Frequency Of Gene Mutations Research Articles

BIOM-68. OUTCOMES IN PATIENTS WITH HIGH-GRADE MENINGIOMA (HGM): A MULTI-INSTITUTIONAL STUDY

Abstract BACKGROUND High-grade meningiomas (HGMs) are associated with increased risk of recurrence after primary treatment. This study aimed to evaluate factors affecting survival. METHODS We performed a multi-institutional retrospective chart review study of patients with HGM (defined as grade 2 or 3 meningioma) whose tumor had undergone next-generation sequencing. Statistical testing was performed in Stata/MP version 16.1 (StataCorp, College Station, TX) on the patients’ demographic, anatomic, clinical, and survival data (using Kaplan-Meier survivor function and long-rank test). Data are presented as mean±SD, median [interquartile range], or percent. Age/time reported in years. RESULTS There were 46 patients (45.7% female) with an age of 57.9±14.0 at initial HGM diagnosis. The most frequent HGM sites were middle cranial fossa (37.0%), frontal (28.3%), parietal (15.2%), posterior fossa (13.0%), parasagittal (10.9%), and petrous (10.9%). The most common presenting symptoms were headache (37.0%), seizure (23.9%), weakness (21.7%), vision changes (19.6%), memory issues (10.9%), and diplopia (10.9%). The most frequent gene mutations were in NF2 (58.7%), CDKN2A (13.0%), and TERT (8.7%). Median follow-up was 2.85 [1.4-7], during which time 65.2% of patients experienced recurrence. mPFS was 2.7 [0.83-6]. Kaplan-Meier analysis showed a mPFS of 5 [1.2-9] and 2.3 [0.8-3] in females and males, respectively (p=0.26). Age and Ki67 proliferative index at diagnosis did not significantly predict PFS. mOS was not reached (NR) [7-NR]. NF2 mutation status and presence of extracranial invasion did not significantly separate the PFS Kaplan-Meier curves on log-rank testing. However, the presence of NF2 mutation [mOS NR (5.2-NR) vs. NR (7-NR), p<0.0001], extracranial invasion [mOS 10 (2.4-NR) vs. NR (NR-NR), p<0.0001], and HGM recurrence [mOS NR (2.7-NR) vs. NR (7-NR), p<0.0001], were associated with shorter mOS. CONCLUSIONS These HGM patients experienced a high recurrence rate during the follow-up period. The presence of NF2 mutation, extracranial invasion, and recurrent HGM were associated with shorter OS.

A Prospective Observational Study on Analyzing Lung Cancer Gene Mutation Variant Allele Frequency (VAF) and Its Correlation with Treatment Efficacy.

A few studies have reported on the variability of the variant allele frequency (VAF) of gene mutations and the relationship between VAF and the therapeutic effect of molecular-targeted drugs. This joint study was conducted from May 2020 to January 2022 between St. Marianna University School of Medicine and the DNA Chip Research Institute. Cytology samples were used to verify the usefulness of a lung cancer compact panel test, which is a high-sensitivity next-generation sequencing (NGS) gene panel test. We analyzed the distribution of VAF and the duration of the initial molecular-targeted drug administration in patients with advanced-stage epidermal growth factor receptor (EGFR) mutations. Of the 196 patients diagnosed with non-small cell carcinoma (NSCLC), gene mutations were detected in 114 (58.2%) cases and in 68.7% of patients with adenocarcinomas (an increased detection rate). A VAF of 30% or more for DNA mutations was confirmed in 35 patients (33.7%), 10% to <30% in 38 (36.5%), and <10% in 31 (29.8%), including 18 patients (17.3%) with <6%, which is considered the lower limit of the LOD for other companion diagnostic kits. EGFR mutations were detected in 59 patients (30%), of whom 35 were in an advanced stage and received molecular-targeted drugs as their initial treatment. Groups A and B comprised patients with a VAF of ≥10% and <10%, respectively, with 27 patients (median VAF 30.6%, range 11.4-77%) in group A and 8 (median VAF 5.4%, range 0.1-8.5%) in group B. The duration of the administration of molecular-targeted drugs was 17 months (range 3-42 months) in group A and 14 months (range 1-45 months) in group B, with no statistically significant difference between the two groups (p-value = 0.7). Twenty-seven percent of patients had a VAF < 10%. Even in patients with a low VAF for gene mutations, sufficient therapeutic effects were observed with molecular-targeted drugs, suggesting the importance of detecting mutations using a highly sensitive method at initial diagnosis. Further prospective validation studies of a larger number of cases are warranted.

