Mutations In Patients Research Articles

A homozygous nonsense variant in HENMT1 causes male infertility in humans and mice.

HENMT1 encodes a small RNA methyltransferase that plays a crucial role in mouse spermatogenesis through the methylation of the 3' end of PIWI-interacting RNAs. Our study aims to elucidate the relationship between HENMT1 and male infertility in humans. A consanguineous family, having a single non-obstructive azoospermia patient was recruited for pathogenic variants screening. The research includes genetic analysis and experimental validation using mouse models. The patient was diagnosed with non-obstructive azoospermia. Whole-exome sequencing and subsequent bioinformatic analyses were performed to screen for candidate pathogenic variants. The pathogenicity of the identified variant was assessed and studied in vivo using a mouse model that mimicked the patient's mutation. Through whole-exome sequencing, we identified a homozygous nonsense variant (c.555G>A, p.Trp185*) in HENMT1 in the patient. The presence of the mutant HENMT1 mRNA was detected in the patient's blood, and the truncated HENMT1 protein was observed in transfected HEK293T cells. The mutant mice modeling this HENMT1 variant displayed an infertile phenotype similar to that of the patient, characterized by spermiogenesis arrest. Further analysis revealed a significant derepression of retrotransposon LINE1 in the testes of the Henmt1 mutant mice, and increased apoptosis of spermatids. Our findings provide the evidence of pathogenicity of the identified HENMT1 variant, thus shedding light on the indispensable role of HENMT1 in human spermatogenesis.

Predicting Drug Resistance in Gastric Cancer with Mutation in the Human Epidermal Growth Factor Receptor 2 (HER2) And Machine Learning Technique

Gastric cancer with mutations in the human epidermal growth factor receptor (HER2) can be regarded as one of the leading causes of cancer mortality in the world. Targeted tyrosine kinase inhibitors (TKIs) developed against HER2 yielded optimistic results in improving patients' survival rates and life quality. Nevertheless, drug resistance can influence the critical supportive documents of treatment plans and decrease the treatment effectiveness after about one year. Predicting the efficacy of HER2-TKI drugs or therapies for patients with HER2-mutated gastric cancer is a critical research field. In the present study, a personalized drug response prediction model based on molecular dynamics simulations and machine learning is presented to predict response to first-generation drugs approved by the Ministry of Health in patients with gastric cancer. In the molecular dynamics simulation, the patient's mutation status is considered. The patient's unique mutation status was modeled using molecular dynamics simulations to extract geometric features at the molecular level.Furthermore, additional clinical features are incorporated into the machine learning model to predict drug response. The complete features encompass demographic and clinical characteristics, geometrical properties of the drug-target binding site, and binding free energy (RBFE) of the drug-target complex from molecular dynamics simulations. Drug response prediction utilizes the XGBoost classifier, which achieved leading-edge performance for a 4-level drug response prediction task (PDRP) with 97.5% accuracy, 93% sensitivity, 96.5% specificity, and 94% F1 score. The present research has demonstrated that modeling the binding cavity geometry, in tandem with the binding free energy, can effectively predict drug response. Interestingly, the clinical information, while significant, did not significantly influence the model's performance. This exciting finding opens up new avenues for testing the proposed model on various types of cancers, potentially revolutionizing drug development strategies. DOI: https://doi.org/10.52783/pst.391

Efficacy of immune checkpoint inhibitors in non-small cell lung cancer with NTRK family mutations

BackgroundThe efficacy of immune checkpoint inhibitors (ICIs) in non-small cell lung cancer (NSCLC) patients harboring neurotrophin receptor kinase (NTRK) family mutations remains obscure.MethodsThe Zehir cohort from cBioPortal was used to analyze the mutations (MT) frequency of NTRK family in patients with NSCLC, and their correlation with clinical characteristics and patient survival. The influence of NTRK MT on ICIs efficacy was evaluated in ICIs-treated patients from Samstein cohort and further validated by use of data from OAK/POPLAR cohort.ResultsIn the Zehir cohort, a significant difference was observed in median overall survival (mOS) between patients with NTRK MT and wild-type (WT) (mOS: 18.97 vs. 21.27 months, HR = 1.34, 95%CI 1.00-1.78; log-rank P = 0.047). In Samstein cohort, the mOS of NTRK mutant patients receiving ICIs has improved compared to WT patients (mOS: 21.00 vs. 11.00 months, log-rank P = 0.103). Notably, in subgroup analysis, ICIs significantly prolonged mOS in patients with NTRK3 MT than in WT patients (mOS: not available vs. 11.00 months, HR = 0.36, 95%CI 0.16–0.81; log-rank P = 0.009). Identical mOS between NTRK MT and WT patients receiving ICIs treatment (mOS: 13.24 vs. 13.50 months, log-rank P = 0.775) was observed in OAK/POPLAR cohort. Moreover, a similar programmed death ligand 1 (PD-L1) expression, but higher tumor mutational burden (TMB), blood TMB (bTMB) and enriched anti-tumor immunity were observed in NTRK MT compared to WT (P < 0.05).ConclusionTaking high TMB or bTMB into consideration, patients with NTRK mutant NSCLC could benefit from ICIs treatment.

Clonal Dynamics and Deterministic Clinical Fate Mapping of Patients with Myelodysplastic Neoplasms and Acute Myeloid Leukemia with TP53 Disruption

