Genetic Aberrations Research Articles

Circulating Tumor DNA as Measurable Residual Disease in Aggressive B-Cell Lymphoma: A Narrative Review.

Achieving remission is the first step toward a cure in treating aggressive B-cell lymphomas. Radiographic imaging, such as fluorodeoxyglucose-positron emission tomography/computed tomography scans are the current standard to define remission at the end of therapy but lack specificity for lymphoma and cannot detect disease at the molecular level. Identifying measurable residual disease with ultrasensitive detection of circulating tumor DNA potentially offers the possibility of improving clinical outcomes. Early studies of circulating tumor DNA in aggressive B-cell lymphomas showed a strong association with overall tumor burden, and baseline quantitative levels are associated with clinical outcomes after frontline chemotherapy. Next-generation sequencing methods that detect lymphoma-relevant genetic aberrations in circulating tumor DNA can also be used for noninvasive genotyping that strongly mirror tissue biopsies. Rapid changes in circulating tumor DNA dynamics after 1 or 2 cycles of frontline chemotherapy or within weeks of treatment with chimeric antigen receptor T-cell salvage therapy are also highly prognostic. Although serial monitoring of circulating tumor DNA can detect molecular relapse 3 to 6 months before clinical relapse, improved analytical thresholds are required to detect measurable residual disease at a singular point at the end of therapy. Modern advances in circulating tumor DNA methods now allow for the reliable detection of measurable residual disease, with an analytical detection threshold of 1 in 1 million cell-free DNA molecules. The results of this review suggest that modern ultrasensitive methods of detecting circulating tumor DNA may improve the current definition of remission in aggressive B-cell lymphomas. Incorporating circulating tumor DNA at the end of therapy assessment identifies patients who do not require surveillance monitoring and introduces paradigms of treating measurable residual disease within clinical trials. Practical barriers, including standardization of collection, availability, turnaround times, and cost, remain hurdles preventing widespread implementation into clinical practice.

Clinical, Etiological, and Therapeutic Profile of Early-Onset Absence Seizures: A Case Series Analysis

Typical absence seizures represent a distinctive form of epileptic activity typically observed in pediatric populations, predominantly manifesting between the ages of 4 and 10, constituting Childhood Absence Epilepsy (CAE). However, a subset of patients presents with Early-onset Absence Epilepsy (EOAE), characterized by seizure onset before the fourth year of life, often displaying favorable outcomes with antiseizure medication. Conversely, atypical absence seizures exhibit prolonged duration and frequently entail tonic, atonic, or myoclonic motor elements, suggesting a more severe clinical course, commonly associated with epileptic encephalopathies of childhood onset.Recent genetic investigations have highlighted the involvement of specific genes, notably the SLC1A2 mutation, identified in 10% of EOAE cases, underlying the GLUT1 deficiency syndrome. Timely recognition of such genetic anomalies facilitates tailored interventions, including ketogenic dietary regimes, shown to ameliorate epileptic symptomatology and neurocognitive sequelae.This retrospective study aimed to delineate the distinct features of EOAE and early-onset atypical absence seizures, facilitating prompt diagnosis, particularly emphasizing genetic aberrations, and initiating precision therapeutic approaches to optimize patient outcomes. Evaluation of 23 patients with absence epilepsy onset within the first four years of life, conducted at the Neuropediatrics Outpatient Clinic of the Policlinico of Modena, revealed that children with atypical absences often exhibit a complex clinical and electroencephalographic phenotype, frequently associated with genetic abnormalities. Notably, neurocognitive prognosis appears less favorable in this subgroup, with half of the patients displaying pharmacoresistance. In contrast, all EOAE cases demonstrated seizure freedom, corroborating previous literature suggesting a relatively benign clinical course in these individuals.

Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors

BackgroundA number of genetic aberrations are associated with the BCL6-correpresor gene (BCOR), including internal tandem duplications (ITDs) and gene fusions (BCOR::CCNB3 and BCOR::MAML3), as well as YWHAE::NUTM2, which are found in clear cell sarcoma of the kidney (CCSK), sarcoma with BCOR genetic alterations, primitive myxoid mesenchymal tumor of infancy, and high-grade neuroepithelial tumors in children. Detecting these gene aberrations is crucial for tumor diagnosis. ITDs can be identified by Sanger sequencing or agarose gel electrophoresis. However, gene fusions are usually detected through reverse transcription-polymerase chain reaction (RT-PCR) or fluorescence in situ hybridization. Methods that analyze these variants simultaneously in a sensitive and convenient manner are lacking in clinical practice.MethodsThis study validated a Universal Fluorescence Multiplex PCR-based assay that assessed BCOR ITDs, BCOR::CCNB3, BCOR::MAML3 and YWHAE::NUTM2 fusions simultaneously.ResultsThe assay achieved a detection threshold of 10 copies for fusion genes and 0.32 ng genomic DNA for BCOR ITDs. The performance of this assay was also tested in a cohort of 43 pediatric tumors (17 undifferentiated small round cell sarcomas, and 26 tumors with a histological diagnosis of CCSK). In total, 20 BCOR ITDs, 4 BCOR::CCNB3 and one YWHAE::NUTM2 were detected. When compared with the final diagnosis, the assay achieved 93% sensitivity and 100% specificity.ConclusionsAccordingly, this assay provided an effective and convenient method for detecting BCOR- and YWHAE-related abnormalities in tumors.

The mutational spectrum of NRAS gene discovers a novel frameshift mutation (E49R) in Saudi colorectal cancer patients

Colorectal cancer (CRC) is a major health problem the world face currently and one of the leading causes of death worldwide. CRC is genetically heterogeneous and multiple genetic aberrations may appear on course of the disease throughout patient’s lifetime. Genetic biomarkers such as BRAF, KRAS, and NRAS may provide early precision treatment options that are crucial for patient survival and well-being. The aim of this study was to identify pathogenic mutations in the NRAS gene causing colorectal cancer in the Saudi population. We enrolled 80 CRC tumor tissue samples and performed molecular analyses to establish the mutation spectrum status in the western region of Saudi Arabia. We identified 5 different mutations in 10 patients, 4 of whom were reported previously (G10R, E37K, Q61K, and Q61*) in the literature while we discovered one novel lethal insertion mutation (E49R). A novel identified insertion mutation was present in the third codon of the NRAS gene [c.145 insA (p.Glu49ArgTer85)], causing a frameshift in the amino acid sequence of the protein, and leading to an aberrant and truncated protein of 85 amino acids. Subsequent bioinformatics analysis showed that the mutation was highly deleterious and affected protein function to a greater extent. This identification may further improve the prognosis of CRC and benefit subsequent treatment choices.

TLE4 is a repressor of the oncogenic activity of TLX3 in T-cell acute lymphoblastic leukemia.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological disease originating from the malignant transformation of T-cell progenitors, caused by the accumulation of genetic aberrations. One-fifth of T-ALL patients are characterized by ectopic expression of the homeobox transcription factor TLX3. However, the role of TLX3 in T-ALL remains elusive, partly due to the lack of suitable study models. Strikingly, this TLX3-positive subgroup has a high frequency of FLT3 mutations, predominantly FLT3-ITD, in pediatric cases. To investigate this, we generated ex vivo cultured pro-T cells driven by the co-expression of TLX3 and FLT3-ITD, which conferred IL7 independent growth. This model allowed us to confirm that TLX3 expression and FLT3 signaling cooperate to transform T-cells and induce an oncogenic context. Data from this cell model, combined with gene expression data from TLX3 positive T-ALL cases, revealed a strong downregulation of the transcriptional repressor TLE4. Furthermore, TLE4 showed to have a repressive effect on ex vivo TLX3 T-ALL cell growth, likely caused by a partial reversal of the TLX3 transcriptional profile. In conclusion, we developed a TLX3+FLT3-ITD pro-T cell model and used it to illustrate that TLX3 directly represses TLE4 expression, which is beneficial for the oncogenic function of TLX3.

Asymptomatic HyperCKemia in the Pediatric Population: A Prospective Study Utilizing Next-Generation Sequencing and Ancillary Tests.

