Majority Of Mutations Research Articles

An In Vivo Metastasis Model Using Genotype-Defined Tumor Organoids.

Recent cancer genome analyses have identified frequently mutated genes that are responsible for the development and malignant progression of cancers, including colorectal cancer (CRC). We previously constructed mouse models that carried major driver mutations of CRC, namely Apc, Kras, Tgfbr2, Trp53, and Fbxw7, in combinations. Comprehensive histological analyses of the models showed a link between mutation combinations and malignant phenotypes, such as invasion, epithelial-mesenchymal transition (EMT), and metastasis. The major cause of cancer-related death is metastasis, making it important to understand the mechanism underlying metastasis in order to develop novel therapeutic strategies. To this end, we have established intestinal tumor-derived organoids from different genotyped mice and generated liver metastasis models via transplantation of the organoids into the spleen. Through histological and imaging analyses of the transplantation models, we have determined that the combination of Apc, Kras, Tgfbr2, and Trp53 mutations promotes liver metastasis at a high incidence. We also demonstrated polyclonal metastasis of tumor cell clusters consisting of genetically and phenotypically distinct cells through our model analysis. These organoid transplantation models recapitulate human CRC metastasis, constituting a useful tool for basic and clinical cancer research as a preclinical model. We herein report the experimental protocols of the organoid culture and generation of metastasis models.

Multidimensional analysis of TMEM132A in pan-cancer: unveiling its potential as a biomarker for treatment response prediction.

Background: TMEM132A is a transmembrane protein that regulates gastric cancer cell malignancy and overall survival in bladder cancer patients. However, while some studies have investigated the involvement of TMEM132A in specific cancers, further systematic studies are required to elucidate its specific mechanisms of action in different cancer types. Methods: We investigated the pan-cancer role of TMEM132A using several databases. We analyzed TMEM132A expression and its correlation with clinical survival, immune checkpoints, tumor stemness score, prognostic value, immunomodulators, genomic profiles, immunological characteristics, immunotherapy and functional enrichment. Results: First, it was observed that TMEM132A expression levels were higher in the majority of tumors compared to non-tumor tissues. In addition, high TMEM132A expression may have a higher prognostic value in some cancers. Furthermore, TMEM132A was significantly associated with immune checkpoints, immunomodulators, prognosis, immunomodulatory genes, tumor stemness score, cell function status and immune infiltration in most tumors. Further analysis of TMEM132A-related gene enrichment, mutation sites and types, RNA modification and genomic heterogeneity showed that the major mutations of TMEM132A were missense mutations and that TMEM132A plays a very important role in UCEC, LUAD and LIHC. Finally, these results suggest that high TMEM132A expression may be associated with a better response to specific immunotherapies. Conclusion: This comprehensive study uncovers an important function for TMEM132A in different types of cancer. It also has the potential to identify TMEM132A as a potential biomarker for predicting treatment response. This may help us to better understand how TMEM132A plays a role in cancer and provide valuable insights for developing personalised treatments.

Identifying the probability of genetic mutations in lung cancer using predictive and prognostic biomarkers from histopathological images

Background: Lung cancer is the highest deadliest disease and second largest disease being diagnosed worldwide. In the age of precision medicine, determining a patient’s genetic status is critical. Finding the percentage of gene mutation of a particular biomarker will help in targeted therapy of a patient at an early stage. Objective: Histopathology images are larger in size which needs to be converted into smaller tiles for the computational purpose. Deep Learning Techniques could be applied on this huge number of histopathological images to derive the probability of gene mutation occurrence in predictive and prognostic biomarkers of lung cancer. Methods: In this work, a deep learning convolutional neural network (CNN) model (InceptionV3) is trained on histopathology images obtained from The Cancer Genome Atlas (TCGA) to accurately predict the mutated genes in lung adenocarcinoma. The convolutional neural network-based model predicts 10 major genetic mutations percentage, i.e., EGFR, FAT1, FAT4, KEAP1, KRAS, LRP1B, NF1, SETBP1, STK11, TP53. Results: InceptionV3 predicted the probability of gene mutation from the histopathology images and categorized the genes as predictive and prognostic. InceptionV3 yielded an accuracy of 82.36% and cross entropy of 37.62%. Conclusion: InceptionV3 was trained on histopathology images to predict gene mutations with an accuracy of 82%. Prediction of gene mutations with different CNN models like AlexNet and ResNet can be explored further.

Exploring the Effect of High-Energy Heavy Ion Beam on Rice Genome: Transposon Activation.

High-energy heavy ion beams are a new type of physical mutagen that can produce a wide range of phenotypic variations. In order to understand the mechanism of high-energy heavy ion beams, we resequenced the whole genome of individual plants with obvious phenotypic variations in rice. The sequence alignment results revealed a large number of SNPs and InDels, as well as genetic variations related to grain type and heading date. The distribution of SNP and InDel on chromosomes is random, but they often occur in the up/downstream regions and the intergenic region. Mutagenesis can cause changes in transposons such as Dasheng, mPing, Osr13 and RIRE2, affecting the stability of the genome. This study obtained the major gene mutation types, discovered differentially active transposons, screened out gene variants related to phenotype, and explored the mechanism of high-energy heavy ion beam radiation on rice genes.

Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory.

Detection of HIV drug resistance (HIVDR) is vital to successful anti-retroviral therapy (ART). HIVDR testing to determine drug-resistance mutations is routinely performed in Australia to guide ART choice in newly diagnosed people living with HIV or in cases of treatment failure. In 2022, our clinical microbiology laboratory sought to validate a next-generation sequencing (NGS)-based HIVDR assay to replace the previous Sanger-sequencing (SS)-based ViroSeq. NGS solutions for HIVDR offer higher throughput, lower costs and higher sensitivity for variant detection. We sought to validate the previously described low-cost probe-based NGS method (veSEQ-HIV) for whole-genome recovery and HIVDR-testing in a diagnostic setting. veSEQ-HIV displayed 100% and 98% accuracy in major and minor mutation detection, respectively, and 100% accuracy of subtyping (provided > 1000 mapped reads were obtained). Pairwise comparison exhibited low inter-and intrarun variability across the whole-genome (Jaccard index [J] = 0.993; J = 0.972) and the Pol gene (J = 0.999; J = 0.999), respectively. veSEQ-HIV met all our pre-set criteria based on WHO recommendations and successfully replaced ViroSeq in our laboratory. Scaling-down veSEQ-HIV to a limited batch size and sequencing on Illumina iSeq. 100, allowed easy implementation of the assay into the workflow of a small sequencing laboratory with minimal staff and equipment and the ability to meet clinically relevant test turn-around times. As HIVDR-testing moves from SS- to NGS-based methods and new ART drugs come to market (particularly those with targets outside the Pol region), whole-genome recovery using veSEQ-HIV provides a robust, cost-effective and "future-proof" NGS method for HIVDR-testing.

Abstract A144: HM99462, a Novel & potent SOS1 inhibitor, induces tumor regressions in combination with KRAS G12C inhibitor, MEK inhibitor, or EGFR mutant inhibitor

Abstract Son of sevenless homolog 1 (SOS1) is one of guanine nucleotide exchange factor (GEF) responsible for a binary molecular switch to activate KRAS as well as a node in the negative feedback loop in the RTK-KRAS-MAPK signaling pathway. Therefore, combination strategies with a SOS1 inhibitor are being explored as a promising therapeutic options to target the MAPK-mediated bypass, which may improve antitumor activity or delay the induction of resistance after treatment. Herein, we presented a novel and potent SOS1 inhibitor, HM99462, which abrogates GTP-binding to KRAS and the profile of drug potency and mechanism of action was examined with in vitro and in vivo models. Biochemical activity on SOS1 was evaluated by a GTP-exchange assay on diverse KRAS G12X mutant types, NRAS Q61H, and HRAS G12V, and HM99462 showed excellent inhibitory activity, while SOS2 action was not affected. Moreover, HM99462 decreased ERK phosphorylation in various cancer cell lines harboring different major KRAS mutation statuses such as KRAS G12C, G12D, G12V, or G13D. Growth inhibition assay was performed using a three-dimensional (3D) conformation culture that mimics the complexity and heterogeneity of tumors and has elevated p-ERK. In this 3D spheroid growth inhibition assay, HM99462 demonstrated significantly effective GI50 against various KRAS mutant cancer cell lines. Additionally, HM99462 was evaluated in cancer cell xenograft mouse models harboring KRAS or EGFR mutation. The combination of HM99462 with KRAS G12C, MEK, or EGFR mutant inhibitor led to significantly synergistic anti-tumor activity in both in vitro and in vivo models with several KRAS or EGFR mutations. Based on our exploratory study, a novel and potent SOS1 inhibitor, HM99462 could be suggested as an appropriate therapeutic agent for diverse inhibitory activity against cancers causing by the hyperactivation of oncogenic KRAS or RTK signaling. And it has the potential to overcome the limitations of KRAS G12C, MEK or EGFR inhibitor through combination. IND enabling GLP-toxicity studies with HM99462 are currently underway, and we planned to initiate clinical study in early 2024. Citation Format: Jaeyul Choi, Seung Hyun Jung, Wongi Park, Jooyun Byun, Semi Lim, Youngjoo Lee, Soye Jeon, Yu-Yon Kim, Young Gil Ahn, Young Hoon Kim, Kwee Hyun Suh. HM99462, a Novel & potent SOS1 inhibitor, induces tumor regressions in combination with KRAS G12C inhibitor, MEK inhibitor, or EGFR mutant inhibitor [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A144.

Forces driving transposable element load variation during Arabidopsis range expansion.

Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.