Background: Myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML) with multi-hit TP53 comprise the highest risk subgroup of all myeloid malignancies. TP53 aberration is recognized as a diagnostic category in the 2022 International Consensus Classification (ICC) and the 5 th edition of the WHO. However, these systems do not discern among the subtypes of TP53 aberrations regarding response to therapy. In this study, we explore the clonal dynamics that underlie such prognostic heterogeneity within distinct subgroups of TP53-aberrant MDS and AML, with a specific focus on the effect of hypomethylating agent (HMA) vs. araC-based chemotherapy on TP53 variant allele frequency (VAF). Methods: The UMass Leukemia Registry from the UMass Data Lake identified 76 patients harboring TP53 aberration(s) plus ICD-10 code of either D46.9 (MDS and its subentities) or C92.00 (AML and its subentities) between 2011-2023. Data was integrated with hematopathology records. TP53 exome sequencing was performed with coverage depth 500X to 6500X, and VAFs were adjusted for copy number variation (CNV), as previously described (Patel SA et al., Leuk Lymphoma 2021; 62: 3348-60). Patients with serial bone marrow biopsy samples were included. We defined multi-hit TP53 status as per the ICC: two or more distinct TP53 mutations with VAF ≥ 10%, or a single TP53 mutation plus one of the following abnormalities: (1) del(17p13.1), (2) TP53 VAF &amp;gt;50%, (3) copy-neutral loss-of-heterozygosity, or (4) any complex karyotype. Clonal dynamics were assessed for MDS vs. AML and for varying TP53 allelic states as a function of therapeutic intervention. Clinical fate mapping was performed based on management decisions at various points of clinical care. Results: For patients with TP53-aberrant MDS, 17 patients underwent serial bone marrow biopsies during treatment. Of these, 11 (64.7%) had multi-hit status. Eight patients (47.1%) underwent hematopoietic cell transplant (HCT), and 7 of these 8 patients had received HMA-based front-line therapy. For patients with MDS, we assessed the effect of HMA-based therapy on TP53 VAF. The mean TP53 VAF (sum of VAFs) was significantly lower after HMA-based treatment (35% vs. 12.6%) ( p = 0.0075) (Panel A). For patients with TP53-aberrant AML, 19 patients underwent serial bone marrow biopsies. Of these, 14 (73.7%) had multi-hit status. Only 2 patients (10.5%) underwent HCT. Five patients (26.3%) received araC-based induction, while 11 patients (57.9%) initially received HMA-based induction. For patients with AML with multi-hit TP53, we assessed the effect of HMA-based vs. araC-based front-line therapy on TP53 VAF. HMA therapy led to mean fold reduction in TP53 VAF (pre-treatment to post-treatment) of 11.7 ± 5.8 ( p = 0.019), while araC-based therapy actually led to mean fold increase (but not statistically significant) in TP53 VAF (pre-treatment to post-treatment) of 2.6 ± 1.05 ( p = 0.319) (Panel B). HMA-based treatment resulted in significantly greater reduction in the VAF in aberrant clones and subclones compared to araC-based treatment. Compared to AML, most patients with MDS (62.9%) proceeded with palliative intent therapy at the time of diagnosis. Although patients with AML (53.7%) attempted to proceed with curative intent at the time of diagnosis, only 14.6% eventually proceeded with HCT, largely due to clinical decompensation or disease progression during front-line therapy. Among HCT recipients for MDS ( n =10), 7 (70%) remained in remission. Among HCT recipients for AML (n = 6), 4 (66.7%) remained in morphologic leukemia-free state. Conclusion: There is limited literature on clonal and subclonal diversity in patients with MDS or AML with TP53 aberrations. Such considerations constitute an important therapeutic issue, as certain interventions may only eliminate a fraction of a patient's mutant cells. In our study, HMA- and araC-based regimens had differential effects on various subclones: HMA was more effective in reducing the TP53 mutational burden and increasing patient ability to proceed with HCT. AraC-based therapy appeared less effective, perhaps due to selection pressure in favor of TP53-mutant cells. Prospective trials are required to identify optimal regimens that lead to the best long-term outcomes, and single-cell resolution might assist with more definitively assessing dynamics of clonal response to treatment.

Wilms' Tumor 1 Functions As a Tumor Suppressor to Suppress FLT3-STAT Signaling and Epigenetic Remodeling in Acute Myeloid Leukemia (CALGB 8461, 9665 and 20202; Alliance)

The Wilms' Tumor 1 ( WT1) gene is a transcription factor that is recurrently mutated or commonly overexpressed in several cancer types. In acute myeloid leukemia (AML), frequent overexpression of WT1 and poor patient outcomes associated with WT1 mutations highlight its importance in the disease; however, there are no tailored treatments for these patients. Furthermore, WT1's fundamental role as either an oncogene or tumor-suppressor remains unresolved. Here we examine the roles of both wild-type and mutant WT1 in AML through epigenetic and mechanistic studies. Using our findings we propose a personalized treatment strategy. WT1 mutations are enriched in the NPM1 mut subset of AML; thus we first focused our study on a cohort of 581 patients with de novo AML and NPM1 mutations enrolled on Alliance for Clinical Trials in Oncology studies. Transcriptomic analyses revealed that WT1 mut patientsphenocopied a distinct, aberrant gene expression signature associated with FLT3 internal tandem duplications (ITD), a mutation known to activate STAT signaling and associated with poor outcome in AML. We observed that WT1 expression levels were remarkably elevated in FLT3-ITD patients and were driven by STAT5A binding to the WT1 promoter. STAT5A binding and subsequent WT1 upregulation were blocked by small molecule FLT3 inhibitors. These findings linking FLT3 activity with WT1 expression raise two possibilities: either WT1 is an oncogene cooperating with the FLT3-STAT pathway, or WT1 naturally functions to suppress FLT3 signaling in a negative feedback loop subverted by WT1 mutations. As WT1 interacts with TET2 to facilitate epigenetic remodeling and DNA binding, we performed genome-wide DNA methylation analysis on WT1 mut AML patients and observed selective hypermethylation of WT1 binding motifs consistent with loss of function. We confirmed that WT1 mutations in AML commonly cause truncation of the C-terminal DNA binding domain in our patient cohort. Using co-immunoprecipitation, ChIP-sequencing and luciferase reporter assays, we found that mutant WT1 functions as a dominant-negative, inhibiting WT1 derived from the wild-type allele. Investigation of WT1 target genes by intersecting transcriptomic and DNA methylation profiles identified hypermethylation and downregulation of miR-193a, leading to a significant downregulation of miR-193a-3p in WT1 mut AML patients. Overexpression of wild-type, but not mutated, WT1 rescued miR-193a expression in AML cell lines. Enforced expression of miR-193a significantly delayed AML onset in vivo. In addition, overexpression of miR-193a in multiple human AML cell lines and primary patient samples impaired AML cell growth and colony-forming capacity while promoting monocytic differentiation, underscoring its role as potent tumor suppressor. Therapeutic modulation of miRNA levels in cancer patients has been limited by inefficient delivery and tissue enrichment. To overcome this, we tested a novel lipid-nanoparticle (LNP) formulation of miR-193a-3p (INT-1B3), currently being investigated in a phase I clinical trial (NCT04675996). Biweekly i.v. treatments of INT-1B3 in the immunocompetent Hoxa9/Meis1 (H9M)-transduced model system prevented AML formation, highlighting the potent anti-leukemic activity of this miRNA based therapeutic. Overexpression of miR-193a-loaded LNPs downregulated FLT3 expression and suppressed STAT signaling in primary AML samples. Finally, treatment of primary AML cells with FLT3 inhibitors revealed enhanced sensitivity of WT1 mut cells in the absence of FLT3-ITD, highlighting the role of wild-type FLT3 in WT1 mut cells. In summary, we uncovered a critical negative-feedback loop maintained by WT1 to suppress FLT3 activity. Loss-of-function WT1 mutations subvert the tumor suppressor function of WT1 via failure to maintain miR-193a expression, leading to increased FLT3 expression and STAT5 signaling, subsequently impairing differentiation, increasing proliferation and disease aggressiveness in AML (Figure 1). Our findings advocate for use of FLT3 inhibition and miR-193a supplementation for treatment of WT1 mut patients, a subgroup with poor outcomes and no targeted treatment options.

