Solid Samples Research Articles

Abstract 862: Multi-omic analysis of allelic expression patterns of imprinted and non-imprinted genes in cancer and their association with drug response

Abstract Malignant cells undergo a broad array of epigenetic changes, including changes in imprinting patterns. In normal cells, imprinted genes have parent of origin-specific monoallelic expression, which is controlled via epigenetic mechanisms. Imprinted gene loci are often complex and frequently include multiple isoforms, which have different individual patterns of parent-of-origin monoallelic or biallelic expression in the normal tissues. Many imprinted genes promote cell proliferation and body growth, and their expression is important during embryonic and postnatal development. Dysregulation of imprinting in tumors has been suggested to contribute to growth and proliferation of cancer cells. Previously we reported that chemotherapy responses of cancer cell lines from a variety of tumors and of patient-derived acute myeloid leukemia samples were associated with copy number, expression, or DNA methylation of selected imprinted genes. In the current project, we examined allele-specific patterns of expression (monoallelic vs. biallelic) of imprinted genes and isoforms in tumors and studied their potential effect on response of cancer cells to drug treatment. We analyzed expression patterns at the whole gene, isoform, and exon levels of 59,283 autosomal protein-coding genes and ncRNA genes, with a special focus on 94 imprinted genes and their isoforms. We developed a computational pipeline to evaluate monoallelic and biallelic expression patterns of each gene in cancer cell lines and in tumor samples based on available matched RNA-seq expression data, whole exome sequencing information, and copy number data. Our initial analysis included 108 cell lines from the Cancer Cell Line Encyclopedia (CCLE), which had been derived from 9 pediatric and adult tumor histologies. We observed variation of allelic expression patterns of imprinted genes and their isoforms in tumor cell lines, including differences across and within cancer histologies. We also observed predominantly monoallelic expression of multiple additional genes. Some of them (PRIM2, BCLAF1, MAP2K3, and SEC22B) had been previously reported as potentially imprinted. Monoallelic expression of other genes identified in our analysis (e.g., GRK2, CBX4, and additional genes) was likely caused by molecular mechanisms other than imprinting. Allelic expression patterns and overall expression levels of isoforms of multiple imprinted and non-imprinted monoallelically expressed genes (e.g., CPA4, MAP2K3, and other genes) were associated with in vitro drug response. We also report our ongoing validation of allelic expression patterns of imprinted and non-imprinted genes, isoforms, and exons in primary bladder and breast tumors and in matched solid normal tissue samples using patient data from the Cancer Genome Atlas (TCGA). These results provide new knowledge about epigenetic dysregulation in cancer. Citation Format: Julia Krushkal, Travis L. Jensen, George Wright, Yingdong Zhao. Multi-omic analysis of allelic expression patterns of imprinted and non-imprinted genes in cancer and their association with drug response [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 862.

Abstract 4946: ssTimiGP: Equip the TimiGP system with a single-sample module, facilitating the cell-cell interaction inference of the tumor microenvironment in any sample

Abstract Understanding the tumor microenvironment (TME) is essential in cancer treatment and risk assessment. While single-cell RNA-seq (scRNA-seq) offers in-depth insights into the TME, its expensive cost results in limited data sets and size. In contrast, microarray and RNA-seq provide rich datasets from larger cohorts, but they yield bulk data with lower resolution. To leverage the strengths of both approaches and comprehensively study the TME, we developed the computational framework TimiGP (Tumor Immune Microenvironment Illustration through Gene Pairs). It is inspired by the dynamic balance of the immune system and extended to the entire TME. TimiGP utilizes scRNA-seq to define cell type of interest, and bulk transcriptomic profiles to deduce clinically relevant cell-cell interaction networks and cell functions. Our recent release includes both prognosis and response modules to study the association between TME and the corresponding clinical outcomes. However, their applicability is constrained by the necessity for paired clinical information. In response to this limitation, we present a significant enhancement, a single sample module slightly modified from the TimiGP framework (ssTimiGP). This upgraded version enables TME analysis in any individual sample, requiring only bulk RNA-seq data and cell-type markers. It exports a cell-cell interaction network representing the relative expression of functional markers and the abundance of cells. This optimization expands the utility of TimiGP, making it more accessible across diverse samples and species. We have further expanded the application of ssTimiGP from solid tumors to liquid samples (e.g., peripheral blood). To validate its performance, we conducted a comparative analysis between the interactions of eight immune cell types observed in experimental results using FACS and the computational results derived from ssTimiGP based on paired RNA-seq data. As a result, ssTimiGP not only successfully identified interactions between different cell types that exhibited a significant correlation with experimental findings (e.g., CD4+ naïve T cells → Monocyte, R=0.75, p< 0.001, accuracy = 0.8), but also demonstrated its capability to achieve higher resolution in capturing interactions between immune cell subpopulations (e.g., CD4 naïve T cells → activated CD4+ memory T cells, R=0.57, p=0.008, accuracy = 1.0). In our benchmark analysis, ssTimiGP demonstrated superior performance compared to CIBERSORTx (e.g., CD4+ naïve T cells → Monocyte, R=0, Accuracy=0.3). In summary, ssTimiGP signifies an expansion of the TimiGP system, enabling the inference of the TME in individual solid tumors and liquid samples at various resolutions by integrating the strengths of both scRNA-seq and bulk RNA-seq. This approach offers substantial potential for advancing personalized cancer treatment. Citation Format: Chenyang Li, Jianjun Zhang, Chao Cheng. ssTimiGP: Equip the TimiGP system with a single-sample module, facilitating the cell-cell interaction inference of the tumor microenvironment in any sample [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 4946.

