Mutation Profiles Research Articles

A bioinformatics analysis of gene expression in endometrial cancer, endometriosis and obesity

ABSTRACT Endometrial cancer (EC), endometriosis (ENDO), and obesity (OBY) are interconnected conditions in women that may share underlying genetic pathways. This study aimed to identify shared genetic pathways and differential gene expressions across these conditions to uncover potential therapeutic targets. A bioinformatics pipeline was applied using gene expression datasets from the GEO database, incorporating differential expression analysis, functional and pathway enrichment, PPI network construction, survival analysis, and mutational profiling across 198 samples. The analysis revealed 26 shared differentially expressed genes (DEGs), with IGF-1, CREBBP, EP300, and PIAS1 identified as key hub genes. Elevated IGF-1 expression was significantly linked to poorer survival outcomes in EC patients (p < .05). Frequent mutations were observed in these hub genes, suggesting their critical role in disease mechanisms. This study highlights genetic links among EC, ENDO, and OBY, emphasizing high IGF-1 expression as a potential prognostic marker in EC and recurrent alterations in hub genes as promising therapeutic targets. These findings provide insights into the shared genetic underpinnings of these conditions and present new avenues for targeted therapies.

Abstract A018: Somatic mutations in the PIK3CA gene and its prognostic implications among Ethiopian Breast cancer patients

Abstract Purpose: The phosphatidylinositol-4, 5-bisphosphate 3-kinase (PIK3CA), catalytic subunit alpha (c) is frequently mutated in breast cancer (BC). Although the biological impact of PIK3CA mutations in BC has been studied in various parts of the world, limited data is available from sub-Saharan Africa. In this study, the frequency and the prognostic role of PIK3CA mutations were investigated among BC patients from Ethiopia. Objective: The aim of the study was to determine the frequency of PIK3CA mutations and its prognostic role in patients with breast cancer in Ethiopia. Methods: Formalin-fixed paraffin-embedded blocks and fresh frozen BC tissue samples were collected from patients newly diagnosed with BC. Histopathological evaluation was carried out using immunohistochemistry (IHC). PIK3CA mutation profiling was carried out using TaqMan® Mutation detection assay. The association between PIK3CA mutation status and clinical and histopathological features was evaluated. A survival regression (Cox’s model) was employed to assess the effect of PIK3CA mutation and other variables on survival. Results: The prevalence of the PIK3CA mutations was 20.4%. Mutation of the PIK3CA gene was mainly observed among younger (24%), early pT stage (19.4%), and G1/G2 tumors (22.3%). The proportion of mutation was 24.4%, 27.3% and 20% in ER+, PR+ and HER2- tumors, respectively. A marked difference was observed in the PIK3CA mutation frequency across the four major tumor subgroups. However, most of the mutated tumors were found among HR+/HER2− (24.1%) followed by HR+/HER2+ tumors (27.8%). In his study, only TNBC was negatively associated with the proportion of mutation in the PIK3CA gene (p-value= 0.02) in comparison to HR+/HER2- tumors. In multivariate Cox’s regression analysis, the advanced pT stage and HR−/HER2- IHC group independently predicted worse overall survival. However, PIK3CA mutation status was not associated with survival. Conclusions: The PIK3CA mutation was relatively high in HR+ tumors. Mutation rates of PIK3CA in Ethiopian BC tumors are similar to those reported for other populations. This finding highlighted that molecular aberrations including mutations in a specific could give insight on prognosis and clinical outcome. Citation Format: Zelalem Desalegn Woldesonbet. Somatic mutations in the PIK3CA gene and its prognostic implications among Ethiopian Breast cancer patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr A018.

