Identification of a novel intronic variant of ATP6V0A2 in a Han-Chinese family with cutis laxa

BACKGROUND

Cutis laxa is a connective tissue disease caused by abnormal synthesis or secretion of skin elastic fibers, leading to skin flabby and saggy in various body parts. It can be divided into congenital cutis laxa and acquired cutis laxa, and inherited cutis laxa syndromes is more common in clinic.

METHODS

In this study, we reported a case of a Han-Chinese male newborn with ATP6V0A2 gene variant leading to cutis laxa. The proband was identified by whole-exome sequencing to determine the novel variant, and their parents were verified by Sanger sequencing. Bioinformatics analysis and minigene assay were used to verify the effect of this variant on splicing function.

RESULTS

The main manifestations of the proband are skin laxity, abnormal facial features, and enlargement of the anterior fontanelle. Whole-exome sequencing showed that the newborn carried a non-canonical splicing-site variant c.117 + 5G > T, p. (?) in ATP6V0A2 gene. Sanger sequencing showed that both parents of the proband carried the heterozygous variant. The results of bioinformatics analysis and minigene assay displayed that the variant site affected the splicing function of pre-mRNA of the ATP6V0A2 gene.

CONCLUSIONS

In this study, it was identified that ATP6V0A2 gene c. 117 + 5G > T may be the cause of the disease. The non-canonical splicing variants of ATP6V0A2 gene were rarely reported in the past, and this variant expanded the variants spectrum of the gene. The functional study of minigene assay plays a certain role in improving the level of evidence for the pathogenicity of splicing variants, which lays a foundation for prenatal counseling and follow-up gene therapy.

Case Report: A developmental and epileptic encephalopathy 45 due to de novo variant of GABRB1

Background

The gamma-aminobutyric acid (GABA) variant causes developmental and epileptic encephalopathy 45 (DEE45), an autosomal dominant disorder that results in oculocortical visual impairment, reduced muscle tone, psychomotor retardation, and epilepsy. Analysis of the clinical features and genetics of DEE45 may be helpful in complementing genotype-phenotype studies.

Case presentation

We collected peripheral blood samples from the affected children and parents and extracted genomic DNA. Whole exome sequencing (WES) was utilized to identify the underlying disease-causing variant. WES showed that the prior carried a heterozygous variant c.686C > T p.(Ala229Val) in exon 7 of the GABRB1 (NM_000812.4), and no variant was detected in either parental sample. The child has DEE45.

Conclusion

The variant c.686C > T of the GABRB1 is a possible cause of DEE45. Gene variant analysis of the relevant family lines using WES provides effective genetic counseling for developing and regressing such patients in the clinic. However, further studies are needed to verify the pathogenic mechanism.

Phosphoserine aminotransferase deficiency diagnosed by whole-exome sequencing and LC-MS/MS reanalysis: A case report and review of literature

BACKGROUND

Phosphoserine aminotransferase deficiency (PSATD) is an autosomal recessive disorder associated with hypertonia, psychomotor retardation, and acquired microcephaly. Patients with PSATD have low concentrations of serine in plasma and cerebrospinal fluid.

METHODS

We reported a 2-year-old female child with developmental delay, dyskinesia, and microcephaly. LC-MS/MS was used to detect amino acid concentration in the blood and whole-exome sequencing (WES) was used to identify the variants. PolyPhen-2 web server and PyMol were used to predict the pathogenicity and changes in the 3D model molecular structure of protein caused by variants.

RESULTS

WES demonstrated compound heterozygous variants in PSAT1, which is associated with PSATD, with a paternal likely pathogenic variant (c.235G>A, Gly79Arg) and a maternal likely pathogenic variant (c.43G>C, Ala15Pro). Reduced serine concentration in LC-MS/MS further confirmed the diagnosis of PSATD in this patient.

CONCLUSIONS

Our findings demonstrate the importance of WES combined with LC-MS/MS reanalysis in the diagnosis of genetic diseases and expand the PSAT1 variant spectrum in PSATD. Moreover, we summarize all the cases caused by PSAT1 variants in the literature. This case provides a vital reference for the diagnosis of future cases.

A novel MMUT splicing variant causing mild methylmalonic acidemia phenotype

Objectives

Methylmalonic acidemia (MMA) is a rare inborn genetic disorder that is characterized by increased levels of methylmalonic acid in blood plasma and urine. Isolated methylmalonic acidemia is one of the most common types of MMA and is caused by mutations in the gene encoding methyl-malonyl coenzyme A mutase (MMUT). In this study, we investigated the possible mechanisms underlying the symptoms of isolated MMA in a patient by molecular analysis.

Methods

PCR amplification and Sanger sequencing analysis was performed to identify variants in the MMUT gene in the proband and his family. Furthermore, minigene constructs were generated to validate the splicing defects in the MMUT gene variant identified in the proband.

Results

The 3-year-old patient was admitted to the hospital with symptoms of MMA, including fever, convulsions, and vomiting. He showed metabolic acidosis, high levels of methylmalonic acid in blood and urine, and normal blood homocysteine levels. Genetic analysis demonstrated that the patient was a compound heterozygous carrier of two variants in the MMUT gene: a missense c.278G > A variant that has already been reported in a patient with the severe mut⁰ phenotype; and a novel splice site variant c.2125-2A > G. RT-PCR analysis showed that, while the novel variant clearly alters splicing, a minor amount of a full-length transcript is generated, suggesting that a wild-type protein may be produced although at a lower quantitative level. The patient's condition improved after treatment with vitamin B12. Serious complications were not reported during follow-up at age 5.

Conclusions

We identified a novel splice site variant that partially disrupts normal splicing of the MMUT pre-mRNA. Production of a reduced amount of full-length transcript is responsible for the mild clinical phenotype observed in this patient. Functional studies have proven useful in exploring the genotype-phenotype association and in providing guidance for the genetic diagnosis of MMA.

Network-based analysis on the genes and their interactions reveals link between schizophrenia and Alzheimer's disease

Schizophrenia (SCZ) is a heterogeneous psychiatric disorder marked by impaired thinking, emotions, and behaviors. Studies have suggested a strong connection between SCZ and Alzheimer's disease (AD), however, controversies exist and the underlying mechanisms linking these two disorders remain largely unknown. Therefore, systematic studies of SCZ- and AD-related genes will provide valuable insights into the molecular features of these two diseases and their comorbidities. In this study, we obtained 331 SCZ-related genes, 650 AD-related genes, 65 shared genes between SCZ and AD. Enrichment analysis shown that these 65 shared genes were mainly involved in cognition, neural development, synaptic transmission, drug reactions, metabolic processes and immune related processes, suggesting a complex mechanism for the co-existence of SCZ and AD. In addition, we performed pathway enrichment analysis and found a total of 57 common pathways between SCZ and AD, which could be largely grouped into three modules: immune module, neurodevelopment module and cancer module. We eventually identified the potential disease-related genes whose interactions provide clues to the overlapping symptoms between SCZ and AD.

Whole exome sequencing approach for identification of the molecular etiology in pediatric patients with hematuria

BACKGROUND

Hematuria is a common condition in clinical practice of pediatric patients. It is related to a wide spectrum of disorders and has high heterogeneity both clinically and genetically, which contributes to challenges of diagnosis and lead many pediatric patients with hematuria not to receive accurate diagnosis and early management.

METHODS

In this single center study, 42 children with hematuria were included in Tianjin Children's Hospital between 2019 and 2020. We analyzed the clinical information and performed WES (Whole exome sequencing) for all cases. Then the classification of identified variants was performed according to the American College of Medical Genetics and Genomics (ACMG) guidelines for interpreting sequence variants. For the fragment deletion, qPCR was performed to validate and confirm the inherited pattern.

RESULTS

For the 42 patients, 16 cases had gross hematuria and 26 had microscopic hematuria. Molecular genetic causes were uncovered in 9 (21.4%) children, including 7 with Alport syndrome (AS), one with polycystic nephropathy and one with lipoprotein glomerulopathy. The genetic causes for other patients were not related with hematuria.

CONCLUSIONS

WES is a rapid and effective way to evaluate patients with hematuria. The analysis of genotype-phenotype correlations of patients with AS indicated that severe variants were associated with early kidney failure. Secondary findings were not rare in Chinese children, thus the clinician should pay more attention to the clinical interpretation of sequencing results and properly interaction with patients and their family.

Genetic Association of Lipids and Lipid-Lowering Drug Target Genes With Attention Deficit Hyperactivity Disorder

BACKGROUND

Lipid metabolism plays an essential role in nervous system development. Cholesterol deficiency leads to a variety of neurodevelopmental disorders, such as autism spectrum disorder and fragile X syndrome. There have been a lot of efforts to search for biological markers associated with and causal to ADHD, among which lipid is one possible etiological factor that is quite widely studied. We aimed to evaluate the causal relationship between lipids traits, lipid-lowering drugs, and attention deficit hyperactivity disorder (ADHD) outcomes using Mendelian randomization (MR) studies.

METHODS

We used summary data from genome-wide association studies to explore the causal relationships between circulating lipid-related traits and ADHD. Then, quantitative trait loci for the expression of lipid-lowering drug target genes and genetic variants associated with lipid traits were extracted. Summary-data-based MR and inverse-variance-weighted MR (IVW-MR) were used to investigate the correlation between the expression of these drug-target genes and ADHD.