Abstract 6129: Emerging disparities in the clinical actionability landscape for patients with inferred African ancestry

Abstract The past decade has seen a surge in the approval and availability of precision oncology therapies targeting distinct genomic alterations. We sought to determine whether these advances have benefitted patients with cancer from various ancestral backgrounds equally over time. We therefore annotated all genomic alterations identified in a pan-cancer cohort of 55,970 solid tumor samples sequenced with the MSK-IMPACT clinical assay using incremental versions of the precision oncology knowledge base OncoKB and computed the fraction of samples with OncoKB Level 1 alterations (biomarkers included in the FDA drug label) per year based on the annual cumulative FDA-approved targeted therapies. In 2010, 4.4% of patients with inferred African ancestry (AFR), and 2.4% of patients with inferred non-Ashkenazi Jewish European ancestry (EUR) had Level 1 alterations, largely explained by differences in cancer type prevalence between these groups. However, by mid-2023, AFR had a significantly lower percent of Level 1 alterations (25.3%) compared to EUR (31.2%), and this difference remained significant after adjusting for cancer type and disease status (q-value = 2.6e-08). Next, we compared AFR versus EUR percentages of Level 1 alterations over time in breast and colorectal (CRC) patient samples, two cancers in which racial disparities of cancer incidence and outcomes are well-documented. We observed that prior to 2019, the fraction of breast cancer patient samples with a Level 1 alteration was similar among AFR (13%) and EUR (12.2%), primarily due to comparable rates of ERBB2 amplifications (12.4% in AFR, 11.7% in EUR). However, following the breast cancer-specific FDA approvals of alpelisib+fulvestrant for PIK3CA-mutant disease in 2019 and elacestrant for ESR1-mutant disease in 2023, a significant shift in Level 1 actionability was observed between EUR (45%) and AFR (34%) attributed in part to the paucity of PIK3CA (26.3% vs. 36.2% in EUR) and ESR1 (4.1% vs. 7.5% in EUR) oncogenic alterations in AFR. We further observed AFR with CRC to have lower prevalence of MSI-H (5.8% vs.10.7% in EUR), TMB (12.5% vs. 18.8% in EUR) and BRAF V600E (5.1% vs. 9% in EUR). Correspondingly, in 2023, 16.4% of AFR with CRC have Level 1 alterations compared to 25.4% of EUR. Moreover, while AFR have higher rates of KRAS mutations (57.2% vs. 42.6% in EUR), they have a lower prevalence of the standard care biomarker KRAS G12C (3.4% vs. 7% of KRAS-mutant CRC in EUR) further exacerbating the disparities in CRC clinical actionability. Taken together, here we demonstrate that a significant disparity exists in the clinical actionability landscape of AFR with cancer compared to EUR, largely due to differences in relative mutational frequencies of Level 1 genomic alterations. Citation Format: Kanika Arora, Sarah P. Suehnholz, Hongxin Zhang, Ritika Kundra, Subhiksha Nandakumar, Moriah Nissan, A. Rose Brannon, Chaitanya Bandlamudi, Marc Ladanyi, Alexander Drilon, David B. Solit, Nikolaus Schultz, Michael F. Berger, Debyani Chakravarty. Emerging disparities in the clinical actionability landscape for patients with inferred African ancestry [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 6129.

Abstract 331: Ion TorrentTM NGS sequencing of the TERT promoter hotspots with Ion AmpliSeqTM HD technology

Abstract Introduction: Recurrent mutations C228T and C250T in the TERT gene promoter are prevalent in cancer and serve as important biomarkers for aggressive disease. Ion Torrent™ NGS sequencing, combined with Ion AmpliSeqTM HD technology, enables comprehensive genomic profiling with ultra-high sensitivity for low-frequency variants in cell-free DNA (cf-DNA) and highly heterogeneous solid tumor samples. However, the high GC content (>80%) and the presence of G repeats that are known to adopt a compact stacked three-G-quadruplex conformation in the TERT gene promoter region pose sequencing challenges such as low read depth and strand-bias, i.e. prematurely truncated reads on one strand. Methods: We designed nine AmpliSeqTM HD panels with amplicon sizes of 70 to 104 bp, ideal for cf-DNA and FFPE samples, to target the recurrent TERT promoter hotspots. The designs were tested alone and combined with a larger Ion AmpliSeqTM HD DNA research panel resulting in highly multiplexed libraries. The libraries were used for Ion 540TM chip template preparation on the Ion ChefTM instrument and subsequently sequenced using the Ion GeneStudioTM S5 System. Sequencing data was used to evaluate coverage of the target hotspots by each design for each condition, and additional panels were designed to test single amplicons covering both TERT promoter hotspots. Results: Through performance evaluation, we selected two overlapping amplicons, each effectively amplifying one of the two hotspots. Individually tested, these amplicons yielded approximately 3000 families each from a 10ng gDNA input and when combined into the larger Ion AmpliSeqTM HD DNA research panel, they produced several thousand reads across various libraries, providing molecular coverage of around 200 functional molecules. While capture efficiency was lower compared to TERT amplicon-only libraries, these improved amplicons allow downstream analysis of variants. A single-pool solution (single amplicon/s covering both hotspots) will be explored further using the second batch of amplicons/primers. Conclusions: The optimized amplicons in two pools developed in this study enable the detection of challenging yet clinically significant TERT promoter hotspot mutations using the ultra-sensitive Ion AmpliSeqTM HD technology. For Research Use Only. Not for use in diagnostic procedures. © 2023 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Citation Format: Anupma Sharma, Guobin Luo, Na Li, Giorgio Pea, Fiona Hyland. Ion TorrentTM NGS sequencing of the TERT promoter hotspots with Ion AmpliSeqTM HD technology [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 331.

