Significant Molecular Heterogeneity Research Articles

OP04 Multi-Omics Biomarkers for Predicting Therapeutic Efficacy in Inflammatory Bowel Disease: Advancing Towards Tailored Treatments

Abstract Background Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are complex conditions characterized by significant clinical, immunological, molecular, genetic, and microbiological heterogeneity. Current therapeutic strategies, particularly biologics and Janus kinase (JAK) inhibitors, are effective for inducing clinical remission and controlling inflammation. However, one-third of patients fail to respond to these treatments, highlighting the need for predictive biomarkers to better tailor therapy and improve outcomes. Methods In this study, we conducted a multi-omic approach, integrating transcriptomics, proteomics, metabolomics, and metagenomics to identify biomarkers of treatment response in IBD. A cohort of 57 active CD and 70 active UC patients was analyzed before and after 14 weeks of treatment with anti-TNF, ustekinumab, vedolizumab, or tofacitinib. Response was evaluated using endoscopic criteria, categorizing patients as responders or non-responders. Biological samples [serum, urine, serum extracellular vesicles (EVs), intestinal biopsies, and stool] were analysed using RNA sequencing, liquid chromatography-mass spectrometry, nuclear magnetic resonance, and 16S rRNA gene sequencing to assess molecular and microbial profiles. Results Our results identified multiple mRNAs, proteins and metabolites associated with treatment response (Table 1). Gene expression analysis in intestinal tissue showed significant differences between UC patients responders and non-responders to vedolizumab. Proteomic analysis of serum EVs and intestinal tissue samples revealed differentially expressed proteins between different study groups. Metabolomic analysis identified deregulation of 24 serum lipoproteins from CD responders to ustekinumab compared to non-responders. Pathway analysis highlighted significant enrichment in ketone and butyrate metabolism, mitochondrial electron transport chain activity, carnitine synthesis, and fatty acid oxidation pathways. Metagenomic analysis revealed microbial differences in UC patients responders to anti-TNF therapy compared to non-responders (Figure 1). Conclusion This multi-omics analysis uncovers promising biomarkers that could serve as predictive indicators of therapeutic response to biologics and JAK inhibitors. Nevertheless, further studies are crucial to confirm these findings and evaluate their clinical relevance in identifying patients most likely to respond to tailored therapeutic interventions. One of the challenges is integrating results from different omics approaches to create a more holistic understanding of the disease, potentially opening doors for more precise/early detection through multipanel biomarkers.

Identification of Molecular Subtypes and Prognostic Traits Based on Chromosomal Instability Phenotype-Related Genes in Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) exhibits significant molecular heterogeneity; however, previous studies have not fully explored its classification into distinct molecular subtypes. Here, we identified LUAD-significant chromosomal instability (CIN) phenotype genes (n = 24) using a TCGA-LUAD cohort (n = 592) and evaluated their ability to predict pathologic grade. Unsupervised clustering and principal component analysis revealed that LUAD patients could be classified into CIN phenotype-related subtypes (GroupLow, GroupModerate, and GroupHigh), each exhibiting distinct transcriptomic patterns. Notably, the GroupHigh showed significantly poor overall survival [OS; hazard ratio (HR) = 1.43, p-value < 10-3] and disease-free survival (DFS; HR = 1.27, p-value < 10-3). Univariate and multivariate analysis confirmed that its expression status was an independent prognostic predictor (p-value < 10-3, HR = 2.18, 95% C.I = 1.26-3.76) of the clinical outcomes, outperforming pathologic grade (p-value < 10-3, HR = 1.2, 95% C.I = 1.08-1.33). Moreover, analysis of surfactant metabolism-related genes revealed higher expression in the GroupLow, which was associated with a favorable prognosis. By integrating multiple independent cohorts (n = 779), we validated these findings and confirmed that CIN phenotype gene status serves as a critical prognostic marker in LUAD. Furthermore, genomic profiling showed that the GroupHigh exhibited frequent mutations in key genes such as KEAP1, LYST, SETD2, and TP53, with oncogenes in this group preferentially showing copy number gains. Our study highlights the significance of CIN phenotype gene status as a predictor of LUAD prognosis and its association with transcriptomic and genomic alterations, paving the way for further clinical validation and potential therapeutic interventions.

The cyclin-G associated kinase (GAK) is a novel mitotic kinase and therapeutic target in diffuse large B-cell lymphoma.

