MPN-760: Investigating Gender-Based Differences in the Molecular Profile of Myeloid Neoplasms: Insights From an Institutional Genomic Database

Impact of spliceosome mutation on outcomes of myelodysplastic syndrome and chronic myelomonocytic leukemia patients undergoing allogeneic hematopoietic cell transplantation

Herein is reported a series of five patients with myeloid neoplasms presenting hepatic complications in whose liver biopsy revealed obstruction of sinusoids by platelet aggregates associated to liver extramedullary haematopoiesis. Indication of liver biopsies was jaundice, unexplained hepatomegaly or portal hypertension. Haematological disorders were classified according to the World Health Organisation. Molecular profile was established in all cases as well as grade of liver extramedullary haematopoiesis and myelofibrosis. The patients were four men and one woman aged from 50 to 82years. Two patients had myeloproliferative neoplasm (triple negative primary myelofibrosis and JAK2-mutated essential thrombocytopenia), two patients had unclassifiable myelodysplastic/myeloproliferative neoplasm and one patient had chronic myelomonocytic leukaemia type 1. Liver biopsies revealed platelet aggregates occluding sinusoids in association with extramedullary haematopoiesis grade 1 in one patient, grade 2 in two patients and grade 3 in two patients. Two of these patients presented co-existing liver fibrosis due to chronic alcoholic consumption and ischemic heart failure. These five patients died from 2 to 23months after liver biopsy due to acute myeloblastic leukaemia (three patients), portal hypertension (one patient) or other causes (acute heart failure). Intrahepatic sinusoidal microthromboses through platelet aggregates might cause portal hypertension or liver deficiency in patients with myeloid neoplasms, independently of JAK2 mutational status and grade of extramedullary haematopoiesis.

Background: Personalized medicine has revolutionized cancer treatment by tailoring therapies to individual genetic and molecular profiles, enabling more targeted and effective interventions. Advances in genomic technologies, such as Next-Generation Sequencing (NGS), and biomarker analyses have allowed for precise identification of actionable mutations and personalized treatment strategies. However, understanding the clinical and economic implications of these approaches remains a priority to optimize their application in cancer care. Objective: This study aims to evaluate the clinical and economic impact of personalized medicine on cancer treatment outcomes, focusing on progression-free survival (PFS), overall survival (OS), quality of life, and cost-effectiveness. By comparing patients receiving personalized treatments with those undergoing standard care, the study seeks to assess the benefits and challenges associated with precision oncology. Methods: A retrospective cohort study was conducted at tertiary cancer centers, including patients diagnosed with breast, lung, and pancreatic cancer who underwent personalized medicine interventions. Genomic and molecular profiling was performed using NGS and biomarker analyses (e.g., PD-L1, EGFR, BRCA mutations). Outcomes such as PFS and OS were analyzed using Kaplan-Meier survival analysis and Cox proportional hazards models. Cost-effectiveness was evaluated through incremental cost-effectiveness ratio (ICER) calculations. Data sources included electronic health records (EHRs), cancer registries, and genomic databases such as The Cancer Genome Atlas (TCGA). Results: Patients receiving personalized medicine interventions demonstrated significantly improved PFS and OS compared to those on standard therapies (PFS: median 12.4 vs. 8.3 months; OS: median 24.6 vs. 18.7 months, p < 0.05). Biomarker-driven therapies exhibited the highest efficacy, particularly among patients with actionable mutations such as EGFR and BRCA. Cost-effectiveness analysis revealed that personalized medicine, while initially more expensive, resulted in better quality-adjusted life years (QALYs), making it economically viable in the long term. Conclusion: The findings underscore the transformative potential of personalized medicine in enhancing cancer treatment outcomes, with notable improvements in survival and quality of life. However, high costs and accessibility challenges must be addressed to ensure broader adoption. Future research should focus on scaling these interventions and exploring their utility across diverse populations and cancer types.

