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J Med Virol ; 94(1): 197-204, 2022 01.
Article En | MEDLINE | ID: mdl-34427922

Coronavirus disease 2019 (COVID-19) has had different waves within the same country. The spread rate and severity showed different properties within the COVID-19 different waves. The present work aims to compare the spread and the severity of the different waves using the available data of confirmed COVID-19 cases and death cases. Real-data sets collected from the Johns Hopkins University Center for Systems Science were used to perform a comparative study between COVID-19 different waves in 12 countries with the highest total performed tests for severe acute respiratory syndrome coronavirus 2 detection in the world (Italy, Brazil, Japan, Germany, Spain, India, USA, UAE, Poland, Colombia, Turkey, and Switzerland). The total number of confirmed cases and death cases in different waves of COVID-19 were compared to that of the previous one for equivalent periods. The total number of death cases in each wave was presented as a percentage of the total number of confirmed cases for the same periods. In all the selected 12 countries, Wave 2 had a much higher number of confirmed cases than that in Wave 1. However, the death cases increase was not comparable with that of the confirmed cases to the extent that some countries had lower death cases than in Wave 1, UAE, and Spain. The death cases as a percentage of the total number of confirmed cases in Wave 1 were much higher than that in Wave 2. Some countries have had Waves 3 and 4. Waves 3 and 4 have had lower confirmed cases than Wave 2, however, the death cases were variable in different countries. The death cases in Waves 3 and 4 were similar to or higher than Wave 2 in most countries. Wave 2 of COVID-19 had a much higher spread rate but much lower severity resulting in a lower death rate in Wave 2 compared with that of the first wave. Waves 3 and 4 have had lower confirmed cases than Wave 2; that could be due to the presence of appropriate treatment and vaccination. However, that was not reflected in the death cases, which were similar to or higher than Wave 2 in most countries. Further studies are needed to explain these findings.

COVID-19 Vaccines , COVID-19/epidemiology , SARS-CoV-2/genetics , Asia/epidemiology , COVID-19/mortality , COVID-19/transmission , COVID-19/virology , Europe/epidemiology , Global Health , Humans , Mutation , Severity of Illness Index , South America/epidemiology , United States/epidemiology
Dermatol Clin ; 40(1): 1-8, 2022 Jan.
Article En | MEDLINE | ID: mdl-34799030

Clinical genetic testing enables the detection of specific gene mutations and variants that predispose individuals and their family members to disease. In recent years, tremendous strides have been made in the variety of clinically useful tests. Targeted testing for specific mutations that cause well-known syndromes enables the efficient diagnosis of genetic diseases with cutaneous manifestations. Testing for specific genes, however, may not always reveal a diagnosis. Expanded options are available. This review outlines the major types of available technology with a focus on those tests most useful for pediatric dermatologists.

Dermatology , Child , Genetic Testing , Humans , Mutation
Talanta ; 237: 122977, 2022 Jan 15.
Article En | MEDLINE | ID: mdl-34736699

Nucleic acid extraction and purification before amplification is considered an essential step for nucleic acid amplification testing. However, this may cause losses or introduce errors that can lead to inaccurate results, especially when using samples with a small nucleic acid concentration. Here, we developed a direct digital chip that enabled us to detect nucleic acid without DNA extraction and purification. We have developed a self-priming liquid-dispensing digital PCR chip that does not require any external power. This is a robust anti-evaporation digital PCR chip with fast sampling and accurate quantification performance. Using this chip, we have established an on-chip direct nucleic acid amplification method that does not require nucleic acid extraction and purification for liquid biopsy samples. In order to verify the feasibility of this chip for clinical samples, we detected the EGFR T790M mutation from plasma. Results showed that EGFR T790M mutation could be detected with an accuracy of 100% and a sensitivity of 0.01%. Without nucleic acid extraction and purification, the assay avoids complex pre-processing, thus saving time and achieving precise quantification. We expect our direct digital PCR chip to have practical applications in diagnosis, screening, and research, especially in resource-deprived regions.

Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Drug Resistance, Neoplasm , ErbB Receptors/genetics , Humans , Mutation , Polymerase Chain Reaction , Protein Kinase Inhibitors
Zhongguo Dang Dai Er Ke Za Zhi ; 23(10): 1058-1063, 2021 Oct 15.
Article En, Zh | MEDLINE | ID: mdl-34719423

A 15-day-old boy was admitted to the hospital due to repeated convulsions for 14 days. The main clinical manifestations were uncontrolled seizures, hypoergia, feeding difficulties, limb hypotonia, and bilateral hearing impairment. Clinical neurophysiology showed reduced brainstem auditory evoked potential on both sides and burst-suppression pattern on electroencephalogram. Measurement of very-long-chain fatty acids in serum showed that C26:0 was significantly increased. Genetic testing showed a pathogenic compound heterozygous mutation, c.101C>T(p.Ala34Val) and c.1448_1460del(p.Ala483Aspfs*37), in the HSD17B4 gene. This article reports a case of D-bifunctional protein deficiency caused by HSD17B4 gene mutation and summarizes the epidemiological and clinical features, diagnosis, and treatment of this disease, with a focus on the differential diagnosis of this disease from Ohtahara syndrome.

Muscle Hypotonia , Protein Deficiency , Genetic Testing , Humans , Infant, Newborn , Male , Mutation , Peroxisomal Multifunctional Protein-2/genetics , Protein Deficiency/genetics
Zhonghua Xue Ye Xue Za Zhi ; 42(9): 752-756, 2021 Sep 14.
Article Zh | MEDLINE | ID: mdl-34753230

Objective: To evaluate the safety and efficacy of vemurafenib in the treatment of BRAF(V600E)-mutated Erdheim-Chester disease (ECD) . Methods: We retrospectively analyzed the clinical data, response rate, adverse events and survival of 12 patients with ECD treated with vemurafenib from March 2015 to October 2020 in Peking Union Medical College Hospital. Results: Of 12 patients [7 males and 5 females, median age = 51.5 (range, 32-66) years old], the median number of organs involved was 6 (range, 4-8) , and the median treatment duration of vemurafenib was 11 (3-60) months. All patients had improvement of clinical symptoms, of which 2 cases were completely relieved, and 10 cases were partially relieved. Seven patients evaluated by (18)F-FDG-positron emission tomography/computed tomography achieved a metabolic response, including 2 patients with a complete metabolic response and 5 patients with a partial metabolic response. The common adverse events in the overall cohort were grade 1 to 2 (Common Terminology Criteria for Adverse Events 5.0) , including skin rash (58.3%) , arthralgia (25.0%) , and digestive tract reactions (16.7%) . The median follow-up time was 13.5 (3-60) months. One patient with central nervous system involvement died due to a cerebrovascular event, and one patient relapsed 10 months after drug withdrawal. The estimated 2-year overall survival rate and 2-year progression free survival rate were 88.89% and 66.67%, respectively. Conclusions: Vemurafenib is safe and effective in the treatment of BRAF(V600E)-mutated ECD.

Erdheim-Chester Disease , Proto-Oncogene Proteins B-raf , Adult , Aged , Erdheim-Chester Disease/drug therapy , Erdheim-Chester Disease/genetics , Female , Fluorodeoxyglucose F18 , Humans , Male , Middle Aged , Mutation , Proto-Oncogene Proteins B-raf/genetics , Retrospective Studies , Vemurafenib
World J Gastroenterol ; 27(39): 6515-6521, 2021 Oct 21.
Article En | MEDLINE | ID: mdl-34754149

In this editorial, we comment on pancreatic cancer (PC), one of the most aggressive and lethal cancers. Only minimal improvements in survival rates have been achieved over recent years. Available chemotherapeutic regimens have little impact, and surgical resection remains the only reliable curative approach. We address current treatment options for these patients, focusing on the usefulness of breast cancer (BRCA) gene mutation as a prognostic biomarker and predictor of response to chemotherapy. Superior survival outcomes have been reported in patients with PC and mutant BRCA gene treated with first-line platinum-based chemotherapy. Therefore, it appears appropriate to include BRCA gene status among clinical criteria used to select the chemotherapy regimen. In addition, maintenance treatment with poly(ADP-ribose) polymerase inhibitors has been found to improve progression-free survival in patients with PC and mutated BRCA whose disease does not progress after first-line platinum-based chemotherapy. This combination has therefore been proposed as the optimal treatment regimen for these patients.

