Molecular Genetic Characterization Research Articles

Biphasic squamoid alveolar papillary renal cell carcinoma: A unique papillary renal cell carcinoma with distinctive morphology, immunophenotype and molecular genetic features.

Biphasic squamoid alveolar papillary renal cell carcinoma (BSARCC) is a recently described renal tumor, considered as a unique rare morphological pattern of PRCC in the 2022 WHO classification. We aimed to further explore the clinicopathological, immunophenotypic, and molecular genetic characteristics of BSARCC in a Chinese cohort. The clinicopathological data of 8 patients with BSARCC were collected for morphology observation and immunohistochemical staining. QRT-PCR was performed to detect BRAF gene mutation. The abnormalities of chromosomes 7, 17 and Y, and CCND1 gene were investigated by fluorescence in situ hybridization (FISH). Among the 8 cases, 5 were males and 3 were females. 6 cases were revealed by physical examination incidentally, and 2 cases were presented with low back pain and hematuria. Microscopically, the tumors were mainly composed of small cells with different proportions of large cells. The small cells were arranged in acinar, compact and long narrow tubular, solid sheet or papillary structures. Single or clustered large cells were arranged in glomerular structures in the acinar cavity formed by small cells. Among the 8 cases, 2 cases had a small amount of typical type I papillary renal cell carcinoma without large cells at the edge of the tumor. And 5 cases presented the swallowing phenomenon of lymphocytes or neutrophils in the cytoplasm of a few large cells. Immunohistochemical staining showed both large and small cells were diffusely and strongly positive for CK7, P504s, EMA, and vimentin. MET was expressed in most tumors (6/8), and large cells (70-90%) exhibited a prominent higher positive rate than small cells (20-90%). CD57 was positive in both large and small cells in 5 cases. Notably, CyclinD1 was exclusively expressed in large cells, while RCC marker was mainly expressed in small cells. Large cells showed a higher ki67 index than small cells. BRAF V600E mutation was negative in all cases. FISH showed 4 cases had chromosome 7 trisomy, 2 cases had chromosome 17 trisomy, and 4 of 5 male patients had Y chromosome deletion. CCND1 gene amplification or rearrangement was not revealed in any case. Follow-up data were available in 8 cases ranging from 3 to 66 months, and there was no recurrence or metastasis of the tumor. BSARCC is a rare unique morphological pattern of papillary renal cell carcinoma, featured by the presence of two cell populations of different morphology and immunophenotype. Distinctive CyclinD1 and RCC immunostainings are essential in diagnosing this type of renal tumor. Large and small cells may be tumor cells in different stages of proliferation and differentiation, and large cells immunoreactive to CyclinD1 and presenting higher ki67 index might be more aggressive than small cells. The anomalous expression of CyclinD1 in large cells is not due to the aberrance of CCND1 gene itself. Most BSARCC is low-stage and inert with a favorable prognosis. Our study not only validates previously described clinicopathological features, but also supplements the clinicopathological features and expands the potential genetic alterations and available clinical outcome data of BSARCC.

189P LncRNA NKILA as a negative regulator of NFkB in ascites in ovarian cancer

NF-κB-interacting LncRNA (NKILA) plays an inhibitory role in the NF-κB pathway, which is a key regulator of inflammatory cytokines. These mediators, freely floating in ascitic fluid (AF), reflecting the molecular genetic characteristics of tumor cells in ovarian cancer (OC), and associated with epigenetic switches of key pathways of carcinogenesis remain poorly understood. The aim of the work was to study the expression of LncRNA NKILA and marker cytokines of the NF-kB pathway in ascites of patients with OC.