Picalm::MLLT10 can Identify a New Subgroup of Acute Leukemias of Ambiguous Lineage with Unique Extramedullary Disease and Treatment Response

Background: Mixed-phenotype acute leukemias (MPAL), which is included in acute leukemias of ambiguous lineage (ALAL), can be classified as four different subtypes based on recurring genetic alterations including BCR::ABL, KMT2A and ZNF384 gene rearrangement as well as BCL11B activation. The 2022 WHO classification has already mentioned PICALM::MLLT10 fusions are also enriched in MPAL but need more data. In 2022 ELN classification, PICALM::MLLT10 was identified as acute myeloid leukemia (AML) with other rare recurring translocations but not ALAL. In addition, there is no separate classification for PICALM::MLLT10 in the new ICC classification. Therefore, it is still confused whether PICALM::MLLT10 corresponds to AML or acute lymphoblastic leukemia (ALL) or ALAL. Methods: Fourteen PICALM::MLLT10 positive patients of 390 AL patients (14/390, 3.6%) were identified by RNA sequencing (RNA-seq) in our center from 2020-2022, including 8 female and 6 male, with a median age of 33 years (16-50 years). These patients were newly diagnosed AL according to bone marrow morphology and immunology including 5 ALAL, 5 T-ALL [ 4 early T-cell precursor ALL (ETP-ALL), 1 cortical T-ALL], 2 AML, 1 B-ALL with aberrant expression of myeloid antigen, and 1 B/T MPAL. Results: The mean white blood cell counts of these patients was 8.25×10 9/L (2.34-51×10 9/L) and platelet counts was 168.5×10 12/L (39-429×10 12/L) individually. It should be mentioned that extramedullary disease (EMD) was found in 7 cases (7/14), including mediastinum, tonsil, and skin. In terms of immunotyping, CD7 was identified in all patients (14/14) and CD33 in 71.4% (10/14) patients. The major concurrence mutations were PHF6 mutation (8/14), JAK3 mutation (5/14), and SUZ12 mutation (4/14). Characteristic cytogenetic abnormality t(10;11)(p12.3;q14.2) was only found in three cases (3/14) (Table 1). The PICALM breakpoints are mainly concentrated in exon 17 (n=6) and exon 19 (n=8). Exon 4 (n=8), exon 6 (n=2), exon 9 (n=2) and exon 10 (n=2) are the most commonbreakpointsof MLLT10. To our knowledge, this is the first report about the breakpoints and fusion gene forms of PICALM::MLLT10. For initial treatment, these patients individually received standard ALL induction chemotherapy (VDPCP, vincristine, idarubicin, pegaspargase, cyclophosphamide, prednisone) and AML induction chemotherapy (3+7 IA regimen including idarubicin, cytarabine). The initial complete remission (CR) rate was only 35.7% (5/14), and 9 patients showing no remission (NR). These NR patients subsequently received salvage chemotherapy. It is worth mentioning that 6 of them received combined chemotherapy regimen including low doses of cytarabine (LDAC), granulocyte colony-stimulating factor (G-CSF) and anthracyclines such as aclarubicin or idarubicin or homoharringtonine (CAG or IAG or HAG), and 2 of 6 patients also further received combination therapy with venetoclax (CAG or IAG +VEN). Finally, 5 of them dramatically achieved CR (5/6). In the other 3 patients, 1 patient who was failure to initial Hyper-CVAD A/B regimen also dramatically achieved CR after the more Hyper-CVAD A regimen combined with venetoclax, and 1 patient achieved CR while another still NR with both receiving CLAG (cladribine, cytarabine, G-CSF) regimen. Subsequently 11 patients (9 CR, 2 with refractory disease) received allogenic hematopoietic stem cell transplantation (allo-HSCT), and all the CR patients survived well after HSCT (follow up 3-24 months, median 15 months) without relapse, while 2 NR patients died soon after transplantation because of severe complications (Table 2). Conclusions: Our data suggested PICALM::MLLT10 positive AL should be more appropriately recognized as an independent ALAL entity and may benefit from LDAC, G-CSF and anthracyclines combination chemotherapy as well as venetoclax. Sequential HSCT after chemotherapy combined with venetoclax may further improve long-term survival in AL patients with CR even MRD positive.