Persistent elevation of serum creatine kinase levels (hyperCKemia) as an isolated manifestation presents a diagnostic challenge. Genetic myopathies are frequently involved; however, studies using next-generation sequencing (NGS) in pediatric patients are lacking, and the significance of genetic aberrations remains poorly understood. This study, therefore, aimed to investigate the relevance of NGS and the support of contemporary diagnostic tools in the diagnosis of pediatric asymptomatic hyperCKemia. This was a prospective cohort study enrolling pediatric (0-18 years old) patients meeting the predefined criteria for asymptomatic/paucisymptomatic hyperCKemia, excluding DMD gene deletion/duplication, recruited from a referral center. NGS, muscle MRI, EMG, and muscle biopsies with immunolabeling and inflammatory markers were performed according to a prespecified protocol. Data analysis was performed using descriptive/univariate statistics and Bayesian logistic regression. The series comprised 65 patients (78% male). NGS diagnosis was achieved in 55% of the cohort, with 70% of the pathogenic variants involving 7 genes (DMD, CAPN3, ANO5, DYSF, RYR1, GAA, and CAV3). The diagnostic rate was similar across all age groups; however, the gene profiles varied between the childhood and juvenile groups. EMG yielded myopathic features in 48% of the investigated cases, being predictive for diagnosis (p < 0.05; odds ratio [OR] 13.484, 95% CI 1.358-705.297). MRI showed normal (64%), focal fatty change (26%), or short-tau inversion recovery hyperintensity (10%) profiles, which were not predictive of diagnosis but supported muscle biopsy indications. Muscle biopsy provided a significant diagnostic effect (p < 0.05; OR 0.028, 95% CI 0.001-0.238), contributing to myopathologic features clarifying the variant pathogenicity and identifying inflammatory myopathies. The diagnoses remained inconclusive and unresolved in 14% and 29% of the cohorts, respectively. The diagnostic rate for patients with CK levels below the threshold of 3× was 42%. In multivariate analysis, NGS was the only variable achieving a significant diagnostic effect (β = 9.85, 95% CI 4.65-16.09). NGS, as the primary diagnostic tool for investigating hyperCKemia in the pediatric population, yielded a higher diagnostic rate. However, muscle biopsies are necessary to define variants of uncertain pathogenicity and aid in identifying inflammatory myopathies. EMG and MRI may play a role in hyperCKemia characterization, guiding the decision to perform muscle biopsy. The primary limitation of this study was that not all ancillary tests were performed in all recruited patients owing to ethical restrictions, which lowered the power of the predictive analysis.

Identifying Genetic Predisposition to Dozer Lamb Syndrome: A Semi-Lethal Muscle Weakness Disease in Sheep.

Lamb health is crucial for producers; however, the percentage of lambs that die before weaning is still 15-20%. One factor that can contribute to lamb deaths is congenital diseases. A novel semi-lethal disease has been identified in newborn Polypay lambs and termed dozer lamb syndrome. This study aims to determine if there is a genetic predisposition to dozer lamb syndrome. These lambs are weak and unable to lift their heads, suckle, and swallow, resulting in nasal reflux. Genetic analyses, including a genome-wide association, runs of homozygosity, and fine mapping to determine haploblock within regions of interest, were utilized in determining genetic predispositions to dozer lamb syndrome. The genome-wide association study identified a region of chromosome 15 with three significant SNPs (p-values of 6.81 × 10-6, 5.71 × 10-6, and 8.52 × 10-6). Genetic analysis identified a run of homozygosity on the same region of chromosome 15 with an odds ratio of 236.7. Fine mapping of this region identified three haploblocks associated with the dozer lamb syndrome (p-value = 2.41 × 10-5). The most significant and promising gene in this region is CELF1, which is known to play an important role in muscle development. Abnormal CELF1 abundance and cellular location are reported to result in abnormal muscle development. Identification of genetic aberrations associated with dozer lamb syndrome provides a tool for decreasing or eliminating the genotype and, thus, the associated phenotype(s) from Polypay sheep.