English

Fonio (Digitaria exilis [Kippist] Stapf) species is from Africa. In Burkina Faso, the genetic diversity of fonio is little known. It is the same for its mode of management and the understanding of its culture. The objective of this study is to contribute to a better knowledge of fonio grown in Burkina Faso. Prospecting collects a permit to identify production areas and collect 60 accessions. The ethnobotanical survey made it possible to collect endogenous knowledge relating to the plant. Fourteen ethnic groups were encountered in 231 people surveyed. Both explained and unexplained vernacular names have been observed. Fonio is a plant of great importance for populations in terms of food and is part of the cultural identity of several ethnic groups. It is also a source of income for the local populations. A gradual abandonment (35.30% of respondents) of its cultivation has been observed because of the painful post-harvest transformation process. The endogenous knowledge collected within the local population will serve as a guide for the valuation of the species. The required accessions will be used for other studies such as agromorphological, biochemical and molecular genetic characterization to better identify its diversity, conserve it and better enhance the species. Key words: Fonio, genetic diversity, indigenous knowledge, Burkina Faso, postharvest quality, shelf life.

Distribution and Current State of Molecular Genetic Characterization in Pathogenic Free-Living Amoebae.

Free-living amoebae (FLA) are protozoa widely distributed in the environment, found in a great diversity of terrestrial biomes. Some genera of FLA are linked to human infections. The genus Acanthamoeba is currently classified into 23 genotypes (T1-T23), and of these some (T1, T2, T4, T5, T10, T12, and T18) are known to be capable of causing granulomatous amoebic encephalitis (GAE) mainly in immunocompromised patients while other genotypes (T2, T3, T4, T5, T6, T10, T11, T12, and T15) cause Acanthamoeba keratitis mainly in otherwise healthy patients. Meanwhile, Naegleria fowleri is the causative agent of an acute infection called primary amoebic meningoencephalitis (PAM), while Balamuthia mandrillaris, like some Acanthamoeba genotypes, causes GAE, differing from the latter in the description of numerous cases in patients immunocompetent. Finally, other FLA related to the pathologies mentioned above have been reported; Sappinia sp. is responsible for one case of amoebic encephalitis; Vermamoeba vermiformis has been found in cases of ocular damage, and its extraordinary capacity as endocytobiont for microorganisms of public health importance such as Legionella pneumophila, Bacillus anthracis, and Pseudomonas aeruginosa, among others. This review addressed issues related to epidemiology, updating their geographic distribution and cases reported in recent years for pathogenic FLA.

Attenuated African swine fever virus through serial passaging of viruses in cell culture: a brief review on the knowledge gathered during 60 years of research.

African swine fever virus (ASFV) is a highly pathogenic double-stranded DNA virus. It affects various breeds of pigs, causing serious economic losses and health threats because of its rapid spread and high pathogenicity and infectivity. This situation is not helped by the lack of a validated vaccine or effective therapies. Since the 1960s, different strains of ASFV have been subjected to serial passage in a variety of cell lines. The attenuated ASFV strains obtained through serial passage are not only candidates for ASF vaccine research, but also are useful to study the molecular genetic characteristics and pathogenic mechanism of the virus. This review summarizes related studies on the attenuated strains of ASFV acquired through cell passage over the last 60 years, with the aim of providing inspiration for the rational design of vaccines in future.

Molecular epidemiology and genetic characterization of Clostridium perfringens infections in lambs

Clostridium perfringens is gram positive bacterium, wide spread in environment causing various diseases in animals and human. The current study was conducted to indentify the genetic identity of C. perfringens isolates from lambs from Egypt. Using specific primers amplifying genes associated to the toxins produced by C. perfringens, multiplex PCR was used to confirm C. perfringens in 87 out of 140 samples were collected from diseased and suspected lambs. The isolates were classified as type A in 49.4%, type B in 31.1% and type D in 19.5% of isolates. The phylogenetic analysis for the partial sequences of C. perfringens strains based on plc gene, cpb gene and etx gene obtained in the present study showed high degree of similarity with other sequences of C. perfringens strains in GenBank, isolating from sheep from Egypt and other countries. According to the findings, lambs with enterotoxaemia more frequently have C. perfringens type A and an efficient hygienic control program is necessary to reduce the infection spreading among susceptible animals.

