Non-synonymous Single Nucleotide Variants Research Articles

Abstract LB132: In silico mutant neoantigen prediction - a promising avenue for target identification in human adrenocortical carcinoma

Abstract Introduction: Adrenocortical carcinoma (ACC) is one of the most aggressive endocrine malignancies and confers a poor prognosis in advanced stages. Effective treatments are lacking. The results of immune checkpoint inhibition were disappointing with few responders only deriving clinical benefit. For the development of novel immunotherapies such as tumor vaccines and T cell-based treatments, target identification is essential. Tumor-specific mutant neoantigens that may be recognized by T cells in the context of major histocompatibility complex (MHC) I are promising candidates. Methods: We performed whole exome-sequencing in 10 ACC samples with matched blood controls. Somatic mutations were identified using an in house bioinformatics pipeline. By coupling POLYSOLVER for HLA typing with netMHCpan, in silico binding affinity of tumor-specific neoantigens to MHC was calculated taking into account both peptide and HLA sequence information. Strong binding (SB) was defined as <0.5% rank, weak binding (WB) as 0.5-1.9% rank and no binding (NB) as >2.0% rank of all peptides to MHC. Results: Across 10 ACC patients, we identified 1067 unique somatic mutations (median 49.5, ranging from 15-590), affecting 989 different genes. Binding affinity changed for 414 predicted neoantigens from NB to WB, 80 from NB to SB and 82 from WB to SB. The mutant neoantigen load per patient ranged from 10 to 235 (mean 66.2) and was positively correlated to the total number of non-synonymous single nucleotide variants (R2 0.8977, 95% CI 0.79-0.99; p<0.0001). Discussion: This is the first study that demonstrates successful in silico neoantigen profiling in ACC. Mutant neoantigens were predicted to be present both in ACC with high and low tumor mutational burden. These data will pave the way for in vitro validation and hold potential to develop therapeutic cancer vaccines and T cell-based cancer immunotherapy in ACC. Citation Format: Laura-Sophie Landwehr, Silke Appenzeller, Laura Ölsner, Isabel Weigand, Silviu Sbiera, Martin Fassnacht, Matthias Kroiss. In silico mutant neoantigen prediction - a promising avenue for target identification in human adrenocortical carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB132.

Abstract 4528: Evaluation of plasma circulating tumor DNA (ctDNA)-based whole genome sequencing (pWGS) and whole exome sequencing (pWES) and concordance with tumor tissue whole exome sequencing (tWES): a pilot study in patients with recurrent or metastatic head and neck squamous cell carcinoma or metastatic urothelial carcinoma

Abstract Background: The genetic heterogeneity and clonal evolution of tumors is hypothesized to influence disease response and acquisition of resistance during treatment. However, comprehensive analysis of the changing tumor molecular landscape to support evaluation of such a hypothesis is often difficult to quantify due to the lack of accessibility to longitudinal biopsy samples in a large number of patients (pts). Longitudinal analyses using pWGS or pWES may allow the delineation of the genetic evolution of tumors and its impact on treatment outcomes. We conducted a pilot study to evaluate the feasibility of obtaining pWGS and pWES data from ctDNA in pretreatment samples from pts enrolled in 2 phase 3 trials that evaluated second-line pembrolizumab versus chemotherapy/standard-of-care therapy: KEYNOTE-040 (recurrent or metastatic head and neck squamous cell carcinoma; NCT02252042) and KEYNOTE-045 (metastatic urothelial carcinoma, NCT02256436). Concordance between pWES and tWES was also evaluated. Methods: Cell-free DNA was isolated from 1-3 mL of plasma; pWGS (via low-pass WGS) and pWES were performed on samples from pts with available tWES data generated as part of planned tissue biomarker analyses for the respective studies. Tumor burden in ctDNA was estimated from pWES data using single nucleotide variant (SNV)-based maximum somatic allele frequency (MSAF) and from pWGS data using a copy number variation-based measure of mutational burden in the tumor fraction. Concordance between the pWES and tWES mutational spectrum was determined using the Jaccard index. Concordance of key driver somatic events (FGFR3, TP53, and HPV status) was evaluated. Results: Plasma samples from 47 pts (KEYNOTE-040, n = 24; KEYNOTE-045, n = 23) were analyzed. Tumor burden estimates from pWGS (median coverage, 5.84; range, 4.28-8.18) and pWES (median coverage, 1806; range, 1038-2413) data were highly correlated (Spearman ρ = 0.94). A range of 0 to 956 nonsynonymous SNVs (median, 50) per pt was identified in ctDNA. When the ctDNA tumor burden was high (MSAF ≥5%, observed in two-thirds of pts), a relatively high concordance was observed for individual alterations in TP53, FGFR3, and HPV status (overall agreement: 0.87, 0.97, and 0.96, respectively); between tissue- and plasma-based tumor mutational burden (R = 0.49); and in overall mutational landscape overlap (Jaccard index: median, 0.30; range, 0.002-0.53). Conclusions: These data show that pWES exhibits reasonably high concordance with tWES when the tumor burden in ctDNA is relatively high and may be informative regarding tumor genomic characteristics. Extensive longitudinal studies are still needed to understand tumor genetic evolution using plasma ctDNA. Citation Format: Razvan Cristescu, Andrew Albright, Steven Townson, Cai Chen, Blanca Homet Moreno, Nati Lerman, Z. Alexander Cao, Carol Peña. Evaluation of plasma circulating tumor DNA (ctDNA)-based whole genome sequencing (pWGS) and whole exome sequencing (pWES) and concordance with tumor tissue whole exome sequencing (tWES): a pilot study in patients with recurrent or metastatic head and neck squamous cell carcinoma or metastatic urothelial carcinoma. [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 4528.