RESULTS

After rigorous screening, 939 instrumental variables were finally included for univariable mendelian randomization analysis. However, there is no correlation between lipid profile and ADHD risk. Drug target analysis by IVW-MR method observed that APOB-mediated low-density lipoprotein cholesterol was associated with lower ADHD risk (odds ratio [OR] = 0.90, 95% confidence interval [CI] [0.84, 0.97]; p = .007), whereas LPL-mediated triglycerides levels were associated with a higher risk of ADHD (OR = 1.13, 95% CI [1.06, 1.21]; p < .001).

CONCLUSION

Our results suggest that APOB gene and LPL gene may be candidate drug target genes for the treatment of ADHD.

Identification of Two Variants c.2697A > C and c.3305A > C in USP7 by Analysis of Whole-Exome Sequencing in Chinese Patients with Hao-Fountain Syndrome

Background  Variants of ubiquitin-specific protease 7 ( USP7 ) gene in humans are associated with a neurodevelopmental disorder-Hao-Fountain syndrome, its core symptoms including developmental delay, intellectual disability, and speech delay. Other variable symptoms can affect multiple systems. In present study, we report two patients with core features from two unrelated consanguineous families originating from the Tianjin Children's Hospital. Methods and Results  Genomic DNA was extracted from the peripheral blood samples collected from the probands with their family members and whole-exome sequencing (WES) was used to detect the pathogenic genes in the probands. Suspected variants were subsequently validated by Sanger sequencing. In family 1, WES revealed that the proband carried the de novo variant c.2697A > C (p.Leu899Phe) in USP7 (NM_003470.3). In family 2, WES identified the variant c.3305A > C (p.Asn1102Thr) in USP7 (NM_003470.3) from the proband. Conclusion  We reported two cases of Hao-Fountain syndrome caused by novel USP7 variants. In addition, we report the first case of mosaicism with a USP7 variant in Chinese family. Our findings demonstrate the importance of WES in diagnosis of genetic diseases and expands the USP7 variants spectrum in Hao-Fountain syndrome. Moreover, we summarize the cases caused by USP7 variants in the literature. Our study can provide a vital reference for the diagnosis of future cases.

Novel Variants of CEP152 in a Case of Compound-Heterozygous Inheritance of Epilepsy

Introduction   CEP152 encodes protein Cep152, which associates with centrosome function. The lack of Cep152 can cause centrosome duplication to fail. CEP152 mutates, causing several diseases such as Seckel syndrome-5 and primary microencephaly-9. Methods  In this study, we reported a patient diagnosed with epilepsy in Tianjin Children's Hospital. We performed clinical examination and laboratory test, and whole-exome sequencing was performed for the proband's and his parents' peripheral blood. The suspected compound-heterozygous variant in the CEP152 gene was verified by Sanger sequencing and quantitative real-time polymerase chain reaction technology. Results  We discovered three variants-two of them from CEP152 and one from HPD . The result showed the variants in CEP152 only. The patient presented with seizures frequently. Sanger sequencing showed two novel variants in CEP152 are in exon26 (NM_014985.3 c.3968C > A p.Ser1323*) and in exon16 (NM_014985.3 c.2034_2036del p.Tyr678*). Conclusions  We reported a novel compound-heterozygous variant in the CEP152 gene in this study. Most of the phenotypes are Seckel syndrome and primary microencephaly, and the novel variant may cause an atypical phenotype that is epilepsy.

[Clinical, endoscopic, and pathological analyses of 14 cases of gastric adenocarcinoma of the fundic gland type]

Objective: Gastric adenocarcinoma of the fundic gland type (GA-FG) is rare and often occurs in patients who are not infected with Helicobacter pylori. The current study analyzed and summarized the clinical, endoscopic, and pathological features of GA-FG, in an effort to improve its diagnosis. Methods: Patients who were diagnosed with GA-FG and treated with endoscopic submucosal dissection (ESD) resection at the Department of Gastroenterology, First Affiliated Hospital of Zhejiang Chinese Medical University from January 1st 2020 to October 1st 2022 were included in the study. Their clinical manifestations, endoscopic features, pathological immunohistochemistry, and other characteristics were analyzed. Results: A total of 14 patients with GA-FG were included in the study, 5 males and 9 females, with a mean age of 59 years. Most had no substantial clinical manifestations. Twelve patients were H. pylori-negative, all patients underwent ESD resection, and all patients survived during the follow-up period of 13±9 months. Eleven patients had postoperative endoscopic follow-up records, and no recurrence was detected. Fifteen lesions were detected (2 were present in 1 patient). Twelve were located in the upper 1/3 of the stomach, 10 were ≤ 1 cm in diameter, 12 had a morphology of type 0-Ⅱa, 8 had visible discoloration changes, and 12 had visible vasodilation on the surface. Magnified endoscopy and narrow-band imaging indicated that 12 of the lesions had enlarged marginal crypt epithelium, without any obvious microvascular pattern abnormalities and no obvious borderline. After resection the pathological specimens were all without vascular infiltration, and there was no atrophy of the mucosa at the edge of the lesion. In immunohistochemistry analyses MUC-2 was negative in all cases. MUC5AC was negative in 11 cases, MUC-6 was positive in all cases, and Ki-67 was ≤ 5% in 12 cases. Conclusions: GA-FG is a newly identified type of gastric cancer with low malignancy and a good prognosis. Characteristic discoloration and surface dilated vessels are often evident endoscopically. Enlarged marginal crypt epithelium and no visible boundary lines are often apparent in magnification endoscopy and narrow band imaging.

A Pair of Compound Heterozygous IARS2 Variants Manifesting West Syndrome and Electrolyte Disorders in a Chinese Patient

Background  Aminoacyl-tRNA synthetases (ARSs) are evolutionarily conserved enzymes that ensure the accuracy of the translation process. Isoleucyl-tRNA synthetase 2 ( IARS2 ) gene is a type of ARS that encodes mitochondrial isoleucine-tRNA synthetase. Pathogenic variants in the IARS2 gene are associated with mitochondrial disease which involves several patients presenting broad clinical phenotypes. These clinical phenotypes include West syndrome, Leigh syndrome, and Cataract, growth hormone deficiency, sensory neuropathy, sensorineural hearing loss, and skeletal dysplasia syndrome. Only 29 cases have been reported worldwide. The patient manifested recurrent convulsions, and specific clinical manifestations included electrolyte disorders and recurrent infections. Methods  Whole-exome sequencing was performed on the child with West syndrome. Three-dimensional structure reconstruction and thermodynamic stability prediction were performed to further analyze the relationship between variation and phenotype. Conclusion  This study further expands the clinical spectrum of IARS2 pathogenic variants. The case summaries help raise clinical awareness of IARS2 -associated disease and reduce misdiagnosis. Result  In this report, a 13-month-old girl was diagnosed with West syndrome and Leigh syndrome for 7 months. Compound heterozygous variants in the IARS2 gene (NM_018060.4), c.2450G>A (Arg817His) and copy number variation (NC_000001. 11: g. (220267549_220284289) del), were detected by WES. This study further expands the clinical spectrum of IARS2 pathogenic variants. The case summaries help raise clinical awareness of IARS2-associated disease and reduce misdiagnosis.

Comprehensive systematic review and meta-analysis of the association between common genetic variants and autism spectrum disorder

BACKGROUND

Autism spectrum disorder (ASD) is neurodevelopmental disorder characterized by stereotyped behavior and deficits in communication and social interactions. To date, numerous studies have investigated the associations between genetic variants and ASD risk. However, the results of these published studies lack a clear consensus. In the present study, we performed a systematic review on the association between genetic variants and ASD risk. Meanwhile, we conducted a meta-analysis on available data to identify the association between the single nucleotide polymorphisms (SNPs) of candidate genes and ASD risk.

METHODS

We systematically searched public databases including English and Chinese from their inception to August 1, 2022. Two independent reviewers extracted data and assessed study quality. Odds ratio and 95 % confidence interval were used as effect indexes to evaluate the association between the SNPs of candidate genes and the risk of ASD. Heterogeneity was explored through subgroup, sensitivity, and meta-regression analyses. Publication bias was assessed by using Egger's and Begg's tests for funnel plot asymmetry. In addition, TSA analysis were performed to confirm the study findings.

RESULTS

We summarized 84 SNPs of 32 candidate genes from 81 articles included in the study. Subsequently, we analyzed 16 SNPs of eight genes by calculating pooled ORs, and identified eight significant SNPs of contactin associated protein 2 (CNTNAP2), methylentetrahydrofolate reductase (MTHFR), oxytocin receptor (OXTR), and vitamin D receptor (VDR). Results showed that seven SNPs, including the CNTNAP2 rs2710102 (homozygote, heterozygote, dominant and allelic models) and rs7794745 (heterozygote and dominant models), MTHFR C677T (homozygote, heterozygote, dominant, recessive and allelic models) and A1298C (dominant and allelic models), OXTR rs2254298 (homozygote and recessive models), VDR rs731236 (homozygote, dominant, recessive and allelic models) and rs2228570 (homozygote and recessive models), were showed to be correlated with an increased ASD risk. By contrast, the VDR rs7975232 was correlated with a decreased the risk of ASD under the homozygote and allelic models.

CONCLUSION

Our study summarized research evidence on the genetic variants of ASD and provides a broad and detailed overview of ASD risk genes. The C677T and A1298C polymorphisms of MTHFR, rs2710102 and rs7794745 polymorphisms of CNTNAP2, rs2254298 polymorphism of OXTR, and rs731236 and rs2228570 polymorphisms of VDR were genetic risk factors. The rs7975232 polymorphism of VDR was a genetic protective factor for ASD. Our study provides novel clues to clinicians and healthcare decision-makers to predict ASD susceptibility.