Abstract 2417: Detection and quantification of site-specific DNA methylation from liquid biopsies as a pharmacodynamic biomarker of OTX-2002, a novel MYC-targeting epigenomic mRNA therapeutic

Abstract Omega Therapeutics has developed a novel platform of programmable epigenomic mRNA medicines capable of modifying chromatin state to specifically tune gene expression at the pre-transcriptional level. Epigenomic controllers (ECs) unlock targets that have been historically considered “undruggable,” with one of the most elusive being the MYC oncogene. A direct MYC-targeting anti-cancer agent has previously remained intangible, largely due to the absence of a drug binding pocket and tight autoregulation. A clinical trial is underway (MYCHELANGELO, NCT05497453) to investigate pre-transcriptional inhibition of MYC with OTX-2002 in patients with hepatocellular carcinoma (HCC). OTX-2002, a first-in-class mRNA therapeutic delivered via lipid nanoparticles (LNP), encodes two proteins that durably modify chromatin, in part, through CpG DNA methylation at the MYC locus. Using both liquid and solid biopsy sampling from in vivo studies, we investigated whether target engagement for OTX-2002 could be assessed by MYC methylation. Detection of DNA methylation has long held promise as an oncology biomarker given its functional roles in various cancer types and the potential signal afforded by methylated CpGs. Indeed, DNA methylation has been shown to serve as a robust analyte in liquid biopsy-derived multi-cancer early detection (MCED) and minimal residual disease (MRD) tests that have recently been utilized in the clinic. Many of these platforms are founded on complex models that leverage methylation signals across >1 million CpGs that can span tens of megabases of genomic space. We faced a distinct challenge when compared to these MCED/MRD tests in developing a pharmacodynamic methylation assay for OTX-2002 as the target region consists of just a few kilobases. With a tissue specific LNP delivery system, ultra-high sensitivity was required to identify rare ctDNA events from the larger cfDNA population. To this end, we designed a minimal hybridization/capture panel that targeted ~50 kb of genomic space, effectively allowing for ultra-deep methylation sequencing of MYC. When this technique was paired with enzymatic (EM) conversion for methylation detection and supported by an analysis pipeline focused on epiallele identification, this assay was able to detect methylation down to the theoretical limit in a dilution series of control genomic DNA, 1 in 104 copies of MYC. This degree of sensitivity translated to successful preclinical detection of on-target methylation by OTX-2002 from DNA extracted from plasma samples collected from mice-bearing human HCC xenografts. Overall, we present a non-invasive and exquisitely sensitive method of assessing target engagement and site-specific pharmacodynamic activity of a novel epigenomic medicine that can be directly translated to the clinical setting. Citation Format: Justin Chen, William Senapedis, Stephen Siecinski, Elmer Figueroa, Adam Katz, Samuel Mildrum, Yaoyu E. Wang, Houda Belaghzal, Kayleigh Gallagher, Graeme Hodgson, Charles W. O'Donnell, Thomas G. McCauley. Detection and quantification of site-specific DNA methylation from liquid biopsies as a pharmacodynamic biomarker of OTX-2002, a novel MYC-targeting epigenomic mRNA therapeutic [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 2417.

Abstract 2359: New insights into targeting the CD200R1 pathway in T and NK cells using 23ME-00610 as a single agent or in combination

Abstract 23ME-00610 is a monoclonal antibody that is being evaluated as a single agent in a Phase 1/2a clinical trial for advanced solid malignancies (NCT05199272). It binds with high affinity (KD < 0.1 nM) to CD200R1, a promising immune-oncology (IO) target identified by surveying the 23andMe genetic and health survey database. CD200R1 is an inhibitory receptor that when bound to its ligand CD200, reduces pro-inflammatory cytokine production, and leads to an immunosuppressive tumor environment. To gain further insight into the mechanism of action of 23ME-00610 and its potential for combination therapy, we profiled CD200R1 and other immune inhibitory receptors in human dissociated solid tumor samples using spectral flow cytometry. CD200R1 was broadly expressed across tumor-infiltrating immune cells, including T cells and NK cells, cytotoxic cell types with known antitumor functions. Notably, CD200R1 expression pattern was differentiated from PD-1, which is mostly restricted to T cells, indicating differences in patient populations that could potentially benefit from anti-CD200R1 and anti-PD-1 treatments. The ligand, CD200 was broadly expressed, including on tumor cells and endothelial cells. The differential expression profiles of CD200R1 and PD-1 on immune cells, along with CD200 expression on endothelial cells, suggest that combining 23ME-00610 with other clinically validated immunomodulatory agents could enhance antitumor responses. Follow-up experiments were conducted to validate and extend these findings. In an in vitro assay with cancer patient-derived PBMCs, 23ME-00610 promoted higher production of IFNγ, a key functional antitumor cytokine, compared to anti-PD-1 in 9 of 10 donors. Subsequent attempts were made to pinpoint immune cells responsible for 23ME-00610's anti-tumor activity. 23ME-00610 reversed CD200-mediated suppression of chronically stimulated primary T cells and CD200-mediated inhibition of NK cell degranulation, suggesting that 23ME-00610 can mediate tumor cell killing through at least two different cell types. To test the potential of 23ME-00610 to combine with anti-PD-1 to enhance T cell function, an artificial antigen-presenting cell (aAPC) line overexpressing PD-L1 and CD200 was co-cultured with chronically stimulated primary human T cells. Anti-PD-1 and 23ME-00610 each independently enhanced IFNy secretion levels compared to isotype control, yet their combination resulted in a more than additive effect. Taken together, these data demonstrate that 23ME-00610 can enhance both NK and T cell antitumor effector functions, and 23ME-00610 could synergize with anti-PD-1 to further increase the activity of T cells against cancer cells. The results of this study provide evidence that 23ME-00610 could expand IO treatment options for patients with advanced solid malignancies as a single agent or in combination with other anti-tumor therapeutics. Citation Format: Mithra R. Kumar, Shiteng Duan, Shruti Yadav, Abigail Jarret, Zhonghao Yan, Jill Fenaux, Martin Kinisu, Zuoan Yi, Mauro Poggio, Patrick Collins, Antony Symons, Lorena Riol Blanco, Maike Schmidt, Sophia Majeed, Anh Diep, Clarissa Lee. New insights into targeting the CD200R1 pathway in T and NK cells using 23ME-00610 as a single agent or in combination [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 2359.