Immunogenicity in renal cell carcinoma: shifting focus to alternative sources of tumour-specific antigens.

Renal cell carcinoma (RCC) comprises a group of malignancies arising from the kidney with unique tumour-specific antigen (TSA) signatures that can trigger cytotoxic immunity. Two classes of TSAs are now considered potential drivers of immunogenicity in RCC: small-scale insertions and deletions (INDELs) that result in coding frameshift mutations, and activation of human endogenous retroviruses. The presence of neoantigen-specific T cells is a hallmark of solid tumours with a high mutagenic burden, which typically have abundant TSAs owing to non-synonymous single nucleotide variations within the genome. However, RCC exhibits high cytotoxic T cell reactivity despite only having an intermediate non-synonymous single nucleotide variation mutational burden. Instead, RCC tumours have a high pan-cancer proportion of INDEL frameshift mutations, and coding frameshift INDELs are associated with high immunogenicity. Moreover, cytotoxic T cells in RCC subtypes seem to recognize tumour-specific endogenous retrovirus epitopes, whose presence is associated with clinical responses to immune checkpoint blockade therapy. Here, we review the distinct molecular landscapes in RCC that promote immunogenic responses, discuss clinical opportunities for discovery of biomarkers that can inform therapeutic immune checkpoint blockade strategies, and identify gaps in knowledge for future investigations.

Whole-Genome Analysis of Mycobacterium neoaurum DSM 1381 and the Validation of Two Key Enzymes Affecting C22 Steroid Intermediates in Sterol Metabolism.

Mycobacterium neoaurum DSM 1381 originated from Mycobacterium neoaurum ATCC 25790 by mutagenesis screening is a strain of degrading phytosterols and accumulating important C22 steroid intermediates, including 22-hydroxy-23, 24-bisnorchola-4-en-3-one (4-HP) and 22-hydroxy-23, 24-bisnorchola-1,4-dien-3-one (HPD). However, the metabolic mechanism of these C22 products in M. neoaurum DSM 1381 remains unknown. Therefore, the whole-genome sequencing and comparative genomics analysis of M. neoaurum DSM 1381 and its parent strain M. neoaurum ATCC 25790 were performed to figure out the mechanism. As a result, 28 nonsynonymous single nucleotide variants (SNVs), 17 coding region Indels, and eight non-coding region Indels were found between the genomes of the two strains. When the wild-type 3-ketosteroid-9α-hydroxylase subunit A1 (KshA1) and β-hydroxyacyl-CoA dehydrogenase (Hsd4A) were overexpressed in M. neoaurum DSM 1381, the steroids were transformed into the 4-androstene-3, 17- dione (AD) and 1,4-androstadiene-3,17-dione (ADD) instead of C22 intermediates. This result indicated that 173N of KshA1 and 171K of Hsd4A are indispensable to maintaining their activity, respectively. Amino acid sequence alignment analysis show that both N173D in KshA1 and K171E in Hsd4A are conservative sites. The 3D models of these two enzymes were predicted by SWISS-MODEL and AlphaFold2 to understand the inactivation of the two key enzymes. These results indicate that K171E in Hsd4A may destroy the inaction between the NAD+ with the NH3+ and N173D in KshA1 and may disrupt the binding of the catalytic domain to the substrate. A C22 steroid intermediates-accumulating mechanism in M. neoaurum DSM 1381 is proposed, in which the K171E in Hsd4A leads to the enzyme's inactivation, which intercepts the C19 sub-pathways and accelerates the C22 sub-pathways, and the N173D in KshA1 leads to the enzyme's inactivation, which blocks the degradation of C22 intermediates. In conclusion, this study explained the reasons for the accumulation of C22 intermediates in M. neoaurum DSM 1381 by exploring the inactivation mechanism of the two key enzymes.

