Specific Mutation Patterns Research Articles

Mutations in the X Gene of the Hepatitis B Virus and Their Influence on Outcome CHB Infection in Three-Generations in the Family

Background: The occurrence of specific mutations within the Hepatitis B virus (HBV) genome is associated with the progression of chronic hepatitis B infection towards more severe outcomes. Objectives: This study aimed to investigate mutational patterns in the X-gene and their influence on the outcome of chronic HBV infection (CHB) across three generations in a family. Methods: Ninety CHB patients, meeting the inclusion criteria, were recruited from cases referred to the Center of Hepatology at Golestan University of Medical Sciences between September 2020 and January 2021. The HBx gene was amplified using semi-nested PCR from serum samples and then subjected to sequencing. Results: A comparison of the sequences from CHB patients indicated that children and mothers in the two-generation group exhibited the highest similarity (79.3%) in the X-gene, with the lowest mutation rate (20.7%). The N-terminal region of the X-gene showed the highest mutation frequency in the three-generation group, including C1491G (25%), G1613T (23.9%), C1500T (43.4%), and G1658T (33.4%). The mutation rate was notably higher in HBeAg-negative patients across the three groups compared to HBe-Ag-positive CHB patients, with a statistically significant difference (P = 0.03). A1762T/G1764A mutations were observed in 15.6% of patients, and their presence showed a significant difference (P = 0.03). Additionally, in the three-generation group, a silent mutation (A1727G, 10%) and a missense mutation (A1727T, 30%) were detected. Conclusions: Specific mutational patterns in the HBx gene may be valuable in predicting clinical outcomes in CHB patients and could serve as warning indicators for increased susceptibility to hepatocellular carcinoma (HCC).

Mutational signatures and their association with cancer survival and gene expression in multiple cancer types.

Different endogenous and exogenous mutational processes cause specific patterns of somatic mutations and mutational signatures. Although their biological research has been intensive, there are only rare studies assessing the possible prognostic role of mutational signatures. We used data from The Cancer Genome Atlas to study the associations between the activity of the mutational signatures and four survival endpoints in 18 types of malignancies. We further explored the prognostic differences according to, for example, the HPV status in head and neck squamous cell carcinomas and smoking status in lung cancers. The predictive power of the signatures over time was evaluated with a dynamic area under the curve model, and the links between mutational signature activities and differences in gene expression patterns were analyzed. In 12 of 18 studied cancer types, we identified at least one mutational signature whose activity predicted survival outcomes after adjusting for the established prognostic factors. For example, overall survival was associated with the activity of mutational signatures in nine cancer types and disease-specific survival in seven cancer types. The clock-like signatures SBS5 and SBS40 were most commonly associated with survival endpoints. The genes of the myosin binding protein and melanoma antigen families were among the most substantially dysregulated genes between the signatures of low and high activity. The differences in gene expression also revealed various enriched pathways. Based on these data, specific mutational signatures associate with the gene expression and have the potential to serve as strong prognostic factors in several cancer types.

Unveiling divergent treatment prognoses in IDHwt-GBM subtypes through multiomics clustering: a swift dual MRI-mRNA model for precise subtype prediction

