Gene Mutation Patterns Research Articles

The heterogeneity and clonal evolution analysis of the advanced prostate cancer with castration resistance

BackgroundNowadays, the incidence rate of advanced and metastatic prostate cancer at the first time of diagnosis grows higher in China yearly. At present, androgen deprivation therapy (ADT) is the primary treatment of advanced prostate cancer. However, after several years of ADT, most patients will ultimately progress to castration-resistant prostate cancer (CRPC). Previous studies mainly focus on Caucasian and very few on East Asian patients.MethodsIn this study, the pre- and post-ADT tumor samples were collected from five Chinese patients with advanced prostate cancer. The whole-exome sequencing, tumor heterogeneity, and clonal evolution pattern were analyzed.ResultsThe results showed that the gene mutation pattern and heterogeneity changed significantly after androgen deprivation therapy. Tumor Mutational Burden (TMB) and Copy Number Alteration (CNA) were substantially reduced in the post-treatment group, but the Mutant-allele tumor heterogeneity (MATH), Socio-Demographic Index (SDI), Intratumor heterogeneity (ITH), and weighted Genome Instability Index (wGII) had no significant difference. According to the clone types and characteristics, the presence of main clones in five pre-and post-treatment samples, the clonal evolution pattern can be further classified into two sub-groups (the Homogeneous origin clonal model or the Heterogeneous origin clonal model). The Progression-free survival (PFS) of the patients with the “Homogeneous origin clonal model” was shorter than the “Heterogeneous origin clonal model”. The longer PFS might relate to MUC7 and MUC5B mutations repaired. ZNF91 mutation might be responsible for resistance to ADT resistance.ConclusionOur findings revealed potential genetic regulators to predict the castration resistance and provide insights into the castration resistance processes in advanced prostate cancer. The crosstalk between clonal evolution patterns and tumor microenvironment may also play a role in castration resistance. A multicenter-research including larger populations with different background are needed to confirm our conclusion in the future.

Bioinformatics-based analysis of programmed cell death pathway and key prognostic genes in gastric cancer: Implications for the development of therapeutics.

Gastric cancer (GC) represents a major global health burden as a result of its high incidence and poor prognosis. The present study examined the role of the programmed cell death (PCD) pathway and identified key genes influencing the prognosis of patients with GC. Bioinformatics analysis, machine learning techniques and survival analysis were systematically integrated to identify core prognostic genes from the The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset. A prognostic model was then developed to stratify patients into high-risk and low-risk groups, and further validated in the GSE84437 dataset. The model also demonstrated clinical relevance with tumor staging and histopathology. Immune infiltration analysis and the potential benefits of immunotherapy for each risk group were assessed. Finally, subgroup analysis was performed based on the expression of three key prognostic genes. Three core prognostic genes (CAV1, MMP9 and MAGEA3) were identified. The prognostic model could effectively differentiate patients into high-risk and low-risk groups, leading to significantly distinct survival outcomes. Increased immune cell infiltration was observed in the high-risk group, and better potential for immunotherapy outcomes was observed in the low-risk group. Pathways related to cancer progression, such as epithelial-mesenchymal transition and tumor necrosis factor-α signaling via nuclear factor-kappa B, were enriched in the high-risk group. By contrast, the low-risk group showed a number of pathways associated with maintenance of cell functionality and immune responses. The two groups differed in gene mutation patterns and drug sensitivities. Subgroup analysis based on the expression of the three key genes revealed two distinct clusters with distinct survival outcomes, tumor immune microenvironment characteristics and pathway enrichment. The present study offers novel insights into the significance of PCD pathways and identifies key genes associated with the prognosis of patients with GC. This robust prognostic model, along with the delineation of distinct risk groups and molecular subtypes, provides valuable tools for risk stratification, treatment selection and personalized therapeutic interventions for GC.

Mutational landscape of cancer-driver genes across human cancers

The genetic mutations that contribute to the transformation of healthy cells into cancerous cells have been the subject of extensive research. The molecular aberrations that lead to cancer development are often characterised by gain-of-function or loss-of-function mutations in a variety of oncogenes and tumour suppressor genes. In this study, we investigate the genomic sequences of 20,331 primary tumours representing 41 distinct human cancer types to identify and catalogue the driver mutations present in 727 known cancer genes. Our findings reveal significant variations in the frequency of cancer gene mutations across different cancer types and highlight the frequent involvement of tumour suppressor genes (94%), oncogenes (93%), transcription factors (72%), kinases (64%), cell surface receptors (63%), and phosphatases (22%), in cancer. Additionally, our analysis reveals that cancer gene mutations are predominantly co-occurring rather than exclusive in all types of cancer. Notably, we discover that patients with tumours displaying different combinations of gene mutation patterns tend to exhibit variable survival outcomes. These findings provide new insights into the genetic landscape of cancer and bring us closer to a comprehensive understanding of the underlying mechanisms driving the development of various forms of cancer.

