Urinary glyphosate and AMPA levels in a cross-sectional study of postmenopausal women: Associations with organic eating behavior and dietary intake

Animal and epidemiologic studies suggest that there may be adverse health effects from exposure to glyphosate, the most highly used pesticide in the world, and its metabolite aminomethylphosphonic acid (AMPA). Meanwhile, consumption of organic foods (presumably grown free of chemical pesticides) has increased in recent years. However, there have been limited biomonitoring studies assessing the levels of human glyphosate and AMPA exposure in the United States. We examined urinary levels of glyphosate and AMPA in the context of organic eating behavior in a cohort of healthy postmenopausal women residing in Southern California and evaluated associations with demographics, dietary intake, and other lifestyle factors. 338 women provided two first-morning urine samples and at least one paired 24-h dietary recall reporting the previous day's dietary intake. Urinary glyphosate and AMPA were measured using LC-MS/MS. Participants reported on demographic and lifestyle factors via questionnaires. Potential associations were examined between these factors and urinary glyphosate and AMPA concentrations. Glyphosate was detected in 89.9% of urine samples and AMPA in 67.2%. 37.9% of study participants reported often or always eating organic food, 30.2% sometimes, and 32.0% seldom or never. Frequency of organic food consumption was associated with several demographic and lifestyle factors. Frequent organic eaters had significantly lower urinary glyphosate and AMPA levels, but not after adjustment for covariates. Grain consumption was significantly associated with higher urinary glyphosate levels, even among women who reported often or always eating organic grains. Soy protein and alcohol consumption as well as high frequency of eating fast food were associated with higher urinary AMPA levels. In conclusion, in the largest study to date examining paired dietary recall data and measurements of first-void urinary glyphosate and AMPA, the vast majority of subjects sampled had detectable levels, and significant dietary sources in the American diet were identified.

Abstract 2013: Integrated proteomic analysis identifies four distinct subtypes of high-risk neuroblastoma

Neuroblastoma is the most common solid extracranial tumor in children. Despite intensive multi-modal therapy, 5-year survival rates for patients with high-risk disease remain at approximately 50%. Neuroblastomas typically have low mutational burden and harbor few recurrent mutations making the identification of new therapeutic targets challenging. To characterize the proteomic landscape of high-risk neuroblastoma, we performed liquid chromatography-mass spectrometry-based deep expression proteomics and phosphoproteomics on 30 neuroblastoma tumors from 26 patients with high-risk disease. Our integrated analysis identified four distinct proteomic subgroups of high-risk neuroblastoma that were not otherwise apparent based on clinical or genomic features. The four subgroups were named based on their defining proteomic signature: C1-Mixed, C2-Neuronal, C3-Functional MYCN and C4-Stromal. Only one third of C3-Functional MYCN tumors had amplification of MYCN. Segmental chromosomal losses and gains were enriched in, but not exclusive to, C1-Mixed and C3-Functional MYCN tumors. The activities of multiple kinases including CDK2, CDK7 and MEK2 differed significantly between subgroups. C3-Functional MYCN and C4-Stromal tumors were enriched for immune and stromal cells, respectively. Focal adhesion signaling was specifically upregulated in C4-Stromal tumors suggesting increased extracellular matrix interactions in this tumor subgroup. C2-Neuronal tumors were enriched for axon guidance and neurotrophin signaling pathways. Rho family GTPase signaling was also evident in multiple tumor subgroups. C1-Mixed and C3-Functional MYCN tumors had elevated expression of RNA processing proteins which was associated with increased alternative splicing. Splicing analysis also identified multiple novel protein coding splice events that were shared amongst multiple neuroblastoma tumors and outliers compared to both the Genotype-Tissue Expression (GTEx) dataset and a panel of commercial reference tissues. Protein domain analysis of these novel splice variants suggested that these novel protein isoforms may have aberrant functions that contribute to tumorigenesis. In conclusion, phosphoproteomic analysis can identify candidate pathways for the development of new therapies for patients with high-risk neuroblastoma.

Citation Format: Kristin L. Leskoske, Sara A. Byron, Seema Plaisier, Apurva M. Hegde, Krystine Garcia-Mansfield, Ritin Sharma, Genevieve Bergendahl, Abhinav Nagulapally, William Ferguson, Jaqueline Kraveka, Javier Oesterheld, William P. Hendricks, Giselle L. Saulnier Sholler, Jeffrey M. Trent, Patrick Pirrotte. Integrated proteomic analysis identifies four distinct subtypes of high-risk neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2013.