Amino Acid Metabolism Subtypes in Neuroblastoma Identifying Distinct Prognosis and Therapeutic Vulnerabilities.

Although amino acid (AA) metabolism is linked to tumor progression and could serve as an attractive intervention target, its association with neuroblastoma (NB) is unknown. Based on AA metabolism-related genes, we established three NB subtypes associated with distinct prognoses and specific functions, with C1 and C2 having better outcomes. The C1 displayed enhanced metabolic activity and recruited metabolism-associated cells. The C2 exhibited an activated immune microenvironment and was more vulnerable to immunotherapy. The C3, characterized by cell cycle peculiarity, possessed a dismal prognosis and high frequency of gene mutations and was susceptible to chemotherapy. Furthermore, single-cell RNA sequencing analysis revealed that the C3-associated Scissor+ cell subpopulation was characterized by notorious functional states and orchestrated an immunosuppressive microenvironment. Additionally, we identified that ALK and BIRC5 contributed to the shorter lifespan of C3 and their corresponding inhibitors were potential interventions. In conclusion, we identified three distinct subtypes of NB, which help us foster individualized therapeutic strategies to improve the prognosis of NB.

Population Characteristics of the Spectrum and Frequencies of CFTR Gene Mutations in Patients with Cystic Fibrosis from the Republic of Bashkortostan (Russia).

Cystic fibrosis (CF) is one of the most common autosomal-recessive disorders worldwide. The incidence of CF depends on the prevalence of cystic fibrosis transmembrane conductance regulator gene (CFTR) mutations in the population, which is determined by genetic diversity and ethnicity. The search for the causes of mutations in the transmembrane conductance regulator gene (CFTR) was carried out using targeted next-generation sequencing (NGS) on the Illumina platform in patients with cystic fibrosis from the Republic of Bashkortostan (Russia), taking into account the ethnic structure of the sample. A total of 35 distinct causal variants were found in 139 cases from 129 families. Five (F508del, E92K, 3849+10kbC>T, CFTRdele2.3, L138ins) explain 78.7% of identified CF causal alleles. Variants N13103K and 394delTT were found in four families each. Variants 2143delT, S1196X, W1282X, Y84X, G194R, and 1525-1G>A, as well as the two previously described complex alleles-c. [S466X; R1070Q] and str.[G509D;E217G]-were found in two or three families each. Twenty additional variants occurred only once. Variant c.3883_3888dup has not been described previously. Thus, regional and ethnic features were identified in the spectrum of frequencies of pathogenic variants of the CFTR gene in the three major sub-groups of patients-Russians, Tatars, and Bashkirs. Taking into account these results, highlighting the genetic specificity of the region, a more efficient search for CFTR mutations in patients can be performed. In particular it is possible to choose certain test kits for quick and effective genetic screening before use of NGS sequencing.

Next-generation sequencing (NGS) of anaplastic thyroid carcinoma identifies unreported mutations in 25 recurring genes

Abstract Introduction/Objective Anaplastic thyroid carcinoma (ATC) is a rare, aggressive form of thyroid cancer. Our prior work identified 6 molecular clusters of ATC with a possible de novo group. Secondary analysis of NGS data from 713 ATC cases was undertaken to identify less frequent and unreported gene mutations. Methods/Case Report Deidentified NGS results of 713 ATC cases were obtained from Foundation Medicine (FoundationOne CDx). The results were analyzed for frequency of gene mutations. A search of the literature and genomic databases (TCGA, NCI Genomic Data Commons, and cBioPortal) was performed to determine gene association with thyroid cancers including ATC. Results (if a Case Study enter NA) There are 25 gene mutations present in 5 or more cases that have not previously been reported in ATC and one gene found, MTAP, which has been discussed in a limited number of cases. The gene mutations found are listed from highest to lowest frequency (14.77% to 0.69%) as follows: MTAP, LRP1B, ASXL1, NUP93, MUTYH, NOTCH3, RAD21, CRKL, PIK3R1, FANCA, STAG2, BRCA2, FGF4, FGF3, FGF19, FBXW7, BRCA1, BCORL1, QKI, VHL, PRKN, GATA6, NKX2_1, KDM5C, CCND3, and BAP1. There are also 99 other gene mutations with 4 or fewer cases (0.14% to 0.77%) that have not previously been associated with ATC. MTAP was previously reported to be lost by immunohistochemistry in 6/27 (22.2%) ATC cases; MTAP loss was also reported to indicate a potential CDKN2A abnormality. Our larger data set supports that MTAP is lost in ATC with 98.6% of MTAP- deleted ATC also harboring CDKN2A deletion and 92.3% showing CDKN2B deletion (p-values &amp;lt; 0.0001), supporting MTAP and CDKN2A/B are often deleted together. Other significant genes include the hereditary cancer genes MUTYH, FANCA (autosomal recessive), and BRCA1/2 (autosomal dominant) and genes associated with clonal hematopoiesis. ASXL1 and STAG2 have previously been unreported in ATC while others such as DNMT3A, TET2, and BCOR were also present in our dataset. Conclusion Our findings demonstrate 124 genes mutated in ATC that have not been previously reported. Besides the previously reported MTAP in 6 cases, genes associated with hereditary cancer and clonal hematopoiesis were identified. MTAP is located adjacent to CDKN2A/B and is often codeleted with MTAP at a much higher frequency than previously reported. Identifying associations with other diseases could improve surveillance and options for earlier therapy of ATC. Finally, these findings warrant further research to determine their role in the pathogenesis and treatment targets of ATC.

