Passed Quality Control Research Articles

Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens

BackgroundAlthough cavitating ultrasonic aspirators are commonly used in neurosurgical procedures, the suitability of ultrasonic aspirator-derived tumor material for diagnostic procedures is still controversial. Here, we explore the feasibility of using ultrasonic aspirator-resected tumor tissue to classify otherwise discarded sample material by fast DNA methylation-based analysis using low pass nanopore whole genome sequencing.MethodsUltrasonic aspirator-derived specimens from pediatric patients undergoing brain tumor resection were subjected to low-pass nanopore whole genome sequencing. DNA methylation-based classification using a neural network classifier and copy number variation analysis were performed. Tumor purity was estimated from copy number profiles. Results were compared to microarray (EPIC)-based routine neuropathological histomorphological and molecular evaluation.Results19 samples with confirmed neuropathological diagnosis were evaluated. All samples were successfully sequenced and passed quality control for further analysis. DNA and sequencing characteristics from ultrasonic aspirator-derived specimens were comparable to routinely processed tumor tissue. Classification of both methods was concordant regarding methylation class in 17/19 (89%) cases. Application of a platform-specific threshold for nanopore-based classification ensured a specificity of 100%, whereas sensitivity was 79%. Copy number variation profiles were generated for all cases and matched EPIC results in 18/19 (95%) samples, even allowing the identification of diagnostically or therapeutically relevant genomic alterations.ConclusionMethylation-based classification of pediatric CNS tumors based on ultrasonic aspirator-reduced and otherwise discarded tissue is feasible using time- and cost-efficient nanopore sequencing.

O09 Microsatellite-unstable sporadic sebaceous and duodenal tumours are associated with loss of mismatch protein expression

Abstract Introduction and aims Lynch syndrome (LS) is a common heritable cancer predisposition syndrome. Tumours from patients with LS demonstrate microsatellite instability (MSI-high), a genetic signature detectable by low-cost DNA sequencing assays that is currently utilized in colorectal cancer screening. The utility of MSI assays for LS detection has not been extensively studied in unselected sebaceous skin tumours or duodenal tumours, where currently immunohistochemical (IHC) expression of mismatch repair (MMR) proteins is used. In addition, it has recently been suggested that cutaneous squamous cell carcinoma (cSCC) could be linked to LS; however MSI status has not been studied in patients with early-onset cSCC. Methods We investigated MSI status in archival formalin-fixed paraffin-embedded cases with ethical approval. We examined 110 sebaceous tumours (STs) (45 female patients, 65 male patients; median age 77 years), 50 duodenal tumours (DTs) (28 female patients, 22 male patients; median age 64 years), and 148 cSCCs selected from patients under 50 years of age (69 female patients, 79 male patients; median age 49 years). Immunohistochemistry (IHC) was performed on each MSI-high sample to determine the expression of MMR proteins MLH1, MSH2, MSH6 and PMS2. Samples that passed quality control were included in the analysis. Results A total of 42 of 106 STs (39.6%) were MSI-high. All STs had loss of at least one MMR protein. Overall, 10 of 41 (24%) DTs were MSI-high. All DTs had loss of at least one MMR protein. We found that 12 of 148 (8.1%) cSCCs were MSI-high and 5 of 12 SCCs exhibited loss of at least one MMR protein expression (41%). Conclusions MSI-high status correlated well with loss of MMR protein expression in STs and DTs samples. Future studies will help establish MSI status in tumours initially selected by MMR loss on IHC, informing its use as an adjunct to MMR IHC in LS detection in patients with STs and DTs.

Relative vaccine protection, disease severity, and symptoms associated with the SARS-CoV-2 omicron subvariant BA.2.86 and descendant JN.1 in Denmark: a nationwide observational study

During the 2023 Danish COVID-19 vaccination campaign, an updated monovalent mRNA vaccine targeting the SARS-CoV-2 omicron XBB.1.5 subvariant was administered. However, the rapid spread of a genetically divergent omicron BA.2.86 subvariant, JN.1, since September, 2023, poses potential challenges due to its rapid dominance and possible immune escape. Using national electronic health registry data from all regions of Denmark, we aimed to investigate whether the SARS-CoV-2 subvariant BA.2.86, and its descendant JN.1, differed from other circulating variants in terms of their ability to escape vaccine protection, the risk of infection leading to severe disease, and self-reported symptoms among infected people. In this observational study, we included all residents of Denmark aged 65 years and older who tested positive for SARS-CoV-2 by PCR between Oct 1 and Dec 31, 2023, and for whom genomic data on the SARS-CoV-2 variant that had caused their infection were available. Data from clinical testing, sentinel, and self-sampling-based surveillance were linked with national electronic civil, vaccination, and hospitalisation registers. The relative protection of the XBB.1.5 updated COVID-19 vaccine against BA.2.86 infections versus infections with other variants was analysed in a case-only study, and the relative risk of hospitalisation in people infected with BA.2.86 versus other variants was analysed in a case-control study. Both analyses were adjusted for time, comorbidities, and previous vaccination history, among other potential confounders. Additionally, prevalence patterns in self-reported symptoms among people of all ages infected with SARS-CoV-2 were reported separately by subvariant. Of the 7581 people in Denmark aged 65 years or older who tested positive for SARS-CoV-2 by PCR during the study period, 5882 (78%) samples were eligible for sequencing. 3862 (66%) of these passed quality control, were successfully sequenced, and the SARS-CoV-2 variant and subvariant identified, and these individuals were included in the study. Of these 3862 people, 2184 (57%) were infected with the BA.2.86 subvariant, including 1615 JN.1 infections. Participants infected with BA.2.86 had 1·52 (95% CI 1·25-1·86) times the odds, and those infected with JN.1 had 1·60 (1·27-2·02) times the odds, of having received the XBB.1.5 vaccine at least 7 days before their infection compared with participants infected with a non-BA.2.86 variant. The severity analysis showed no evidence of association between the infecting variant and the risk of COVID-19 hospitalisation (odds ratio 1·04 [95% CI 0·86-1·26] for BA.2.86 and 1·07 [0·85-1·34] for JN.1). Similarly, there was no evidence of differences in self-reported symptoms by variant strain. Compared with other SARS-CoV-2 variants, BA.2.86 and the JN.1 sublineage were less sensitive to vaccine-induced immune protection from the XBB.1.5 updated COVID-19 vaccine; however, we found no evidence that infection with BA.2.86 or JN.1 resulted in increased disease severity or different symptom profiles. Although less effective against the new variants, XBB.1.5 vaccination remains protective and reduces the risk of infection and COVID-19 disease. The Danish Government and the EU's EU4Health programme.

Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip

This study aimed to evaluate the genetic diversity and structure within the Dengchuan cattle population and effectively protect and utilize their germplasm resources. Herein, the single-nucleotide polymorphisms (SNPs) of 100 Dengchuan cattle (46 bulls and 54 cows) were determined using the GGP Bovine 100K SNP Beadchip. The results showed that among the Dengchuan cattle, a total of 101,220 SNPs were detected, and there were 83,534 SNPs that passed quality control, of which 85.7% were polymorphic. The average genetic distance based on identity-by-state (IBS) within the conservation population of Dengchuan cattle was 0.26 ± 0.02. A total of 3,999 genome-length runs of homozygosity (ROHs) were detected in the Dengchuan cattle, with ROH lengths primarily concentrated in the range of 1–5 Mb, accounting for 87.02% of the total. The average inbreeding coefficient based on ROHs was 4.6%, within the conservation population of Dengchuan cattle, whereas it was 4.9% for bulls, and the Wright inbreeding coefficient (FIS) value was 2.4%, demonstrating a low level of inbreeding within the Dengchuan cattle population. Based on neighbor-joining tree analysis, the Dengchuan cattle could be divided into 16 families. In summary, the conservation population of Dengchuan cattle displays relatively abundant diversity and a moderate genetic relationship. Inbreeding was observed among a few individuals, but the overall inbreeding level of the population remained low. It is important to maintain this low level of inbreeding when introducing purebred bloodlines to expand the core group. This approach will ensure the long-term conservation of Dengchuan cattle germplasm resources and prevent loss of genetic diversity.

Transcriptomic Profiles Associated with Experimental Placebo Effects in Chronic Pain.

Gene expression networks associated with placebo effects are understudied; in this study, we identified transcriptomic profiles associated with placebo responsivity. Participants suffering from chronic pain underwent a verbal suggestion and conditioning paradigm with individually tailored thermal painful stimulations to elicit conditioned placebo effects. Participants reported pain intensity on a visual analog scale (VAS) anchored from zero = no pain to 100 = maximum imaginable pain. RNA was extracted from venous blood and RNA sequencing and validation tests were performed to identify differentially expressed genes (DEGs) associated with placebo effects, controlling for sex and level of pain. Unbiased enrichment analyses were performed to identify biological processes associated with placebo effects. Of the 10,700 protein-coding genes that passed quality control filters, 667 were found to be associated with placebo effects (FDR <0.05). Most genes (97%) upregulated were associated with larger placebo effects. The 17 top transcriptome-wide significant genes were further validated via RT-qPCR in an independent cohort of chronic pain participants. Six of them (CCDC85B, FBXL15, HAGH, PI3, SELENOM, and TNFRSF4) showed positive and significant (P < 0.05) correlation with placebo effects in the cohort. The overall DEGs were highly enriched in regulation of expression of SLITs and ROBOs (R-HSA-9010553, FDR = 1.26e-33), metabolism of RNA (R-HSA-8953854, FDR = 1.34e-30), Huntington's disease (hsa05016, FDR = 9.84e-31), and ribosome biogenesis (GO:0042254, FDR = 2.67e-15); alternations in these pathways might jeopardize the proneness to elicit placebo effects. Future studies are needed to replicate this finding and better understand the unique molecular dynamics of people who are more or less affected by pain and placebo.

Formulation, Optimization and Evaluation of Solid SMEDDS of Pioglitazone

This investigation assessed 32 formulations of liquid self-microemulsifying drug delivery system (L-SMEDDS) for pioglitazone (PGZ). The optimal PLS12 formulation comprises 40% capmul MC8 (oil), 40% cremophore RH40 (surfactant), and 20% PEG (co-surfactant). PLS12 exhibited approximately 75 nm droplet size, below 200 nm, and a PDI of 0.47, indicating nanosized droplets with uniform distribution. The formulation demonstrated stability, and achieved supreme drug loading capacity. The enhanced L-SMEDDS was solidified into solidified SMEDDS utilizing Sylloid 244 FP, subsequently in a free-flowing powder without drug interactions. Tablets were successfully formulated by incorporating S-SMEDDS with diverse tableting excipients. The selected tablet batch passed quality control and stability tests. The tablet exhibited a rapid and pH-independent release profile. The combined impact of SMEDDS and tablets collectively enhanced the solubility and dissolution of PGZ hydrochloride