Characterization of aberrant alternative splicing landscape in patients with renal cell carcinoma (RCC)

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Background: Aberrant alternative splicing (AS) events have been implicated in the initiation and progression of various cancers; however, the detailed nature of their role in RCC is yet to be fully elucidated. Our study aims to characterize AS events in RCC tumors using a novel AS pipeline (Bisbee). Methods: We retrospectively identified patients (pts) with RCC who had tumor-normal whole exome sequencing and tumor whole transcriptome sequencing (GEMExtra, Ashion Analytics) performed as part of their routine clinical care. AS events from RNA sequencing data were identified and further characterized as (1) alternative splice 3’ site (A3), (2) alternative splice 5’ site (A5), (3) exon skipping (ES), (4) intron retention (IR), and (5) mutually exclusive exons splice events (MUT). The Bisbee outlier analysis was performed against normal kidney tissues from the GTEx tissue library to further identify tumor-associated splice events. Outlier splice events were categorized as either non-coding/protein loss/silent, isoform switch, novel, or unknown. Results: Overall, 147 RCC pts (77% male) with RNA sequencing data were included in this analysis. Median age at diagnosis was 60 (range 31-94) and 97% of pts had metastatic RCC. The distribution of histology was 85% clear cell RCC followed by 11% papillary RCC. The AS analysis identified 25,928 outlier splice events. Approximately 60% of these were predicted to be protein-coding events, with the majority arising from IR and ES. These were followed by A3, A5, and MUT, in descending order of frequency. We also examined tumor-associated novel outlier events where 70% of analyzed RCC tumor samples noted 34 tumor-associated novel events were present, shared in most of the cohort and found an enrichment for IR events leading to frame disruptions. Data of splice variants will be presented at the meeting. Conclusions: In depth examination of this large cohort suggests that IR resulting from AS events occur frequently within RCC. Further efforts to investigate the association of AS events and clinical outcomes are underway.

Genomic and Transcriptomic Analysis of Relapsed and Refractory Childhood Solid Tumors Reveals a Diverse Molecular Landscape and Mechanisms of Immune Evasion

Children with treatment-refractory or relapsed (R/R) tumors face poor prognoses. As the genomic underpinnings driving R/R disease are not well defined, we describe here the genomic and transcriptomic landscapes of R/R solid tumors from 202 patients enrolled in Beat Childhood Cancer Consortium clinical trials. Tumor mutational burden (TMB) was elevated relative to untreated tumors at diagnosis, with one-third of tumors classified as having a pediatric high TMB. Prior chemotherapy exposure influenced the mutational landscape of these R/R tumors, with more than 40% of tumors demonstrating mutational signatures associated with platinum or temozolomide chemotherapy and two tumors showing treatment-associated hypermutation. Immunogenomic profiling found a heterogenous pattern of neoantigen and MHC class I expression and a general absence of immune infiltration. Transcriptional analysis and functional gene set enrichment analysis identified cross-pathology clusters associated with development, immune signaling, and cellular signaling pathways. While the landscapes of these R/R tumors reflected those of their corresponding untreated tumors at diagnosis, important exceptions were observed suggestive of tumor evolution, treatment resistance mechanisms, and mutagenic etiologies of treatment.

Integrated whole-exome and transcriptome analysis of 250 treatment-refractory or relapsed (R/R) childhood solid tumors

