Specific Genetic Abnormalities Research Articles

BRUGADA SYNDROME: NEWEST DATA ON RISK STRATIFICATION

Abstract Background Brugada Syndrome (BrS) is a rare genetically based channelopathy responsible for malignant arrhythmias and sudden cardiac death (SCD) in young adults. Objectives The aims was to evaluate prognostic indicators useful for accurate arrhythmic risk stratification in BrS by studying genetic, clinical, anamnestic, instrumental parameters, and those derived from electrophysiological study (EPS) and intracavitary mapping. Materials and Methods 209 patients with Brugada type 1 were recruited between 01/01/2018 and 01/10/2023. Results In the first study, predictive factors related to high arrhythmic risk from the data obtained for the total population of 209 Brugada patients enrolled in our case series include a positive history of cardiogenic syncope (p value 0.000041), having had a resuscitated cardiac arrest (p value 0.00025), presenting positive EPS for inducibility of ventricular tachycardia (p value 0.00032), having a family history of sudden cardiac death (p value < 0.00001), and presenting positive cardiac mapping and MRI for pathological alterations (both with p value > 0.00001). From the data obtained for the subset of 80 Brugada patients with ICD in our case series, predictive factors related to high arrhythmic risk are different from the previously analyzed population: presenting spontaneous type 1 ECG (p value 0.0015), having had a resuscitated cardiac arrest (p value 0.014028), having a family history of sudden cardiac death (p value < 0.00001), and presenting positive mapping, genetics, and cardiac MRI for pathological alterations. Positive EPS and syncope in this subset do not appear to be risk factors, unlike the population of all 209 enrolled patients. Conclusions Multiparametric scores, including the mentioned markers, have been introduced in clinical practice for a better approach in selection. However, new markers are needed to improve risk stratification in BrS patients, especially those in the so–called "gray zone" with intermediate risk. In the future, it will be evaluated through experimental models and genotype–phenotype integration whether such electrical heterogeneity is also associated with specific genetic or structural abnormalities and may represent a new therapeutic target for etiological treatment in BrS patients. In conclusion, there is an urgent need to develop new methods for risk stratification in Brugada syndrome that are sufficiently sensitive, specific, reproducible, and easy to apply.

Myelodysplastic Neoplasms (MDS): The Current and Future Treatment Landscape.

Myelodysplastic neoplasms (MDS) are a heterogenous clonal disorder of hemopoietic stem cells characterized by cytomorphologic dysplasia, ineffective hematopoiesis, peripheral cytopenias and risk of progression to acute myeloid leukemia (AML). Our understanding of this disease has continued to evolve over the last century. More recently, prognostication and treatment have been determined by cytogenetic and molecular data. Specific genetic abnormalities, such as deletion of the long arm of chromosome 5 (del(5q)), TP53 inactivation and SF3B1 mutation, are increasingly associated with disease phenotype and outcome, as reflected in the recently updated fifth edition of the World Health Organization Classification of Hematolymphoid Tumors (WHO5) and the International Consensus Classification 2022 (ICC 2022) classification systems. Treatment of lower-risk MDS is primarily symptom directed to ameliorate cytopenias. Higher-risk disease warrants disease-directed therapy at diagnosis; however, the only possible cure is an allogenic bone marrow transplant. Novel treatments aimed at rational molecular and cellular pathway targets have yielded a number of candidate drugs over recent years; however few new approvals have been granted. With ongoing research, we hope to increasingly offer our MDS patients tailored therapeutic approaches, ultimately decreasing morbidity and mortality.

SALL3 mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss

Human pluripotent stem cell (hPSC) cultures are prone to genetic drift, because cells that have acquired specific genetic abnormalities experience a selective advantage invitro. These abnormalities are highly recurrent in hPSC lines worldwide, but their functional consequences in differentiating cells are scarcely described. In this work, we show that the loss of chromosome 18q impairs neuroectoderm commitment and that downregulation of SALL3, a gene located in the common 18q loss region, is responsible for this failed neuroectodermal differentiation. Knockdown of SALL3 in control lines impaired differentiation in a manner similar to the loss of 18q, and transgenic overexpression of SALL3 in hESCs with 18q loss rescued the differentiation capacity of the cells. Finally, we show that loss of 18q and downregulation of SALL3 leads to changes in the expression of genes involved in pathways regulating pluripotency and differentiation, suggesting that these cells are in an altered state of pluripotency.