Platelet-Restricted Clonal Hematopoiesis

Clonal hematopoiesis (CH) is a common age-related condition in which somatic mutations accumulate in hematopoietic stem cells (HSCs), leading to the clonal expansion of mutated cells. CH has been causatively linked with risk of disease, including atherosclerotic cardiovascular disease (CVD), and reduced overall survival. The current model of hematopoiesis suggests substantial heterogeneity and lineage-priming within the HSC compartment, including the existence of multipotent but platelet (PLT)-biased HSCs. However, all CH studies to date are based on whole blood or granulocyte (GRA) DNA, and therefore they do not assess for PLT-restricted clones, which we reasoned could be particularly important given the association of CH with CVD. We aimed to assess for presence of PLT-biased CH in a cohort of normal individuals, hypothesizing that PLT-biased CH might represent a distinct subgroup of persons with CH. We analysed a cohort of 151 individuals, aged 22.0 to 98.6 years ( x̅ = 74.9; 95% CI, 50.0 to 91.8), with normal blood counts, and no known hematological malignancy. We first established a method for isolation of high-purity cDNA from PLTs alongside isolation of gDNA and cDNA from matched GRAs. Myeloid cell contamination was extremely low in the PLT fraction as assessed by flow cytometry and molecular analysis. We first performed targeted analysis for presence of the JAK2V617F mutation in PLT and GRA fractions due to the known association of JAK2V617F with CVD and myeloid neoplasms, including essential thrombocythemia. We developed a high sensitivity allele specific JAK2V617F droplet digital PCR (ddPCR) assay (variant allele frequency [VAF] limit of detection 0.1%) for parallel assessment of gDNA and cDNA from GRAs and PLTs respectively. When including all cases with a VAF > 0.1%, JAK2V617F CH was detected in 21 (13.9%) individuals, consisting of 2 cases of non-lineage-restricted CH (present in both GRA and PLT fractions), 6 cases of GRA-restricted CH, and 13 cases of PLT-restricted CH. Only 6 cases showed VAF ≥ 2% (consistent with CH of indeterminate potential) and all were PLT restricted. Comparison of median JAK2V617F VAF in PLT cDNA with VAF in GRA gDNA revealed significantly higher VAF in the PLT-derived material (1.00% vs. 0.26%; p = 0.04). We next developed a custom, targeted, hybridisation capture next-generation sequencing (NGS) panel for parallel ultra-deep sequencing of both gDNA and cDNA, covering the major genes and hotspot mutations involved in CH ( DNMT3A, TET2, ASXL1, IDH2, JAK2, CALR, MPL, CBL, KRAS, GNB1, SF3B1, SRSF2, U2AF1, PPM1D and TP53). The panel comprised a total of 250 120-nucleotide-long probes (including 27 cDNA-specific probes) with a combined footprint size 25,083 bp. Performance studies showed acceptable off-target effect and good coverage, alignment rate, uniformity, and complexity. Agreement between the NGS-measured VAF for GRA gDNA and GRA cDNA was high (ρ c = 0.952, alpha = 0.05). In total, we screened GRA gDNA and matched PLT cDNA samples from 42 individuals. At the resolution of VAF ≥ 2%, analysis of PLTs substantially enhanced the number of individuals with detected CH from 12 (28.6%) to 26 (61.9%) (Fig. 1). Amongst the detected variants (n = 44), mutations detected in the GRA fraction (n = 20) accounted for less than half of the detected variants, while the PLT fraction included ~75% of the variants (n = 33), including 55% (n = 24) that were PLT-restricted. Notably, lineage-restriction for the above variants held true when taking into consideration clones with VAF < 2% too. Median VAF for all CH variants was 3.9% (95% CI, 2.2% to 32.3%), with no difference between GRA and PLT CH. The detected variants were distributed across DNMT3A, TET2, ASXL1, JAK2, SF3B1, and PPM1D genes, with evidence of lineage bias towards PLTs for TET2- and JAK2-related CH. PLT-restricted clones included high-VAF (> 5%) variants in DNMT3A (n = 4; x̅VAF = 13.2%), TET2 (n = 2; x̅VAF = 7.7%), JAK2 (n = 2; x̅VAF = 21.6%), and SF3B1 (n = 1), including an individual with DNMT3AQ842R and the SF3B1K666N at VAFs 16.7% and 12.5% respectively. Selected NGS-detected variants were orthogonally validated. We describe PLT-restricted CH as a frequent phenomenon in persons with normal blood parameters. Given the known association between CH and risk of CVD and hematological malignancy, further studies on larger patient cohorts are warranted to determine the importance of PLT vs. GRA CH in relation to clinical endpoints.

2163. Prevalence and geographic distribution of mutations in TonB-dependent receptors in the Prospective Observational Pseudomonas aeruginosa (PA) Study

Abstract Background Cefiderocol (FDC) is a last line treatment for carbapenem-resistant Pseudomonas aeruginosa (CR-PA). FDC retains activity against CR-PA by inhibition of penicillin-binding proteins facilitated by active uptake of drug via TonB-dependent receptors (TBDR). Prior, we have shown an association between mutations in TBDR genes and loss of FDC susceptibility, particularly in association with changes at the PA-derived cephalosporinase (PDC/AmpC) active site. Here, we outline geographic variation and prevalence of TBDR mutations in the Prospective Observational Pseudomonas (POP) study.Figure 1.SNP frequency in the pirR, pirS, pirA, and piuA/piuD genes across geographic location.Figure 2.Genotypic variation of PirRS and PiuA/D genes in the 972 P. aeruginosa isolates of the POP cohort. Black versus gray differentiates presence of either PiuA versus PiuD homologous proteins. Color legend corresponds to presence of TBDR gene variants/SNPs per gene pirR, pirS, pirA, piuA/piuD, and ampC. Methods The genomes of 972 CR-PA isolates collected across 10 countries in North America, South America, Asia, and Oceania were screened for single nucleotide polymorphisms (SNP) resulting in missense, insertion/deletion (indel), frameshift, and early stop codon mutations in the TBDR genes pirR, pirS, pirA, piuA/piuD, and ampC using PAO1 as a reference. SNPs were defined as variant mutations occurring in ≤10% of isolates. A core genome maximum likelihood phylogenetic tree was used to assess distribution and prevalence of genotypic variants. Neighbor-joining trees of the variants in each gene were used to analyze clusters across lineages. Results Across all regions except Oceania, SNPs were most frequently seen in pirS and pirA (Fig 1). Gene variants comprised from 8% up to 50% of each geographic population. On phylogenetic mapping, isolates within the same lineage tended to have clustering of shared mutations across the TBDR genes pirS, pirR, and pirA, and the majority of piuA/piuD mutations clustered within two distinct lineages (Fig 2). Major mutations, including indel, frameshift, and early stop codon mutations occurred in 16 isolates (1.6%), predominantly in isolates from the United States (n=14). Variations in PDC were frequently observed, with 57 different variants across 35.8% of the population. Seven of the PDC variants (n=10 isolates) have been associated with decreased susceptibility to ceftolozane/tazobactam, but these variants did not co-occur with major TBDR mutations. Conclusion TBDR mutations occur in PA isolates worldwide. Mutations previously associated with reduced susceptibility to FDC occurred most frequently in isolates from the United States. Disclosures Michael J. Satlin, MD, AbbVie: IDMC member|Biomerieux: Grant/Research Support|Merck: Grant/Research Support|Shionogi: Advisor/Consultant|SNIPRBiome: Grant/Research Support William R. Miller, M.D., Merck: Grant/Research Support|UpToDate: Honoraria