BackgroundIDH1-wildtype glioblastoma multiforme (IDHwt-GBM) is a highly heterogeneous and aggressive brain tumour characterised by a dismal prognosis and significant challenges in accurately predicting patient outcomes. To address these issues and personalise treatment approaches, we aimed to develop and validate robust multiomics molecular subtypes of IDHwt-GBM. Through this, we sought to uncover the distinct molecular signatures underlying these subtypes, paving the way for improved diagnosis and targeted therapy for this challenging disease.MethodsTo identify stable molecular subtypes among 184 IDHwt-GBM patients from TCGA, we used the consensus clustering method to consolidate the results from ten advanced multiomics clustering approaches based on mRNA, lncRNA, and mutation data. We developed subtype prediction models using the PAM and machine learning algorithms based on mRNA and MRI data for enhanced clinical utility. These models were validated in five independent datasets, and an online interactive system was created. We conducted a comprehensive assessment of the clinical impact, drug treatment response, and molecular associations of the IDHwt-GBM subtypes.ResultsIn the TCGA cohort, two molecular subtypes, class 1 and class 2, were identified through multiomics clustering of IDHwt-GBM patients. There was a significant difference in survival between Class 1 and Class 2 patients, with a hazard ratio (HR) of 1.68 [1.15–2.47]. This difference was validated in other datasets (CGGA: HR = 1.75[1.04, 2.94]; CPTAC: HR = 1.79[1.09–2.91]; GALSS: HR = 1.66[1.09–2.54]; UCSF: HR = 1.33[1.00–1.77]; UPENN HR = 1.29[1.04–1.58]). Additionally, class 2 was more sensitive to treatment with radiotherapy combined with temozolomide, and this sensitivity was validated in the GLASS cohort. Correspondingly, class 2 and class 1 exhibited significant differences in mutation patterns, enriched pathways, programmed cell death (PCD), and the tumour immune microenvironment. Class 2 had more mutation signatures associated with defective DNA mismatch repair (P = 0.0021). Enriched pathways of differentially expressed genes in class 1 and class 2 (P-adjust < 0.05) were mainly related to ferroptosis, the PD-1 checkpoint pathway, the JAK-STAT signalling pathway, and other programmed cell death and immune-related pathways. The different cell death modes and immune microenvironments were validated across multiple datasets. Finally, our developed survival prediction model, which integrates molecular subtypes, age, and sex, demonstrated clinical benefits based on the decision curve in the test set. We deployed the molecular subtyping prediction model and survival prediction model online, allowing interactive use and facilitating user convenience.ConclusionsMolecular subtypes were identified and verified through multiomics clustering in IDHwt-GBM patients. These subtypes are linked to specific mutation patterns, the immune microenvironment, prognoses, and treatment responses.

Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma

Cholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed not only commonly mutated genes, such as TP53, JAK3, and KMT2C, consistent with the reports in CCA, but also specific mutation patterns in each cell line. In addition, specific expression patterns with distinct biological functions and pathways involved were also observed in the PDPCs at the transcriptomic level. Furthermore, the drug-sensitivity results revealed that the PDPCs exhibited different responses to the six commonly used compounds. Our findings indicate that the established PDPCs can serve as novel in vitro reliable models to provide a crucial molecular basis for improving the understanding of tumorigenesis and its treatment.

Identifying PTPRJ As a Novel Mediator of CEBPA-Mutated AML

10-20% of acute myeloid leukaemia (AML) cases in children and adults carry mutations in the transcription factor CCAAT/enhancer binding protein alpha (CEBPA). CEBPA is transcribed from a single exon and produces two isoforms, p30 and p42, with characteristic mutations, either frameshift mutations in the N-terminal portion ( CEBPA Nterm) leading to production of only the p30 isoform, or in frame mutations in the C-terminal portion ( CEBPA Cterm), disrupting DNA binding. The most frequent secondary driver mutation in CEBPA-mutated AML, is the second allele of CEBPA. Additionally, in rare germline CEBPA cases, the founding mutation is usually CEBPA Nterm, with allindividuals showing acquisition of a second hit mutation in the CEBPA Cterm on the alternate CEBPA allele at the time of AML diagnosis, which has near 100% penetrance in these families. This highlights a strong selective pressure for this very specific biallelic mutation pattern. We have developed zebrafish models with germline cebpa Nterm and cebpa Cterm mutations that faithfully recapitulates the disease, with all homozygous and double heterozygous mutants showing loss of mature myeloid cells, and impaired survival. All double or compound mutants die by 10 weeks of age, with haematopoietic stem and progenitor cell (HSPC) expansion, and leukaemia in around 30% of these animals. Our model also demonstrates distinct phenotypes for cebpa Nterm and cebpa Cterm mutations during developmental haematopoiesis prior to leukaemia onset. We observed that cebpa Nterm and cebpa Cterm mutations have opposite effects on the expression of c-myb, a transcription factor expressed by proliferating HSPC, from 3 days post fertilization. cebpa Nterm/Nterm mutants show an increase in c-myb while cebpa Cterm/Cterm show reduced c-myb expression during development. To uncover the mechanisms by which cebpa Nterm and cebpa Cterm effect HSPCs we undertook RNASeq of sorted Tg(cd41:eGFP) lo HSPCs from fish of all possible genotype combinations. We identified both shared and unique expression profiles between genotypes. We also identified 4 genes that that were differentially regulated in both cebpa Nterm/Nterm and cebpa Cterm/Cterm HSPC, but in opposing vectors (upregulated in cebpa Cterm/Cterm and downregulated in cebpa Nterm/Nterm) (Figure 1). We hypothesised that these 4 genes are candidate drivers of selective pressure for the common CEBPA Cterm/Ntermmutation combination in human AML, and thus the malignant phenotype it confers. One of these candidate genes, PTPRJ, has also recently been identified as a frequently mutated gene in CEBPA-mutated AML in children thereby validating the relevance of our dataset and our approach. To define the effects of these 4 candidate genes we then conducted an F0 CRISPR knock-out screen in all cebpa mutant combinations in our zebrafish model, using c-myb expression as a phenotypic readout. We identified ptprja as our primary candidate gene and showed that loss of ptprja alone and in combination with cebpa Cterm/+ reduced expression of c-myb but had no effect on expression of c-myb in cebpa Cterm/Cterm, indicating that ptprja loss reduces c- myb-expressing HSPC and that this is dependent on functional cebpa DNA binding. We then examined the impact of ptprja knockout in juvenile zebrafish. Homozygous and double heterozygous mutants develop a pre-leukaemia expansion of HSPC before they succumb to death. We showed that that loss of ptprja in cebpa Cterm/Cterm fish accelerates this pre-leukaemic expansion of Tg(cd41:eGFP) lo HSPCs in 4 week fish (Figure 2). We also showed an opposing effect in the cebpa Nterm/Nterm mutants at 2 weeks, where loss of ptprja resulted in decreased pre-leukemic expansion of HSPC. These data indicate a role for PTPRJ in mediating HSPC expansion in CEBPA-mutated AML and suggest that PTPRJ may mediate the mechanism of clonal selection in those with a CEBPA mutation that drives the acquisition of a second CEBPA mutation on the opposing allele, leading to the common CEBPA Cterm/Nterm in patients with CEBPA-mutated AML.

Early Identification of Refractory/Relapsed Diffuse Large B Cell Lymphoma with Serial Ctdna Sampling

Background: Diffuse Large B Cell Lymphoma (DLBCL) is an aggressive lymphoma that is curable in 60% of patients with chemoimmunotherapy. Outcomes are poor for those experiencing relapsed or refractory disease (rrDLBCL), particularly for patients with primary refractory disease (REFR, &amp;lt; 9 months from diagnosis) and early relapse (ER, 9 months to 2 years from diagnosis). Some of these patients would be candidates for chimeric antigen receptor T cell therapy (CART) in second line, where outcomes are superior when the disease burden is low. Therefore, exploring strategies to identify these high-risk patients early is important. Plasma circulating tumor DNA has been shown to be prognostic in various DLBCL cohorts. Method: We developed a custom panel of 170 genes to identify early treatment failure in a cohort of 171 patients that had profiling performed on 323 plasma samples. Plasma samples were taken serially starting at diagnosis and as patients progressed through frontline treatment. All plasma samples underwent DNA extraction, library preparation and subsequent sequencing using a panel of DLBCL related genes at high read depth (~1000x). Single nucleotide variant (SNV) calling was carried out using a custom pipeline including paired normal DNA for improved somatic variant detection. ctDNA fraction was estimated based on the highest variant allele fraction detected, using a loss of heterozygosity somatic model. Our ctDNA analysis focused on samples at diagnosis, cycle 2 of therapy, and end of treatment in order to identify early determinants of refractory disease. Changes in ctDNA levels between time points were represented as log2 ratio of ctDNA fraction. Results: rrDLBCL cases were separated into 3 categories based on the time between diagnosis and progressive disease (PD): 47 REFR, 34 ER, and 31 late relapse (LR, &amp;gt;24 months). The remaining patients were disease free after frontline therapy for over 24 months (CR, n=59), resulting in a cohort enriched for rrDLBCL (65% of cases). The average international prognostic index (IPI) of each group at diagnosis was REFR=3.38, ER=2.87, LR=2.81, and CR=2.41. Cell of Origin, as determined by Hans algorithm, showed a higher number of non-GCB samples in ER and LR groups (53% and 60%, respectively) while REFR and CR displayed increased GCB cases (63% and 66%, respectively). The REFR patients were significantly more likely to be of a 4/5 IPI score at diagnosis than other groups (p=0.0203). Progression-free survival (PFS2) at relapse therapy for REFR (median=0.29 years) was shorter when compared to both ER (p=0.0104, median=0.44 years) and LR (p=0.0012, median=0.80 years). Using the diagnostic plasma sample, there was no significant difference in ctDNA fraction in any of the three groups. When the sample with the highest ctDNA fraction was compared between patients, REFR had significantly higher levels than LR and CR, consistent with a higher overall tumor burden (p=0.001 and 0.026, respectively). There was a trend towards higher ctDNA fraction at the end of treatment in both REFR and ER groups. As ctDNA dynamics are known to be informative of molecular response, we compared patients using the change in ctDNA fraction at cycle 2 of therapy (log2 ratio). This value was significantly different in REFR patients (p=0.0073 vs ER), consistent with a lower rate of molecular response to treatment. Conclusions: While refractory and later relapsed DLBCL have similar ctDNA features at diagnosis, we find they have distinct ctDNA dynamics during treatment. REFR had higher maximal ctDNA levels across time points and both REFR and ER patients exhibited higher levels of ctDNA at end of treatment. Moreover, patients with minimal change in ctDNA levels at cycle 2 of therapy are at a high risk of treatment failure and refractory disease. Further exploration of the specific mutational patterns is ongoing. These results could enable the earlier identification of rrDLBCL and facilitate the prioritization of approaches for therapeutic intervention in rrDLBCL.

Impact of core protein naturally selected mutants associated with HBeAg-negative status in HBV biosynthesis.

Hepatitis B e antigen (HBeAg) loss represents a late stage of chronic hepatitis B virus (HBV) infection associated with a drastic decrease in HBV-DNA, a lower risk of disease progression, and the occurrence of several mutations in the preCore/core region. However, the underlying mechanisms supporting the downregulation of viral replication have yet to be elucidated. In the present study, the analysis of the frequency of subgenotype D1 core protein (HBc) mutations associated with HBeAg status revealed a higher mutation rate in HBeAg-negative sequences compared to HBeAg-positive ones. Particularly, 22 amino acids exhibited a higher frequency of mutation in HBeAg-negative sequences, while the remaining residues showed a high degree of conservation. Subsequently, the assessment of HBc mutants derived from HBeAg-negative patients in viral structure and replicative capacity revealed that HBc mutations have the ability to modulate the subcellular localization of the protein (either when the protein was expressed alone or in the context of viral replication), capsid assembly, and, depending on specific mutation patterns, alter covalently closed circular DNA (cccDNA) recycling and up- or downregulate viral replication. In conclusion, HBc mutations associated with HBeAg-negative status impact on various stages of the HBV life cycle modulating viral replication during the HBeAg-negative stage of infection.

Non-homogeneous Poisson and renewal processes as spatial models for cancer mutation

Advances in sequencing technology assisted biologists in revealing signatures of DNA cancer mutation process and in demonstrating the mutagenesis behind. However, most of these signatures proposed by majority of work focus only on the type and frequency of mutations, without considering spatial information which is non-negligible in exploring mechanisms of mutation occurrence, e.g., Kataegis. Statistical characterization of the distance between consecutive mutations can give us relative spatial information; however, it ignores location information which is as important as distance information. In this work, we assume that DNA cancer mutations are location-dependent and that integrating the two variables, location and inter-distance, is beneficial to study DNA cancer mutation processes more accurately. Particularly, instead of following a specific distribution over the whole DNA sequence, we found out that the distribution of distance between successive mutations alternates between exponential and power-law distributions. Apart from this, the parameters of either of the two distributions vary with DNA locations. The cancers with kataegis phenomenon, a specific mutation pattern caused by abnormal activity of APOBEC protein family, are more likely to be accompanied by higher parameter values of distance distribution, implying higher occurrence rate of mutation. Therefore, we propose non-homogeneous Poisson and Renewal processes to spatially model DNA cancer mutations and to describe mutation patterns quantitatively and more accurately through a statistical perspective.

Clonal dynamics and copy number variants by single-cell analysis in leukemic evolution of myeloproliferative neoplasms.

Transformation from chronic (CP) to blast phase (BP) in myeloproliferative neoplasm (MPN) remains poorly characterized, and no specific mutation pattern has been highlighted. BP-MPN represents an unmet need, due to its refractoriness to treatment and dismal outcome. Taking advantage of the granularity provided by single-cell sequencing (SCS), we analyzed paired samples of CP and BP in 10 patients to map clonal trajectories and interrogate target copy number variants (CNVs). Already at diagnosis, MPN present as oligoclonal diseases with varying ratio of mutated and wild-type cells, including cases where normal hematopoiesis was entirely surmised by mutated clones. BP originated from increasing clonal complexity, either on top or independent of a driver mutation, through acquisition of novel mutations as well as accumulation of clones harboring multiple mutations, that were detected at CP by SCS but were missed by bulk sequencing. There were progressive copy-number imbalances from CP to BP, that configured distinct clonal profiles and identified recurrences in genes including NF1, TET2, and BCOR, suggesting an additional level of complexity and contribution to leukemic transformation. EZH2 emerged as the gene most frequently affected by single nucleotide and CNVs, that might result in EZH2/PRC2-mediated transcriptional deregulation, as supported by combined scATAC-seq and snRNA-seq analysis of the leukemic clone in a representative case. Overall, findings provided insights into the pathogenesis of MPN-BP, identified CNVs as a hitherto poorly characterized mechanism and point to EZH2 dysregulation as target. Serial assessment of clonal dynamics might potentially allow early detection of impending disease transformation, with therapeutic implications.

Genomic and transcriptional characterization of early esophageal squamous cell carcinoma

BackgroundEsophageal squamous cell carcinoma (ESCC) is a highly heterogeneous cancer that lacks comprehensive understanding and effective treatment. Although multi-omics study has revealed features and underlying drivers of advanced ESCC, research on molecular characteristics of the early stage ESCC is quite limited.Materials and methodsWe presented characteristics of genomics and transcriptomics in 10 matched pairs of tumor and normal tissues of early ESCC patients in the China region.ResultsWe identified the specific patterns of cancer gene mutations and copy number variations. We also found a dramatic change in the transcriptome, with more than 4,000 genes upregulated in cancer. Among them, more than one-third of HOX family genes were specifically and highly expressed in early ESCC samples of China and validated by RT-qPCR. Gene regulation network analysis indicated that alteration of Hox family genes promoted the proliferation and metabolism remodeling of early ESCC.ConclusionsWe characterized the genomic and transcriptomic landscape of 10 paired normal adjacent and early ESCC tissues in the China region, and provided a new perspective to understand the development of ESCC and insight into potential prevention and diagnostic targets for the management of early ESCC in China.

In Vitro and In Vivo Models for Metastatic Intestinal Tumors Using Genotype-Defined Organoids.

It has been established that the accumulation of driver gene mutations causes malignant progression of colorectal cancer (CRC) through positive selection and clonal expansion, similar to Darwin's evolution. Following this multistep tumorigenesis concept, we previously showed the specific mutation patterns for each process of malignant progression, including submucosal invasion, epithelial mesenchymal transition (EMT), intravasation, and metastasis, using genetically engineered mouse and organoid models. However, we also found that certain populations of cancer-derived organoid cells lost malignant characteristics of metastatic ability, although driver mutations were not impaired, and such subpopulations were eliminated from the tumor tissues by negative selection. These organoid model studies have contributed to our understanding of the cancer evolution mechanism. We herein report the in vitro and in vivo experimental protocols to investigate the survival, growth, and metastatic ability of intestinal tumor-derived organoids. The model system will be useful for basic research as well as the development of clinical strategies.

Analysis of rod-cone dystrophy genes reveals unique mutational patterns

BackgroundRod-cone dystrophy (RCD) is the most common inherited retinal disease that is characterised by the progressive degeneration of retinal photoreceptors. RCD genes classification is based exclusively on gene mutations’ prevalence...

Specific Nucleotide Substitutions and Stressors Erode Highly Conserved Genomic Regions in Acute Myelogenous Leukemia

Background: "Leukemia stressors” refer to extrinsic factors that may facilitate clonal progression. We previously reported that smoking initiates unique leukemogenic signatures in acute myelogenous leukemia (AML) characterized by a higher proportion of C>A and G>A single base substitutions (SBS) [Hoang. ASH. 2021]. These G>A SBS are known to be particularly prevalent in CpG islands due to cytosine methylation. However, toxic smoking metabolites could potentially induce specific genomic signatures in patients with AML that resemble COSMIC SBS4 in lung cancer [i.e. enrichment in C>A transversion], and spontaneous C>T SBS1 signatures within specific genomic clusters or nodes. In this study, we investigate how these SBS1/SBS4 signatures distribute within hot-spot regions and evaluate whether G>A mutations (mut), commonly observed in methylated CpG islands, are differentially expressed in AML patients who are older and/or are smokers. In our study, these hot-spot regions or nodes were referenced as a genomic pool 1 (GP1). Methods: After IRB approval, the incidence of specific SBS densities were investigated in vulnerable hot-spot regions affected by exogenous [SBS4] and endogenous [SBS1] mutagenesis. Next generation sequencing (NGS) was used in patients to obtain data regarding specific mutation types and locations. In known gene exons, we examined genomic coordinates corresponding to individual mut. COSMIC browser allowed genomic coordinate examination to "aggregate” mut within putative "vulnerable exon neighborhoods". "Hot-spot neighborhoods” were described as genomic pool 1 (GP1). Descriptive and inferential statistics were used to analyze data, which was obtained from a single institution. Results: 80 patients (pt) diagnosed with hematopoietic malignancies with available next generation sequencing (NGS) were selected for analysis. 73/80 (91%) were AML pt. The median age was 63 years (y) (range, 22-88). 42% and 64% of pt were smokers and older than 63 y, respectively. With respect to specific hot spots or nodes, AML pt showed increased G>A mutagenicity in GP1 cluster 1 (Fig 1). Specifically, for G>A, smoking increased the rate from 18.4% to 37.5% (p=0.01) (Fig 1 A and B). Age > 63 y led to an increased mutagenicity rate of 17.1% to 30.5% (p=0.03) (Fig 1 C and D). A synergistic effect in mutagenicity was observed when combining age > 63 y plus smoking (10.3% to 41.9%, p=0.01) (Fig 1. E and F). In regards to hotspots in specific genes, smoking has the ability to increase NRAS (G>A), P53 (G>A) and SRSF2 (C>A) frequencies within GP1. Interestingly, smoking increased C>A mutagenicity in the SRSF2 gene in GP1 from 50% vs 82%. Conclusions: Our data suggests that aging and smoking globally and locally erode the AML genome by potentially accelerating cytosine methylation and thus G>A mutagenicity, most likely in CpG islands within genes like NRAS and P53. These genes likely contain hot spots aggregated in GP1 that, when mutated, can de-stabilize the genome and increase the risk of AML. Importantly, we observed similar COSMIC SBS4 substitutions seen in lung cancer associated with C>A transversions in older AML pt who had a history of smoking, which is specifically found in the SRSF2 gene. Overall, our data advances our understanding on how risk factors for AML affect the human AML genome. These have strong implications for AML prevention, pathogenesis and therapy. Future studies should be aimed at identifying other intrinsic and extrinsic risk factors for AML seeking to explore their specific mutational patterns and locations within the human genome. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Development of extrahepatic bile ducts and mechanisms of tumorigenesis: Lessons from mouse models.

The biliary system is a highly branched tubular network consisting of intrahepatic bile ducts (IHBDs) and extrahepatic bile ducts (EHBDs). IHBDs are derived from hepatic progenitor cells, while EHBDs originate directly from the endoderm through a separate branching morphogenetic process. Traits that are important for cancer are often found to overlap in developmental and other processes. Therefore, it has been suggested that intrahepatic cholangiocarcinomas (iCCAs) and extrahepatic cholangiocarcinomas (eCCAs) have different developmental mechanisms. While much evidence is being gathered on the mechanism of iCCAs, the evidence for eCCA is still very limited. The main reason for this is that there are very few appropriate animal models for eCCA. We can gain important insights from these animal models, particularly genetically engineered mouse models (GEMMs). GEMMs are immunocompetent and mimic human CCA subtypes with a specific mutational pattern, allowing the development of precancerous lesions, that is, biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of the bile duct (IPNB). This review provides a summary of the pathogenesis and mechanisms of eCCA that can be revealed by GEMMs. Furthermore, we discuss several clinical questions, such as whether BilIN and IPNB really become malignant, whether the peribiliary gland is the origin of eCCAs, and others.

Molecular predictors of immunophenotypic measurable residual disease clearance in acute myeloid leukemia.

Measurable residual disease (MRD) is a powerful prognostic factor in acute myeloid leukemia (AML). However, pre-treatment molecular predictors of immunophenotypic MRD clearance remain unclear. We analyzed a dataset of 211 patients with pre-treatment next-generation sequencing who received induction chemotherapy and had MRD assessed by serial immunophenotypic monitoring after induction, subsequent therapy, and allogeneic stem cell transplant (allo-SCT). Induction chemotherapy led to MRD- remission, MRD+ remission, and persistent disease in 35%, 27%, and 38% of patients, respectively. With subsequent therapy, 34% of patients with MRD+ and 26% of patients with persistent disease converted to MRD-. Mutations in CEBPA, NRAS, KRAS, and NPM1 predicted high rates of MRD- remission, while mutations in TP53, SF3B1, ASXL1, and RUNX1 and karyotypic abnormalities including inv (3), monosomy 5 or 7 predicted low rates of MRD- remission. Patients with fewer individual clones were more likely to achieve MRD- remission. Among 132 patients who underwent allo-SCT, outcomes were favorable whether patients achieved early MRD- after induction or later MRD- after subsequent therapy prior to allo-SCT. As MRD conversion with chemotherapy prior to allo-SCT is rarely achieved in patients with specific baseline mutational patterns and high clone numbers, upfront inclusion of these patients into clinical trials should be considered.

Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan.

(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, an in-depth molecular phylogenetic characterization of HIV-1 sub-subtype A1 strains in Pakistan have not been presented. We performed a detailed characterization of the HIV-1 sub-subtype A1 epidemic in Pakistan using state-of-the-art molecular epidemiology and phylodynamics. (2) Methods: A total of 143 HIV-1 sub-subtype A1 gag sequences, including 61 sequences generated specifically for this study from PLHIVs part of our cohort, representing all sub-subtype A1 gag sequences from Pakistan, were analyzed. Maximum-likelihood phylogenetic cluster analysis was used to determine the relationship between Pakistani sub-subtype A1 strains and pandemic sub-subtype A1 strains. Furthermore, we used signature variation, charge distribution, selection pressures, and epitope prediction analyses to characterize variations unique to Pakistani HIV-1 strains and establish the association between signature variations and Gag epitope profile. (3) Results: The HIV-1 sub-subtype A1 sequences from Pakistan formed three main clusters: two that clustered with Kenyan sequences (7 and 10 sequences, respectively) and one that formed a Pakistan-specific cluster of 123 sequences that were much less related to other sub-subtype A1 sequences available in the database. The sequences in the Pakistan-specific cluster and the Kenyan reference strains exhibited several signature variations, especially at amino acid positions 312, 319, 331, 372, 373, 383, and 402. Structural protein modeling suggested that amino acid changes in these positions result in alterations of the Gag protein structure as well as in Gag-specific T-cell epitopes. (4) Conclusions: Our results suggest that the majority of the Pakistan HIV-1 sub-subtype A1 strains were unique to Pakistan and with a specific mutation pattern in Gag.

Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19

Infection with SARS-CoV-2 variant Omicron is considered to be less severe than infection with variant Delta, with rarer occurrence of severe disease requiring intensive care. Little information is available on comorbid factors, clinical conditions and specific viral mutational patterns associated with the severity of variant Omicron infection. In this multicenter prospective cohort study, patients consecutively admitted for severe COVID-19 in 20 intensive care units in France between December 7th 2021 and May 1st 2022 were included. Among 259 patients, we show that the clinical phenotype of patients infected with variant Omicron (n = 148) is different from that in those infected with variant Delta (n = 111). We observe no significant relationship between Delta and Omicron variant lineages/sublineages and 28-day mortality (adjusted odds ratio [95% confidence interval] = 0.68 [0.35–1.32]; p = 0.253). Among Omicron-infected patients, 43.2% are immunocompromised, most of whom have received two doses of vaccine or more (85.9%) but display a poor humoral response to vaccination. The mortality rate of immunocompromised patients infected with variant Omicron is significantly higher than that of non-immunocompromised patients (46.9% vs 26.2%; p = 0.009). In patients infected with variant Omicron, there is no association between specific sublineages (BA.1/BA.1.1 (n = 109) and BA.2 (n = 21)) or any viral genome polymorphisms/mutational profile and 28-day mortality.

342. GENOMIC ANALYSIS OF RESPONSE TO NEOADJUVANT CHEMOTHERAPY IN OESOPHAGEAL ADENOCARCINOMA

Abstract Oesophageal adenocarcinoma (OAC) is the ninth most common cancer worldwide, with a mortality of &amp;gt;500,000 deaths yearly. Neoadjuvant chemotherapy (NAC) followed by surgery is the standard of care (SOC) for locally advanced OAC. Although almost all patients receive chemotherapy as SOC, but &amp;lt;20% respond and benefit from chemotherapy before surgery. The OAC genome is complex and heterogeneous between patients, and it is not yet understood whether specific mutational patterns may result in chemotherapy sensitivity or resistance. To identify associations between genomic events and response to NAC in OAC, a comparative genomic analysis was performed in 65 patients using whole-genome sequencing. We defined response to NAC using Mandard Tumour Regression Grade TRG), with responders classified as TRG1–2 (n = 27) and non-responders classified as TRG4–5 (n = 38). We report a higher non-synonymous mutation burden in responders (median 2.08/Mb vs 1.70/Mb, P = 0.036) and elevated copy number variation (CNV) in non-responders (282 vs 136/patient, P &amp;lt; 0.001). We identified CNVs unique to each group, with cell cycle (CDKN2A, CCND1), c-Myc (MYC), RTK/PIK3 (KRAS, EGFR) and gastrointestinal differentiation (GATA6) pathway genes being specifically altered in non-responders. Of particular interest was the identification of the Neuron Navigator-3 (NAV3), a known tumour suppressor downstream of EGFR, which was mutated exclusively in 22% of non-responders. Our work characterises genetic features and mutations that are uniquely associated with response to NAC. We envision a treatment pipeline that incorporates driver mutation profiling in OAC, combining response prediction with targeted therapies to enhance response to NAC and improve survival outcomes.

Clonal hematopoiesis of indeterminate potential: clinical relevance of an incidental finding in liquid profiling

Abstract Clonal hematopoiesis of indeterminate potential (CHIP) is a hematologic precursor lesion that is defined by the presence of somatic mutations in peripheral blood cells but without evidence for the presence of leukemia or another hematologic neoplasm. CHIP is frequent in elderly individuals and can be detected as incidental finding in liquid profiling of cell-free DNA. While liquid profiling assays aim to reduce the biological noise generated by CHIP and to discriminate solid cancer-associated from CHIP-associated mutation profiles, the finding of CHIP is of potential clinical relevance at its own. Overall, CHIP is associated with a moderate risk of progression to an overt hematologic neoplasm of 1% per year. The risk increases substantially in patients with unexplained blood count abnormalities, multiple mutations, or specific patterns of mutations. In patients with solid cancer, the presence of CHIP increases the risk for development of treatment-related myeloid neoplasms. In addition, CHIP has been associated with a number of non-hematological diseases and represents a previously unrecognized major risk factor for cardiovascular disease. The management of individuals diagnosed with CHIP includes both hematologic and cardiovascular risk assessment in a multidisciplinary setting. Additional evidence from interventional studies is needed to integrate CHIP into a personalized treatment approach for patients with solid cancer.

O086 Genomic analysis of response to neoadjuvant chemotherapy in oesophageal adenocarcinoma

Abstract Introduction Oesophageal adenocarcinoma (OAC) is the ninth most common cancer worldwide with a mortality of over 500,000 deaths yearly. Neoadjuvant chemotherapy (NAC) followed by surgery is the standard of care (SOC) for locally advanced OAC. Although almost all patients receive chemotherapy as SOC, fewer than 20% obtain a clinically meaningful response and benefit before surgery. The OAC genome is complex and heterogeneous between patients, and it is not yet understood whether specific mutational patterns result in chemotherapy sensitivity or resistance. Methods To identify associations between genomic events and response to NAC in OAC, a comparative genomic analysis was performed in 65 patients using whole-genome sequencing. We defined response to NAC using Mandard Tumour Regression Grade TRG), with responders classified as TRG1-2 (n=27) and non-responders classified as TRG4- 5 (n=38). Results We report a higher non-synonymous mutation burden in responders (median 2.08/Mb vs 1.70/Mb, P=0.036) and elevated copy number variation (CNV) in non-responders (282 vs 136/patient, P&amp;lt;0.001). We identified CNVs unique to each group, with cell cycle (CDKN2A, CCND1), c-Myc (MYC), RTK/PIK3 (KRAS, EGFR) and gastrointestinal differentiation (GATA6) pathway genes being specifically altered in non-responders. Of particular interest was the identification of the Neuron Navigator-3 (NAV3), a known tumour suppressor downstream of EGFR, which was mutated exclusively in 22% of non-responders. Conclusion We characterise genetic features and mutations that are uniquely associated with response to NAC. We envision a treatment pipeline that incorporates driver mutation profiling in OAC, combining response prediction with targeted therapies enhancing response to NAC and improving survival outcomes. Take-home message Developing a method of determining an OAC patient's response to neoadjuvant chemotherapy before treatment is administered is desperately needed and will improve patient outcome and quality of life. We identified a number of aberrations in the genome that were unique to non-responders to chemotherapy compared to responders, particularly a known tumour suppressor gene namely Neuron Navigator-3, suggesting that these events may contribute to chemoresistance in these patients. Our work characterises pre-existing genomic alterations that have potential as biomarkers for resistance or sensitivity to NAC.