Food allergy as one of the faces of primary immunodeficiency

Food allergy is characterized by an abnormal immune reaction that occurs reproducibly upon exposure to a specific food. This immune response can lead to a variety of symptoms, the prevalence of food allergies has increased in recent decades, most likely due to environmental factors that likely play a role in the expression of genetic susceptibility. Recent understanding of the immunopathogenesis of allergic diseases has suggested that these atopic diseases may be due to monogenic mutations associated with inborn errors of immunity (IEI). Aspects to be assessed in suspected IEI involve the onset of atopic disease within the initial months of life, the progression of the condition, and the response to conventional therapy. A prospective study was conducted on 385 patients admitted to the clinic with suspected immunodeficiency. Most children were referred for recurrent respiratory infections, but almost half had concurrent atopy (44%), atopy and autoimmunity (3%), autoimmunity (6%) and malignancy (1%). The results of the study underline the importance of the allergic phenotype and suggest that children with more severe allergic diseases should be screened for possible underlying inborn defects of immunity. If a congenital disorder of immunity is suspected, comprehensive immunologic testing is required, and genetic testing is essential to identify the specific genetic abnormalities. Molecular diagnosis provides a comprehensive understanding of congenital immune disorders, allowing tailored interventions and personalized surveillance strategies.

Measuring response to therapy in AML: Difference from normal flow cytometry vs RQ-PCR.

Multiple technologies have been used to monitor response to therapy in acute myeloid leukemia (AML) to improve detection of leukemia over the standard of practice, morphologic counting of blasts. The two techniques most frequently used in a routine clinical setting, flow cytometry and RQ-PCR, differ in their targets, sensitivity, and ability to detect residual disease. Both flow cytometry and RQ-PCR detect the expression of abnormal gene products, at the protein level or RNA level, respectively. Flow cytometry can be applied to a broad range of AML cases while RQ-PCR is limited to specific genetic abnormalities identified in subsets of AML. This article compares the results when both techniques were used in a reference laboratory to monitor AML over the course of treatment, comparing quantitative and qualitative results.

10171-MPC-13 IDH-WILDTYPE LOWER-GRADE ASTROCYTOMA

Abstract BACKGROUND AND PURPOSE In the WHO 2021 classification, glioblastoma is limited to IDH-wildtype and is diagnosed when microvascular proliferation and necrosis are present. Furthermore, even in the presence of morphologically low-grade findings, the diagnosis of glioblastoma is made if there is either EGFR gene amplification, TERT promoter mutation, or +7/-10 chromosome copy number alterations. Therefore, we investigated IDH wild-type lower-grade astrocytoma. CASES 10 patients were included in this study. Sanger sequencing was performed for TERT promoter mutations, and MLPA was further implemented using probes for EGFR and PTEN genes in TERT wild-type cases. The threshold values for copy number change were homozygous deletion (x≤0.4), loss of heterozygosity (LOH) (0.4<x≤0.7), gain (1.3≤x<2.0), and amplification (x≥2.0). EGFR gain and PTEN LOH were used as surrogate markers for +7/-10 chromosome copy-number alterations. RESULTS Seven of these patients were diagnosed with glioblastoma, IDH-wildtype with a TERT promoter mutation. All three did not meet the diagnostic criteria for glioblastoma. All patients received temozolomide combination radiotherapy and maintenance temozolomide therapy. The median survival time of seven glioblastoma, IDH-wildtype patients was 616 days. Two patients who did not meet the diagnostic criteria for glioblastoma survived 510 and 583 days after initial surgery, respectively, and one patient was given the best supportive care policy at 518 days. Genetic analysis of all three cases showed TP53 LOH. CONCLUSION It was suggested that tumors with IDH wild-type low-grade astrocytoma that do not meet the diagnostic criteria for glioblastoma may have a poor prognosis. Although TP53 LOH was common, further investigation of specific genetic abnormalities is needed, and the classification and treatment strategy of these disease groups may be a challenge in the future.