TWIST1/miR-199a axis promotes tumor aggressiveness through inhibiting oxidative phosphorylation in carcinomas

Background Metabolic reprogramming has emerged as a key hallmark of cancer progression, though its role in tumor aggressiveness is still evolving. Here, using a pan-cancer genome approach, we aimed to comprehensively assess the metabolic reprogramming involved in tumor aggressiveness in carcinomas and identify metabolic hubs which can be therapeutically targeted to treat aggressive tumors in the clinic. Methods In this study, we employed a stringent pan-cancer multi-omic metabolism-targeted differential expression approach to identify the metabolic hubs regulating tumor aggressiveness. mRNA, miRNA, DNA methylation and mutation profiling data of tumors representing 14 different types of carcinomas was downloaded from TCGA database. Cell line expression profiling and drug response data was downloaded from CCLE database. Pathway enrichment, GSEA, String protein-protein interaction, miRNA-mRNA prediction, network random-walk and CCLE drug response analyses were carried out. Results We identified downregulated expression of enzymes involved in oxidative phosphorylation as a key common factor across carcinomas, aligning with the Warburg effect. Additionally, we established that the decreased dependence on oxidative phosphorylation is driven by elevated expression of miR-199 family miRNAs that inhibit their expression at the post-transcriptional level. Furthermore, we identified the epithelial-to-mesenchymal transition-related transcription factor, TWIST1, as a master regulator of tumor aggressiveness by controlling miR-199a-3p and -5p expression. Random walk analysis of established miRNA-mRNA network identified NDUFA2, DLD, COX15, NDUFB5, and TIMM13 as crucial metabolic hubs downregulated as tumors become aggressive. Drug response analysis suggested that targeting PDGFR signaling may offer a novel therapeutic approach to counteract the aggressiveness driven by the loss of oxidative phosphorylation. Conclusion We identified TWIST1/miR-199a axis mediated suppression of oxidative phosphorylation as major metabolic contributor towards tumor aggressiveness in carcinomas. These insights underscore the critical interplay between metabolic reprogramming and tumor aggressiveness, opening avenues for potential metabolic therapies in clinical settings.

Comprehensive genetic profile of Chinese muscle-invasive bladder cancer cohort

ObjectiveThe aim of our study was to characterize the spectrum of mutations in muscle-invasive bladder cancer (MIBC) in the Chinese population, identifying mutational features and exploring potential therapeutic targets. MethodsWe collected samples from 62 Chinese patients with MIBC. For each patient, tumor tissues or blood samples were collected and sequenced by whole exome sequencing. ResultsOur findings revealed the most frequently mutated genes included TP53 (41%), TTN (41%), HYDIN (34%), FRG1 (33%), ZNF717 (23%), AHNAK2 (21%), MUC4 (21%), KMT2D (20%), CDC27 (18%) and IGSF3 (18%). The most frequently mutated DNA damage repair (DDR) genes were TP53 (49%), SMARCA4 (10%), ERCC2 (8%), BRAC2 (6%), HERC2 (6%), HLTF (6%), PALB2 (6%) and POLG (6%). Additionally, our analysis confirmed an association between DDR mutations and high TMB (P = 0.022). Significant differences in MSI were observed between smokers and nonsmokers (P = 0.022), drinkers and nondrinkers (P = 0.018). By analyzing the data of 323 white MIBC samples from TCGA database, we identified frequently mutated driver genes in both our cohort and TCGA white cohort, including TP53, KMT2D, KMT2C, and FGFR3. Our study also revealed genes with distinct mutation frequencies compared to the TCGA white cohort, including FRG1, CDC27, IGSF3, MUC16, and ARID1A. ConclusionsOur study provided comprehensive insights into genomic alterations in a cohort of Chinese MIBC, which could provide potential clues for clinical applications. MicroAbstractThis study aimed to characterize mutations in muscle-invasive bladder cancer (MIBC) in the Chinese population, identifying mutational features and potential therapeutic targets. Samples from 62 Chinese MIBC patients were sequenced using whole exome sequencing, revealing frequent mutations in genes like TP53, TTN, and HYDIN. The study also found associations between DNA damage repair mutations and high tumor mutational burden, as well as differences in mutational profiles between Chinese and white MIBC cohorts. These findings offer valuable insights for clinical applications in Chinese MIBC patients.