Abstract 4233: Rapid and robust generation of ex vivo tumoroid samples from fresh patient samples in a serum-free, conditioned medium-free system

Abstract Functional precision oncology describes a method in which an individual patient’s cancer cells are tested for response to various treatments ex vivo to aid in therapy selection. In many cases, these cultures take the form of tumoroids, which are 3D, patient-derived “mini tumors” that retain phenotypic and genotypic characteristics of the patient cancer. While interest in functional precision oncology is increasing due to strong correlation between patient responses and those experimentally observed using matched tumoroid models in the literature, a lack of standardization has precluded its widespread translation to clinical settings. To study the ability to generate short-term tumoroid cultures using a commercially available, serum-free, and conditioned medium-free system, we processed fresh tumor resection samples and performed culture in Gibco™ OncoPro™ Tumoroid Culture Medium. Tumor resection samples spanning a variety of indications were stored in supplemented Hibernate™-A Medium (including antibiotics) and shipped overnight on gel packs to a central tissue processing site. Samples were minced, enzymatically dissociated, and counted. Average yields of ~2000-12,000 cells per mg of tumor resection tissue were observed, with lower yields in lung, head and neck, and breast cancer samples and higher yields in endometrial and colorectal cancer samples. Donor-to-donor variability generated a wide range of yields within a given indication. Similarly, cell viability following dissociation ranged widely, reaching as low as 20% for some samples and exceeding 90% for others. Though yields and initial viability varied, dissociated cells that were plated in OncoPro Tumoroid Culture Medium formed tumoroids in >85% of samples within 7 days of tissue receipt. Both mutational profiles and gene expression patterns were highly conserved (>90%) between initial tumor samples and cells cultured in OncoPro for 7 days. Computational approaches designed to identify cell-type specific signatures from bulk RNA sequencing data indicated that immune cell population signatures were present after one week in OncoPro medium. Additionally, we have developed methods to analyze tumoroid response to compounds and candidate cell therapies by both plate reader- and imaging-based analyses using ~1.2e6 initial tumor cells per 96-well plate. Due to the high success rate of tumoroid formation from fresh tumor samples and retention of donor-specific characteristics in OncoPro Tumoroid Culture Medium, we believe that it will be a valuable tool for functional precision oncology of solid tumor samples. Citation Format: Colin Paul, Amber Bullock, Anthony Chatman, Brittany Balhouse, Chris Yankaskas, Pradip Shahi Thakuri, Matt Dallas, David Kuninger. Rapid and robust generation of ex vivo tumoroid samples from fresh patient samples in a serum-free, conditioned medium-free system [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 4233.

Abstract 6396: Ex vivo 3D micro tumor testing to assess chemotherapy and immunotherapy responses for NSCLC patients