This issue of Molecular Oncology focuses on two key topics: blood cancers and liquid biopsy research. We pick the Blood Cancer Awareness month of September to feature the Review Article by Karen Keeshan and colleagues; providing a comprehensive picture of genetic, epigenetic, transcriptional and metabolic profiles of acute myeloid leukemia (AML) in paediatric and adult patients, while also discussing clonality and molecular signatures of stem cells and chemoresistant cells in AML [[1]]. Further Research Articles in this issue investigate specific molecular signatures of AML and other myeloid neoplasms. Indicatively, Andrés-Zayas et al. used a 15-gene panel to identify and characterize myeloid neoplasms with germline predisposition through next-generation sequencing [[2]]. Moreover, Hellesøy et al. observed sex-dependent differences in mutational and transcriptional profiles and ex vivo drug responses of a total of 1755 patients with AML, therefore recommending sex-adjusted clinical management of this heterogeneous disease [[3]]. Liquid biopsy is a valuable tool for diagnosis, patient stratification and treatment follow-up of blood cancers and solid cancers alike, as also reviewed in a recent thematic issue of Molecular Oncology [https://febs.onlinelibrary.wiley.com/toc/18780261/2021/15/6]. Ongoing research aspires to address challenges related to testing sensitivity of liquid biopsy samples. Tyrosine kinase inhibitors (TKIs) are currently being used for the treatment of patients with non-small cell lung cancer (NSCLC) that carry EGFR mutations. However, during the course of treatment, patients often develop resistance to TKI therapies. Thus, mutation profiling of circulating tumour DNA (ctDNA) has been recommended in international guidelines and has entered clinical practice, in order to improve treatment decisions for patients with NSCLC. Unfortunately, ctDNA-based tests show limited sensitivity in detecting EGFR mutations. The research of Luigi Pasini et al. [[4]] proposes the use of RNA contained in blood-derived extracellular vesicles (EVs) for quantitative EGFR profiling in patients with NSCLC subjected to TKI treatment. The study employed longitudinal EGFR mRNA profiling in a representative cohort of patients treated with first- or second-generation TKIs. The authors established a workflow for the ultrasensitive detection of EGFR mutations in circulating EVs and compared the data to previously established ctDNA-based methods. Both methods adequately identified the type of EGFR mutations, where EV-RNA profiling showed superior sensitivity in mutation detection. Additionally, changes in tumour EV burden were observed during disease progression and were associated with clinical features and disease outcomes in patients receiving TKI therapy. The study also suggests that EV-RNA and ctDNA represent independent biological sources in liquid biopsy and that the molecular analysis of both could offer a more comprehensive understanding of tumour dynamics during NSCLC progression. While the role of CTCs in cancer progression, as well as in clinical cancer management, is well established, reaching reproducible and adequate sensitivity of CTC detection and molecular profiling may represent a challenge for cancer diagnostics and treatment selection. Peng-Xiang Wang and colleagues developed a new workflow for CTC enrichment, detection and single-cell analysis [[5]]. The workflow was tested and validated in healthy donors and patients with different types of cancer. In summary, automated CTC enrichment at the ChimeraX-i120 platform was combined with machine learning-based CTC identification and single CTC sequencing. Apart from establishing the novel automated workflow for single CTC enumeration and molecular characterization in different cancer types, the authors employed the workflow in a cohort of patients with hepatocellular carcinoma (HCC) to evaluate the prognostic and clinical feasibility of their method. While the workflow yielded moderate diagnostic potential in distinguishing patients with HCC, it could be efficiently used for an accurate estimation of CTC numbers and as a complementary tool in screening and early diagnosis of patients with different types of cancer. Moreover, single CTC profiling could offer a comprehensive analysis of the tumour clonal composition and tumour heterogeneity before and after treatment. In their article, Bade at al. [[6]] explore a novel strategy aimed at increasing the detection rate of circulating tumour cells (CTCs) in patients with advanced clear cell renal cell carcinoma (ccRCC). Peripheral blood CTCs were isolated and enumerated from a heterogeneous cohort of patients having various disease stages, metastasis sites and types of treatment. Captured CTCs were further characterized for several tumour-specific markers. Analysis of the isolated CTCs demonstrated pronounced heterogeneity of CTC biomarker expression among patients, as well as a significant correlation of CTC numbers with clinical progression. Furthermore, longitudinal CTC characterization showed that CTCs could hold a pharmacodynamic potential for the evaluation of patients during therapy. The novel approach of CTC capture maximized the specificity of CTC identification and advanced the noninvasive evaluation of intra- and intertumoural heterogeneity. The authors propose deployment of these novel assays in prospective clinical trials to explore the clinical potential of their approach in patients with ccRCC. The authors declare no conflict of interest.