Predictive significance of circulating tumor DNA against patients with T790M-positive EGFR-mutant NSCLC receiving osimertinib

Circulating tumor DNA (ctDNA) provides molecular information on tumor heterogeneity. The prognostic usefulness of ctDNA after first-line epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are limited. Therefore, the present study evaluated ctDNA during osimertinib administration as a second-line or more setting to identify the relationship between EGFR mutation levels and outcomes in patients with advanced non-small cell lung cancer (NSCLC). Forty patients with EGFR T790M-positive NSCLC receiving osimertinib after prior EGFR-TKI treatment were registered. Plasma samples were collected at osimertinib pretreatment, after 1 month of treatment, and at the time of progressive disease (PD). ctDNA analysis was performed by digital polymerase chain reaction. The detection rate of copy numbers of exon 19 deletion, L858R, and T790M in plasma samples was significantly lower 1 month after osimertinib than at pretreatment, and significantly higher at PD than at 1 month, whereas that of C797S was significantly higher at PD than at 1 month. No statistically significant difference was observed in the copy numbers of exon 19 deletion, L858R, T790M, and C797S between complete response or partial response and stable disease or PD. The detection of T790M at PD after osimertinib initiation was a significant independent prognostic factor for predicting shorter prognosis, and the presence of major EGFR mutations at pretreatment and PD was closely linked to worse survival after osimertinib initiation. Molecular testing based on ctDNA is helpful for predicting outcomes of osimertinib treatment in T790M-positive NSCLC after previous EGFR-TKI treatment.

Time point and scale measurement of carbon sink trading market risk based on catastrophe entropy and potential function

According to the principle of total entropy change of dissipative structure, the carbon trading market is defined as a nonlinear complex system that follows the law of entropy increase in this paper. Based on the potential function of sudden change theory, this paper studies the risk point and scale of the carbon trading market. The results show that (1) the theory of dissipative structure and catastrophe theory can be used as the theoretical basis of carbon financial market risk research, and its core technology can be used to measure and predict risks. (2) The risk mutation point measurement model based on the total entropy change principle and potential function technology effectively detected 16 major risk mutation points in the financial crisis, the European debt crisis, and the European new energy efficiency plan. The empirical test shows that the model has a good ability to capture abrupt changes and prediction accuracy. The fitting effect is very good. (3) The risk index value of the risk abrupt point can be calculated effectively by the risk scale measurement technique based on information entropy and the potential function surface equation. Furthermore, we judge the degree and grade of risk. From 2008 to 2021, amongst the 16 risk mutation points in the EU carbon trading market, there are three extremely high risk mutation points, seven high-risk mutation points, two medium-risk mutation points, two low-risk mutation points, and two very low risk mutation points. High risk or above grade accounted for 62.5%. Empirical analysis supports this conclusion.

Prognostic outcomes and recurrence patterns in resected stage I lung adenocarcinoma harbouring atypical epidermal growth factor receptor mutations.

Limited data exist on the characteristics of atypical epidermal growth factor receptor (EGFR) mutations in early-stage lung cancer. Our goal was to elucidate the associations with outcomes and recurrence patterns in resected stage I lung adenocarcinoma harbouring atypical EGFR mutations. Eligible patients between 2014 and 2019 were retrospectively identified and grouped into exon20 insertion mutations and major atypical mutations, which included G719X, L861Q and S768I. Disease-free survival (DFS) was evaluated in the entire cohort and stratified by radiologic characteristics. Recurrence patterns were investigated and compared between groups. A competing risk model was used to estimate the cumulative incidence of recurrence. A total of 710 patients were finally included. Among them, 289 (40.7%) patients had exon 20 insertion mutations and 421 (59.3%) patients had major atypical mutations. There was no significant difference regarding DFS (P = 0.142) between groups in the entire cohort. The interaction between mutation subtype and the presence of ground-glass opacities was significant (hazard ratio 2.00, 95% confidence interval 1.59-2.51, P < 0.001), indicating DFS between exon 20 insertion mutations and major atypical mutations may be different among subsolid and solid tumours. Survival analysis consistently revealed no significant difference in subsolid tumours (P = 0.680), but favourable DFS of exon 20 insertion mutations in solid tumours (P = 0.037). Furthermore, patients with exon 20 insertion mutations had a lower risk of developing bone metastases did those with radiologic solid tumours (Gray's test, P = 0.012). Exon 20 insertion mutations were correlated with favourable DFS and lower incidence of bone metastases in radiologic solid lung adenocarcinomas harbouring atypical EGFR mutations.