Polymorphism of PGR, ERα, CYP1A1, CYP1A2 Genes in Patients with Endometrial Hyperplastic Processes

Цель исследования. Определить частоту полиморфных вариантов генов рецептора эстрогена ERα, прогестерона PGR, цитохрома Р450 (CYP1A1, CYP1A2) у пациенток с гиперпластическими процессами эндометрия.Материалы и методы. Пациенткам проводили молекулярно-генетическое типирование полиморфных вариантов генов, участвующих в метаболизме половых гормонов (ERα 351A>G rs9340799; полиморфный вариант гена PGR, содержащего Alu-инсерцию в интроне G (Progins – аллель T2); CYP1A1 (T264C в 30-некодирующем регионе, rs4646903); CYP1A2 (C734A, rs762551)).Результаты. Основную группу составили 35 (46,67%) пациенток с гиперпластическими процессами эндометрия, 40 (53,33%) женщин с нормальным эндометрием вошли в контрольную группу. Индекс массы тела у пациенток основной группы составил 27 (25,0; 32,2), в группе сравнения – 22 (20,0; 24,0) (p<0,001). У пациенток основной группы отмечена высокая частота ожирения (p=0,001) и избыточной массы тела (p<0,001). При сравнении частоты выявления полиморфных аллелей генов PGR, ERα, CYP1A1, CYP1A2 в группах не выявлено значимых различий. Среди пациенток с гиперпластическими процессами эндометрия и ожирением установлена высокая частота полиморфного аллеля гена PGR Т1/Т2 – 5 (50,00%) (χ2=9,76, p=0,008, ОР 4,50, 95% ДИ 1,888–10,724).Заключение. Полученные результаты свидетельствуют о том, что у обследованных пациенток не выявлена ассоциация изученных полиморфных локусов генов PGR, ERα, CYP1A1, CYP1A2 с гиперпластическими процессами эндометрия. Однако отмечена тенденция к увеличению частоты полиморфных аллелей T1/T2 (PGR), G/A (ERα), для установления значимости которой необходимо изучение большей выборки пациенток. У женщин с гиперпластическими процессами эндометрия и ожирением установлена высокая частота полиморфного аллеля Т1/Т2 гена PGR (p=0,008), что указывает на взаимный вклад ожирения и молекулярно-генетических особенностей гена рецептора прогестерона в патогенез гиперпластических процессов эндометрия у данного контингента пациенток. Purpose of the study. To determine the frequency of polymorphic variants of estrogen ERα and progesterone receptors PGR, cytochromes P450 (CYP1A1, CYP1A2) genes in patients with endometrial hyperplastic processes.Materials and methods.The patients underwent molecular genetic typing of polymorphic variants of genes involved in the metabolism of sex hormones (ERα 351A>G rs9340799; polymorphic variant of the PGR gene containing Alu insertion in intron G (Progins – allele T2); CYP1A1 (T264C in the 30-non-coding region, rs4646903); CYP1A2 (C734A, rs762551)). Results. 35 (46.67%) patients with endometrial hyperplastic processes were included in the study group, 40 (53.33%) women with normal endometrium were included in the comparison group. The body mass index in the patients of the main group was 27 (25.0; 32.2), in the group 22 (20.0; 24.0) (p<0.001). The patients of the study group had a significantly higher incidence of obesity (p=0.001) and overweight (p<0.001). No significant differences of the frequency of detection of polymorphic alleles of the PGR, ERα, CYP1A1, CYP1A2 genes were found. A high frequency of the polymorphic allele of the T1/T2 (PGR) – 5 (50.00%) was established among patients with endometrial hyperplastic processes and obesity (χ2=9.76, p=0.008, RR 4.50, 95% CI 1.888–10.724).Conclusion. The results indicate that there is not association between the studiedpolymorphic loci of the PGR, ERα, CYP1A1, CYP1A2 genes and endometrial hyperplastic processes. However, there is a tendency to increase the frequency of polymorphic alleles T1/T2 PGR, G/A ERα, to establish the significance it is necessary to study a larger sample of patients. In women with endometrial hyperplastic processes and obesity, a high frequency of the polymorphic allele T1/T2 of the PGR gene (p=0.008) was established, which indicates the mutual contribution of obesity and the molecular genetic features of the progesterone receptor gene to the pathogenesis of endometrial hyperplastic processes in this cohort of patients.

Molecular characterization of SARS-CoV-2 from the saliva of patients in the Republic of Korea in 2020.