Deciphering Thrombosis Risk in Vexas Syndrome Patients through Thrombin Generation Assay Andthromboelastography

Introduction: VEXAS syndrome (for Vacuoles in myeloid progenitors, E1 ubiquitin ligase, X-linked, Autoinflammatory manifestations and Somatic) is the consequence of the clonal expansion of hematopoietic stem or progenitor cells with somatically acquired mutation of UBA1. VEXAS is a rare disease characterized by a variety of autoinflammatory manifestations and frequently associated with other hematological malignancies. Venous (VTE) and arterial thrombosis (AT) are recurrently observed in disease course and may affect up to 50% of patients. The exact pathophysiological mechanism underlying thrombosis genesis in UBA1 mut patients is not yet elucidated. Thrombin generation assay (TGA) and thromboelastography (ROTEM) are global hemostasis assays that might be used to identify hemostatic profiles at risk of thrombosis (Ay C et al. J Clin Oncol 2011). In this study, we aimed to evaluate TGA and ROTEM as potential surrogate markers of clot formation in UBA1 mut patients to predict their risk for thrombosis. Methods: TGA and ROTEM assays were performed in UBA1 mut patients between March 2022 and July 2023 , in Hospices Civils de Lyon, France. Patients were tested whether or not they had a personal history of VTE/AT. For patients already treated with oral anticoagulant interfering with exploratory assays, a temporary heparin switch was realized. TGA allows to evaluate concentration of generated thrombin through time, resulting in a dynamic thrombin generation curve, from which various parameters can be determined that describe thrombin activity, such as endogenous thrombin potential (ETP; area under the TG curve). Regarding ROTEM, analyses have been performed on citrated tubes using the ROTEM delta. For each test, the parameters CT (clotting time in seconds), A5 and A10 (measured clot amplitude at 5 and 10 minutes in mm), angle alpha (velocity in °), maximum clot firmness (in mm) and LI30 (% clot lysis at 30 minutes) have been measured. Results: We screened 15 UBA1 mut patients, while only 14 were evaluable for TGA/ROTEM (1 patient excluded due to concomitant use of apixaban the day of TGA). Five out of 15 (33%) had an history of VTE (N=3) or AT (N=2) at the time of TGA/ROTEM blood tests. With a median follow-up of 11.8 months after hmostastic explorations, none of screened patients experienced VTE/AT. On the 14 evaluable patients, TGA/ROTEM exploration was performed in 4 of them at the time of diagnosis prior any treatment onset (including steroids). Active disease (defined by increased CRP and/or clinical manifestations) at the time of TGA did not influence significantly time to peak (mins), peak thrombin (nM) and endogeneous thrombin potential (ETP, nM. min) either in platelet rich- and platelet poor- plasma. Interestingly, patients with prior history of VTE/AT (N=4) had significantly higher ETP compared to those without thrombosis history (N=10) either in platelet rich- and platelet poor-plasmas. Moreover, UBA1 mut patients without thrombosis history exhibited similar ETP values than controls ( figure 1). There was no significant correlation between type of UBA1 mutation, UBA1 allelic frequency, concomitant MDS, type of treatment at the time of TGA assay. Regarding ROTEM analysis, there was no significant differences in clot formation between patients with or without thrombosis history in EXTEM, NATEM, and FIBTEM channels. However, in TEMACT channel (activation as in EXTEM but with a plasminogen activator), we observed higher MCF (Maximum Clot Firmness) in UBA1 mutpatients with prior history of VTE/AT ( Figure 2). Acquired and inherited thrombophilia (protein C and S activities, lupus anticoagulant, anticardiolipine antibodies, anti-beta2 GP1 antibodies, factor V Leiden and prothrombin G20210A mutations, antithrombin evels) were explored in 8 out 15 of our patients. Two of them harbored lupus anticoagulant but without antiphospholipid antibodies. They do not have eitherthrombosis history or higher ETP levels. Conclusions: Based on these preliminary results, TGA and more specifically ETP might identify UBA1 mutpatients at risk of VTE or AT. ROTEM identified an hypofibrinolytic phenotype UBA1 mutpatients with thrombosis history paving the way for future explorations. The small sample size and the retrospective (post-VTE/AT) nature of these explorations are main limitations of this study, which need to be confirmed with a larger follow-up.

TRAF3-Inactivated Chronic Lymphocytic Leukemia Cells Show an Enhanced Metabolic Plasticity That Can be Attenuated By Glutaminolysis and Mitochondrial Pyruvate Import Inhibition