Imaging Flow Cytometric Identification of Chromosomal Defects in Paediatric Acute Lymphoblastic Leukaemia.

Acute lymphoblastic leukaemia is the most common childhood malignancy that remains a leading cause of death in childhood. It may be characterised by multiple known recurrent genetic aberrations that inform prognosis, the most common being hyperdiploidy and t(12;21) ETV6::RUNX1. We aimed to assess the applicability of a new imaging flow cytometry methodology that incorporates cell morphology, immunophenotype, and fluorescence in situ hybridisation (FISH) to identify aneuploidy of chromosomes 4 and 21 and the translocation ETV6::RUNX1. We evaluated this new "immuno-flowFISH" platform on 39 cases of paediatric ALL of B-lineage known to have aneuploidy of chromosomes 4 and 21 and the translocation ETV6::RUNX1. After identifying the leukaemic population based on immunophenotype (i.e., expression of CD34, CD10, and CD19 antigens), we assessed for copy numbers of loci for the centromeres of chromosomes 4 and 21 and the ETV6 and RUNX1 regions using fluorophore-labelled DNA probes in more than 1000 cells per sample. Trisomy 4 and 21, tetrasomy 21, and translocations of ETV6::RUNX1, as well as gains and losses of ETV6 and RUNX1, could all be identified based on FISH spot counts and digital imagery. There was variability in clonal makeup in individual cases, suggesting the presence of sub-clones. Copy number alterations and translocations could be detected even when the cell population comprised less than 1% of cells and included cells with a mature B-cell phenotype, i.e., CD19-positive, lacking CD34 and CD10. In this proof-of-principle study of 39 cases, this sensitive and specific semi-automated high-throughput imaging flow cytometric immuno-flowFISH method has been able to show that alterations in ploidy and ETV6::RUNX1 could be detected in the 39 cases of paediatric ALL. This imaging flow cytometric FISH method has potential applications for diagnosis and monitoring disease and marrow regeneration (i.e., distinguishing residual ALL from regenerating haematogones) following chemotherapy.

Recipient sex and donor leukemic cell characteristics determine leukemogenesis in patient-derived models.

In acute myeloid leukemia (AML), leukemogenesis depends on cell-intrinsic genetic aberrations and thus, studies on AML require investigations in an in vivo setting as provided by patient derived xenografts (PDX) models. Here we report that, next to leukemic cell characteristics, recipient sex highly influences the outgrowth of AML cells in PDX models, with females being much better repopulated than males in primary as well as secondary transplantation assays. Testosterone may be the more important player since, strikingly, better engraftment was seen in castrated versus control male recipients, while ovariectomy did not significantly impair engraftment in females. Shorter time-to-engraftment and mouse survival were observed with adverse molecular risk, and respectively with high FLT3-ITD ratio mutated AML cells. Adverse risk AML furthermore showed higher percentages of phenotypic leukemic stem cells (LSCs), suggesting impaired differentiation capacity in these AML subtypes. Overall, we achieved successful repopulation with 14/23 (61%) favorable, 18/30 (60%) intermediate and 4/8 (50%) adverse risk AML cases in female recipient PDX models. Our data identify recipient sex as an important experimental confounder in leukemia PDX models, and the contribution of the sex hormones to leukemogenesis as an intriguing, underexplored research area.

Depletion of TP53 in Human Pluripotent Stem Cells Triggers Malignant-Like Behavior.

Human pluripotent stem cells (hPSCs) tend to acquire genetic aberrations upon culture in vitro. Common aberrations are mutations in the tumor suppressor TP53, suspected to confer a growth-advantage to the mutant cells. However, their full impact in the development of malignant features and safety of hPSCs for downstream applications is yet to be elucidated. Here, TP53 is knocked out in hPSCs using CRISPR-Cas9 and compared them with isogenic wild-type hPSCs and human germ cell tumor lines as models of malignancy. While no major changes in proliferation, pluripotency, and transcriptomic profiles are found, mutant lines display aberrations in some of the main chromosomal hotspots for genetic abnormalities in hPSCs. Additionally, enhanced clonogenic and anchorage-free growth, alongside resistance to chemotherapeutic compounds is observed. The results indicate that common TP53-depleting mutations in hPSCs, although potentially overlooked by standard analyses, can impact their behavior and safety in a clinical setting.

