HLA-DQA1*04:01 is related to a higher multiple sclerosis lesion load on T2/Flair MRI sequences

ABSTRACT Background: The genetic predisposition to multiple sclerosis (MS) is associated with HLA alleles, especially HLA-DRB1*15:01. Objective: To identify associations between findings in magnetic resonance imaging (MRI) and genetic features in a Brazilian cohort of patients with MS. Methods: We retrospectively studied data from 95 consecutive patients with MS. Two independent observers who were blinded to the clinical data identified black holes and enhanced lesions on T1 MRI sequences, and counted and measured contrast-enhanced lesions on T2 and Flair (fluid attenuation inversion recovery) sequences. Cases were classified according to lesion size, number, and volume. The HLA-DRB1, HLA-DQB1, and HLA-DQA1 alleles, and the rs4774, rs3087456, rs6897932, rs731236, and rs1033182 single nucleotide polymorphisms were identified by polymerase chain reaction amplification with sequence-specific primers using the One Lambda Inc. Kit, Canoga Park, CA, USA. Results: Patients with the HLA-DQA1*04:01 allele had lesion load (adjusted for age, sex, and MS duration) above median compared with patients with other HLA-DQA1 alleles (p=0.02). There were no differences among all the other HLA alleles and single nucleotide polymorphisms and lesion load. Conclusions: The correlation of the HLA-DQA1*04:01 allele with a higher lesion load on T2/Flair MRI sequences suggests that the presence of this allele is associated with the risk of greater MS severity.

New Delhi metallo-β-lactamase-1 among Escherichia coli strains isolated from leukemia patients in Iran: two case reports

Background Escherichia coli has appeared as an important opportunistic pathogen responsible for nosocomial infections in patients with immunodeficiency, particularly in leukemia patients. New Delhi metallo-beta-lactamase is an enzyme originally found in Enterobacteriaceae. Case presentation In this study, 80 isolates of Escherichia coli and Klebsiella pneumoniae were collected over the course of 2 years from two medical centers in Tehran, Iran. Production of carbapenemase was detected in the isolates using modified Hodge test. New Delhi metallo-beta-lactamase-1 genes were detected by polymerase chain reaction amplification with specific primers. Two New Delhi metallo-beta-lactamase-1-producing Escherichia coli strains were isolated from two Iranian patients with leukemia. These two patients were 6 and 15 years old, one female and the other male, from two oncology centers in Iran. The isolates were resistant to carbapenems (imipenem, meropenem), and two isolates were positive for carbapenemase production by modified Hodge test. Conclusions The emergence of New Delhi metallo-beta-lactamase-1-producing Escherichia coli is a threat for leukemia patients in oncology and hematology departments. We conclude that the incidence of multidrug resistant pathogens has increased among patients with leukemia and is life threatening.

Bioinformatics analysis of tumor-educated platelet microRNAs in patients with hepatocellular carcinoma

Background: Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies that seriously threaten global health. The primary reason for its grim prognosis is the lack of sensitive tools for early diagnosis. The purpose of this study was to apply bioinformatics analysis to explore tumor-educated platelet miRNA expression and its potential diagnostic utility in HCC. Methods:Twenty-five HCC patients and 25 healthy controls were included. RNA sequencing was utilized to screen microRNA alterations in platelets derived from HCC patients (n=5) and controls (n=5). Gene set enrichment analysis was performed to analyze the targeted mRNAs of differentially expressed miRNAs by using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases, aiming at main functions and pathways, respectively. We then verified the selected platelet microRNAs in another cohort by quantitative reverse transcription-polymerase chain reaction amplification (qRT-PCR). Results: A total of 250 differentially expressed microRNAs were identified, among which 111 were down-regulated and 139 were up-regulated. The functional enrichment analysis of differentially expressed miRNAs suggested that their target genes were involved primarily in pathways related to HCC. Expression levels of miR-495-3p and miR-1293 were further validated by qRT-PCR, which yielded results consistent with the sequencing analysis. The area under the receiver operating characteristic curve of miR-495-3p and miR-1293 as diagnostic tests for HCC were 0.76 and 0.78, respectively. Conclusion: Tumor-educated platelet microRNAs such as miR-495-3p and miR-1293 were differentially expressed in HCC patients, and may be involved in the pathophysiology of HCC.

Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay

Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT and the effect of inhibitors, utilizing the methylation-sensitive B-Z transition of DNA without bisulfite conversion, methylation-sensing proteins, and polymerase chain reaction amplification. With the high sensitivity of single-molecule FRET, this method detects the event of DNA methylation in a single DNA molecule and circumvents the need for amplification steps, permitting direct interpretation. This method also responds to hemi-methylated DNA. Dispensing with methylation-sensitive nucleases, this method preserves the molecular integrity and methylation state of target molecules. Sparing methylation-sensing nucleases and antibodies helps to avoid errors introduced by the antibody’s incomplete specificity or variable activity of nucleases. With this new method, we demonstrated the inhibitory effect of several natural bio-active compounds on DMT. All taken together, our method offers quantitative assays for DMT and DMT-related anticancer drugs.