Abstract 2265: Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma

Abstract Advances in sequencing techniques have made molecular subgrouping of Diffuse Large B-cell Lymphoma (DLBCL) based on DNA cahnges, which has led to the development of Lymphgen classification. By the way, although alternative splicing (AS) in cancer cells contributes to proliferation, invasion and metastasis, and immune escape, their role and association with DLBCL molecular subtypes are unknown. Therefore, we analyzed whole-exome sequencing (WES) and bulk RNA-Seq data paired in the public EGA dataset (EGAD00001003600) to explore the patterns of AS events that differ between Lymphgene subtypes. The WES data of 620 DLBCL samples that passed quality control were aligned to the reference using BWA-MEM, and variants were called with Mutect2. We used the information of copy number variants provided by cBioPortal. The RNA-Seq analysis was performed using the STAR-RSEM pipeline and differential splicing events were detected using rMATS to compare subtypes. Among 620 DLBCL samples, there were 19 MCDs, 95 EZBs, 22 BN2s, and 137 ST2s (50 samples with multiple genetic classes, and 291 samples unclassified). Mutations in spliceosome complex genes (ZRSR2 and SF1) were found in 14 and 27 samples, respectively. In BN2 and MCD subtypes, splicing events with significantly different exon inclusion levels were observed at a high frequency of 29 and 16 occurrences, respectively, compared to other subtypes. (P-value &amp;lt; 0.05). In contrast, retained intron is the only event observed in the EZB subtype (Table 1). Samples with mutations in ZRSR2 and SF1 showed four and two aberrant events, respectively, compared to samples without these mutations. Of note, rMATS detected an alternative 3’ splice site event in exon 6 of CD37 in the MCD. CD37 is involved in tumorigenesis in leukocytes and has been suggested as a potential biomarker in blood cancer, and its dysregulation may have influenced the poor prognosis of MCD. In summary, molecular subtypes of DLBCL had unique features in terms of alternative splicing. Functional consequences of these selective exon usages for each DLBCL subtype are being warranted. Citation Format: Sanyeowool An, Youngil Koh, Sung-Soo Yoon. Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2265.

Abstract 973: Plasma androgen receptor (AR) copy number gain at progression in patients randomized in the STAMPEDE phase 3 abiraterone acetate, prednisolone (AAP) and enzalutamide (ENZ) trial: An ancillary biomarker study

Abstract Addition of ENZ or AAP to androgen deprivation therapy (ADT) as first-line treatment for advanced prostate cancer improves survival compared to ADT alone. Genomic alterations in AR associate with resistance to ENZ/AAP when started for castration-resistant prostate cancer (CRPC). We aimed to test whether early use of AAP/ENZ altered the incidence of AR alterations at progression. Between July 2014 and March 2016, 1976 patients with metastatic or high-risk locally advanced prostate cancer were randomized to ADT or ADT+ENZ+AAP in the STAMPEDE trial (NCT00268476). Consenting patients were given the option to donate blood for the ancillary biomarker study at trial-defined progression and prior to start of the next line of treatment. We focused on patients who progressed within 4 years from the end of recruitment (early progressors), as these patients represent the greatest unmet need. We obtained plasma DNA at emergence of CRPC from 115 early progressors (ADT n=63, ADT+ENZ+AAP n=52). We performed liquid biopsy-focused, custom, high-coverage targeted enrichment sequencing (PCF-SELECT, Orlando et al, NAR Cancer 2022). We used a bespoke computational pipeline, leveraging allelic imbalance and fragmentome analysis, to detect circulating tumor DNA (ctDNA) in plasma samples and copy number changes. Of 108 samples that passed quality control, 94 were positive for tumor (ADT n=52, ADT+AAP+ENZ n=42). The detection rate and ctDNA fractions were similar between the two treatment groups [ADT: 86.7% (52/60), mean ctDNA fraction 0.18; ADT+ENZ+AAP: 87.5% (42/48), mean ctDNA fraction 0.21; p=0.34]. The proportion of plasma with detectable ctDNA and AR gain was significantly higher with ADT+AAP+ENZ vs ADT alone (15/42, 35.7% vs 8/52, 15.4%, p=0.03). We then implemented the same approach on plasma collected from patients progressing on ENZ started for metastatic CRPC in a prospective Phase 3b trial (PRESIDE, NCT02288247): we confirmed a high prevalence of AR gain in plasma samples with detectable ctDNA (47.7%, 95% CI 38.8-54.9) in the CRPC setting. Significant copy number aberrations in relevant prostate cancer-related genes/pathways (deletions of TP53, RB1, PTEN or DNA repair genes, or gain of PI3K/AKT1) were identified in 9 out of 42 evaluable samples in the ADT group and 18 out of 38 evaluable samples in the ADT+ENZ+AAP group (21.4% vs 47.4%, p=0.014). Treatment with ADT+ENZ+AAP increases detection of plasma AR gain at emergences of CRPC in early progressors compared to ADT alone. Detection of plasma AR gain increases at progression on ADT+ENZ regardless of the treatment setting. The impact of early use of ENZ/AAP on the detection of copy number aberrations, especially homozygous deletions, in other prostate cancer-related genes in plasma requires further investigation. Citation Format: Gianmarco Leone, Francesco Orlando, Suparna Thakali, Sharanpreet Lall, Daniel Wetterskog, Anna Wingate, Noel W. Clarke, Nicholas D. James, Francesca Demichelis, Gerhardt Attard. Plasma androgen receptor (AR) copy number gain at progression in patients randomized in the STAMPEDE phase 3 abiraterone acetate, prednisolone (AAP) and enzalutamide (ENZ) trial: An ancillary biomarker study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 973.