Deleterious mutation load in the admixed mice population

Deleterious mutation loads are known to correlate negatively with effective population size (Ne). Due to this reason, previous studies observed a higher proportion of harmful mutations in small populations than that in large populations. However, the mutational load in an admixed population that derived from introgression between individuals from two populations with vastly different Ne is not known. We investigated this using the whole genome data from two subspecies of the mouse (Mus musculus castaneus and Mus musculus musculus) with significantly different Ne. We used the ratio of diversities at nonsynonymous and synonymous sites (dN/dS) to measure the harmful mutation load. Our results showed that this ratio observed for the admixed population was intermediate between those of the parental populations. The dN/dS ratio of the hybrid population was significantly higher than that of M. m. castaneus but lower than that of M. m. musculus. Our analysis revealed a significant positive correlation between the proportion of M. m. musculus ancestry in admixed individuals and their dN/dS ratio. This suggests that the admixed individuals with high proportions of M. m. musculus ancestry have large dN/dS ratios. We also used the proportion of deleterious nonsynonymous SNVs as a proxy for deleterious mutation load, which also produced similar results. The observed results were in concordance with those expected by theory. We also show a shift in the distribution of fitness effects of nonsynonymous SNVs in the admixed genomes compared to the parental populations. These findings suggest that the deleterious mutation load of the admixed population is determined by the proportion of the ancestries of the subspecies. Therefore, it is important to consider the status and the level of genetic admixture of the populations whilst estimating the mutation loads.

Genomic profiles of Indonesian colorectal cancer patients.

Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes.

Intra-Host Evolution Provides for the Continuous Emergence of SARS-CoV-2 Variants.

Variants of concern (VOC) in SARS-CoV-2 refer to viruses whose viral genomes differ from the ancestor virus by ≥3 single-nucleotide variants (SNVs) and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Still, too little is known regarding how frequently new viral variants emerge and under what circumstances. We report a study to determine the degree of SARS-CoV-2 sequence evolution in 94 patients and to estimate the frequency at which highly diverse variants emerge. Two cases accumulated ≥9 SNVs over a 2-week period and one case accumulated 23 SNVs over 3 weeks, including three nonsynonymous mutations in the spike protein (D138H, E554D, D614G). The remainder of the infected patients did not show signs of intra-host evolution. We estimate that in as much as 2% of hospitalized COVID-19 cases, variants with multiple mutations in the spike glycoprotein emerge in as little as 1 month of persistent intra-host virus replication. This suggests the continued local emergence of variants with multiple nonsynonymous SNVs, even in patients without overt immune deficiency. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of reinfection, and (iii) patients with diminished immune function may offer broad public health benefits. IMPORTANCE New SARS-CoV-2 variants can potentially disrupt ongoing public health measures and vaccine efforts. Still, little is known regarding how frequently new viral variants emerge and under what circumstances. Based on this study, we estimate that in hospitalized COVID-19 cases, variants with multiple mutations may emerge locally in as little as 1 month, even in patients without overt immune deficiency. Surveillance by sequencing for continuously shedding patients, patients suspected of reinfection, and patients with diminished immune function may offer broad public health benefits.

A plasma-based analysis and genomic landscape of patients with high tumor mutational burden (TMB-H), microsatellite stable (MSS) colorectal cancer (CRC).