Breast Neoplasms , Ovarian Neoplasms , Pancreatic Neoplasms , BRCA1 Protein/genetics , BRCA2 Protein/genetics , Female , Humans , Mutation , Ovarian Neoplasms/drug therapy , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/genetics , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use
Zhonghua Wai Ke Za Zhi ; 59(11): 897-901, 2021 Nov 01.
Article Zh | MEDLINE | ID: mdl-34743450

Objective: To examine the clinical features and prognostic value of TP53 mutation in circulating tumor DNA(ctDNA) of Chinese prostate cancer patients. Methods: A prospective cohort of 239 prostate cancer patients diagnosed in the Department of Urology, Fudan University Shanghai Cancer Center from May 2018 to June 2019 was included. The age of diagnosis was(65.4±7.6) years(range: 45 to 85 years). Clinical data were collected from patient diagnosis and treatment records as well as follow-up surveys. TP53 mutations in plasma were detected by target sequence capture and second-generation sequencing. The relationship between TP53 mutation status and progression-free survival(PFS) was analyzed in patients who received any treatment lines. Kaplan-Meier analysis was performed in different subgroups, survival curves were drawn, and Log-rank test was used for comparison. Cox regression models were used to estimate multivariate adjusted HR and 95%CI associated with PFS. Results: In the cohort, 15.9%(38/239) patients had TP53 mutation. Patients with TP53 mutations had a higher rate of metastases initially diagnosed with prostate cancer (78.9% (30/38) vs. 60.2% (121/201), χ²=4.829, P=0.028), as well as a higher rate of castration resistance (68.4% (26/38) vs. 42.8% (86/201), χ²=8.434, P=0.004). Kaplan-Meier analysis revealed a median androgen-deprivation therapy-PFS of 13.0 months in patients with TP53 mutation and 17.0 months in patients with TP53 wild-type. The median abiraterone-PFS was 4.7 months for patients with TP53 mutation and 11.0 months for TP53 wild-type patients. The median docetaxel-PFS was 3.0 months in patients with TP53 mutation and 5.0 months in patients with TP53 wild-type. TP53 mutation was the undependent prognosis factor of PFS in patients treated with abiraterone(HR=2.23, 95%CI: 1.26 to 3.94, P=0.006) and docetaxel(HR=1.92, 95%CI: 1.01 to 3.66, P=0.047) had significant differences in PFS. Conclusions: TP53 mutations were associated with the presence of metastasis and castration resistance, and were also an independent prognostic factor for progression-free survival in patients treated with abiraterone and docetaxel.

Androgen Antagonists , Prostatic Neoplasms, Castration-Resistant , Aged , Aged, 80 and over , China , Humans , Male , Middle Aged , Mutation , Prognosis , Prospective Studies , Prostatic Neoplasms, Castration-Resistant/genetics , Tumor Suppressor Protein p53/genetics
Pediatr Endocrinol Diabetes Metab ; 27(3): 201-208, 2021.
Article En | MEDLINE | ID: mdl-34743503

Mucopolysaccharidoses (MPSs) are known as rare genetic diseases which are caused by mutation in the enzyme heparin sulfate, which normally leads to degradation and accumulation of glycosaminoglycans in the cells. There are 11 types of MPSs, whereby neuropathy may occur in seven of them (MPS I, II, IIIA, IIIB, IIIC, IIID and VII). Accumulation of degraded heparin sulfate in lysosomes causes cellular dysfunction and malfunction of several organs. However, the exact molecular mechanism how protein degradation and storage leads to cellular dysfunction is not understood, yet. Nonetheless, several genetic and biochemical methods for diagnosis of MPSs are available nowadays. Here we provide an overview on known molecular basis of MPS in general, including enzyme defects and symptoms of MPS; however, the main focus is on MPS type III together with potential and perspective therapy-options.