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Background: The major genomic profiling studies that have helped define the molecular landscapes of pediatric cancers have typically focused on untreated pediatric cancers at diagnosis. Despite improvements in overall survival for childhood cancers, patients with treatment-refractory or relapsed (R/R) solid tumors face a poor prognosis. The genomic underpinnings of R/R disease are less well-characterized. Here, we describe the integrated genomic and transcriptomic analysis of 250 R/R solid tumors from 202 children profiled within precision medicine studies (NCT01355679, NCT01802567, NCT02162732) conducted by the Beat Childhood Cancer Consortium. Methods: Tumor-normal whole-exome and tumor mRNA sequencing was performed by Ashion Analytics (Phoenix, Arizona), a CAP-accredited, CLIA-certified laboratory, or within the research setting at TGen. Longitudinal tumor samples were sequenced for 20 patients. Variant calling included single nucleotide variants, indels, copy number alterations, and fusions. Integrated genomic and transcriptomic research analysis included microsatellite instability assessment, immunogenomic profiling, and functional gene set enrichment analysis. Results: Forty-six tumor types were represented, grouped into four general categories: sarcomas (36.1%; n = 73), neuroblastomas (29.2%; n = 59), CNS tumors (23.3%; n = 47), and other rare tumors (11.4%; n = 23). For patients with whole exome sequencing data, 78.3% (n = 144/184) of tumors bore a somatic alteration in at least one known cancer gene. Over one-third (39.1%; 72/184) of the cohort bore oncogenic fusions and/or oncogenic/likely-oncogenic hotspot mutations in a known cancer gene. Pathognomonic fusions were identified in 25% (46/184) of tumors, occurring most frequently in sarcomas. Pathogenic or likely pathogenic germline variants were identified in 8.7% (16/184) of patients. Microsatellite instability was detected in five different tumor types. Despite nearly all tumors (94%, 173/184) having at least one predicted strong binding neoantigen, over a quarter of tumors lacked transcript expression of these neoantigens or exhibited low MHC class I expression. Further, a subset of tumors showed elevated expression of the co-inhibitory immune checkpoint molecule PDL1. Transcriptional analysis and functional gene set enrichment analysis identified cross-pathology tumor clusters associated with immune signaling, development, and cellular signaling pathways. Longitudinal analysis revealed temporal heterogeneity pointing to the importance of re-biopsy at relapse for targeted treatment planning. Conclusions: Together, these data suggest R/R childhood solid tumors exhibit shared molecular features that are reflective of underlying biology, demonstrating the importance of comprehensive profiling to inform molecularly-guided treatment of R/R disease.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.

Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer

The majority of the targeted therapeutic agents in clinical use target proteins and protein function. Although DNA and RNA analyses have been used extensively to identify novel targets and patients likely to benefit from targeted therapies, these are indirect measures of the levels and functions of most therapeutic targets. More importantly, DNA and RNA analysis is ill-suited for determining the pharmacodynamic effects of target inhibition. Assessing changes in protein levels and function is the most efficient way to evaluate the mechanisms underlying sensitivity and resistance to targeted agents. Understanding these mechanisms is necessary to identify patients likely to benefit from treatment and to develop rational drug combinations to prevent or bypass therapeutic resistance. There is an urgent need for a robust approach to assess protein levels and protein function in model systems and across patient samples. While "shot gun" mass spectrometry can provide in-depth analysis of proteins across a limited number of samples, and emerging approaches such as multiple reaction monitoring have the potential to analyze candidate markers, mass spectrometry has not entered into general use because of the high cost, requirement of extensive analysis and support, and relatively large amount of material needed for analysis. Rather, antibody-based technologies, including immunohistochemistry, radioimmunoassays, enzyme-linked immunosorbent assays (ELISAs), and more recently protein arrays, remain the most common approaches for multiplexed protein analysis. Reverse-phase protein array (RPPA) technology has emerged as a robust, sensitive, cost-effective approach to the analysis of large numbers of samples for quantitative assessment of key members of functional pathways that are affected by tumor-targeting therapeutics. The RPPA platform is a powerful approach for identifying and validating targets, classifying tumor subsets, assessing pharmacodynamics, and identifying prognostic and predictive markers, adaptive responses and rational drug combinations in model systems and patient samples. Its greatest utility has been realized through integration with other analytic platforms such as DNA sequencing, transcriptional profiling, epigenomics, mass spectrometry, and metabolomics. The power of the technology is becoming apparent through its use in pathology laboratories and integration into trial design and implementation.

Dermatoglyphic peculiarities in children with oral clefts

In humans, the development of the primary palate and the lip is completed by the 7th week of intra uterine life and that of secondary palate by 12th week. The dermal ridges develop in relation to the volar pads, which are formed by the 6th week of gestation and reach maximum size between 12th and 13th weeks. This means that the genetic message contained in the genome--normal or abnormal is deciphered during this period and is also reflected by dermatoglyphics. Hence this study was done in order to observe the differences in dermatoglyphic patterns between the children with oral clefts and normal children and to determine the usefulness of dermatoglyphics in studying the genetic etiology of oral clefts. Dermatoglyphic data from 50 oral cleft children and 50 normal children were collected using the ink method and comparison was done between them. In the present study, we found an increase in the ulnar loop patterns on the distal phalanges of the ten fingers, an increase in the atd angle and an increase in the fluctuating asymmetry of the atd angle in the oral cleft children which indicates the degree of developmental instability of the oral cleft individual.

Use of EMLA: is it an injection free alternative?