Anaplastic thyroid carcinoma: a genome-based search for new targeted therapy options

Abstract Introduction/Objective Anaplastic thyroid carcinoma (ATC) is a rare, aggressive thyroid cancer. Precision medicine, particularly gene-targeted therapy has emerged as a promising avenue in cancer treatment. However, few targeted therapies have been approved for ATC. Here, we present a genome-based search for new targeted therapy options using next-generation sequencing (NGS) data of 727 ATC cases. Methods/Case Report Deidentified NGS results in 727 ATC cases were obtained from Foundation Medicine. A search of the literature and genomic databases (TCGA, My Cancer Genome, and DGIdb) was performed to analyzed frequency of gene mutations and corresponding gene targeted drugs. Results (if a Case Study enter NA) Remarkably, 99.17% of the 727 ATC cases had at least one targeted drug option available. Among the 254 unique genes identified with pathogenic mutations, 150 (59.06%) were found to have at least 1 corresponding targeted drug. Among the top 35 most frequently mutated genes (frequency &amp;gt; 2.0%), 27 (80.00%) had available targeted therapies. Notably, most drug categories (70.83%) exhibited multi-gene targeting capabilities. The drug categories based on the percentage of genes targeted from highest to lowest are Serine/Threonine and Tryosine kinase inhibitors, therapeutic antibodies, MEK inhibitors, CDK inhibitors, AKT inhibitors, PI3K inhibitors and immunotherapies. There are an additional 16 drug categories that target 1 to 5 of the 35 frequently mutated genes identified. Of particular interest is MTAP, a previously unreported frequently mutated gene which is most often deleted (14.77%). Several drugs are undergoing phase 1 and/or phase 2 clinical trials for MTAP-deleted solid tumors. MTAP loss holds promise for identifying expanding therapeutic options in ATC. Conclusion Our genome-based analysis indicates that 99.17% of the 727 ATC cases have targeted drug options, targeting 59.06% of identified gene mutations. Among the 24 categories of targeted drugs 17 (70.83%) target more than one gene. The 2018 FDA approval of combination BRAF/MEK inhibitor therapy for management of BRAF V600E-positive ATC was a major first step in gene targeted therapies. Besides that, Tyrosine kinase inhibitors, mTOR inhibitor, PPAR-γ agonist, ALK inhibitor, VEGF inhibitor and several combined treatment and immunotherapeutic agents are currently being tested in ATC clinical trials. These promising findings highlight the expanding repertoire of gene-targeted therapy options in ATC and emphasizes the importance of combined strategies and identifying driver mutations.

CYSLTR1 antagonism displays potent anti-tumor effects in uveal melanoma

Uveal Melanoma (UM) is the most common primary intraocular malignancy in adults. Although rare, it is a deadly tumor, with a long-term prognosis of death occurring in more than 50% of the cases. It is characterized by frequent (∼80%) driver mutations in GNAQ and GNA11 genes, both of which are activated by cysteinyl leukotriene receptors (CYSLTRs). CYSLTR1 is upregulated and participated in the progression of several cancers. In the present study, we sought to determine the expression levels of CYSLTR1 in 31 human UM specimens and cell lines (3 primary and 1 metastatic), and its role in the proliferation and viability of these cells by analyzing cell metabolic activity, cell confluence and apoptosis levels. We show that all analyzed UM specimens and cells expressed CYSLTR1 at high levels. Notably, the pharmacological blockage of this receptor, using the inverse agonist MK571, reduced the growth and metabolic activity, and increased the apoptotic cell death of all analyzed UM cell lines. We provide evidence that CYSLTR1 is expressed in human UM and plays a significant role in UM progression behavior. Our data highlight the potential beneficial effects of targeting CYSLTR1 in the control of UM progression.