Machine learning models-based on integration of next-generation sequencing testing and tumor cell sizes improve subtype classification of mature B-cell neoplasms.

Next-generation sequencing (NGS) panels for mature B-cell neoplasms (MBNs) are widely applied clinically but have yet to be routinely used in a manner that is suitable for subtype differential diagnosis. This study retrospectively investigated newly diagnosed cases of MBNs from our laboratory to investigate mutation landscapes in Chinese patients with MBNs and to combine mutational information and machine learning (ML) into clinical applications for MBNs, especially for subtype classification. Samples from the Catalogue Of Somatic Mutations In Cancer (COSMIC) database were collected for ML model construction and cases from our laboratory were used for ML model validation. Five repeats of 10-fold cross-validation Random Forest algorithm was used for ML model construction. Mutation detection was performed by NGS and tumor cell size was confirmed by cell morphology and/or flow cytometry in our laboratory. Totally 849 newly diagnosed MBN cases from our laboratory were retrospectively identified and included in mutational landscape analyses. Patterns of gene mutations in a variety of MBN subtypes were found, important to investigate tumorigenesis in MBNs. A long list of novel mutations was revealed, valuable to both functional studies and clinical applications. By combining gene mutation information revealed by NGS and ML, we established ML models that provide valuable information for MBN subtype classification. In total, 8895 cases of 8 subtypes of MBNs in the COSMIC database were collected and utilized for ML model construction, and the models were validated on the 849 MBN cases from our laboratory. A series of ML models was constructed in this study, and the most efficient model, with an accuracy of 0.87, was based on integration of NGS testing and tumor cell sizes. The ML models were of great significance in the differential diagnosis of all cases and different MBN subtypes. Additionally, using NGS results to assist in subtype classification of MBNs by method of ML has positive clinical potential.

Survey of Helicobacter pylori levofloxacin and clarithromycin resistance rates and drug resistance genes in Ningxia, 2020-2022

Objective: To explore the rate of Helicobacter pylori (Hp) resistance to levofloxacin and clarithromycin and the common mutation patterns of resistance genes in Ningxia, and to assess the concordance between phenotypic resistance and genotypic resistance. Methods: Cross-sectional study. Patients diagnosed with Hp infection in 14 hospitals in Ningxia region from February 2020 to May 2022 were retrospectively selected. Hp strains were isolated from gastric biopsy specimens of Hp-infected patients and subjected to phenotypic drug sensitivity testing and detection of resistance genes to analyze the rate of Hp resistance to levofloxacin and clarithromycin and the common mutation patterns of resistance genes in Ningxia region; and the concordance rate and Kappa concordance test were used to assess the concordance between phenotypic resistance and genotypic resistance. Results: A total of 1 942 Hp strains were isolated and cultured, and among the infections, 1 069 cases (55.0%) were male and 873 cases (45.0%) were female, aged (50.0±12.5) years (15-86 years). The rates of Hp resistance to levofloxacin and clarithromycin in Ningxia were 42.1% (818/1 942) and 40.1% (779/1 942), respectively, and the rate of dual resistance to both was 22.8% (443/1 942). The rate of resistance to levofloxacin and clarithromycin of Hp strains from female patients was higher than in male patients (levofloxacin: 50.4%(440/873) vs 35.4%(378/1 069); clarithromycin: 44.4%(388/873) vs 36.6%(391/1 069), both P<0.001). Among the GyrA gene mutations associated with levofloxacin resistance, the differences in mutation rate of amino acid at positions 87 and 91 were statistically significant in both drug-resistant and sensitive strains(both P<0.001), except for Asn87Thr. Hp strains were statistically significant for levofloxacin (Kappa=0.834, P<0.001) and clarithromycin (Kappa=0.829, P<0.001) had good concordance in resistance at the phenotypic and genotypic levels. Conclusion: The resistance of Hp to levofloxacin and clarithromycin in Ningxia region is severe, and there is good consistency between genotypic and phenotypic resistance.

Genomic and transcriptional characterization of early esophageal squamous cell carcinoma

BackgroundEsophageal squamous cell carcinoma (ESCC) is a highly heterogeneous cancer that lacks comprehensive understanding and effective treatment. Although multi-omics study has revealed features and underlying drivers of advanced ESCC, research on molecular characteristics of the early stage ESCC is quite limited.Materials and methodsWe presented characteristics of genomics and transcriptomics in 10 matched pairs of tumor and normal tissues of early ESCC patients in the China region.ResultsWe identified the specific patterns of cancer gene mutations and copy number variations. We also found a dramatic change in the transcriptome, with more than 4,000 genes upregulated in cancer. Among them, more than one-third of HOX family genes were specifically and highly expressed in early ESCC samples of China and validated by RT-qPCR. Gene regulation network analysis indicated that alteration of Hox family genes promoted the proliferation and metabolism remodeling of early ESCC.ConclusionsWe characterized the genomic and transcriptomic landscape of 10 paired normal adjacent and early ESCC tissues in the China region, and provided a new perspective to understand the development of ESCC and insight into potential prevention and diagnostic targets for the management of early ESCC in China.