I ntroduction: TRAF3 gene is located in 14q32.32 and has been identified as a tumor suppressor gene involved in B-cell survival, immune response, and cellular metabolism. TRAF3 is frequently encompassed within 14q deletion and affected by inactivating mutations in 4% of chronic lymphocytic leukemia (CLL) patients. Recently, our group found that CLL patients harboring biallelic TRAF3 inactivation (deletion and mutation) showed a dismal prognosis, with a short time to first treatment (Pérez Carretero, AJH 2022). However, the biological role of TRAF3 alterations in CLL pathogenesis remains to be elucidated. Thus, the aims of this study wereto assess the functional consequences of these alterations and to determine their impact on therapy response. Methods: Previously reported TRAF3 mutations were mimicked in a CRISPR/Cas9-edited CLL model by using the PGA1 cell line (PGA1- TRAF3 mut). Metabolomic (liquid chromatography-mass spectrometry), transcriptomic (RNAseq) and functional analyses were carried out. To evaluate the metabolic specificities of PGA1- TRAF3 mut cells, oxidative phosphorylation (OXPHOS) and glycolytic capacity were studied by assessing the mitochondrial oxygen consumption rate (OCR) and extracellular acidification (ECAR), respectively. Additionally, we assessed the metabolite profile of 25 primary CLL cells (n=3 TRAF3 mut cells, n=22 TRAF3 wt cells) and their response to a library of drugs (CLL drugs and metabolic inhibitors), in the presence and absence of microenvironment (with and without HS-5 co-culture and IL-2 and CpG stimulation). Results: Metabolomic analysis of CRISPR/Cas9-edited CLL models showed an enrichment of metabolites involved in Warburg effect (pyruvate, phosphoenolpyruvate, and lactate), citric acid cycle (TCA- acetyl-CoA, α-ketoglutarate, succinate) and glutamate metabolism (α-ketoglutarate) in PGA1- TRAF3 mut cells. Moreover, PGA1- TRAF3 mut cells exhibited higher basal and maximal respiration levels and a more important spare capacity and generation of ATP-linked to mitochondrial respiration. Glycolysis was also slightly enhanced in the TRAF3 mut cells. Remarkably, primary CLL cells with TRAF3 mutations presented a higher concentration of phosphoenolpyruvate, glutamate and the TCA intermediates fumarate and malate, as well as higher levels of NADH and ATP, proving an increased energy production in these cells. Altogether, these results reveal that TRAF3 mut cells showed an enhanced mitochondrial glycolytic metabolism. Given the metabolic changes identified in TRAF3 mut cells, we subsequently assessed their OCR and ECAR after treatment with metabolic inhibitors. Unlike in WT cells, UK5099 administration (inhibitor of the mitochondrial pyruvate transporter that regulates mitochondrial glycolysis) induced an increase in the maximal respiration of TRAF3 mut cells, suggesting a metabolic reprogramming towards an alternative metabolic way fueling mitochondrial metabolism. Therefore, we tested the effect of C968 (glutaminolysis inhibitor), finding the same effect on TRAF3 mut cells, which reveals a specific metabolic plasticity (mitochondrial glycolysis/glutaminolysis). Notably, the transcriptomic analysis revealed an upregulation of the glutamine transporter SLC1A4 (p-adj=0.007), what could be favoring glutamine uptake for an enhanced glutaminolysis. Interestingly, by blocking pyruvate import and glutaminolysis simultaneously, a decrease in TRAF3 mut CLL cells proliferation was observed (p=0.03), with equal levels of the previously dysregulated metabolites to those of the WT, which may indicate that this treatment sensitizes TRAF3 mut cells through its relieving effect on metabolic reprogramming. Moreover, primary CLL cells with TRAF3 mutations were also sensitive to the combination, in the presence and absence of microenvironment (p=0.01, p=0.04 respectively), demonstrating the potential of the combination of metabolic inhibitors as a new therapeutic approach in TRAF3 mut patients. Conclusion: Our work identifies a novel role of TRAF3 alterations in the CLL cellular metabolism. Specifically, TRAF3 inactivation induced an increased mitochondrial glycolytic activity and distinct metabolic dependencies in CLL cells, contributing to an enhanced metabolic plasticity (mitochondrial glycolysis/glutaminolysis) potentially targetable in CLL. Funding: PI21/00983 FEHH-GELLC(CPC), JYCL(ARS)

Analysis of the clinical characteristics and prognosis of adult de novo acute myeloid leukemia (none APL) with PTPN11 mutations.

We discuss the clinical characteristics and prognostic significance of adult individuals with PTPN11 mutations who have developed acute myeloid leukemia (AML) (none acute promyelocytic leukemia). Next generation sequencing and Sanger sequencing were used to detect 51 gene mutations, and multiplex-PCR was used to detect 41 fusion genes from 232 de novo adult AML patients retrospectively. About 7.76% patients harbored PTPN11 mutations, 20 PTPN11 alterations were identified, all of which were missense mutations in the N-SH2 (n = 16) and PTP (n = 4) domains located in exon 3. Patients with PTPN11 mut had significantly higher platelet counts and hemoglobin levels (p < 0.001), which were mainly detected in M5 (n = 12, 66.67%, p < 0.001) subtype. Patients with MLL-AF6 positive showed a higher frequency of PTPN11 mut (p = 0.018) in the 118 AML cases. PTPN11 mut were accompanied by other mutations, which were NPM1 (44.44%), DNMT3A (38.89%), FLT3 (38.89%), and NRAS (17.2%). PTPN11 mut had a negative impact on the complete remission rate in M5 subtype patients (p < 0.001). However, no statistically significant effect on overall survival (OS) with PTPN11 mut patients in the whole cohort and age group (p > 0.05) was observed. Further analysis revealed no significant difference in OS among NPM1 mut/PTPN11 mut, NPM1 mut/PTPN11 wt, DNMT3A mut/PTPN11 mut, and DNMT3A mut/PTPN11 wt patients (p > 0.05). Multivariate analysis showed the proportion of bone marrow blasts ≥65.4% was a factor significantly affecting OS in PTPN11 mut patients (p = 0.043).

Parallel Genomic Analysis from Paired Bone Marrow and Peripheral Blood Samples of 200 Cytopenic Patients