Determination of the frequency and distribution of APC, PIK3CA, and SMAD4 gene mutations in Ugandan patients with colorectal cancer

Uganda is a developing low-income country with a low incidence of colorectal cancer, which is steadily increasing. Ugandan colorectal cancer (CRC) patients are young and present with advanced-stage disease. In our population, there is a scarcity of genetic oncological studies, therefore, we investigated the mutational status of CRC tissues, focusing in particular on the adenomatous polyposis coli (APC), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), and SMAD4 genes. Our objective was to determine whether there were any differences between other populations and Ugandan patients. We performed next-generation sequencing on the extracted DNA from formalin-fixed paraffin-embedded adenocarcinoma samples from 127 patients (mean (SD) age: 54.9 (16.0) years; male:female sex ratio: 1.2:1). Most tumours were located in the rectum 56 (44.1%), 14 (11%) tumours were high grade, and 96 (75.6%) were moderate grade CRC. Stage III + IV CRC tumours were found in 109 (85.8%) patients. We identified 48 variants of APC, including 9 novel APC mutations that were all pathogenic or deleterious. For PIK3CA, we found 19 variants, of which 9 were deleterious or pathogenic. Four PIK3CA novel pathogenic or deleterious variants were included (c.1397C > G, c.2399_2400insA, c.2621G > C, c.2632C > G). Three SMAD4 variants were reported, including two pathogenic or deleterious variants (c.1268G > T, c.556dupC) and one tolerant (c.563A > C) variant. One novel SMAD4 deleterious mutation (c.1268G > T) was reported. In conclusion, we provide clinicopathological information and new genetic variation data pertinent to CRC in Uganda.

Abstract C091: Uncovering genetic regulators of metabolic plasticity in renal cell carcinoma

Abstract We aim to offer new insights on the regulation of metabolic plasticity in renal cell carcinoma (RCC) and identify novel metabolic regulatory targets that can be used for potential treatment therapies of the disease. RCC affects an estimated 400,000 people worldwide each year with over 100,00 deaths annually that disproportionately affects racial/ethnic minorities in the United States. RCC is a term that covers an array of kidney cancer subtypes differing in incidence, histopathology, genetic and molecular alterations, as well as in clinical outcomes and prognoses. However, a common characteristic of many RCCs is that they are driven by metabolic rewiring, due to a high frequency of mutations in genes that regulate major metabolic processes in the cell. It was recently discovered that patient overall survival and prognosis has been linked to the expression of certain metabolic signatures in RCC tumor cells. Metabolic plasticity allows cancer cells to survive and adapt to different environments and metabolic stress conditions, such as nutrient deprivation. Therefore, exploring and exploiting metabolic rewiring in these cells may reveal genetic vulnerabilities and dependencies. This could lead to discovery of novel biomarkers and molecular targets that can be implicated as future therapeutic interventions for this disease. To this end, we applied functional genomic screening to expose genetic dependencies and vulnerabilities under different physiologic and metabolic conditions in patient derived medullary (PDM) RCC cells. The medullary RCC is a rare and aggressive RCC subtype that disproportionately affects the African American/Black population. We applied a CRISPR- based combinatorial screening platform that is based on co-expression of Cas9 and Cas12a nucleases and libraries of hybrid guide RNAs (hgRNA) to achieve ultra-efficient gene knockout (Aregger et al., 2021; Gonatopoulos-Pournatzis et al., 2020) in PDM RCC cells. Additionally, cells were screened under different media conditions that mimic human physiological nutrient conditions and a media deprived of lipids, one of the major metabolic substrates of the cell. By utilizing a genome-wide pooled CRISPR gene knockout screen we were able to systematically uncover genes required for cell survival and proliferation in a panel of patient-derived RCCs. We have begun to uncover genetic dependencies and major metabolic pathways that can be elucidated and exploited for future studies, such as those involving ferroptosis which is a targetable pathway for the development of cancer treatment therapies. Our findings demonstrate some of the key genetic drivers underlying cellular adaptations to different physiological environments and nutrient deprivation. In future studies we will further explore the relationship between different key metabolic regulatory genes in RCC and map for genetic interactions in major metabolic pathways. Citation Format: Chelsee Holloway, Josef Horak, Youngkyu Jeon, Michael Aregger. Uncovering genetic regulators of metabolic plasticity in renal cell carcinoma [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C091.