Analysis of characteristics of drug resistance gene mutation in HBV RT region of hepatitis B infected patients

Objective: This article investigated the clinical characteristics and distribution of drug resistance mutation sites in HBV RT region of hepatitis B infected patients. Methods: Retrospective analysis was made on 1 948 patients with HBV infection, who had been tested for NAs resistance mutation and had a medical history of NAs in the Laboratory Department of the Fifth Medical Center of the PLA General Hospital from January 2020 to December 2021. Basic clinical information and drug resistance related mutation information were recorded. Meanwhile, the serological index data of hepatitis B were collected. Drug resistance gene mutant group and non-mutated group were grouped according to whether the drug resistance genes had a mutation in HBV RT region, and the clinical characteristics and genotype distribution of the two groups were statistically analyzed. The pattern of drug resistance gene mutation, number of mutation sites, drug resistance type and mutation of NAs resistance-related sites were analyzed in 917 patients with drug resistance gene mutation in HBV RT region. χ2 Inspection was used for counting data. Meanwhile, two independent samples t-test and Wilcoxon rank sum test were used for measurement data. Results: Among the 1 948 patients with chronic HBV infection, 917 patients had drug resistance gene mutation in RT region (47.07%). The proportion of patients with acute hepatitis B and CHB in HBV RT resistance gene mutant group was lower than that in the non-mutated group, while the proportion of patients with HBV-related cirrhosis was higher than that in the non-mutated group, these differences were statistically significant. Compared with the non-mutated group in HBV RT region, the age, the positive rates of HBeAg and HBV DNA, and HBV DNA load of these patients were increased in drug resistance gene mutant group, these differences were statistically significant. Genotypes of patients in both groups were dominated by C, followed by B and D. The proportion of patients with genotype C in HBV RT drug resistance gene mutant group was higher than that of non-mutated group, the difference was statistically significant. There were 53 gene mutation patterns in 917 patients with drug resistance gene mutation in HBV RT region, and the main pattern was rtL180M+rtM204V+rtS202G (9.70%). The mutation sites were dominated by 3 (20.74%). There were 5 types of drug resistance, LAM+Ldt (21.25%) was the most. Among the 18 sites that were clearly associated with LAM, ADV, ETV and Ldt resistance in the HBV RT region, 14 sites were mutated, and the most common mutation sites were rtL180M, rtM204V, rtM204 and rtS202G. what's more, the proportion of patients with NAs drug resistance was LAM>Ldt>ETV>ADV. Conclusion: In order to prevent adverse consequences of this study such as disease recurrence or disease progression caused by HBV drug resistance, HBV infected patients, who have long-term use of NAs antiviral therapy, should monitor the level of HBV DNA and drug resistance genes in HBV RT region in order to optimize the treatment plan in time or guide individualized treatment.

Genetic heterogeneity of thalassemia major patients in Rembang Regency, Central Java, Indonesia

Link of Video Abstract: https://www.youtube.com/watch?v=RG95aJkUndg Background: Thalassemia and hemoglobinopathies are caused by mutations in the globin genes that reduce haemoglobin synthesis. In many Asian countries, including Indonesia, thalassemia is a common inherited disorder. Thalassemia has specific characteristics due to the wide variability of the mutations from various populations. Therefore, screening protocol should be designed on specific populations’ regional gene mutation patterns. This study aims to investigate the mutational diversity of the globin genes in thalassemia major patients in Rembang Regency, Central Java, Indonesia. Methods: Genetic mutations were carried out in all major thalassemia patients who were recorded and underwent routine blood transfusions at the Rembang District Hospital from 2018 – 2020. Mutation identification was carried out using a PCR- RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) based method, the ACRS (Amplified Created Restriction Site) method, and genome sequencing. Results: The most common genotypes are double heterozygous HbE and Cd 35 mutation (-C) (42.87%), HbE and IVS1-nt.5 mutations (G&gt; C) (28.57%), HbE and IVS1- nt.2 mutations (T&gt; C), HbE and codon 8/9 (insertion + G), codon 8/9 (insertion + G) and Hb Malay, as well as Hb Adana and Hb Constant Spring (1.74%). Conclusion: The β-thalassemia and α-thalassemia mutations most commonly found in Rembang Regency are Cd 35 (-C) and non-deletional mutations.

Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer.