Prevalence and analysis of acquired and transmitted integrase strand transfer inhibitor-associated HIV-1 drug resistance in Chongqing, China

ABSTRACT In this study, we examined the occurrence of acquired and transmitted drug resistance to integrase strand transfer inhibitor (INSTI) in HIV-1 strains in Chongqing (China) for guiding for the routine testing of INSTI-associated HIV-1 genotype resistance. Plasma samples were obtained from HIV-1 patients at Chongqing Public Health Medical Center from July 2019 to August 2022. Besides, amplification, sequence, and analysis of the portion of the HIV-1 pol gene that encodes the integrase protein were implemented to identify INSTI resistance. Integrase sequence data was harvested for a comprehensive cohort of 1032 patients infected with HIV-1. This cohort consisted of 564 ART-naive patients, 465 ART-treated patients, and 3 patients with an unknown treatment history. Within the study group, we identified INSTI resistance in 21 patients (2.03%, 21/1032), including 17 ART-treated patients (3.66%, 17/465). Among the ART-treated patients, 12 were INSTI-treated (11.76%, 12/102), 5 were INSTI-naive (1.38%, 5/363), and 4 were ART-ineffective patients (0.71%, 4/564). The prevalent major resistance mutation was Q148R (0.48%, 5/1032), while the most prevalent accessory resistance mutation was E157Q (1.65%, 17/1032). In light of the above, it is recommended that the incidence of accessory genotype analysis should be considered before starting any future INSTI-based therapy, especially in patients with drug resistance to NRTIs and NNRTIs and the reduction of INSTI sensitivity should be carefully monitored and investigated. Regular monitoring for resistance should be implemented after the use of INSTIs, and, importantly, ongoing monitoring of the decreasing susceptibility to INSTIs is crucial following the initiation of treatment with INSTIs.

Genomic Mutations in SARS-CoV-2 Genome following Infection in Syrian Golden Hamster and Associated Lung Pathologies.

The continuous evolution of the SARS-CoV-2 virus led to constant developments and efforts in understanding the significance and impacts of SARS-CoV-2 variants on human health. Our study aimed to determine the accumulation of genetic mutations and associated lung pathologies in male and female hamsters infected with the ancestral Wuhan strain of SARS-CoV-2. The present study showed no significant difference in the viral load between male and female hamsters and peak infection was found to be on day four post infection in both sexes of the animals. Live virus particles were detected up to 5 days post infection (dpi) through the TCID-50 assay, while qRT-PCR could detect viral RNA up to 14 dpi from all the infected animals. Further, the determination of the neutralizing antibody titer showed the onset of the humoral immune response as early as 4 dpi in both sexes against SARS-CoV-2, and a significant cross-protection against the delta variant of SARS-CoV-2 was observed. Histopathology showed edema, inflammation, inflammatory cell infiltration, necrosis, and degeneration of alveolar and bronchial epithelium cells from 3 dpi to 14 dpi in both sexes. Furthermore, next-generation sequencing (NGS) showed up to 10 single-nucleotide polymorphisms (SNPs) in the SARS-CoV-2 (ancestral Wuhan strain) genome isolated from both male and female hamsters. The mutation observed at the 23014 position (Glu484Asp) in the SARS-CoV-2 genome isolated from both sexes of the hamsters plays a significant role in the antiviral efficacy of small molecules, vaccines, and the Mabs-targeting S protein. The present study shows that either of the genders can be used in the pre-clinical efficacy of antiviral agents against SARS-CoV-2 in hamsters. However, considering the major mutation in the S protein, the understanding of the genetic mutation in SARS-CoV-2 after passing through hamsters is crucial in deciding the efficacy of the antiviral agents targeting the S protein. Importance: Our study findings indicate the accumulation of genomic mutations in SARS-CoV-2 after passing through the Syrian golden hamsters. Understanding the genomic mutations showed that either of the hamster genders can be used in the pre-clinical efficacy of antiviral agents and vaccines.

Outcome of Acute Myeloid Leukemia in Adults Treated with Standard Chemotherapy-a Single Center Retrospective Study

Background: Acute Myeloid Leukemia (AML) is a heterogenous Hematopoietic stem cell disorder and standard therapy being intensive chemotherapy (IC) followed by consolidation with either high dose Cytarabine or Allogeneic Hematopoietic stem cell transplantation in intermediate and high-risk patients. Though the outcome in younger &amp; fit patients with IC in terms of CR rates and survivability are reasonable, however patients above 60 years may not benefit owing to increasing frailty, co-morbidities, adverse disease risk factors, chemo resistance and toxicities. Newer approaches with Novel/Targeted agents are being incorporated in treatment strategies in order to acheive better results and long-term survival. We report outcome of AML patients treated on standard chemotherapy at our institution. Methods: Total 208 Acute Myeloid Leukemia (AML) patients were treated at our institution between January 2017 and December 2022 and analyzed after institutional review board (IRB) approval. Data was collected from institutional data base and summarized by medians and Range for continuous variables, numbers and percentages for categorical variables &amp; Survival estimates were obtained by Kaplan-Meier method. Results: Median age of our cohort was 46.5 years (range,17-90), Male patients were 57% (n-118) and 43% (n-90) were Female. Seventy-five (36%) were locals and 133 (64%) of other nationalities. Median WBC 11.5 x10^9/L (range 0.60-381); Hemoglobin 83 g/L (range 27-103), Platelets 53x10^9/L (range 2-791), Median Bone marrow blast were 50% and median LDH 357 U/L. Normal cytogenetics was present in 54.4% (n-111); 19%(n-39) were Core binding Factor (CBF), 3.5% trisomy 8 and 3.5% were complex cytogenetics. Major molecular mutations included FLT3-ITD (21%), NPM1 (18.3%), DNMT3A (11%), IDH1&amp;2 (7%), TET2(5%), TP53(3.5%) and ASXL1(3%). As per European Leukemia Net (ELN 2017) risk stratification, Intermediate risk were 50% (n-104), Favorable 30% (n-63) and Adverse 20% (n-41). Total of 164 (79%) patients received intensive chemotherapy, 13(7%) Azacytidine and Venetoclax, 16(8%) low intensity and 12(6%) best supportive care (BSC). Intensive chemotherapy included Anthracyclines +Cytarabine and FLAG/FLAG-Ida (Fludarabine, Idarubicin, Cytarabine and G-CSF). Total of 136(65%) of patients achieved Complete Remission (CR/Cri) after 1 or 2 inductions. Major adverse events during induction were grade 4 cytopenia's and pneumonias. There were 26(13.6%) deaths during induction. Majority of patients received consolidation therapy with high dose cytarabine 1-3 g/M2 twice a day for 3 days for two to 3 cycles and 28(14%) underwent Allogeneic stem cell Transplantation. At a median follow up of 9.1 months, the 2 year and 5-year overall survival (OS) were 65% and 57% in whole cohort. ELN Favorable Risk group had a better survivability at 2 years (80%). Two-year OS in Patients above 60 and less than 60 years were 37% and 75% respectively. Conclusion: Intensive chemotherapy resulted in significant survival improvement in AML and has been standard of care for more than 3 decades. However significant advances in understanding the biology, risk categorization and development of newer novel therapies has led to alter the treatment strategy with better outcome. Our study underlines the fact that we need to incorporate the newer therapies in treatment plan to achieve these goals.

Temporal trend of drug-resistance and APOBEC editing in PBMC genotypic resistance tests from HIV-1 infected virologically suppressed individuals.

We aimed at evaluating the temporal trend of drug-resistance and APOBEC editing from HIV-DNA genotypic resistance tests (GRT) in virologically suppressed individuals. Major resistance mutations (MRM), genotypic susceptibility score (GSS) for the current regimen and APOBEC-related mutations (APO-M) were evaluated. Potential changes in trends of MRM and APO-M over-time were assessed and predictors of MRM detection or sub-optimal GSS (GSS<2) at HIV-DNA-GRT were estimated through logistic regression analyses. Among the 1126 individuals included, 396 (35.2%) harboured at least one MRM (23.4% to NRTI, 18.8% to NNRTI, 7.7% to PI and 1.4% to INSTI [N=724]); 132 (12.3%) individuals showed a GSS <2. APO-M and stop codons were found in 229 (20.3%) and 105 (9.3%) individuals, respectively. APO-DRMs were found in 16.8% of individuals and were more likely observed in those individuals with stop codons (40.0%) compared to those without (14.4%, P<0.001). From 2010 to 2021 no significant changes of resistance or APO-M were found. Positive predictors of MRM detection at HIV-DNA GRT were drug abuse, subtype B infection, and a prolonged and complex treatment history. Perinatal infection and having at least 2 stop codons were associated with a current suboptimal regimen. In virologically suppressed individuals, resistance in HIV-DNA and the extent of APOBEC editing were generally stable in the last decade. A careful evaluation of APOBEC editing might be helpful to improve the reliability of HIV-DNA GRT. Further investigations are required to understand how to apply the estimation of APOBEC editing in refining genotypic evaluation.

Screening and verifying the mutations in the LDLR and APOB genes in a Chinese family with familial hypercholesterolemia

BackgroundFamilial hypercholesterolemia (FH) is an autosomal dominant genetic disorder. The primary objective of this study was to identify the major pathogenic mutations in a Chinese family with FH.MethodsWhole-genome sequencing (WGS) was used to identify variants of FH-related genes, including low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin 9 (PCSK9). Bioinformatics software was used to predict signal peptides, transmembrane structures, and spatial construction information of the mutated sequences. Western blotting was performed on the mutant protein to determine the presence of the major structural domains of the LDLR. The PCSK9 and APOB genes were screened and analyzed. Moreover, the proband and his brother were treated with a PCSK9 inhibitor for 1 year, and the effect of the treatment on lipid levels was assessed.ResultsWGS revealed two potentially pathogenic mutations in the LDLR gene. One was a novel mutation, c.497delinsGGATCCCCCAGCTGCATCCCCCAG (p. Ala166fs), and the other was a known pathogenic mutation, c.2054C>T (p. Pro685Leu). Bioinformatics prediction and in vitro experiments revealed that the novel mutation could not be expressed on the cell membrane. Numerous gene variants were identified in the APOB gene that may have a significant impact on the family members with FH. Thus, it is suggested that the severe manifestation of FH in the proband primarily resulted from the cumulative genetic effects of variants in both LDLR and APOB. However, a subsequent study indicated that treatment with a PCSK9 inhibitor (Evolocumab) did not significantly reduce the blood lipid levels in the proband or his brother.ConclusionsThe cumulative effect of LDLR and APOB variants was the primary cause of elevated blood lipid levels in this family. However, PCSK9 inhibitor therapy did not appear to be beneficial for the proband. This study emphasizes the importance of genetic testing in determining the most suitable treatment options for patients with FH.