249 Background: An estimated 85% of CRC are microsatellite stable (MSS) and this population has limited response to immune checkpoint inhibitors (ICIs). Biomarkers are needed to identify responders. Although pembrolizumab received FDA universal approval for chemorefractory cancers with tissue TMB-H > 10 mut/Mb, it is not effective across all TMB-H cancers. We aim to identify TMB-H/MSS CRC patients that derive benefit from ICIs through analysis of circulating tumor DNA (ctDNA). Methods: We retrospectively queried Guardant Health database (2020-2022) for patients with advanced CRC who had ctDNA NGS (Guardant360, Redwood City, CA) as part of routine clinical care. The assay covers a 1Mb panel for TMB that counts synonymous and non-synonymous somatic SNVs and indels to calculate a TMB score. Co-mutations were evaluated for MSS cancers with plasma TMB-H; ≥20mut/Mb vs those with low TMB (TMB-L; < 20mut/Mb). RAS- mutated signature was defined as those harboring an activating somatic alteration in KRAS, NRAS, or BRAF. Statistical significance was calculated using Fisher’s exact test. Results: We identified 6412 CRC patients: 11% (711) TMB-H/MSS (median age 64), 69% (4426) TMB-L/MSS (median age 62), 3% MSI-H, and 17% unevaluable. When compared to TMB-L/MSS, patients with TMB-H/MSS had a significantly higher frequency of select genetic mutations, including TP53, APC, KRAS, EGFR, and PIK3CA (p < 0.001). Treatment-naïve TMB-H/MSS cancers had a higher frequency of ARID1A (p = 0.05) and TERT (p = 0.02) alterations, while those post therapy progression had higher frequency of KRAS (p = 0.02), EGFR (p < 0.001), and MAP2K1 (p = 0.002) alterations. A total of 556 (78%) CRC patients in the TMB-H/MSS cohort harbored a RAS-mutated genetic signature. Of those, 432 (78%) belonged to the post therapy progression group, likely representing adaptive clones post anti-EGFR therapy. While RAS-mutated tumors had a higher prevalence of PIK3CA (p = 0.001) and SMAD4 (p = 0.007) co-alterations, RAS-wildtype ones carried a higher frequency of ERBB2 (p = 0.068) alterations. Conclusions: We describe the genomic landscape of patients with plasma TMB-H/MSS CRC. A clinical cohort of TMB-H/MSS CRC patients identified by ctDNA and treated with ICIs will be presented.

Role of Stress-Induced Proteins RpoS and YicC in the Persistence of Salmonella enterica subsp. enterica Serotype Typhimurium in Tomato Plants.

Understanding the functional role of bacterial genes in the persistence of Salmonella in plant organs can facilitate the development of agricultural practices to mitigate food safety risks associated with the consumption of fresh produce contaminated with Salmonella spp. Our study showed that Salmonella enterica subsp. enterica serotype Typhimurium (strain MDD14) persisted less in inoculated tomato plants than other Salmonella Typhimurium strains tested (JSG210, JSG626, JSG634, JSG637, JSG3444, and EV030415; P < 0.01). In-vitro assays performed in limited-nutrient conditions (growth rate, biofilm production, and motility) were inconclusive in explaining the in-planta phenotype observed with MDD14. Whole-genome sequencing combined with non-synonymous single nucleotide variations analysis was performed to identify genomic differences between MDD14 and the other Salmonella Typhimurium strains. The genome of MDD14 contained a truncated version (123 bp N-terminal) of yicC and a mutated version of rpoS (two non-synonymous substitutions, i.e., G66E and R82C), which are two stress-induced proteins involved in iron acquisition, environmental sensing, and cell envelope integrity. The rpoS and yicC genes were deleted in Salmonella Typhimurium JSG210 with the Lambda Red recombining system. Both mutants had limited persistence in tomato plant organs, similar to that of MDD14. In conclusion, we demonstrated that YicC and RpoS are involved in the persistence of Salmonella in tomato plants in greenhouse conditions and, thus, could represent potential targets to mitigate persistence of Salmonella spp. in planta. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A strategy for uncovering germline variants altering anti-tumor CD8 T cell response