Abstract C086: Somatic mutation variations in minority populations at the University of New Mexico Comprehensive Cancer Center

Abstract The global burden of cancer underscores the urgency to understand its genetic underpinnings. Genetic testing has revolutionized clinical practice, identifying driver mutations crucial for tumorigenesis, including TP53, PIK3CA, KRAS, PTEN, and ARID1A. However, minority populations are underrepresented in major genomic projects, hindering tailored therapies. Variations in genetic polymorphisms among ethnicities, exemplified by distinct patterns in mutations like BRCA and EGFR, underscore the imperative for diversity in genomic research. We conducted a retrospective study at the University of New Mexico Comprehensive Cancer Center, analyzing 5,045 patients' genetic testing data. Significant differences in somatic gene mutation frequencies and survival outcomes were observed across racial and ethnic groups, highlighting the importance of personalized approaches in cancer care. Specific gene mutations, such as IDH1, JAK2, KITX11, and TP53, were associated with distinct survival outcomes. Integrating genetic testing into routine practice could enhance patient stratification and treatment efficacy. Future research should explore underlying mechanisms and include larger, diverse populations to advance personalized medicine in oncology. Citation Format: Isabella Doan, Jonathan Coy, Bernard Tawfik. Somatic mutation variations in minority populations at the University of New Mexico Comprehensive Cancer Center [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C086.

An updated AL-Base reveals ranked enrichment of immunoglobulin light chain variable genes in AL amyloidosis.

Each monoclonal antibody light chain associated with AL amyloidosis has a unique sequence. Defining how these sequences lead to amyloid deposition could facilitate faster diagnosis and lead to new treatments. Light chain sequences are collected in the Boston University AL-Base repository. Monoclonal sequences from AL amyloidosis, multiple myeloma and the healthy polyclonal immune repertoire were compared to identify differences in precursor gene use, mutation frequency and physicochemical properties. AL-Base now contains 2,193 monoclonal light chain sequences from plasma cell dyscrasias. Sixteen germline precursor genes were enriched in AL amyloidosis, relative to multiple myeloma and the polyclonal repertoire. Two genes, IGKV1-16 and IGLV1-36, were infrequently observed but highly enriched in AL amyloidosis. The number of mutations varied widely between light chains. AL-associated κ light chains harbored significantly more mutations compared to multiple myeloma and polyclonal sequences, whereas AL-associated λ light chains had fewer mutations. Machine learning tools designed to predict amyloid propensity were less accurate for new sequences than their original training data. Rarely-observed light chain variable genes may carry a high risk of AL amyloidosis. New approaches are needed to define sequence-associated risk factors for AL amyloidosis. AL-Base is a foundational resource for such studies.

Analysis of the Mechanism Underlying Radiotherapy Resistance Caused by Oligodendroglia Cells in Glioblastoma by Applying the Single-cell RNA Sequencing Technology.

Glioblastoma (GBM) is an aggressive malignancy. The inherent resistance of GBM to radiotherapy poses great challenges for clinical treatment. The primary objective of this study is to explore the molecular mechanisms of radiotherapy resistance in GBM and identify the key influencing factors that contribute to this phenomenon. The single-cell RNA sequencing (scRNA-seq) data of GBM were downloaded from the Gene Expression Omnibus (GEO) database. Cells were clustered using the Seurat R package, and the clusters were annotated using the CellMarker database. Pseudotime analysis was conducted using Monocle2. Marker scores were calculated based on the RNA-seq data of GBM from the UCSC database, and the enrichment of Hallmark gene sets was measured with the AUCell package. Furthermore, the most frequently mutated genes were identified using the simple nucleotide variation data from The Cancer Genome Atlas (TCGA) applying the maftools package. This study identified two oligodendrocyte subsets (ODC3 and ODC4) as radiotherapy-resistant groups in GBM. Enrichment and Pseudotime analysis revealed that the inflammatory response and immune activation pathways were enriched in ODC3, while the cell division and interferon response pathways were enriched in ODC4. The enrichment scores of hallmark gene sets further confirmed that ODC3 and ODC4 subpopulations developed radiotherapy resistance via distinct molecular mechanisms. Analysis of gene mutation frequencies showed that TP53 exhibited the most significant change in mutation frequency, indicating that it was an important risk factor involved in radiotherapy resistance in GBM. We identified two ODC subpopulations that exhibited resistance to radiotherapy, providing a new perspective and potential targets for personalized treatment strategies for GBM.

