Genetic Driver Mutations Research Articles

Myeloproliferative Neoplasms Transcriptome Reveals Pro-Inflammatory Signature and Enrichment in Peripheral Blood Monocyte-Related Genes

Myeloproliferative neoplasms (MPN) are hematological diseases associated with genetic driver mutations in the JAK2, CALR, and MPL genes and exacerbated oncoinflammatory status. Analyzing public microarray data from polycythemia vera (n = 41), essential thrombocythemia (n = 21), and primary myelofibrosis (n = 9) patients’ peripheral blood by in silico approaches, we found that pro-inflammatory and monocyte-related genes were differentially expressed in MPN patients’ transcriptome. Genes related to cell activation, secretion of pro-inflammatory and pro-angiogenic mediators, activation of neutrophils and platelets, coagulation, and interferon pathway were upregulated in monocytes compared to controls. Together, our results suggest that molecular alterations in monocytes may contribute to oncoinflammation in MPN.

Assessing Radiological Response to Immunotherapy in Lung Cancer: An Evolving Arena.

In the past decade, immune checkpoint inhibitors (ICIs) have entered the treatment landscape of non-small-cell lung cancer, signalling a paradigm shift within the field characterized by significant survival benefits for patients with advanced and metastatic disease, and especially those with non-targetable genetic oncogenic driver mutations. However, the shift towards immune-based treatments has created new challenges in oncology. Atypical immunotherapy response patterns, including pseudo-progression and hyperprogressive disease, as well as immune-related adverse events have generated the need for new methods to predict patient response to treatment. Hence, new versions of the traditional Response Evaluation Criteria for Solid Tumors (RECIST) have emerged to help characterise with better accuracy radiological findings concerning patient response classification to immunotherapy. This review discusses response evaluation criteria relevant to unique radiological findings observed in patients treated with immunotherapy for non-small-cell lung cancer.

Development of an in vivo syngeneic mouse transplant model of invasive intestinal adenocarcinoma driven by endogenous expression of Pik3caH1047R and Apc loss.

Preclinical models that replicate patient tumours as closely as possible are crucial for translational cancer research. While in vitro cancer models have many advantages in assessing tumour response therapy, in vivo systems are essential to enable evaluation of the role of the tumour cell extrinsic factors, such as the tumour microenvironment and host immune system. The requirement for a functional immune system is particularly important given the current focus on immunotherapies. Therefore, we set out to generate an immunocompetent, transplantable model of colorectal cancer suitable for in vivo assessment of immune-based therapeutic approaches. Intestinal tumours from a genetically engineered mouse model, driven by expression of a Pik3ca mutation and loss of Apc, were transplanted into wild type C57BL/6 host mice and subsequently passaged to form a novel syngeneic transplant model of colorectal cancer. Our work confirms the potential to develop a panel of mouse syngeneic grafts, akin to human PDX panels, from different genetically engineered, or carcinogen-induced, mouse models. Such panels would allow the in vivo testing of new pharmaceutical and immunotherapeutic treatment approaches across a range of tumours with a variety of genetic driver mutations.

Abstract C063: Frequency and spectrum of KRAS mutations in lung adenocarcinoma from Black/African American and White/European patients