Severe neonatal hypotonia due to SLC30A5 variant affecting function of ZnT5 zinc transporter.

The tightly-regulated spatial and temporal distribution of zinc ion concentrations within cellular compartments is controlled by two groups of Zn2+ transporters: the 14-member ZIP/SLC39 family, facilitating Zn2+ influx into the cytoplasm from the extracellular space or intracellular organelles; and the 10-member ZnT/SLC30 family, mobilizing Zn2+ in the opposite direction. Genetic aberrations in most zinc transporters cause human syndromes. Notably, previous studies demonstrated osteopenia and male-specific cardiac death in mice lacking the ZnT5/SLC30A5 zinc transporter, and suggested association of two homozygous frameshift SLC30A5 variants with perinatal mortality in humans, due to hydrops fetalis and hypertrophic cardiomyopathy. We set out to decipher the molecular basis of a severe hypotonia syndrome. Combining homozygosity mapping and exome sequencing studies of consanguineous Bedouin kindred, as well as transfection experiments and zinc monitoring in HEK293 cells, we demonstrate that a bi-allelic in-frame 3bp deletion variant in SLC30A5, deleting isoleucine within the highly conserved cation efflux domain of the encoded ZnT5, results in lower cytosolic zinc concentrations, causing a syndrome of severe non-progressive neonatal axial and limb hypotonia with high-arched palate and respiratory failure. There was no evidence of hydrops fetalis, cardiomyopathy or multi-organ involvement. Affected infants required nasogastric tube or gastrostomy feeding, suffered from various degrees of respiratory compromise and failure to thrive and died in infancy. Thus, a biallelic variant in SLC30A5 (ZnT5), affecting cytosolic zinc concentrations, causes a severe hypotonia syndrome with respiratory insufficiency and failure to thrive, lethal by 1 year of age.

CTGCT, Centre of Excellence for the Technologies of Gene and Cell Therapy: Collaborative Translation of Scientific Discoveries into Advanced Treatments for Neurological Rare Genetic Diseases and Cancer

The emerging field of precision medicine relies on scientific breakthroughs to understand disease mechanisms and develop cutting-edge technologies to overcome underlying genetic and functional aberrations. The establishment of the Centre of Excellence for the Technologies of Gene and Cell Therapy (CTGCT) at the National Institute of Chemistry (NIC) in Ljubljana represents a significant step forward, as it is the first centre of its kind in Slovenia. The CTGCT is poised to spearhead advances in cancer immunotherapy and personalised therapies for neurological and other rare genetic diseases. The centre’s overarching mission is to extend beyond the NIC’s scientific excellence in basic research and bring new therapeutic solutions toward clinical application. The CTGCT aims to develop a broad pipeline of biomedical tools, including innovative synthetic biology tools, gene editing and splicing technologies, RNA-based technologies, immune regulation engineering and novel viral and non-viral delivery systems. The CTGCT is supported by partner institutions from the UK, the Netherlands and Germany, which already have academic good manufacturing practice (GMP) facilities for the manufacture of advanced therapy medicinal products (ATMPs) and is committed to active collaboration with clinicians and patient organizations at all stages of development to improve access to gene and cell therapies (GCTs) for patients. The Centre also seeks to collaborate with national and international academic and industrial partners, and the newly established GMP facilities will address a critical bottleneck in the translation of GCTs from research to practice. Finally, CTGCT's translational research and technology transfer units will ensure the impactful dissemination of research and innovation activities in Slovenia, throughout the Western Balkans and Eastern Europe region, and beyond. With its comprehensive approach and forward-looking vision, the CTGCT will drive transformative advances in gene and cell therapies for the benefit of patients on a global scale.

How Have Massively Parallel Sequencing Technologies Furthered Our Understanding of Oncogenesis and Cancer Progression?