Diffuse large B cell lymphoma (DLBCL) is an aggressive non-Hodgkin lymphoma and the most frequently diagnosed hematologic malignancy in the United States. DLBCL exhibits significant molecular and clinical heterogeneity, and at least a third of patients are left uncured with standard frontline chemoimmunotherapy. As such, there is a critical need to identify novel targeted therapies to improve outcomes. We conducted a phenotypic screen of kinase inhibitors against DLBCL cell lines and non-malignant controls. We identified the cyclin G-associated kinase (GAK) as a tumor-selective, readily druggable target whose inhibition killed DLBCL cell lines, while sparing non-malignant blood cells. Upon investigation of GAK's cellular function, we discovered that inhibition results in G2/M-phase cell cycle arrest. Immunofluorescent confocal microscopy revealed significant chromosome misalignment and spindle distortion in DLBCL cells following GAK-inhibition, disrupting progression through mitosis. Analysis of RNA-seq data from clinical samples showed increased GAK expression associates strongly with RB1 deficiency in DLBCL cases, suggesting dependency on GAK for proper mitotic progression linked to retinoblastoma associated protein (RB) loss of function, a common DLBCL driver. In cell-cycle analyses and under microscopy, RB-deficient DLBCL cells treated with an exquisitely selective GAK inhibitor showed complete arrest at G2/M, pronounced distortion of mitotic spindles, and widespread chromosomal damage. Finally, in vivo studies of DLBCL xenograft-bearing NSG mice achieved a dramatic tumor-burden reduction in response to targeted GAK inhibition. These results reveal a novel cell cycle kinase suitable for therapeutic exploitation in DLBCL patients and linked to the common, undruggable biomarker of RB loss of function.

Metabolic and Epigenetic Mechanisms in Hepatoblastoma: Insights into Tumor Biology and Therapeutic Targets.

Hepatoblastoma, the most common pediatric liver malignancy, is characterized by significant molecular heterogeneity and poor prognosis in advanced stages. Recent studies highlight the importance of metabolic reprogramming and epigenetic dysregulation in hepatoblastoma pathogenesis. This review aims to explore the metabolic alterations and epigenetic mechanisms involved in hepatoblastoma and how these processes contribute to tumor progression and survival. Relevant literature on metabolic reprogramming, including enhanced glycolysis, mitochondrial dysfunction, and shifts in lipid and amino acid metabolism, as well as epigenetic mechanisms like DNA methylation, histone modifications, and non-coding RNAs, was reviewed. The interplay between these pathways and their potential as therapeutic targets were examined. Hepatoblastoma exhibits metabolic shifts that support tumor growth and survival, alongside epigenetic changes that regulate gene expression and promote tumor progression. These pathways are interconnected, with metabolic changes influencing the epigenetic landscape and vice versa. The dynamic interplay between metabolism and epigenetics in hepatoblastoma offers promising avenues for therapeutic intervention. Future research should focus on integrating metabolic and epigenetic therapies to improve patient outcomes, addressing current gaps in knowledge to develop more effective treatments.

Interactions between nanobiochar and arsenic: Effects of biochar aging methods on arsenic binding capacity and mechanisms

Nano-biochar (nanoBC), produced from biochar aging, exhibits significant molecular heterogeneity that may affect the fate and toxicity of co-occurring pollutants. However, the interaction between nanoBC and arsenic (As) remains unclear. Herein, we simulated biochar aging through water erosion, photoaging, and thermal chemical decomposition to generate three types of nanoBC (nUBC, nPBC, and nHBC). We then investigated their distinct binding affinities and interaction mechanisms with arsenite (AsIII) and arsenate (AsV). Complementary analysis using optical spectrophotometer and high-resolution mass spectrometry revealed significant differences in properties and chemical compositions among the three nanoBCs at a size of 100 nm. Specifically, nHBC had higher yield, nPBC had higher aromaticity, and nUBC had more intricate molecular compositions and larger molecular weights. Binding experiments showed that nHBC and nUBC exhibited the highest conditional distribution coefficient (KD) for AsIII and AsV, respectively. In nHBC, a higher proportion of humic-like fluorescent component C3 enhanced its affinity for AsIII, attributed to lignin-like molecules with CHONS formulas where thiol acted as active binding sites. In contrast, the robust AsV binding capacity of nUBC stemmed from its richness in humic-like fluorescent component C1 and tryptophan-like fluorescent component C2. This is facilitated by lipid-like molecules and CHO formulas in C1 and aliphatic/peptide-like molecules and CHON formulas in C2, which provided oxygenic and nitrogen-containing groups for binding. All nanoBC had a significantly higher binding affinity for As than bulk BC. These findings provide a deeper understanding of As-nanoBC binding mechanisms at the molecular level, facilitating more accurate prediction of As fate in biochar-amended soil and associated ecosystem risks.

Introducing FISCAS, a Tool for the Effective Generation of Single Cell MALDI-MSI Data.