Background and aimsDespite global vaccination efforts, the number of confirmed cases of coronavirus disease 2019 (COVID‐19) remains high. To overcome the crisis precipitated by the ongoing pandemic, characteristic studies such as virus diagnosis, isolation, and genome analysis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are necessary. Herein, we report the isolation and molecular characterization of SARS‐CoV‐2 from the saliva of patients who had tested positive for COVID‐19 at Proving Ground in Taean County, Republic of Korea, in 2020.MethodsWe analyzed the whole‐genome sequence of SARS‐CoV‐2 isolated from the saliva samples of patients through next‐generation sequencing. We also successfully isolated SARS‐CoV‐2 from the saliva samples of two patients by using cell culture, which was used to study the cytopathic effects and viral replication in Vero E6 cells.ResultsWhole‐genome sequences of the isolates, SARS‐CoV‐2 ADD‐2 and ADD‐4, obtained from saliva were identical, and phylogenetic analysis using Bayesian inference methods showed SARS‐CoV‐2 GH clade (B.1.497) genome‐specific clustering. Typical coronavirus‐like particles, with diameters of 70–120 nm, were observed in the SARS‐CoV‐2 infected Vero E6 cells using transmission electron microscopy.ConclusionIn conclusion, this report provides insights into the molecular diagnosis, isolation, genetic characteristics, and diversity of SARS‐CoV‐2 isolated from the saliva of patients. Further studies are needed to explore and monitor the evolution and characteristics of SARS‐CoV‐2 variants.

RESULTS OF MONITORING THE INCIDENCE OF NON-POLIO ENTEROVIRUS INFECTION IN THE PRE-PANDEMIC AND PANDEMIC PERIODS

The results of monitoring the incidence of non-polio enterovirus infection (EVI) in the pre-pandemic and pandemic periods in the Khanty-Mansiysk Autonomous Okrug (2006-2021) are presented. It was found that the predominant share in the total incidence of EVI was urban population with a predominance of children under 6 years of age and school age. In the period 2020-2021. The low incidence of EVI was due to ongoing anti-epidemic measures against COVID-19 and was accompanied by the spread of enterovirus serotype CVA6, which is able to effectively implement the aspiration mechanism of transmission of the infectious agent and cause respiratory and exanthemic diseases. The spread of CVA6 was influenced by the growth of migration activity of the population, due to the partial lifting of restrictions and an increase in the non-immune stratum of the population due to a decrease in the incidence of EVI in 2020. The results of the study will contribute to the adoption of measures leading to a decrease in the incidence of EVI in the Khanty-Mansiysk Autonomous Okrug, rational planning of preventive measures, by improving the information and diagnostic subsystems of epidemiological surveillance. To solve these tasks, it is necessary to further study the spectrum of enteroviruses circulating on the territory of the Khanty-Mansi Autonomous Okrug, the frequency of their occurrence in subclinical forms of EVI and as etiological agents of enterovirus meningitis, the development of molecular genetic typing techniques using mass parallel high-performance sequencing technology, the study of molecular genetic characteristics. All this will reduce the risks of EVI morbidity in the post-pandemic period and ensure the sanitary and epidemiological well-being of the population and prevent the spread of EVI in the Khanty-Mansi Autonomous Okrug.

Bacillus anthracis strain differentiation based on SNP and VNTR loci.

Bacillus anthracis is the anthrax causative agent. For its epidemiology, it is important not only to identify the etiological agent but also to determine the patterns of its evolution and spread. Modern methods of molecular biology make it possible to detect a number of genetic markers suitable for indicating and differentiating the strains of B. anthracis, including the loci arranged as variable number tandem repeats (VNTRs) and SNPs, one nucleotide-sized differences in the DNA sequence of the loci being compared. The objective of the present study was to examine the effectiveness of SNP analysis and PCR amplif ication of VNTR loci combined with the high-resolution amplicon melting analysis for identif ication and differentiation of the anthrax agent strains. In the study, seven strains of B. anthracis obtained from soil samples and animal carcasses were investigated using vaccine strain STI-1 as a reference. For molecular genetic characterization of these bacteria, analysis of 12 SNPs and variability analysis of eight VNTR loci were carried out. To detect the differences between the strains, their PCR product melting points were measured in the presence of the EvaGreen (Sintol, Russia) intercalating dye. For SNP detection, a PCR assay with double TaqMan probes was applied. It was found that the studied virulent strains, except for B. anthracis No. 1 and 3, could not be attributed to any phylogenetic subgroup of the anthrax agents. The proposed method made it possible to differentiate four out of the seven investigated strains. Strains No. 5–7 had identical SNP and HRM prof iles and, as a result, formed a single cluster. Our investigation has conf irmed that the proposed method can be successfully used for preliminary analysis of an epizootic situation in the case of anthrax.