Abstract 7570: Molecular subtyping and immunohistochemistry validation identifies muscle Invasive bladder cancer subgroups with poorer overall survival

Abstract Introduction: Muscle-invasive bladder cancers (MIBC) are molecularly heterogeneous and have poor clinical outcomes, compared to non-muscle invasive disease. The molecular characterization of subtypes and immune status has shown prognostic value and the potential to guide precision intervention. However, a more comprehensive understanding of the association between subtypes and immune cells is still required. To this end, an integrative multi-omics analysis was performed on patients with MIBC. Methods: From a cohort of 244 MIBC patients who did not receive neoadjuvant chemotherapy, cystectomy tissue was collected to assess molecular features associated with poor outcomes. Macro-dissected FFPE slides were used to perform whole transcriptome RNA sequencing (N=208, passing quality control) and both the consensus single-sample classifier and TCGA classifier were applied to the RNAseq data to determine molecular subtypes. Immunohistochemistry (IHC) staining for canonical markers of basal (KRT5, 14 and CD44), luminal (KRT20, GATA3, FOXA1) and immune cells (CD3, CD8, PD-L1 (SP263)) was performed, and scoring was assessed by two independent pathologists. Tumor subtypes derived from either RNAseq or IHC were compared and correlated with disease specific survival. Results: Among the 244 MIBC patients 30.7% were T2, 47.6% were T3 and 21.7% were T4. The consensus molecular classification identified mRNA subtypes and showed agreement with the TCGA molecular classification. Correlations with disease specific survival revealed that luminal subtypes trended towards best outcome while stroma-rich subtype trended towards poorest outcomes compared to other subtypes. IHC markers associated with luminal-like and basal-like tumors recapitulated the molecularly defined luminal/basal subtype assignment. Stroma-rich subtypes were enriched with fibroblast signatures, implying high desmoplastic stromal cell infiltration and low immune cell infiltration. By integrating molecular classification and IHC immune markers (PD-L1, CD3, CD8 - serving as a proxy for ‘immune signature’), we found that the immune signatures themselves stratified the survival benefit, as previously shown. Interestingly, we observed heterogeneity of the IHC-immune signature within mRNA subtypes. Conclusions: Integrating MIBC subtyping, IHC of immune markers and patient outcomes data provides a biological framework that allows for potential biomarker identification for this lethal disease. The studies presented here underscore the existence of heterogeneity in immune phenotypes within tumor subtypes. A deeper understanding of the association between these tumor subtypes and their immunological states is crucial to guide treatment decisions, particularly for patients facing worse prognostic outcomes. Citation Format: Jiarui Zhang, Mingxiao Feng, Neil Beeharry, Shibu Thomas, Ralph Wirtz, Arndt Hartmann, Markus Eckstein, Woonyoung Choi. Molecular subtyping and immunohistochemistry validation identifies muscle Invasive bladder cancer subgroups with poorer overall survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7570.

Abstract 666: ASTX295 engages p53-mediated apoptosis and an inflammatory response in patient derived mesothelioma explants

Abstract Mesothelioma is a universally lethal, rare cancer caused by asbestos that is lacking effective targeted treatments, particularly in the relapsed setting. P53 is predominantly wildtype (WT 83%) but is likely restrained by MDM2 particularly in the context of 9p21 deletion, a common, clonal somatic event affecting around half of all mesotheliomas that results in deletion of the MDM2 suppressor ARF. 9p21 deletion is also associated with a cold, immunosuppressed microenvironment. Unleashing p53WT by inhibiting its interaction with MDM2 has therapeutic potential in mesothelioma. To test this hypothesis, we employed live patient derived explants (PDEs) as a model that reflects the genomic inter-patient heterogeneity of mesotheliomas, and harbours an intact tumour microenvironment. Between August 2017 and April 2021 a total of 71 patients were consented prior to extended pleurectomy decortication, and PDEs were harvested at the time of surgery. PDEs were then cultured and treated with ASTX295, an inhibitor of p53-MDM2 interaction, using two concentrations (0.5 and 1 micromolar) and two timepoints (48 and 72 hours). PDEs passing quality control were subjected to spatial profiling using multiplex immunofluorescence microscopy. PDEs harbouring p53WT showed ASTX295-induced p21 (CDK1A) upregulation, which correlated with induction of apoptosis (p=0.04). PDE rank-order sensitivity was conserved across different doses and exposure-times. Transcriptome analysis confirmed ASTX295 induced p53 pathway activation in conjunction with a pro-inflammatory phenotype; both of which were absent in one PDE harbouring an inactivating p53 single nucleotide variant. Constitutive epithelial mesenchymal transition (EMT) was enriched in responding PDEs, as well as MDM2 inhibitor sensitive mesothelioma cell lines. 9p21 deletion (revealed by exome sequencing) was detected in both responding and non-responding PDEs. In summary, inhibition of MDM2-P53 interaction triggers robust p53 activation and a pro-inflammatory phenotype, which is potentiated in EMT enriched mesothelioma PDEs. ASTX295 is currently under clinical investigation (NCT03975387). Citation Format: Dean Anthony Fennell, Joanna Dzialo, Jan Rogel, Daniel Faulkner, Nada Nusrat, Aleksandra Bzura, Kudzayi Kutywayo, Peter Wells-Jordan, Charlotte Poile, Andrea Biondo, Martin Sims, Apostolos Nakas, Jin-Li Luo, Min Zhang, Maria Ahn. ASTX295 engages p53-mediated apoptosis and an inflammatory response in patient derived mesothelioma explants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 666.