NPM1+/FLT3- Patients with Acute Myeloid Leukemia (AML) Have Excellent Clinical Outcome Independent of Age When Treated with Cytotoxic Chemotherapy: Mayo Clinic Experience

The extensively employed limited-gene coverage NGS panels lead to clinically inadequate molecular profiling of myeloid neoplasms. The aim of the present investigation was to assess performance and clinical utility of a comprehensive DNA panel for myeloid neoplasms. Sixty-one previously well characterized samples were sequenced using TSO500 library preparation kit on NextSeq550 platform. Variants with a VAF ≥ 5% and a total read depth of >50X were filtered for analysis. The following results were recorded-for clinical samples: clinical sensitivity (97%), specificity (100%), precision (100%) and accuracy (99%) whereas reference control results were 100% for analytical sensitivity, specificity, precision and accuracy, with high intra- and inter-run reproducibility. The panel identified 880 variants across 292 genes, of which, 749 variants were in genes not covered in the 54 gene panel. The investigation revealed 14 variants in ten genes, and at least one was present in 96.2% patient samples that were pathogenic/ likely pathogenic in myeloid neoplasms. Also, 15 variants in five genes were found to be pathogenic/ likely pathogenic in other tumor types. Further, the TMB and MSI scores ranged from 0–7 and 0–9, respectively. The high analytical performance and clinical utility of this comprehensive NGS panel makes it practical and clinically relevant for adoption in clinical laboratories for routine molecular profiling of myeloid neoplasms.

e23269 Background: Mutations like EZH2, BRAF, KRAS, EGFR and others have been widely studied in lymphoid and solid malignancies where they are implicated in tumorigenesis and serve as therapeutic targets. However, the prevalence, characteristics, and clinical impact of these mutations in myeloid Neoplasms (MNs) remain underexplored. This study aims to assess the prevalence of these mutations in a cohort of MNs, providing a foundation for future research to explore their potential as therapeutic targets. Methods: We conducted a descriptive study using data from the AACR GENIE v17.0 (cBioPortal) on patients with MNs, including AML, MDS, and MPNs, excluding subtypes with fewer than 10 cases. The analysis was limited to a single distinct sample per patient to avoid duplication. Mutations were categorized as driver or Variant of Unknown Significance (VUS). Results: Among 7122 patients with MNs, 4644 unique patient samples were identified. Mutation frequencies were as follows (see Table): NRAS mutations in 384 cases (8.3%) with 426 total mutations (411 driver, 15 VUS); EZH2 mutations in 197 cases (4.3%) with 237 total mutations (104 driver, 133 VUS); KRAS mutations in 182 cases (3.9%) with 192 total mutations (186 driver, 6 VUS); NF1 mutations in 62 cases (2.8%) with 83 total mutations ( 56 driver, 27 VUS); BRCA2 mutations in 33 cases (1.5%) with 34 total mutations (3 driver, 31 VUS); BRAF mutations in 24 cases (0.5%) with 25 total mutations (21 driver, 4 VUS); ROS1 mutations in 23 cases (1%) with 25 total mutations, all VUS; EGFR mutations in 13 cases (0.5%) with 13 total mutations (2 driver, 11 VUS); NTRK1 mutations in 12 cases (0.5%) with 13 total mutations, all VUS; and RET mutations in 11 cases (0.4%) with 11 total mutations (1 driver, 10 VUS). Among significant mutations ( > 1.5% frequency), most were somatic, except for NF1 and BRCA2, with somatic mutation frequencies of 1.3% and 0.7%, respectively. Conclusions: Our findings identify actionable mutations in MNs (KRAS, EZH2, NF1, BRAF) with FDA-approved targeted therapies (e.g. sotorasib, tazemetostat, selumetinib, vemurafenib). These mutations are underexplored in MNs, though some studies have assessed MEK inhibitors for certain subtypes. The high prevalence of these mutations underscores the need for clinical trials evaluating these inhibitors starting in the relapsed/refractory setting, when outcomes are poor and alternatives are limited. This highlights the value of seeking care at dedicated Phase I programs like the Novel Therapeutics Centre at the Cleveland Clinic. Reference: The AACR Project GENIE Consortium. AACR Project GENIE: Powering Precision Medicine Through An International Consortium, Cancer Discov. 2017 Aug;7(8):818-831 v 17.0- public. Target mutation Cases Altered Altered % NRAS 384 8.30% EZH2 197 4.30% KRAS 182 3.90% NF1 62 2.80% BRCA2 33 1.50% BRAF 24 0.50% EGFR 13 0.50% RET 11 0.40%