We introduce Fluorescence Integrated Single-Cell Analysis Script (FISCAS), which combines fluorescence microscopy with MALDI-MSI to streamline single-cell analysis. FISCAS enables automated selection of tight measurement regions, thereby reducing the acquisition of off-target pixels, and makes use of established algorithms for cell segmentation and coregistration to rapidly compile single-cell spectra. MALDI-compatible staining of membranes, nuclei, and lipid droplets allows the collection of fluorescence data prior to the MALDI-MSI measurement on a timsTOF fleX MALDI-2. Usefulness of the software is demonstrated by the example of THP-1 cells during stimulated differentiation into macrophages at different time points. In this proof-of-principle study, FISCAS was used to automatically generate single-cell mass spectra along with a wide range of morphometric parameters for a total number of roughly 1300 cells collected at 24, 48, and 72 h after the onset of stimulation. Data analysis of the combined morphometric and single-cell mass spectrometry data shows significant molecular heterogeneity within the cell population at each time point, indicating an independent differentiation of each individual cell rather than a synchronized mechanism. Here, the grouping of cells based on their molecular phenotype revealed an overall clearer distinction of the different phases of differentiation into macrophages and delivered an increased number of lipid signals as possible markers compared with traditional bulk analysis. Utilizing the linkage between mass spectrometric data and fluorescence microscopy confirmed the expected positive correlation between lipid droplet staining and the overall signal for triacylglyceride (TG), demonstrating the usefulness of this multimodal approach.

Lipid imaging mass spectrometry: Towards a new molecular histology

Lipid research is attracting greater attention, as these molecules are key components to understand cell metabolism and the connection between genotype and phenotype. The study of lipids has also been fueled by the development of new and powerful technologies, able to identify an increasing number of species in a single run and at decreasing concentrations. One of such key developments has been the image techniques that enable the visualization of lipid distribution over a tissue with cell resolution. Thanks to the spatial information reported by such techniques, it is possible to associate a lipidome trait to individual cells, in fixed metabolic stages, which greatly facilitates understanding the metabolic changes associated to diverse pathological conditions, such as cancer. Furthermore, the image of lipids is becoming a kind of new molecular histology that has great chances to make an impact in the diagnostic units of the hospitals. Here, we examine the current state of the technology and analyze what the next steps to bring it into the diagnosis units should be. To illustrate the potential and challenges of this technology, we present a case study on clear cell renal cell carcinoma, a good model for analyzing malignant tumors due to their significant cellular and molecular heterogeneity.

Amyotrophic lateral sclerosis diagnosis using machine learning and multi-omic data integration

Amyotrophic Lateral Sclerosis (ALS) is a complex and rare neurodegenerative disorder characterized by significant genetic, molecular, and clinical heterogeneity. Despite numerous endeavors to discover the genetic factors underlying ALS, a significant number of these factors remain unknown. This knowledge gap highlights the necessity for personalized medicine approaches that can provide more comprehensive information for the purposes of diagnosis, prognosis, and treatment of ALS. This work utilizes an innovative approach by employing a machine learning-facilitated, multi-omic model to develop a more comprehensive knowledge of ALS. Through unsupervised clustering on gene expression profiles, 9,847 genes associated with ALS pathways are isolated and integrated with 7,699 genes containing rare, presumed pathogenic genomic variants, leading to a comprehensive amalgamation of 17,546 genes. Subsequently, a Variational Autoencoder is applied to distil complex biomedical information from these genes, culminating in the creation of the proposed Multi-Omics for ALS (MOALS) model, which has been designed to expose intricate genotype-phenotype interconnections within the dataset. Our meticulous investigation elucidates several pivotal ALS signaling pathways and demonstrates that MOALS is a superior model, outclassing other machine learning models based on single omic approaches such as SNV and RNA expression, enhancing accuracy by 1.7 percent and 6.2 percent, respectively. The findings of this study suggest that analyzing the relationships within biological systems can provide heuristic insights into the biological mechanisms that help to make highly accurate ALS diagnosis tools and achieve more interpretable results.

Abstract C147: Impact of genetic ancestry in triple-negative breast cancer subtypes