Abstract 3858: Peripheral CD38+ effector memory (EM) T cells are dynamic biomarkers of response to neoadjuvant immune checkpoint blockade (NeoICB) in patients (pts) with resectable dedifferentiated liposarcoma (DDLPS) and undifferentiated pleomorphic sarcoma (UPS)

Abstract Introduction: NeoICB is a promising approach for pts with DDLPS and UPS. However, biomarkers to identify which pts benefit from this treatment and understanding the mechanisms of response and resistance to ICB remains a challenge. Methods: We conducted a randomized phase 2 trial of neoICB (anti-PD1 +/- CTLA4) in pts with resectable DDLPS (n=17) and UPS (n=10). Pts with UPS received concurrent neoICB and radiation. The primary endpoint of the trial was pathological response; 3 DDLPS and 9 UPS pts were responders (R) and 14 DDLPS and 1 UPS pts were non-responders (NR). Peripheral blood mononuclear cells (PBMCs) were collected at baseline, prior to cycle 2 of neoICB (C2D1), and at the time of surgery (SURG). We performed mass cytometry (CyTOF) to identify immune cells associated with response and their dynamic changes with neoICB. We designed a custom 41-parameter panel using CD45 live cell barcoding with 31 markers for immune profiling, of which 23 were selected to detect key cell lineage and 8 to detect signaling markers. Batch correction and high dimensional data analyses were performed using CyCombine and CyTOF workflow R packages. Longitudinal comparisons between immune cell populations were conducted using Mann-Whitney U Test. Results: Of 79 available PBMC samples from 27 pts, 63 passed quality control after thawing (≥30% viability) and data clean-up (at least 10,000 events). Data was down-sampled to 5000 events for analysis. Of 19 immune cell types identified, monocytes were the most common followed by CD4+ and CD8+ T cells. There was an early increase in CD38+ effector/effector memory (EM) T cells at C2D1 in pts with DDLPS (CD8+ p=0.005, CD4+ p&amp;lt;0.001) and a similar increase observed in pts with UPS (CD8+ C2D1 p=NS, SURG p=0.034; CD4+ C2D1 p=0.024, SURG p=0.06) and these cells had higher Ki67 expression than CD38- T cells (p&amp;lt;0.005). At baseline, R pts with DDLPS had higher fractions of CD38+ EM CD8+ T cells than NR pts (p=0.044). Analysis in the UPS cohort was limited by the low number of NR pts. Higher expression of TIGIT was observed on CD38+ EM CD8+ T cells compared to CD38- counterparts at all time points. Conclusion: Peripheral CD38+ EM CD8+ T cells are associated with response to neoICB in pts with DDLPS. Longitudinal peripheral immune profiling reveals an increase in CD38+ EM CD8+ and CD4+ T cells with neoICB in pts with DDLPS and UPS. These cells are proliferative and express higher levels of TIGIT, which could be a future target for therapeutic exploration. Importantly, changes in the peripheral immune populations may precede changes in the tumor microenvironment (TME) as preliminary analyses of the TME did not identify early (C2D1) changes. TME imaging mass cytometry analyses are currently underway to associate peripheral and intratumor changes in immune populations. Citation Format: Elise F. Nassif, Hsinyi Lu, Michael Stanford, Karen Millerchip, Diana Romero, Jared Malke, Brenna Matejka, Jeffrey E. Gershenwald, Susmita Kumari, Duncan H. Mak, Angelique J. Lin, Jared K. Burks, Wei-Lien Wang, Alexander J. Lazar, Neeta Somaiah, Cara Haymaker, Christina L. Roland, Emily Z. Keung. Peripheral CD38+ effector memory (EM) T cells are dynamic biomarkers of response to neoadjuvant immune checkpoint blockade (NeoICB) in patients (pts) with resectable dedifferentiated liposarcoma (DDLPS) and undifferentiated pleomorphic sarcoma (UPS) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3858.

Abstract 1058: Immune biomarkers for recurrence in stage II and III melanoma to guide patient stratification

Abstract Stage II-III melanoma patients lack needed biomarkers to avoid over-treatment and determine need for combination immunotherapy. A “hot” tumor immune micro-environment (TIME) is predictive of survival and immunotherapy benefit in multiple tumor types. We have previously identified the ratio of CD8+/CD68+ cells as well as a 53-gene melanoma immune panel (MIP) as indicative of a favorable “hot” TIME. CD8/CD68 ratio and MIP were evaluated in specimens from 213 previously untreated patients including 164 from Roswell Park Comprehensive Cancer Center (RPCCC) and 49 from Geisinger Health Systems (GHS, n=36). Tumors were stained with Sox10, CD8, CD68, MPO, PDL1 and HLA-DR using the MOTiF workflow (Akoya Biosciences, AB). Image analysis was completed using inForm software (AB). RNA was extracted and NanoString analysis performed using published methods. Receiving Operator Curves (ROC) were generated and KM curves using cutoffs selected using maximally selected log-rank statistics to quantify survival benefit. We tested whether the CD8/CD68 ratio correlated with disease specific survival (DSS) and distant metastatic recurrence (DMR). In the RPCCC cohort (n=164), 138 specimens were evaluated by a pathologist and stained of which 15 were excluded based on tissue quality, and inForm analysis was completed on 80. Of these 80, 16 had DMR of whom 8 had died. ROC showed CD8/CD68 ratio to correlate with DMR (p=0.0397). KM analysis showed high CD8/CD68 ratio correlated with DMR free survival (p=0.00079). Within the GHS samples, 36 of 49 patients had sufficient quality tissue, of whom 13 had died. DMR data was not available. A high CD8/CD68 ratio correlated with DSS by ROC curve (p=0.027) and KM analysis (p=0.0009). MIP was run on 166 patients of whom 147 passed quality control for analysis. MIP correlated with DSS in the RPCCC cohort by ROC analysis (p=0.025) and cutoff defined based on prior cohort showed correlation with DSS (p=0.01) and trend towards correlation with DMRFS (p=0.065). To include diverse samples in the training set, MIP was retrained with the addition of 81 patients from Columbia University (CUMC). KM analysis performed using the retrained signature showed a favorable signature correlated with DSS (p=0.032) and DMRFS (p=0.00077). Immune based biomarkers including CD8/CD68 ratio and immune gene signature have potential to assist clinicians in selecting early-stage melanoma patients for more intensive immunotherapy regimens. Full analysis of the data from the RPCCC and GHS cohorts will be presented at the conference. Citation Format: Gerardo A. Espinoza, Chenxin Zhang, Jee-Young Moon, Divya B. Kenchappa, Matteo Abbruzzese, Lydia Bioh, Yadriel M. Bracero, Sharmin Sultana, Ajay Singh, Thazin Aung, John J. Krolewski, Robyn D. Gartrell, Larisa J. Geskin, Lawrence W. Leung, Tammie Ferringer, Rui Chang, Basil Horst, Kent Nastiuk, Yvonne M. Saenger. Immune biomarkers for recurrence in stage II and III melanoma to guide patient stratification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1058.

