Molecular Genetic Characterization Research Articles

Prevalence and genetic diversity of the <i>Alongshan virus (Flaviviridae)</i> circulating in ticks in the south of Eastern Siberia

Introduction. Tick-borne infections are of great importance for many regions of Russia, including Eastern Siberia. This unfavorable epidemiological situation can be characterized not only by the circulation of well-known tick-borne infections, but also by the identification of new pathogens, the role of which remains little or generally unexplored. Multicomponent flavi-like viruses can cause infectious diseases in humans and pose a threat to public health. The purpose of the study was the identification and molecular genetic characterization of the Alongshan virus (Flaviviridae, ALSV) isolates, transmitted by ticks in the south of Eastern Siberia. Materials and methods. Total 1060 ticks were collected and analyzed from the territory of the Republics of Khakassia, Tuva, Buryatia, Irkutsk Region and Transbaikal Territory (Zabaykalsky Krai) in the spring-summer period 2023. ALSV RNA was detected by RT-PCR followed by nucleotide sequence determination and phylogenetic analysis for each segment of the genome. Results. The ALSV infection rate in Ixodes persulcatus ticks collected in the Republic of Khakassia was 3.3% (95% CI: 1.4–7.5); in Irkutsk Oblast – 1.0% (95% CI: 0.3–3.7); in the Republic of Tuva – 0.9% (95% CI: 0.3–3.4) and in Transbaikal Krai – 0.7% (95% CI: 0.2–3.6). Sequences of all four segments of ALSV genetic variants circulating in I. persulcatus ticks in the south of Eastern Siberia are grouped with sequences found in China and clustered into the Asian subgroup transmitted by taiga ticks. The level of difference in the nucleotide sequences of genome fragments among the identified genetic variants of ALSV ranged from 2 to 3%. Conclusion. The article shows the widespread distribution of ALSV in I. persulcatus ticks in the Republics of Khakassia and Tyva, Irkutsk Oblast and Transbaikal Territory. The obtained data actualize monitoring of changes in the area of distribution of potentially dangerous for humans flavi-like viruses and their vectors.

Molecular genetic characterization analysis of a novel HIV-1 circulating recombinant form (CRF156_0755) in Guangdong, China.

The characteristic of human immunodeficiency virus type 1 (HIV-1) is its susceptibility to erroneous replication and recombination, which plays a crucial role in the diverse and dynamic variation of HIV-1. The spread of different subtypes in the same population often leads to the emergence of circulating recombination forms (CRFs). At present, the main recombinant subtypes of HIV-1 in China are CRF07_BC, CRF01_AE, CRF08_BC and B' subtypes, while CRF55_01B has become the fifth major epidemic strain in China after rapid growth in recent years since it was first reported in 2013. In this study, we obtained five nearly full-length genomes (NFLGs) and one half-length genome from five different cities in Guangdong. Here, we focused on analyzing their characteristics, parental origin and drug resistance. Plasma samples were collected from six HIV-1 infected patients in Guangdong Province who had no epidemiological association with each other. The NFLGs of HIV-1 were amplified in two overlapping segments by the near-terminal dilution method. The positive products were sequenced directly to obtain genomic sequences. The recombinant patterns and breakpoints of the NFLGs were determined using the Simplot software and confirmed by the maximum likelihood trees for segments using the IQ-TREE and BEAST software. The genotypic resistance profiles of the protease reverse transcriptase and integrase were resolved by the Stanford HIV drug resistance database. The six genomes shared highly similar recombinant pattern, with the CRF55_01B backbone substituted by CRF07_BC segments, therefore assigned as CRF156_0755. The evolutionary analysis of the segments showed that CRF07_BC segments were not clustered with the Chinese MSM variants in the CRF07_BC lineage. All the five NFLGs were identified with the non-nucleoside reverse-transcription inhibitors (NNRTIs) resistance mutation V179E. With the accumulation and evolution of recombination between CRF55_01B and CRF 07_BC, the prevalence of more recombinant strains of CRF55_01B and CRF 07_BC may occur. Therefore, it is necessary to strengthen the identification and monitoring of the recombination of CRF55_01B and CRF 07_BC.

An overview on liposarcoma subtypes: Genetic alterations and recent advances in therapeutic strategies.

Liposarcoma (LPS) is a rare malignancy of adipocytic differentiation. According to World Health Organization classification, LPS comprises of four principle subtypes Atypical lipomatous tumor/Well-differentiated liposarcoma (ATL/WDLPS), Dedifferentiated liposarcoma (WDLPS), Myxoid liposarcoma (MLPS), and Pleomorphic liposarcoma (PLPS). Each subtype can develop at any location and shows distinct clinical behavior and treatment sensitivity. ATL/ WDLPS subtype has a higher incidence rate, low recurrence, and is insensitive to radiation and chemotherapy. DDLPS is the focal progression of WDLPS, which is aggressive and highly metastasizing. MLPS is sensitive to radiation and chemotherapy, with a higher recurrence rate and metastasis. PLPS subtype is highly metastasizing, has a poor prognosis, and exhibiting higher recurrence rate. Initial histological analysis provides information for the characterization of LPS subtypes', further molecular and genetic analysis provides certain subtype specifications, such as gene amplifications and gene fusions. Such molecular genetic alterations will be useful as therapeutic targets in various cancers, including the LPS subtypes. A wide range of novel therapeutic agents based on genetic alterations that aim to target LPS subtypes specifically are under investigation. This review summarizes the LPS subtype classification, their molecular genetic characteristics, and the implications of genetic alterations in therapeutics.

Molecular detection and genetic characteristics of porcine circovirus 3 and porcine circovirus 4 in central China.

Porcine circoviruses (PCVs) are a significant cause of concern for swine health, with four genotypes currently recognized. Two of these, PCV3 and PCV4, have been detected in pigs across all age groups, in both healthy and diseased animals. These viruses have been associated with various clinical manifestations, including porcine dermatitis and nephropathy syndrome (PDNS) and respiratory and enteric signs. In this study, we detected PCV3 and PCV4 in central China between January 2022 and February 2023. We tested fecal swabs and tissue samples from growing-finishing and suckling pigs with or without respiratory and systemic manifestations and found the prevalence of PCV3 to be 15.15% (15/99) and that of PCV3/PCV4 coinfection to be 4.04% (4/99). This relatively low prevalence might be attributed to the fact that most of the clinical samples were collected from pigs exhibiting respiratory signs, with only a few samples having been obtained from pigs with diarrhea. In some cases, PCV2 was also detected, and the coinfection rates of PCV2/3, PCV2/4, and PCV2/3/4 were 6.06% (6/99), 5.05% (5/99), and 3.03% (3/99), respectively. The complete genomic sequences of four PCV3 and two PCV4 isolates were determined. All four of the PCV3 isolates were of subtype PCV3b, and the two PCV4 isolates were of subtype PCV4b. Two mutations (A24V and R27K) were found in antibody recognition domains of PCV3, suggesting that they might be associated with immune escape. This study provides valuable insights into the molecular epidemiology and evolution of PCV3 and PCV4 that will be useful in future investigations of genotyping, immunogenicity, and immune evasion strategies.

Comparative Morphological and Molecular Genetic Characteristics of Cell and Tissue Strains of Experimental Rat Glioma 10-17-2 (Astrid-17).

In order to obtain models of gliomas of varying degrees of malignancy, we performed morphological and molecular genetic study of a tissue strain of glioma 10-17-2 (Astrid-17) obtained by intracranial passaging of tumor fragments of chemically induced rat brain tumor, and a cell strain isolated from it. More or less pronounced changes in the expression levels of Mki67, Trp53, Vegfa, and Gfap genes in the tissue and cell strain of glioma 10-17-2 (Astrid-17) compared with intact brain tissue were shown. The tissue model of glioma 10-17-2 (Astrid-17) according to the studied characteristics shows features of grade 3-4 astrocytoma and the cellular model - grade 2-3 astrocytoma.

Management of High-Risk Neuroblastoma with Soft-Tissue-Only Disease in the Era of Anti-GD2 Immunotherapy.

Neuroblastoma presents with two patterns of disease: locoregional or systemic. The poor prognostic risk factors of locoregional neuroblastoma (LR-NB) include age, MYCN or MDM2-CDK4 amplification, 11q, histology, diploidy with ALK or TERT mutations, and ATRX aberrations. Anti-GD2 immunotherapy has significantly improved the outcome of high-risk (HR) NB and is mostly effective against osteomedullary minimal residual disease (MRD), but less so against soft tissue disease. The question is whether adding anti-GD2 monoclonal antibodies (mAbs) benefits patients with HR-NB compounded by only soft tissue. We reviewed 31 patients treated at SJD for HR-NB with no osteomedullary involvement at diagnosis. All tumors had molecular genetic features of HR-NB. The outcome after first-line treatment showed 25 (80.6%) patients achieving CR. Thirteen patients remain in continued CR, median follow-up 3.9 years. We analyzed whether adding anti-GD2 immunotherapy to first-line treatment had any prognostic significance. The EFS analysis using Cox models showed a HR of 0.20, p = 0.0054, and an 80% decrease in the risk of relapse in patients treated with anti-GD2 immunotherapy in the first line. Neither EFS nor OS were significantly different by CR status after first-line treatment. In conclusion, adding treatment with anti-GD2 mAbs at the stage of MRD helps prevent relapse that unequivocally portends poor survival.

Microbiological and molecular genetic characteristics of Klebsiella pneumoniae isolates, extracted under conditions of cardiac surgery hospital

Klebsiella pneumoniae is one of the main causative agents of healthcare-associated infections (HAI) worldwide. The study was aimed at molecular characterization of beta-lactam antibiotic resistance in K. pneumoniae isolated in the cardiac surgery hospital, identify hypervirulent isolates and assess isolate genetic relatedness. K. pneumoniae isolated from the clinical material of patients (n = 50) at cardiac surgery departments as well as anesthesiology and reanimation department treated at the cardiovascular surgery hospital in Perm from July 2021 to December 2022 were analyzed. Bacteriological studies were performed on an automatic analyzer WalkAway-96Plus (Beckman Coulter, USA). The sensitivity to thirteen antimicrobials, production of extended-spectrum beta-lactamases (ESBL) and multidrug resistance (MDR) phenotype were assessed. The string test was used to screen hypermucoviscous K. pneumoniae. Isolate relatedness (ERIC-PCR), presence of beta-lactamase genes (blaTEM, blaCTX-M, blaSHV, blaOXA, blaKPC, blaVIM-2, blaIMP-1, blaNDM-1), as well as genes associated with hypervirulence (prmpA, iucA, peg-344, wzyK2, magA) were analyzed by PCR. Amplifications were performed in a DNA Engine Dyad Thermal Cycler (Bio-Rad, USA). Gel documentation system Gel-Doc XR (Bio-Rad, USA) was used for band visualization and data documentation. According to the study results, it was found that carbapenem-resistant isolates accounted for almost 76% of all isolates, the ESBL-phenotype had 90%, and MDR-phenotype — 88% of studied isolates. According to the string test results, 8% of K. pneumoniae isolates had a hypermucoviscous phenotype. As for genes associated with hypervirulence, it was shown that the iucA gene was the most common, amplified in 54% of isolates, prmpA was detected in 38% of isolates, 48% of isolates had wzyK2 or magA genes encoding capsular type K1/K2. Almost a third of K. pneumoniae samples contained a combination of the rmpA and iucA genes, and they were isolated more often in the group of patients with active infection. Only carbapenem-sensitive microorganisms had hypermucoviscous phenotype, K1 capsular type, and a combination of prmpA, iucA, peg-344 genes, whereas the K2 capsular type was most common among carbapenem-resistant K. pneumoniae. Based on molecular genetic typing, it was found that 24% of K. pneumoniae isolates were assigned to four genome groups of identical cultures, 76% of the isolates had individual profiles. Closely related isolates were found among patients from different departments that indicates a potential pathogen circulation in the closed circuit “surgery department–department of anesthesiology” and “reanimation–surgery department”.

Molecular investigation and genetic characterization of feline leukemia virus (FeLV) in cats referred to a veterinary teaching hospital in Northern Italy

Feline leukemia virus (FeLV) is responsible for feline leukemia syndrome in domestic cats. The prevention and control of disease caused by FeLV are primarily based on vaccination and identification and isolation of infected subjects. Antigen diagnostic methods, which are the most widely used in clinical practices, can be associated to molecular tests to characterize the FeLV detected. In this study, a quantitative SYBR Green Real-Time PCR (qPCR) assay was used to detect FeLV proviral DNA in blood samples from antigen positive cats referred to a veterinary teaching hospital in Northern Italy in 2018–2021. To genetically characterize the identified viruses, a portion of the viral envelope (env) gene was amplified using six different end-point PCRs and sequenced. Twenty-two of 26 (84.6%) cats included in the study tested positive by qPCR assay. This suggests a high performance of the qPCR adopted but further studies are required to investigate the cause of discordant results between the antigen test and qPCR in four cats. From env gene analysis, 15/22 qPCR-positive cats were infected by FeLV subtype A and 5/15 shown coinfection with subtype B.

Mutations in the NUP93, NUP107 and NUP160 genes cause steroid-resistant nephrotic syndrome in Chinese children

BackgroundThe variants of nucleoporins are extremely rare in hereditary steroid-resistant nephrotic syndrome (SRNS). Most of the patients carrying such variants progress to end stage kidney disease (ESKD) in their childhood. More clinical and genetic data from these patients are needed to characterize their genotype–phenotype relationships and elucidate the role of nucleoporins in SRNS.MethodsFour patients of SRNS carrying biallelic variants in the NUP93, NUP107 and NUP160 genes were presented. The clinical and molecular genetic characteristics of these patients were summarized, and relevant literature was reviewed.ResultsAll four patients in this study were female and initially presented with SRNS. The median age at the onset of the disease was 5.08 years, ranging from 1 to 10.5 years. Among the four patients, three progressed to ESKD at a median age of 7 years, ranging from 1.5 to 10.5 years, while one patient reached stage 3 chronic kidney disease (CKD3). Kidney biopsies revealed focal segmental glomerulosclerosis in three patients. Biallelic variants were detected in NUP93 in one patient, NUP107 in two patients, as well as NUP160 in one patient respectively. Among these variants, five yielded single amino acid substitutions, one led to nonsense mutation causing premature termination of NUP107 translation, one caused a single nucleotide deletion resulting in frameshift and truncation of NUP107. Furthermore, one splicing donor mutation was observed in NUP160. None of these variants had been reported previously.ConclusionThis report indicates that biallelic variants in NUP93, NUP107 and NUP160 can cause severe early-onset SRNS, which rapidly progresses to ESKD. Moreover, these findings expand the spectrum of phenotypes and genotypes and highlight the importance of next-generation sequencing in elucidating the molecular basis of SRNS and allowing rational treatment for affected individuals.

SOX11 expression is restricted to EBV-negative Burkitt lymphoma and is associated with molecular genetic features

AbstractSRY-related HMG-box gene 11 (SOX11) is a transcription factor overexpressed in mantle cell lymphoma (MCL), a subset of Burkitt lymphomas (BL) and precursor lymphoid cell neoplasms but is absent in normal B cells and other B-cell lymphomas. SOX11 has an oncogenic role in MCL but its contribution to BL pathogenesis remains uncertain. Here, we observed that the presence of Epstein-Barr virus (EBV) and SOX11 expression were mutually exclusive in BL. SOX11 expression in EBV-negative (EVB-) BL was associated with an IG∷MYC translocation generated by aberrant class switch recombination, whereas in EBV-negative (EBV−)/SOX11-negative (SOX11−) tumors the IG∷MYC translocation was mediated by mistaken somatic hypermutations. Interestingly, EBV− SOX11-expressing BL showed higher frequency of SMARCA4 and ID3 mutations than EBV−/SOX11− cases. By RNA sequencing, we identified a SOX11–associated gene expression profile, with functional annotations showing partial overlap with the SOX11 transcriptional program of MCL. Contrary to MCL, no differences on cell migration or B-cell receptor signaling were found between SOX11− and SOX11-positive (SOX11+) BL cells. However, SOX11+ BL showed higher adhesion to vascular cell adhesion molecule 1 (VCAM-1) than SOX11− BL cell lines. Here, we demonstrate that EBV− BL comprises 2 subsets of cases based on SOX11 expression. The mutual exclusion of SOX11 and EBV, and the association of SOX11 with a specific genetic landscape suggest a role of SOX11 in the early pathogenesis of BL.

Clinicopathological and molecular genetic features of Crohn's disease

Objective: To investigate the clinicopathological and molecular genetic characteristics of Crohn's disease (CD). Methods: A retrospective analysis was conducted on 52 CD patients who underwent surgical resection at the First Affiliated Hospital of Nanjing Medical University between January 2014 and June 2023. Clinical presentations and histopathological features were assessed. Whole-genome sequencing was performed on 17 of the samples, followed by sequencing and pathway enrichment analyses. Immunohistochemistry was used to assess the expression of frequently mutated genes. Results: Among the 52 patients, 34 were males and 18 were females, male-to-female ratio was 1.9∶1.0, with a median age of 45 years at surgery and 35 years at diagnosis. According to the Montreal classification, A3 (51.9%,27/52), B2 (61.5%, 32/52), and L3 (50.0%,26/52) subtypes were the most predominant. Abdominal pain and diarrhea were the common symptoms. Histopathological features seen in all 52 patients included transmural inflammation, disruption of cryptal architecture, lymphoplasmacytic infiltration, varying degrees of submucosal fibrosis and thickening, increased enteric nerve fibers and neuronal proliferation. Mucosal defects, fissure ulcers, abscesses, pseudopolyps, and adenomatous proliferation were also observed in 51 (98.1%), 38 (73.1%), 28 (53.8%), 45 (86.5%), and 28 (53.8%) cases, respectively. Thirty-one (59.6%) cases had non-caseating granulomas, and 3 (5.8%) cases had intestinal mucosal glandular epithelial dysplasia. Molecular analysis showed that 12/17 CD patients exhibited mutations in at least one mucin family gene (MUC2, MUC3A, MUC4, MUC6, MUC12, MUC17), and MUC4 was the most frequently mutated in 7/17 of cases. Immunohistochemical stains showed reduced MUC4 expression in epithelial cells, with increased MUC4 expression in the epithelial surface, particularly around areas of inflammatory cell aggregation; and minimal expression in the lower half of the epithelium. Conclusions: CD exhibits diverse clinical and pathological features, necessitating a comprehensive multidimensional analysis for diagnosis. Mutations and expression alterations in mucin family genes, particularly MUC4, may play crucial roles in the pathogenesis of CD.

Congenital spindle cell/sclerosing rhabdomyosarcoma: a clinicopathological analysis

Objective: To investigate the clinicopathological features, immunophenotype and molecular genetic characteristics of congenital spindle cell/sclerosing rhabdomyosarcoma. Methods: Sixteen cases (including 10 consultation cases) of congenital spindle cell/sclerosing rhabdomyosarcoma diagnosed at the Beijing Children's Hospital, Capital Medical University, Beijing China, from April 2017 to January 2022 were collected. These cases were evaluated for clinical profiles, histomorphological features, immunophenotype and molecular characteristics. Results: Among the 16 patients, 9 were male and 7 were female. Five cases were present during maternal pregnancy and 11 cases were found immediately after birth. The tumors were located in the chest wall, low back, retroperitoneum, extremities or perineum. The tumors consisted of fasciculated spindle-shaped cells with localized mesenchymal sclerosis and vitreous metaplasia. Immunohistochemistry showed that the tumor cells expressed Desmin, Myogenin, MyoD1, SMA, CD56 and ALK to varying degrees, but not other markers such as CD34, CD99, pan-TRK, S-100 and BCOR. FISH analyses with NCOA2 (8q13) and VGLL2 (6q22) gene breakage probes revealed a breakage translocation in chromosome NCOA2 (8q13) in 4 cases (4/11). In the 6 cases subject to sequencing, a mutation at the p.L122R locus of MYOD1 gene was detected in 1 case (1/6). Two cases were examined by electron microscopy, which showed bundle-arranged myofilaments with some primitive myofilament formation. Five cases were resected with simple surgery, 2 cases were biopsied and followed up with observation only, and 9 cases were treated with surgery and adjuvant chemotherapy. Follow-up was available in 12 cases. At the end of the follow-up, 2 of the 12 patients developed local recurrences and 2 patients survived with disease. Conclusions: Congenital spindle cell/sclerosing rhabdomyosarcoma is a rare subtype of congenital rhabdomyosarcoma. It more commonly occurs in the chest, back and lower limbs of infants than other sites. NCOA2/VGLL2 gene fusion seems to be the most common genetic change. Its prognosis is better than other subtypes of rhabdomyosarcoma and those in adolescents and adults with the same subtype. Analysis and summary of its clinicopathological features can help differentiate it from other soft tissue tumors in infants and children and provide the information for appropriate treatments.

Genetic diversity of hepatitis C virus and the prevalence of resistance mutations to NS5A inhibitors in the Krasnoyarsk region

To research the molecular genetic characteristics of the HCV population circulating among HIV‐infected residents of the Krasnoyarsk Territory, including analysis of resistance‐associated mutations to NS5A inhibitors. Total RNA was isolated from 94 blood plasma samples from HIV/HCVinfected residents of the region and the nucleotide sequences of the Core/E1 gene and NS5A gene regions were obtained and deciphered, which were used for genotyping and searching for resistance mutations.In the HCV samples studied, the circulation of five virus subtypes was recorded: 1b (47,9 %), 3a (37,2 %), 1a (10,6 %), 2a (3,2 %) and 2k (1,1 %). Phylogenetic analysis of HCVs revealed partial clustering within subtypes 1a and 3a on a territorial basis. HCV subtypes 1b, 2a and 2k were grouped with other HCVs previously isolated in Russia, Armenia and Kyrgyzstan. Among the HCVs studied, no clusters were found that were common to HIV‐infected individuals with the same route of infection. Among patients who had no experience of taking DAAs, HCV resistance mutations in the NS5A region were found in 42,3 % of cases for those infected with subtype 3a virus and in 75,6 % of cases for those infected with HCV subtype 1b.The analysis of the diversity and occurrence of mutations of HCV drug resistance to direct antiviral drugs is extremely important for the development of tactics for effective treatment of CHC. The high prevalence of polymorphic mutations that affect sensitivity to DAAs indicates the relevance of introducing HCV resistance analysis into clinical practice.

Contemporary views on the clinical, epidemiological and molecular genetic characteristics of melanoma of the skin and mucous membranes

Melanoma of the skin and mucous membranes remains a global medical problem, which is associated with the increasing prevalence of this disease and the lack of adequate molecular genetic markers for its diagnosis and prognosis. The development of molecular approaches in the treatment of this type of tumor is associated with the identification of mutations, and with the development of immunotherapeutic and targeted drugs that can improve the effectiveness of treatment of patients with this pathology. However, the heterogeneity of the mechanisms of tumor development and the formation of resistance are a problem. It is worth noting the presence of many epigenetic mechanisms that are promising markers of the development, diagnosis and prognosis of the effectiveness of treatment of melanoma of the skin and mucous membranes. This review contains up-to-date information on the molecular mechanisms of the disease associated with the genetic characteristics of the tumor and biological factors of resistance to therapy. Of particular interest is the intersection of signaling pathways associated with melanocyte-inducing transcription factor (MITF), which is associated with transcription and growth factors, and is a target of epigenetic regulation using microRNAs and long non-coding RNAs.

Plasmablastic Lymphoma and Plasmablastic Myeloma: А Diagnostic Dilemma (Literature Review)

Plasmablastic lymphoma and plasmablastic myeloma are similar in morphology. Tumor substrate in both is characterized by large cells with blastic morphology, central or somewhat eccentric nuclei, large central nucleolus or some distinct nucleoli, and abundant eosinophilic cytoplasm. The common characteristic of both B-cell tumors is the expression of plasma cell differentiation markers (CD38, CD138, MUM-1/IRF-4, interferon regulatory factor 4, PRDM-1, PR domain zinc finger protein 1, and/or XBP-1, X-box-1 binding protein) with a frequent loss of CD20. These rare nosological entities with similar morphological and immunohistochemical features present a challenge for differential and reliable diagnosis. The present review deals with clinical signs, diagnostically significant immunohistochemical markers, and molecular genetic characteristics which are essential for differential diagnosis of plasmablastic lymphoma and plasmablastic myeloma.

Gene Expression Profile-Guided Personalized Intraperitoneal Chemotherapy for Gastric Cancer Peritoneal Carcinomatosis.

Peritoneal carcinomatosis (PC) is one of the most unfavorable sites of metastasis for malignant tumors of various localizations, especially gastric cancer (GC). According to the literature, synchronous PC in GC is common in 15-52% of patients. The purpose of this study was to examine the long-term results using personalized systemic and intraperitoneal chemotherapy as part of the combined treatment of stomach cancer presenting with synchronous PC. Cytoreductive surgical treatment was performed for 70 patients at the first stage. The control group (n = 35) received standard postoperative chemotherapy according to the FOLFOX scheme. Personalized postoperative systemic and intraperitoneal chemotherapy was administered in the basic group (n = 35), based on the expression levels of the eight genes in the primary tumor, lymph node, and peritoneal metastases. The median progression-free survival was 14.9 months in the basic group, and in the control group it was 11.2 months (P < 0.001). The median life expectancy in the basic group was 16.8 (13.7 - 18.8) months, in the control group it was 12.5 (11.3 - 13.1) months (P < 0.001). Developing algorithms of personalized systemic and intraperitoneal chemotherapy in patients with GC with synchronous carcinomatosis, based on the analysis of molecular genetic characteristics of the tumor and metastases, allows to improve the long-term results of combined treatment.

ALK-mutated thyroid cancer

At the moment, the standard of treatment in the Russian Federation for late stages of well-differentiated thyroid cancer (hereinafter referred to as WDTC) with a recorded radioiodine-resistant tumor status is the sequential administration of multikinase inhibitors: Sorafenib, Lenvatinib. Treatment protocols for subsequent lines have not been developed. The purpose of this article is to review the main molecular genetic features of WDTC and present the clinical observation of a patient with metastatic radioiodine-resistant follicular varient of papillary thyroid cancer (hereinafter referred to as PTC), which has progressed after previous lines of therapy. The patient’s tumor biological material was submitted for next-generation sequencing (NGS), which allows detection of all classes of molecular changes for a large number of genes. Due to the discovery of an ALK mutation and the lack of registered standards for subsequent treatment, ALK inhibitors were prescribed. This attempt to individualize therapy was successful: a partial response was registered during therapy and a significant clinical improvement in the patient’s general condition was noted. Therapy with ALK inhibitors continues to this day (46 months as of October 2023) and has a favorable toxicity profile. Thus, we can conclude that when the basic standards for the treatment of metastatic well-differentiated thyroid cancer have been exhausted, there is an individual selection of targeted therapy depending on the molecular genetic characteristics of the tumor process.

Abstract 5053: Clinicopathologic and molecular genetic features of STAT3-mutated myeloid neoplasms

Abstract STAT3 is a key transcription factor that can mediate cancer progression through phosphorylation or gain-of-function mutations. STAT3 mutations have been mainly associated with large granular lymphocytic T-cell leukemia. Whereas STAT3 activation is common in myeloid neoplasms, it is primarily mediated through STAT3 phosphorylation. STAT3 mutation has only rarely been reported in myeloid neoplasms. We assessed the clinicopathologic and molecular genetic features of 32 STAT3-mutated myeloid neoplasms. Twenty (62.5%) cases were classified as acute myeloid leukemia (AML), 7 (21.9%) as myelodysplastic syndrome (MDS), and 5 (15.6%) as chronic myelomonocytic leukemia (CMML). It is of note that STAT3 mutation was not detected in myeloproliferative neoplasms (MPN). STAT3 mutations were detected at the initial diagnosis in 22 of 25 (88%) cases, suggesting STAT3 mutation is an early event in pathogenesis. However, STAT3 mutations represented the dominant clone in only 6 (18.8%) cases, all classified as AML. Most are missense mutations, located at the SH2 domain. The median variant allele frequencies were 6.8%, 4.6% and 3.1% for AML, MDS and CMML, respectively, and in a case of CMML, the VAF increased from 2.4% to 34.8% upon leukemic transformation. STAT3 mutation was accompanied by co-existing mutations in all cases, with SRSF2 (40.6%), TET2 (40.6%), ASXL1 (37.5%), and SETBP1 (34.4%) being most common. Cases with STAT3 mutations were usually associated with morphologic dysplasia and increased blasts. Monosomy 7/del7q was the most common cytogenetic abnormality, seen in 11 (34.4%) cases. With a median follow-up of 24.5 months, 21 patients died, 6 had persistent disease, and 5 achieved complete remission. We summarize that STAT3 mutation is present in a variety of myeloid neoplasms, but not seen in MPN. It is often an early events and always with concurrent mutations. It may play an important role in the pathogenesis and progression of myeloid neoplasms by activating JAK-STAT pathway, and may serve as a potential therapeutic target. Citation Format: Matthew T. Ye, Zhuang Zuo, Steliana Calin, Fengxi Ye, Hua He, Wataru Kamata, M. James You. Clinicopathologic and molecular genetic features of STAT3-mutated myeloid neoplasms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5053.

Identification of four novel mutations in VSP13A in Iranian patients with Chorea-acanthocytosis (ChAc).

Chorea-acanthocytosis (ChAc) is a rare autosomal recessive neurodegenerative disorder characterized by a variety of involuntary movements, predominantly chorea, and the presence of acanthocytosis in peripheral blood smears. ChAc is caused by mutations in the vacuolar protein sorting-associated protein 13A (VPS13A) gene. The aim of the present study was to conduct a clinical and genetic analysis of five patients with suspected ChAc in Iran.This study included five patients who were referred to the genetic department of the Endocrinology and Metabolism Research Institute between 2020 and 2022, with a suspicion of ChAc. Clinical features and the presence of characteristic MRI findings were evaluated in the patients. Whole-exome sequencing (WES) followed by Sanger sequencing was employed to identify the disease-causing variants. The functional effects of novel mutations were analyzed by specific bioinformatics prediction tools.WES and data analysis revealed the presence of five distinct VPS13A mutations in the patients, four of which were novel. Theseincluded one nonsense mutation (p.L984X), and three splice site mutations (c.755-1G>A, c.144+1 G>C, c.2512+1G>A). All mutations were validated by Sanger sequencing, and in silico analysis predicted that all mutations were pathogenic.This study provides the first molecular genetic characteristics of Iranian patients with ChAc, identifying four novel mutations in the VPS13A gene. These findings expand the VPS13A variants spectrum and confirm the clinical variability in ChAc patients.

Progression-free survival after first recurrence in patients with glioblastoma.

Relevance. Despite all the treatment glioblastoma recurs as an aggressive and therapy-resistant tumor, and patients quickly die from these neoplasms. The study of glioblastoma recurrence processes and search for prognostic factors of the disease should lead to the improvement of survival rates of patients with this pathology. Purpose of the study. To study the influence of clinical and molecular-genetic factors on the median second recurrence-free period. Materials and methods. Progression-free survival after first recurrence in 34 patients aged 28 to 81 years with recurrent glioblastoma was analyzed. The diagnosis was established according to the WHO 2021 classification of CNS tumors. In each observation we studied such clinical parameters as patient’s age, functional status according to the Karnovsky scale pre- and postoperatively, peculiarities of neuroimaging picture (prevalence of tumor process, localization of recurrence, tumor volume), conducted treatment and molecular-genetic characteristics of the tumor (determination of mRNA expression level of genes: MGMT, VEGF, PDGFRA, β-tubulin III, ERCC-1, TOP2A). Results. Among the clinical and demographic characteristics, the median of the survival was influenced by the patients’ age and functional status after surgery. The median of the survival was more than 2 times higher in the group of patients under 50 years old, compared to patients over 50 years old (18.5 vs 8 weeks). The dependence of the median of the survival on the post- operative functional status (according to the Karnovsky scale) was determined (p = 0.001). The median of the survival in case of a single brain lobe lesion was more than 5 times higher than in case of widespread tumor process, though without statistical reliability (p = 0.09, 21.5 vs 4 weeks). Survival rates were higher when recurrence was localized within 2 cm of the area of removal of the primary neoplasm. After disease progression, the MGMT gene lost its predictive value. Patients with low expression of the TOR2A gene had a higher survival rate than those with medium and high expression (47.5 vs 3 weeks, p = 0.001; 47.5 vs 22.5 weeks, p = 0.06). The median of survival was higher than at high levels at low and medium PDGFRA gene expression levels (29 vs 0 weeks, p = 0.04; 21 vs 0 weeks; p = 0.05, respectively). Maximum survival rates were recorded in the group of patients after total and subtotal removal of tumor recurrence (22 and 18.5 weeks, p = 0.05). Administration of second-line chemotherapy with temozolomide statistically significantly increased the median of the second BRS (p = 0.01). Conclusion. Recurrent glioblastomas are characterized by an extremely aggressive course. Therefore, such prognostic factors as patient age, degree of tumor resection, tumor process prevalence, degree of tumor resection and 2nd line chemotherapy come to the forefront. It should be noted that the MGMT gene loses its predictive value during disease progression, while the TOR2A gene and PDGFRA gene become prognostic markers.