Functional Characterization of a Novel SLC4A4 Variant and Uniparental Isodisomy in Proximal Renal Tubular Acidosis Patient

SLC4A4 variants are the etiologies of inherited proximal renal tubular acidosis (pRTA), which results in metabolic acidosis, hypokalemia, glaucoma, band keratopathy, and cataract. This study aims to characterize SLC4A4 variant and uniparental isodisomy of chromosome 4 in a patient, and analyse the functional characterization of SLC4A4 variants. This study analyzed renal tubular acidosis disease genes by whole exome sequencing (WES). H3M2 algorithm was used to analyze the run of homozygosity region in chromosomal regions in trio-WES data. The pathogenicity analysis of variants was performed using bioinformatics tools. Additionally, protein stability was analyzed by cycloheximide chase assay. Whole-cell patch clamping was used to examine the electrophysiological properties of NBCe1-A. A novel homozygous SLC4A4 variant was identified in the patient: a missense variant c.496C > T, p. Arg166Trp (NM_003759.4). But the father was heterozygous variant carrier, and the mother did not detect the variant. The H3M2 and UPDio algorithm revealed paternal uniparental isodisomy on chromosome 4 in the patient. SIFT, Poly Phen-2, FATHMM and Mutant Taster showed that the variant might be pathogenic. The tertiary structure analysis showed that the variant could cause structural damage to NBCe1 protein. Foldx results showed that the protein stability of the variant was slightly reduced. Cycloheximide chase assay demonstrated that the variant affects protein stability. The result of electrophysiological studies showed that the variant altered Na+/HCO3- cotransport activity of protein. In conclusion, the study is the first to report a pRTA patient with Arg166Trp variant with UPiD (4) pat and analyze the function of Arg166Trp variant.

Pathogenicity analysis and splicing rescue of a classical splice site variant (c.1343+1G>T) of CNOT1 gene associated with neurodevelopmental disorders

Mutations in the CNOT1 gene lead to an incurable rare neurological disorder mainly manifested as a clinical spectrum of intellectual disability, developmental delay, seizures, and behavioral problems. In this study, we investigated a classical splice site variant of CNOT1 (c.1343+1G>T) associated with neurodevelopmental disorders, which was a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. To link CNOT1 dysfunction with the neurodevelopmental phenotype observed in a patient, in vitro minigene assay was used to verify the effect of CNOT1 gene splice site variant c.1343+1G>T on mRNA splicing. We also explored the impact of transient transfection introducing modified U1 snRNA on correcting the splicing variant. Through minigene expression in mammalian cells, we demonstrated that the variant induced complete exon 12 skipping, which explained the patient's clinical condition and provided additional genetic diagnosis evidence for the clinical significance of the variant. Moreover, we confirmed that the aberrant splice pattern could be partially corrected by the modified U1 snRNA at the mRNA level, which provided strong evidence for the therapeutic potential of modified U1 snRNA in neutralizing the hazardous effect of incorrect splicing patterns.

Review on neuroimaging in pediatric-type diffuse low-grade gliomas

The fifth edition of the World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS5) has identified a new classification system for tumors of the brain and spinal cord, highlighting the pivotal role of molecular diagnosis in accurately categorizing neoplasms. In addition to previous classifications, one of the key distinctions lies in categorizing pediatric-type diffuse low-grade gliomas (pDLGGs) and pediatric-type diffuse high-grade gliomas (pDHGGs) as distinct tumor types. Although similar in histology and morphology, pediatric diffuse gliomas are completely different from the adult type with respect to the molecular genetic characteristics, prognosis, and treatment strategies. pDLGG includes four tumor types, namely, diffuse astrocytoma, MYB- or MYBL1-altered; angiocentric glioma; polymorphous low-grade neuroepithelial tumor of the young (PLNTY); and diffuse low-grade glioma, MAPK pathway-altered, three types of which are newly recognized tumor types. Herein, we review the clinical characteristics, histopathological and molecular genetic characteristics, neuroimaging features, and prognosis of pDLGG and summarize the neuroimaging key points in diagnosing different tumor types. This review aims to evaluate and update the relevant pDLGG features and advances in neuroimaging that may assist in differential diagnosis, surgery planning, and prognostic determination of these tumor types and provide accurate diagnostic information for clinical colleagues.

Multi-dimensional Insight into the Coexistence of Pathogenic Genes for ADAR1 and TSC2: Careful Consideration is Essential for Interpretation of ADAR1 Variants

Aicardi-Goutières syndrome 6 (AGS6) is a serious auto-immunization-associated acute neurologic decompensation. AGS6 manifests as acute onset of severe generalized dystonia of limbs and developmental regression secondary to febrile illness mostly. Dyschromatosis symmetrica hereditaria (DSH), as pigmentary genodermatosis, is a characterized mixture of hyperpigmented and hypopigmented macules. Both AGS6 and DSH are associated with ADAR1 pathogenic variants. To explore the etiology of a proband with developmental regression with mixture of hyperpigmentation and hypopigmentation macules, we used the trio-WES. Later, to clarify the association between variants and diseases, we used guidelines of ACMG for variants interpretation and quantitative Real-time PCR for verifying elevated expression levels of interferon-stimulated genes, separately. By WES, we detected 2 variants in ADAR1 and a variant in TSC2, respectively, were NM_001111.5:c.1096_1097del, NM_001111.5:c.518A>G, and NM_000548.5:c.1864C>T. Variants interpretation suggested that these 3 variants were both pathogenic. Expression levels of interferon-stimulated genes also elevated as expected. We verified the co-occurrence of pathogenic variants of ADAR1 and TSC2 in AGS6 patients with DSH. Our works contributed to the elucidation of ADAR1 pathogenic mechanism, given the specific pathogenic mechanism of ADAR1, and it is necessary to consider with caution when variants were found in ADAR1.

Polo-like kinase 1 Decrease During Induction Therapy Could Indicate Good Treatment Response, Favorable Risk Stratification, and Prolonged Survival in Pediatric Acute Lymphoblastic Leukemia

OBJECTIVE

Polo-like kinase 1 (PLK1) modulates leukemia cell apoptosis, proliferation, and cell cycle arrest in the progression of acute lymphoblastic leukemia (ALL). This study intended to investigate the dysregulation of PLK1 and its association with induction therapy response and prognosis in pediatric ALL patients.

MATERIALS AND METHODS

Bone marrow mononuclear cell samples were collected from 90 pediatric ALL patients at baseline and on the 15th day of induction therapy (D15), as well as from 20 controls after enrollment, for the detection of PLK1 by reverse transcription-quantitative polymerase chain reaction.

RESULTS

PLK1 was increased in pediatric ALL patients compared with controls ( P <0.001). In pediatric ALL patients, PLK1 decreased from baseline to D15 ( P <0.001). Lower PLK1 at baseline was associated with a good prednisone response ( P =0.002), while decreased PLK1 at D15 was related to good prednisone response ( P =0.001), better bone marrow response ( P =0.025), and favorable risk stratification ( P =0.014). In addition, reduced PLK1 at baseline was linked with better event-free survival (EFS) ( P =0.046), and decreased PLK1 at D15 was related to prolonged EFS ( P =0.027) and overall survival (OS) ( P =0.047). Moreover, PLK1 decline ≥25% was linked to favorable EFS ( P =0.015) and OS ( P =0.008). Further multivariate Cox proportional regression analysis revealed that PLK1 decline ≥25% was independently linked with prolonged EFS (hazard ratio (HR)=0.324, P =0.024) and OS (HR=0.211, P =0.019).

CONCLUSION

The reduction of PLK1 after induction therapy reflects a good treatment response and correlates with a favorable survival profile in pediatric ALL patients.

A novel variant in ALG1 gene associated with congenital disorder of glycosylation: A case report and short literature review

BACKGROUND

The congenital disorder of glycosylation associated with ALG1 (ALG1-CDG) is a rare autosomal recessive disease. Due to the deficiency of β1,4 mannosyltransferase caused by pathogenic variants in ALG1 gene, the assembly and processing of glycans in the protein glycosylation pathway are impaired, resulting in a broad clinical spectrum with multi-organ involvement. To raise awareness of clinicians for its manifestations and genotype, we here reported a new patient with a novel variant in ALG1 gene and reviewed the literature to study the genotype-phenotype correlation.

METHOD

Clinical characteristics were collected, and clinical exome sequencing was used to identify the causative variants. MutationTaster, PyMol, and FoldX were used to predict the pathogenicity, changes in 3D model molecular structure of protein, and changes of free energy caused by novel variants.

RESULTS

The proband was a 13-month-old Chinese Han male characterized by epileptic seizures, psychomotor development delay, muscular hypotonia, liver and cardiac involvement. Clinical exome sequencing revealed the biallelic compound heterozygosity variants, a previously reported variant c.434G>A (p.G145N, paternal) and a novel variant c.314T>A (p.V105N, maternal). The literature review found that in severe phenotypes, the incidences of clinical manifestations were significantly higher than that in mild phenotypes, including congenital nephrotic syndrome, agammaglobulinemia, and severe hydrops. Homozygous c.773C>T was a strongly pathogenic variant associated with a severe phenotype. When heterozygous for c.773C>T, patients with another variant leading to substitution in amino acids within the strongly conserved regions (c.866A>T, c.1025A>C, c.1182C>G) may cause a more severe phenotype than those within less-conserved regions (c.434G>A, c.450C>G, c.765G>A, c.1287T>A). c.1129A>G, c.1076C>T, and c.1287T>A were more likely to be associated with a mild phenotype. The assessment of disease phenotypes requires a combination of genotype and clinical manifestations.

CONCLUSIONS

The case reported herein adds to the mutations identified in ALG1-CDG and a review of this literature expands the study of the phenotypic and genotypic spectrum of this disorder.