Evolution of Rapid Clonal Dynamics and Non-Cross-Resistance in Response to Alternating Targeted Therapy and Chemotherapy in BRAF-V600E-Mutant Colon Cancer.

Combined BRAF, MEK, and EGFR inhibition can induce clinical responses in BRAF-V600E-mutant colon cancer, but rapid resistance often occurs. We use serial monitoring of circulating tumor DNA cell-free plasma DNA (cfDNA) in a patient case study in addition to organoids derived from mouse models of BRAF-V600E-mutant intestinal cancer, which emulated the patient's mutational profile to assess drug treatment efficacy. We demonstrate dynamic evolution of resistance to combined EGFR/BRAF/MEK inhibition in a pediatric patient with metastatic BRAF-V600E-mutant, mismatch repair-stable colon cancer. Initial resistance to targeted therapy was associated with development of MET amplification. Sequential treatment with chemotherapy and targeted therapy resulted in clearing of the resistant MET-amplified clone. Rechallenge with combined BRAF/EGFR inhibition resulted in clinical and radiographic response, demonstrating these treatments may be non-cross-resistant. Tumor organoids were used to model clinical findings and demonstrated effectiveness of combined targeted therapy and chemotherapy. These findings suggest rational strategies for combining sequential chemotherapy and BRAF-/EGFR-directed therapy in BRAF-V600E-mutant colon cancer to prevent resistance and improve outcome. The data demonstrate rapid clonal dynamics in response to effective therapies in BRAF-V600E-mutant colon cancer that can be monitored by serial cfDNA analysis. Moreover, in mismatch repair-proficient BRAF-V600E-mutant colon cancers, combined EGFR and BRAF/MEK therapy is not cross-resistant with standard chemotherapy, suggesting new rational combination treatment strategies.

Engineered FnCas9 mediated mutation profiling for clarithromycin resistance in Helicobacter pylori strains isolated from Indian patients with gastrointestinal disorders

Helicobacter pylori is a highly prevalent gut pathogen with reported implications in a wide range of gastrointestinal disorders. Antibiotic based therapy, especially with clarithromycin is one of most effective treatment strategies against H. pylori. However, rising global prevalence of clarithromycin resistance in certain H. pylori strains, primarily attributed to point mutations in the 23 s ribosomal RNA coding gene, pose a major challenge in the effective eradication of this pathogen. There are a number of established methodologies devised for H. pylori mutation detection, so as to provide a tailored treatment plan to the patients and resist further transmissions of antibiotic resistant strains. However, there is no ‘gold standard’ method available to detect mutation status in clinical isolates of H. pylori from infected patients. CRISPR-Cas9 based technologies have revolutionized the field of mutation detection in biological samples, particularly during the recent COVID-19 pandemic. Although multiple assays have been reported for detection of H. pylori in clinical samples including CRISPR diagnostics (CRISPRDx) platforms, there is no such assay reported till date to detect specific mutations that confer antibiotic resistance to this pathogen. In this study, we have developed an assay using engineered FnCas9 (en31-FnCas9) protein to effectively detect the A2142G and A2143G mutations in the 23 s rDNA of H. pylori strains isolated from gastric biopsy samples. The data from in vitro cleavage assays and strip-based lateral flow tests using en31-FnCas9 and guide RNAs targeting the conserved and mutated loci of H. pylori 23 s rDNA are in perfect congruence with the data from Sanger sequencing and restriction fragment length polymorphism (RFLP) analysis. Our results indicate that en31-FnCas9 based mutation analysis can be deployed as an efficient diagnostic methodology to detect clarithromycin susceptibility in patients with suspected H. pylori infections.

Diagnosing recipient- vs. donor-derived posttransplant myelodysplastic neoplasm via targeted single-cell mutational profiling.