Background: Analysis of bone marrow is the gold standard in patients with unexplainable cytopenia for diagnosing (or excluding) myelodysplastic neoplasm (MDS). Besides morphology also molecular genetics and cytogenetics are currently assessed from BM as both are required for diagnosis and risk stratification. Substitution of BM analysis with peripheral blood (PB) analysis would be a substantial progress especially in the elderly to allow for a less invasive strategy. Aims: Validate, whether PB reliably reflects molecular and cytogenetic aberrations of BM by evaluating somatic mutations and copy number variations (CNVs) in concurrent PB and BM samples. Methods: We analyzed paired BM and PB samples (time difference of sampling: &amp;lt;15 days) of 200 cytopenic patients. All samples were subjected to targeted panel sequencing analyzing mutations (assessed as positive at variant allelic frequencies/VAFs &amp;gt;1%) in 40 genes associated with myeloid neoplasms (coverage: 1500x). If available, BM chromosome analysis (CA) and BM FISH analysis were compared to NGS CNV analysis from PB using a human CNV backbone hybridization panel (coverage: 50x). Results: In 69 patients (35%) no mutations (MUTs) were detected in either BM or PB (Figure 1A). For the remaining 131 patients at least one MUT was found in BM (median MUTs/patient: 2; range 1-10). In 130/131 patients MUTs were detected in both BM and PB (same number of MUTs: n=121; higher number of MUTs in BM than in PB: n=9) while in only one patient harboring a DNMT3A MUT as the sole MUT in BM (VAF: 9%) no MUT was detected in PB. This resulted in a negative predictive value of 98.6% (69/70). Overall, we detected 364 MUTs in 29 of the analyzed genes (BM MUTs: n=362; PB MUTs: n=349) and a concordance between BM and PB of 95% (347/364; Figure 1A). The median VAF was lower in PB compared to BM across all MUTs (median VAF: 20% vs. 12%; p&amp;lt;0.001). All MUTs detected in BM at VAF ≥13% (n=229) were also detected in corresponding PB. Next, we compared CNVs detected by PB NGS to BM karyotype (KT). For 119/200 patients PB NGS including a CNV-backbone panel was available. BM CA revealed a normal KT in 71 and an aberrant KT in 48 patients. In total, 126 aberrations were detected in BM CA including 7 balanced aberrations that can technically not be detected using the CNV backbone panel. CNV analysis from PB revealed 68 aberrations (of 119 detectable BM CNVs; 54%) with 64 being concordant with BM CA. In total, in 88/119 patients (74%) concordant results were found in BM and PB (70/71 with normal and 18/48 with aberrant BM KT). In 3 patients (2.5%) different CNVs were detected (1/3: no CNV in BM CA), while in 28 (23.5%) either fewer CNVs (n=8; all complex KTs) or no CNVs (n=20) were detected in PB compared to BM. The majority (76%) of BM CNVs not detected by PB NGS with available BM FISH data were small BM clones (clone size ≤30%) and therefore not reliably captured by NGS PB with a technical sensitivity of 30%. Interestingly, 4 of the discordant patients with aberrant BM KT did not harbor any somatic MUT in BM and PB. Regarding the IPSS-R cytogenetic risk group, 95 (80%) patients fell into the same category, while 22 (18%; all with aberrant BM KT) were assigned to a better risk category by NGS PB than based on BM CA data and 2 patients (2%) to a worse risk category by NGS PB (Figure 1B). Conclusion: In cytopenic patients mutations can be reliably detected from PB showing a concordance with BM of individual mutations of 95% and a consistency regarding overall mutation detection between PB and BM in 99.5% of patients. Cytogenetic risk group assignment based on NGS CNV analysis from PB compared to chromosome analysis from BM resulted in the same risk group in 80% of patients. However, to further decrease the number of discrepant cases, the technical limitations (sensitivity, inability to detect balanced CNVs) of the CNV backbone method might be overcome by increasing the sequencing depth and/or using CD34-enriched PB samples and adding probe sets. Alternatively, FISH on PB smears could be used for CNV detection. Overall, our data indicate a high degree of overlap between PB and BM regarding mutational and cytogenetic analysis in patients with unexplained cytopenia and suggest PB as reliable surrogate especially in patients without any genetic aberrations.

ZMYM3 Mutations Cooperate with NOTCH1 Alterations, Reduce Histone H4 Acetylation and Promote Apoptosis Evasion in Chronic Lymphocytic Leukemia

Introduction: Recent next-generation sequencing (NGS) studies have identified up to 200 recurrently mutated genes in chronic lymphocytic leukemia (CLL), the vast majority of which appear mutated in &amp;lt;5% of CLL cases. Among the long list of CLL candidate driver genes is ZMYM3, a gene mutated in 2-4% of CLL patients. Since the impact of ZMYM3 mutations is unknown, we aimed to identify their clinical and biological consequences in CLL. Methods: 487 CLL patients were analyzed by targeted NGS using a customized panel of 54 CLL-related genes to characterize the mutational profile of ZMYM3 mutated patients ( ZMYM3MUT) and the clinical impact of these variants. In addition, we introduced ZMYM3 truncating mutations into the CLL-derived HG3 cell line with two genetic backgrounds: wild-type (WT), and NOTCH1 mutated cells ( NOTCH1MUT), to generate cells with either single ZMYM3MUT, NOTCH1MUT or combined ZMYM3MUTNOTCH1MUT. In these CLL models, we evaluated the impact of these alterations in gene expression, apoptosis, growth and DNA damage response (DDR). Results: A total of 32 ZMYM3 variants were identified in 30 CLL patients, most of which were loss-of-function mutations (24/32; 75%). These variants were distributed throughout the protein sequence, with a particular recurrent frameshift mutation occurring in 6 patients (p.P48fs) that was subsequently reproduced in our CLL model. Attending to their mutational profile, we identified that 70% (21/30) of ZMYM3MUT patients harbored mutations in the NOTCH pathway, either in NOTCH1 (60%) or in negative regulators such as MED12, FBXW7 and SPEN, suggesting a cooperation between ZMYM3 dysfunction and NOTCH1 signaling mutations in CLL evolution. Interestingly, ZMYM3MUT patients exhibited significantly shorter time to first treatment (TFT) than ZMYM3WT cases (median: 35 vs 52 months; p=0.010). Furthermore, ZMYM3 mutations shortened TFT of early stage CLL patients, including Binet A (48 vs 108 months, p=0.002) or Rai 0/1 (48 vs 91 months, p=0.016), as well as in low-risk cytogenetics del(13q) patients (median: 45 vs 93 months; p=0.033). We next addressed the biological implications of ZMYM3 mutations and their co-occurrence with NOTCH1 mutations in HG3 cells. First, we performed RNA-sequencing and analyzed the number of differentially expressed genes (DEGs) (|fold change|&amp;gt;2, adjusted p-value&amp;lt;0.05). Comparing with WT cells, we detected 155 DEGs in ZMYM3MUT and 83 DEGs in NOTCH1MUT, whereas ZMYM3MUTNOTCH1MUT cells showed 690 DEGs,indicating that the combination of both mutations profoundly dysregulate gene expression. Immune regulation, apoptosis and DNA damage response were some of the biological processes dysregulated by ZMYM3 mutations (p&amp;lt;0.05). Furthermore, considering the suggested role of ZMYM3 in chromatin remodeling (Puente et al, Nature. 2015) and that ZMYM3MUT cells showed altered expression of histone acetylation related genes (p&amp;lt;0.05), we identified that ZMYM3 mutations reduced global acetylation levels of histone H4 (p&amp;lt;0.05), which may underlie the ZMYM3-related changes in gene expression. To further define the functional effects of ZMYM3 mutations, we assessed in vitro their impact in the main dysregulated pathways identified by RNA-seq. First, we identified that ZMYM3 mutations impair DNA damage response, as reflected by the difficulties to arrest cell cycle in G2/M phase after irradiation. Moreover, we detected more γH2AX foci (p&amp;lt;0.05) in ZMYM3MUTcells, indicating persistent DNA damage; and fewer RAD51 and BRCA1 foci than WT cells (p&amp;lt;0.001) after irradiation, suggesting defective DNA damage response. In parallel, we identified that ZMYM3 mutations promote apoptosis evasion, especially in the context of NOTCH1 mutations (p&amp;lt;0.001), which led to enhanced growth of ZMYM3MUTNOTCH1MUT cells (p&amp;lt;0.05). Of note, ZMYM3MUT cells showed down-expression of caspases (-8, -7 and -3) and slightly higher levels of anti-apoptotic proteins (BCL2, MCL1 and BCL-XL), which may explain this apoptosis resistance. Conclusions: Mutations in ZMYM3 are mainly loss-of-function, associate with NOTCH1 signaling mutations and shorten TFT in CLL patients, suggesting that ZMYM3 mutational status may be a useful marker in the management of early stage CLL patients. Moreover, ZMYM3 mutations reduce histone H4 acetylation and cooperate with NOTCH1 mutations to dysregulate gene-expression, leading to impair DNA damage response and apoptosis evasion.