Comparison of the 2022 ICC and Who Classification Systems of Myelodysplastic Neoplasms

Introduction: Recently, the World Health Organization (WHO) updated the 5th edition classification of myelodysplastic neoplasms (MDS) and the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemia was published. In this study, we aimed to compare several differences between WHO 2022 and ICC classifications. Methods: Our study consisted of 989 newly-diagnosed primary MDS subjects classified using the WHO 2016 criteria from 08/2016 to 07/2022. CD34 and CD117 immunostaining were used in 30 of 38 subjects with low blasts and BM fibrosis to evaluate a proportion of immature myeloid precursors. All subjects were negative for CD117+ cells. CD34+ BM cells ranged from 0% to 5%. Results: According to WHO 2022 classification, 36 MDS subjects with NPM1 mutation were reclassified as AML and 10 MDS-U subjects were reclassified as clonal cytopenia of undetermined significance (CCUS). Applying to the ICC criteria, 20 MDS subjects with NPM1 mutation were reclassified as AML and 8 MDS-U subjects were reclassified as CCUS. We analyzed the remaining patients. Among the 81 subjects classified as MDS-biTP53 according to WHO 2022, 10 subjects did not meet ICC criteria for MDS or MDS/AML with mutated TP53 because the VAF of TP53 mutation(s) was less than 10%. Subjects not qualifying for MDS or MDS/AML with mutated TP53 had lower Revised International Prognostic Scoring System (IPSS-R) scores, better IPSS-R-defined cytogenetics, a higher frequency of SF3B1 mutations and longer survival compared with subjects with MDS or MDS/AML with mutated TP53 according to ICC (All P-values＜ 0.005, Figure 1 Left). Our data suggested that TP53 mutational burden should also be considered in the diagnostic classification and the cut-off value of 10% seems reasonable. An additional difference between these two classifications is that ≥15% ring sideroblasts may be a surrogate for SF3B1 mutation in WHO 2022. But only those with SF3B1 mutation (VAF≥10%), without 5q-, -7 or complex karyotype and RUNX1 mutation can be diagnosed as MDS with mutated SF3B1(MDS- SF3B1) according to ICC. 23 of 76 subjects (30.3%) with MDS- SF3B1 according to the WHO 2022 classification did not meet the ICC criteria for MDS- SF3B1. Subjects not meeting the ICC for MDS- SF3B1 had lower WBCs ( P = 0.003) ,platelet concentrations ( P = 0.001), higher IPSS-M categories ( P = 0.024) and shorter survival compared with those with MDS- SF3B1 according to ICC( P = 0.003, Figure 1 middle). Therefore, our study shown that SF3B1-unmutated MDS-RS cases have different clinical features and outcome in comparison with SF3B1-mutated subjects and ICC criteria defined a more homogeneous disease entity of MDS- SF3B1. Apart from MDS with defining genetic abnormalities, substantial differences in morphologically defined MDS subtypes between WHO 2022 and ICC also need to be addressed. According to the WHO 2022 classification, only MDS-EB patients were furtherly categorized into MDS-EB with or without BM fibrosis. Here, we explore the impact of BM fibrosis in patients with MDS-LB. Among MDS patients without excess blasts and specific genetic abnormalities, 38 patients had fibrosis. Subjects with low blasts and fibrosis (MDS-LBf) had lower platelet concentrations ( P = 0.002), worse IPSS-R-defined cytogenetics and IPSS-R categories ( P ＜0.05) compared with those without excess blasts and myelofibrosis. MDS-LBf had worse survival compared with those with low blasts and without fibrosis (Figure 1 right, P = 0.007). Conclusion: Both the WHO 2022 and ICC criteria allow more accurate diagnoses and risk stratification. However, the presence of two separate classifications leads to the dilemma in clinical application. When it comes to MDS with defining genetic abnormalities, our analyses suggest ICC defines more homogeneous disease entities of MDS-SF3B1, MDS or MDS/AML with mutated TP53 subjects compared with WHO 2022. Although WHO 2022 places an emphasis on morphologically defined MDS and listed hypoplastic MDS (MDS-h) and MDS with fibrosis (MDS-f) as new entities. Our data shown that fibrosis is a poor prognostic factor in MDS subjects without excess blasts. These subjects tend to have more aggressive clinical manifestations than other MDS subjects with low blasts. Collectively, we propose to integrate these two classifications into one pipeline for diagnosis of MDS (Figure 2), avoiding disadvantages for each one. Bing Liand Zhijian Xiao were co-corresponding authors

Selinexor, Ixazomib, Pomalidomide and Dexamethasone in Functionally High-Risk Multiple Myeloma: Results from the Myeloma Developing Regimens Using Genomics (MyDRUG) Sub-Protocol Y3