First Dark Matter Search with Nuclear Recoils from the XENONnT Experiment

We report on the first search for nuclear recoils from dark matter in the form of weakly interacting massive particles (WIMPs) with the XENONnT experiment, which is based on a two-phase time projection chamber with a sensitive liquid xenon mass of 5.9 ton. During the (1.09±0.03)  ton yr exposure used for this search, the intrinsic ^{85}Kr and ^{222}Rn concentrations in the liquid target are reduced to unprecedentedly low levels, giving an electronic recoil background rate of (15.8±1.3)  events/ton yr keV in the region of interest. A blind analysis of nuclear recoil events with energies between 3.3 and 60.5 keV finds no significant excess. This leads to a minimum upper limit on the spin-independent WIMP-nucleon cross section of 2.58×10^{-47}  cm^{2} for a WIMP mass of 28  GeV/c^{2} at 90% confidence level. Limits for spin-dependent interactions are also provided. Both the limit and the sensitivity for the full range of WIMP masses analyzed here improve on previous results obtained with the XENON1T experiment for the same exposure.

Searching for Heavy Dark Matter near the Planck Mass with XENON1T

Multiple viable theoretical models predict heavy dark matter particles with a mass close to the Planck mass, a range relatively unexplored by current experimental measurements. We use 219.4 days of data collected with the XENON1T experiment to conduct a blind search for signals from multiply interacting massive particles (MIMPs). Their unique track signature allows a targeted analysis with only 0.05 expected background events from muons. Following unblinding, we observe no signal candidate events. This Letter places strong constraints on spin-independent interactions of dark matter particles with a mass between 1×10^{12} and 2×10^{17}  GeV/c^{2}. In addition, we present the first exclusion limits on spin-dependent MIMP-neutron and MIMP-proton cross sections for dark matter particles with masses close to the Planck scale.

[Efficacy of video-assisted thoracoscopic surgical decortication for stage Ⅲ tuberculous empyema]

Objective: To investigate the clinical efficacy, safety and feasibility of "double-portal" video-assisted thoracoscopic surgical(VATS) decortication among patients with stage Ⅲ tuberculous empyema, and then to evaluate the recovery of chest deformity. Method: This study was a single center retrospective study. A total of 49 patients with stage Ⅲ tuberculous empyema who underwent VATS pleural decortication at the Department of Thoracic Surgery, Public Health Clinical Center of Chengdu between June 2017 and April 2021 were enrolled, including 38 males, and 11 females, aged 13-60 (27.5±10.4) years. The safety and feasibility of VATS were further evaluated. The inner circumference of the chest on sternal and xiphoid planes on chest CT scans before and 1, 3, 6, 12months after decortication were collected through the measuring software of the CT. The samples in-pair test was used to compare the changes in the chest to reflect the recovery of the chest deformity. Results: In the 49 patients, The surgical time was (186±61) min, and the volume of blood loss was (366±267) ml. There were 8 cases (16.33%) with postoperative complications during the perioperative period. Constant air leak and pneumonia were the main postoperative complications. No relapse of empyema or dissemination of tuberculosis occured during the period of follow-up. Before surgery, the inner thoracic circumference of the thorax at the level of the carina plane was (655±54) mm, and the inner thoracic circumference of the thorax at the level of the xiphoid plane was (720±69) mm. Patients were followed for 12-36 months. The inner thoracic circumference of the thoracic cavity at the level of carina was (666±51), (667±47) and (671±47) mm at the 3rd, 6th and 12th months after operation, which were significantly larger than that at the level of carina before operation (all P<0.05). The inner thoracic circumference diameter of the thoracic cavity measured at the xiphoid level at the 3rd, 6th and 12th months after the operation was (730±65), (733±63) and (735±63) mm respectively(all P<0.05).The inner thoracic circumference of the thoracic cavity increased significantly than that before surgery (P<0.05). At 6 months after operation, there was significant difference in the improvement of the inner thoracic circumference of the carina plane in patients with age less than 20 years and FEV₁% less than 80% (P=0.015, P=0.003). The improvement in the inner thoracic circumference of the carina plane in patients with pleural thickening≥8 mm compared with those with less than 8 mm was not statistically different(P=0.070). Conclusions: For some patients with stage Ⅲ tuberculous empyema, pleural decortication under thoracoscopy is safe and feasible, and can significantly restore the inner thoracic circumference of the patient's chest, improve the collapse of the patient's chest, and have significant clinical effect. The "double-portal VATS" surgical technology has the advantage of less trauma, wide operation field, large operation space and is easy to master, which is worth further exploring for clinical application.

[Study of incubation period of infection with 2019-nCoV Omicron variant BA.5.1.3]

Objective: To study the incubation period of the infection with 2019-nCoV Omicron variant BA.5.1.3. Methods: Based on the epidemiological survey data of 315 COVID-19 cases and the characteristics of interval censored data structure, log-normal distribution and Gamma distribution were used to estimate the incubation. Bayes estimation was performed for the parameters of each distribution function using discrete time Markov chain Monte Carlo algorithm. Results: The mean age of the 315 COVID-19 cases was (42.01±16.54) years, and men accounted for 30.16%. A total of 156 cases with mean age of (41.65±16.32) years reported the times when symptoms occurred. The log-normal distribution and Gamma distribution indicated that the M (Q₁, Q₃) of the incubation period from exposure to symptom onset was 2.53 (1.86, 3.44) days and 2.64 (1.91, 3.52) days, respectively, and the M (Q₁, Q₃) of the incubation period from exposure to the first positive nucleic acid detection was 2.45 (1.76, 3.40) days and 2.57 (1.81, 3.52) days, respectively. Conclusions: The incubation period by Bayes estimation based on log-normal distribution and Gamma distribution, respectively, was similar to each other, and the best distribution of incubation period was Gamma distribution, the difference between the incubation period from exposure to the first positive nucleic acid detection and the incubation period from exposure to symptom onset was small. The median of incubation period of infection caused by Omicron variant BA.5.1.3 was shorter than those of previous Omicron variants.

Identification of a Splicing Variant c.3813-3A&gt;G in NPHP3 by Reanalysis of Whole Exome Sequencing in a Chinese Boy with Nephronophthisis

Nephronophthisis is an autosomal recessive cystic kidney disease characterized by tubular injury and commonly results in kidney failure. We reported a case of 4-year-old Chinese boy presented with severe anemia, kidney, and liver dysfunction. Whole exome sequencing (WES) was performed to identify the candidate variant with a negative result initially. After complete collection of clinical information, reanalysis of WES identified a homozygous NPHP3 variant c.3813-3A>G (NM_153240.4). The effect on mRNA splicing of the intronic variant was predicted through software (three in silico splice tools). Furthermore, in vitro minigene assay was conducted to validate the predicted deleterious effects of the intronic variant. All of the splice prediction programs and minigene assay indicated that the variant had an impact on the normal splicing pattern of NPHP3. Our study confirmed the effect of the c.3813-3A>G variant on NPHP3 splicing in vitro, which gives additional evidence for the clinical significance of the variant and provides a basis for genetic diagnosis of nephronophthisis 3. In addition, we think that it is essential to reanalyze WES data after the complete clinical information collection to avoid missing some important candidate variants.

Valgus-varus deformity induced abnormal tissue metabolism, inflammatory damage and apoptosis in broilers

1. This study explored the tissue metabolic status and the relationship with inflammation in valgus-valgus deformity (VVD) broilers with increasing age.2. Tissue and blood from VVD and healthy broilers were collected at two, four and five weeks old. A fully automated biochemical analyser, real-time PCR, HE staining and enzyme-linked immunosorbent assay were used to detect tissue metabolic indexes, mRNA levels of inflammation and apoptosis cytokines in immune organs, histological changes and serum inflammation and immune-related protein contents in VVD broilers.3. The results showed that VVD increased the levels of total protein, albumin, alanine aminotransferase at five weeks of age, aspartate aminotransferase, urea and creatine kinase in blood at two weeks of age. It upregulated the gene expression of inflammatory factors IL-1β, IL-6, IL-8, TNF-α, NF-κB and TGF-β and apoptotic factors FAS, Bcl-2, caspase-3 and 9 in immune organs; increased levels of serum proteins TNF-α, IL-1β and IL-6 and decreased levels of serum immunoglobulins IgY and CD3⁺.4. In addition, with increasing age, IL-10 gene expression gradually increased in the BF and decreased in the spleen.5. In conclusion, VVD broilers have disorders of liver and kidney metabolism, inflammation and apoptosis of immune organs and increased levels of serum inflammatory factor proteins.

MiR-185-5p measurement assists in reflecting Th1/Th2 cell imbalance, inflammatory cytokine production, and exacerbation risk for childhood asthma

BACKGROUND

MicroRNA (miR)-185-5p participates in the pathology of asthma by regulating immune imbalance, inflammation, periostin synthesis, and smooth muscle contraction. This study intended to explore the dysregulation of miR-185p and its correlation with T-helper (Th)1, Th2 cells, and inflammatory cytokines in childhood asthma.

METHODS

In 150 childhood asthma patients and 30 healthy controls (HCs), miR-185-5p from peripheral blood mononuclear cells was detected using reverse transcription-quantitative polymerase chain reaction, Th cells from peripheral blood samples were detected using flow cytometry, inflammatory cytokines from serum samples were detected using enzyme-linked immunosorbent assay.