Among many factors known to alter the outcomes of T cell receptor (TCR)-induced proximal signaling, the role of human germline variants in dictating the individuality of the anti-tumor CD8 T cell response has remained challenging to address. Here, we describe a convenient strategy for molecular and functional characterization of phosphotyrosine-altering non-synonymous single nucleotide variations (pTyr-SNVs) that directly impact TCR-induced proximal phosphotyrosine motif-based signaling pathways. We devise an experimental co-cultivation set-up comprising a C57BL/6 mouse-derived metastatic melanoma cell line engineered to constitutively present ovalbumin (OVA) antigens and retrovirally engineered syngeneic major histocompatibility complex (MHC) Class I restricted OVA TCR-transgenic CD8 T cells (OT-I). Using the synthetic version of pTyr-SNV rs1178800678-G/T-encoding integrin alpha 4 (ITGA4) p.S1027I variant as a prototype, we show that under identical TCR stimulation conditions, genetically determined membrane-proximal immunoreceptor tyrosin activation motif (ITAM) results in increased tyrosine phosphorylation of 70 kDa zeta-chain-associated protein (ZAP70) and the levels of cytotoxic effector molecule granzyme B (GZMB), which in turn result in enhanced cytotoxic activity against metastatic melanoma cell line. This strategy paves the way for rapid molecular and functional characterization of anti-tumor immune response-linked germline pTyr-SNVs so as to improve our understanding of the genetic basis of individual-to-individual differences in anti-tumor CD8 T cell response.

Comprehensive biomarker analysis from phase II study of nivolumab in patients with thymic carcinoma.

In a phase II trial of nivolumab in advanced thymic carcinoma (UMIN000022007), long SD (SD for more than 24 weeks) was seen in three patients and irAE (Gr2 or higher) was seen in four patients among 15 patients. Here, we report preplanned comprehensive biomarker analyses. We obtained tumor samples for immunohistochemistry, peripheral blood mononuclear cells (PBMCs), plasma and serum for pharmacokinetic analysis of nivolumab and cytokine evaluations, and whole blood for immuno pharmacogenomic (PGx) analysis. PD-L1 expression on tumor cells were not associated with therapeutic efficacy, but FOXP3 expression in tumor area and stroma, CD204 expression in stroma, and MHC class I in tumor area were all low among long SD patients. PBMC of long SD patients presented with larger number of naïve/memory cells prior to treatment, suggesting priming after nivolumab administration. Immuno-PGx analysis showed non-synonymous SNVs in ITGAX and PDCD1 had some correlation with PFS. Concentration of nivolumab in blood during the treatment was not related to PFS, with their overall trend towards decreased nivolumab concentration in patients with irAEs. Low immunogenicity of thymic carcinoma demonstrated in our study may require the activation of immune systems via a combination of immune checkpoint blockades.

ARgus: Multilevel visualization of non-synonymous single nucleotide variants & advanced pathogenicity score modeling for genetic vulnerability assessment

The widespread use of high-throughput sequencing techniques is leading to a rapidly increasing number of disease-associated variants of unknown significance and candidate genes. Integration of knowledge concerning their genetic, protein as well as functional and conservational aspects is necessary for an exhaustive assessment of their relevance and for prioritization of further clinical and functional studies investigating their role in human disease. To collect the necessary information, a multitude of different databases has to be accessed and data extraction from the original sources commonly is not user-friendly and requires advanced bioinformatics skills. This leads to a decreased data accessibility for a relevant number of potential users such as clinicians, geneticist, and clinical researchers. Here, we present aRgus (https://argus.urz.uni-heidelberg.de/), a standalone webtool for simple extraction and intuitive visualization of multi-layered gene, protein, variant, and variant effect prediction data. aRgus provides interactive exploitation of these data within seconds for any known gene of the human genome. In contrast to existing online platforms for compilation of variant data, aRgus complements visualization of chromosomal exon-intron structure and protein domain annotation with ClinVar and gnomAD variant distributions as well as position-specific variant effect prediction score modeling. aRgus thereby enables timely assessment of protein regions vulnerable to variation with single amino acid resolution and provides numerous applications in variant and protein domain interpretation as well as in the design of in vitro experiments.