Background: Multiple myeloma (MM) is characterized by somatic mutations involving cancer-associated genes. The MyDRUG trial was initiated to explore the efficacy of specific molecularly-targeted therapies in combination with a standard triplet combination in MM. Methods: MyDRUG (NCT03732703) is a genomically-guided umbrella trial for patients with functional high-risk MM, defined as early relapse following primary therapy (3 years for transplant with maintenance, 18 months without), with specific genetic abnormalities. Patients with no actionable mutation or mutations with allelic burden below 30% were randomly assigned to one of the “non-actionable” arms. Here we present the data for the Y3 arm which combines selinexor (60mg po days 1,8,15), ixazomib (4mg po days 1,8,15), pomalidomide (3mg po days 1-21) and dexamethasone (40mg po weekly) (Seli-IPD), given on a 28-day cycle. The primary objective of the Y3 sub-protocol was to evaluate the overall response rate (ORR) according to the International Myeloma Working Group consensus criteria. Secondary objectives included assessment of adverse events (AEs). Results: 17 patients were enrolled into the Y3 arm. The average age was 62 (51-79), 65% were male with a median of 29 months since initial diagnosis and a median of 2 prior lines of therapy. The ORR (> PR) was 52.9% with a clinical benefit rate (> MR) of 58.8%. The median progression free survival was 10.2 months ( 95% CI: 3.9; 12.9) with a median overall survival which has not yet been reached; with all 17 patients still alive at the current data cutoff. No dose-limiting toxicities were seen. Eight patients (47.1%) experienced a serious AE with 2 patients (11.8%) experiencing an AE leading to treatment discontinuation. Two patients (11.8%) required dose reductions. The most common non-hematologic AEs were fatigue, nausea and constipation; all of which were grade 1 and 2. Conclusions: In this platform study of patients with relapsed, functionally high-risk MM, patients who received Seli-IPd exhibited significant efficacy and a manageable AE profile. Furthermore, this provides an all-oral option for patients wishing to minimize their office visits and parenteral therapy administrations.

Effective venetoclax-based treatment in relapsed/refractory multiple myeloma patients with translocation t(6;14).

Introduction: The selective Bcl-2 inhibitor venetoclax has shown promising therapeutic potential in multiple myeloma, particularly in cases associated with t(11;14) IGH::CCND1 translocation. However, the efficacy of venetoclax in myeloma patients with the t(6;14) IGH::CCND3 translocation remains less investigated. Methods: In this study, we conducted a retrospective analysis to investigate the efficacy of venetoclax-based therapy in relapsed/refractory myeloma patients with t(6;14) translocation. The treatment courses of three patients, that included previous therapies and responses to venetoclax, were assessed. Clinical data, laboratory results, and adverse events were analyzed to evaluate treatment outcomes. Results: Our findings demonstrated remarkable therapeutic responses in three consecutive patients with t(6;14) translocation-associated myeloma who received venetoclax-based therapy. Patient 1, a lenalidomide-bortezomib-daratumumab and alkylator treatment refractory patient, achieved sustained stringent complete remission (sCR) after combining carfilzomib-dexamethasone with venetoclax, which was his best response ever. Similarly, Patient 2, refractory to frontline bortezomib-thalidomide-dexamethasone therapy, attained CR following a transition to bortezomib-dexamethason-venetoclax treatment. Patient 3, who was immunomodulatory (IMID)-intolerant, showed a highly favorable response to venetoclax-dexamethasone therapy after his first relapse following autologous stem cell transplantation. No significant adverse effects were observed in any of the patients. Discussion: Our study provides compelling preliminary evidence for the efficacy of venetoclax in t(6;14) translocation-associated myeloma. The outcomes observed in our patients suggest that venetoclax-based therapy holds substantial promise as an effective treatment option for this specific genetic subgroup. Furthermore, the similarities in treatment response between t(11;14) and t(6;14) translocation subgroups highlight the importance of personalized approaches targeting specific genetic abnormalities to optimize therapeutic outcomes.

Elevated IgE Levels-An Allergy or an Underlying Inborn Error of Immunity in Children with Recurrent Infections?

Elevated immunoglobulin E (IgE) is a hallmark of allergic diseases. However, high IgE levels also occur in a number of other infectious and noninfectious diseases. In most cases, elevated IgE levels indicate allergy, eczema, or chronic skin infection. Very high IgE levels are not uncommon in patients with active eczema but more often indicate monogenic atopic disorder or inborn errors of immunity with an atopic phenotype. We conducted a retrospective study of 385 children with suspected immune deficiency referred to the clinic over a 9-year period. Measurement of IgE, IgG, IgA, IgM, and IgG subclasses in blood samples revealed that nearly one-third of the patients had elevated serum IgE levels. Most of the cases with elevated IgE were children with underlying atopy-mainly atopic dermatitis and, to a lesser extent, bronchial asthma-whereas 40.12% (37 children) had no atopy at all. In the most severe cases (with extremely elevated IgE or severe dermatitis), we confirmed genetic mutations for underlying immunodeficiency. Our results indicate that allergic phenotype should not be underestimated and that children with more severe allergic disease should be evaluated for an underlying inborn error of immunity. If inborn error of immunity (IEI) is suspected, a comprehensive immunologic evaluation is required. Genetic testing helps identify the specific genetic abnormality, which provides important insight into the immunopathogenesis of the disease and accurate determination of optimal therapy.