Somatic variants as a cause of drug-resistant epilepsy including mesial temporal lobe epilepsy with hippocampal sclerosis.

The contribution of somatic variants to epilepsy has recently been demonstrated, particularly in the etiology of malformations of cortical development. The aim of this study was to determine the diagnostic yield of somatic variants in genes that have been previously associated with a somatic or germline epilepsy model, ascertained from resected brain tissue from patients with multidrug-resistant focal epilepsy. Forty-two patients were recruited across three categories: (1) malformations of cortical development, (2) mesial temporal lobe epilepsy with hippocampal sclerosis, and (3) nonlesional focal epilepsy. Participants were subdivided based on histopathology of the resected brain. Paired blood- and brain-derived DNA samples were sequenced using high-coverage targeted next generation sequencing to high depth (585× and 1360×, respectively). Variants were identified using Genome Analysis ToolKit (GATK4) MuTect-2 and confirmed using high-coverage Amplicon-EZ sequencing. Sequence data on 41 patients passed quality control. Four somatic variants were validated following amplicon sequencing: within CBL, ALG13, MTOR, and FLNA. The diagnostic yield across 41 patients was 10%, 9% in mesial temporal lobe epilepsy with hippocampal sclerosis and 20% in malformations of cortical development. This study provides novel insights into the etiology of mesial temporal lobe epilepsy with hippocampal sclerosis, highlighting a potential pathogenic role of somatic variants in CBL and ALG13. We also report candidate diagnostic somatic variants in FLNA in focal cortical dysplasia, while providing further insight into the importance of MTOR and related genes in focal cortical dysplasia. This work demonstrates the potential molecular diagnostic value of variants in both germline and somatic epilepsy genes.

Structural connectivity at term equivalent age and language in preterm children at 2 years corrected.

We previously reported interhemispheric structural hyperconnectivity bypassing the corpus callosum in children born extremely preterm (<28 weeks) versus term children. This increased connectivity was positively associated with language performance at 4-6 years of age in our prior work. In the present study, we aim to investigate whether this extracallosal connectivity develops in extremely preterm infants at term equivalent age by leveraging a prospective cohort study of 350 very and extremely preterm infants followed longitudinally in the Cincinnati Infant Neurodevelopment Early Prediction Study. For this secondary analysis, we included only children born extremely preterm and without significant brain injury (n = 95). We use higher-order diffusion modelling to assess the degree to which extracallosal pathways are present in extremely preterm infants and predictive of later language scores at 22-26 months corrected age. We compare results obtained from two higher-order diffusion models: generalized q-sampling imaging and constrained spherical deconvolution. Advanced MRI was obtained at term equivalent age (39-44 weeks post-menstrual age). For structural connectometry analysis, we assessed the level of correlation between white matter connectivity at the whole-brain level at term equivalent age and language scores at 2 years corrected age, controlling for post-menstrual age, sex, brain abnormality score and social risk. For our constrained spherical deconvolution analyses, we performed connectivity-based fixel enhancement, using probabilistic tractography to inform statistical testing of the hypothesis that fibre metrics at term equivalent age relate to language scores at 2 years corrected age after adjusting for covariates. Ninety-five infants were extremely preterm with no significant brain injury. Of these, 53 had complete neurodevelopmental and imaging data sets that passed quality control. In the connectometry analyses adjusted for covariates and multiple comparisons (P < 0.05), the following tracks were inversely correlated with language: bilateral cerebellar white matter and middle cerebellar peduncles, bilateral corticospinal tracks, posterior commissure and the posterior inferior fronto-occipital fasciculus. No tracks from the constrained spherical deconvolution/connectivity-based fixel enhancement analyses remained significant after correction for multiple comparisons. Our findings provide critical information about the ontogeny of structural brain networks supporting language in extremely preterm children. Greater connectivity in more posterior tracks that include the cerebellum and connections to the regions of the temporal lobes at term equivalent age appears to be disadvantageous for language development.