Mucopolysaccharidoses , Mucopolysaccharidosis III , Mucopolysaccharidosis I , Glycosaminoglycans , Humans , Mucopolysaccharidoses/drug therapy , Mucopolysaccharidoses/genetics , Mutation
BMJ Case Rep ; 14(11)2021 Nov 02.
Article En | MEDLINE | ID: mdl-34728514

Fanconi-Bickel syndrome (FBS) is a rare autosomal recessive disease, resulting from mutations in the SLC2A2 gene, causing impaired glucose transporter 2 protein transporter protein function, impaired glucose and galactose utilisation, hepatorenal glycogen accumulation and organ dysfunction. Clinical features include failure to thrive, hepatomegaly, rickets, short stature and delayed puberty. Therapy includes electrolyte supplementation and uncooked cornstarch. We present a 15-year-old boy diagnosed with FBS in infancy. Growth velocity was normal on standard treatment until age 8.5 years, at which time growth failure led to a diagnosis of acquired growth hormone (GH) deficiency. Initiation of recombinant human GH (rhGH) replacement of 0.25 µg/kg/week resulted in marked improvement in growth velocity and height. While short stature is expected in FBS, growth velocity that falls below the normal range despite adequate therapy should prompt further evaluation. Our case suggests that acquired GH deficiency can arise in FBS and benefits from rhGH therapy.

Fanconi Syndrome , Adolescent , Child , Failure to Thrive , Fanconi Syndrome/diagnosis , Fanconi Syndrome/drug therapy , Fanconi Syndrome/genetics , Glucose , Growth Hormone , Humans , Male , Mutation
Nat Commun ; 12(1): 6304, 2021 11 02.
Article En | MEDLINE | ID: mdl-34728625

Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus display remarkable efficacy against authentic B.1.351 virus. Surprisingly, structural analysis has revealed that 58G6 and 13G9 both recognize the steric region S470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly binds to another region S450-458 in the RBD. Significantly, 58G6 and 510A5 both demonstrate prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. Together, we have evidenced 2 potent neutralizing Abs with unique mechanism targeting authentic SARS-CoV-2 mutants, which can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic.

Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/prevention & control , SARS-CoV-2/immunology , Animals , Antibodies, Monoclonal/administration & dosage , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/administration & dosage , Antibodies, Neutralizing/chemistry , Antibodies, Viral/administration & dosage , Antibodies, Viral/chemistry , Binding Sites , COVID-19/pathology , COVID-19/virology , Epitopes , Humans , Mice , Mice, Transgenic , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Viral Load/drug effects , Weight Loss/drug effects
BMJ ; 375: e066288, 2021 11 03.
Article En | MEDLINE | ID: mdl-34732400

OBJECTIVE: To determine whether whole genome sequencing can be used to define the molecular basis of suspected mitochondrial disease. DESIGN: Cohort study. SETTING: National Health Service, England, including secondary and tertiary care. PARTICIPANTS: 345 patients with suspected mitochondrial disorders recruited to the 100 000 Genomes Project in England between 2015 and 2018. INTERVENTION: Short read whole genome sequencing was performed. Nuclear variants were prioritised on the basis of gene panels chosen according to phenotypes, ClinVar pathogenic/likely pathogenic variants, and the top 10 prioritised variants from Exomiser. Mitochondrial DNA variants were called using an in-house pipeline and compared with a list of pathogenic variants. Copy number variants and short tandem repeats for 13 neurological disorders were also analysed. American College of Medical Genetics guidelines were followed for classification of variants. MAIN OUTCOME MEASURE: Definite or probable genetic diagnosis. RESULTS: A definite or probable genetic diagnosis was identified in 98/319 (31%) families, with an additional 6 (2%) possible diagnoses. Fourteen of the diagnoses (4% of the 319 families) explained only part of the clinical features. A total of 95 different genes were implicated. Of 104 families given a diagnosis, 39 (38%) had a mitochondrial diagnosis and 65 (63%) had a non-mitochondrial diagnosis. CONCLUSION: Whole genome sequencing is a useful diagnostic test in patients with suspected mitochondrial disorders, yielding a diagnosis in a further 31% after exclusion of common causes. Most diagnoses were non-mitochondrial disorders and included developmental disorders with intellectual disability, epileptic encephalopathies, other metabolic disorders, cardiomyopathies, and leukodystrophies. These would have been missed if a targeted approach was taken, and some have specific treatments.