Machine Learning Models Predict Molecular Genetic Subtypes of Multiple Myeloma from Whole-Slide Bone Marrow Aspirate Smears

Multiple myeloma (MM) is a plasma cell neoplasm and the second most common hematologic malignancy. Current guidelines recommend multiple myeloma cases undergo karyotyping and fluorescence in situ hybridization (FISH) analysis on bone marrow biopsy samples to assess for specific recurrent genetic abnormalities. Results of this testing help to predict differences in patient prognosis over time and to guide appropriate selection of therapy. Refinements in risk stratification incorporated additional complex molecular testing which, along with karyotyping and FISH, are costly and not available to all patients. Myeloma cell cytomorphologies have been associated in a subset of cases with more aggressive disease, when plasmablastic, and with a subset of t(11;14) cases, when lymphoplasmacytoid. Nonetheless, cellular features as assessed by manual microscopy have not been shown to identify biologic subtypes of disease reproducibly and broadly, such that these features are not a component of current prognostic systems. Whether accurate risk-stratification information can be extracted from microscopic images of myeloma cells through machine-based approaches is uncertain. Thus, in this study, we tested the feasibility of using machine learning models to predict multiple myeloma molecular genetic subtypes from analysis of neoplastic plasma cell morphology on Wright-stained aspirate smears. We first improved upon a previously developed computational pipeline that identifies and classifies hematopoietic cells from scanned whole-slide images (400x) of bone marrow aspirate smears, including classification of plasma cells with 94% accuracy. Using this pipeline, we obtained images from all plasma cells (up to 68,569 plasma cells per slide) from aspirate smears of 18 patients without plasma cell neoplasms and 96 patients with plasma cell neoplasms (including 20 with t(11;14) and 23 with gain(1q); 44 with standard risk FISH and 22 with high risk FISH (t(4;14), t(14;16), del(17p), or >4 copies 1q+)). We then developed convolutional neural network (CNN)-based multi-instance machine learning models to perform patient-level classifications of disease status and molecular genetic classification from image-level analysis of plasma cell cytomorphology. These models demonstrated strong performance for classifying patients without versus with plasma cell neoplasms (AUROC 0.80), and are capable of making patient-level predictions of multiple myeloma molecular genetic subtypes (t(11;14), AUROC 0.73; gain(1q), AUROC 0.71) as well as prediction of FISH risk level (AUROC 0.68). Finally, by assessing cell attention scores and CNN model weights, this machine learning pipeline can assess which individual plasma cells and which specific morphologic features provided the most utility in the prediction of molecular genetic subtypes for individual patients, hence providing explainability for model output. Importantly, our findings suggest that cytomorphologic features of plasma cells on routine aspirate smear slides contain information, extractable through machine-based approaches, that correlates with molecular genetic subtypes employed for risk stratification. With further refinement these promising computational digital pathology models can potentially yield tools not only for use in low resource settings, but also provide a potential basis for development of multimodal models that incorporate and improve upon results of currently used risk stratification tools.

A di-electrophoretic simulation procedure of iron-oxide micro-particle drug attachment system for leukemia treatment using COMSOL software: a potential treatment reference for LMICs.

Leukemia encompasses various subtypes, each with unique characteristics and treatment approaches. The challenge lies in developing targeted therapies that can effectively address the specific genetic mutations or abnormalities associated with each subtype. Some leukemia cases may become resistant to existing treatments over time making them less susceptible to chemotherapy or other standard therapies. Developing new treatment strategies to overcome resistance is an ongoing challenge particularly in Low and Middle Income Countries (LMICs). Computational studies using COMSOL software could provide an economical, fast and resourceful approach to the treatment of complicated cancers like leukemia. Using COMSOL Multiphysics software, a continuous flow microfluidic device capable of delivering anti-leukemia drugs to early-stage leukemia cells has been computationally modeled using dielectrophoresis (DEP). The cell size difference enabled the micro-particle drug attachment to the leukemia cells using hydrodynamic focusing from the dielectrophoretic force. This point of care application produced a low voltage from numerically calculated electrical field and flow speed simulations. Therefore, such a dielectrophoretic low voltage application model can be used as a computational treatment reference for early-stage leukemia cells with an approximate size of 5 μm.