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive BC subtype characterized by significant molecular and clinical heterogeneity, influenced by genetic, phenotypic, and environmental factors, as well as interactions of the tumor with its surrounding milieu. A significant racial disparity has been observed between African American (AA) and European American (EA) women regarding the incidence and clinical progression of TNBC. TNBC frequently occurs in young parous women who self-identify as AA and in women who harbor a germline BRCA1 mutation. Notably, AA women are diagnosed with TNBC at a younger age and exhibit a higher risk of developing stage IV disease. Studies examining gene expression signatures that distinguish AA and EA TNBC have reported distinct tumor-associated immunologic profiles in AA patients. We have developed a novel cell type-driven subtyping system based on a racially diverse TNBC sample set that identified three TNBC subtypes, each with distinct biology and prognosis: CC1- immune signaling/T-cell response; CC2- pro- migratory/inflammatory; CC3- fatty acid and hormone and nuclear receptor signaling. In this study, we propose to examine ancestry-inferred differences within each TNBC subtype between patients with African and European ancestry. Methods: RNA-Sequencing data for the Louisiana Tumor Registry, a TNBC cohort of 250 diverse women [EA: 123 and AA: 127], was obtained from our collaborators at Louisiana State University Health Sciences Center. Genetic admixture was performed on 227/250 patients using the method described by Pakstis, A. J. et al. Differentially expressed genes (DEGs) were identified in pairwise comparisons at p-adj ≤ 0.05. Survival was assessed using log-rank tests. Results: We investigated DEGs within each subtype between patients with &amp;gt;60% African (Aa, n=102) or &amp;gt;60% European ancestry (Ea, n=99) (identified via admixture analysis). In all three subtypes, upregulated genes, and their associated enrichment in Aa were related to immune pathways, while DEGs in Ea patients were related to epithelial cell regulation. In CC1, Aa was associated with the upregulation of immunoglobulin genes involved in immunoglobulin production and antigen recognition, while Ea was associated with the upregulation of embryonic development genes. In CC2, Aa showed enriched complement activation and immunoglobulin genes, while Ea exhibited upregulation of basal cytokeratin and growth factor EGFR. In CC3, Aa was associated with the upregulation of inflammatory genes, whereas Ea showed upregulation of cellular senescence genes. Survival analysis demonstrated favorable outcomes for Aa in CC1 and less favorable outcomes for Aa in CC2. Conclusion: Our study highlights significant ancestry-inferred differences in gene expression within TNBC subtypes, with Aa patients showing immune pathways enrichment and Ea patients exhibiting differential epithelial cell regulation. These findings underscore the importance of considering genetic ancestry in TNBC prognosis and treatment strategies. Citation Format: Zahra Mesrizadeh, Kavitha Mukund, Fokrul Hossain, Jovanny Zabaleta, Denise Danos, Luis De Valle, Xiao-Cheng Wu, Chindo Hicks, Augusto Ochoa, Lucio Miele, Victoria L. Seewaldt, Shankar Subramaniam. Impact of genetic ancestry in triple-negative breast cancer subtypes [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C147.

Advances, recognition, and interpretation of molecular heterogeneity among conventional and subtype histology of urothelial carcinoma (UC): a survey among urologic pathologists and comprehensive review of the literature.

Urothelial carcinoma (UC) demonstrates significant molecular and histologic heterogeneity. The WHO 2022 classification has hinted at adding molecular signatures to the morphologic diagnosis. As morphology and associated molecular repertoire may potentially translate to choices of and response to therapy and relapse rate, broader acceptability of recognizing these key features among uropathologists is needed. This prompted an international survey to ascertain the practice patterns in classical/subtype UC among uropathologists across the globe. A survey instrument was shared among 98 uropathologists using SurveyMonkey software. Anonymized respondent data were analysed. The response rate was 85%. A majority were in concordance with the profiles of luminal (93%) and basal (82%) types. Opinion on the FGFR3 testing platform was variable. While 95% concurred that TERT promoter mutation is the key driver in UC, 72% had the opinion that APOBEC mutagenesis is the main signature in muscle invasive bladder cancer (MIBC). Uropathologists have divergent opinions on MIBC and ERCC2 mutations. Among the participants, 94% would quantify aggressive micropapillary and sarcomatoid histology, while 88% would reevaluate another transurethral resection of the bladder tumour specimen in nonmuscle invasive tumour with micropapillary, small cell, or sarcomatoid histology. A leading number agreed to specific molecular signatures of micropapillary (93%), plasmacytoid (97%), and small cell (86%) subtypes. Ninety-six percent of participants agreed that a small-cell component portends a more aggressive course and should be treated with neoadjuvant chemotherapy and 63% would perform HER2/neu testing only on oncologist's request in advanced tumours. Ninety percent agreed that microsatellite instability testing, although not a standard protocol, should be considered in young patients with upper tract UC. Eighty-six percent agreed that UC with high tumour mutational burden would be a better candidate for immunotherapy. In the era of precision medicine, enhanced understanding of molecular heterogeneity of UC will contribute to better therapeutic options, novel biomarker discovery, innovative management protocols, and outcomes. Our survey provides a broad perspective of pathologists' perceptions and experience regarding incorporation of histomolecular approaches to "personalize" therapy. Due to variable clinical adoption, there is a need for additional data using uniform study criteria. This will drive generation of best practice guidelines in this area for widespread and consistent clinical utility.