Clinicopathological Features of FGFR3 - Mutated Upper Tract Urothelial Carcinoma: A Genomic Database Analysis.

Genetic Diversity Drives Differing Morphological and Clinical Presentation and Survival in Myelodysplastic-Type CMML with a Low Absolute Monocyte Count

Diagnosis, risk stratification, and response evaluation in classical myeloproliferative neoplasms

POSTER: MPN-760 Investigating Gender-Based Differences in the Molecular Profile of Myeloid Neoplasms: Insights From an Institutional Genomic Database

The number of molecular abnormalities identified in hematopoietic and lymphocytic neoplasms has grown exponentially over the past decades. Patients with genetic biomarker-matched targeted therapies have experienced significantly improved survival rates. Modern molecular laboratories, equipped with advanced technologies such as next-generation sequencing, can simultaneously test hundreds of genes and thousands of hotspots in a single run with multiple samples analyzed side by side. Bioinformatics tools provide seamless, evidence-based information to determine whether the detected mutations are benign or pathogenic, somatic or germline, druggable or diagnostic. This review is divided into five sections, each aiming to provide a comprehensive overview of the genetic landscape of myeloid and lymphocytic neoplasms. It highlights the challenges and proposes potential solutions to facilitate interpretation and maximize the clinical utility of molecular profiling results.