Distinguishing donor- vs. recipient-derived myelodysplastic neoplasm (MDS) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is challenging and has direct therapeutical implications. Here, we took a translational approach that we used in addition to conventional diagnostic techniques to resolve the origin of MDS in a 38-year-old patient with acquired aplastic anemia and evolving MDS after first allo-HSCT. Specifically, we used single-cell transcriptional profiling to differentiate between donor- and recipient-derived bone marrow cells and established a strategy that additionally allows identification of cells carrying the MDS-associated U2AF1S34Y variant. The patient exhibited mixed donor chimerism combined with severely reduced erythropoiesis and dysplastic morphology within the granulocytic and megakaryocytic lineage along with the MDS-associated U2AF1S34Y mutation in the bone marrow. Single-cell transcriptional profiling together with targeted enrichment of the U2AF1S34Y-specific locus further revealed that, while the immune compartment was mainly populated by donor-derived cells, myelopoiesis was predominantly driven by the recipient. Additionally, concordant with recipient-derived MDS, we found that U2AF1S34Y-mutated cells were exclusively recipient derived with X but not Y chromosome-specific gene expression. Our study highlights the clinical potential of integrating high-resolution single-cell techniques to resolve complex cases for personalized treatment decisions. The study was funded by intramural resources of the Charité- Universitätsmedizin Berlin and the Berlin Institute of Health.

At what cost? The impactof bacteriophage resistance on the growth kinetics and protein synthesis of Escherichia coli.

Cost of bacteriophage resistance (COR) is important in explaining processes of diversification and coexistence in microbial communities. COR can be expressed in different traits, and the lack of universally applicable methods to measure fitness trade-offs makes COR challenging to study. Due to its fundamental role in growth, we explored protein synthesis as a target for quantifying COR. In this study, the growth kinetics of three genome-sequenced strains of phage-resistant Escherichia coli, along with the phage-susceptible wild-type, were characterized over a range of glucose concentrations. Bioorthogonal non-canonical amino acid tagging (BONCAT) was used to track differences in protein synthetic activity between the wild-type and phage-resistant E. coli. Two of the resistant strains, with different levels of phage susceptibility, showed mucoid phenotypes corresponding with mutations in genes associated with the Rcs phosphorelay. These mucoid isolates, however, had reduced growth rates and potentially lower protein synthetic activity. Another resistant isolate with a different mutational profile maintained the same growth rate as the wild-type and showed increased BONCAT fluorescence, but its yield was lower. Together, these findings present different patterns of trade-offs resulting from the phage-induced mutations and demonstrate the potential applicability of BONCAT as a tool for measuring COR.

Mutational Stability Profiling and Functional Analysis of Spike Protein In Indian Sars Cov-2 Delta Variants: An In Silico Analysis

Mutational Stability Profiling and Functional Analysis of Spike Protein In Indian Sars Cov-2 Delta Variants: An In Silico Analysis

Validation of two predictive models for survival in anaplastic thyroid cancer (ATC)

BackgroundThe prognosis of patients with anaplastic thyroid cancer (ATC) remains dismal. A small portion of patients experience longterm survival and need to be identified before treatment allocation. Survival scores may guide clinicians making more informed decisions about treatment options and improve the understanding of patients’ prognosis. The aim of this study was to validate two prognostic scores using an independent dataset to analyze which prognostic index is superior in discriminating survival.MethodsThirty-four patients with histologically confirmed ATC diagnosed between January 2009 and December 2019 were consecutively treated at our department and evaluated. Next generation sequencing was performed in 7 (21%) patients, but no druggable mutation was found. 50% of all patients received surgery and 56% were treated with chemoradiotherapy. The median radiation dose in equivalent dose in 2 Gy fractions (EQD2) was 50 Gy (SD:21 Gy). The study compared the discrimination of the Sugitani Prognostic Index (SPI) and the Marchand-Crety Prognostic Score (MCPS) using concordance statistics, area under the receiver-operating characteristics curve (AUC), net reclassification index, and integrated discrimination improvement for 6-month survival.ResultsThe median survival of the entire cohort was 5 months (range: 1-133). The AUC for 6-month survival was 0.85 (95% confidence interval [CI]:0.72–0.97) for SPI and 0.69 (95% CI: 0.56–0.83) for MCPS (p < 0.0001). Using the net reclassification index (NRI), 73% of patients were correctly reclassified using SPI instead of MCPS for 6-month survival (p = 0.0237).ConclusionThe SPI was more accurate than the MCPS to determine patients’ life expectancies and should be recommended for clinical guidance and treatment allocation. In the last decade, comprehensive genetic profiling of actionable mutations in ATC has become vital to guide targeted therapy.