The impact of genetic analysis on the early detection of colorectal cancer

Although the 5-year survival rate for colorectal cancer is below 10%, it increases to greater than 90% if it is diagnosed early. We hypothesized from our research that analyzing non-synonymous single nucleotide variants (SNVs) in a patient's exome sequence would be an indicator for high genetic risk of developing colorectal cancer. First, the patient's exome sequence and the reference exome sequence were repeatedly aligned to identify the regions of similarity. The alignment between the two sequences that resulted in the most similar regions (optimal alignment) was selected. Next, we performed variant calling and identified variants in the patient's exome sequence. We applied a quality control check to assess sequencing data quality and filtered out the variants that did not pass the quality control check. Finally, the remaining selected variants were annotated with biologically pertinent information and explored for their potential roles in human disease by cross-referencing databases. A variant in the FGFR4 gene, known to cause accelerated cancer progression and tumor cell motility, was found in the patient's exome sequence. Studies suggest that this variant corresponds with an increased risk of colorectal cancer, supporting the usefulness of this procedure in early detection of colorectal cancer. This research was expanded to demonstrate that exome sequencing methods are capable of identifying other genetic variants. With higher computational power, one can produce more accurate alignment readings, detecting even the smallest of deviations from the reference exome sequence and thus enhancing the ability to evaluate genetic risk of disease.

The eighth International Forum on Stem Cells: virtual meeting, October 20-21, 2022.

The eighth International Forum on Stem Cells: virtual meeting, October 20-21, 2022.

139. Development of cefiderocol resistance in an Enterobacter hormaechei strain following prolonged antibiotic exposure

Abstract Background Cefiderocol (FDC) is a novel antimicrobial agent used for multi-drug resistant Gram-negative pathogens. To date, reports of mutations in β-lactamase and siderophore complex genes have been described and may contribute to FDC resistance. This case describes a New Dehli metallo-β-lactamase (NDM)-producing strain of Enterobacter hormaechei that developed FDC resistance following antibiotic exposure. Methods Serial respiratory and blood cultures were collected from a lung transplant recipient throughout 72 days of hospitalization. Confirmatory susceptibility and combination minimal inhibitory concentration (MIC) testing were performed using broth dilution and E-test assays. Short-read sequencing libraries were prepared using a seqWell plexWell 96 kit, and whole-genome sequencing was performed using the Illumina NovaSeq platform. Reads from the sample genomes were aligned to the chromosome and three plasmid sequences of reference genome ENCL48880. Results Four serial respiratory E. hormaechei isolates and one blood isolate were evaluated. Although initial isolates were susceptible to FDC (MICs 1-2 µg/mL), two respiratory isolates cultured after 41 days of FDC therapy had MICs of 128 µg/mL. The blood isolate remained FDC susceptible despite respiratory resistance. The combination of ceftazidime/avibactam and aztreonam was determined to be active via synergy MIC testing in all isolates, and aztreonam therapeutic drug monitoring confirmed an adequate dosing strategy. Whole-genome sequencing revealed no nonsynonymous single nucleotide variants (SNVs) within the chromosomes but identified a deletion of a large urease island in the resistant isolates. In four of the five isolates, a plasmid (p48880_mcr) was identified and analyzed for possible contributions to FDC resistance. Enterobacter Isolate Assemblies This figure demonstrates genomic assemblies from the five Enterobacter clinical isolates, noting an absence of sequence from ECResp2. Conclusion This case demonstrates development of FDC resistance in E. hormaechei isolates during a 41 day course of FDC therapy. Possible causes of resistance include a large chromosomal deletion and plasmid alleles, demonstrating a potential novel mechanism for FDC resistance. Partnering molecular testing and enhanced antimicrobial stewardship should be encouraged to optimize selection of regimens and durations to prevent resistance to FDC. Disclosures Michael G. Ison, MD MS, GlaxoSmithKlein: Grant/Research Support|Pulmocide: Grant/Research Support|Viracor Eurfins: Advisor/Consultant Nathaniel J. Rhodes, PharmD, MSc, American Academy of Colleges of Pharmacy: Grant/Research Support|Paratek: Grant/Research Support|Third Pole Therapeutics: Advisor/Consultant.

Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus.