Updated AWMF Guideline on the Diagnosis and Treatment of Acute Lymphoblastic Leukaemia in Children

Depending on the initial risk factors survival rates of childhood acute lymphoblastic leukemia (ALL) nowadays reach an average of 85%. The successful treatment of this severe disease is based on the development of multi-modal treatment concepts, on the basis of a continuously improving molecular genetic characteri-zation of the disease with the identification of new risk factors. The diagnosis of the response to therapy and the resulting stratification of patients into different therapy strata plays an essential role in this progress. These risk-adapted treatment approaches have minimized therapy-associated complications as well as late effects. In the upcoming years, the goal will be to improve the cure rate of patients with unfavorable prognosis. The development of im-munotherapeutic approaches, which are currently being tested in clinical trials in the con-text of ALL therapy, can play an important role in this context.

Molecular Epidemiology and Genetic Characterization of PCV2 Circulating in Wild Boars in Southwestern Ethiopia.

Porcine circovirus type 2 (PCV2) is one of the most relevant infectious agents affecting domestic pigs. Recently, a surprising PCV2 genetic heterogenicity has been reported in Africa. Nevertheless, the knowledge of the epidemiology of PCV2 in African countries, in both domestic and wild species, is limited and sparse. Having this in mind, in the present study, the PCV2 circulation and its molecular epidemiology in Southwestern Ethiopia have been investigated by collecting 64 samples from domestic pigs, wild boars, and warthogs. PCV2 genome presence was detected and quantified using qPCR and ORF2 sequencing was attempted on positive samples. Ten samples, 8 wild boars, 1 domestic pig, and 1 warthog, tested PCV2 positive. Complete ORF2 sequences were obtained from 5 wild boars; 4 of those were classified as PCV2d and 1 as PCV2b. Both PCV2b and PCV2d were related to strains of Asian origin, most commonly from China. The role of this country in the exportation of PCV2 strains in Ethiopia, and Africa in general, might be supported by the crescent economic relationship between the two continents. The obtained evidence also testifies to the inadequacy and/or poor application of biosecurity measures separating wild and domestic animals. Further, extensive and systematic studies should be performed to more deeply characterize the molecular epidemiology of PCV2 in this region, in order to improve our understanding of these ecological niches in the evolution and dispersal of PCV2.

Molecular genetics and epidemiological characteristics of HIV-1 epidemic strains in various sexual risk behaviour groups in developed Eastern China, 2017–2020

ABSTRACT In this study, we conducted a detailed molecular epidemiological analysis of HIV-1 epidemic strains in various sexual risk behaviour groups in a developed area in eastern China based on phylogenetic inference, molecular transmission networks, and Bayesian analyses. A total of 1083 pol sequences (91.23%, 1083/1187) from newly diagnosed HIV-1-positive patients from 2017 to 2020 were successfully obtained and involved thirteen HIV-1 subtypes, in which the major HIV-1 subtypes were CRF07_BC (36.10%, 391/1083) and CRF01_AE (34.63%, 375/1083). 485 individuals (44.78%,485/1083) formed 146 clusters in the network. Of which CRF07_BC showed extensive clustering driven by men who have sex with men (MSM) within larger networks, CRF01_AE and other subtypes were generally driven by small clusters (SCs) and medium clusters (MCs) among various risk groups. Through Sankey diagrams, the MSM group infected with CRF07_BC had a greater impact on the non-commercial heterosexual group among all cross-risk groups. In addition, a higher number of key individuals infected with CRF07_BC (40.22%, 74/127), suggests the crucial role of CRF07_BC-infected individuals as a local epidemic driver in the context of a mixed HIV-1 epidemic. Further Bayesian analysis confirmed that CRF07_BC was introduced into Jiaxing city from other provinces multiple times and spread rapidly among MSM and heterosexual individuals. Overall, our study provided some insights and information to explore the local transmission dynamics of HIV-1 epidemic strains involving various sexual risk groups, and emphasize that it is necessary to conduct in-depth research and precise intervention targeting key clusters/ individuals to effectively block the continued transmission of AIDS.