The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel.

Next-generation sequencing (NGS) technology detects specific mutations that can provide treatment opportunities for colorectal cancer (CRC) patients. We analyzed the mutation frequencies of common actionable genes and their association with clinicopathological characteristics and oncologic outcomes using targeted NGS in 107 Saudi Arabian patients without a family history of CRC. Approximately 98% of patients had genetic alterations. Frequent mutations were observed in BRCA2 (79%), CHEK1 (78%), ATM (76%), PMS2 (76%), ATR (74%), and MYCL (73%). The APC gene was not included in the panel. Statistical analysis using the Cox proportional hazards model revealed an unusual positive association between poorly differentiated tumors and survival rates (p = 0.025). Although no significant univariate associations between specific mutations or overall mutation rate and overall survival were found, our preliminary analysis of the molecular markers for CRC in a predominantly Arab population can provide insights into the molecular pathways that play a significant role in the underlying disease progression. These results may help optimize personalized therapy when drugs specific to a patient's mutation profile have already been developed.

Clinical and cellular phenotypes resulting from a founder mutation in IL10RB.

Inborn errors of immunity are a group of rare genetically determined diseases that impair immune system development or function. Many of these diseases include immune dysregulation, autoimmunity, or autoinflammation as prominent clinical features. In some children diagnosed with very early onset inflammatory bowel disease (VEOIBD), monogenic inborn errors of immune dysregulation underlie disease. We report a case of VEOIBD caused by a novel homozygous loss of function mutation in IL10RB. We use cytometry by time-of-flight with a broad panel of antibodies to interrogate the immunophenotype of this patient and detect reduced frequencies of CD4 and CD8 T cells with additional defects in some populations of T helper cells, innate-like T cells, and memory B cells. Finally, we identify the patient's mutation as a founder allele in an isolated indigenous population and estimate the age of this variant by studying the shared ancestral haplotype.

Temporal correlation between the first melanoma and the first noncutaneous tumor in CKDN2A genotyped patients.

CDKN2A pathogenic variants are well known to be associated with cutaneous melanoma and noncutaneous tumors (NCTs). Herein, we investigated the temporal correlation between the first cutaneous melanoma and NCT both in CDKN2A mutation carriers (MUT) and in wild-type melanoma patients, a poorly explored issue to date. Two hundred forty-five cutaneous melanoma patients were genotyped for the CDKN2A gene and divided into 51 MUT and 189 wild-type; the remaining five variant carriers were excluded from the analyses. MUT developed a significantly higher number of cutaneous melanoma than wild-type, while 13.7% in both genotyped groups received a diagnosis of at least one malignant NCT, without statistically significant differences. The onset of the first cutaneous melanoma preceded that of the first malignant or benign NCT in both MUT and wild-type patients by an average of 4.5 and 3.02 years, respectively. Considering only malignant tumors, the diagnosis of melanoma preceded that of the first NCT on an average of 8 and 4.34 years, in MUT and wild-type patients respectively. We emphasize the relevance to adopt a global vision for the primary and secondary surveillance of patients affected by cutaneous melanoma, not only limited to high-risk for multiple primary skin cancers but also to NCT that may develop several years after the diagnosis of the first cutaneous melanoma.

GLA GENE MUTATION IN PATIENTS WITH FABRY DISEASE

Introduction: For the first time in the Lenkoran-Astara administrative area of Azerbaijan Republic, a genetic screening was conducted on patients with cardiomyopathies to identify Fabry metabolic disease. The screening involved the assessment of alpha-galactosidase enzyme activity and the globotriasylsphingosine level. This article aims to present the results of the screening and the subsequent molecular genetic analysis of the GLA gene in the identified patients. Materials and Methods. The genetic screening was based on applying fluorimetry and liquid chromatography methods. The Sanger sequencing technique was employed for direct sequencing of the GLA gene, enabling the detection of existing mutations. This technique was developed in CENTOGENE laboratories, Rostock, Germany. The initial tests were conducted at the Centogene laboratory in Rostock, Germany, followed by further testing at the GENOM clinical laboratory in Baku, Azerbaijan Republic. Ultrasonic and echocardiography studies were performed simultaneously with blood sampling at the central regional hospital. Results: 21 individuals out of 76 involved in the study had a deficiency in αgalactosidase enzyme activity and elevated levels of globotriasylsphingosine, indicative of Fabry disease. Among them, seven women exhibited X-linked inheritance as heterozygous, and three men were identified as homozygous. Molecular genetic analysis revealed two different mutations in the GLA gene: 801+3A&gt;G and 137 A&gt;G. To prevent Fabry disease, it is recommended to screen family members of affected individuals for α-galactosidase enzyme activity. Conclusion: This study represents the first genetic screening for Fabry disease conducted in the Azerbaijan Republic among patients with cardiological diseases. 21 individuals out of 76 examined patients were identified as having Fabry disease and carrying two different GLA gene mutations: c.801+3A&gt;G and c.137A&gt;G. The obtained genetic results will aid cardiologists to make accurate diagnosis and to select appropriate management for patients with cardiomyopathy, considering the presence of Fabry disease, as well as enabling prenatal foetus diagnostics during pregnancies in families at genetic risk.