Yellow fever virus (YFV) is the agent of the most severe mosquito-borne disease in the tropics. Recently, Brazil suffered major YFV outbreaks with a high fatality rate affecting areas where the virus has not been reported for decades, consisting of urban areas where a large number of unvaccinated people live. We developed a machine learning framework combining three different algorithms (XGBoost, random forest and regularized logistic regression) to analyze YFV genomic sequences. This method was applied to 56 YFV sequences from human infections and 27 from non-human primate (NHPs) infections to investigate the presence of genetic signatures possibly related to disease severity (in human related sequences) and differences in PCR cycle threshold (Ct) values (in NHP related sequences). Our analyses reveal four non-synonymous single nucleotide variations (SNVs) on sequences from human infections, in proteins NS3 (E614D), NS4a (I69V), NS5 (R727G, V643A) and six non-synonymous SNVs on NHP sequences, in proteins E (L385F), NS1 (A171V), NS3 (I184V) and NS5 (N11S, I374V, E641D). We performed comparative protein structural analysis on these SNVs, describing possible impacts on protein function. Despite the fact that the dataset is limited in size and that this study does not consider virus-host interactions, our work highlights the use of machine learning as a versatile and fast initial approach to genomic data exploration.

Recurrent posterior fossa group A (PFA) ependymoma in a young child with constitutional mismatch repair deficiency (CMMRD).

Recurrent posterior fossa group A (PFA) ependymoma in a young child with constitutional mismatch repair deficiency (CMMRD).

Targeted Next-Generation Sequencing Identifies Additional Mutations Other Than BCR-ABL in Chronic Myeloid Leukemia Patients: A Chinese Monocentric Retrospective Study

The discovery of tyrosine kinase inhibitors (TKIs) has drastically changed the treatment of chronic myeloid leukemia (CML) patients. However, a proportion of patients still show resistance or intolerance to TKI therapy. These patients often carry somatic variants related to myeloid malignancies, indicating that additional mutations other than BCR-ABL1 may lead to TKI treatment failure or disease progression. We retrospectively evaluated 151 CML patients receiving TKI therapy and performed next-generation sequencing (NGS) analysis of 22 CML patients to explore the mutation spectrum other than BCR-ABL1 affecting the achievement of molecular responses. We also performed a comprehensive evaluation of clinical characteristics, distinct TKI options and scoring systems in the correlation with the molecular response of TKI. In total, 161 variants were detected by NGS, most of which were nonsynonymous SNVs (Figure A). The coexistence pattern among high-frequency variants was quite intricate(Figure B). Among 25 genes with allele mutation frequency (VAF) ≥5%, the most frequently mutated gene was ASXL1 (40.9%), followed by KMT2C (27.3%), DIS3 (18.2%), ATM (13.6%), DNMT3A (13.2%) and NOTCH3 (13.6%) (Figure C). NOTCH3 and RELN mutations were only carried by subjects failing to achieve a major molecular response (MMR) at 12 months, suggesting CML patients with NOTCH3 and RELN mutations might have poor long-term treatment effects (Figure D, Figure E). The distribution frequency of ASXL1 mutations was higher in the group that did not achieve MR4.0 at 36 months (P=0.023), indicating that ASXL1 mutation was an adverse factor for the achievement of MR4.0. Furthermore, subjects in this group possessed more mutations related to activation signaling pathway genes (P=0.003) and chromatin modification genes (P=0.029) (Figure F). In the group that failed to achieve MR4.5 at 12 months, there were more subjects carrying >2 gene mutations (9.1% vs. 63.6%, P=0.024), implying that it is less likely to achieve MR4.5 with the increase in the number of mutated genes and that the existence of more than two mutations is a poor prognostic factor for achieving deep molecular response (DMR) (Figure G, Figure H). However, no statistical significance was found in the effects of mutations in ASXL1 (P=0.371), KMT2C (P=0.079), DIS3 (P=0.467), ATM (P=0.280), DNMT3A (P=0.479) and NOTCH3 (P=0.479) on PFS. In the analysis of clinical characteristics, multivariate analysis identified hemoglobin concentration (HB) (relative risk, [RR], 1.023; P=0.08) and BCR-ABLIS level at 12 months (RR, 2.485; P＜0.001) as independent predictive covariates for MR4.5(Figure I). Subjects who received initial second-generation TKI (2GTKI) were more likely to achieve early molecular response (EMR) at 3 months (P=0.012), BCR-ABLIS ≤1% at 6 months (P=0.012) and MMR at 12 months (P=0.018) than initial first-generation TKI (1GTKI). And there did not show statistical significance in achieving BCR-ABLIS≤1% at 6 months, MMR at 12 months and MR4.5 between original 1GTKI (Group A1, Glevic, Novartis, Switzerland) and generic 1GTKI (Group A2, Genike, Chiatai Tianqing Pharmaceutical Group Co., Ltd.). As for scoring system, ELTS score was sensitive in differentiating whether patients could achieve EMR (P=0.001) and MMR (P=0.004). EUTOS scoring system had a significant difference in achieving MMR at 12 months (P=0.049). However, there was no significant difference in subjects stratified by the Hasford and Sokal scoring systems. In conclusion, ASXL1 mutation, activation signal pathway genes, chromatin modification genes and the presence of >2 mutations were adverse factors in achieving molecular response with TKI treatment. HB and MMR were independent factors for DMR, and initial 2GTKI therapy was better than 1GTKI in the achievement of molecular response. For the scoring system, we found that the ELTS score was the best in predicting the efficacy of TKI therapy. Acknowledgement: The work was supported by the Key R&D Program of Zhejiang (No. 2022C03137.), Public Technology Application Research Program of Zhejiang, China (No. LGF21H080003.), the Key Project of Jinhua Science and Technology Plan, China (No. 2020-3-011.), the 2019-2022 Key Medical Discipline (Haematology) Fund of Jinhua, China. Correspondence to: Dr Jian Huang, The First Affiliated Hospital of Zhejiang University School of Medicine. No. 79 Qingchun Road. Hangzhou, Zhejiang, PR China. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Targeted resequencing of the 13q13 spondyloarthritis-linked locus identifies a rare variant in FREM2 possibly associated with familial spondyloarthritis.