Loss-of-function mutations in the adenomatous polyposis coli (APC) gene are common in metastatic colorectal cancer (mCRC). However, the characteristic of APC specific mutations in mCRC is poorly understood. Here, we explored the clinical and molecular characteristics of N-terminal and C-terminal side APC mutations in Chinese patients with mCRC. Hybrid capture-based next-generation sequencing was performed on tumor tissues from 275 mCRC pati-ents to detect mutations in 639 tumor-associated genes. The prognostic value and gene-pathway difference between APC specific mutations in mCRC patients were analyzed. APC mutations were highly clustered, accounting for 73% of all mCRC patients, and most of them were truncating mutations. The tumor mutation burden of the N-terminal side APC mutations group (n=76) was significantly lower than that of the C-terminal side group (n=123) (p < 0.001), further confirmed by the public database. Survival analysis showed that mCRC patients with N-terminus side APC mutations had longer overall survival than C-terminus side. Tumor gene pathway analysis showed that gene mutations in the RTK/RAS, Wnt and transforming growth factor β signaling pathways of the C-terminal group were significantly higher than those of the N-terminal group (p < 0.05). Additionally, KRAS, AMER1, TGFBR2, and ARID1A driver mutations were more common in patients with C-terminal side APC mutations. APC specific mutations have potential function as mCRC prognostic biomarkers. There are obvious differences in the gene mutation patterns between the C-terminus and N-terminus APC mutations group, which may have certain guiding significance for the subsequent precise treatment of mCRC.

Clinical implications of myeloid malignancy‑related somatic mutations in aplastic anemia

Aplastic anemia (AA) is a potentially fatal bone marrow failure syndrome characterized by a paucity of hematopoietic stem cells and progenitor cells with varying degrees of cytopenia and fatty infiltration of the bone marrow space. Recent advances in genomics have uncovered a link between somatic mutations and myeloid cancer in AA patients. At present, the impact of these mutations on AA patients remains uncertain. We retrospectively investigated 279 AA patients and 174 patients with myelodysplastic syndromes (MDS) and performed targeted sequencing of 22 genes on their bone marrow cells using next-generation sequencing (NGS). Associations of somatic mutations with prognostic relevance and response to treatment were analyzed. Of 279 AA patients, 25 (9.0%) patients had somatic mutations, and 20 (7.2%) patients had one mutation. The most frequently mutated genes were ASXL1(3.2% of the patients), DNMT3A (1.8%) and TET2 (1.8%). In the MDS group, somatic mutations were detected in 120 of 174 (69.0%) patients, and 81 patients (46.6%) had more than one mutation. The most frequently mutated genes were U2AF1 (24.7% of the patients), ASXL1 (18.4%) and TP53 (13.2%). Compared with MDS patients, AA patients had a significantly lower frequency of somatic mutations and mostly one mutation. Similarly, the median variant allele frequency was lower in AA patients than in MDS patients (6.9% vs. 28.4%). The overall response of 3 and 6 months in the somatic mutation (SM) group was 37.5% and 66.7%, respectively. Moreover, there was no significant difference compared with the no somatic mutation (N-SM) group. During the 2-years follow-up period, four (20%) deaths occurred in the SM group and 40 (18.1%) in the N-SM group, with no significant difference in overall survival and event-free survival between the two groups. Our data indicated that myeloid tumor-associated somatic mutations in AA patients were detected in only a minority of patients by NGS. AA and MDS patients had different gene mutation patterns. The somatic mutations in patients with AA were characterized by lower mutation frequency, mostly one mutation, and lower median allelic burden of mutations than MDS. Somatic mutations were a common finding in the elderly, and the frequency of mutations increases with age. The platelet count affected the treatment response at 3 months, and ferritin level affected the outcome at 6 months, while somatic mutations were not associated with treatment response or long-term survival. However, our cohort of patients with the mutation was small; this result needs to be further confirmed with large patient sample.

Abstract 4666: PDX, mini-brain co-cultures and patient-derived tumor organoids: Preclinical models to study the prion protein in glioblastoma biology

Abstract Glioblastoma (GBM), supported by a subpopulation of glioblastoma stem cells (GSCs), stands among the most harmful tumors. Its invasive and aggressive behavior has been correlated with poor therapy outcomes and reduced patient survival, which remains difficult to model and treat due to its cellular and molecular heterogeneity. GSCs are responsible for the malignant features of this cancer, including increased recurrence rates and resistance to therapy. Efforts have been employed to understand the molecular and cellular mechanisms underlying GSCs biology. The cellular prion protein (PrPC), encoded by the PRNP gene, is a key player in GBM biology, and our group has proposed PrPC as a scaffold protein that integrates signaling platforms involved in GSCs maintenance. A deeper understanding of the intracellular pathways modulated by PrPC is essential to identify novel targets for GBM treatment. We have analyzed bulk-RNA sequencing (RNA-seq) data from patient-derived xenografts (PDX) and in vitro preclinical experimental models. RNA-seq analyses identified differentially expressed genes (DEGs) associated with adhesion and migration signaling pathways in PDX cells with high PRNP expression (PRNP−HIGH). Morphological characterization of PDX samples with PRNP−HIGH levels showed an increase in morphologically undifferentiated cell groups, that are more commonly found in younger GBM patients. Furthermore, molecular profiling using Exome data showed that groups PRNP−HIGH present enhanced global patterns of gene mutations. Due to the importance of experimental models to translate basic science into clinical applications, we are establishing emerging models to study PrPC function in GBM biology: glioblastoma organoids (GBO) from patient’s surgically resected GBM tumors; and brain organoids derived from human-induced pluripotent stem cells. We noticed a morphological and molecular reproducibility of the cytoarchitecture of brain organoids and GBO, similar to that described in the literature, indicating consistency in 3D structures, despite the variability between patients. Furthermore, brain organoids will be co-cultured with GSCs, providing platforms for studying the interaction between tumor cells and brain parenchyma. The establishment of these models will improve our comprehension of the role of PrPC in GSCs maintenance and provide additional tools to understand GBM biology and predict tumor progression and response to treatment. Citation Format: Maria Clara da Silva Souza, Barbara P. Coelho, Camila F. Fernandes, Tiago G. Dos Santos, Stefan Knorst, Cibele Masotti, Maria Rita S. Passos-Bueno, Marilene H. Lopes. PDX, mini-brain co-cultures and patient-derived tumor organoids: Preclinical models to study the prion protein in glioblastoma biology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4666.