Abstract Lung cancer is the most common cause of cancer death in the United States and a major source of cancer health disparity. Lung cancer incidence and mortality rates are higher in Black/African American (B/AA) men than in men from other racial/ethnic groups. Lung adenocarcinoma, arising in the alveoli or air sacs of the lung, is the most common subtype of lung cancer in all ethnic/racial groups. Genetic driver mutations can differ among racial/ethnic groups, in the identity of the mutated genes, their mutation frequencies, and the spectrum of mutations for each given gene. In addition, the same mutation could have different effects depending on an individual patient’s genetic background, resulting in differential responses to therapies. Therefore, it is important to identify the frequency and spectrum of driver mutations in different population groups. Protooncogenes from the RAS family, KRAS, NRAS, and HRAS, play a crucial role in cell growth regulation, cell proliferation, and survival. KRAS is frequently mutated in numerous cancer types, including lung adenocarcinoma, and has been reported to be the driver gene in ~30% of lung adenocarcinomas from White/European (W/E) patients. Due to the much lower number of lung cancer samples analyzed from B/AA patients, it has been unclear if the KRAS mutational frequency and spectrum in B/AA lung adenocarcinoma patients differs from that in W/E patients. Here we collected available existing data sets with mutational information on KRAS muations in lung adenocarcinoma from B/AA and W/E patients. We obtained data for 1555 B/AA and 13840 White lung adenocarcinoma patients. While B/AA lung adenocarcinoma patients had a lower prevalence of KRAS mutations (27% vs. 35%) than W/E patients, (χ2 p-value= 5.877e-10), KRAS was still the most frequently mutated cancer driver gene in both groups. The most common KRAS mutations in both B/AA and W/E patients were alterations of glycine 12 to cysteine (G12C), valine (G12V), aspartic acid (G12D), and alanine (G12A), as well as glutamine 61 to histidine (Q61H) and glycine 13 to cysteine (G13C). Given that a substantial proportion of lung adenocarcinoma patients carry a mutated KRAS gene, investigating new potential KRAS-targeting therapies remains especially urgent. To this end, we are investigating polyisoprenylated cysteinyl amide inhibitors (PCAIs), a group of potential cancer therapy agents designed to specifically disrupt and suppress hyperactive G-protein signaling, as caused by mutated RAS proteins. We are testing PCAI efficiacy on B/AA and W/E lung adenocarcinoma cell lines carrying various KRAS mutations. Citation Format: Daniel J. Mullen, Pablo E. Puente, Christopher Leon, Diana I. Romero, Kweku Ofosu-Asante, Yong Huang, Nazarius S. Lamango, Ite A. Offringa. Frequency and spectrum of KRAS mutations in lung adenocarcinoma from Black/African American and White/European patients [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C063.

Transcriptional Heterogeneity and Clonal Evolution between Diagnosis and Relapse in Pediatric Acute Myeloid Leukemia

Clonal evolution of leukemia is driven by different selection pressures operating on a heterogeneous population of cells. These pressures may include therapy-induced and immune-mediated effects which eradicate the majority of cells, but which simultaneously provide a selective advantage to a minor population of cells that is genetically or transcriptionally distinct and which grow out towards relapse. We integrated single-cell RNA-seq, DNA-seq, ATAC-seq and long-read Oxford Nanopore sequencing of matched diagnosis and relapse samples of 20 pediatric AML patients with various genetic driver mutations representative of the mutational spectrum to map the genetic and transcriptional evolution of these cancers (Figure 1). We investigated whether and how differences in AML-initiating mutations impact on transcriptional programs in AML blasts and their surrounding microenvironmental cells and how the mutational and transcriptional features of these cells are impacted by cancer therapy. Specifically, we traced the progression of these traits from the point of diagnosis to the occurrence of relapse. Our single cell RNA and ATAC data showed high patient-to-patient heterogeneity, with gene expression patterns that were largely conserved between diagnosis and relapse. Analyses of the differentially expressed genes and factorization into “metaprograms” revealed gene sets that were shared between relapse samples but could not be tied to interpretable common “biological signatures”. Exome-seq revealed highly significant changes in somatic variants, most notably in members of the RAS-signaling pathway (i.e., KRAS, NRAS, PTPN11, NF1 and CBL). Interestingly, pathogenic RAS mutations were often gained, but also lost, or switched between different RAS-pathway members, indicating that RAS-mutations are associated with extensive clonal evolution/rewiring. To unveil the effect of accumulation or loss of (sub)clones with RAS mutations on the transcriptional phenotype and epigenetic landscape of leukemic blasts, we performed targeted screening of somatic variants at single-cell resolution. To this aim, we combined long-read nanopore sequencing with 10x Genomics single-cell technologies, enabling us to directly link genetic, transcriptomics and epigenetic changes in distinct (sub)clones. Taken together, we successfully reconstructed patient-specific genetic and transcriptional evolutionary trajectories in pediatric AML. This knowledge will be essential for our understanding of AML relapse and therapy resistance.