Abstract Background: Systemic treatment options for NSCLC patients consists of chemo-, targeted or immunotherapy. Although predictive biomarkers can guide treatment decisions, response prediction for chemo- and immunotherapy is still a challenge. Recent studies showed the potential of functional testing to assess patient sensitivity to drugs in various cancers, but NSCLC is lacking. This study reports the feasibility of ex vivo 3D micro lung tumor testing with native tumor microenvironment (TME) to enable treatment sensitivity profiling for all drug classes in parallel. Methods: Fresh NSCLC tumor tissue was collected from pleural fluid stage IVa/b (N=24) or resected primary tumor for stage I-III disease (N=11). Tumor clusters were isolated and exposed to drugs, while preserving the TME. Thirteen therapies were included, including cisplatin, pembrolizumab, osimertinib, and positive control for immune sensitivity (SEA). Morphological features were extracted from high-throughput 3D imaging data. Chemo- and targeted therapy sensitivity was based on AUC comparison of fitted dose-response curves. Immunotherapy sensitivity was classified on percentage and statistical significance of tumor killing, immune cell proliferation and cytokine profiling. Results: The overall assay success rate for solid samples was 64% (7/11), with 100% (4/4) success after protocol optimization. For pleural fluids, the overall success rate was 33% (8/24), caused by many samples arriving without tumor content (13/24, 54%). Excluding these samples, a technical success rate of 73% (8/11) was obtained. The assay was robust and reproducible (mean Z’ = 0.38, CV = 16.1%). Results were delivered in two weeks and on average, eight treatments were tested in parallel per sample. Patient-specific response profiles were observed for chemo-, targeted and immunotherapy. General immunotherapy sensitivity (SEA) was measured in 50% (6/12) of the tissues. Distinct responses were observed for the different immunotherapies: 33% (4/12), 17% (2/12) and 8% (1/12) of the patients responded to pembrolizumab, atezolizumab and/or ipilimumab, respectively. Strong response to osimertinib was observed in a patient with EGFR exon 19 mutation (AUC = 0.26) versus resistance in a WT patient (AUC=0.92). Conclusion: Ex vivo 3D micro tumor testing using liquid and solid tissues is feasible for NSCLC patients with resected primary tumor or pleuritis carcinomatosa. Distinct patient sensitivity profiles for chemo-, targeted and immunotherapies were measured. A preliminary correlation of targeted therapy response with mutation status was found. Discussion: The ex vivo 3D micro tumor testing platform is proven predictive for platinum-based therapy. The current study established the methods to accurately measure ex vivo NSCLC responses to all drug classes to correlate with clinical measures and further validate the platform for guiding treatment decisions. Citation Format: Esmee Koedoot, Timothy J. Sijsenaar, Lieke J. Ceton, Dieudonné J. van der Meer, Thomas J. van Brakel, Peter van Zwam, Erica Geraedts, Willemijn Vader, Egbert F. Smit, Laurie C. Steinbusch, Christi M. Steendam. Ex vivo 3D micro tumor testing to assess chemotherapy and immunotherapy responses for NSCLC patients [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 6396.

Abstract 1618: Highly populated phylogenetic reconstruction in patients with hormone receptor positive - HER2 non-amplified metastatic breast cancer

Abstract Background: Tumor progression still needs to be further elucidated in hormone receptor positive (HR+) breast cancer, the most common subtype of breast cancer. Here, leveraging the extensive sampling approach of our postmortem rapid tissue donation program UPTIDER (NCT04531696), we used phylogenic reconstruction to analyze disease progression. Patients and Methods: Thirteen patients with HR+/HER2 non-amplified primary breast cancer, recruited in UPTIDER between 12/2020 and 05/2022, were considered. Shallow whole-genome sequencing was performed on 495 solid samples including a matched germline DNA and archived primary tumor sample for each patient. Log2 coverage ratios were computed with CNVkit and profiles with median absolute pairwise deviation < 0.35 were co-segmented per patient using the copynumber R package. Purity and ploidy were assessed by ABSOLUTE and manually reviewed. Samples with purity > 30% were kept for downstream analysis. Phylogenetic reconstruction was performed using MEDICC2 for each patient. Metrics derived from the trees were: (i) tree length, (ii) trunk length, (iii) trunk ratio as trunk length/tree length*100. Overall survival (OS) was defined as time between primary diagnosis and death. Comparison was done using Wilcoxon test, time to event analysis using cox regression. Endocrine resistance was defined as per the ESMO guidelines (PMID:34678411). Results: 81% (399/495) of the samples passed QC. Phylogenies included a median of 28 samples per patient (range: 9-59) and 10/13 phylogenies included primary samples at diagnosis. Multi-seeding from the primary tumor was observed in 7 patients, suspected in 1, and a single seeding was observed in 2 patients. Median OS was 8.0 years. Higher trunk ratios tended to associate with poorer OS (Hazard ratio: 1.08 per 1% increase, 95% confidence interval: 0.99-1.16, p=0.06). In organs where multiple metastatic lesions were sampled (n= 73 organs, median of 3 samples/organ, range: 2-18 and median of 5 organs per patient, range: 1-10) seeding from at least 2 organs was detected in 48% (35/73) of the organs. Phylogenies from patients with secondary endocrine resistance (7 patients) tended to have a shorter trunk compared to patients with primary endocrine resistance (5 patients, median of 18 and 48 alterations respectively, p=0.15). Conclusion: Branching evolution from the primary tumor was more frequently observed than linear evolution. Phylogenies revealed extensive tumor heterogeneity, questioning treatment decisions based on a single biopsy. Additionally, evaluation of multiple metastatic samples per organ showed seeding from multiple organs in 48% of organs evaluated, indicating greater disease heterogeneity than previously thought. Phylogenetic differences were also noted according to the type of endocrine resistance (primary versus secondary). Citation Format: Francois Richard, Tatjana Geukens, Maxim De Schepper, Amena Mahdami, Karen Van Baelen, Marion Maetens, Gitte Zels, Ha-Linh Nguyen, Anirudh Pabba, Sophoa Leduc, Edoardo Isnaldi, Josephine Van Cauwenberge, Kristien Borremans, Hava Izci, Imane Bachir, Sigrid Hatse, Peter Vermeulen, Evy Vanderheyden, Bram Boeckx, Diether Lambrechts, Ann Smeets, Ines Nevelsteen, Kevin Punie, Patrick Neven, Hans Wildiers, Wouter Van Den Bogaert, Jonas Demeulemeester, Elia Biganzoli, Giuseppe Floris, Christine Desmedt. Highly populated phylogenetic reconstruction in patients with hormone receptor positive - HER2 non-amplified metastatic breast cancer [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 1618.