Massive parallel sequencing of head and neck conventional squamous cell carcinomas: A comprehensive review.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and is a cause of significant mortality and morbidity. The epidemiology of this cancer varies worldwide due to either genetic differences in populations or differences in carcinogen exposure. The application of massive parallel sequencing-based techniques in HNSCC should provide a helpful understanding of the genetic alterations that eventually lead to HNSCC development and progression, and ideally, could be used for personalized therapy. In this review, the reader will find an overview of the mutational profile of conventional HNSCC according to published results on massive parallel sequencing data that confirm the pivotal role of TP53 and the frequent involvement of CDKN2A and PIK3CA. The reader will also find a more detailed description of the genes, such as NOTCH1 and FBXW7, that were not identified in HNSCCs before the development of these techniques, the differences that can be site-specific, such as the different mutational signatures that indicate specific carcinogens for various subsites of the head and neck, and finally, the actionability of these findings that should allow more personalized therapy for patients.

SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies.

Many tumours show deficiencies in DNA damage response (DDR), which influence tumorigenesis and progression, but also expose vulnerabilities with therapeutic potential. Assessing which patients might benefit from DDR-targeting therapy requires knowledge of tumour DDR deficiency status, with mutational signatures reportedly better predictors than loss of function mutations in select genes. However, signatures are identified independently using unsupervised learning, and therefore not optimised to distinguish between different pathway or gene deficiencies. We propose SNMF, a supervised non-negative matrix factorisation that jointly optimises the learning of signatures: (1) shared across samples, and (2) predictive of DDR deficiency. We applied SNMF to mutation profiles of human induced pluripotent cell lines carrying gene knockouts linked to three DDR pathways. The SNMF model achieved high accuracy (0.971) and learned more complete signatures of the DDR status of a sample, further discerning distinct mechanisms within a pathway. Cell line SNMF signatures recapitulated tumour-derived COSMIC signatures and predicted DDR pathway deficiency of TCGA tumours with high recall, suggesting that SNMF-like models can leverage libraries of induced DDR deficiencies to decipher intricate DDR signatures underlying patient tumours. https://github.com/joanagoncalveslab/SNMF .

Atypical Teratoid Rhabdoid Tumor of the Brain in a Young Adult With Down Syndrome: Case Report and Literature Review.

Atypical teratoid/rhabdoid tumor (ATRT) is an aggressive, malignant embryonal tumor with dismal long-term survival despite aggressive multimodal therapy. While this tumor typically presents in infancy or early childhood, there are published case reports of adult-onset ATRT. Making prognostic conclusions or therapeutic decisions for this older patient population remains challenging due to the paucity of these reports. A 25-year-old female with Down syndrome presented with dysphagia and facial droop and was found to have an avidly enhancing, cerebellopontine angle mass. Histology demonstrated sheets of rhabdoid cells with loss of INI1 expression, pathognomonic for ATRT. Further sequencing detected a frameshift SMARCB1 mutation and methylation profiling matched with high confidence to the MYC subclass of ATRT. The patient was treated with subtotal surgical resection and focal proton beam irradiation, followed by chemotherapy on a modified regimen due to concern for heightened risk of treatment-related toxicity. On most recent follow-up 22 months from diagnosis, the patient remains without evidence of disease. This report represents the first known case of ATRT in a young adult patient with Down syndrome, offering unique mechanistic insight into the tumorigenesis of ATRT. Further studies are needed to define an appropriate risk-adapted and standardized therapeutic approach for this patient population.

Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach

Biological mechanisms related to cancer development can leave distinct molecular fingerprints in tumours. By leveraging multi-omics and epidemiological information, we can unveil relationships between carcinogenesis processes that would otherwise remain hidden. Our integrative analysis of DNA methylome, transcriptome, and somatic mutation profiles of kidney tumours linked ageing, epithelial–mesenchymal transition (EMT), and xenobiotic metabolism to kidney carcinogenesis. Ageing process was represented by associations with cellular mitotic clocks such as epiTOC2, SBS1, telomere length, and PBRM1 and SETD2 mutations, which ticked faster as tumours progressed. We identified a relationship between BAP1 driver mutations and the epigenetic upregulation of EMT genes (IL20RB and WT1), correlating with increased tumour immune infiltration, advanced stage, and poorer patient survival. We also observed an interaction between epigenetic silencing of the xenobiotic metabolism gene GSTP1 and tobacco use, suggesting a link to genotoxic effects and impaired xenobiotic metabolism. Our pan-cancer analysis showed these relationships in other tumour types. Our study enhances the understanding of kidney carcinogenesis and its relation to risk factors and progression, with implications for other tumour types.

Evaluation of Heterogeneity in the Coding Region of BRAF, MAP2K1, and MAP2K2 Genes in Primary and Metastatic Melanomas.

The incidence of melanoma has been increasing in recent decades. BRAF mutations appear in 50%-70% of melanomas. The BRAF-targeted therapy increased the disease-free survival of patients with metastatic melanoma, but this response may be short, due to several resistance mechanisms, such as the presence of other subclones with mutations. Evaluation of mutations and heterogeneity in the coding region of the BRAF, MAP2K1, and MAP2K2 genes in primary and metastatic melanomas. Twenty-seven samples of primary and metastatic superficial spreading melanoma (SSM) and acral lentiginous melanoma (ALM) were analyzed for BRAF, MAP2K1, and MAP2K2 mutations using the next-generation sequencing technique. In ALM, the mutation rate found was 50% in the BRAF and MAP2K1 genes and 28.6% in MAP2K2. In the SSM, BRAF was mutated in 76.9%, MAP2K1 in 30.8%, and MAP2K2 in 23.2% of the cases. All samples were formed by distinct tumor subclones in the same lesion. Intertumoral heterogeneity was present between primary and metastatic lesions of ALM in BRAF, MAP2K1, and MAP2K2; the cases of SSM were heterogeneous for BRAF and MAP2K1. We sought to evaluate the mutations in the BRAF, MAP2K1, and MAP2K2 genes, revealing a heterogeneous mutation profile in samples of ALM and SSM.

Transcriptomic, mutational and structural bioinformatics approaches to explore the therapeutic role of FAP in predominant cancer types

Fibroblast activating protein (FAP) is a cell surface marker of cancer-associated fibroblasts with a distinct pro-tumorigenic role. The present study analyzed the pan-cancer expression; and clinical and mutational profiles of the FAP coding gene. Molecular dynamics simulation (MDS) deciphered the backbone dynamics and energetics of FAP. Virtual screening and subsequent pharmacokinetic-profiling (PK) filtered lead molecules, which were subjected to molecular docking. MDS projected a stable trajectory for the protein, as dynamics evidenced by low residue-level fluctuations, stable backbone dynamics, and energetics. Around five stabilization and deleterious mutations in the catalytic domain were identified. The low binding energy (BE) profiles from molecular docking studies screened the top five lead molecules for site-specific intermolecular interaction studies. Lead-16 (ZINC000245289699) exhibited a significant BE and inhibition constant of −6.87 kcal/mol and 12.27 μM, respectively, across FAP and its mutants. Interestingly, the docked complexes of Lead-16 interacted with the catalytic triad residues (S624, D702, and H734). The docked complexes of Lead-16 with FAP showed lower average root-mean-square fluctuations compared to the unbound protein, suggesting a stable ligand–protein complex. The tumor-specific expression and its critical overall survival suggest the inhibitors of FAP for potential cancer therapeutic intervention and hindering tumor microenvironment-driven cancer progression.

Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana

Abstract Botswana, like the rest of the world, has been significantly impacted by SARS-CoV-2. In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.1.529.5.3.1.1.1.1.1.1.74.1 (alias FN.1, clade 22E). These genomes were sourced from both epidemiologically linked and unlinked samples collected in three close locations within the district of Greater Gaborone. In this study, we assessed the worldwide prevalence of the FN.1 lineage, evaluated its mutational profile, and conducted a phylogeographic analysis to reveal its global dispersal dynamics. Among approximately 16 million publicly available SARS-CoV-2 sequences generated by September 30, 2023, only 87 were of the FN.1 lineage, including 22 from Botswana, 6 from South Africa, and 59 from the United Kingdom. The estimated time to the most recent common ancestor (tMRCA) of the 87 FN.1 sequences was October 22, 2022 (95% highest posterior density (HPD): September 02, 2022 - November 24, 2022), with the earliest of the 22 Botswana sequences having been sampled on December 7, 2022. Discrete trait reconstruction of FN.1 identified Botswana as the most probable place of origin. The FN.1 lineage is derived from the BQ.1.1 lineage and carries two missense variants in the Spike protein, S:K182E in NTD and S:T478R in RDB. Among the over 90 SARS-CoV-2 lineages circulating in Botswana between September 2020 and July 2023, FN.1 was most closely related to BQ.1.1.74 based on maximum likelihood phylogenetic inference, differing only by the S:K182E mutation found in FN.1. Given the early detection of numerous novel variants from Botswana and its neighboring countries, our study underscores the necessity of continuous surveillance to monitor the emergence of potential VOCs, integrating molecular and spatial data to identify dissemination patterns enhancing preparedness efforts.

Elevated risk of lung cancer among asian American females who have never smoked: an emerging cancer disparity.

Lung cancer is a leading cause of cancer mortality for most ethnic groups of Asian American females, including Chinese, Korean, Japanese, and Vietnamese Americans, a striking pattern given the exceedingly low prevalence of smoking among Asian American females in the general population. Recent research demonstrates that among Asian American females diagnosed with lung cancer, the vast majority of patients have never smoked, as high as > 80% among Chinese and Asian Indian American females. Despite declining rates in lung cancer overall in the United States, rates among Asian American females who have never smoked appear to be increasing. This Commentary articulates extant knowledge, based on studies in Asia, of a range of risk factors such as a family history of lung cancer, history of lung diseases including tuberculosis and chronic obstructive pulmonary diseases, exposure to cooking fumes and second-hand smoke, and various putative risk factors. Unique mutational profiles at the tumor level, including higher prevalence of EGFR mutations among Asian populations, highlight the importance of tumor genomic testing of newly-diagnosed patients. Additional research is essential, given the high burden of disease among Asian American females who have never smoked, and limited knowledge regarding contributing risk factors specific to Asian American females, as the risk factors identified in Asians living in Asia may not apply.

Distinct metabolic phenotype renders β-catenin mutant hepatocellular carcinoma susceptible to treatment-induced ischemia.