Enhancing Therapeutic Approaches in Glioblastoma with Pro-Oxidant Treatments and Synergistic Combinations: In Vitro Experience of Doxorubicin and Photodynamic Therapy.

Glioblastoma (GBM) is an aggressive brain cancer characterized by significant molecular and cellular heterogeneity, which complicates treatment efforts. Current standard therapies, including surgical resection, radiation, and temozolomide (TMZ) chemotherapy, often fail to achieve long-term remission due to tumor recurrence and resistance. A pro-oxidant environment is involved in glioma progression, with oxidative stress contributing to the genetic instability that leads to gliomagenesis. Evaluating pro-oxidant therapies in brain tumors is crucial due to their potential to selectively target and eradicate cancer cells by exploiting the elevated oxidative stress levels inherent in these malignant cells, thereby offering a novel and effective strategy for overcoming resistance to conventional therapies. This study investigates the therapeutic potential of doxorubicin (DOX) and photodynamic therapy (PDT) with Me-ALA, focusing on their effects on redox homeostasis. Basal ROS levels and antioxidant gene expression (NFE2L2, CAT, GSR) were quantitatively assessed across GBM cell lines, revealing significant variability probably linked to genetic differences. DOX and PDT treatments, both individually and in combination, were analyzed for their efficacy in inducing oxidative stress and cytotoxicity. An in silico analysis further explored the relationship between gene mutations and oxidative stress in GBM patients, providing insights into the molecular mechanisms underlying treatment responses. Our findings suggest that pro-oxidant therapies, such as DOX and PDT in combination, could selectively target GBM cells, highlighting a promising avenue for improving therapeutic outcomes in GBM.

Analysis of regulation of cell death pathway genes in CSC-enriched TNBC after treatment with doxorubicin: A potencial biomarker.

e13154 Background: Breast cancer is one of the most common cancers in women worldwide, and triple-negative breast cancer (TNBC) accounts for approximately 10-20% of all cases globally. TNBC has the worst prognosis among other types of breast cancer due to the lack of targeted therapy. In addition, TNBC tumors exhibit significant cellular and molecular heterogeneity, along with the presence of cells with cancer stem cell (CSC) characteristics, which contribute to the low response to available chemotherapy treatments, leading to chemoresistance, recurrence and metastasis. objective of this study is to evaluate the expression of genes related to cell death and survival pathways in CSCs-enriched spheroids DOX-treated obtained of BT-549 cells, a human TNBC cell line. The death receptor genes include TNFRSF10B, TNFRSF10C, CFLAR, RIPIK1, CASP8, NFKB1, RELA, and MLKL. Methods: To achieve this, gene expression was analyzed through RT-qPCR, comparing the expression in DOX-treated CSCs-enriched spheroids (IC50 55.7 μM/ 48h incubation) and untreated CSCs-enriched spheroids. Preliminary results indicated that, among the evaluated genes, only CFLAR, NFKB1, and RELA were expressed in the untreated CSCs-enriched spheroids, while the others were not expressed under any condition. Results: The genes CFLAR, NF- κ B and RELA showed considerable Ct values, while the remaining genes did not exhibit a Ct value in one or more samples. The gene CFLAR showed an overexpression, both in monolayers vs. spheroids and in treated spheroids vs. untreated spheroids, which can be related to the inhibition of Caspase 8 and consequently, the apoptotic activity of cells. The overexpression of the RELA, same as CFLAR, suggests increased inflammation pathway activation in the tumor microenvironment. However, the lower expression of the NF-κB1 gene in treated spheroids vs. untreated spheroids may be related to the production of ROS, suppressing its activation. Conclusions: The expression of NFKB1 and RELA genes is associated with the cellular survival pathway, which may be linked to the resistance to the drug observed in many patients. Previous studies of our group have shown that achieving a satisfactory result of DOX action on CSCs-enriched spheroids requires using a dose 100 times higher than that used in monolayer cells. This may be related to the non-expression of the TNFRSF10B, TNFRSF10C, RIPIK1, CASP8, and MLKL genes in CSCs-enriched spheroid DOX-treated. Thus, the results obtained so far indicate that DOX may have an impact on the expressed genes in CSCs-enriched spheroids and demonstrate the expression of apoptosis inhibitors in treated breast spheres. Consequently, the expression of these genes in BT-549 cells TNBC indicates a pro-inflammatory, anti-apoptotic, and pro-cell survival profile of CSC-enriched spheroids.

