and identify the changes in the main input flows, wealth production, emissions and waste in the city. Results The results of the analysis are then compared with those for other selected large urban agglomerations in Latin America and worldwide to highlight similarities and make inferences. The results show that in Bogotá, there was a decrease in some of the material flows, such as the consumption of water and the generation of discharge, in recent years, while there was an increase in the consumption of energy and cement and in the production of CO2 emissions and construction materials. Solid waste production remained relatively stable. With respect to the other large cities considered, we observe that the 10-year growth rates of the flows with respect to population growth are lower in Bogotá, particularly when compared with the other urban agglomerations in Latin America. Conclusions The findings of this study are important for advancing characterizations of the trends of material and energy flows in cities, and they contribute to the establishment of a benchmark that allows for the definition and evaluation of the different impacts of public policy while promoting the sustainability of Bogotá in the coming decades.

scholarly journals Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wen-juan Li ◽  
Yao-hui He ◽  
Jing-jing Yang ◽  
Guo-sheng Hu ◽  
Yi-an Lin ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cell Growth ◽  
Rna Splicing ◽  
Synergistic Effects ◽  
Arginine Methylation ◽  
Type I ◽  
Prostate Cancer Cells ◽  
Cancer Cell Growth ◽  
Cancer Mutations ◽  
Substrate Spectrum

AbstractNumerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy.

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