Interstitial 6q deletion in a patient presenting with drug-resistant epilepsy and Prader-Willi like phenotype: An electroclinical description with literature review

PurposeInterstitial 6q deletions are associated with rare genetic syndromes characterized by different signs, including developmental delay, dysmorphisms, and Prader-Willi (PWS)-like features. Drug-resistant epilepsy, a relatively rare finding in this condition, is often a challenge in terms of therapeutic approach. Our aim is to present a new case of interstitial 6q deletion and to conduct a systematic review of the literature with an emphasis on the neurophysiological and clinical traits of afflicted individuals. MethodsWe report a patient with an interstitial 6q deletion. Standard electroencephalograms (EEG), video-EEG with polygraphy and MRI features are discussed. We also conducted a literature review of previously described cases. ResultsWe describe a relatively small interstitial 6q deletion (2 Mb circa), detected by CGH-Array, not encompassing the previously described 6q22 critical region for epilepsy occurrence. The patient, a 12-year-old girl, presented with multiple absence-like episodes and startle-induced epileptic spasms since the age of 11, with partial polytherapy control. Treatment with lamotrigine induced the resolution of startle-induced phenomena. From the literature review, we identified 28 patients with overlapping deletions, often larger than our patient's mutation. Seventeen patients presented with PWS-like features. Epilepsy was reported in 4 patients, and 8 patients presented abnormal EEG findings. In our patient, the deletion included genes MCHR2, SIM1, ASCC3, and GRIK2, but, interestingly, it did not encompass the 6q22 critical region for epilepsy occurrence. The involvement of GRIK2 in the deletion may play a role. ConclusionLiterature data are limited, and specific EEG or epileptological phenotypes cannot yet be identified. Epilepsy, although uncommon in the syndrome, deserves a specific diagnostic workup. We speculate on the existence of an additional locus in the 6q16.1–q21 region, different from the already hypothesized q22, promoting the development of epilepsy in affected patients.

IRF2BP2 mutation with autoimmune enteropathy, immune deficiency, and respiratory failure

Case historyWe present the case of a 31-year-old Hispanic male with history of recurrent bronchiectasis, invasive aspergillosis, and severe persistent asthma, who is now status post lung transplant for end-stage lung disease. He initially presented at 7 years of age with diarrhea, failure to thrive, and nearly absent immunoglobulin levels (IgG < 33 mg/dL, IgA < 7 mg/dL, IgM = 11 mg/dL, IgE = 4 IU/dL) necessitating IVIG treatment. Small intestinal biopsy showed villous atrophy consistent with autoimmune enteropathy. Sweat chloride was reported as indeterminate (44 me/dL). Initial WBC, platelet, and T- and NK-cell counts were within normal range, and B-cell count and percentage were borderline low. Most recently, he was found to have increased immature B-cell count (CD21low), decreased memory B-cells, and poor pneumococcal vaccine antibody response. Patient has been hospitalized numerous times with increasingly severe bronchiectasis, pneumonitis, and COVID-19 infections twice despite vaccination, leading to respiratory failure and lung transplantation. Family history is negative for immune deficiency and lung diseases. DiscussionOf these 3 VUSs (see the table), the one in IRF2BP2 has the most pathogenic potential due to its autosomal dominant inheritance, its location in a conserved domain (Ring), and previous case reports of pathogenic variants at the same or adjacent alleles 1–3. Baxter et al reported a de novo truncating mutation in IRF2BP2 at codon 536 (c.1606CinsTTT), which is similar to our patient's mutation. This patient was noted to have an IPEX-like presentation, with chronic diarrhea, hypogammaglobulinemia, and recurrent infections. Variant Functional Prediction Score for our variant predicts a potentially high damage effect. There are 2 other case reports of heterozygous mutations in loci adjacent to this allele; one (c.1652G>A)2 with a similar clinical phenotype to our patient and the other (C.625-665 del)3 with primarily inflammatory features and few infections. ImpactThis case highlights a variant in IRF2BP2 associated with severe hypogammaglobulinemia, recurrent pulmonary infections, and autoimmune enteropathy.Table 1(abstract: 126)ClassificationGeneExon/IntronDNA changeProtein changeZygosityInheritanceOMIMAssociated diseaseUncertain significanceIRF2BP22c.1606C>Tp.Gln536TerHeterozygousAutosomal Dominant615332Immunodeficiency Common variable, 14Uncertain SignificanceLRBA30c.4832C>Tp.Thr1611lleHeterozygousAutosomal Recessive606453Immunodeficiency Common variable, 8, with autoimmunityPathogenicCFTR4c.350G>Ap.Arg117HisHeterozygousAutosomal Recessive602421CFTR- related disorders

Abstract A07: Single-cell proteomic assessment of FLT3-ITD AML landscape identifies distinct resistance patterns

Abstract Acute myeloid leukemia (AML) represents a heterogeneous hematopoietic disorder characterized by accumulation of immature hematopoietic precursors with differentiation block. FLT3 internal tandem duplications (FLT3-ITD) are commonly occurring genetic alterations in AML and are associated with poor prognosis. Preclinical studies showed combining FLT3 inhibitor with MDM2 inhibitor, which is a negative regulator of p53, was synergistic in FLT3-ITD/TP53 wild type (WT) AML. We performed single-cell proteomic evaluation of leukemia landscape in FLT3-ITD patients treated with FLT3i and MDM2i to assess proteomic profiles associated with response and resistance. We performed CyTOF analysis of leukemia cells in serially collected samples from six FLT3-ITD and TP53 WT AML patients following treatment with FLT3i+MDM2i treatment. Using 51 features assessed in CyTOF, we first performed UMAP dimension reduction and clustering to identify distinct cells in leukemia compartment. Notably, the frequencies of blasts identified through CyTOF data analysis were compatible with clinical lab reports. In line with previous reports, we also detected that NPM mutant AML cells did not express CD34. Of note, CD34+ and CD34- leukemia cells were clustered together in NPM1 mut patients, indicating that they have overlapping proteomic profiles. Interestingly, the CD34+ leukemia cells were eliminated at the early time points in CR patients while the CD34- leukemia cells were still detectable after two months. On the other hand, CD34+ leukemia cells in nonresponders(NR) persisted despite therapy. These findings indicate CD34+ leukemia cells were more sensitive to the treatment compared to NPM1 mutant CD34- leukemia cells. Next, we interrogated leukemia proteomic landscape in serial samples, evaluated the therapy-induced alterations in proteomic profiles and sought to identify potential adaptive mechanisms. To this end, we performed differential expression analysis and observed that signaling pathways (p-4EBP1, p-GSK3, p-MEK1/2, p-S6) and differentiation markers(CD33, CD68,CXCR4 HLADR) were more enriched on day 8 post treatment in NR patients, revealing that compensatory signaling activity, phenotypic profiles and differentiation status could be associated with therapy response. Moreover, we found that leukemia cells in NR patients had distinct phenotypic profiles(CD11b,CD68,CXCR4), higher levels of anti-apoptotic molecules (BCL2,MCL1) and enriched survival pathways (p-GSK3, YTHDF2) compared to baseline. In contrast, we did not observe rebound increases in CR patients post-therapy. These findings demonstrate high levels of BCL2 and MCL1 and preferential survival of more differentiated cells may be associated with therapy resistance and treatment failure in NR patient treated with MDM2i and FLT3i. In conclusion, multiplexed single-cell proteomic analysis permitted longitudinal monitoring of leukemia landscape and identified proteomic alterations associated with therapy resistance. Citation Format: Li Li, Muharrem Muftuoglu, Mahesh Basyal, Naval Daver, Michael Andreeff. Single-cell proteomic assessment of FLT3-ITD AML landscape identifies distinct resistance patterns [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A07.