Abstract LB006: Cell marker-based classification of TNBC subtypes and patient outcomes

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive BC subtype characterized by significant molecular and clinical heterogeneity, influenced by genetic, phenotypic, and environmental factors, as well as interactions of the tumor with its surrounding milieu. In the recent past, gene expression-based subtyping methods have provided a functional understanding for the observed molecular diversity/heterogeneity. In this study, we propose an approach to reclassifying TNBC while considering the cellular heterogeneity of the tumor as well as the tumor milieu. Methods: RNA-Sequencing data for TNBC cohort of 250 diverse women [European (EA, self-reported race, SRR): 114 and African (AA, SRR): 136)], was obtained from our collaborators at LSUHSC. 38/250 were labeled ERhi via IHC but histologically confirmed to be TNBC patients. We utilized 261 breast specific cell type markers to classify our cohort via hierarchical (HC) and consensus (CC) clustering. Differentially expressed genes (DEGs) were identified at p-adj ≤ 0.05. Endotype specific networks were generated using protein-protein interactions, DEGs, and genes regulated by transcription factor. Survival was assessed via log-rank tests. Genetic admixture was performed on 227/250 patients using method described by Pakstis, A. J. et al. Results: We identified three distinct mechanistic subtypes (endotype, CC1-3) containing nine distinct groups (HC1-9), revealing substantial heterogeneity in cell-type and tissue-state within TNBC. Each subtype exhibited unique biomarkers, reflecting diverse immune, extracellular matrix, adipogenesis, and inflammatory signatures. Endotype specific networks revealed patients in CC1 exhibited upregulation of CD8 T cell activation, interferon and interleukin markers, while CC2 showed upregulation of extracellular matrix genes, and CC3, the subtype containing ERhi patients, showed upregulation of fatty acid regulation, hormone sensitivity, and pro-inflammatory genes. Survival analysis demonstrated favorable outcomes for CC1 and less favorable outcomes for CC2. Additionally, SRR-inferred survival differences highlighted poorer outcomes for CC2 groups. We found SRR-inferred prognostic biomarkers such as TTC6, ANKRD30A, and KRT86 associated with distinct prognostic profiles in CC2. Genetic admixture showed a comparable distribution of SRR and genetic ancestry across subtypes. We developed a user-friendly Shiny App for our subtyping method and validated it using TCGA TNBC data. Conclusion: TNBC subtyping using cellular heterogeneity of biopsied samples provides a mechanistic approach to patient classification. Subtype-specific mechanisms suggest tailored therapeutic strategies and provide survival outcomes specific to each subtype. Our method can be applied to other cohorts using the application developed in this work. Citation Format: Zahra Mesrizadeh, Kavitha Mukund, Fokrul Hossain, Jovanny Zabaleta, Denise Danos, Luis Del Valle, Xiao-Cheng Wu, Chindo Hicks, Yuan Chun Ding, Augusto Ochoa, Lucio Miele, Victoria L. Seewaldt, Shankar Subramaniam. Cell marker-based classification of TNBC subtypes and patient outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB006.

Aberrantly Glycosylated GLUT1 as a Poor Prognosis Marker in Aggressive Bladder Cancer.

Muscle-invasive bladder cancer (MIBC) remains a pressing health concern due to conventional treatment failure and significant molecular heterogeneity, hampering the development of novel targeted therapeutics. In our quest for novel targetable markers, recent glycoproteomics and bioinformatics data have pinpointed (glucose transporter 1) GLUT1 as a potential biomarker due to its increased expression in tumours compared to healthy tissues. This study explores this hypothesis in more detail, with emphasis on GLUT1 glycosylation patterns and cancer specificity. Immunohistochemistry analysis across a diverse set of human bladder tumours representing all disease stages revealed increasing GLUT1 expression with lesion severity, extending to metastasis, while remaining undetectable in healthy urothelium. In line with this, GLUT1 emerged as a marker of reduced overall survival. Revisiting nanoLC-EThcD-MS/MS data targeting immature O-glycosylation on muscle-invasive tumours identified GLUT1 as a carrier of short glycosylation associated with invasive disease. Precise glycosite mapping uncovered significant heterogeneity between patient samples, but also common glycopatterns that could provide the molecular basis for targeted solutions. Immature O-glycosylation conferred cancer specificity to GLUT1, laying the molecular groundwork for enhanced targeted therapeutics in bladder cancer. Future studies should focus on a comprehensive mapping of GLUT1 glycosites for highly specific cancer-targeted therapy development for bladder cancer.