Prevalence of Lewis Blood Group Polymorphisms in Southern Thai Blood Donors

Objective: To determine the frequencies of five of the most common (59T>G, 202T>C, 314C>T, 508G>A and 1067T>G) single nucleotide polymorphisms (SNPs) of the FUT3 gene in Thai blood donors and examine their associations with the presence or absence of Lewis antigens on red blood cells.Material and Methods: A total of 364 donor specimens from Songklanagarind Hospital and Regional Blood Centre XII Songkhla, Thailand, were recruited for the study. Molecular analysis of each SNP was performed by polymerase chain reaction amplification with sequence-specific primers (PCR-SSP). The Lewis phenotype was investigated in 159 individuals using the standard hemagglutination test.Results: The frequencies of the SNPs were 32.0% (59T>G), 46.6% (202T>C), 21.7% (314C>T), 37.9% (508G>A), and 25.0% (1067T>A). The prevalences of the Lewis phenotype were 61.0% for Le(a-b+), 7.6% for Le(a+b-), 11.3% for Le(a+b+), and 20.1% for Le(a-b-). The Lewis-negative phenotype was significantly associated with homozygosity in 59T>G and 1067T>A (χ2 =49.873, and χ2 =44.520, respectively).Conclusion: Our findings suggest that le59,1067 is largely responsible for the Lewis-negative phenotype in our southern Thai population. Genetic variations in FUT3 polymorphisms may be used as molecular markers for ethnicity and to help understand the roles of the Lewis blood group in infections or clinical diseases.

Successful recovery from COVID-19 pneumonia with awake early self-proning

Background Since COVID-19 global pandemic, “early awake proning in non-intubated patients with COVID-19” has been suggested as anecdotal evidence. Hereby, we report an awake and non-intubated patient with COVID-19 pneumonia who was successfully managed with early self-proning. Case presentation A 68-year-old male presented to the emergency department with a respiratory distress. He was non-smoker and denied any significant past medical history. His chest computed tomography scan showed “ground glass opacities” and “consolidation areas” located especially in the peripheral sites of both lungs which were consistent with a coronavirus pneumonia and reverse transcription polymerase chain reaction amplification by a nasopharyngeal swab sample for SARS-Cov-2 was also positive. His initial therapy with hdroxychloroquine and favipiravir was started. Due to deterioration of the patient’s oxygenation, he was transferred to the intensive care unit for further treatment with non-invasive mechanical ventilation on supine position and intermittent “awake early self-proning positioning” was applied. Additionally, antibiotherapy, anticoagulant therapy, and convalescent plasma therapy were also administered to the patient. On the 17th day of the ICU admission, he was transferred back to the ward. And the patient was discharged from the hospital on the 19th day of his initial admission. Conclusions Although some case reports and small case series initially noted potential improvement in oxygenation by awake proning, further research is required to evaluate the exact benefits and proper applications of prone positioning in awake patients with COVID-19 pneumonia.

Rat bite fever due to Streptobacillus notomytis complicated by meningitis and spondylodiscitis: a case report

Background Only three other cases of rat bite fever caused by Streptobacillus notomytis in humans have been reported since this species was identified in 2015. Data specific to the differences in clinical features and geographic distribution between S. notomytis infection and S. moniliformis infection are scarce. All previous cases of human S. notomytis infection were reported from Japan. This is the first case of S. notomytis infection reported from outside of Japan. Case presentation A 72-year-old Thai woman was admitted to Siriraj Hospital (Bangkok, Thailand)—Thailand’s largest university-based national tertiary referral center—in August 2020 with fever, myalgia, and polyarthralgia for 3 days, and gradually decreased consciousness for the past 1 day. Physical examination and laboratory investigations revealed septic arthritis of both knee joints, meningitis, and hepatitis. She was initially misdiagnosed as rheumatoid arthritis in the elderly since the initial investigations were unable to detect a causative pathogen. However, S. notomytis infection was later confirmed by polymerase chain reaction amplification of a part of the 16S rRNA gene and sequencing from synovial fluid. Her clinical course was also complicated by spondylodiscitis and epidural abscess caused by S. notomytis, which was detected from tissue biopsy. Therefore, rat bite fever in this patient manifested as meningitis, septic polyarthritis, hepatitis, and spondylodiscitis. The patient was treated with intravenous ceftriaxone then switched to oral amoxicillin with complete recovery. Conclusions The clinical manifestations of S. notomytis infection are similar to those demonstrated in S. moniliformis infection. This case also showed that arthritis caused by S. notomytis mimics rheumatoid arthritis, and that meningitis and spondylodiscitis are potential coexisting complications that can be found in S. notomytis infection.