First implementation of quality control procedures on selected X-ray machines in South of Benin

Abstract Introduction: The use of X-ray equipment for medical diagnostic radiography procedures has increased due to advances and complexity of radiological procedures. Achieving good image quality while keeping exposure of workers, public and patient exposure to an acceptable level has become a prerequisite for the radiology department in order to comply with best international practices. The aim of this study was to undertake quality control measurement of seven (7) diagnostic radiography equipment in the south of Benin, the first of its kind. Material and methods: Multifunction detector (Piranha) and beam alignment test tool were used to perform quality control tests on seven (7) X-ray units. The method used as well as the interpretation of the results was based on the American Association of Physicists in Medicine (AAPM), United States Food and Drug Administration (FDA), Healing Arts Radiation Protection (HARP), Institute of Physics and Engineering in Medicine (IPEM), International Atomic Energy Agency (IAEA) and Canadian Safety code 35 (S.C 35) recommendations. Results: The quality control results showed that all X-ray equipment investigated were within standard limits for accuracy of exposure time below 10 ms; reproducibility of kVp, exposure time and dose output; specific dose-kVp2 linearity; and specific dose-mAs linearity. Five (5) out of seven (7) diagnostic X-ray machines passed quality control tests such as X-ray beam alignment, exposure time above 10 ms and kVp accuracy. One (1) X-ray machine failed the quality control test of beam filtration at 70 kVp and above. Conclusions: The findings of this study have provided baseline data for other radiology departments to embark on similar QA/QC activities, and also explore options for optimization of patient dose. However, there is a need to extend the study to cover more diagnostic X-ray machines throughout the country. It is anticipated that this would ultimately assist in improving radiation protection and safety during medical diagnostic radiological procedures.

Abstract B030: DNA methylation profiling identifies subset of low-grade endometrial neoplasms with poor response to progestin therapy

Abstract Purpose: We aimed to investigate the DNA methylation profile of low-grade endometrial neoplasms before and after progestin therapy. Methods: This is a retrospective cohort of patients with endometrial intraepithelial neoplasia/atypical hyperplasia (EIN/AH) and grade 1 endometrial endometrioid carcinoma (EEC) treated with progestin therapy. DNA was extracted from 24 formalin-fixed paraffin-embedded (FFPE) tumors before and 19 tumors after progestin therapy (median interval between specimens: 12.1 months). Methylation profiling was performed using the Illumina Infinium Methylation EPIC array. Laser-capture microdissection was used to enrich samples with low tumor content. Results: Twenty-four patients with a median age of 38 years were included. Majority of patients were nulligravid (58%), and self-identified as non-Hispanic (83%) and white (42%). Ten patients had a diagnosis of EIN/AH, while 14 were grade 1 EEC. Ten cases showed complete response, 7 partial responses, 8 showed no response between the pre- and post-treatment samples. Ten patients had regression of disease on follow-up, while 9 showed persistent tumor. In 5 patients, clinical outcome could not be assessed due to short time of exposure (&amp;lt;6 months). Unsupervised clustering based on top 3,000 differentially methylated sites (DMS) in 24 pre-treated tumors identified 2 different groups. Cluster 1 (n= 11) was composed of significantly older patients (p=0.047; median age: 39 vs 37 years) and more likely to have EEC on histologic examination (p=0.016; 100% vs 54%). Tumors in Cluster 1 were more likely to show absence of pathologic response following progestin therapy (p= 0.038; 55% vs 8%). Although no statistical significance was reached regarding clinical outcome (p=0.2), patients in Cluster 1 showed regression of disease in only 29% of cases (2/7), while in Cluster 2, 67% of patients showed regression of tumor (8/12). There was no difference regarding gravidity, race/ethnicity, body mass index, type of progestin, and follow-up time. KEGG pathways analysis revealed that the most significantly different pathways between the 2 clusters were: maturity onset diabetes of young, neuroactive ligand-receptor interaction, and signaling pathways regulating pluripotency of stem cells. Pairwise differential DNA methylation analysis between 15 pairs of pre- and post-treatment samples that passed quality control showed a hypermethylation effect of progestin therapy in the majority of DMS, including sites in open sea, northern and southern shores and shelves. Although there were sites in CpG islands with a hypermethylation pattern after treatment, progestin therapy had a predominantly hypomethylation effect on CpG islands. The gene set enrichment based on DMS showed significant change in genes mostly related to cell-cell adhesion following progestin therapy. Conclusion: DNA methylation profiling identifies a subset of EIN/AH and grade 1 EEC with poor response to progestin therapy. The methylation landscape of these low-grade neoplasms undergoes changes after progestin treatment. Citation Format: Lawrence H. Lin, Kyriaki Founta, Nyasha Chambwe, Deborah F. DeLair. DNA methylation profiling identifies subset of low-grade endometrial neoplasms with poor response to progestin therapy [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr B030.

Demonstrating the reliability of in vivo metabolomics based chemical grouping: towards best practice

While grouping/read-across is widely used to fill data gaps, chemical registration dossiers are often rejected due to weak category justifications based on structural similarity only. Metabolomics provides a route to robust chemical categories via evidence of shared molecular effects across source and target substances. To gain international acceptance, this approach must demonstrate high reliability, and best-practice guidance is required. The MetAbolomics ring Trial for CHemical groupING (MATCHING), comprising six industrial, government and academic ring-trial partners, evaluated inter-laboratory reproducibility and worked towards best-practice. An independent team selected eight substances (WY-14643, 4-chloro-3-nitroaniline, 17α-methyl-testosterone, trenbolone, aniline, dichlorprop-p, 2-chloroaniline, fenofibrate); ring-trial partners were blinded to their identities and modes-of-action. Plasma samples were derived from 28-day rat tests (two doses per substance), aliquoted, and distributed to partners. Each partner applied their preferred liquid chromatography–mass spectrometry (LC–MS) metabolomics workflows to acquire, process, quality assess, statistically analyze and report their grouping results to the European Chemicals Agency, to ensure the blinding conditions of the ring trial. Five of six partners, whose metabolomics datasets passed quality control, correctly identified the grouping of eight test substances into three categories, for both male and female rats. Strikingly, this was achieved even though a range of metabolomics approaches were used. Through assessing intrastudy quality-control samples, the sixth partner observed high technical variation and was unable to group the substances. By comparing workflows, we conclude that some heterogeneity in metabolomics methods is not detrimental to consistent grouping, and that assessing data quality prior to grouping is essential. We recommend development of international guidance for quality-control acceptance criteria. This study demonstrates the reliability of metabolomics for chemical grouping and works towards best-practice.

Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water

The quantity and quality of DNA isolated from environmental samples are crucial for getting robust high-throughput sequencing data commonly used for microbial community analysis. The differences in the nature and physicochemical properties of environmental samples impact DNA yields, and therefore, an optimisation of the protocols is always recommended. For instance, samples collected from corroded areas contain high concentrations of metals, salts, and hydrocarbons that can interfere with several steps of the DNA extraction protocols, thereby reducing yield and quality. In this study, we compared the efficiency of commercially available DNA extraction kits and laboratory-adopted methods for microbial community analysis of iron incrustations and oilfield-produced water samples. Modifications to the kits manufacturers’ protocols were included to maximise the yield and quality. For iron incrustations, the modified protocol for FastDNA Spin Kit for Soil yielded higher DNA and resulted in higher diversity, including the recovery of low-abundant and rare taxa in the samples, compared to DNeasy PowerSoil Pro Kit. The DNA extracted with modified phenol–chloroform methods yielded higher DNA but failed to pass quality control PCR for 16S sequencing with and without purification. The protocols mentioned here can be used to maximise DNA recovery from iron incrustations and oilfield-produced water samples.

Prospective study of a multi-modal blood-based test for colorectal cancer screening.

70 Background: Colorectal cancer (CRC) screening has proven to be a useful tool for the detection and prevention of CRC. However, adherence is low despite the multiple screening options available. A blood-based CRC screening test with optimized sensitivity and specificity may improve screening adherence. We aimed to prospectively evaluate the performance of a multimodal blood-based colorectal neoplasia screening test in individuals presenting for colonoscopy. Methods: This prospective, observational study was developed in four hospitals in Spain and enrolled individuals (45 – 84 years of age) undergoing colonoscopy, including diagnostic and screening colonoscopies, between March 2020 and September 2021. Eligible individuals consented to use of medical records for research and to provide a blood sample prior to colonoscopy procedure. Individuals were followed for one year. Whole blood was collected and shipped ambient to a central laboratory for analysis (Shield, Guardant Health, Redwood City, CA, USA). The blood-based colorectal neoplasia test is a 500kb next-generation sequencing based panel and bioinformatic platform that incorporates cell-free DNA (cfDNA) methylation-based partitioning to identify cancer related genomic alterations and epigenomic modifications (methylation and modifications in chromatin state). Results are integrated to yield a binary “positive” or “negative” result. Here we present findings correlating the blood-based test results with colonoscopy findings and findings from available 1-year follow-up data. Results: 556 out of 598 eligible individuals had an evaluable colonoscopy and a blood-based test result that passed quality control standards. Of the 556 individuals, 52% were female; median age was 55 years (21% age 45 – 49, 74% age 50 – 74, 4% age 75+). Reasons for colonoscopy were symptoms (49%), average risk screening (33%), positive stool-based test (6%), positive family history (11%) or other reasons (1%). Colorectal adenocarcinoma prevalence rate was 1.4%. Sensitivity for CRC detection was 100% (8/8; Stage I, 1; Stage II, 3; Stage III, 2; Stage IV, 2). Sensitivity for advanced adenoma (AA) detection was 22%. Specificity for advanced neoplasia (CRC + AA) was 91%. Negative predictive value (NPV) for CRC detection was 100% and positive predictive value (PPV) was 13%. 1-year follow-up data was available for 504 individuals, of whom 9 patients developed cancer (none CRC), of whom 1 had an initial positive Shield result. Conclusions: In this prospective study of individuals eligible for colonoscopy, sensitivity and specificity of the blood-based test showed a performance consistent with the available stool-based non-invasive screening options. This, combined with a more acceptable mode of testing suggests that this blood-based test may be a viable CRC screening option.

Molecular subtyping of head and neck cancer – Clinical applicability and correlations with morphological characteristics

AimWe aimed to evaluate the applicability of a customized NanoString panel for molecular subtyping of recurrent or metastatic head and neck squamous cell carcinoma (R/M−HNSCC). Additionally, histological analyses were conducted, correlated with the molecular subtypes and tested for their prognostic value. Material and MethodsWe conducted molecular subtyping of R/M−HNSCC according to the molecular subtypes defined by Keck et al. For molecular analyses a 231 gene customized NanoString panel (the most accurately subtype defining genes, based on previous analyses) was applied to tumor samples from R/M−HNSCC patients that were treated in the CeFCiD trial (AIO/IAG-KHT trial 1108). A total of 130 samples from 95 patients were available for sequencing, of which 80 samples from 67 patients passed quality controls and were included in histological analyses. H&E stained slides were evaluated regarding distinct morphological patterns (e.g. tumor budding, nuclear size, stroma content). ResultsDetermination of molecular subtypes led to classification of tumor samples as basal (n = 46, 45 %), inflamed/mesenchymal (n = 31, 30 %) and classical (n = 26, 25 %). Expression levels of Amphiregulin (AREG) were significantly higher for the basal and classical subtypes compared to the mesenchymal subtype. While molecular subtypes did not have an impact on survival, high levels of tumor budding were associated with poor outcomes. No correlation was found between molecular subtypes and histological characteristics. ConclusionsUtilizing the 231-gene NanoString panel we were able to determine the molecular subtype of R/M−HNSCC samples by the use of FFPE material. The value to stratify for different treatment options remains to be explored in the future. The prognostic value of tumor budding was underscored in this clinically well annotated cohort.