Mutation patterns of resistance genes for macrolides, aminoglycosides, and rifampicin in non-tuberculous mycobacteria isolates from Kenya.

Non-tuberculous mycobacteria (NTM) treatment constitutes a macrolide-based antibiotic regimen in combination with aminoglycosides for Rapid-Growing Mycobacteria (RGM), and rifampicin for Slow-Growing Mycobacteria (SGM). Mutations in the anti-NTM drug target regions promote NTM evolution to mutant strains that are insusceptible to NTM drugs leading to treatment failure. We, therefore, described the mutation patterns of anti-NTM drug target genes including rrl, rrs, and rpoB in NTM isolates from Kenya. Methods: We carried out a cross-sectional study that included 122 NTM obtained from the sputum of symptomatic tuberculosis-negative patients in Kenya. All 122 NTM underwent targeted sequencing of the rrl gene. The 54 RGM were also sequenced for rrs, and the 68 SGM were sequenced for rpoB genes using ABI 3730XL analyzer. The obtained sequences were aligned to their wild-type reference sequences for each gene using Geneious then mutations were identified. Pearson chi-square at a 95% confidence interval tested the association of NTM to mutation patterns for each gene. NTM harboring mutations associated with resistance to at least one of the antibiotics used in the macrolide-based therapy were 23% (28/122). Of these NTM, 10.4% (12/122) had mutations in the rrl gene with 58.3% (7/12) comprising RGM and 41.7% (5/12) being SGM. Mutation at position 2058 (A2058G, A2058C, A2058T) of the rrl gene was seen for 83.3% (10/12) of NTM, while 16.6% (2/12) harbored a A2059G mutation. Of the 54 RGM included for rrs characterization, 11.1% (6/54) exhibited mutations at position 1408(A1408G), while 14.7% (10/68) of the SGM had mutations in the rpoB gene at positions S531W, S531L, S531Y, F506L, E509H with M.gastri having multiple mutations at positions D516V, H526D and, S531F. We demonstrated a significant level of mutations associated with drug resistance for macrolides, aminoglycosides, and rifampicin in NTM isolated from symptomatic TB negative patients in Kenya.

MP41-14 PROGNOSTIC IMPACT AND GENOMIC BACKGROUNDS OF RENAL PARENCHYMAL INFILTRATION OR MICRONODULAR SPREAD IN CLEAR CELL RENAL CELL CARCINOMA