Synthesis, studies on properties of Eu3+/Dy3+ co–doped BaMoO4 nanophosphors via hydrothermal method

AbstractThe article shows the outstanding properties and luminescence ability of Eu3+/Dy3+ co–doped BaMoO4 (BMED) materials, which have been successfully fabricated by the hydrothermal method. The crystalline structure analysis of BMED nanophosphor by X–ray diffraction (XRD) shows that it has a structure single–phase structure, with tetragonal BaMoO4 (JCPDS 029–0193), consist of spherical nanoparticles with a size diameter of 31.79–52.99 nm. The characteristic vibrational modes of molybdate lattice in the Raman spectroscopy confirmed the successful Eu3+/Dy3+ co–doped into the host matrix. The field emission scanning electron microscopy (FE–SEM) image shows that the BMED consists of quite uniform nanoparticle with sizes less than 50 nm. The energy dispersive spectra (EDS) confirm the purity and uniform distribution of elements Eu, Dy, Mo, O, Ba throughout in the solid sample. The BMED nanophosphor has is small bandgap from 2.83 to 3.00 eV. The photoluminescence spectra show that BMED have strong red emission at 616 nm of the transition (5D0 → 7F2) with luminescence lifetime from 0.330 to 1.429 ms. The BMED nanophosphor have potential application for the production of warm wLEDs, agricultural lighting and biomedical marking.

Enhancing room temperature performance of solid-state lithium cell via a facile solid electrolyte-cathode interface design

Herein, we report the enhanced electrochemical performance of a solid-state cell realized through an engineered solid electrolyte-cathode interface via a simple casting technique. The ceramic-in-polymer solid electrolyte sample with 15 wt% NASICON-type Li1·2Sn0·9Zr0·9Al0·2(PO4)3 ceramic filler in a P(VDF-HFP) matrix (CPSE15) showed the highest room temperature conductivity of ∼1.1 × 10−4 S cm−1 and lithium-ion transference number of ∼0.60. The symmetric Li|CPSE15|Li cell showed a consistent voltage profile with an over-potential of ∼45 mV for 750 h at a current density of 0.1 mA cm−2. CPSE15 slurry was directly cast onto the LiFePO4 (LFP) cathode layer using a doctor-blade coating method to obtain a cathode-electrolyte assembly. Subsequently, a full cell fabricated using this assembly and lithium metal delivered an initial discharge capacity of ∼157 mAh g−1 at 0.2C. Further, the cell exhibited ∼90 mAh g−1 discharge capacity at 1C and sustained 500 charge-discharge cycles at room temperature. The engineered interface in cathode-electrolyte assembly enabled this cell to outperform its conventionally fabricated counterpart with a stacked LFP cathode sheet and freestanding CPSE15 electrolyte membrane, which was attributed to a lower interfacial resistance (∼51%) of the former.

Characterization of solid carbon from hydrocarbon pyrolysis in molten aluminum

This study analyzed the synthesized solid carbon from the pyrolysis of methane, ethane, propane, and natural gas using molten aluminum at 1000 °C. Microscopic examination revealed the formation of spherical structures and capped-carbon nanotubes with average primary particle sizes of 0.18–1.29 μm for the spheres and 0.31–0.39 μm for the capped-carbon nanotubes. Methane and ethane pyrolysis generated spherical carbon exclusively, while propane and natural gas pyrolysis produced spheres and capped-carbon nanotubes. The analysis of interlayer spacing indicated the presence of nanocrystalline properties in all carbon samples. X-ray diffraction analysis indicated broad graphitic phases in methane, ethane, and natural gas-derived carbon, and a broad and sharp graphitic carbon peak in propane-derived carbon. Raman spectroscopy confirmed the presence of graphitic structures and disorder, with capped-carbon nanotubes demonstrating more ordered structures than spheres. The thermogravimetric analysis uncovered differences in oxidation behavior, with the mixture of spherical carbon and capped-carbon nanotubes resulting from propane pyrolysis displaying superior thermal stability compared to samples composed solely of spherical carbon. Additionally, the solid carbon samples from the pyrolysis of methane, ethane, and natural gas displayed a final decomposition curve corresponding with commercial carbon black N991. The surface area analysis unveiled that carbon samples derived from ethane and natural gas exhibited surface areas that were 2.4–5.2 times larger than those of commercial carbon black N991 and graphite flakes. These findings underscore the adaptability of tailoring solid carbon materials by selecting the appropriate feed gas to suit specific applications.

Crystal Structure, Luminescence and Electrical Conductivity of Pure and Mg2+-Doped β-Ga2O3-In2O3 Solid Solutions Synthesized in Oxygen or Argon Atmospheres.