Genetic Testing/methods , Mitochondrial Diseases/diagnosis , Mitochondrial Diseases/genetics , Whole Genome Sequencing , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , DNA, Mitochondrial/genetics , Female , Follow-Up Studies , Genetic Markers , Humans , Infant , Infant, Newborn , Male , Middle Aged , Mutation , Phenotype , Young Adult
Zhonghua Yi Xue Za Zhi ; 101(42): 3501-3505, 2021 Nov 16.
Article Zh | MEDLINE | ID: mdl-34775709

Objective: To investigate the relationship between V444A mutation of the ABCB11 gene and primary intrahepatic stone (PIS). Methods: A total of 164 patients (including 91 males and 73 females, with an average age of (46.0±13.0) years) with PIS and 164 healthy (including 99 males and 65 females, with an average age of (43.8±16.7) years) volunteers were enrolled in this case-control study between October 2017 and June 2019. TaqMan-MGB was used for detecting the V444A polymorphism site of the ABCB11 gene. All the genotypes and allele frequencies were calculated. Pearson chi-squared test was performed to detect the differences in allele and genotype distribution between the two groups. Logistic regression analysis was used to identify genotypes associated with PIS. Results: There was no significant difference in age and gender between the two groups(both P>0.05). The distributions of V444A allele and genotype accorded with Hardy-Weinberg equilibrium law (P=0.161), which indicated that the selected control group represented statistically acceptable sample. Two alleles of T and C, and three genotypes of TT, TC and CC were detected in the locus of V444A. The T and C allele frequencies in the PIS group and the control group were 28.4% vs 35.4%, and 71.6% vs 64.6%, respectively. The frequencies of the T and C alleles were not different between the two groups (P=0.054). The frequencies of TT, TC and CC genotypes in the two groups were 5.5%, 45.7%, 48.8%, and 14.6%, 41.5%, 43.9%, respectively, with significant difference between the two groups (P=0.023). Logistic regression analysis revealed the V444A polymorphism (TC heterozygous mutation) was associated with PIS. Conclusion: ABCB11 gene polymorphism at the site of V444A may be related to the susceptibility of PIS.

Polymorphism, Genetic , Polymorphism, Single Nucleotide , ATP Binding Cassette Transporter, Subfamily B, Member 11 , Adult , Alleles , Case-Control Studies , Female , Gene Frequency , Genetic Predisposition to Disease , Genotype , Humans , Male , Middle Aged , Mutation
ACS Chem Neurosci ; 12(22): 4361-4366, 2021 11 17.
Article En | MEDLINE | ID: mdl-34735109

Research on misfolding of tau proteins will help to better understand the formation process of neurofibrillary tangles, a hallmark of Alzheimer's disease. Mutation and histidine tautomeric effects have been considered the two most important inherent factors for tau protein misfolding. In current research, replica-exchange molecular dynamics (REMD) were performed to characterize the structural properties of the key fragment R3 of tau protein under the collective effects of P332L mutation and histidine tautomerism. Simulation results suggest that though the content ß-sheet of P332L R3 εδ isomer is slightly lower than that of the WT P332L R3 fragment, the total stable secondary structures including ß-sheet and helix of P332L R3 isomers are generally more prevalent than those of wild type R3, which may be the reason that P332L R3 has a higher aggregation tendency. Further analysis showed that the hydrogen bond networks are affected by the mutation and histidine tautomerism. Furthermore, the interactions between N-terminus and C-terminus play a crucial role in ß-hairpin formation in all isomers. The current study will contribute to revealing the collective effects of P332L and histidine tautomerism on the misfolding of tau proteins.

Alzheimer Disease , tau Proteins , Alzheimer Disease/genetics , Histidine/genetics , Humans , Mutation/genetics , Neurofibrillary Tangles/metabolism , Protein Conformation, beta-Strand , tau Proteins/genetics , tau Proteins/metabolism
J Int AIDS Soc ; 24(11): e25833, 2021 11.
Article En | MEDLINE | ID: mdl-34762770