Transarterial chemoembolization (TACE) is the most common treatment for hepatocellular carcinoma (HCC) worldwide; however, response rates and durability vary widely. With the growing armamentarium of therapies for HCC patients, identifying predictors of response to TACE has become increasingly important for a patient population with limited hepatic reserve. We hypothesized that a distinct metabolic phenotype associated with β-catenin pathway mutations render HCC tumors more susceptible to TACE-induced ischemia. HCC patients referred for TACE were enrolled in a prospective cohort study at two academic medical centers from April 2016 to October 2021. Liver biopsies were acquired at the time of TACE, and mutational profiles were determined using next generation sequencing. Tumor response was determined by MRI using modified Response Evaluation Criteria in Solid Tumors. HCC cell lines with and without B-catenin mutations were grown in standard and ischemic cell culture conditions (1% O 2 , low nutrient media). Cell viability was measured by WST-1 reagent and Annexin-V PI assay. ATP concentration and metabolites were measured using CellTiter Glo and a YSI biochemical analyzer, respectively. Mitochondrial function was assessed through Seahorse XF Mito Stress Test. 53 HCC tumors from 50 HCC patients were biopsied prior to TACE, including 22/53 (41.5%) tumors with β-catenin pathway mutations. Despite larger tumor size (4.9 cm vs 3.0 cm p=0.01), tumors with these mutations demonstrated increased rates of complete response after TACE at first imaging (9/22, 40.9% vs 6/31, 19.4%, p=0.06) and best response (12/22, 54.5% vs 7/31, 22.6%, p=0.02), as well as a longer time to tumor progression (median not yet reached vs 8.3 months, p=0.02). In vitro modeling confirmed that β-catenin mutant HCC cells have reduced viability (21.4% vs 59.9%, p<0.01) and ATP levels (8.47 vs 4.26 pM/cell, p<0.001) under ischemic conditions compared to β-catenin wild type HCC cells. β-catenin mutant HCC cells had a dramatic increase in their susceptibility to glycolysis inhibition that was not seen in wild type HCC cells (0.09 vs 0.79 IC50 ration for ischemic vs standard conditions, p=0.004), suggesting a change from predominantly aerobic to anaerobic metabolism under ischemia specific to β-catenin mutant. This was further supported by increased sensitivity of β-catenin mutant cells to inhibition of the electron transport chain (43.9% vs 59.5%, p=0.02,) as well as significantly higher basal oxygen consumption rates (0.74 vs 0.39 pmoles/min, p=0.04), maximal respiratory capacity (1.46 vs 0.51 pmoles/min, p=0.01) and ATP-linked respiration (0.58 vs 0.29 pmoles/min, p=0.04). HCC tumors with activating B-catenin pathway mutations demonstrate a superior response to TACE, driven by enhanced susceptibility to ischemia due to a greater dependence on oxidative phosphorylation for bioenergetic homeostasis. These findings hold the potential to provide a molecular basis for treatment selection in patients with HCC. With the growing armamentarium of locoregional and systemic therapies for patients with HCC, identifying predictors of response to individual therapies has become increasingly important for a patient population with limited hepatic reserve. Current treatment guidelines fail to incorporate molecular biomarkers to inform therapy. In a prospective clinical study of HCC patients undergoing transarterial chemoembolization (TACE), we demonstrated that tumors with activating mutations in the Wnt/B-catenin pathway have increased rates of complete response and longer time to local progression. We further characterized this finding in vitro by modeling the post-TACE ischemic environment and demonstrated that B-catenin mutant HCC cells have a distinct metabolic phenotype that renders this subtype more susceptible to ischemia. These findings provide the rationale for genotype-based strategies to enable precision medicine for patients with HCC patients.

Analysis of shared variants between cancer biospecimens.

Mutational data from multiple solid and liquid biospecimens of a single patient is often integrated to track cancer evolution. However, there is no accepted framework to resolve if individual samples from the same individual share variants due to common identity versus coincidence. Utilizing 8,000 patient tumors from The Cancer Genome Atlas (TCGA) across 33 cancer types, we estimated background rates of co-occurrence rates of mutations between discrete pairs of samples across cancers and by cancer type. We developed a mutational profile similarity score (MPS) that uses a large background database to produce confidence estimates that two tumors share a unique, related molecular profile. The MPS algorithm was applied to randomly paired tumor profiles, including patients who underwent repeat solid tumor biopsies sequenced with MSK-IMPACT (n=53,113). We also evaluated the MPS in sample pairs from single patients with multiple cancers (n=2,012), as well as patients with plasma and solid-tumor variant profiles (n=884 patients). In unrelated tumors, nucleotide-specific variants are shared in 1.3% (cancer-type agnostic) and in 10-13% (cancer-type specific) of cases. The mutational profile similarity (MPS) method contextualized shared variants to specify whether patients had a single cancer versus multiple distinct cancers. When multiple tumors were compared from the same patient, and an initial clinicopathologic diagnosis was discordant with molecular findings, the MPS anticipated future diagnosis changes in 28% of examined cases. Use of a novel shared variant framework can provide information to clarify the molecular relationship between compared biospecimens with minimal required input.