RESULTS

MiR-185-5p was increased in childhood asthma patients versus HCs [median (interquartile range (IQR)): 2.315 (1.770-3.855) versus 1.005 (0.655-1.520)] (P < 0.001). Meanwhile, miR-185-5p was negatively associated with Th1 cells (P = 0.035) but positively correlated with Th2 cells (P = 0.006) and IL-4 (P = 0.003) in childhood asthma patients; however, miR-185-5p was not linked to Th1 cells, Th2 cells, IFN-γ, or IL-4 in HCs (all P > 0.05). In addition, miR-185-5p was positively related to TNF-α (P < 0.001), IL-1β (P = 0.015), and IL-6 (P = 0.008) in childhood asthma patients, miR-185-5p was only linked to TNF-α (P = 0.040) but not IL-1β or IL-6 (both P > 0.05) in HCs. Moreover, miR-185-5p was increased in exacerbated childhood asthma patients versus remissive patients [median (IQR): 3.170 (2.070-4.905) versus 1.900 (1.525-2.615)] (P < 0.001). Besides, miR-185-5p was highest in patients with severe exacerbation followed by patients with moderate exacerbation, and lowest in patients with mild exacerbation (P = 0.010).

CONCLUSION

MiR-185-5p is associated with imbalanced Th1/Th2 cells, increased inflammatory cytokines along with elevated exacerbation risk, and severity in childhood asthma patients.

Prognostic Value of Four Preimplantation Malnutrition Estimation Tools in Predicting Heart Failure Hospitalization of the Older Diabetic Patients with Right Ventricular Pacing

OBJECTIVES

The prognostic value of preimplantation nutritional status is not yet known for older diabetic patients that received right ventricular pacing (RVP). The study aimed to investigate the clinical value of the four malnutrition screening tools for the prediction of heart failure hospitalization (HFH) in older diabetic patients that received RVP.

DESIGN

Retrospective observational cohort study.

SETTING AND PARTICIPANTS

This study was conducted between January 2017 and January 2018 at the Fuwai Hospital, Beijing, China, and included older (age ≥ 65 years) diabetic patients that received RVP for the first time Measurements: The Prognostic Nutritional Index (PNI), Geriatric Nutritional Risk Index (GNRI), Naples Prognostic Score (NPS), and the Controlling Nutritional Status (CONUT) score were used to estimate the preimplantation nutritional status of the patients. Univariate and multivariate Cox proportional hazard regression analyses were performed to investigate the association between preimplantation malnutrition and HFH.

RESULTS

Overall, 231 older diabetic patients receiving RVP were included. The median follow-up period after RVP was 53 months. HFH was reported for 19.9% of the included patients. Our results showed preimplantation malnutrition for 18.2%, 15.2%, 86.6% and 66.2% of the included patients based on the PNI, GNRI, NPS, and CONUT score, respectively. The cumulative rate of HFH during follow-up period was significantly higher for patients in the preimplantation malnutrition group based on the PNI (log-rank = 13.0, P = 0.001), GNRI (log-rank = 8.5, P = 0.01), and NPS (log-rank = 15.7, P < 0.001) compared to the normal nutrition group, but was not statistically significant for those in the preimplantation malnutrition group based on the CONUT score (log-rank = 2.7, P = 0.3). As continuous variables, all the nutritional indices showed significant correlation with HFH (all P < 0.05). However, multivariate analysis showed that only GNRI was independently associated with HFH (HR = 0.97, 95% CI: 0.937-0.997, P = 0.032). As categorical variables, PNI, GNRI, and NPS showed significant correlation with HFH. After adjustment of confounding factors, moderate-to-severe degree of malnutrition was an independent predictor of HFH based on the PNI (HR = 4.66, 95% CI: 1.03-21.00, P = 0.045) and GNRI (HR = 3.02, 95% CI: 1.02-9.00, P = 0.047).

CONCLUSION

Preimplantation malnutrition was highly prevalent in older diabetic patients that received RVP. The malnutrition prediction tools, PNI and GNRI, showed significant prognostic value in accurately predicting HFH in older diabetic patients with RVP.

Dendritic Spine in Autism Genetics: Whole-Exome Sequencing Identifying De Novo Variant of CTTNBP2 in a Quad Family Affected by Autism Spectrum Disorder

Autism spectrum disorder (ASD) affects around 1% of children with no effective blood test or cure. Recent studies have suggested that these are neurological disorders with a strong genetic basis and that they are associated with the abnormal formation of dendritic spines. Chromosome microarray (CMA) together with high-throughput sequencing technology has been used as a powerful tool to identify new candidate genes for ASD. In the present study, CMA was first used to scan for genome-wide copy number variants in a proband, and no clinically significant copy number variants were found. Whole-exome sequencing (WES) was used further for genetic testing of the whole quad family affected by ASD, including the proband, his non-autistic sister, and his parents. Sanger sequencing and MassARRAY-based validation were used to identify and confirm variants associated with ASD. WES yielded a 151-fold coverage depth for each sample. A total of 98.65% of the targeted whole-exome region was covered at >20-fold depth. A de novo variant in CTTNBP2, p.M115T, was identified. The CTTNBP2 gene belongs to a family of ankyrin repeat domain-containing proteins associated with dendritic spine formation. Although CTTNBP2 has been associated with ASD, limited studies have been developed to identify clinically relevant de novo mutations of CTTNBP2 in children with ASD; family-based WES successfully identified a clinically relevant mutation in the CTTNBP2 gene in a quad family affected by ASD. Considering the neuron-specific expression of CTTNBP2 and its role in dendritic spine formation, our results suggest a correlation between the CTTNBP2 mutation and ASD, providing genetic evidence for ASD spine pathology. Although the present study is currently insufficient to support the assertion that the de novo mutation M115T in CTTNBP2 directly causes the autism phenotype, our study provides support for the assertion that this mutation is a candidate clinically relevant variant in autism.

Inductively coupled plasma mass spectrometry based urine metallome to construct clinical decision models for autism spectrum disorder

BACKGROUND

The global prevalence of autism spectrum disorder (ASD) is on the rise, and high levels of exposure to toxic heavy metals may be associated with this increase. Urine analysis is a noninvasive method for investigating the accumulation and excretion of heavy metals. The aim of this study was to identify ASD-associated urinary metal markers.

METHODS

Overall, 70 children with ASD and 71 children with typical development (TD) were enrolled in this retrospective case-control study. In this metallomics investigation, inductively coupled plasma mass spectrometry was performed to obtain the urine profile of 27 metals.

RESULTS

Children with ASD could be distinguished from children with TD based on the urine metal profile, with ASD children showing an increased urine metal Shannon diversity. A metallome-wide association analysis was used to identify seven ASD-related metals in urine, with cobalt, aluminum, selenium, and lithium significantly higher, and manganese, mercury, and titanium significantly lower in the urine of children with ASD than in children with TD. The least absolute shrinkage and selection operator (LASSO) machine learning method was used to rank the seven urine metals in terms of their effect on ASD. On the basis of these seven urine metals, we constructed a LASSO regression model for ASD classification and found an area under the receiver operating characteristic curve of 0.913. We also constructed a clinical prediction model for ASD based on the seven metals that were different in the urine of children with ASD and found that the model would be useful for the clinical prediction of ASD risk.

CONCLUSIONS

The study findings suggest that altered urine metal concentrations may be an important risk factor for ASD, and we recommend further exploration of the mechanisms and clinical treatment measures for such alterations.

Single nucleotide polymorphisms of PCP pathway related genes participate in the occurrence and development of neural tube defect

BACKGROUND

To screen the single nucleotide polymorphisms (SNPs) in the coding regions of VANGL and FZD family members related to the plane cell polarity (PCP) signaling pathway in neural tube defects (NTDs) patients, so as to provide theoretical and experimental basis for the prevention and treatment of NTDs by intervening PCP signal transduction.

METHODS

112 NTDs patients were collected as the case group and 112 craniocerebral trauma patients as control. Afterwards, blood genomic DNA was extracted and sequenced. The distribution of SNP alleles and genotypes between case and control groups was analyzed. Finally, the NTD rat model was constructed, and the effect of SNPs on the expression level of VANGL and FZD genes was verified by qRT-PCR.

RESULTS

GC genotype was newly found at VANGL1 c.346G>A, as well as AT genotype in FZD6 c.97A>G. The distribution of VANGL1 c.346g>A allele and genotype was statistically different between the case and control groups (p < 0.05). The newly found genotype GC increased the risk of NTDs (OR = 9.918, 95% CI: 1.234%-79.709%). The results of qRT-PCR showed that the expression level of FZD6 in E11 NTD fetuses were significantly increased (p < 0.05), but there was no obvious difference in the expression of VANGL1.

CONCLUSION

We found a new variant of VANGL1 c.346G>A, whose GC genotype might play an important role in the pathogenesis of NTDs. The SNPs of VANGL1 had no significant effect on its expression level, indicating that it may induce NTDs through other ways. FZD6 was significantly overexpressed in NTDs fetuses.

The health system and health impacts of primary healthcare reform in China: A systematic review

Background

China has undergone a comprehensive primary healthcare(PHC) reform since 2009 aiming to deliver accessible, higher-quality, and equitable healthcare. However, there is limited understanding of the effectiveness of this reform. This systematic review synthesizes evidence on health system and health impacts of this reform.

Methods

We searched 13 international databases and three Chinese databases for quantitative studies assessing the impacts of this reform published between January 2009 and March 2020. We searched for studies in English or Mandarin. Eligible study designs were RCTs, quasi-experimental studies and controlled before-after studies. We included studies that: assessed PHC policies since 2009; had geographical, temporal or population comparators; and assessed any outcome measures of health expenditures, health service utilisation, quality of care or health outcomes. Study quality was assessed using ROBINS-I, and results synthesized narratively. PROSPERO: CRD42021239991.