Nanopore Sequencing of Cell-free DNA: An Emerging Liquid Biopsy Approach for Brain Tumor Molecular Profiling

Background: Brain tumors exhibit significant molecular heterogeneity, complicating diagnosis, prognosis, and treatment. Traditional tissue biopsies are invasive and often fail to capture the full tumor landscape due to intratumoral heterogeneity. Liquid biopsy, which analyzes cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA), offers a minimally invasive alternative for tumor profiling. Nanopore sequencing, a novel long-read sequencing technology, is emerging as a valuable tool in this context. Purpose: This review explores the application of nanopore sequencing in molecular profiling of brain tumors using liquid biopsy, focusing on its ability to detect both genetic and epigenetic alterations with clinical relevance. Main body: Brain tumors, such as gliomas and medulloblastomas, are characterized by diverse molecular profiles, which influence patient outcomes and treatment strategies. Nanopore sequencing offers unique advantages for profiling cfDNA from biofluids like cerebrospinal fluid (CSF) and plasma, including the ability to generate long reads and detect structural variants, copy number alterations, and methylation patterns. Several studies have demonstrated its potential to identify key mutations (e.g., IDH1/2, H3K27 M) and track tumor evolution through serial cfDNA monitoring. However, challenges remain, including low ctDNA fractions in biofluids and bioinformatic complexities. Conclusion: Nanopore sequencing holds significant promise for advancing non-invasive molecular profiling of brain tumors, offering real-time insights into tumor genomics and evolution. This technology could revolutionize personalized brain tumor management, but further validation and optimization are needed before it can be routinely applied in clinical practice.

Molecular Characteristics, Antimicrobial Susceptibility, Biofilm-Forming Ability of Clinically Invasive Staphylococcus aureus Isolates.

This study aimed to investigate the molecular characteristics, antimicrobial resistance, and biofilm-forming ability of Staphylococcus aureus isolates from invasive infections. A total of 92 non-repetitive S. aureus isolates from invasive infections were analyzed by Multi-locus Sequence Typing (MLST), spa typing, and chromosomal cassette mec (SCCmec) typing. Antibiotic susceptibility testing was performed using the disk diffusion and agar dilution methods. Biofilm-forming ability was assessed using crystal violet assay. The presence and expression of biofilm-associated genes were examined using PCR and RT-qPCR. Among the 55 Methicillin-resistant S. aureus (MRSA) and 41 Methicillin-sensitive S. aureus (MSSA) isolates, ST59 (43.6%) predominated in MRSA, while ST7 (39.0%) was most common in MSSA. As expected, MRSA exhibited higher antibiotic resistance rates compared to MSSA isolates. Biofilm formation assays revealed that the majority of isolates (88.5%) produced biofilms, with 26.0% classified as strong producers (OD570 ≥ 1.0) and 62.5% as weak producers (0.2 ≤ OD570<1.0). MSSA exhibited a higher biofilm-forming ability than MRSA (P < 0.01), with variations across clones. Notably, ST7 isolates displayed greater biofilm-forming ability than other sequence types (ST59, ST5, and ST239). RT-qPCR results revealed that ST7 isolates exhibited higher expression levels of icaA compared to other sequence types. This study revealed significant molecular heterogeneity among invasive S. aureus isolates, with ST59 and ST7 as dominant clones. The strong biofilm-forming capacity of ST7 merits concern given its rising prevalence regionally. Continuous surveillance of emerging successful lineages is critical to help guide infection control strategies against invasive S. aureus infections.

SYST-27 INTERROGATION OF THE TUMOR IMMUNE MICROENVIRONMENT REVEALS DISTINCT IMMUNOSUPPRESSIVE LANDSCAPES IN GLIOBLASTOMA

Abstract High-resolution sequencing technologies have revealed significant inter-and intra-tumoral molecular heterogeneity in glioblastoma (GBM), leading to an urgent need for novel targeted therapies. Our research using representative murine GBM models and various experimental techniques has shown that classical GBMs (e.g., EGFRvIII+, TIMElow) and mesenchymal GBMs (e.g., NF1ko/PTENko/p53ko, TIMEhigh) are both immunosuppressive but in distinct ways. TIMElow GBMs have a more impaired and less functional tumor vasculature, resulting in low infiltration of T cells with anergic features. TIMEhigh GBMs have a more intact BBB revealing overall more adaptive and innate immune cell infiltrates, but with highly dysfunctional T cells and immunosuppressive TME. Congruently, GSEA analysis of both human and murine GBM scRNA-seq data demonstrated enriched immunosuppressive signatures in the myeloid cell populations of TIMEhigh GBM compared to TIMElow GBM. Our findings have also revealed potential adaptive and intrinsic resistant mechanisms to antiangiogenic immunotherapy in TIMElow and TIMEhigh GBMs, respectively, with TIMElow GBMs exhibiting a transitory response to the treatment, while TIMEhigh GBMs being intrinsically resistant due to their intact tumor vasculature and reliance on dysfunctional T cells. We then tested the efficacy of different immunotherapies, including dendritic cell vaccination, a CD40 agonist, and a myeloid cell PI3K activity inhibitor in TIMElow and TIMEhigh tumors. Surprisingly, our results revealed that the response to these treatments can be either beneficial or detrimental and may depend on factors such as tumor antigenicity and TIME subtype. Overall, our study provides new insights into the intricate immune landscape of GBMs, emphasizes the importance of considering tumor subtypes as they may lead to potential unintended consequences of immunotherapies.