INTRODUCTION: A potential concern with the use of dapivirine (DPV) for HIV prevention is the selection of a drug-resistant virus that could spread and reduce the effectiveness of non-nucleoside reverse transcriptase (NNRTI)-based first-line antiretroviral therapy. We evaluated HIV-1 seroconversions in MTN-020/ASPIRE for selection of drug resistance and evaluated the genetic basis for observed reductions in susceptibility to DPV. METHODS: MTN-020/ASPIRE was a placebo-controlled, Phase III safety and effectiveness study of DPV ring for HIV-1 prevention conducted at 15 sites in South Africa, Zimbabwe, Malawi and Uganda between 2012 and 2015. Plasma from individuals who seroconverted in ASPIRE was analysed for HIV-1 drug resistance using both population Sanger sequencing and next-generation sequencing (NGS) with unique molecular identifiers to report mutations at ≥1% frequency. DPV susceptibility of plasma-derived recombinant HIV-1 containing bulk-cloned full-length reverse transcriptase sequences from MTN-020/ASPIRE seroconversions was determined in TZM-bl cells. Statistical significance was calculated using the Fisher's exact test. RESULTS: Plasma from all 168 HIV seroconversions were successfully tested by Sanger sequencing; 57 of 71 DPV arm and 82 of 97 placebo (PLB) arm participants had NGS results at 1% sensitivity. Overall, 18/168 (11%) had NNRTI mutations including K101E, K103N/S, V106M, V108I, E138A/G, V179D/I/T and H221Y. Five samples from both arms had low-frequency NNRTI mutations that were not detected by Sanger sequencing. The frequency of NNRTI mutations from the DPV arm (11%) was not different from the PLB arm (10%; p = 0.80). The E138A mutation was detected in both the DPV (3 of 71 [4.2%]) and PLB arm (5 of 97 [5.2%]) and conferred modest reductions in DPV susceptibility in some reverse transcriptase backgrounds but not others. CONCLUSIONS: HIV-1 drug resistance including NNRTI resistance did not differ between the DPV and placebo arms of the MTN-020/ASPIRE study, indicating that drug resistance was not preferentially acquired or selected by the DPV ring and that the preventive benefit of DPV ring outweighs resistance risk.

Anti-HIV Agents , HIV Infections , HIV Seropositivity , HIV-1 , Anti-HIV Agents/pharmacology , Anti-HIV Agents/therapeutic use , Drug Resistance, Viral/genetics , HIV Infections/drug therapy , HIV Reverse Transcriptase/genetics , HIV Reverse Transcriptase/pharmacology , HIV Reverse Transcriptase/therapeutic use , HIV Seropositivity/drug therapy , HIV-1/genetics , Humans , Mutation , Pyrimidines , Reverse Transcriptase Inhibitors/therapeutic use
BMC Med ; 19(1): 269, 2021 11 17.
Article En | MEDLINE | ID: mdl-34784919

BACKGROUND: There is no consensus regarding the clinical target volume (CTV) margins in radiotherapy for glioma. In this study, we aimed to perform a complete macropathologic analysis examining microscopic tumor extension (ME) to more accurately define the CTV in glioma. METHODS: Thirty-eight supra-total resection specimens of glioma patients were examined on histologic sections. The ME distance, defined as the maximum linear distance from the tumor border to the invasive tumor cells, was measured at each section. We defined the CTV based on the relationships between ME distance and clinicopathologic features. RESULTS: Between February 2016 and July 2020, a total of 814 slides were examined, corresponding to 162 slides for low-grade glioma (LGG) and 652 slides for high-grade glioma (HGG). The ME value was 0.69 ± 0.43 cm for LGG and 1.29 ± 0.54 cm for HGG (P < 0.001). After multivariate analysis, tumor grade, O6-methylguanine-DNA-methyltransferase promoter methylated status (MGMTm), isocitrate dehydrogenase wild-type status (IDHwt), and 1p/19q non-co-deleted status (non-codel) were positively correlated with ME distance (all P < 0.05). We defined the CTV of glioma based on tumor grade. To take into account approximately 95% of the ME, a margin of 1.00 cm, 1.50 cm, and 2.00 cm were chosen for grade II, grade III, and grade IV glioma, respectively. Paired analysis of molecularly defined patients confirmed that tumors that had all three molecular alterations (i.e., MGMTm/IDHwt/non-codel) were the most aggressive subgroups (all P < 0.05). For these patients, the margin could be up to 1.50 cm, 2.00 cm, and 2.50 cm for grade II, grade III, and grade IV glioma, respectively, to cover the subclinical lesions in 95% of cases. CONCLUSIONS: The ME was different between the grades of gliomas. It may be reasonable to recommend 1.00 cm, 1.50 cm, and 2.00 cm CTV margins for grade II, grade III, and grade IV glioma, respectively. Considering the highly aggressive nature of MGMTm/IDHwt/non-codel tumors, for these patients, the margin could be further expanded by 0.5 cm. These recommendations would encompass microscopic disease extension in 95% of cases. TRIAL REGISTRATION: The trial was registered with Chinese Clinical Trial Registry ( ChiCTR2100049376 ).