Genomic profiles of IDH-mutant gliomas: MYCN-amplified IDH-mutant astrocytoma had the worst prognosis

This study aimed to find any ambiguous genetic outlier for “oligodendroglioma, IDH-mutant and 1p/19q-codeleted (O_IDH_mut)” and “astrocytoma, IDH-mutant (A_IDH_mut)” and to redefine the genetic landscape and prognostic factors of IDH-mutant gliomas. Next-generation sequencing (NGS) using a brain tumor-targeted gene panel, methylation profiles, and clinicopathological features were analyzed for O_IDH_mut (n = 74) in 70 patients and for A_IDH_mut (n = 95) in 90 patients. 97.3% of O_IDH_mut and 98.9% of A_IDH_mut displayed a classic genomic landscape. Combined CIC (75.7%) and/or FUBP1 (45.9%) mutations were detected in 93.2% and MGMTp methylation in 95.9% of O_IDH_mut patients. In A_IDH_mut, TP53 mutations were found in 86.3% and combined ATRX (82.1%) and TERTp (6.3%) mutations in 88.4%. Although there were 3 confusing cases, NOS (not otherwise specified) category, based on genetic profiles, but they were clearly classified by combining histopathology and DKFZ methylation classifier algorithms. The patients with MYCN amplification and/or CDKN2A/2B homozygous deletion in the A_IDH_mut category had a worse prognosis than those without these gene alterations and MYCN-amplified A_IDH_mut showed the worst prognosis. However, there was no prognostic genetic marker in O_IDH_mut. In histopathologically or genetically ambiguous cases, methylation profiles can be used as an objective tool to avoid a diagnosis of NOS or NEC (not elsewhere classified), as well as for tumor classification. The authors have not encountered a case of true mixed oligoastrocytoma using an integrated diagnosis of histopathological, genetic and methylation profiles. MYCN amplification, in addition to CDKN2A/2B homozygous deletion, should be included in the genetic criteria for CNS WHO grade 4 A_IDH_mut.

Circulating tumor DNA–based genomic landscape of KRAS wild-type pancreatic adenocarcinoma.

747 Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer deaths. KRAS is a primary oncogenic driver in the majority of PDAC patients. KRAS wild-type (wt) PDAC (~10%) is a molecularly heterogeneous subgroup that may harbor alternate drivers and targetable alterations. In this study, we sought to characterize the circulating tumor DNA (ctDNA) landscape of alterations in PDAC patients harboring KRAS mutations ( KRAS mut) compared to KRAS wt. Methods: We analyzed ctDNA samples from 2000 patients ( N= 1000 each for KRAS mut and KRAS wt) collected prospectively between 2019-2022 using a 74-83 gene next generation sequencing panel (Guardant360). KRAS mutation not detected was used as a proxy for KRAS wt. To limit bias from low tumor shed, samples were excluded if they did not have maximum variant allele fraction (VAF) &gt; 0.34% and if the only maximum VAF &gt; 0.34% was within putative germline range (40-60%). Statistical analyses were performed using Fisher’s exact test or t-test. Results: No significant gender differences were noted between KRAS wt and KRAS mut patients. Median age was 72yo in KRAS wt and 69yo in KRAS mut patients. Overall, KRAS wt patients had higher frequency of alterations in ATM, BRAF, ERBB2, FGFR2, JAK3, MET and NOTCH1 compared to KRAS mut (all p &lt; 0.05). Meanwhile, KRAS wt patients had lower frequency of alterations in CDKN2A, SMAD4, CDK6, ARID1A, and TP53 compared to KRAS mut (all p &lt; 0.05). The most frequently mutated gene in KRAS wt PDAC was TP53 (46%), followed by ATM (26%) and EGFR (11%). The most common currently targetable alterations identified in KRAS wt patients were ATM (26%), BRCA1/2 (12%), EGFR (11%; 70% mutations, 30% amplifications), FGFR1/2 (9%), BRAF (8%; 91% mutations, 9% amplifications), PIK3CA (7%), MET (7%; 80% mutations, 20% amplifications) and ERBB2 (5.8%; 79% mutations, 21% amplifications) among others. Median tumor mutational burden for KRAS wt patients was higher than KRAS mut (10.0 vs. 7.77 mut/Mb, p = 0.035). There were no significant differences in rates of MSI-H between KRAS wt and KRAS mut patients (1.9% vs. 1.3%, p = 0.37). KRAS wt patients harbored higher number of oncogenic gene fusions compared to KRAS mut (1.6% vs 0.2%, p = 0.0013). The most common fusion partners among KRAS wt patients included FGFR2 (0.4%), BRAF (0.4%), ALK (0.2%), NTRK (0.2%), RET (0.2%), FGFR3 (0.1%) and EGFR (0.1%). Potential germline variants (pathogenic/likely pathogenic) were detected in both KRAS wt and mut patients, most commonly in the DNA-damage repair genes, including ATM (3.5%), BRCA2 (1.8%) and BRCA1 (0.6%). Conclusions: Targetable alterations and oncogenic rearrangements are enriched in KRAS wt PDAC compared to KRAS mut. These analyses provide additional therapeutic options and may improve outcomes for KRAS wt patients, warranting blood-based ctDNA genomic profiling in PDAC, especially when a tissue biopsy is not feasible or sufficient for comprehensive genomic profiling.

Gene therapy strategies using CRISPR/Cas9 for RyR1-related myopathies.

Type 1 ryanodine receptor (RyR1) is the intracellular calcium channel responsible for skeletal muscle contraction. Mutations in the RYR1 gene can lead to RyR1-related myopathies (RyR1-RM), a group of genetic disorders. They are characterised by abnormal calcium homeostasis and muscle weakness of variable severity. Currently, there is no treatment for these pathologies. This study aims to present proof of concept for gene therapy approaches. Immortalized skeletal muscle cells from patients affected by RyR1-Related myopathies have been edited using Clustered Regularly Interspaced Short Palindromic Repeats associated protein 9 (CRISPR/Cas9). CRISPR guides targeting different part of the gene were design in order to adapt the strategy depending on the patient's mutation and its localisation. The consequences of the expected editing will be verified at the DNA, RNA and functional level. The objective is to determine if these therapeutic approaches could improve calcium release in patient's cells and skeletal muscle contraction.