Massively parallel sequencing technologies have been a boon to many fields of biological science, including oncology. Cancer is an umbrella term for many diseases featuring abnormal cellular growth due to genetic and epigenetic aberrations. Advances in sequencing technology allow for interrogation of the DNA and RNA of cancer cells and other cells in the tumor microenvironment down to a single-base resolution. However, these strides come after a rich history of ground-breaking biological assays, like the discovery of the Philadelphia chromosome in the context of leukemia. Many specific genetic and epigenetic modifications have been implicated in oncogenesis, cancer progression, and response to treatment. Sequencing technologies have also helped to associate populations of bacteria in the microbiome to cancer development and prognosis. However, all this new information, especially when procured via high-throughput methods, comes at the cost of being more computationally and staff-resource intensive. There is also more risk to the privacy of the individuals with sequenced genomes. Notwithstanding, the overall benefit of sequencing technologies can greatly outweigh the risks with careful advancements and continued focus on the goal: helping those affected by cancer via precision medicine. Cancer biology has been and will continue to be elucidated by sequencing innovations in ways unimaginable without it.

Disease characteristics and outcomes of acute myeloid leukemia in germline RUNX1 deficiency (Familial Platelet Disorder with associated Myeloid Malignancy).

Familial Platelet Disorder with associated Myeloid Malignancy (FPDMM, FPD/AML, RUNX1-FPD), caused by monoallelic deleterious germline RUNX1 variants, is characterized by bleeding diathesis and predisposition for hematologic malignancies, particularly myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Clinical data on FPDMM-associated AML (FPDMM-AML) are limited, complicating evidence-based clinical decision-making. Here, we present retrospective genetic and clinical data of the largest cohort of FPDMM patients reported to date. We describe 159 European patients (from 94 families) of whom 134 were evaluable for the development of malignant disease. Sixty developed a hematologic malignancy (44.8%), most frequently AML (36/134, 26.9%) or MDS (18/134, 13.4%). Somatic alterations of RUNX1 by gene mutation (48%) and chromosome 21 aberrations (14.3%) were the most common somatic genetic aberrations in FPDMM-AML, followed by FLT3-ITD mutations (24.1%). Somatic RUNX1 and FLT3-ITD mutations were not detected in FPDMM-associated MDS, suggesting important contributions to leukemic transformation. Remission-induction chemotherapy resulted in complete remission in 80% of FPDMM-AML patients with a 5-year overall survival (OS) of 50.4%. Survival outcome was non-inferior compared to a large cohort of newly diagnosed adult RUNX1-mutated AML (5-year OS 36.6%, p = 0.5), with relatively infrequent concurrent adverse risk somatic aberrations (ASXL1 mutation, monosomal karyotype, monosomy 5/del 5q) in FPDMM-AML. Collectively, data support the notion that step-wise leukemic evolution in FPDMM is associated with distinct genetic events and indicate that a substantial subset of FPDMM-AML patients achieves prolonged survival with conventional AML treatment, including allogeneic stem cell transplant. These findings are anticipated to inform personalized clinical decision-making in this rare disorder.

Oncogenic IDH1mut drives robust loss of histone acetylation and increases chromatin heterogeneity

Malignant gliomas are heterogeneous tumors, mostly incurable, arising in the central nervous system (CNS) driven by genetic, epigenetic, and metabolic aberrations. Mutations in isocitrate dehydrogenase (IDH1/2mut) enzymes are predominantly found in low-grade gliomas and secondary high-grade gliomas, with IDH1 mutations being more prevalent. Mutant-IDH1/2 confers a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), resulting in an aberrant hypermethylation phenotype. Yet, the complete depiction of the epigenetic alterations in IDHmut cells has not been thoroughly explored. Here, we applied an unbiased approach, leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, to systematically profile the effect of mutant-IDH1 expression on a broad panel of histone modifications at single-cell resolution. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH1, with the most prominent being deregulation of histone acetylation marks. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Notably, the changes in acetylation are not predominantly driven by 2-HG, can be rescued by pharmacological inhibition of mutant-IDH1, and reversed by acetate supplementations. Furthermore, cells expressing mutant-IDH1 show higher epigenetic and transcriptional heterogeneity and upregulation of oncogenes such as KRAS and MYC, highlighting its tumorigenic potential. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma and highlights epigenetic and oncogenic pathways affected by mutant-IDH1-driven metabolic rewiring.