Unlocking the power of precision medicine for pediatric low-grade gliomas: molecular characterization for targeted therapies with enhanced safety and efficacy.

In the past decade significant advancements have been made in the discovery of targetable lesions in pediatric low-grade gliomas (pLGGs). These tumors account for 30-50% of all pediatric brain tumors with generally a favorable prognosis. The latest 2021 WHO classification of pLGGs places a strong emphasis on molecular characterization for significant implications on prognosis, diagnosis, management, and the potential target treatment. With the technological advances and new applications in molecular diagnostics, the molecular characterization of pLGGs has revealed that tumors that appear similar under a microscope can have different genetic and molecular characteristics. Therefore, the new classification system divides pLGGs into several distinct subtypes based on these characteristics, enabling a more accurate strategy for diagnosis and personalized therapy based on the specific genetic and molecular abnormalities present in each tumor. This approach holds great promise for improving outcomes for patients with pLGGs, highlighting the importance of the recent breakthroughs in the discovery of targetable lesions.

Tumeurs de Bellini et carcinomes médullaires rénaux à l’ère des nouvelles thérapies

Collecting duct carcinoma (also known as Bellini tumour) and renal medullary carcinoma are two extremely rare and aggressive renal cancers. They are both less responsive to conventional treatments used in clear cell renal carcinoma. There are very few studies evaluating their optimal management and currently, at the metastatic stage, polychemotherapy based on platinum salts remains the most widely used. The emergence of new treatments such as anti-angiogenic TKIs, immunotherapy or treatments targeting specific genetic abnormalities, opens up a new field of possibilities in the management of these cancers. The evaluation of the response to these treatments is therefore essential. In this article, we will review the status of their management and the various studies that have evaluated recent treatments in these two cancers.

The targeted next-generation sequence revealed SMAD4, AKT1, and TP53 mutations from circulating cell-free DNA of breast cancer and its effect on protein structure – A computational approach

Breast cancer biomarkers that detect marginally advanced stages are still challenging. The detection of specific abnormalities, targeted therapy selection, prognosis, and monitoring of treatment effectiveness over time are all made possible by circulating free DNA (cfDNA) analysis. The proposed study will detect specific genetic abnormalities from the plasma cfDNA of a female breast cancer patient by sequencing a cancer-related gene panel (MGM455 – Oncotrack Ultima), including 56 theranostic genes (SNVs and small INDELs). Initially, we determined the pathogenicity of the observed mutations using PredictSNP, iStable, Align-GVGD, and ConSurf servers. As a next step, molecular dynamics (MD) was implemented to determine the functional significance of SMAD4 mutation (V465M). Lastly, the mutant gene relationships were examined using the Cytoscape plug-in GeneMANIA. Using ClueGO, we determined the gene’s functional enrichment and integrative analysis. The structural characteristics of SMAD4 V465M protein by MD simulation analysis further demonstrated that the mutation was deleterious. The simulation showed that the native structure was more significantly altered by the SMAD4 (V465M) mutation. Our findings suggest that SMAD4 V465M mutation might be significantly associated with breast cancer, and other patient-found mutations (AKT1-E17K and TP53-R175H) are synergistically involved in the process of SMAD4 translocate to nuclease, which affects the target gene translation. Therefore, this combination of gene mutations could alter the TGF-β signaling pathway in BC. We further proposed that the SMAD4 protein loss may contribute to an aggressive phenotype by inhibiting the TGF-β signaling pathway. Thus, breast cancer’s SMAD4 (V465M) mutation might increase their invasive and metastatic capabilities. Communicated by Ramaswamy H. Sarma

Choosing the Right Cell Line for Acute Myeloid Leukemia (AML) Research.

Immortalized cell lines are widely used in vitro tools in oncology and hematology research. While these cell lines represent artificial systems and may accumulate genetic aberrations with each passage, they are still considered valuable models for pilot, preliminary, and screening studies. Despite their limitations, cell lines are cost-effective and provide repeatable and comparable results. Choosing the appropriate cell line for acute myeloid leukemia (AML) research is crucial for obtaining reliable and relevant results. Several factors should be considered when selecting a cell line for AML research, such as specific markers and genetic abnormalities associated with different subtypes of AML. It is also essential to evaluate the karyotype and mutational profile of the cell line, as these can influence the behavior and response to the treatment of the cells. In this review, we evaluate immortalized AML cell lines and discuss the issues surrounding them concerning the revised World Health Organization and the French-American-British classifications.