Results

Of 35,480 titles, 37 studies were included (27 in English and ten in Mandarin). Eight were considered at low risk of bias. The 37 studies covered all major PHC policies since 2009, but mostly focused on the essential medicine (N = 15) and financing (N = 10). The quantity and quality of studies on service delivery policies(e.g., family physician and essential health services), were low(N = 3,with moderate or serious risk of bias). 17 studies found that the PHC reforms promoted primary care utilisation. Its impacts on quality and health improvement appear limited to people with chronic diseases(N = 11). Evidence on primary care costs and OOPs were not clear. Some evidence showed that the reforms were pro-equity with benefits accrued in disadvantaged regions and groups.

Conclusions

Comprehensive PHC reforms can deliver some benefits related to utilisation and health for high-risk and vulnerable populations. Policymakers should continue to prioritize PHC to achieve Universal Health Coverage.

Key messages

• The finding suggests that large-scale and comprehensive primary healthcare reforms can deliver benefits related to utilisation and health for high-risk and vulnerable populations.

• Future research should include more robust study designs and seek to better understand the impact of major PHC reforms on quality of care, health outcomes and equity.

Search for New Physics in Electronic Recoil Data from XENONnT

We report on a blinded analysis of low-energy electronic recoil data from the first science run of the XENONnT dark matter experiment. Novel subsystems and the increased 5.9 ton liquid xenon target reduced the background in the (1, 30) keV search region to (15.8±1.3)  events/(ton×year×keV), the lowest ever achieved in a dark matter detector and ∼5 times lower than in XENON1T. With an exposure of 1.16 ton-years, we observe no excess above background and set stringent new limits on solar axions, an enhanced neutrino magnetic moment, and bosonic dark matter.

[Effects and mechanism of diammonium glycyrrhizinate on liver injury in severely scalded rats]

Objective: To investigate the effects and mechanism of diammonium glycyrrhizinate (DG) on liver injury in severely scalded rats. Methods: The experimental research method was used. Fifty-four female Sprague-Dawley rats aged 7-9 weeks were divided into sham injury group with simulated injury on the back, and simple scald group and scald+DG group with scald of 30% total body surface area on the back, with 18 rats in each group. Rats in sham injury group were not specially treated after injury, and rats in simple scald group and scald+DG group were rehydrated for antishock. Besides, rats in scald+DG group were injected intraperitoneally with 50 mg/kg DG at post injury hour (PIH) 1, 25, and 49. Rats in the three groups were collected, the serum content of liver function injury related indexes including aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), total protein, and albumin was measured by automatic biochemical assay analyzer, and serum content of ornithine carbamoyl transferase (OCT) was measured by enzyme-linked immunosorbent assay method at PIH 24, 48, and 72; hepatic histopathological changes at PIH 72 were observed by hematoxylin-eosin staining; the mRNA expressions of B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein (Bax), glucose regulated protein 78 (GRP78), activating transcription factor 4 (ATF4), and protein kinase R-like endoplasmic reticulum kinase (PERK) in liver tissue were detected by real-time fluorescent quantitative reverse transcription polymerase chain reaction at PIH 24, 48, and 72. The protein expressions of Bcl-2, Bax, GRP78, PERK, and ATF4 in liver tissue were detected by Western blotting at PIH 72 in sham injury group and PIH 24, 48, and 72 in simple scald group and scald+DG group. The number of samples was 6 in each group at each time point. Data were statistically analyzed with analysis of variance for factorial design, one-way analysis of variance, and Bonferroni test. Results: Compared with that in sham injury group, the serum content of AST, ALT, and LDH was significantly increased (P<0.01), and the serum content of total protein and albumin was significantly decreased (P<0.05 or P<0.01) of rats in simple scald group at all post-injury time points. Compared with those in simple scald group, the serum AST content of rats in scald+DG group at PIH 24 was decreased significantly (P<0.05); the serum AST, ALT, and LDH content of rats in scald+DG group at PIH 48 was decreased significantly (P<0.01), and the serum total protein content was increased significantly (P<0.01); the serum AST, ALT, and LDH content of rats in scald+DG group at PIH 72 was decreased significantly (P<0.01), and the serum total protein and albumin content was increased significantly (P<0.01). At PIH 24, 48, and 72, the serum OCT content of rats in simple scald group was (48.5±3.9), (40.8±2.4), and (38.7±2.0) U/L, which was significantly higher than (15.1±2.5), (15.7±2.6), and (16.4±3.7) U/L in sham injury group (P<0.01), and (39.0±4.5), (31.8±2.0), and (22.1±2.6) U/L in scald+DG group (P<0.05 or P<0.01). At PIH 72, the cells in liver tissue of rats in sham injury group had normal morphology and regular arrangement, with no obvious inflammatory cell infiltration; the cells in liver tissue of rats in simple scald group had disordered arrangement, diffuse steatosis, and moderate inflammatory cell infiltration; the cells in liver tissue of rats in scald+DG group arranged regularly, with scattered steatosis and a small amount of inflammatory cell infiltration. Compared with those in sham injury group, the Bcl-2 mRNA (P<0.05 or P<0.01) and protein expressions of liver tissue were significantly decreased, and the mRNA (P<0.01) and protein expressions of Bax were significantly increased in rats in simple scald group at PIH 24, 48, and 72. Compared with those in simple scald group, the mRNA (P<0.05) and protein expressions of Bax in liver tissue of rats in scald+DG group were decreased significantly at PIH 48; the mRNA (P<0.01) and protein expressions of Bax in liver tissue of rats in scald+DG group were significantly decreased, and the mRNA (P<0.01) and protein expressions of Bcl-2 were significantly increased at PIH 72. Compared with those in sham injury group, the mRNA (P<0.05 or P<0.01) and protein expressions of ATF4, GRP78, and PERK in liver tissue were significantly increased in rats in simple scald group at all post-injury time points. Compared with those in simple scald group, the mRNA (P<0.01) and protein expressions of ATF4 in liver tissue of rats in scald+DG group at PIH 48 were significantly decreased, and the mRNA (P<0.05 or P<0.01) and protein expressions of ATF4, GRP78, and PERK were significantly decreased in liver tissue of rats in scald+DG group at PIH 72. Conclusions: DG can effectively reduce the degree of liver injury in rats after severe scald, and the mechanism may involve alleviating endoplasmic reticulum stress and mitigating mitochondrial damage.

What is the impact of a novel DEPDC5 variant on an infant with focal epilepsy: a case report

Background

Variants in the DEPDC5 have been proved to be main cause of not only various dominant familial focal epilepsies, but also sporadic focal epilepsies. In the present study, a novel variant in DEPDC5 was detected in the patient with focal epilepsy and his healthy father. We aimed to analyze the pathogenic DEPDC5 variant in the small family of three.

Case presentation

A 5-month-old male infant presented with focal epilepsy. Whole exome sequencing identified a novel heterozygous variant c.1696delC (p.Gln566fs) in DEPDC5, confirmed by Sanger sequencing. The variant was inherited from healthy father.

Conclusions

Our study expands the spectrum of DEPDC5 variants. Moreover, We discuss the relation between the low penetrance of DEPDC5 and the relatively high morbidity rate of DEPDC5-related sporadic focal epilepsy. Besides, due to interfamilial phenotypic and genetic heterogeneity, we speculate the prevalence of familial focal epilepsy with variable foci might be underestimated in such small families. We emphasize the importance of gene detection in patients with sporadic epilepsy of unknown etiology, as well as their family members. It can identify causative mutations, thus providing help to clinicians in making a definitive diagnosis.

Beware of missed diagnosis in patients with multiple genetic diseases: a case report

Background

Duchenne muscular dystrophy (DMD) is an X-linked recessive inherited disorder caused by the absence of the Dystrophin protein. Cerebral cavernous malformations (CCMs) are the most common vascular abnormalities in the central nervous system caused by the absence of the products of the CCM genes. Most CCMs cases reported occurring in a sporadic form are often asymptomatic.

Case presentation

We report a rare case of a 7-year-old Chinese boy with a co-existing DMD and sporadic CCMs. We found classic clinical features of DMD and non-specific pathological changes in his brain. We made the definitive diagnosis based on the results of whole-exome sequencing (WES), a repeat from exon 3 to exon 9 of the DMD inherited from his mother, and a de novo heterozygote nonsense mutation C.418G > T of the PDCD10 exon 6.

Conclusion

We should take care to avoid missed diagnoses in patients with multiple genetic disorders.

Case Report: Cardiac Multiple Thrombus and Pulmonary Embolism Associated With Mycoplasma Pneumonia Infection in a Child

Mycoplasma pneumoniae (MP) is a common pathogen of lower respiratory tract infection in children and adolescents. Some patients with MP infection are self-limiting, while with the increase of severe or refractory Mycoplasma pneumoniae pneumonia (MPP) in recent years, there is a great increase in reports of thromboembolism in multiple organs, including lung, brain, spleen, and peripheral arteries. Cardiac multiple thrombi and pulmonary embolism associated with MP infection have not been reported. The most effective treatment option for cardiac thrombus was surgical resection for fear of thrombus detachment and causing new thromboembolism. Herein, we present a patient with cardiac multiple thrombi and pulmonary embolism in MPP for the first time. In our case, the child recovered after conservative medical treatment, which provides a therapeutic option for children with cardiac multiple thrombi.

Identification of two aberrant transcripts by RNA sequencing for a novel variant c.3354 + 5 G > A of MED12 in a Chinese girl with non-syndromic intellectual disability

BACKGROUND

Missense variants in MED12 are associated with MED12-related disorders. We aimed to clarify the molecular level changes and underlying pathogenic mechanism of a female patient in our study.