HIV Drug Resistance Patterns and Characteristics Associated with Clinically Significant Drug Resistance among Children with Virologic Failure on Antiretroviral Treatment in Kenya: Findings from the Opt4Kids Randomized Controlled Trial.

Increasing HIV drug resistance (DR) among children with HIV (CHIV) on antiretroviral treatment (ART) is concerning. CHIV ages 1-14 years enrolled from March 2019 to December 2020 from five facilities in Kisumu County, Kenya, were included. Children were randomized 1:1 to control (standard-of-care) or intervention (point-of-care viral load (POC VL) testing every three months with targeted genotypic drug resistance testing (DRT) for virologic failure (VF) (≥1000 copies/mL)). A multidisciplinary committee reviewed CHIV with DRT results and offered treatment recommendations. We describe DR mutations and present logistic regression models to identify factors associated with clinically significant DR. We enrolled 704 children in the study; the median age was 9 years (interquartile range (IQR) 7, 12), 344 (49%) were female, and the median time on ART was 5 years (IQR 3, 8). During the study period, 106 (15%) children had DRT results (84 intervention and 22 control). DRT detected mutations associated with DR in all participants tested, with 93 (88%) having major mutations, including 51 (54%) with dual-class resistance. A history of VF in the prior 2 years (adjusted odds ratio (aOR) 11.1; 95% confidence interval (CI) 6.3, 20.0) and less than 2 years on ART at enrollment (aOR 2.2; 95% CI 1.1, 4.4) were associated with increased odds of major DR. DR is highly prevalent among CHIV on ART with VF in Kenya. Factors associated with drug resistance may be used to determine which children should be prioritized for DRT.

Synchronous detection of Burkholderia pseudomallei and its ceftazidime resistance mutation based on RNase-HII hydrolysis combined with lateral flow strip assay.

Melioidosis is a severe and often fatal infectious disease caused by Burkholderia pseudomallei, which poses significant challenges due to its high mortality rate and frequent misdiagnosis. To effectively treat infected patients, especially in epidemic regions like Hainan with a high resistance rate to ceftazidime (CAZ), early diagnosis and resistance testing are critical. Here, we designed a strategy that combines RNase-HII-dependent PCR with lateral flow strip assay (LFSA) for simultaneous detection of B. pseudomallei and its CAZ resistance mutation. In this strategy, we utilized rhPCR technology to design specific primers with a C3-spacer modification. These primers target a 115-base pair region within the ORF2 of the B. pseudomallei type III secretion system gene cluster, as well as the P174L mutation in the penA gene, which is a major mutation associated with CAZ resistance in Hainan. The primers contain complementary RNA bases that can be hydrolyzed only in the presence of thermostable RNase-HII enzymes, facilitating subsequent PCR reactions. Additionally, we introduced two pairs of universal probes carrying fluorescein isothiocyanate (FITC) and biotin, as well as digoxin and biotin. The sequences of these universal probes align with specific regions of the primers, resulting in target products labeled with different tags. The resulting amplification products are then subjected to LFSA, where the presence of specific markers is visually interpreted based on color development. These markers flow to test line 1 (T1) and are captured by a fixed anti-FITC antibody, generating a red line that indicates the presence of B. pseudomallei. Similarly, the occurrence of a red line on test line 2 (T2), which is fixed with anti-digoxin antibodies, indicates the presence of the P174L mutation in B. pseudomallei. This protocol serves as an excellent tool for the rapid diagnosis of melioidosis and provides a basis for selecting appropriate antibiotic medication. It has the potential to revolutionize the diagnosis of melioidosis, particularly in resource-limited settings. Furthermore, this technique holds promise as a versatile tool for disease diagnosis in general. IMPORTANCE This study focused on the development of a reaction system using rhPCR to amplify a specific gene, ORF2, of B. pseudomallei and to identify the P174L mutation associated with increased drug resistance to ceftazidime (CAZ). The system incorporated universal primer probes and a simple temperature cycle reaction. The amplified products were then analyzed using lateral flow strip assay (LFSA) for strain identification and mutation interpretation. The developed system provides a reliable basis for diagnosing melioidosis and selecting appropriate drugs. Its potential impact is particularly significant in resource-limited settings where access to advanced diagnostic techniques is limited. This platform stands out for its simplicity, convenience, sensitivity, specificity, and portability. It shows promise as a point-of-care testing method for detecting single nucleotide polymorphism in genes associated with other diseases. By leveraging the advantages of this platform, researchers and healthcare professionals can potentially expand its use beyond melioidosis and apply it to the rapid detection of genetic variations in other disease-related genes.