Molecular genetic characteristics of Vibrio cholerae nonO1/nonO139 strains isolated on the territory of Russian Federation from patients with otitis

Introduction. In 2017–2020 for the first time in many years strains of Vibrio cholerae nonO1/nonO139 (NAGs) were isolated in Russia from patients with otitis.Aim — bioinformatic analysis of whole genome sequences (WGSs) and sequences of individual genes of NAG strains - causative agents of otitis isolated in Russia.Materials and methods. Analysis of WGSs of eight NAG clinical isolates obtained on the MiSeq Illumina platform was carried out using BioEdit, BLASTN, BLASTP, Vector NTI programs; antibiotic resistance was determined according to MUK 4.2.2495-09.Results. The strains differed in SNP content, sets of determinants of pathogenicity/persistence factors and their alleles. All lacked CTX, preCTX, RS1 prophages, VPI pathogenicity island, thermostable toxin gene, mobile elements associated with antibiotic resistance, pandemicity island VSP-I; two strains contained VSP-II island. Genes of a number of proteases, cholix toxin, type 3 secretion system (T3SS) cluster and additional T6SS clusters formed different combinations. Products of the altered genes retained or lost their characteristic active domains. In the cytotoxin MARTX of 6 strains, the key ACD domain was absent; in 4 strains a new rtxA-like domain was revealed. Biofilm gene clusters varied in their structure. The presence of genes for antibiotic resistance did not always correlate with antibioticograms. All strains were susceptible to most antibiotics, but some showed resistance to 1–4 drugs.Conclusion. All the studied strains — causative agents of otitis, in spite of revealed differences, have sufficient sets of determinants responsible for realization of pathogenic and persistent potential. Due to discrepancy between the genotypic and phenotypic characteristics of antibiotic resistance, one should rely mainly on the phenotype when choosing drugs for the etiotropic therapy of NAG infections. Emergence of patients with otitis caused by NAG-vibrios in Russia indicates the advisability of the inclusion of tests for their identification in the scheme of bacteriological analysis for extraintestinal infections and, in cases of their isolation, for prompt determination of sensitivity to antibiotics.

Integrated genomic analysis reveals actionable targets in pediatric spinal cord low-grade gliomas

Gliomas are the most common central nervous tumors in children and adolescents. However, spinal cord low-grade gliomas (sLGGs) are rare, with scarce information on tumor genomics and epigenomics. To define the molecular landscape of sLGGs, we integrated clinical data, histology, and multi-level genetic and epigenetic analyses on a consecutive cohort of 26 pediatric patients. Driver molecular alteration was found in 92% of patients (24/26). A novel variant of KIAA1549:BRAF fusion (ex10:ex9) was identified using RNA-seq in four cases. Importantly, only one-third of oncogenic drivers could be revealed using standard diagnostic methods, and two-thirds of pediatric patients with sLGGs required extensive molecular examination. The majority (23/24) of detected alterations were potentially druggable targets. Four patients in our cohort received targeted therapy with MEK or NTRK inhibitors. Three of those exhibited clinical improvement (two with trametinib, one with larotrectinib), and two patients achieved partial response. Methylation profiling was implemented to further refine the diagnosis and revealed intertumoral heterogeneity in sLGGs. Although 55% of tumors clustered with pilocytic astrocytoma, other rare entities were identified in this patient population. In particular, diffuse leptomeningeal glioneuronal tumors (n = 3) and high-grade astrocytoma with piloid features (n = 1) and pleomorphic xanthoastrocytoma (n = 1) were present. A proportion of tumors (14%) had no match with the current version of the classifier. Complex molecular genetic sLGGs characterization was invaluable to refine diagnosis, which has proven to be essential in such a rare tumor entity. Moreover, identifying a high proportion of drugable targets in sLGGs opened an opportunity for new treatment modalities.