Characterization of driver mutations identifies gene signatures predictive of prognosis and treatment sensitivity in multiple myeloma.

In multiple myeloma (MM), while frequent mutations in driver genes are crucial for disease progression, they traditionally offer limited insights into patient prognosis. This study aims to enhance prognostic understanding in MM by analyzing pathway dysregulations in key cancer driver genes, thereby identifying actionable gene signatures. We conducted a detailed quantification of mutations and pathway dysregulations in 10 frequently mutated cancer driver genes in MM to characterize their comprehensive mutational impacts on the whole transcriptome. This was followed by a systematic survival analysis to identify significant gene signatures with enhanced prognostic value. Our systematic analysis highlighted 2 significant signatures, TP53 and LRP1B, which notably outperformed mere mutation status in prognostic predictions. These gene signatures remained prognostically valuable even when accounting for clinical factors, including cytogenetic abnormalities, the International Staging System (ISS), and its revised version (R-ISS). The LRP1B signature effectively distinguished high-risk patients within low/intermediate-risk categories and correlated with significant changes in the tumor immune microenvironment. Additionally, the LRP1B signature showed a strong association with proteasome inhibitor pathways, notably predicting patient responses to bortezomib and the progression from monoclonal gammopathy of unknown significance to MM. Through a rigorous analysis, this study underscores the potential of specific gene signatures in revolutionizing the prognostic landscape of MM, providing novel clinical insights that could influence future translational oncology research.

Advances in the understanding of molecular genetics and therapy of Richter transformation in chronic lymphocytic leukemia.

Richter's transformation (RT) is defined as the evolution of chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL) into an aggressive lymphoma, most commonly diffuse large B-cell lymphoma. This complication is rare and aggressive, with poor prognosis and dismal survival. Clonal relationship with the underlying CLL/SLL, observed in ∼80% of cases, represents one of the main factors affecting prognosis. Treatment has been historically based on chemoimmunotherapy, but frequent mutations in genes involved in cell survival and proliferation-such as TP53, NOTCH1, MYC, CDKN2A-confer resistance to standard treatments. During the last years, advances in the knowledge of the biological mechanisms underlying RT allowed to identify genetic and molecular lesions that can potentially be targeted by novel selective agents. Pathway and checkpoint inhibitors, bispecific antibodies and CAR T-cell therapy are currently under investigation and represent promising treatment options. This review summarizes current biological evidence and available data on novel therapeutic agents.

The pattern of rpoB gene mutation of Mycobacterium tuberculosis and predictors of rifampicin resistance detected by GeneXpert MTB/RIF assay in Tanzania.

Antimicrobial resistance in Mycobacterium tuberculosis (MTB) poses a significant challenge to tuberculosis (TB) management worldwide. Rifampicin resistance (RR) has been associated with the rpoB gene mutation. No study was conducted in Tanzania to determine the commonest mutation. The inconsistent findings from various studies support the need to determine whether reported mutation patterns are applicable in our setting. We determined the frequency of rpoB gene mutation and factors associated with RR, which were detected using GeneXpert MTB/RIF assay. We conducted a retrospective cross-sectional study involving data from the National Tuberculosis and Leprosy Program database from 2020 to 2022 for cases investigated using GeneXpert MTB/RIF assay. Descriptive analysis was performed to determine the frequency of categorical variables. The chi-square test and logistic regression analysis assessed the relationship between the independent variables and outcome. The 95% confidence interval and a significance level of p<0.05 were used to assess the strength of association. A total of 56,004 participants had a status of MTB and RR, where 38,705/56,004 (69.11%) were males. Probe E mutation (codon 529-533), 89/219 (40.64%) was predominant. Human immunodeficiency virus (HIV)-positive patients had a higher gene mutation, 134/10601 (1.26%) than HIV-negative, 306/45016 (0.68%) (p<0.001). Patients with both pulmonary and extra-pulmonary TB had about four times greater odds of developing rifampicin resistance (AOR 3.88, 95%CI: 1.80-8.32). RR was nearly nine times higher in previously treated patients than new patients (AOR 8.66, 95% CI: 6.97-10.76). HIV-positive individuals had nearly twice the odds of developing RR than HIV-negative individuals (AOR 1.91, 95%CI: 1.51-2.42). The rate of RR was lower compared to other studies in Tanzania, with probe E mutations the most prevalent. Patients with disseminated TB, HIV co-infection and those with prior exposure to anti-TB had more risk of RR. The findings highlight the need to strengthen surveillance of multidrug-resistant TB among high risk patients.