What's new in the WHO 2022 classification of kidney tumours?

The World Health Organization (WHO) 2022 classification of urinary and male genital tumours (5th edition) has significantly improved our understanding of the morphologic, immunohistochemical, and molecular characteristics of renal tumours. The aim of this review is to outline the most important changes and diagnostic updates in the WHO 2022 classification of kidney tumours. A major change in this edition is the grouping of renal tumours into broader categories that include "clear cell renal tumours", "papillary renal tumours", "oncocytic and chromophobe renal tumours", "collecting duct tumours" as well as adding two categories of "other renal tumours" and "molecularly defined renal carcinomas". Novel entities included in the WHO 2022 classification are eosinophilic solid and cystic renal cell carcinoma (ESC RCC), anaplastic lymphoma kinase (ALK)-rearranged RCC and ELOC (formerly TCEB1)-mutated RCC. The category of "other renal tumours" includes a group of diverse, unrelated renal tumours that do not fit into other categories. The group of "molecularly defined renal carcinomas" reflects recent discoveries in the renal tumour genomics. These molecularly-defined renal entities demonstrate a set of morphologic features reflecting genotype-phenotype relationships. Final diagnosis of such entities rests on phenotypic and immunohistochemical (IHC) correlation, usually associated with IHC surrogate makers that reflect specific genetic abnormalities.

Profiling of mitochondrial heteroplasmy in single human oocytes by next-generation sequencing.

Mitochondrial DNA (mtDNA) plays a crucial role in the development of a competent oocyte. Indeed, mtDNA alterations may predispose to chromosome nondisjunction, resulting in infertility due to a reduced vitality and quality of oocytes and embryos. In this methods paper, the multiple displacement amplification approach was applied in combination with next-generation sequencing (NGS) to amplify and sequence, in single-end, the entire mtDNA of single human oocytes to directly construct genomic NGS libraries, and subsequently, to highlight and quantify the mutations they presented. The bioinformatic workflow was carried out with a specific ad hoc developed in-house software. This approach proved to be sensitive and specific, also highlighting the mutations present in heteroplasmy, showing deletion, insertion or substitution mutations in the genes involved in the respiratory chain, even if the found variants were benign or of uncertain meaning. The analysis of mtDNA mutations in the oocyte could provide a better understanding of specific genetic abnormalities and of their possible effect on oocyte developmental competence. This study shows how this approach, based on a massive parallel sequencing of clonally amplified DNA molecules, allows to sequence the entire mitochondrial genome of single oocytes in a short time and with a single analytical run and to verify mtDNA mutations.

Overview on Common Genes Involved in the Onset of Glioma and on the Role of Migraine as Risk Factor: Predictive Biomarkers or Therapeutic Targets?

Gliomas are relatively rare but fatal cancers, and there has been insufficient research to specifically evaluate the role of headache as a risk factor. Nowadays, gliomas are difficult to cure due to the infiltrative nature and the absence of specific adjuvant therapies. Until now, mutations in hundreds of genes have been identified in gliomas and most relevant discoveries showed specific genes alterations related to migraine as potential risk factors for brain tumor onset. Prognostic biomarkers are required at the time of diagnosis to better adapt therapies for cancer patients. In this review, we aimed to highlight the significant modulation of CLOCK, BMLA1 and NOTCH genes in glioma onset and development, praising these genes to be good as potentially attractive therapeutic markers for brain tumors. A improved knowledge regarding the role of these genes in triggering or modulating glioma maybe the key to early diagnosing brain tumor onset in patients affected by a simple headache. In addition, investigating on these genes we can suggest potential therapeutic targets for treating brain tumors. These considerations open up the possibility of personalized treatments that can target each brain tumor's specific genetic abnormality.