The strong heritability of spondyloarthritis remains poorly explained, despite several large-scale association studies. A recent linkage analysis identified a new region linked to SpA on 13q13. Here we searched for variants potentially explaining this linkage signal by deep-sequencing of the region. Re-sequencing of the 1.4 Mb target interval was performed in 92 subjects from the 43 best-linked multicases families (71 spondyloarthritis and 21 unaffected relatives), using hybridization capture-based protocol (Illumina Nextera®). Variants of interest were then genotyped by TaqMan and high resolution melting to check their co-segregation with disease in the same families and to test their association with spondyloarthritis in an independent cohort of 1,091 unrelated cases and 399 controls. Expression of FREM2 was assessed by immunostaining. Of the 7,563 variants identified, 24 were non-synonymous coding single-nucleotide variants. Two of them were located in the FREM2 gene on a haplotype co-segregating with the disease, including one common variant (R1840W, minor allele frequency=0.11) and one rare variant (R727H, minor allele frequency=0.0001). In the case-control analysis, there was no significant association between R1840W and spondyloarthritis (P-value=0.21), whereas R727H was not detected in any of the genotyped individuals. Immunostaining experiments revealed that FREM2 is expressed in synovial membrane, cartilage and colon. Targeted re-sequencing of a spondyloarthritis-linked region allowed us to identify a rare non-synonymous coding variant in FREM2, co-segregating with spondyloarthritis in a large family. This gene is expressed in several tissues relevant to spondyloarthritis pathogenesis, supporting its putative implication in spondyloarthritis.

Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria)

PurposeThis study aimed to explore whether evidence of pathogenicity from prior variant classifications in ClinVar could be used to inform variant interpretation using the American College of Medical Genetics and Genomics/Association for Molecular Pathology clinical guidelines. MethodsWe identified distinct single-nucleotide variants (SNVs) that are either similar in location or in functional consequence to pathogenic variants in ClinVar and analyzed evidence in support of pathogenicity using 3 interpretation criteria. ResultsThousands of variants, including many in clinically actionable disease genes (American College of Medical Genetics and Genomics secondary findings v3.0), have evidence of pathogenicity from existing variant classifications, accounting for 2.5% of nonsynonymous SNVs within ClinVar. Notably, there are many variants with uncertain or conflicting classifications that cause the same amino acid substitution as other pathogenic variants (PS1, N = 323), variants that are predicted to cause different amino acid substitutions in the same codon as pathogenic variants (PM5, N = 7692), and loss-of-function variants that are present in genes in which many loss-of-function variants are classified as pathogenic (PVS1, N = 3635). Most of these variants have similar computational predictions of pathogenicity and splicing effect as their associated pathogenic variants. ConclusionBroadly, for >1.4 million SNVs exome wide, information from previously classified variants could be used to provide evidence of pathogenicity. We have developed a pipeline to identify variants meeting these criteria that may inform interpretation efforts.