Molecular precision medicine: Multi-omics-based stratification model for acute myeloid leukemia

Acute myeloid leukemia (AML), as the most common malignancy of the hematopoietic system, poses challenges in treatment efficacy, relapse, and drug resistance. In this study, we have utilized 151 RNA sequencing datasets, 194 DNA methylation datasets, and 200 somatic mutation datasets from the AML cohort in the TCGA database to develop a multi-omics stratification model. This model enables comparison of prognosis, clinical features, gene mutations, immune microenvironment and drug sensitivity across subgroups. External validation datasets have been sourced from the GEO database, which includes 562 mRNA datasets and 136 miRNA datasets from 984 adult AML patients. Through multi-omics-based stratification model, we classified 126 AML patients into 4 clusters (CS). CS4 had the best prognosis, with the youngest age, highest M3 subtype proportion, fewest copy number alterations, and common mutations in WT1, FLT3, and KIT genes. It showed sensitivity to HDAC inhibitors and BCL-2 inhibitors. Both the M3 subtype and CS4 were identified as independent protective factors for survival. Conversely, CS3 had the worst prognosis due to older age, high copy number alterations, and frequent mutations in RUNX1, DNMT3A, and TP53 genes. Additionally, it showed higher proportions of cytotoxic cells and Tregs, suggesting potential sensitivity to mTOR inhibitors. CS1 had a better prognosis than CS2, with more copy number alterations, while CS2 had higher monocyte proportions. CS1 showed good sensitivity to cytarabine, while CS2 was sensitive to RXR agonists. Both CS1 and CS2, which predominantly featured mutations in FLT3, NPM1, and DNMT3A genes, benefited from FLT3 inhibitors. Using the Kappa test, our stratification model underwent robust validation in the miRNA and mRNA external validation datasets. With advancements in sequencing technology and machine learning algorithms, AML is poised to transition towards multi-omics precision medicine in the future. We aspire for our study to offer new perspectives on multi-drug combination clinical trials and multi-targeted precision medicine for AML.

IGFBP1 promotes the proliferation and migration of lung adenocarcinoma cells through the PPARα pathway

BackgroundThe immune status is closely linked to cancer progression, metastasis, and prognosis. Lipid metabolism, crucial for reshaping immune status, plays a key role in regulating the advancement of lung adenocarcinoma (LUAD) and deserves further investigation. MethodsThis study classifies LUAD patients into different immune subtypes based on lipid metabolism-related genes and compares the clinical characteristics among these subtypes. Single-multi COX analysis screens out key genes related to prognosis, and a risk feature and prognostic model are constructed. Cell cloning, scratch, transwell, western blotting and flow cytometry cell cycle analysis to detect the function of key genes. A subcutaneous tumor animal model is used to investigate the in vivo function and molecular mechanisms of key genes. ResultsLUAD patients are classified into three immune subtypes, among which C3 subtype has lower immune status and higher frequency of gene mutations, and show lower immunoreactivity in immunotherapy. COX analysis identified a prognostic model for four lipid metabolism factors (IGFBP1, NR0B2, PPARA, and POMC). IGFBP1, a core gene in this model, is highly expressed in the C3 subtype. Functionally, knocking down IGFBP1 significantly inhibits tumor cell cloning, scratch, and migration abilities, and downregulates the expression of cell cycle and EMT-related proteins. Knocking down IGFBP1 significantly inhibits tumor burden (P < 0.05). Mechanistically, knocking down IGFBP1 inhibits the activation of PPARα to regulate tumor cell growth. ConclusionsThis study found that lipid metabolism genes are closely related to LUAD, and IGFBP1 may be a key gene in regulating tumor growth and development.