e15160 Background: Advances in genomic technology and the development of an increased repertoire of targeted treatments are helping achieve better outcomes for patients with cancer. Sequencing may expose a genomic target that would not have been predicted based on patients’ cancer histology results alone. The results of basket clinical trials focusing on all solid (Pan-Solid) tumors have led the FDA to approve some drugs based on a particular genomic target regardless of histology. Methods: We analyzed the comprehensive molecular genomic profiling of FFPE tumor samples sent to a commercial CLIA-certified laboratory from our private cancer institute since 2016. Profiling included whole exome and transcriptome sequencing, as well as immunohistochemistry (IHC). cBioPortal is a Cancer Genomics database that provides visualization, interrogation, and analysis of cancer genomics datasets. We retrospectively queried our instance of cBioPortal for Pan-Solid FDA-approved biomarkers. Results: As of January 9, 2025, we have data from 6,773 solid tumor samples in 5,855 patients. In total, 632/5,855 (10.8%) patients harbored at least one indication for which there is a tumor agnostic FDA drug approval, including 288 patients whose tumors had high tumor mutational burden (TMB-H), for which immunotherapy is FDA-approved, 115 had tumors with a BRAF V600E mutation for which BRAF-targeted therapy is approved, 18 with RET fusion (RET targeted therapy), and 6 with fusions in NTRK1/2/3 genes. We identified 144 patients whose tumors exhibited microsatellite instability (MSI-H), and 92 with deficient mismatch repair (dMMR). Lastly, 33 had HER2 IHC-positive tumors. We assessed the treatment history of the patients with tumor alterations that are not commonly associated with the identified biomarker. One patient with colorectal cancer ( RET fusion/dMMR/MSI-H, and TMB-H) is receiving immunotherapy. While most patients were provided standard-of-care treatment (SOC), 7 of 19 patients with a BRAF V600E mutation who were diagnosed with cancers other than lung, melanoma, and thyroid cancers started targeted therapy based on this finding. Three patients discontinued treatment due to toxicity; one patient was recently started on dual BRAF inhibition and the rest resumed SOC treatment. Conclusions: Although most patients were provided SOC treatment, the option of targeted therapy is available. Additional studies are needed to determine whether initial targeted therapy would be more beneficial than SOC cytotoxic treatment. The use of somatic testing is increasing with an increased understanding of the potential clinical utility of molecular testing.

Aim:This study reports structural modeling, molecular dynamics profiling of hypothetical proteins in Chlamydia abortus genome database.Methodology:The hypothetical protein sequences were extracted from C. abortus LLG Genome Database for functional elucidation using in silico methods.Results:Fifty-one proteins with their roles in defense, binding and transporting other biomolecules were unraveled. Forty-five proteins were found to be nonhomologous to proteins present in hosts infected by C. abortus. Of these, 31 proteins were related to virulence. The structural modeling of two proteins, first, WP_006344020.1 (phosphorylase) and second, WP_006344325.1 (chlamydial protease/proteasome-like activity factor) were accomplished. The conserved active sites necessary for the catalytic function were analyzed.Conclusion:The finally concluded proteins are envisioned as possible targets for developing drugs to curtail chlamydial infections, however, and should be validated by molecular biological methods.

Treatment-related myeloid neoplasms (t-MN) represent a severe complication of cancer therapy, characterized by poor prognosis and limited treatment options. This study presents a preliminary, exploratory bioinformatic analysis aimed at characterizing the expression landscape and potential regulatory roles of pyroptosis-related genes (PRGs) in a murine model of t-MN. Utilizing RNA-seq data (GEO: GSE135866), differential expression analysis identified 1286 DEGs. Cross-referencing 367 curated mouse PRGs revealed 46 pyroptosis-related DEGs (PRDEGs). Functional enrichment analysis (GO, KEGG) showed these PRDEGs are significantly involved in autophagy, inflammatory regulation, apoptosis, NOD-like receptor signaling, and the AMPK pathway. GSEA associated the broader gene set with PI3K-Akt and Notch signaling. Protein-protein interaction network analysis identified five critical hub genes: Trp53, Mtor, Gpx3, Foxo3, and Cybb. ROC curve analysis confirmed these hub genes exhibit significant differential expression and high diagnostic accuracy (AUC > 0.9) in distinguishing t-MN from controls. Furthermore, immunoinfiltration analysis (CIBERSORT) revealed significant differences in immune cell composition between t-MN and control samples and identified notable correlations between hub gene expression and specific immune cell abundances. Importantly, given the limited sample size and the use of murine bone marrow data, the statistical findings should be interpreted strictly at the exploratory and hypothesis-generating level. This study does not support definitive biological conclusions or causal inferences but rather aims to delineate the pyroptosis-related molecular profile in a preclinical t-MN model. The results are intended to inform and guide future investigations-including validation in larger cohorts, independent experimental models, and human clinical samples-to assess the translational potential of these candidate biomarkers and therapeutic targets.