You have accessJournal of UrologyCME1 Apr 2023MP41-14 PROGNOSTIC IMPACT AND GENOMIC BACKGROUNDS OF RENAL PARENCHYMAL INFILTRATION OR MICRONODULAR SPREAD IN CLEAR CELL RENAL CELL CARCINOMA Hajime Tanaka, Yuki Fukawa, Kouhei Yamamoto, Kousuke Tanimoto, Akira Takemoto, Hisashi Hasumi, Akihiro Hirakawa, Yudai Ishikawa, Shohei Fukuda, Yuma Waseda, Soichiro Yoshida, Minato Yokoyama, Steven C. Campbell, and Yasuhisa Fujii Hajime TanakaHajime Tanaka More articles by this author , Yuki FukawaYuki Fukawa More articles by this author , Kouhei YamamotoKouhei Yamamoto More articles by this author , Kousuke TanimotoKousuke Tanimoto More articles by this author , Akira TakemotoAkira Takemoto More articles by this author , Hisashi HasumiHisashi Hasumi More articles by this author , Akihiro HirakawaAkihiro Hirakawa More articles by this author , Yudai IshikawaYudai Ishikawa More articles by this author , Shohei FukudaShohei Fukuda More articles by this author , Yuma WasedaYuma Waseda More articles by this author , Soichiro YoshidaSoichiro Yoshida More articles by this author , Minato YokoyamaMinato Yokoyama More articles by this author , Steven C. CampbellSteven C. Campbell More articles by this author , and Yasuhisa FujiiYasuhisa Fujii More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003279.14AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: The efficacy of adjuvant immune checkpoint inhibition has been reported recently for locally advanced clear cell renal carcinoma (ccRCC); however, further exploration is required to define optimal candidates for this strategy, who are at high risk for recurrence. In this study, we defined renal parenchymal infiltration or micronodular spread (RPI/MNS) in ccRCC and investigated its prognostic impact and genomic backgrounds. METHODS: We retrospectively analyzed 333 M0 ccRCC patients treated with radical nephrectomy (approval # M2019-172 and M2021-272). Two pathologists evaluated the whole tissue sections of surgical specimens and performed the focused analysis on the tumor interface with normal renal parenchyma. Recurrence-free survival (RFS) was analyzed as an endpoint. Genomic DNA was extracted from tumor tissue in eligible cases (n=51), and variants were screened using a panel of 440 cancer-related genes. RESULTS: Overall, ≥pT3a, WHO/ISUP grade 3-4, and microvascular invasion were observed in 107 (32%), 138 (41%), and 199 (60%) patients, respectively. Histological assessment revealed the variations of the tumor interface with normal renal parenchyma and identified the specific pattern at high risk for recurrence. This finding was defined as RPI/MNS, in whichcancer cells infiltrated or spread into the renal parenchyma by involving normal renal tissue and/or by forming micronodules. RPI/MNS was finally identified in 40 patients (12%). During the median follow-up of 6.0 years, 67 patients (20%) developed recurrence. On multivariable analysis, ≥pT3a, grade 3-4, and RPI/MNS were independently associated with shorter RFS; RPI/MNS showed the highest hazard ratio (4.63) followed by grade 3-4 (2.03) and ≥pT3a(1.99). 2y-RFS rates were 38% and 95% in patients with and without RPI/MNS, respectively. The genomic analysis revealed significantly different patterns of representative gene mutations in ccRCC (figure). Patients with RPI/MNS (n=18) had significantly more frequent mutations in SETD2 (28% vs. 6%) and TSC1 (17% vs. 0%) in comparison to those without RPI/MNS (n=33). CONCLUSIONS: RPI/MNS had a strong impact on recurrence after surgery with the background of aggressive genomic features in ccRCC. Adjuvant therapy may be recommended for patients showing RPI/MNS. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e560 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Hajime Tanaka More articles by this author Yuki Fukawa More articles by this author Kouhei Yamamoto More articles by this author Kousuke Tanimoto More articles by this author Akira Takemoto More articles by this author Hisashi Hasumi More articles by this author Akihiro Hirakawa More articles by this author Yudai Ishikawa More articles by this author Shohei Fukuda More articles by this author Yuma Waseda More articles by this author Soichiro Yoshida More articles by this author Minato Yokoyama More articles by this author Steven C. Campbell More articles by this author Yasuhisa Fujii More articles by this author Expand All Advertisement PDF downloadLoading ...

Molecular characterisation of colistin and carbapenem-resistant clinical isolates of Acinetobacter baumannii from Southeast Europe

ObjectivesTo characterise 11 colistin- and carbapenem-resistant Acinetobacter baumannii isolates recently emerging in hospital settings. MethodsA. baumannii isolates were collected from hospitalised patients under colistin treatment in three countries of Southeast Europe: Turkey, Croatia, and Bosnia and Herzegovina. Isolates were identified using molecular methods. ResultsIsolates from Turkey and Croatia belong to the sequence types ST195 or ST281 of the clone lineage 2, while the single isolate from Bosnia and Herzegovina belongs to the ST231 of clone lineage 1. All isolates turned out to be highly resistant to colistin (MIC ≥ 16 mg/L) and have point mutations in pmrCAB operon genes. The colistin-resistant isolate from Bosnia and Herzegovina had a unique P170L point mutation in the pmrB gene and the R125H point mutation in the pmrC gene. The L20S mutation in the pmrA gene was detected only in isolates from Croatia and has never been reported before in isolates from this country. ConclusionColistin resistance in A. baumannii in hospitalised patients receiving colistin treatment is a result of chromosomal mutations. The pattern of point mutations in pmrCAB genes suggests a spread of specific colistin-resistant isolates within the hospital.

Prevalence and Patterns of Gene Mutations Associated with &lt;i&gt;M. tuberculosis&lt;/i&gt; Resistance to Isoniazid and Rifampicin in Patients with Different Clinical Manifestations of Tuberculosis

The objective: to study prevalence and patterns of mutations in the katG, inhA, ahpC, rpoB genes associated with Mycobacterium tuberculosis (MTB) resistance to isoniazid (H) and rifampicin (R) in patients with various clinical manifestations of pulmonary tuberculosis (TB).Subjects and Methods. 441 sputum samples collected in tuberculosis patients were tested using biological microchips. Tests were carried out in Group 1 - patients with confirmed bacterial excretion (n = 256) and in Group 2 (n = 185) - patients without bacterial excretion. The same patients were enrolled in Group 3 - patients with acute progressing tuberculosis (n = 52) and Group 4 (n = 99) - patients with localized tuberculosis.Results. In Group 1, DNA of Mycobacterium tuberculosis was found in 79.3% of patients, in Group 2 - in 57.8%. Among all samples, mutations in the genes encoding resistance to isoniazid were detected in 15.5%, resistance to rifampicin - in 58.1%. Resistance to isoniazid was more often caused by mutations in the katG gene (49%) versus the inhA (29%) and ahpC (4.2%) genes. We found 13 most common types of mutations in the rpoB gene associated with resistance to rifampicin. The dominant mutations in both groups were Seu531-&gt;Leu mutations - 19.7% in Group 1 and 24.3% in Group 2. In Group 1, mutations in the katG gene (53.7%) were observed more often than mutations in the inhA gene (27.7%). In Group 3, mutations in the katG gene were registered in 30.8%, in the inhA gene - in 25%. There were no statistically significant differences in patterns of mutations in the katG, inhA, ahpC, rpoB genes between Groups 1, 2 and 3, 4. Thus, patients without bacterial excretion and patients with localized tuberculosis are a hidden dangerous reservoir of tuberculous mycobacteria with multiple drug resistance to rifampicin and drug resistance to isoniazid.

Mutation patterns of resistance genes for macrolides, aminoglycosides, and rifampicin in nontuberculous mycobacteria isolates from Kenya

Background: Nontuberculous mycobacteria (NTM) treatment constitutes a macrolide-based antibiotic regimen in combination with aminoglycosides for Rapid-Growing mycobacteria (RGM), and rifampicin for Slow-Growing mycobacteria (SGM). Mutations in the anti-NTM drug target regions promote NTM evolution to mutant strains that are insusceptible to NTM drugs leading to treatment failure. We, therefore, described the mutation patterns of anti-NTM drug target genes including rrl, rrs, and rpoB in NTM isolates from Kenya. Methods: We carried out a cross-sectional study that included 122 NTM obtained from the sputum of symptomatic tuberculosis-negative patients in Kenya. All 122 NTM underwent targeted sequencing of the rrl gene. The 54 RGM were also sequenced for rrs, and the 68 SGM were sequenced for rpoB genes using ABI 3730XL analyzer. The obtained sequences were aligned to their wild-type reference sequences for each gene using Geneious then mutations were identified. Pearson chi-square at a 95% confidence interval tested the association of NTM to mutation patterns for each gene. Results: Twenty-eight (23%) of the NTM harbored mutations associated with resistance to at least one of the macrolide-based therapy antibiotics. Twelve (10.4%) NTM comprising 7(58.3%) of RGM and 5(41.7%) of SGM had mutations in the rrl gene. For ten (83.3%) NTM, mutations were found at position 2058, while for two (16.6%) NTM, mutations were found at position 2059. Six (11.1%) of the 54 RGM exhibited mutations in the aminoglycoside target gene rrs at location 1408. Ten (14.7%) of the 68 SGM harbored mutations in the rpoB gene with 40 percent having mutations at codon 531. Conclusion: We demonstrated a significant level of mutations associated with drug resistance for macrolides, aminoglycosides, and rifampicin in NTM isolated from symptomatic TB negative patients in Kenya.

Whole-exome sequencing and bioinformatic analyses revealed differences in gene mutation profiles in papillary thyroid cancer patients with and without benign thyroid goitre background.

Papillary thyroid cancer (PTC) is the most common thyroid malignancy. Concurrent presence of cytomorphological benign thyroid goitre (BTG) and PTC lesion is often detected. Aberrant protein profiles were previously reported in patients with and without BTG cytomorphological background. This study aimed to evaluate gene mutation profiles to further understand the molecular mechanism underlying BTG, PTC without BTG background and PTC with BTG background. Patients were grouped according to the histopathological examination results: (i) BTG patients (n = 9), (ii) PTC patients without BTG background (PTCa, n = 8), and (iii) PTC patients with BTG background (PTCb, n = 5). Whole-exome sequencing (WES) was performed on genomic DNA extracted from thyroid tissue specimens. Nonsynonymous and splice-site variants with MAF of ≤ 1% in the 1000 Genomes Project were subjected to principal component analysis (PCA). PTC-specific SNVs were filtered against OncoKB and COSMIC while novel SNVs were screened through dbSNP and COSMIC databases. Functional impacts of the SNVs were predicted using PolyPhen-2 and SIFT. Protein-protein interaction (PPI) enrichment of the tumour-related genes was analysed using Metascape and MCODE algorithm. PCA plots showed distinctive SNV profiles among the three groups. OncoKB and COSMIC database screening identified 36 tumour-related genes including BRCA2 and FANCD2 in all groups. BRAF and 19 additional genes were found only in PTCa and PTCb. "Pathways in cancer", "DNA repair" and "Fanconi anaemia pathway" were among the top networks shared by all groups. However, signalling pathways related to tyrosine kinases were the most significantly enriched in PTCa while "Jak-STAT signalling pathway" and "Notch signalling pathway" were the only significantly enriched in PTCb. Ten SNVs were PTC-specific of which two were novel; DCTN1 c.2786C>G (p.Ala929Gly) and TRRAP c.8735G>C (p.Ser2912Thr). Four out of the ten SNVs were unique to PTCa. Distinctive gene mutation patterns detected in this study corroborated the previous protein profile findings. We hypothesised that the PTCa and PTCb subtypes differed in the underlying molecular mechanisms involving tyrosine kinase, Jak-STAT and Notch signalling pathways. The potential applications of the SNVs in differentiating the benign from the PTC subtypes requires further validation in a larger sample size.