Prognostic Impact of the 2022 European Leukemia Net Risk Classification in Patients with Acute Myeloid Leukemia Undergoing Allogeneic Stem Cell Transplantation

Introduction: For most acute myeloid leukemia (AML) patients (pts) an allogeneic stem cell transplantation (HSCT) offers the highest chance of cure. Recently, the European LeukemiaNet (ELN) published updated recommendations on the risk classification in AML pts. In addition to the risk at diagnosis, which is now based on cytogenetics and the mutation status of several genes, a dynamic adjustment according to the measurable residual disease (MRD) status in favorable (fav) and intermediate (int) risk pts at informative time points - such as prior to an allogeneic HSCT - was recommended. A validation of the new ELN2022 risk classification has not been reported. Methods: We retrospectively analyzed 522 AML pts who received an allogeneic HSCT between 2000 and 2021 in first complete remission (CR, 54%), second CR (11%), CR with incomplete count recovery (CRi, 13%), or relapsed/refractory (22%) at our center. Median age at HSCT was 59 (range 16-76) years (y), 53% of pts were younger than 60 y. Conditioning regimens were myeloablative (27%), reduced-intensity (23%) or non-myeloablative (50%). At diagnosis, cytogenetics, and the mutation status of CEBPA, NPM1, and FLT3-ITD were assessed. Using next-generation sequencing we analyzed a panel of 54 recurrently mutated genes in myeloid malignancies (MiSeq platform, Illumina). In pts with material available in remission prior to HSCT, the MRD status based on NPM1mutations, BAALC, MN1, and WT1 expression was evaluated as published previously (Jentzsch 2021). MRD positivity (MRDpos) was defined as positivity of any of the analyzed markers. Median follow up after HSCT was 3.0 y. Results: ELN2022 risk at diagnosis was 22% fav, 26% int, and 52% adverse (adv). Older pts (≥ 60 y at HSCT) had significantly worse ELN2022 genetic risk (P<.001). Comparing the ELN2017 and the new ELN2022, 83% (fav), 70% (int), and 90% (adv) of pts kept their allocation, while 15% and 2% of fav ELN2017 risk pts changed to int and adv ELN2022, 30% of int ELN2017 risk pts changed to adv ELN2022 & 1% and 10% of adv ELN2017 risk pts changed to fav and int ELN2022. Analyzing the c-statistic (area under the curves [AUC]) produced by the ELN2017 and ELN2022 for relapse (AUC2017 = 0.64 vs AUC2022 = 0.64, P=.21) and overall survival (OS) prediction (AUC2017 = 0.60 vsAUC2022 = 0.57, P=.06), the ELN2022 did not perform significantly better. However, the ELN2022 risk at diagnosis impacted cumulative incidence of relapse/progression (CIR, P<.001) and OS (P<.001, Figure 1), which was especially seen in pts < 60 y (CIR P<.001, OFS P<.001), but less so in pts ≥ 60 y at HSCT (CIR P=.002, OS P=.10). At diagnosis, outcomes did not differ significantly with respect to the specific genetic abnormality defining the ELN2022 fav or the ELN2022 int risk. Also a high or low FLT3-ITD allelic ratio (0.5 cut) within the ELN2022 int risk did not result in distinct outcomes (CIR P=.13, OS P=.30). In contrast, within pts harboring adv ELN2022 risk, CIR (P=.05) and OS (P<.001) significantly differed according to the presence of specific genetic abnormalities; i.e. a complex karyotype (at 3 y: CIR 59%, OS 30%), other adverse cytogenetic aberrations (at 3 y: CIR 50%, OS 54%), adverse-risk gene mutation (i.e.ASXL1, RUNX1, or TP53, at 3 y: CIR 47%, OS 58%), or secondary AML-like gene mutations (at 3 y: CIR 30%, OS 73%). When we adjusted fav and int risk pts according to the MRD status at HSCT as proposed by the ELN2022 recommendations, 49% of fav risk pts at diagnosis had persisting MRD and were reclassified as int risk at HSCT while 53% of int risk pts at diagnosis were MRD negative and reclassified as fav risk at HSCT. Outcomes of MRD-adjusted fav risk pts improved (at 3 y: CIR 12%, OS 75%), while that of MRD-adjusted int risk pts (at 3 y: CIR 53%, OS 49%) was similar to that of adv risk pts transplanted in morphologic CR/CRi (at 3 y: CIR 47%, OS 54%). Conclusion: In the context of an allogeneic HSCT, the proposed risk assessments by the ELN2022 significantly impacted outcomes at diagnosis as well as after adjustment according to MRD status prior to HSCT of AML pts. However, it did not perform significantly better than the previous ELN2017 risk stratification. The FLT3-ITD allelic ratio did not significantly impacted outcomes within the ELN2022 int risk, justifying the removal from the risk stratification. Noteworthy, in pts receiving allogeneic HSCT, secondary AML-like gene mutations did not associate with adverse outcomes when no other adverse-risk characteristics were present. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal