Frequency Of TP53 Mutations Research Articles

Abstract 55: High frequency of TP53 mutations in canine skin tumors recapitulates solar induced human lesions representing an important research model of spontaneous diseases

Abstract Skin tumors are the most common type of neoplastic lesion affecting humans and dogs, and their incidence is increasing for both species. Skin tumor initiation and progression are associated with chronic exposure to ultraviolet (UV) radiation, mainly for light-skinned individuals, that can activate different oncogenes and pathways. Solar UV-induced mutations, characterized by C to T or CC to TT mutations, are well described in the TP53 gene in human skin cancers such as ​​basal cell carcinoma, squamous cell carcinoma and melanoma. This study evaluated TP53 mutations in 2201 canine tumors enrolled in FidoCure Precision Medicine Platform. Tumors were classified in 26 different types according to their histology and anatomic location. Gastrointestinal tumors, insulinomas and mesotheliomas did not carry any TP53 mutation as opposed to cutaneous squamous cell carcinoma (CSCC) and cutaneous hemangiosarcoma (CHSA) that had higher number of TP53 mutations in 88.9% and 77.8% of cases, respectively. Canine CSCC had a similar frequency of TP53 mutations compared to humans, previously identified in 83.64% of cases (MSKCC, Nat Med 2017). The C to T transitions were the most prevalent type of mutations in both canine CSCC and CHSA representing 66.67% and 55.55% of TP53 mutations, respectively. On the other hand, C>T corresponded to just 23.36% of TP53 mutations for the other 24 tumor types. R261H, G290R, R184*, S229F, N143K and R201* variants were identified more than 10 times in all canine tumors. Canine CSCC and CHSA were enriched with R201* (P<0.0001; P=0.004) and R184*(P<0.0001; P=0.048). These two nonsense variants are C>T changes at the position 601 and 550, respectively. They are homologous to human R213* (637C>T) and R196* (586C>T). Canine R201* was identified in 44.4% of CSCC, and human R213* in 73.91% of cases (MSKCC, Nat Med 2017). This study identified a high frequency of TP53 mutations in canine cutaneous tumors consistent with solar induced lesions. These results position canines as excellent spontaneous models of human solar induced cancers that can be utilized to elucidate elements of cancer biology, prognosis and responses across a wide spectrum of therapies. Citation Format: Lucas Rodrigues, Thaynan Vieira, Garrett Harvey, Dorothy Girimonte, Gerald Post, Lindsay Lambert, Aubrey Miller, Abigail Hull, Chase Schwalbach, Christina Lopes, Michelle White. High frequency of TP53 mutations in canine skin tumors recapitulates solar induced human lesions representing an important research model of spontaneous diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 55.

PD10-11 DISTINCT CLINICAL GENOMIC VARIATIONS AMONG MEN WITH LOCALIZED VS METASTATIC PROSTATE CANCER

You have accessJournal of UrologyCME1 Apr 2023PD10-11 DISTINCT CLINICAL GENOMIC VARIATIONS AMONG MEN WITH LOCALIZED VS METASTATIC PROSTATE CANCER Ahmed El-shafie, Mohammed Al-Toubat, Allison H. Feibus, SeyedBehzad Jazayeri, Soroush Bazargani, Devon Thomas, Mark Bandyk, and K.C. Balaji Ahmed El-shafieAhmed El-shafie More articles by this author , Mohammed Al-ToubatMohammed Al-Toubat More articles by this author , Allison H. FeibusAllison H. Feibus More articles by this author , SeyedBehzad JazayeriSeyedBehzad Jazayeri More articles by this author , Soroush BazarganiSoroush Bazargani More articles by this author , Devon ThomasDevon Thomas More articles by this author , Mark BandykMark Bandyk More articles by this author , and K.C. BalajiK.C. Balaji More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003250.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Our objective was to identify unique genetic mutations associated with metastatic prostate cancer (PCa) by comparing next generation sequencing (NGS) data between men with localized and metastatic disease METHODS: We queried the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (GENIE) registry for men diagnosed with PCa. Patients were categorized into localized (m0) and metastatic (m1) groups. The difference in the frequency of genetic mutations between the two groups and the prognostic significance of the differentially expressed genes were analysed using SPSS V24. We included frequency rates of >5% and p values <0.05 were considered statistically significant to maintain over 95% true positive detection rate. RESULTS: A total of 1,027 patients, with localized (n=459) and metastatic PCa (n=568) were included in the study. Patients were mostly non-Hispanic White men (89%) with a median age of 61 years (IQR 56-66 years). 421 (41%) of our cohort had Gleason grade group (GG) 2 disease, 277 (27%) had GG3 disease, and 267 (26%) had GG4 or GG5 disease. We identified alterations in 89 genes in our analyses. Patients with M1PCa had significantly higher genomic aberrations in TMPRSS2 (31.51% vs 11.14%, p<0.001); ERG fusion (23.59% vs 13.13%, p<0.001); PTEN loss (25.7% vs 16.16%, p<0.001); TP53 mutation (38.73% vs 12.23%, p<0.001); FOXA1 (17.43% vs 6.33%, p<0.001); KMT2C (9.51% vs 6.11%, p=0.02) (Figure 1). We then isolated the signalling pathways most likely to be affected by these mutations, and found that the androgen receptor was most often impacted (Figure 2). Patients with alterations in all 6 of the genes listed above had the worst progression-free survival (p = <0.01, log rank test) (Figure 1). CONCLUSIONS: In M1PCa, patients had significantly higher frequency of TMPRSS2, ERG, PTEN loss, TP53, FOXA1, and KMT2C somatic gene mutations compared to samples from patients with m0PCa. Additionally, patients who had mutations in all 6 of these genes harboured more aggressive cancer and poorer outcomes. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e330 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ahmed El-shafie More articles by this author Mohammed Al-Toubat More articles by this author Allison H. Feibus More articles by this author SeyedBehzad Jazayeri More articles by this author Soroush Bazargani More articles by this author Devon Thomas More articles by this author Mark Bandyk More articles by this author K.C. Balaji More articles by this author Expand All Advertisement PDF downloadLoading ...

Decreased transthyretin predicts a poor prognosis in primary myelodysplastic syndrome.

This study aims to investigate the prognostic significance of transthyretin in newly diagnosed myelodysplastic syndromes (MDS). The clinical, laboratory, and follow-up data of 280 newly diagnosed patients with MDS were collected. The relationship between serum transthyretin levels and overall survival (OS) and leukemia-free survival (LFS) were analyzed by Kaplan-Meier analysis and Cox Regression Model. In the MDS cohort, there were 121 cases in the low transthyretin group and 159 cases in the normal transthyretin group. MDS patients with decreased transthyretin had a higher risk score on the Revised International Prognostic Scoring System (IPSS-R) (p = 0.004) and on the molecular IPSS (IPSS-M) (p = 0.005), a higher frequency of TP53 mutation (p < 0.0001), a shorter OS (p < 0.0001) and LFS (p < 0.0001). Multivariate analyses showed that higher IPSS-R and IPSS-M score were adverse factors for OS (p = 0.008 and p = 0.015, respectively) and LFS (p = 0.024 and p = 0.005, respectively). Mutations of TP53 and NRAS were also poor factors for LFS (p = 0.034 and p = 0.018, respectively). Notably, decreased transthyretin was an independent adverse predictor for OS (p = 0.009, HR = 0.097, 95%CI, 0.017-0.561) but not for LFS (p = 0.167) when IPSS-R was included in the Cox regression model and an independent poor one for OS (p = 0.033, HR = 0.267, 95%CI, 0.080-0.898) and LFS (p = 0.024, HR = 0.290, 95%CI, 0.099-0.848) while IPSS-M involved. The results indicate that decreased transthyretin could be an independent adverse prognostic factor in patients with MDS and may provide a supplement to IPSS-R and IPSS-M.

Single-cell and bulk RNA sequencing identifies T cell marker genes score to predict the prognosis of pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the lethal malignancies, with limited biomarkers identified to predict its prognosis and treatment response of immune checkpoint blockade (ICB). This study aimed to explore the predictive ability of T cell marker genes score (TMGS) to predict their overall survival (OS) and treatment response to ICB by integrating single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. Multi-omics data of PDAC were applied in this study. The uniform manifold approximation and projection (UMAP) was utilized for dimensionality reduction and cluster identification. The non-negative matrix factorization (NMF) algorithm was applied to molecular subtypes clustering. The Least Absolute Shrinkage and Selection Operator (LASSO)-Cox regression was adopted for TMGS construction. The prognosis, biological characteristics, mutation profile, and immune function status between different groups were compared. Two molecular subtypes were identified via NMF: proliferative PDAC (C1) and immune PDAC (C2). Distinct prognoses and biological characteristics were observed between them. TMGS was developed based on 10 T cell marker genes (TMGs) through LASSO-Cox regression. TMGS is an independent prognostic factor of OS in PDAC. Enrichment analysis indicated that cell cycle and cell proliferation-related pathways are significantly enriched in the high-TMGS group. Besides, high-TMGS is related to more frequent KRAS, TP53, and CDKN2A germline mutations than the low-TMGS group. Furthermore, high-TMGS is significantly associated with attenuated antitumor immunity and reduced immune cell infiltration compared to the low-TMGS group. However, high TMGS is correlated to higher tumor mutation burden (TMB), a low expression level of inhibitory immune checkpoint molecules, and a low immune dysfunction score, thus having a higher ICB response rate. On the contrary, low TMGS is related to a favorable response rate to chemotherapeutic agents and targeted therapy. By combining scRNA-seq and bulk RNA-seq data, we identified a novel biomarker, TMGS, which has remarkable performance in predicting the prognosis and guiding the treatment pattern for patients with PDAC.

An Analysis Regarding the Association Between Proteasome (PSM) and Hepatocellular Carcinoma (HCC).

The Proteasome (PSM) is a large multi-catalytic protease complex consisting of a 20S core particle and a 19S regulatory particle whose main function is to accept and degrade ubiquitinated substrates, are now considered as one of the potential regulators of tumor proliferation, and stemness maintenance. However, to date, studies on the relationship between PSM and hepatocellular carcinoma (HCC) are limited. This study used a bioinformatics approach combining validation experiments to investigate the biological mechanisms that may be related with PSM. A series of experiments in vivo and in vitro were performed to explore the function of the 26S proteasome non-ATPase regulatory subunit 13 (PSMD13) in HCC. HCC patients can be divided into two clusters. Cluster 1 (C1) patients having a significantly worse prognosis than Cluster (C2). Two subtypes had significant differences in proliferation-related signaling. In particular, the frequency of TP53 mutation was significantly higher in C1 than in C2. In addition, PSM-associated genes were highly consistent with the expression of DNA repair-related signatures, suggesting a potential link between PSM and genomic instability. We also found that downregulation of PSMD13 expression significantly inhibited stemness of tumor cells and impaired the Epithelial mesenchymal transition (EMT) process. Finally, the correlation between the PSMD13 and Ki67 was found to be strong. PSM is a valid predictor of prognosis and therapeutic response in patients with HCC disease. Furthermore, PSMD13 may be a potential therapeutic target.

Genetic Lesions in Russian CLL Patients with the Most Common Stereotyped Antigen Receptors.

Chronic lymphocytic leukemia (CLL) is one of the most common B-cell malignancies in Western countries. IGHV mutational status is the most important prognostic factor for this disease. CLL is characterized by an extreme narrowing of the IGHV genes repertoire and the existence of subgroups of quasi-identical stereotyped antigenic receptors (SAR). Some of these subgroups have already been identified as independent prognostic factors for CLL. Here, we report the frequencies of TP53, NOTCH1, and SF3B1 gene mutations and chromosomal aberrations assessed by NGS and FISH in 152 CLL patients with the most common SAR in Russia. We noted these lesions to be much more common in patients with certain SAR than average in CLL. The profile of these aberrations differs between the subgroups of SAR, despite the similarity of their structure. For most of these subgroups mutations prevailed in a single gene, except for CLL#5 with all three genes affected by mutations. It should be noted that our data concerning the mutation frequency in some SAR groups differ from that obtained previously, which could be due to the population differences between patient cohorts. The research in this area should be important for better understanding the pathogenesis of CLL and therapy optimization.

Exploiting PRMT5 as a target for combination therapy in mantle cell lymphoma characterized by frequent ATM and TP53 mutations

Constant challenges for the treatment of mantle cell lymphoma (MCL) remain to be recurrent relapses and therapy resistance, especially in patients harboring somatic mutations in the tumor suppressors ATM and TP53, which are accumulated as therapy resistance emerges and the disease progresses, consistent with our OncoPrint results that ATM and TP53 alterations were most frequent in relapsed/refractory (R/R) MCL. We demonstrated that protein arginine methyltransferase-5 (PRMT5) was upregulated in R/R MCL, which predicted a poor prognosis. PRMT5 inhibitors displayed profound antitumor effects in the mouse models of MCL with mutated ATM and/or TP53, or refractory to CD19-targeted CAR T-cell therapy. Genetic knockout of PRMT5 robustly inhibited tumor growth in vivo. Co-targeting PRMT5, and ATR or CDK4 by using their inhibitors showed synergistic antitumor effects both in vitro and in vivo. Our results have provided a rational combination therapeutic strategy targeting multiple PRMT5-coordinated tumor-promoting processes for the treatment of R/R MCL with high mutation burdens.

Metabolism-related signatures is correlated with poor prognosis and immune infiltration in hepatocellular carcinoma via multi-omics analysis and basic experiments.

Metabolism is an ordered series of biological processes that occur in an organism. Altered cellular metabolism is often closely associated with the development of cancer. The aim of this research was to construct a model by multiple metabolism-related molecules to diagnose and assess the prognosis of patients. WGCNA analysis was used to screen out differential genes. GO, KEGG are used to explore potential pathways and mechanisms. The lasso regression model was used to filter out the best indicators to construct the model. Single-sample GSEA (ssGSEA) assess immune cells abundance, immune terms in different Metabolism Index (MBI) groups. Human tissues and cells were used to verify the expression of key genes. WGCNA clustering grouped genes into 5 modules, of which 90 genes from the MEbrown module were selected for subsequent analysis. GO analysis was found that BP mainly has mitotic nuclear division, while KEGG pathway is enriched to Cell cycle, Cellular senescence. Mutation analysis revealed that the frequency of TP53 mutations was much higher in samples from the high MBI group than in the low MBI group. Immunoassay revealed that patients with higher MBI have higher macrophage and Regulatory T cells (Treg) abundance, while NK cells were lowly expressed in the high MBI group. RT-qPCR and immunohistochemistry (IHC) revealed that the hub genes expression is higher in cancer tissues. The expression in hepatocellular carcinoma cells was also much higher than that in normal hepatocytes. In conclusion, a metabolism-related model was constructed that can be used to estimate the prognosis of hepatocellular carcinoma, and the clinical treatment of different hepatocellular carcinoma patients with medications was guided.

Multi-omics analysis unravels the underlying mechanisms of poor prognosis and differential therapeutic responses of solid predominant lung adenocarcinoma.

Solid predominant adenocarcinoma (SPA) has been reported to be a subtype with poor prognosis and unsatisfactory response to chemotherapy and targeted therapy in lung adenocarcinoma (LUAD). However, the underlying mechanisms remain largely unknown and the suitability of immunotherapy for SPA has not been investigated. We conducted a multi-omics analysis of 1078 untreated LUAD patients with clinicopathologic, genomic, transcriptomic, and proteomic data from both public and internal cohorts to determine the underlying mechanisms of poor prognosis and differential therapeutic responses of SPA and to investigate the potential of immunotherapy for SPA. The suitability of immunotherapy for SPA was further confirmed in a cohort of LUAD patients who received neoadjuvant immunotherapy in our center. Along with its aggressive clinicopathologic behaviors, SPA had significantly higher tumor mutation burden (TMB) and number of pathways altered, lower TTF-1 and Napsin-A expression, higher proliferation score and a more immunoresistant microenvironment than non-solid predominant adenocarcinoma (Non-SPA), accounting for its worse prognosis. Additionally, SPA had significantly lower frequency of therapeutically targetable driver mutations and higher frequency of EGFR/TP53 co-mutation which was related to resistance to EGFR tyrosine kinase inhibitors, indicating a lower potential for targeted therapy. Meanwhile, SPA was enriched for molecular features associated with poor response to chemotherapy (higher chemoresistence signature score, lower chemotherapy response signature score, hypoxic microenvironment, and higher frequency of TP53 mutation). Instead, muti-omics profiling revealed that SPA had stronger immunogenicity and was enriched for positive biomarkers for immunotherapy (higher TMB and T cell receptor diversity; higher PD-L1 expression and more immune cell infiltration; higher frequency of gene mutations predicting efficacious immunotherapy, and elevated expression of immunotherapy-related gene signatures). Furthermore, in the cohort of LUAD patients who received neoadjuvant immunotherapy, SPA had higher pathological regression rates than Non-SPA and patients with major pathological response were enriched in SPA, confirming that SPA was more prone to respond to immunotherapy. Compared with Non-SPA, SPA was enriched for molecular features associated with poor prognosis, unsatisfactory response to chemotherapy and targeted therapy, and good response to immunotherapy, indicating more suitability for immunotherapy while less suitability for chemotherapy and targeted therapy.

Aminoacyl-tRNA Synthetase-based Prognosis Model and Exploration of Potential Mechanisms in Hepatocellular Carcinoma.

Aminoacyl-tRNA synthetases (ARSs) participate in tumor initiation and progression but their involvement in hepatocellular carcinoma (HCC) is not clear. This study aimed to investigate the prognostic value and underlying mechanisms of ARS in HCC. Data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium, Gene Expression Omnibus and Human Protein Atlas databases. The prognostic model was constructed with the use of Cox regression and least absolute shrinkage and selection operator regression. Kaplan-Meier survival analysis, enrichment analysis, single sample gene set enrichment analysis and tumor mutation burden calculation were performed with R to evaluate the model and explore the underlying mechanism. Wilcoxon tests were used for comparisons between groups. Aspartyl-tRNA synthetase 2 (DARS2), tyrosyl-tRNA synthetase 1 (YARS1) and cysteinyl-tRNA synthetase 2 (CARS2) were identified as prognostic biomarkers and enrolled in model construction. The area under receiver operating characteristic curve of the model was 0.775. The model was used to assign patients from TCGA into low- and high-risk groups. Those in the high-risk group had a worse prognosis (p<0.001). The clinical significance of the model was tested in different clinical subgroups. Genetic mutation analysis had a higher TP53 mutation frequency in high-risk group. Enrichment analysis and study of immune-related cells and molecules found that the high-risk group was characterized by immune-cell infiltration and immunosuppression states. A novel ARS family-based model of HCC prognosis was constructed. TP53 mutation frequency and immune-suppressive status accounted for a worse prognosis in patients included in the high-risk group.

Mutational Landscape of Bladder Cancer in Mexican Patients: KMT2D Mutations and chr11q15.5 Amplifications Are Associated with Muscle Invasion.

Bladder cancer (BC) is the most common neoplasm of the urinary tract, which originates in the epithelium that covers the inner surface of the bladder. The molecular BC profile has led to the development of different classifications of non-muscle invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC). However, the genomic BC landscape profile of the Mexican population, including NMIBC and MIBC, is unknown. In this study, we aimed to identify somatic single nucleotide variants (SNVs) and copy number variations (CNVs) in Mexican patients with BC and their associations with clinical and pathological characteristics. We retrospectively evaluated 37 patients treated between 2012 and 2021 at the National Cancer Institute-Mexico (INCan). DNA samples were obtained from paraffin-embedded tumor tissues and exome sequenced. Strelka2 and Lancet packages were used to identify SNVs and insertions or deletions. FACETS was used to determine CNVs. We found a high frequency of mutations in TP53 and KMT2D, gains in 11q15.5 and 19p13.11-q12, and losses in 7q11.23. STAG2 mutations and 1q11.23 deletions were also associated with NMIBC and low histologic grade.

Characteristics of TP53 mutation in adult precursor B-cell acute lymphoblastic leukemia

Abstract Objectives TP53 is the most intensively studied gene in cancer. However, data on the frequency and prognostic significance of TP53 mutations in acute lymphoblastic leukemia (ALL) are still lacking. This study aimed to determine the characteristics of TP53 mutation, its correlation with clinical and laboratory parameters and other cytogenetic alterations, and their impact on patient outcome on day 21 after induction therapy. Patients and methods This is a prospective cohort clinical study that was conducted on 41 de-novo adult ALL patients, who presented to the Hematology/Oncology Unit of Ain-Shams University Hospitals, where all studied patients were subjected to the treatment regimen. TP53 mutation was investigated in 41 patient samples using the RT-PCR. Results TP53 mutation was detected in 19.5% of studied cases. A highly significant association was detected between 17P deletion and TP53 mutation (P&lt;0.0001). A significant association was detected between TP53 mutation and abnormal karyotyping (P=0.032). The authors found a clear association between TP53 mutation and hypodiploidy (P=0.001) and MYC rearrangements (P=0.001). In contrast, TP53 mutation was clearly underrepresented in ALL patients with t(9;22)(q34;q11). A highly significant association between TP53 mutation and the poor outcome on day 21 (P=0.002) was observed. The patients with TP53 mutation revealed either failure of remission (50%) or incomplete remission (50%). Logistic regression analysis of factors influencing the patient outcome showed that advanced age (&gt;34 years), high total leukocyte count (&gt;40 × 109/l), and abnormal fluorescence in-situ hybridization and karyotyping results due to cytogenetic abnormalities are independent predictors of poor outcome with failure of induction of complete remission on day 21. Conclusion TP53 alterations strongly identify high-risk adult precursor B-ALL patients with poor outcome in this study; yet, this needs further investigation on a larger sample size with a longer follow-up. Investigations of TP53 mutation especially in adult B-cell ALL (accounting 75% of adult ALL) may help with the selection of patients in need of intensive therapeutic strategy or may help with designation of new innovative targeted therapies.

Glycine Decarboxylase (GLDC) Plays a Crucial Role in Regulating Energy Metabolism, Invasion, Metastasis and Immune Escape for Prostate Cancer.

Glycine decarboxylase (GLDC) is one of the core enzymes for glycine metabolism, and its biological roles in prostate cancer (PCa) are unclear. First, we found that GLDC plays a central role in glycolysis in 540 TCGA PCa patients. Subsequently, a metabolomic microarray showed that GLDC enhanced aerobic glycolysis in PCa cells, and GLDC and its enzyme activity enhanced glucose uptake, lactate production and lactate dehydrogenase (LDH) activity in PCa cells. Next, we found that GLDC was highly expressed in PCa, was directly regulated by hypoxia-inducible factor (HIF1-α) and regulated downstream LDHA expression. In addition, GLDC and its enzyme activity showed a strong ability to promote the migration and invasion of PCa both in vivo and in vitro. Furthermore, we found that the GLDC-high group had a higher TP53 mutation frequency, lower CD8+ T-cell infiltration, higher immune checkpoint expression, and higher immune exclusion scores than the GLDC-low group. Finally, the GLDC-based prognostic risk model by applying LASSO Cox regression also showed good predictive power for the clinical characteristics and survival in PCa patients. This evidence indicates that GLDC plays crucial roles in glycolytic metabolism, invasion and metastasis, and immune escape in PCa, and it is a potential therapeutic target for prostate cancer.

Molecular Subtypes of Head and Neck Cancer in Patients of African Ancestry.

The purpose of this study was to better understand the complex molecular biomarkers and signatures of head and neck cancer (HNC) among Black patients and identify possible molecular changes associated with HNC disparities. Molecular subtypes and genomic changes in HNC samples from patients of African and European ancestry in The Cancer Genome Atlas, Memorial Sloan Kettering Cancer Center, Broad Institute, MD Anderson Cancer Center, and John Hopkins University were identified. Molecular features (genomic, proteomic, transcriptomic) associated with race and genomic alterations associated with clinical outcomes were determined. An independent cohort of HNC tumor specimens was used to validate the primary findings using IHC. Black patients were found to have a younger age at diagnosis, more aggressive tumor types, higher rates of metastasis, and worse survival compared with White patients. Black patients had fewer human papillomavirus-positive tumor types and higher frequencies of laryngeal subtype tumors. Higher frequencies of TP53, MYO18B, KMT2D, and UNC13C mutations and a lower frequency of PIK3CA mutations were observed in Black patients. Tumors of Black patients showed significant enrichment of c-MYC and RET-tyrosine signaling and amplifications. A significant increase in tumor expression of c-MYC in Black patients was observed and was associated with poor survival outcomes in the independent cohort. Novel genomic modifications and molecular signatures may be related to environmental, social, and behavioral factors associated with racial disparities in HNC. Unique tumor mutations and biological pathways have potential clinical utility in providing more targeted and individualized screening, diagnostic, and treatment modalities to improve health outcomes.

RB1-deficient squamous cell carcinoma: the proposed source of combined Merkel cell carcinoma

Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine (NE) carcinoma arising from integration of Merkel cell polyomavirus (MCPyV) DNA into a host cell or from ultraviolet light-induced genetic damage (proportions vary geographically). Tumors in the latter group include those with “pure” NE phenotype and those “combined” with other elements, most often squamous cell carcinoma (SCC). We performed comprehensive genomic profiling (CGP) of MCPyV+ and MCPyV− (pure and combined) tumors, to better understand their mutational profiles and shed light on their pathogenesis. Supplemental immunohistochemistry for Rb expression was also undertaken. After eliminating low quality samples, 37 tumors were successfully analyzed (14 MCPyV+, 8 pure MCPyV− and 15 combined MCPyV−). The SCC and NE components were sequenced separately in 5 combined tumors. Tumor mutational burden was lower in MCPyV+ tumors (mean 1.66 vs. 29.9/Mb, P < 0.0001). MCPyV− tumors featured frequent mutations in TP53 (95.6%), RB1 (87%), and NOTCH family genes (95.6%). No recurrently mutated genes were identified in MCPyV+ tumors. Mutational overlap in the NE and SCC components of combined tumors was substantial (‘similarity index' >24% in 4/5 cases). Loss of Rb expression correlated with RB1 mutational (P < 0.0001) and MCPyV− status (P < 0.0001) in MCCs and it was observed more frequently in the SCC component of combined MCC than in a control group of conventional cutaneous SCC (P = 0.0002). Our results (i) support existing evidence that MCPyV+ and MCPyV− MCCs are pathogenetically distinct entities (ii) concur with earlier studies linking the NE and SCC components of combined MCCs via shared genetic profiles and (iii) lend credence to the proposal that an Rb-deficient subset of SCC's is the source of phenotypically divergent combined MCCs.

Integrated systemic analysis of FAM72A to identify its clinical relevance, biological function, and relationship to drug sensitivity in hepatocellular carcinoma.

The family with sequence similarity 72 member A (FAM72A) protein has been identified as an effector of multiple pathological processes in many cancers. The value of FAM72A in HCC remains largely unknown. Data from TCGA-LIHC, ICGC-LIRI-JP, IMvigor210, cBioPortal, GeneMANIA, and TIMER were processed and visualized to explore the association between FAM72A and the prognosis, stemness phenotype, mutational burden, immune cell infiltration, and drug sensitivity in HCC patients. Potential pathways were also revealed. Furthermore, we experimentally verified the results in vivo and in vitro using immunohistochemistry, western blotting, and CCK-8 assays. First, FAM72A mRNA expression was significantly upregulated in HCC. High FAM72A expression was independently associated with a poor prognosis. Experimental validation confirmed that FAM72A was remarkably overexpressed in HCC patients and mice. Moreover, FAM72A knockdown suppressed HCC cell proliferation. In addition, the frequency of TP53 mutations was significantly higher in the high FAM72A expression group. Subsequently, the enrichment analysis revealed that FAM72A was closely related to immune processes and mTOR pathways. Silencing FAM72A increased the expression levels of mTOR in HCC cell lines. The FAM72A-mTOR pathway was strongly associated with a poor prognosis for patients with HCC. Patients with high FAM72A expression levels might be more resistant to sorafenib. Furthermore, the expression of FAM72A and mTOR was significantly associated with the abundance of some tumor-infiltrating immune cells, especially CD4+ T cells. Finally, patients with high levels of FAM72A and mTOR were more sensitive to immunotherapy. FAM72A, a member of the FAM72 family, might be a prognostic and immunotherapeutic target for HCC patients.

Integrative analysis indicates the prognostic value of circadian rhythm disruption in liver cancer: Potential for therapeutic targeting.

Circadian rhythms regulate various biological processes, such as cell division and metabolism. Circadian rhythm disruption (CRD) is often associated with malignant tumor progression and poor prognosis. However, the effect of CRD on liver cancer prognosis has not been systematically analyzed or fully elucidated. Here, we developed a method to quantify and assess intratumoral CRD in a single-cell transcriptomic analysis of liver cancer and systematically analyzed the role of CRD in tumor progression and prognosis. Furthermore, a LASSO-Cox regression model based on 14 CRD genes was used to predict overall patient survival across multiple datasets. We found that malignant cells with high CRD scores were enriched in specific metabolic pathways, such as fatty acid metabolism and the trichloroacetic acid cycle. Intercellular communication analysis suggested that CRD regulates chemokine-mediated interactions. With the bulk transcriptomic datasets, we determined that LiverCRD scores were significantly correlated with macrophage infiltration levels and could guide targeted immunotherapy and chemotherapy strategies. In addition, LiverCRD is also associated with the mutational landscape-for example, TP53 mutation frequency was higher in high-CRD samples. Finally, the 14-gene-based LASSO-Cox regression model could accurately predict overall patient survival across datasets. In conclusion, Our proposed analysis reflects the relationship between CRD and the immune environment in liver cancer, suggesting that CRD may serve as a potential prognostic indicator. Our results may help guide targeted anti-tumor strategies.

In Multiple Myeloma Patients without Known Cytogenetic Risk Features, Genomic Features Contribute to Early Death Risk at Diagnosis

Multiple myeloma (MM) is a heterogeneous disease, and cytogenetic abnormalities such as t(4;14) and del17p are well-established independent high-risk features in newly diagnosed patients. In two clinical trials (N=1422), the IFM2009 and Determination, patients with del17p or t(4;14) had a hazard ratio of 1.9 (95% CI 1.5-2.4) and 1.6 (95% CI 1.2-2.1), respectively. However, the same study also showed that 25% of the remaining patients had a similar short PFS without any identified known high-risk features. To understand the genomic etiology of the high-risk in these patients, we generated WGS data from 640 newly diagnosed patients (GAMER dataset) in 3 categories (low risk [PFS > 36 months] without known risk features (LR), high-risk [PFS < 18 months] without known risk features (unknownHR, uHR) and high-risk with known risk features) (HR). Our primary focus was to find factors that contribute to high-risk without known risk features. As a validation set, we used WGS samples from newly diagnosed patients who enrolled in the DFCI 2009 study. Overall, we observed that t(14;16) was the only primary translocation that differs between uHR (7%) and the LR group (1%) (p value < 0.01). We found more frequent driver mutations in TP53(7%), ATM(6%), and EGR1(4%), in the uHR group (FDR < 0.05). In uHR group, we found that the cancer cell fraction carrying these mutations was significantly lower compared to double hits events observed in HR (p value = 6.4e-05), suggesting their presence in high-risk subclones. Chromosome 1q gain vs amplification were associated with similar outcomes in these patients (p value = 0.81), but both significantly differed from chr1q wild type (p value = 1.8e-07). High-risk patients with and without known risk features had a significant enrichment of mutations in the Genome Integrity pathways (24%) compared to the LR group. However, the enrichment in MAPK signaling pathway mutations (60%) was significantly different between the two high-risk groups. Features that contribute to genome integrity, such as structural variants (insertion, deletion, translocation and inversion, p value<0.001), mutational load (p=0.00025), and genomic scar scores (p=0.0007), were all significantly lower in the low-risk group compared to the uHR. The number of copy number alterations that have not been described before, such as del16, del8p and gain 9 and 19, were also significantly different between low-risk and high-risk patients without known risk features. We further searched for genomic factors that contribute to the classification of uHR using multiple statistical modeling and machine learning tools. All models were run using a 10-fold cross-validation for choosing variables to put into the final model. Using all variables in the final model, we created a classification model using the variables' significance and the model's accuracy. Out of 27 variables, we found that 7 (mutational load, structural variants, del8p, t(14;16), Genome Integrity Pathway, MAPK pathway and ISS > 2) significantly contributed to the classification model. On training and validation data, this model successfully detected the risk group (p value = 3.5e-09 and 0.0027, respectively). Our dataset gives the ability to identify genomic risk markers that are not currently considered in newly diagnosed MM and allows us to extend our understanding beyond traditional risk. The absence of unique and mutually exclusive markers between uHR and LR suggests the additive risk model in MM patients without known high risk markers. Additional risk features might be hidden in the transcriptome and regulation of the transcriptome. We are currently building an integrative model from the same patients with WGS, RNA-seq and methylation data. This will allow us to fine-tune our risk model and help us develop simplified and complex models on MM risk beyond known cytogenetic risk features.

Genomic Characterization of Patients in a Phase 2 Study of Zanubrutinib in BTK Inhibitor-Intolerant Patients with Relapsed/Refractory B-Cell Malignancies

Background/Introduction: Targeting Bruton tyrosine kinase (BTK) to inhibit B-cell receptor signaling is an effective way to treat B-cell malignancies. However, some patients (pts) have experienced toxicities to BTK inhibitors ibrutinib (ibr) and acalabrutinib (acala), which lead to dose reduction or treatment discontinuation. Zanubrutinib (zanu) is a potent and selective next-generation BTK inhibitor (Blood. 2021;138[suppl 1]:1410). BGB-3111-215 (NCT04116437) is an ongoing, phase 2 study of the safety and efficacy of zanu monotherapy in pts with chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), Waldenström macroglobulinemia (WM), mantle cell lymphoma (MCL), or marginal zone lymphoma (MZL) who discontinued ibr, acala, or acala and ibr because of intolerance. Here, we present the gene mutation profile of pts in this study to demonstrate the mutational landscape of pts intolerant to ibr or acala and to explore the association between gene mutations and response to zanu in ibr- and acala- intolerant pts. Methods: Peripheral blood from pts was collected before treatment and at or after the time of disease progression. Genomic DNA was isolated from peripheral blood mononuclear cells or plasma, and the mutational status of targeted genes was assessed using a targeted 106-gene next-generation sequencing (NGS) panel (PredicineHEMETM, Predicine). Samples were sequenced to a median depth of >20,000 reads, with a validated sensitivity of 0.25% mutant allele frequency for all genomic regions. Results: Samples from 63 pts were analyzed, including 63 at baseline and 5 at or after progressive disease (PD). There were 41 pts with CLL, 6 with SLL, 10 with WM, 3 with MCL, and 3 with MZL. The most common mutations at baseline were TP53 (31.7%), SF3B1 (22.2%), ATM (17.5%), NOTCH1 (17.5%), CHEK2 (14.3%), and KRAS (12.7%). Copy number variants were detected, including deletions at ATM locus (9.5%) and RB1 locus (9.5%) and amplifications at CCND2 locus (6.3%). For CLL/SLL, the frequencies of TP53 (27.7%), NOTCH1 (21.3%), SF3B1 (25.5%), ATM (21.3%), and BIRC3 (10.4%) mutations were comparable to those in other studies with high-risk relapsed/refractory CLL pts (Leukemia. 2018;32:3-91; Blood. 2014;123:3247-3254; Leuk Lymphoma. 2018;59[10]:2318-26). For WM, 5 of 10 (50%) samples harbored TP53 mutations, and 4 of 10 samples had MYD88 mutations; all harbored the L265P mutation. Among the 4 pts with MYD88 mutation, CXCR4 gene mutation was detected in 1 case. All 6 pts with MYD88 wild type also had CXCR4 wild type gene, consistent with published data (N Engl J Med. 2015;373:584-6). Baseline mutations were available for the 10 pts with PD, including 8 CLL, 1 SLL, and 1 MCL. Compared to pts without PD, pts with PD had increased frequency of certain mutations: TP53 (60%, P=0.071), ATM (50%, P=0.017), SF3B1 (50%, P=0.035), RB1 (40%, P=0.009), SETD2 (40%, P=0.009), and CDKN2A (30%, P=0.011). This finding suggests that these particular baseline mutations are associated with resistance to zanu. Five pts also had mutations detected at or after PD. Of these, 3 pts had BTK or PLCG2 mutations (submitted). One patient with CLL and without BTK or PLCG2 mutations had ATM and FBXW7 mutations (variant allele frequencies were 86% and 50%, respectively), suggesting DNA damage pathway mutations and NOTCH1 dysregulations may have contributed to disease progression in this patient. Conclusion: Exploratory analysis results confirmed that cell cycle, DNA damage, and NOTCH1 pathway genes were frequently mutated in pts with B-cell malignancies on study BGB-3111-215 (pts intolerant to ibr and/or acala). Pts with mutations associated with poor prognosis at baseline were more likely to develop PD.

Molecular Landscape of Myeloid Neoplasms with Der(1;7)(q10;p10)

Background: Der(1;7)(q10;p10) ((der(1;7)) is a derivative chromosome comprising 7p and 1q, accounting for approximately 1.5-6% of patients with MDS and AML. It is generated by an unbalanced translocation between chrs. 1 and 7, which results in +1q and -7q. Compared to other cases with -7/del(7q) which do not accompany +1q, der(1;7)(+) cases are reported to have a higher frequency of RUNX1 mutations and fewer TP53 mutations, and showed a better prognosis. However, the small number of cases enrolled and the lack of comprehensive analysis of driver mutations and transcriptome analysis in previous studies have prevented more detailed molecular characterization of der(1;7)(+) MDS/AML. Methods: We enrolled 148 cases with der(1;7) and analyzed their genetic profile using whole exome and/or targeted-capture sequencing as well as RNA-sequencing (N=10) and ATAC-sequencing (n=3). To establish the distinct characteristics of der(1;7)(+) we enrolled an additional 3,238 der(1;7)(-) myeloid neoplasm cases. Results: Highly skewed to male, der(1;7) was widely observed across different subtypes of myeloid neoplasms but it was more prevalent in MDS (107/1106, 9.7%) than AML (35/1466, 2.4%) or MDS/MPN (5/130, 3.8%) cases, while rarely found in MPN cases. Der(1;7)(+) AML cases were more frequently derived from MDS or therapy-related than those with -7/del(7q). Targeted-capture sequencing revealed that the profile of driver mutations and copy number alterations (CNAs) substantially differed between cases with der(1;7), -7/del(7q), +1q, and other cases, even after corrected for diagnosis. RUNX1 (37.8%), EZH2 (18.9%) and ETNK1 (18.2%) were more frequently mutated in der(1;7)(+) than other cases (OR=6.13-22.2), whereas TP53 mutations were less common in der(1;7)(+) cases compared to -7/del(7q). +8 and del(20q) were very common in der(1;7)(+) cases (18.9% and 37.4% respectively), compared to those with -7/der(7q),+1q, or other cases. Prognosis of der(1;7)(+) cases was slightly better than that of -7/del(7q) cases (HR=0.71, p=0.098), but worse than +1q cases (HR=1.36, p=0.11) and others cases (HR=1.8, p<0.001). The most frequent cause of deaths in der(1;7)(+) cases was infection (45.5%), followed by disease progression (36.4%), showing a sharp contrast to the cases with -7/del(7q) (13.9% and 72.3%, respectively) and other cases (10.8% and 76.9%, respectively). RNA-sequencing analysis revealed 1,463 differentially expressed genes in der(1;7) MDS cases compared to non-der(1;7) MDS cases. In GSEA analysis, significantly down-regulated pathways were related to cell cycles, innate immunity and TNFα signaling via NFκB. ATAC-seq analysis identified a total of 53,248 peaks, of which 2,243 were significantly upregulated in der(1;7)(+) samples. GATA family motifs were most significantly enriched in upregulated peaks, compared to other motifs. Footprint analysis further revealed that GATA transcription factors were predicted to bound to more peaks in der(1;7)(+) than der(1;7)(-). Consistent with this, expression of GATA2 downstream genes were significantly upregulated in der(1;7)(+) cases, suggesting the role of deregulated GATA2 downstream transcription in the pathogenesis of der(1;7)(+) MDS. Conclusion: Der(1;7)(+) defines a distinct subset of myeloid neoplasms characterized by a unique co-mutation patter, gene expression, and clinical features. Deregulated ETNK1 and GATA2 signaling might play a role in the pathogenesis of der(1;7)(+) myeloid neoplasms. Infections and other non-leukemic complications are the major cause of mortality in der(1;7)(+) cases and should be carefully monitored during their clinical course. Taken together, our findings provide new insight into the understanding of der(1;7)(+) myeloid neoplasms.