Stromal protein CCN family contributes to the poor prognosis in lower-grade gioma by modulating immunity, matrix, stemness, and metabolism.

Background: The CCN family of stromal proteins is involved in the regulation of many important biological functions. However, the role of dysregulated CCN proteins in lower-grade glioma (LGG) remain less understand. Methods: The clinical significance of the CCN proteins was explored based on RNA-seq profiles from multiple cohorts. A CCNScore was constructed using LASSO regression analysis. The PanCanAtlas data and MEXPRESS database were employed to elucidate molecular underpinnings. Results: The expression of CCN4 was associated with poor prognosis in LGG. The CCNScore (CCN1 = 0.06, CCN4 = 0.86) showed implication in prognosis prediction, subtype assessment and therapy selection. The gene mutation pattern of the high-CCNScore group was similar with glioblastoma, including EGFR, PTEN, and NF1 mutation frequently. Besides, the high-CCNScore group was comprised of samples mainly classic-like and mesenchymal-like, had lower methylation levels, higher stemness, higher inflammation, higher levels of extracellular matrix remodel and dysfunction of metabolic pathways. On the other hand, the low-CCNScore group consisted mainly of IDH-mutation LGG, and was characterized by TP53, CIC, and ATRX gene mutations, hyper-methylation status, lower stemness, lower proliferation, immune quietness and low extracellular matrix stiffness. Conclusion: In summary, these results outlined the role of CCN family in LGG and provided a potential and promising therapeutic target.

Mutation patterns of resistance genes for macrolides, aminoglycosides, and rifampicin in nontuberculous mycobacteria isolates from Kenya

Background: Nontuberculous mycobacteria (NTM) treatment constitutes a macrolide-based antibiotic regimen in combination with aminoglycosides for Rapid-Growing mycobacteria (RGM), and rifampicin for Slow-Growing mycobacteria (SGM). Mutations in the anti-NTM drug target regions promote NTM evolution to mutant strains that are insusceptible to NTM drugs leading to treatment failure. We, therefore, described the mutation patterns of anti-NTM drug target genes including rrl, rrs, and rpoB in NTM isolates from Kenya. Methods: We carried out a cross-sectional study that included 122 NTM obtained from the sputum of symptomatic tuberculosis-negative patients in Kenya. All the 122 NTM underwent targeted sequencing of the rrl gene. The 54 RGM were also sequenced for rrs, and the 68 SGM were sequenced for rpoB genes using ABI 3730XL analyzer. The obtained sequences were aligned to their wild-type reference sequences for each gene using Geneious then mutations were identified. Pearson chi-square at 95% confidence interval tested the association of NTM to mutation patterns for each gene. Results: Twenty-eight (23%) of the NTM harbored mutations associated with resistance to at least one of the macrolide-based therapy antibiotics. Twelve (10.4%) NTM comprising 7(58.3%) of RGM and 5(41.7%) of SGM had mutations in the rrl gene. For ten (83.3%) NTM, mutations were found at position 2058, while for two (16.6%) NTM, mutations were found at position 2059. Six (11.1%) of the 54 RGM exhibited mutations in the aminoglycoside target gene rrs at location 1408. Ten (14.7%) of the 68 SGM harbored mutations in the rpoB gene with 40 percent having mutations at codon 531. Conclusion: We demonstrated a significant level of mutations associated with drug resistance for macrolides, aminoglycosides, and rifampicin in NTM isolated from symptomatic TB negative patients in Kenya.

A Case of Epidermolysis Bullosa Simplex (Dowling-Meara 1 Type) in Newborn

Epidermolysis bullosa is a rare genetic skin disease in which skin easily peels off and blisters are formed with mild mechanical trauma. It is classified into simple, borderline, dysmorphic, and mixed type. These four subtypes are further classified according to the location of gene mutation and genetic patterns. Epidermolysis bullosa simplex (EBS) is characterized by separation in the epidermal or subepidermal layer. And it is mostly caused by mutation of keratin 5 (KRT5) and KRT14 genes. Recently, genetic test has become increasingly important for diagnosis, confirming subtypes and genetic counseling. And there are moderate correlation exists between the EBS phenotype and genotype. Here, we report a case of 2-day-old boy with EBS Dowling-Meara type (EBS-DM) diagnosed by mutation analysis in KRT14.