Interaction effects between variants in TOMM40 and PVRL2 with plasma amyloid-β and Alzheimer's disease among Chinese older adults: a population-based study

Background Emerging evidence has linked TOMM40 and PVRL2 polymorphisms with Alzheimer’s disease (AD). We examined their associations with AD and plasma AD biomarkers and interaction on AD risk among Chinese older adults. Methods This population-based study included 4876 participants (age ≥ 65 years, 57.2% women) from MIND-China. TOMM40(rs2075650) and PVRL2(rs6859) polymorphisms were detected using multiple-polymerase chain reaction amplification. Plasma Aβ40, Aβ42, and t-tau were measured using SIMOA in a subsample (n = 1257). Data was analyzed using multiple logistic and general linear regression models. Results AD was diagnosed in 182 participants. The multi-adjusted odds ratio of AD was 6.24(95%CI 1.73–22.48) for TOMM40GG (vs. AA), 1.47(0.89–2.42) for PVRL2AA (vs. GG), and 12.87(3.97–41.73) for having both risk alleles (Pinteraction=0.0003). In the plasma biomarker subsample, TOMM40GG was significantly associated with lower plasma Aβ42 and the Aβ42-to-Aβ40 ratio (p < 0.05). Conclusions TOMM40 and PVRL2 genes could interact to substantially increase the likelihood of AD, possibly through influencing Aβ metabolism.

Molecular diversity of Uzbekistan’s fishes assessed with DNA barcoding

Uzbekistan is one of two doubly landlocked countries in the world, where all rivers are endorheic basins. Although fish diversity is relatively poor in Uzbekistan, the fish fauna of the region has not yet been fully studied. The aim of this study was to establish a reliable barcoding reference database for fish in Uzbekistan. A total of 666 specimens, belonging to 59 species within 39 genera, 17 families, and 9 orders, were subjected to polymerase chain reaction amplification in the barcode region and sequenced. The length of the 666 barcodes was 682 bp. The average K2P distances within species, genera, and families were 0.22%, 6.33%, and 16.46%, respectively. The average interspecific distance was approximately 28.8 times higher than the mean intraspecific distance. The Barcode Index Number (BIN) discordance report showed that 666 specimens represented 55 BINs, of which five were singletons, 45 were taxonomically concordant, and five were taxonomically discordant. The barcode gap analysis demonstrated that 89.3% of the fish species examined could be discriminated by DNA barcoding. These results provide new insights into fish diversity in the inland waters of Uzbekistan and can provide a basis for the development of further studies on fish fauna.

Novel TNC-PDGFD fusion in fibrosarcomatous dermatofibrosarcoma protuberans: a case report

Background Dermatofibrosarcoma protuberans (DFSP) is a superficial fibroblastic tumor characterized by high rate of local recurrence and low metastatic potential. Fibrosarcomatous transformation can rarely arise in DFSP either de novo or as recurrent, which represents a form of tumor progression and carries an increased risk of metastasis over classic DFSP. Cytogenetically, DFSP is characterized by a recurrent unbalanced chromosome translocation t (17;22)(q22;q13), leading to the formation of COL1A1-PDGFB fusion transcript that is present in more than 90% of cases. Alternative fusions involving the PDGFD with partners of COL6A3 or EMILIN2 have recently been documented in less than 2% of cases. Herein, we report a DFSP with fibrosarcomtous morphology harboring a novel TNC-PDGFD fusion. Case presentation A 54-year-old female presented with a slowly growing mass in the right thigh. Excision demonstrated a 2-cm ovoid, well-circumscribed, gray-white, mass. Microscopic examination revealed a partially encapsulated subcutaneous nodule without dermal connection. The neoplasm was composed of cellular and fairly uniform spindle cells with brisk mitoses, arranged in elongated fascicles and herringbone patterns, with focal collagenized stroma. The neoplastic cells were positive for CD34 and smooth muscle actin. Fluorescence in-situ hybridization analyses showed negative for COL1A1-PDGFB fusion as well as NTRK1/2/3 rearrangements. A subsequent RNA sequencing detected an in-frame fusion between exon 15 of TNC and exon 6 of PDGFD. This fusion was further confirmed by nested reverse transcription polymerase chain reaction amplification followed by Sanger sequencing. A diagnosis of fibrosarcomatous DFSP was rendered and the patient was in good status at a follow-up of 12 months after the operation. Conclusions We report a fibrosarcomatous DFSP with novel TNC-PDGFD fusion, which adds to the pathologic and genetic spectrum of PDGFD-rearranged DFSP.