METHODS

We reported a Chinese girl with clinical characteristics similar to MED12-related disorders. Trio whole exome sequencing (WES) was performed to identify related pathogenic variant(s) and RNA sequencing (RNA-seq) was subsequently applied to evaluate the effect of identified variant(s) on mRNA splicing. Moreover, X-chromosome inactivation (XCI) assay based on AR and RP2 was performed to reveal the XCI pattern of the female patient.

RESULTS

The proband manifested mainly as mental retardation and language impairment. Trio WES revealed a novel heterozygous variant c.3354 + 5 G > A in intron 23 of MED12. RNA-seq identified two aberrant transcripts. XCI assay on AR revealed a homozygous result, while XCI based on RP2 showed random pattern in peripheral blood.

CONCLUSION

In conclusion, we identified a novel variant c.3354 + 5 G > A by WES combined with RNA-seq, which extends the spectrum of MED12 variants and provide a basis for further genetic counseling. According to the result of two aberrant transcripts by RNA-seq, we speculate that our patient's milder clinical feature may be the consequence of multiple different transcripts.

[Progress in clinical diagnosis and treatment of gallbladder cancer]

Due to the lack of effective early diagnosis and treatment, gallbladder cancer(GBC) remains a malignant tumor with extremely high malignancy and poor prognosis. Therefore, high quality studies are required to break through the bottleneck in GBC diagnosis and treatment. This article reviewed the domestic and foreign GBC research published in 2021, presenting a comprehensive summary of the important advances in the field of clinical diagnosis and treatment. Latest epidemiological data and risk factors, emerging diagnostic methods of peripheral blood laboratory tests and imaging, new pathologic classification system, hot topics and controversies of surgical treatment as well as the dynamics of systemic treatment of GBC are reviewed in the article. The present findings may contribute to a more efficient means of diagnosis and treatment for GBC and hold the promise of improved outcomes for patients with GBC.

Development and validation of a nomogram to predict plastic bronchitis in children with refractory Mycoplasma pneumoniae pneumonia

Background

Early identification of plastic bronchitis (PB) is of great importance and may aid in delivering appropriate treatment. This study aimed to develop and validate a nomogram for predicting PB in patients with refractory Mycoplasma pneumoniae pneumonia (RMPP).

Methods

A total of 547 consecutive children with RMPP who underwent fiberoptic bronchoscopy (FOB) intervention from January 2016 to June 2021 were enrolled in this study. Subsequently, 374 RMPP children (PB: 137, without PB: 237) from January 2016 to December 2019 were assigned to the development dataset to construct the nomogram to predict PB and 173 RMPP children from January 2020 to June 2021 were assigned to the validation dataset. The clinical, laboratory and radiological findings were screened using Least Absolute Shrinkage and Selection Operator (LASSO) regression and logistic regression was applied to construct a nomogram. The performance of the nomogram was evaluated by discrimination, calibration and clinical utility. Comparsion of ROC analysis and decision curve analysis (DCA) between nomogram and other models was performed to evaluate the discrimination ability and clinical utility.

Results

The development dataset included 374 patients with a mean age of 6.6 years and 185(49.5%) were men. The validation dataset included 173 patients and the mean age of the dataset was 6.7 years and 86 (49.7%) were men. From 26 potential predictors, LASSO regression identified 6 variables as significant predictive factors to construct the nomogram for predicting PB, including peak body temperature, neutrophil ratio (N%), platelet counts (PLT), interleukin-6 (IL-6), actic dehydrogenase (LDH) and pulmonary atelectasis. The nomogram showed good discrimination, calibration and clinical value. The mean AUC of the nomogram was 0.813 (95% CI 0.769–0.856) in the development dataset and 0.895 (95% CI 0.847–0.943) in the validation dataset. Through calibration plot and Hosmer–Lemeshow test, the predicted probability had a good consistency with actual probability both in the development dataset (P = 0.217) and validation dataset (P = 0.183), and DCA showed good clinical utility. ROC analysis indicated that the nomogram showed better discrimination ability compared with model of peak body temperature + pulmonary atelactsis and another model of N% + PLT + IL-6 + LDH, both in development dataset (AUC 0.813 vs 0.757 vs 0.754) and validation dataset (AUC 0.895 vs 0.789 vs 0.842).

Conclusions

In this study, a nomogram for predicting PB among RMPP patients was developed and validated. It performs well on discrimination ability, calibration ability and clinical value and may have the potential for the early identification of PB that will help physicians take timely intervention and appropriate management.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-022-02047-2.

Identifying Rare Genetic Variants of Immune Mediators as Risk Factors for Autism Spectrum Disorder

Autism spectrum disorder (ASD) affects more than 1% of children, and there is no viable pharmacotherapeutic agent to treat the core symptoms of ASD. Studies have shown that children with ASD show changes in their levels of immune response molecules. Our previous studies have shown that ASD is more common in children with folate receptor autoantibodies. We also found that children with ASD have abnormal gut immune function, which was characterized by a significant increase in the content of immunoglobulin A and an increase in gut-microbiota-associated epitope diversity. These studies suggest that the immune mechanism plays an important role in the occurrence of ASD. The present study aims to systematically assess gene mutations in immune mediators in patients with ASD. We collected genetic samples from 72 children with ASD (2−12 years old) and 107 healthy controls without ASD (20−78 years old). We used our previously-designed immune gene panel, which can capture cytokine and receptor genes, the coding regions of MHC genes, and genes of innate immunity. Target region sequencing (500×) and bioinformatics analytical methods were used to identify variants in immune response genes associated with patients with ASD. A total of 4 rare variants were found to be associated with ASD, including HLA-B: p.A93G, HLA-DQB1: p.S229N, LILRB2: p.R322H, and LILRB2: c.956-4C>T. These variants were present in 44.44% (32/72) of the ASD patients and were detected in 3.74% (4/107) of the healthy controls. We expect these genetic variants will serve as new targets for the clinical genetic assessment of ASD, and our findings suggest that immune abnormalities in children with ASD may have a genetic basis.

[Survival analysis since diagnosis of HIV-positive injecting drug users aged 15 years and above in China]

Objective: To understand death's mortality and risk factors among HIV-positive injecting drug users (IDU) aged 15 or above in China and provide further reference to future prevention and treatment policies. Method: Retrospective cohort study was conducted to calculate the mortality rate of HIV-positive IDU based on HIV/AIDS Comprehensive Response Information Management System. Cox proportion hazards regression model was performed to assess the risk factors for deaths. The Excel 2019 and SPSS 22.0 software was used for data cleaning and statistical analysis. Results: Between 2001 and 2020, 119 209 HIV-positive IDU were reported with 59 094 deaths. The all-cause mortality rate was 6.96 per 100 person-years (py), and the AIDS-related mortality rate was 1.91 per 100 py, with a decreasing trend over the years. Multivariate Cox regression indicated for all-cause death risks of HIV-positive IDU, compared with those baseline T⁺ lymphocyte cells (CD4) counts above 500 cells/μl, the HR (95%CI) of those CD4 counts untested, between 0-199, 200-349, 350-500 cells/μl was 2.85 (2.78-2.93), 2.47 (2.40-2.54), 1.58 (1.53-1.62) and 1.24 (1.21-1.28) respectively. The HR (95%CI) of antiretroviral treatment (ART) naïve was 7.13 (6.99-7.27) compared with those under ART. The HR (95%CI) of methadone maintenance treatment (MMT) naïve was 1.07 (1.04-1.10) compared to those receiving MMT. As for AIDS-related death risks, compared with baseline T+ lymphocyte cell CD4 counts >500 cells/μl, the HR (95%CI) of those CD4 counts untested, between 0-199, 200-349, 350-500 cells/μl was 3.26 (3.08-3.46), 5.54 (5.24-5.85), 2.35 (2.21-2.50) and 1.41 (1.32-1.50). HR (95%CI) of ART naïve was 5.96(5.74-6.18) compared to those under ART. Conclusions: Further efforts should be made timely on diagnosis, treatment, and harm reduction programs such as MMT for improvement compliance to reduce mortality risks of HIV-positive IDU.

The biallelic novel pathogenic variants in AGL gene in a chinese patient with glycogen storage disease type III

BACKGROUND

Glycogen storage disease type III (GSD III) is a rare autosomal recessive glycogenolysis disorder due to AGL gene variants, characterized by hepatomegaly, fasting hypoglycemia, hyperlipidemia, elevated hepatic transaminases, growth retardation, progressive myopathy, and cardiomyopathy. However, it is not easy to make a definite diagnosis in early stage of disease only based on the clinical phenotype and imageology due to its clinical heterogeneity.

CASE PRESENTATION

We report a two-year-old girl with GSD III from a nonconsanguineous Chinese family, who presented with hepatomegaly, fasting hypoglycemia, hyperlipidemia, elevated levels of transaminases. Accordingly, Sanger sequencing, whole‑exome sequencing of family trios, and qRT-PCR was performed, which revealed that the patient carried the compound heterogeneous variants, a novel frameshift mutation c.597delG (p. Q199Hfs*2) and a novel large gene fragment deletion of the entire exon 13 in AGL gene. The deletion of AGL was inherited from the proband's father and the c.597delG variant was from the mother.

CONCLUSIONS

In this study, we identified two novel variants c.597delG (p. Q199Hfs*2) and deletion of the entire exon 13 in AGL in a Chinese GSD III patient. We extend the mutation spectrum of AGL. We suggest that high-throughput sequencing technology can detect and screen pathogenic variant, which is a scientific basis about genetic counseling and clinical diagnosis.