Undoped and Mg2+-doped β-Ga2O3-20% In2O3 solid solution microcrystalline samples were synthesized using the high-temperature solid-state chemical reaction method to investigate the influence of native defects on structural, luminescent, and electrical properties. The synthesis process involved varying the oxygen partial pressure by synthesizing samples in either an oxygen or argon atmosphere. X-ray diffraction (XRD) analysis confirmed the monoclinic structure of the samples with the lattice parameters and unit cell volume fitting well to the general trends of the (Ga1-xInx)2O3 solid solution series. Broad emission spectra ranging from 1.5 to 3.5 eV were registered for all samples. Luminescence spectra showed violet, blue, and green emission elementary bands. The luminescence intensity was found to vary depending on the synthesis atmosphere. An argon synthesis atmosphere leads to increasing violet luminescence and decreasing green luminescence. Intense bands at about 4.5 and 5.0 eV and a low-intensity band at 3.3 eV are presented in the excitation spectra. The electrical conductivity of the samples was also determined depending on the synthesis atmosphere. The high-resistance samples obtained in an oxygen atmosphere exhibited activation energy of around 0.98 eV. Samples synthesized in an argon atmosphere demonstrated several orders of magnitude higher conductivity with an activation energy of 0.15 eV. The results suggest that the synthesis atmosphere is crucial in determining the luminescent and electrical properties of undoped β-Ga2O3-In2O3 solid solution samples, offering the potential for various optoelectronic applications.

Photothermal spectroscopy on-chip sensor for the measurement of a PMMA film using a silicon nitride micro-ring resonator and an external cavity quantum cascade laser

Abstract Laser-based mid-infrared (mid-IR) photothermal spectroscopy (PTS) represents a selective, fast, and sensitive analytical technique. Recent developments in laser design permits the coverage of wider spectral regions in combination with higher power, enabling for qualitative reconstruction of broadband absorption features, typical of liquid or solid samples. In this work, we use an external cavity quantum cascade laser (EC-QCL) that emits in pulsed mode in the region between 5.7 and 6.4 µm (1770–1560 cm−1), to measure the absorption spectrum of a thin film of polymethyl methacrylate (PMMA) spin-coated on top of a silicon nitride (Si3N4) micro-ring resonator (MRR). Being the PTS signal inversely proportional to the volume of interaction, in the classical probe–pump dual beam detection scheme, we exploit a Si3N4 transducer coated with PMMA, as a proof-of-principle for an on-chip photothermal sensor. By tuning the probe laser at the inflection point of one resonance, aiming for highest sensitivity, we align the mid-IR beam on top of the ring’s area, in a transversal configuration. To maximize the amplitude of the photoinduced thermal change, we focus the mid-IR light on top of the ring using a Cassegrain reflector enabling for an optimal match between ring size and beam waist of the excitation source. We briefly describe the transducer design and fabrication process, present the experimental setup, and perform an analysis for optimal operational parameters. We comment on the obtained results showing that PTS allows for miniaturized robust sensors opening the path for on-line/in-line monitoring in several industrial processes.

Rational engineering of S-scheme CeO2/g-C3N4 heterojunctions for effective photocatalytic destruction of rhodamine B dye under natural solar radiations

Constructing heterojunction to achieve efficient charge separation and transportation is a significant way to enhance the photocatalytic activity to solve many water crisis. In this novel research, rational sonochemical engineering of S-scheme CeO2/g-C3N4 heterojunctions was carried out by hybridizing CeO2 as oxidative photocatalyst (EVB = +2.37 eV) with g-C3N4 nanosheets as reductive photocatalyst (ECB= −1.2 eV) for removal of rhodamine B dye under natural solar radiations. The morphology, nanostructure, textural properties and optical characteristics of the solid samples were investigated using X-ray diffraction [XRD], N2-adsorption isotherms, diffuse reflectance spectrum [DRS], X-ray photoelectron spectroscopy [XPS], photoluminescence [PL], scanning electron microscope [SEM], mapping, selected area electron diffraction [SAED] and high resolution transmission electron microscope [HRTEM] analysis. The co-existence of CeO2 and g-C3N4 diffraction peaks and the depression in the surface area to half its value implied the strong interfacial interaction between the two semiconductors due to the remarkable difference in the point of zero charge of both semiconductors. CeO2 nanoparticles transported the heterojunction absorbability to deep visible region compared with pristine g-C3N4. With sonochemical incorporation of various proportions of CeO2 on g-C3N4 sheets, the photocatalytic performance was enhanced and optimized for the heterojunction containing 15 wt% CeO2 that mitigated 98.9% of RhB dye during three hours under natural solar radiations. RhB dye decomposed over heterojunction surface containing 15 wt% CeO2 with pseudo-first-order rate of 0.0312 min−1 which is 16.4 and 34.7 times higher than that of g-C3N4 and CeO2 nanoparticles, respectively. The exceptional enhancement of the photocatalytic performance of CeO2/g-C3N4 heterojunctions was ascribed to the strong absorbability of natural solar radiations, limiting the electron-hole recombination rate and production of S-scheme heterojunction with auspicious redox power. Scavenger experimental results and PL analysis of terephthalic acid directed the mechanism of the photocatalytic charge transportation to S-scheme route. The results emerged from this research work revealed that novel S-scheme CeO2/g-C3N4 heterojunctions with robust oxidative-reductive efficiency are capable for destructing various organic pollutants exist in wastewater.

Grinding-Induced Water Solubility Exhibited by Mechanochromic Luminescent Supramolecular Fibers.