Genomic characterization of AML with aberrations of chromosome 7: a multinational cohort of 519 patients

BackgroundDeletions and partial losses of chromosome 7 (chr7) are frequent in acute myeloid leukemia (AML) and are linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood.MethodsTo discover genetic lesions in adult AML patients with aberrations of chromosome 7 [abn(7)], 60 paired diagnostic/remission samples were investigated by whole-exome sequencing in the exploration cohort. Subsequently, a gene panel including 66 genes and a SNP backbone for copy-number variation detection was designed and applied to the remaining samples of the validation cohort. In total, 519 patients were investigated, of which 415 received intensive induction treatment, typically containing a combination of cytarabine and anthracyclines.ResultsIn the exploration cohort, the most frequently mutated gene was TP53 (33%), followed by epigenetic regulators (DNMT3A, KMT2C, IDH2) and signaling genes (NRAS, PTPN11). Thirty percent of 519 patients harbored ≥ 1 mutation in genes located in commonly deleted regions of chr7—most frequently affecting KMT2C (16%) and EZH2 (10%). KMT2C mutations were often subclonal and enriched in patients with del(7q), de novo or core-binding factor AML (45%). Cancer cell fraction analysis and reconstruction of mutation acquisition identified TP53 mutations as mainly disease-initiating events, while del(7q) or −7 appeared as subclonal events in one-third of cases. Multivariable analysis identified five genetic lesions with significant prognostic impact in intensively treated AML patients with abn(7). Mutations in TP53 and PTPN11 (11%) showed the strongest association with worse overall survival (OS, TP53: hazard ratio [HR], 2.53 [95% CI 1.66–3.86]; P < 0.001; PTPN11: HR, 2.24 [95% CI 1.56–3.22]; P < 0.001) and relapse-free survival (RFS, TP53: HR, 2.3 [95% CI 1.25–4.26]; P = 0.008; PTPN11: HR, 2.32 [95% CI 1.33–4.04]; P = 0.003). By contrast, IDH2-mutated patients (9%) displayed prolonged OS (HR, 0.51 [95% CI 0.30–0.88]; P = 0.0015) and durable responses (RFS: HR, 0.5 [95% CI 0.26–0.96]; P = 0.036).ConclusionThis work unraveled formerly underestimated genetic lesions and provides a comprehensive overview of the spectrum of recurrent gene mutations and their clinical relevance in AML with abn(7). KMT2C mutations are among the most frequent gene mutations in this heterogeneous AML subgroup and warrant further functional investigation.

Molecular pathophysiology of germline mutations in acute myeloid leukemia.

Germline (GL) predisposition to acute myeloid leukemia (AML) has been established as an independent disease entity in the latest World Health Organization classification. Following the American College of Medical Genetics and Genomics guidelines, GL variants were interpreted as causal if they were classified as "pathogenic." GL predisposition can be divided into three groups with different phenotypes, and play an important role in the pathogenesis of adult-onset AML. The clinical course and age of onset of myeloid neoplasms varied considerably for each gene. For example, patients with GATA2 GL variants develop AML before the age of 30 along with bone marrow failure, whereas those with DDX41 GL variants tend to develop AML after the age of 50 without any preceding hematological abnormalities or organ dysfunction. A comprehensive analysis of adult-onset myelodysplastic syndromes in transplant donors showed a 7% frequency of pathogenic GL variants, with DDX41 being the most frequent gene mutation at approximately 3.8%. Future research on GL predisposition at any age of myeloid neoplasm onset will assist in early and accurate diagnosis, development of effective treatment strategies, and selection of suitable donors for stem cell transplantation.

Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ.

Background: In melanomas, mutations in the BRAF gene are common and their occurrence represents an early oncogenic event. Our goal was to determine and compare the frequency of BRAF gene mutations in dysplastic nevi (ND) and melanomas in situ (MIS), as well as whether there is a correlation between the presence of BRAF gene mutations and various anamnestic, clinical, and histopathologic variables. Methods: A total of 175 patients-106 with ND, 41 with MIS, and 28 with lentigo maligna (LM) were included in the study. DNA was extracted from tissue samples and analyzed using the competitive allele-specific TaqMan chain reaction by polymerase in real time to detect the presence of BRAF V600E and V600K mutations. The data were compared with anamnestic, clinical, and histopathological data. Results: There is a statistically significant correlation between the presence of BRAF mutation and the diagnosis of melanoma in situ (χ2 test, χ2 = 29.17, p < 0.0001). Patients with LM had a significantly lower incidence of BRAF mutations compared to patients with ND and MIS. There was a significant correlation between the presence of a BRAF mutation and tumor localization, as well as the age of the patient, but no statistically significant correlation between the presence of a BRAF mutation and sex, tumor size, or previous melanoma diagnosis. Conclusions: BRAF mutations in ND are essentially required; however, they are an insufficient oncogenic trigger for the development of melanoma. This research contributes to a better understanding of the etiopathogenesis of melanoma and the role of ND as possible precursor lesions.