Novel Prognostic Signature for Acute Myeloid Leukemia: Bioinformatics Analysis of Combined CNV-Driven and Ferroptosis-Related Genes

Background: Acute myeloid leukemia (AML), which has a difficult prognosis, is the most common hematologic malignancy. The role of copy number variations (CNVs) and ferroptosis in the tumor process is becoming increasingly prominent. We aimed to identify specific CNV-driven ferroptosis-related genes (FRGs) and establish a prognostic model for AML.

Methods: The combined analysis of CNV differential data and differentially expressed genes (DEGs) data from The Cancer Genome Atlas (TCGA) database was performed to identify key CNV-driven FRGs for AML. A risk model was constructed based on univariate and multivariate Cox regression analysis. The Gene Expression Omnibus (GEO) dataset was used to validate the model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to clarify the functional roles of DEGs and CNV-driven FRGs.

Results: We identified a total of 6828 AML-related DEGs, which were shown to be significantly associated with cell cycle and immune response processes. After a comprehensive analysis of CNVs and corresponding DEGs and FRGs, six CNV-driven FRGs were identified, and functional enrichment analysis indicated that they were involved in oxidative stress, cell death, and inflammatory response processes. Finally, we screened 2 CNV-driven FRGs (DNAJB6 and HSPB1) to develop a prognostic risk model. The overall survival (OS) of patients in the high-risk group was significantly shorter in both the TCGA and GEO (all p < 0.05) datasets compared to the low-risk group.

Conclusion: A novel signature based on CNV-driven FRGs was established to predict the survival of AML patients and displayed good performance. Our results may provide potential targets and new research ideas for the treatment and early detection of AML.

Development and Validation of a Novel Gene Signature for Predicting the Prognosis of Idiopathic Pulmonary Fibrosis Based on Three Epithelial-Mesenchymal Transition and Immune-Related Genes

Background: Increasing evidence has revealed that epithelial–mesenchymal transition (EMT) and immunity play key roles in idiopathic pulmonary fibrosis (IPF). However, correlation between EMT and immune response and the prognostic significance of EMT in IPF remains unclear.

Methods: Two microarray expression profiling datasets (GSE70866 and GSE28221) were downloaded from the Gene Expression Omnibus (GEO) database. EMT- and immune-related genes were identified by gene set variation analysis (GSVA) and the Estimation of STromal and Immune cells in MAlignant Tumors using Expression data (ESTIMATE) algorithm. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to investigate the functions of these EMT- and immune-related genes. Cox and least absolute shrinkage and selection operator (LASSO) regression analyses were used to screen prognostic genes and establish a gene signature. Gene Set Enrichment Analysis (GSEA) and Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) were used to investigate the function of the EMT- and immune-related signatures and correlation between the EMT- and immune-related signatures and immune cell infiltration. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to investigate the mRNA expression of genes in the EMT- and immune-related signatures.

Results: Functional enrichment analysis suggested that these genes were mainly involved in immune response. Moreover, the EMT- and immune-related signatures were constructed based on three EMT- and immune-related genes (IL1R2, S100A12, and CCL8), and the K–M and ROC curves presented that the signature could affect the prognosis of IPF patients and could predict the 1-, 2-, and 3-year survival well. Furthermore, a nomogram was developed based on the expression of IL1R2, S100A12, and CCL8, and the calibration curve showed that the nomogram could visually and accurately predict the 1-, 2-, 3-year survival of IPF patients. Finally, we further found that immune-related pathways were activated in the high-risk group of patients, and the EMT- and immune-related signatures were associated with NK cells activated, macrophages M0, dendritic cells resting, mast cells resting, and mast cells activated. qRT-PCR suggested that the mRNA expression of IL1R2, S100A12, and CCL8 was upregulated in whole blood of IPF patients compared with normal samples.

Conclusion: IL1R2, S100A12, and CCL8 might play key roles in IPF by regulating immune response and could be used as prognostic biomarkers of IPF.

Cryptogenic massive hemoptysis caused by bronchial artery-pulmonary artery fistula in a 12-year-old boy: A case report and literature review

BACKGROUND

Hemoptysis is a frequently encountered symptom of the respiratory system in adult but is rare in children. Bronchial artery-pulmonary artery fistula (BPF) is one of the most important and life-threatening cause in pediatric hemoptysis patients. Although the severity of BPF has been proved in previous studies, details about clinical diagnosis and treatment of BPF in children have been rarely reported.

CASE PREPARATION

A 12-year-old boy presented to the hospital with hematemesis after coughing, without any other symptoms. After admission, he had repeated hemoptysis, 20-30 ml each time, and on the 11th night of admission a massive hemoptysis (about 100 ml bright red blood) occurred suddenly. Chest computed tomography demonstrated patchy ground glass opacities in the right lung, suggestive of pulmonary hemorrhage. Bronchial arteriography showed an apparent BPF in the right lobe bronchial artery. Therefore, bronchial artery embolization was performed, following which a thrombus in the bronchial lumen was removed by bronchoscopy. After these interventions, the patient recovered quickly and no recurrence was noted in the following year.

CONCLUSION

We believe that this case should raise awareness of cryptogenic massive hemoptysis caused by BPF. In the event of hemoptysis in a child, it is important to clarify the source of the bleeding. If common etiologies have been excluded, the presence of pulmonary and bronchial vascular malformations should be considered. Moreover, multidisciplinary collaboration is crucial in the diagnosis and management of cryptogenic hemoptysis.

Efficacy and Safety of Diet Therapies in Children With Autism Spectrum Disorder: A Systematic Literature Review and Meta-Analysis

Objective

Autism Spectrum Disorder is a neurodevelopmental disorder, with a rapid increase in recognition over the past decade. Interest in alternative therapies is growing annually, such as dietary therapies including gluten-free and/or casein-free diet, and the ketogenic diet. However, there is no consensus on the efficacy and safety of dietary therapy in children with ASD up to now. This study aimed to assess the efficacy and safety of these diet interventions for children with ASD based on a meta-analysis of global data.

Methods

Seven databases (Cochrane Library, PubMed, EMBASE, Web of Science, VIP, CNKI, and Wanfang) were searched according to the established inclusion criteria, from the inception of the databases to August 18, 2021. The Cochrane Bias risk assessment tool was intended to assess the quality of the included studies. Review Manager 5.4 software was used as an efficacy analysis tool of the included studies, taking the core autistic symptoms and scales of ASD as therapeutic efficacy evaluations.

Results

In total, 7 RCTs with 338 participants were finally obtained. All studies assessed the association between core autistic symptoms and therapeutic diet, showing a statistically significant effect (standard mean difference (SMD) of −0.51, 95% confidence interval (Cl): −0.81 to −0.21), in which two studies which followed the GFD diet reported significant reductions in social behaviors (SMD of−0.41, 95% Cl: −0.75 to −0.06), showing no correlation with the length of the interventions (P < 0.05). Two studies were performed in KD diet suggested a significant effect in core symptoms (SMD of −0.67, 95% Cl: −1.04 to −0.31). No statistically significant changes were observed in the GFCF diet, GFD diet, cognition, communication, and stereotypical behaviors subgroups (all P > 0.05).

Conclusion

The results of a meta-analysis suggest that diet therapies can significantly ameliorate core symptoms of ASD, and GFD diets are conducive to improving social behaviors. Although the results suggest the effectiveness of dietary therapy for ASD, limited by the small sample size of RCTs, more well-designed, and high-quality clinical trials are needed to validate the above conclusions.

Systematic Review Registration

https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42021277565.

Identification of a Novel Deep Intronic Variant by Whole Genome Sequencing Combined With RNA Sequencing in a Chinese Patient With Menkes Disease

Background: Menkes disease (MD) is a rare X-linked connective tissue disorder of copper metabolism caused by pathogenic variant(s) in ATP7A gene. The aim of the present study is to determine the clinical characteristics and molecular basis of one patient with MD.

Methods: One 10-month-old Chinese boy who met the clinical manifestations of MD was enrolled in this study. Whole genome sequencing (WGS) was performed in the patient in order to identify the variant(s), followed by Sanger sequencing. RNA sequencing (RNA-seq) from whole blood was subsequently applied to assess the effect of variant on transcription levels, and reverse transcriptase-polymerase chain reaction (RT-PCR) was performed for further validation. In addition, X chromosome inactivation (XCI) status of the patient’s mother at the DNA level was measured by capillary electrophoresis.

Results: The patient suffered from intermittent convulsions for more than 6 months, with psychomoto retardation and neurodegenerations. The patient also had curly hair, hypopigmented skin, cutis laxa, decreased muscle strength and hypotonia. MRI showed the intracranial arteries were tortuous with some “spiral” changes. The patient’s serum ceruloplasmin level was low. WGS revealed one novel hemizygous variant, c.2627-501C > T (NM_000,052.7), located in the deep intronic sequence of ATP7A gene. Sanger sequencing confirmed that the variant was inherited from his mother. RNA-seq confirmed the variant itself, and identified a pseudo-exon inserted between exons 12 and 13 in mRNA of ATP7A. The sequencing results of RT-PCR from the patient confirmed this finding, while neither of his parents detected aberrant splicing. The Capillary electrophoresis results showed that the patient’s mother had a skewed XCI.

Conclusion: Our finding of the variant enlarges the variant spectrum in the ATP7A gene. This is a novel deep intronic variant which leads to the activation of a pseudo-exons in the ATP7A gene, and it demonstrates the usefulness of WGS combined with RNA-seq, in terms of revealing disease-causing variants in non-coding regions. Furthermore, the fact that the deep intronic variants cause disease by the activation of pseudo-exon inclusion indicates that in MD this might be an important mechanism.