Molecular and genetic features of calpainopathy

Calpainopathy is the most common form of limb-girdle muscular dystrophy, prevalence in the population is approximately 1 in 15,00042,700 individuals. In the Russian Federation, there is an insufficient number of studies, which researched prevalence of calpainopathy among patients with limb-girdle muscular dystrophy, but according to available data, approximately in 43% of cases the disease is associated with mutations of the CAPN3 gene. Molecular genetic analysis is the main method for diagnosing these patients. Studies indicate many pathogenic mutations that cause calpainopathy with corresponding phenotypes, however, it is quite difficult to establish clear correlations between genotype and phenotype due to the high variability of symptoms and severity, even among patients with the same CAPN3 gene mutations. Currently, there is no effective etiotropic treatment for limb-girdle muscular dystrophy, but new technologies are developing to improve patients condition and quality of life. This research collects data from various studies on the prevalence of calpainopathy in different countries and the main molecular genetic features of the CAPN3 gene and calpain-3 protein, which will further allow the development of possible treatment options for patients with limbgirdle muscular dystrophy.

Molecular Detection and Genetic Characterization of Ehrlichia ruminantium Harbored by Amblyomma hebraeum Ticks of Domestic Ruminants in North West Province, South Africa.

Simple SummaryBont ticks (Genus Amblyomma) transmit Ehrlichia ruminantium (E. ruminantium), a pathogen that causes a rickettsial disease called heartwater in ruminants. Heartwater disease is devastating and causes financial loss in livestock farming in most parts of southern Africa. The E. ruminantium tends to have many variants; as a result, it is difficult to develop vaccines for controlling it. Knowledge of E. ruminantium variant occurrence in a particular area may assist in designing appropriate vaccination control strategies. Thus, this study investigated the E. ruminantium variants found in the Ngaka Modiri Molema District, North West Province, South Africa. Diversity of these E. ruminantium variants was determined by PCR and sequencing of DNA pools extracted from the tick vectors. Six different DNA variants of E. ruminantium were detected and compared well with those known to be virulent from other parts of South Africa and other countries. The type of variant commonly used for the massive vaccination was not detected in the study area.Ehrlichia ruminantium (E. ruminantium) is the causative agent of heartwater disease and it is mainly transmitted to livestock by Amblyomma hebraeum (A. hebraeum) tick in South Africa. This study investigated the occurrence of E. ruminantium and its genetic diversity in ticks within Ngaka Modiri Molema district of North West Province in South Africa. Genomic DNA was extracted from whole A. hebraeum ticks totaling 876 and resulted in a total of 292 pooled DNA samples. Firstly, conventional PCR was used to detect Ehrlichia spp. targeting the dsbA gene, followed by nested PCR targeting the Map1 gene performed on DNA pool samples that were positive from the first PCR. One hundred and six tick DNA pool samples were positive by dsbA gene PCR for the presence of Ehrlichia spp. with minimum infection rate (MIR) of 121, while 13/106 were positive by Map1 PCR with MIR of 15. Different E. ruminantium Map1 genotypes (NWUe1, NWUe2, NWUe3, NWUe5, and NWUe6) were detected from tick samples and were closely related to more than 13 gene sequences of E. ruminantium from the NCBI GenBank database. These findings suggest that there is a significant diversity of E. ruminantium infecting ticks in the study area.

Molecular evolution and genetic characteristics of G3P[3] group A canine rotavirus isolated in Wuhan, China.

Rotaviruses can infect multiple animal species and have the potential for cross-recombination based on the segmented genome characteristics. To study the intra-host recombination and zoonotic potential of group A canine rotavirus (CRV), 438 samples were collected from domestic dogs in six animal hospitals and from stray dogs from October 2019 to May 2021 in Wuhan, China. Seven of the samples were positive (7/438) for group A CRV from which a CRV strain was successfully isolated in MA-104 cells. The genotype of the isolated strain was characterized by whole-genome sequencing showing that the genotype was group A CRV G3P[3]. According to the Rotavirus Classification Working Group (RCWG), the genomic constellation of the isolated CRV was G3-P[3]-I3-R3-C3-M3-A9-N2-T3-E3-H6, which belongs to the AU-1-like group with gene segments of AU-1-like and Cat 97-like strains. Based on the phylogenetic analysis of the 11 gene segments, we found that the different segments of the isolated group A CRV were closely related to several reassortment rotaviruses from different animal sources and bat strains. Based on the analysis of the molecular evolution and genetic characteristics, we concluded that the isolated strain might be a reassortment strain. These data further enrich our understanding of rotavirus molecular evolution and genetic characteristics in China.

Influence of clinical and molecular genetic characteristics on the first relapse-free period in patients with glioblastoma in the era of modern chemoradiotherapy

Introduction. Due to the active research of the molecular and genetic features of glioblastoma, the performance of the biological processes occurring in tumor cells has become more distinct. In the modern scientific literature, the number of scientific studies is growing, which emphasizes the priority importance of the genetic status of the tumor in the prognosis of the disease.Purpose statement. To study the influence of clinical and molecular genetic factors on the median of the first relapse-free period.Materials and methods. The first progression-free survival (PFS) was analyzed in 30 patients aged 28 to 81 years with glioblastoma. The diagnosis was established in accordance with the WHO classification of CNS tumors in 2021. After the first operation, all patients underwent a course of radiation therapy (LT) (60Gr) and chemotherapy with temozolomide (2–18 cycles). In each case, clinical parameters such as the patient’s age, functional status on the Karnovsky scale both before and after surgery, features of the neuroimaging picture (prevalence of the tumor process, localization, tumor volume), treatment (degree of tumor resection, radiation therapy with or without temozolomide and the number of cycles of chemotherapy) and molecular genetic parameters of tumor (determination of the mRNA expression level of genes: MGMT, VEGF, PDGFRA, β-tubulin III, ERCC-1, TOP2A) were studied.Results. Of all the studied clinical parameters, only the postoperative functional status on the Karnovsky scale (p = 0.001) influenced the median of PFS. The median of the first PFS was not affected by such radiological characteristics as involvement of basal structures of the brain in the tumor process (p = 0.9), the side of the lesion (p = 0.67), the prevalence of the tumor process (p = 0.6) and the volume of the tumor (p = 0.52). The duration of the first PFS with statistical reliability was higher in the group of patients after subtotal resection of the tumor (14.9 months; p ³ 0.05). The median of the first PFS was influenced by the presence of a mutation in the IDH1 gene (22.5 vs 11.5 months) and the expression level of the MGMT gene (p = 0.036). Total tumor resection increases the first BRP only at a high level of MGMT gene expression, although without statistically significant differences (7.6 vs 2.7 months; p = 0.6). The addition of temozolomide to radiation therapy (75 mg/m2, orally, daily) led to an increase in the first relapse-free period by more than 6.9 months, but only in patients with low expression of the MGMT gene in the tumor.Conclusion. In the conditions of standard patient therapy (surgical removal of the tumor, chemoradiotherapy followed by adjuvant therapy with temozolomide), the first PFS primarily depends on the molecular genetic characteristics of the tumor, namely, the presence of a mutation in the IDH1 gene and the level of MGMT in the tumor. For patients with an expected lack of response to therapy (i.e., a high level of MGMT gene activity), the role of other factors increases, and first of all, the volume of cytoreduction.

Major features of the 2021 WHO Classification of Tumors of the Central Nervous System: clinician’s view

Advances in the understanding of the molecular biology of central nervous system (CNS) tumors have prompted a new WHO classification of brain and spinal cord tumors in 2021 and integration it in routine clinical practice. Nowadays accurate diagnosis verification consists not only of the histological tumor type, but also includes its molecular-genetic characteristics. Differences in the genetic features of a tumor, even within the same histological type, will determine differences in the prognosis of the disease, and in the tactics of anticancer therapy. The introduced changes necessitate a comprehensive diagnosis of CNS tumors, thereby placing the responsibility for formulating the final diagnosis not only on pathologists. New approaches to classification make it possible to personalize anticancer treatment, as well as including new methods of targeted and immunotherapy, which today seems to be a key aspect of improving the survival of this category of patients.