Changes in expression of mesothelial BBS genes in 2D and 3D after lithium chloride and ammonium sulphate induction of primary cilium disturbance: a pilot study

BackgroundMalignant pleural mesothelioma (MPM), a rare and aggressive pleural tumor, has significant histological and molecular heterogeneity. Primary Cilium (PC), an organelle of emerging importance in malignancies, has been scarcely investigated in MPM. A critical molecular complex for the PC function is the BBSome and here we aimed at assessing its expression patterns in ordinary 2D and spheroid 3D cell cultures.MethodsA human benign mesothelial cell line (MeT-5A), MPM cell lines (M14K, epithelioid MPM; MSTO, biphasic MPM), and primary MPM cells (pMPM) were used. Primers specific for the human BBS1, 2, 4, 5, 7, 9, 18 transcripts were designed, and quantitative real-time PCR (qRT-PCR) was done with β-actin as the gene of reference. The relative gene expression across 2D and 3D cultures was analyzed by the expression factor (mean of 1/ΔCt values). With the 2–∆∆Ct method the gene expression fold changes were assessed from qRT-PCR data. Molecular changes using the PC-modulating drugs ammonium sulfate (AS) and lithium chloride (LC) were also determined.ResultsPC was present in all cells used in the study at approximately 15% of the observed area. BBSome transcripts were differentially expressed in different dimensions of cell culture (2D vs. 3D) in all cell lines and pMPM. Treatment with AS and LC affected the expression of the ciliary BBS2 and BBS18 genes in the benign as well as in the MPM cells.ConclusionsThese data indicate distinct BBSome molecular profiles in human benign and MPM cells cultured in 2D and 3D dimensions and support the notion that PC genes should be investigated as potential MPM therapeutic targets.

Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis.

Human Papillomaviruses (HPVs) are associated with around 5%-10% of human cancer, notably nearly 99% of cervical cancer. The mechanisms HPV interacts with stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study viral gene and host cell differentiation-associated heterogeneity of HPV-positive cervical cancer tissue. We examined the HPV16 genes-E1, E6, and E7, and found they expressed differently across nine epithelial clusters. We found that three epithelial clusters had the highest proportion of HPV-positive cells (33.6%, 37.5%, and 32.4%, respectively), while two exhibited the lowest proportions (7.21% and 5.63%, respectively). Notably, the cluster with the most HPV-positive cells deviated significantly from normal epithelial layer markers, exhibiting functional heterogeneity and altered epithelial structuring, indicating that significant molecular heterogeneity existed in cancer tissues and that these cells exhibited unique/different gene signatures compared with normal epithelial cells. These HPV-positive cells, compared to HPV-negative, showed different gene expressions related to the extracellular matrix, cell adhesion, proliferation, and apoptosis. Further, the viral oncogenes E6 and E7 appeared to modify epithelial function via distinct pathways, thus contributing to cervical cancer progression. We investigated the HPV and host transcripts from a novel viewpoint focusing on layer heterogeneity. Our results indicated varied HPV expression across epithelial clusters and epithelial heterogeneity associated with viral oncogenes, contributing biological insights to this critical field of study.

Identification of a novel glycolysis-related prognosis risk signature in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is a particularly aggressive cluster of breast cancer characterized by significant molecular heterogeneity. Glycolysis is a metabolic pathway that is significantly associated with cancer progression, metastasis, recurrence and chemoresistance. However, the potential roles of glycolysis-related genes in TNBC remain unclear. In the present study, we identified 108 glycolysis-related differentially expressed genes (DEGs) between breast cancer (BRCA) tumor tissues and normal tissues, and we divided patients into two different clusters with significantly distinct molecular characteristics, clinicopathological features, prognosis, immune cell infiltration and mutation burden. We then constructed a 10-gene signature that classified all TNBCs into low- and high-risk groups. The high-risk group had significantly lower survival than the low-risk group, which implied that the risk score was an independent prognostic indicator for TNBC patients. Consequently, we constructed and validated a prognostic nomogram, which accurately predicted individual overall survival (OS) of TNBC. Moreover, the risk score predicted the drug sensitivity of chemotherapeutic agents and immunotherapy for TNBC patients. The present comprehensive analysis of glycolysis-related DEGs in TNBC provides new methods for prognosis prediction and more effective treatment strategies.