Most mechanochromic luminescent compounds are crystalline and highly hydrophobic; however, mechanochromic luminescent molecular assemblies comprising amphiphilic molecules have rarely been explored. This study investigated mechanochromic luminescent supramolecular fibers composed of dumbbell-shaped 9,10-bis(phenylethynyl)anthracene-based amphiphiles without any tetraethylene glycol (TEG) substituents or with two TEG substituents. Both amphiphiles formed water-insoluble supramolecular fibers via linear hydrogen bond formation. Both compounds acquired water solubility when solid samples composed of supramolecular fibers are ground. Grinding induces the conversion of 1D supramolecular fibers into micellar assemblies where fluorophores can form excimers, thereby resulting in a large redshift in the fluorescence spectra. Excimer emission from the ground amphiphile without TEG chains is retained after dissolution in water. The micelles are stable in water because hydrophilic dendrons surround the hydrophobic luminophores. By contrast, when water is added to a ground amphiphile having TEG substituents, fragmented supramolecular fibers with the same molecular arrangement as the initial supramolecular fibers are observed, because fragmented fibers are thermodynamically preferable to micelles as the hydrophobic arrays of fluorophores are covered with hydrophilic TEG chains. This leads to the recovery of the initial fluorescent properties for the latter amphiphile. These supramolecular fibers can be used as practical mechanosensors to detect forces at the mesoscale.

Advanced suspect screening of tiamulin and its transformation products in waters: Assessing their persistence, mobility and toxicity

Persistent, Mobile, Organic Compounds (PMOCs) exhibit a propensity to disseminate within the water cycle and as a result, pose a significant threat to the quality of drinking water. To this point of view, considerable research has been initiated to explore the environmental behavior of the omnipresent tiamulin (TIA), being potential PMOC. In contrast to the parent compound (TIA), its transformation products (TPs) have received relatively limited attention, particularly in the context of their PM (persistent-mobile) characteristics. To address this research gap, an investigation into the phototransformation of TIA was conducted, through solar-simulated experiments in combination with Advanced Oxidation Processes (AOPs). To this end, an innovative suspect-screening methodology, involved comparison of the results obtained for the identified photo-TPs with existing literature data. This enabled us to construct an enhanced high-resolution mass spectrometry (HRMS) database for the purpose of environmental assessments of TIA and its TPs in the environment. In total, 32 TPs were identified, with 18 of them being pioneeringly reported. The principal transformation pathways appeared to involve hydroxylation, oxidation, dealkylation, and the cleavage of the C-O bond. Additionally, a comprehensive monitoring of TIA and its TPs in various environmental compartments, including samples from livestock units, leachates, surface water, and groundwater was accomplished. The highest concentration was observed in solid samples from the livestock unit at 2847 ng/g. Furthermore, both the in silico and in vitro methods to assess the toxicity of TIA and its TPs were performed. The results indicated that TIA and many TPs exhibit an alarming toxicity. Consequently, TIA can be classified as a potential PMOC, with a heightened potential for occurrence in different environmental matrices compared to ascertained PM chemicals.

Calibration of MAJIS (Moons And Jupiter Imaging Spectrometer). III. Spectral calibration.

The Moons And Jupiter Imaging Spectrometer (MAJIS) is the visible and near-infrared imaging spectrometer onboard the European Space Agency (ESA)'s Jupiter Icy Moons Explorer mission. Before its integration into the spacecraft, the instrument undergoes an extensive ground calibration to establish its baseline performances. This process prepares the imaging spectrometer for flight operations by characterizing the behavior of the instrument under various operative conditions and uncovering instrumental distortions that may depend on instrumental commands. Two steps of the on-ground calibration campaigns were held at the instrument level to produce the data. Additional in-flight measurements have recently been obtained after launch during the Near-Earth Commissioning Phase. In this article, we present the analyses of these datasets, focusing on the characterization of the spectral performances. First, we describe and analyze the spectral calibration datasets obtained using both monochromatic sources and polychromatic sources coupled with solid and gas samples. Then, we derive the spectral sampling and the spectral response function over the entire field of view. These spectral characteristics are quantified for various operational parameters of MAJIS, such as temperature and spectral binning. The derived on-ground performances are then compared with in-flight measurements obtained after launch and presented in the framework of the MAJIS performance requirements.

Characterisation and agronomic evaluation of acidified food waste anaerobic digestate products

Raw liquid anaerobic digestate was synthesised into nutrient-dense solid digestates via acidification and evaporation. Acidification retained ammonium in the digestate whilst also donating the anion to free ammonium to form an ammonium salt. Digestate was treated with the addition of sulphuric, nitric, and phosphoric acid resulting in the formation of ammonium sulphate, ammonium nitrate and ammonium phosphate, respectively then evaporated into a solid fertiliser product. FTIR, XRD and SEM-EDS collectively confirm that the addition of acids completely converted the free ammonium in the raw digestate into their respective ammonium salt counterparts. Compounds of potassium chloride, silicon dioxide, calcium carbonate, magnesium ammonium phosphate, sodium nitrate, and sodium chloride were identified in all solid digestate samples. Plant growth and grain yield was higher in urea ammonium nitrate, raw liquid digestate and acidified digestate products compared to control and unacidified solid digestate. Urea ammonium nitrate and ammonium nitrate solid digestate had the highest dry shoot, likely due to the high available nitrogen found in both fertilisers. Overall, acidification and evaporation of liquid digestate can efficiently transform it into a valuable solid fertiliser with a high nutrient density. This process not only has the potential to mitigate handling and storage constraints of low nutrient density digestate in anaerobic digestion facilities but also offers a sustainable alternative to conventional fertilisers.

BTN1A1 is a novel immune checkpoint mutually exclusive to PD-L1

BackgroundWhile Programmed cell death protein 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) blockade is a potent antitumor treatment strategy, it is effective in only limited subsets of patients with cancer, emphasizing...