This study was conducted to evaluate the use of Eutectic Mixture of Local Anesthetics (EMLA) for various clinical procedures such as extraction of the mobile primary teeth, root stumps as well as pulpal therapy procedures in the primary teeth. Thirty children in need of routine dental procedures were selected and procedures were done under a single anesthesia of EMLA. Pain perception and the effectiveness of anesthesia were evaluated with the Eland's color scale and Lickert's scale respectively. Results showed that use of EMLA could to some extent eliminate the use of the needle in the procedures performed especially in pediatric dentistry.

Clinical evaluation of Carisolv in the chemico-mechanical removal of carious dentin

The Chemo-mechanical caries removal technique involves the application of chemical agents, to cause a selective softening of the carious dentine and facilitate removal by gentle excavation. Carisolv is one such new chemical agent used in this minimal invasive technique of carious dentine removal. The present study was, therefore, undertaken to evaluate the efficacy of Carisolv in the chemo-mechanical removal of carious dentine, the time taken for caries removal, the perception of the treatment by the patient, and to evaluate the restorations, radiographically. Accordingly, fifty primary and permanent molars with dentinal carious lesions were excavated using this technique of caries removal. The chemo-mechanical caries removal technique using Carisolv proved to be an effective atraumatic treatment modality with potential interest for use in clinical pediatric dentistry.

Ultrasonographic and electromyographic evaluation of the labial musculature in children with repaired cleft lips

Muscle thickness and activity of the labial musculature in twenty seven children aged 4 to 12 years, with repaired cleft lips were measured using ultrasonographic and electromyographic techniques respectively. The results demonstrated that the muscle thickness and muscle activity were more at the repaired area when compared to that at the normal areas, adjacent to the repaired area, on either side. No significant positive correlation was noted between the muscle thickness and muscle activity.

Gallium alloy versus high copper amalgam: a comparative evaluation of corrosion resistance and microleakage in the primary teeth

In vivo corrosion and in vitro microleakage of a gallium based and a high copper amalgam alloys were evaluated. Twenty-five primary molars each were restored with Galloy and DPI alloy respectively and evaluated, over a period of three months, for various aspects of corrosion in the oral cavity. Additionally ten primary molars were utilized for evaluation of microleakage by dye penetration after having them restored with the two materials. Gallium alloy restorations showed better marginal adaptation, clinically when compared to amalgam restorations. No significant difference was observed for the degree of microleakage around gallium alloy and amalgam restorations.

Clinical evaluation of electronic dental anesthesia for various procedures in pediatric dentistry

Electronic dental anesthesia (EDA) is a newer technique for achieving regional anesthesia by the application of transcutaneous electrical nerve stimulation (TENS). The present study intended to be an initial investigation of the attitudes of dentists and patients towards a relatively newly introduced EDA system. The purpose of the study was to evaluate the effectiveness of EDA system, a unit of TENS, in the management of pain during treatment procedures such as minor extractions, restorations (tooth preparations), and pulp therapy, in children. Overall, forty children between the age groups of 5 to 12 years were selected for three different clinical procedures. The response of the patients as well as the opinion of both, the clinician and the patient regarding perception of pain and comfort on administration I effectiveness of electronic anesthesia were recorded and analyzed. Significantly favorable results to the use of EDA were obtained, which indicate that EDA, besides offering safety and psychological advantages, may also be a promising alternative to the conventional methods of local anesthesia.

Caries prevalence amongst handicapped children of South Canara district, Karnataka

This epidemiological investigation was carried out among 524 handicapped children in the age group of 3-30 years, attending 8 different non-residential special schools in South Canara district, Karnataka. The examination procedure and criteria were those recommended by W.H.O. in 1997. The total caries prevalence was found to be 71.56%. The mean deft in the primary dentition was found to be 3.06 +/- 3.14. The mean deft and DMFT in the mixed dentition were 3.32 +/- 2.82 and 1.14 +/- 1.08 respectively. The mean DMFT in the permanent dentition was 4.51 +/- 3.17. The prevalence of dental caries was higher in the mentally subnormal and handicapped children. The decayed component constituted the majority of the dental caries index. Lack of conservative approach to the treatment had been confirmed in the study.

Relationship between the existing caries status, plaque S. mutans and Cariostat caries activity test in children

An attempt was made in this study to find out the sensitivity and specificity of a caries activity test, CARIOSTAT and its relationship to the existing caries status and the plaque S. mutans level. The test proved to be highly sensitive and specific with significant relationship to the S.mutans count in the dental plaque. There also was a significant relationship between both the cultured microorganisms on MSB agar and the plaque in the Cariostat medium.