Brain Neoplasms , Glioma , Brain Neoplasms/genetics , Brain Neoplasms/radiotherapy , Glioma/genetics , Glioma/radiotherapy , Humans , Isocitrate Dehydrogenase/genetics , Mutation
J Coll Physicians Surg Pak ; 31(12): 1494-1496, 2021 Dec.
Article En | MEDLINE | ID: mdl-34794294

Spinal muscular atrophy (SMA) with respiratory distress type 1 (SMARD1) is an exceptionally rare type of SMA. It results from disintegration of alpha motor neurons of the spinal cord. Clinically, children affected with this disorder present between the age of six weeks to six months with respiratory distress and hypotonia. Most of the children die before the age of 13 months. Here, we report a new variant in a female infant with SMARD1 having a novel IGHMBP2 gene mutation. Despite supportive treatment, she died at the age of 5 months in hospital. To the best of our knowledge, the variant has not been described in the literature so far. Key Words:  Spinal muscular atrophy with respiratory distress type-1 (SMARD1), Hypotonia, respiratory distress, infants.

Muscular Atrophy, Spinal , Respiratory Distress Syndrome, Newborn , DNA-Binding Proteins/genetics , Female , Humans , Infant , Muscular Atrophy, Spinal/genetics , Mutation , Respiratory Distress Syndrome, Newborn/genetics , Transcription Factors/genetics
BMC Genomics ; 22(1): 844, 2021 Nov 22.
Article En | MEDLINE | ID: mdl-34802420

BACKGROUND: Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatment. However, a development in the molecular field through Whole-genome sequencing (WGS) can be used as a solution in detecting mutations associated with TB- drugs. This investigation intended to implement this data for supporting the scientific community in deeply understanding any TB epidemiology and evolution in Papua along with detecting any mutations in genes associated with TB-Drugs. RESULT: A whole-genome sequencing was performed on the random samples from TB Referral Laboratory in Papua utilizing MiSeq 600 cycle Reagent Kit (V3). Furthermore, TBProfiler was used for genome analysis, RAST Server was employed for annotation, while Gview server was applied for BLAST genome mapping and a Microscope server was implemented for Regions of Genomic Plasticity (RGP). The largest genome of M. tuberculosis obtained was at the size of 4,396,040 bp with subsystems number at 309 and the number of coding sequences at 4326. One sample (TB751) contained one RGP. The drug resistance analysis revealed that several mutations associated with TB-drug resistance existed. In details, mutations of rpoB gene which were identified as S450L, D435Y, H445Y, L430P, and Q432K had caused the reduced effectiveness of rifampicin; while the mutases in katG (S315T), kasA (312S), inhA (I21V), and Rv1482c-fabG1 (C-15 T) genes had contributed to the resistance in isoniazid. In streptomycin, the resistance was triggered by the mutations in rpsL (K43R) and rrs (A514C, A514T) genes, and, in Amikacin, its resistance was led by mutations in rrs (A514C) gene. Additionally, in Ethambutol and Pyrazinamide, their reduced effectiveness was provoked by embB gene mutases (M306L, M306V, D1024N) and pncA (W119R). CONCLUSIONS: The results from whole-genome sequencing of TB clinical sample in Papua, Indonesia could contribute to the surveillance of TB-drug resistance. In the drug resistance profile, there were 15 Multi Drugs Resistance (MDR) samples. However, Extensively Drug-resistant (XDR) samples have not been found, but samples were resistant to only Amikacin, a second-line drug.

Mycobacterium tuberculosis , Pharmaceutical Preparations , Tuberculosis, Multidrug-Resistant , Antitubercular Agents/pharmacology , Antitubercular Agents/therapeutic use , Bacterial Proteins/genetics , Drug Resistance, Multiple, Bacterial , Humans , Indonesia , Microbial Sensitivity Tests , Mutation , Mycobacterium tuberculosis/genetics , Tuberculosis, Multidrug-Resistant/drug therapy , Tuberculosis, Multidrug-Resistant/epidemiology , Tuberculosis, Multidrug-Resistant/genetics
Pestic Biochem Physiol ; 179: 104969, 2021 Nov.
Article En | MEDLINE | ID: mdl-34802519

Carboxylesterases (CarEs) usually play critical roles in the detoxification of toxic chemicals and therefore may be involved in insecticide resistance in agricultural pests. Previous work has shown that CarE 001C from Helicoverpa armigera was able to metabolize the isomers of cypermethrin and fenvalerate. In this study, seven mutants of CarE 001C with single amino acid substitution were produced and expressed in the Escherichia coli. Enzyme kinetic analysis indicated that all seven mutations dramatically reduced enzymatic activities toward the generic substrate α-naphthyl acetate, but in vitro metabolism assay showed that two of the mutations, H423I and R322L, significantly improved hydrolase activities toward fenvalerate, with their recorded specific activities being 3.5 and 5.1 nM·s-1·mg -1 proteins, respectively. Further, thermostability assay showed that the stability of one mutant enzyme was enhanced. This study will help us better understand the potential of CarEs in insecticide detoxification and resistance in H. armigera.

Insecticides , Moths , Pyrethrins , Animals , Carboxylesterase/genetics , Carboxylesterase/metabolism , Carboxylic Ester Hydrolases/genetics , Insecticide Resistance/genetics , Insecticides/pharmacology , Kinetics , Moths/genetics , Moths/metabolism , Mutation , Nitriles
Pestic Biochem Physiol ; 179: 104956, 2021 Nov.
Article En | MEDLINE | ID: mdl-34802535

Green foxtail [Setaria viridis (L.) P.Beauv.] is a troublesome grass weed that is widely distributed in maize (Zea mays L.) fields across China. Many populations of S. viridis have evolved resistance to the acetolactate synthase (ALS)-inhibiting herbicide nicosulfuron. The objectives of this research were to confirm nicosulfuron resistance in these populations and to investigate the basis of nicosulfuron resistance. Whole-plant dose-response experiments showed 6 out of 13 S. viridis populations were highly resistance (20-30 times) to nicosulfuron. Sequencing of the ALS gene revealed two amino acid mutations, Asp-376-Glu and Pro-197-Ala, in the nicosulfuron-resistant populations. A malathion pretreatment study revealed that the R376 and R197 subpopulations might have cytochrome P450s-mediated herbicide metabolic resistance. The resistant populations were cross-resistant to imazethapyr but sensitive to topramezone and quizalofop-p-ethyl. This is the first report of resistance to ALS inhibitors conferred by target site mutations (Asp-376-Glu or Pro-197-Ser) and possible cytochrome P450s-involved metabolism in S. viridis.

Acetolactate Synthase , Herbicides , Setaria Plant , Acetolactate Synthase/genetics , Cytochrome P-450 Enzyme System/genetics , Herbicide Resistance/genetics , Herbicides/pharmacology , Mutation , Pyridines , Sulfonylurea Compounds
World J Surg Oncol ; 19(1): 330, 2021 Nov 18.
Article En | MEDLINE | ID: mdl-34794435

BACKGROUND: HER2 is a member of the ERBB family of receptor tyrosine kinases, and HER2 mutations occur in 1-4% of non-small cell lung cancer (NSCLC) as an oncogenic driver mutation. We found a rare mutation of HER2 p.Asp769Tyr in NSCLC. CASE PRESENTATION: We presented a case of a 68-year-old nonsmoking male patient with brain metastasis from lung adenocarcinoma harboring a rare mutation of HER2 p.Asp769Tyr. After multiple lines of treatment, he obtained a durable response (10 months) to afatinib and anlotinib. CONCLUSION: We reported for the first time that afatinib and anlotinib have successfully treated lung adenocarcinoma with HER2 p.Asp769Tyr mutation. This finding can provide an insight into the optimal treatment of lung adenocarcinoma patients with novel mutations. Additionally, we summarized the efficacy of targeted therapy for HER2 mutant lung cancer in this article.

Adenocarcinoma of Lung , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/genetics , Afatinib/therapeutic use , Aged , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Humans , Indoles , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Male , Mutation , Prognosis , Protein Kinase Inhibitors , Quinolines , Receptor, ErbB-2/genetics