The importance of targeted next-generation sequencing based genomic profiling in the diagnosis of childhood acute myeloid leukemia: a single center experience.

The management of pediatric acute myeloid leukemia (AML) is based on the prognostic risk classification of initial leukemia. Targeted next-generation sequencing (NGS) is a reliable method used to identify recurrently mutated genes of pediatric AML and associated prognosis. In this study, we retrospectively evaluated the prognostic, and therapeutic utility of a targeted NGS panel covering twenty-five genes, in 21 children with de novo and 8 with relapsed or secondary AML. Results. Variants were detected in 44.8% of patients, and 63.2% of them were in the signaling pathway genes. The number of variants per patient and diversity increased with age. The panel results affected hematopoietic stem cell transplantation decisions, especially in core binding factor AML, and allowed the categorization of diseases according to current classifications. Panel results also pointed out predisposition to germline leukemia to the extent of the panel coverage. No targeted therapy was used based on the variants, and none of the variants were used to monitor minimal residual disease. Targeted NGS results, along with well-known genetic aberrations and treatment responses, can guide treatment modalities. The coverage of the routine panels should include proven mutations of childhood AML and germline leukemia predisposition genes.

Clinical characteristics and prognostic analysis of CDKN2A/2B gene in pediatric acute lymphoblastic leukemia: a retrospective case-control study

ABSTRACT In this retrospective case-control study involving 424 pediatric patients diagnosed with Pediatric Acute Lymphoblastic Leukemia (ALL), the investigation focused on analyzing the clinical characteristics and prognosis associated with the Cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) gene. Treatment and evaluation followed the South China Children's Leukemia Group-ALL-2016 protocol (SCCLG-ALL-2016). Among the cohort, 92 patients (21.7%) exhibited CDKN2A/2B gene deletions, with 11.1% homozygous and 10.6% heterozygous deletions. Notably, ALL patients that do have CDKN2A/2B gene deletions tended to present at an older age (P = 0.001), demonstrate hepatosplenomegaly on palpation (P < 0.001), and exhibit a higher incidence of Central nervous system leukemia (CNSL) (P = 0.037) and T-ALL (P = 0.007). A significant correlation was observed between ALL that does have CDKN2A/2B gene deletions and ETV6::RUNX1-positive (8.7% vs. 19.3%, P = 0.017) and IKZF1 gene deletions (20.7% vs. 8.4%, P = 0.001). Survival analysis of 392 patients revealed no significant differences in 5-year relapse, Overall survival (OS), or Event-free survival (EFS) between ALL that does/ does not have CDKN2A/2B gene deletions. Subgroup analysis highlighted poorer prognosis among hepatosplenomegaly patients in the CDKN2A/2B gene deletion group, with a 5-year EFS of 81.8%, 95%CI (0.695–0.963), P = 0.05. Hepatosplenomegaly emerged as the most significant prognostic factor for EFS [HR = 2.306, 95%CI (1.192–4.461), P = 0.013]. Cox regression analyses identified covariates influencing prognosis, ALL with the CDKN2A/2B gene showing no significant impact on outcomes. In conclusion, while ALL that does have CDKN2A/2B gene deletions is associated with certain clinical characteristics and genetic aberrations, they did not significantly impact OS or EFS. Furthermore, subgroup analysis revealed a potential prognostic role of ALL that does have CDKN2A/2B deletions presenting with hepatosplenomegaly on palpation, emphasizing the importance of comprehensive risk stratification in treatment decision-making for this subgroup.

Combined Cell-Free DNA Screening for Aneuploidies and Selected Single-Gene Disorders for Pregnancies With Sonographically Detected Fetal Anomalies: Detection Rate and Residual Risk.

To determine the additional detection rate (DR) and the residual risk (RR) of combined cell-free DNA (cfDNA) screening for aneuploidies (not including copy number variants) and 25 dominant single-gene disorders (SGD) in pregnancies with sonographic abnormalities. One hundred sixteen singleton pregnant women with abnormal fetal ultrasounds from week 12 were included in the study. They underwent combined cfDNA analysis, while exome sequencing and karyotyping were performed as reference standards. The results of the cfDNA analysis were compared with diagnostic genetic tests. The positive rate of cfDNA analysis was 15/116 (12.9%), with a positive predictive value of 13/15 (86.7%). The incremental DR of combined cfDNA screening for aneuploidies and 25 SGD compared with cfDNA testing for aneuploidies in fetuses with sonographic anomalies was 22.9%. The RR of cfDNA analysis for aneuploidies and pathogenic/likely pathogenic gene variants, after excluding cfDNA testing-detectable findings, was 2/101 (2.0%). The DR of cfDNA analysis for genetic aberrations in pregnancies with abnormal ultrasound was 13/35 (37.1%) compared with diagnostic testing. In fetuses with sonographic anomalies, the additional DR of combined cfDNA analysis for aneuploidies and 25 SGD was remarkable at 22.9% compared with cfDNA testing for aneuploidies; the overall RR of combined cfDNA analysis was approximately 2.0%. It is essential to provide detailed genetic counseling before using cfDNA analysis in these pregnancies.

Diagnostic and prognostic genomic aberrations in upper tract urothelial carcinoma can be identified in focal barbotage samples.

To investigate whether genetic analysis of focal barbotage samples obtained at ureterorenoscopy (URS) is possible, and to identify genetic aberrations that might add prognostic information. This prospective study included barbotage samples from 42 patients with upper urinary tract urothelial carcinoma (UTUC) confirmed at URS. At URS, focal barbotage specimens were collected for cytology and for gene sequencing. Tumour grades were determined from cytology and/or biopsy, or from radical nephroureterectomy samples. Next-generation sequencing using a 385-gene panel was performed and single nucleotide variants (SNVs), deletions/insertions (indels) and copy number aberrations (CNAs) were identified. Manual filtering of the SNVs/indels was performed to identify possible pathogenic mutations. Of the 42 samples, two failed quality control, therefore, 40 focal barbotage samples were sequenced. We identified known and suspected pathogenic mutations and other genomic aberrations in 36 samples. The most common variants were in TERT (78%), FGFR3 (50%), KMT2D (42%), KDM6A (42%), ARID1A (39%), TP53 (19%) and deletion of 9q (50%). Known pathogenic mutations in FGFR3 were common in grade 1 and 2 tumours, but not present in any grade 3 tumour. No patients with an FGFR3 mutation died during follow-up. TP53 variants or deletions, as well as amplifications of MDM2, were only present in high-grade (HG) tumours or low-grade (LG) tumours in patients who had metastasis/died from urinary tract carcinoma. CNAs were detected in 36/40 barbotage samples, 91% of the HG samples and 69% of the LG samples, including those from all five patients with LG tumours with metastasis or who died from urinary tract cancer. Focal barbotage samples enable identification of gene mutations and other genetic aberrations that may add important prognostic information to histopathology and cytology. Refined prognostication of UTUC patients already at diagnosis can guide treatment decisions and follow-up programmes.

Case report: Therapeutic response of front-line cadonilimab plus chemotherapy on patient with advanced lung adenocarcinoma harboring STK11 genetic aberration

The STK11 gene mutation is a common genetic alteration in non-small cell lung cancer (NSCLC) and is significantly associated with poor responses to current immunotherapy regimens. Despite its prevalence, there is currently no established standard for front-line treatment in this subtype of NSCLC, underscoring the increasing need for personalized therapeutic strategies. In this report, we present a case of a patient with STK11-mutant NSCLC who was treated with first-line cadonilimab (10mg/kg) in combination with pemetrexed (500mg/m^2) plus carboplatin (AUC=5), resulting in a notable extension of progression-free survival (PFS). This case highlights the potential efficacy and feasibility of combining immunotherapy with chemotherapy in patients with STK11-mutant NSCLC. Additionally, we provide a review of recent advancements in research related to STK11 mutations in lung cancer as reported in the literature.