TMIC-15. GENETIC AND SPATIAL HETEROGENEITY OF PEDIATRIC HIGH-GRADE GLIOMAS CONFER UNIQUE INFLAMMATORY MICROENVIRONMENTS

Abstract Significant progress has been made molecularly defining pediatric high-grade gliomas (pHGG), including diffuse midline gliomas (DMG), yet little progress has been made with respect to delineating the inflammatory microenvironment. We utilize molecularly defined human samples and immunocompetent genetic mouse models to study how tumor location and genetic driver mutations influence the tumor microenvironment (TME). We report human DMGs have a significant enrichment of Elane+ neutrophils compared to their hemispheric counterparts. We validate this utilizing the RCAS-Tva mouse model, which histologically and genetically recapitulates human pHGGs. Using this model we demonstrate each distinct pHGG/DMG entity confers unique transcriptional identities as made evident by NanoString RNA expression profiles and whole-tumor single-cell RNA sequencing. H3.3WT DMGs and H3.3K27M DMGs cluster together and have high expression of inflammatory genes such as Ptprc, Trem2, Lag3, and Cd274 while H3.3WT and H3.3G34R hemispheric tumors, and H3.1K27M DMGs cluster together with low expression of these genes. Several genes were found to significantly correlate with median survival in human bulk RNA sequencing data including IL13RA2. Flow cytometry and immunohistochemistry demonstrate H3WT DMGs are enriched for monocytes and lymphocytes while H3.3K27M DMGs are enriched for microglia. Genetic perturbations were made to prevent TAM or neutrophil infiltration, including targeting Ccl3, Cxcl1, and Ccl8/12. Only Ccl8/12 knockout resulted in significant extension of survival in H3K27M DMGs, which was met with an increase in CD4+ and CD8+ T-cells and decreased neutrophil infiltration. CD4+ T-cell depletion and anti-PD1 therapy was performed to further study the role of lymphocyte infiltration in DMGs. Lastly, CCR1/CCR5 inhibitors were utilized to abrogate TAM infiltration in DMGs, resulting in decreased microglia infiltration and significant survival extension comparable to radiation therapy. Together, this work provides the foundation for developing or improving immunotherapies designed at specific subgroups of pHGG and DMGs, such as CAR-T-cell, oncolytic viral therapy, and checkpoint blockade.

An Explainable Radiogenomic Framework to Predict Mutational Status of KRAS and EGFR in Lung Adenocarcinoma Patients.

The complex pathobiology of lung cancer, and its spread worldwide, has prompted research studies that combine radiomic and genomic approaches. Indeed, the early identification of genetic alterations and driver mutations affecting the tumor is fundamental for correctly formulating the prognosis and therapeutic response. In this work, we propose a radiogenomic workflow to detect the presence of KRAS and EGFR mutations using radiomic features extracted from computed tomography images of patients affected by lung adenocarcinoma. To this aim, we investigated several feature selection algorithms to identify the most significant and uncorrelated sets of radiomic features and different classification models to reveal the mutational status. Then, we employed the SHAP (SHapley Additive exPlanations) technique to increase the understanding of the contribution given by specific radiomic features to the identification of the investigated mutations. Two cohorts of patients with lung adenocarcinoma were used for the study. The first one, obtained from the Cancer Imaging Archive (TCIA), consisted of 60 cases (25% EGFR, 23% KRAS); the second one, provided by the Azienda Ospedaliero-Universitaria 'Ospedali Riuniti' of Foggia, was composed of 55 cases (16% EGFR, 28% KRAS). The best-performing models proposed in our study achieved an AUC of 0.69 and 0.82 on the validation set for predicting the mutational status of EGFR and KRAS, respectively. The Multi-layer Perceptron model emerged as the top-performing model for both oncogenes, in some cases outperforming the state of the art. This study showed that radiomic features can be associated with EGFR and KRAS mutational status in patients with lung adenocarcinoma.

SINGLE‐CELL RNA‐SEQ OF CLASSIC HAIRY CELL LEUKEMIA REVEALS DISEASE DRIVERS LINKED TO INTRINSIC TREATMENT RESISTANCE AND IDENTIFIES DUSP1 AS POTENTIAL NEW THERAPEUTIC TARGET

Introduction: Standard treatment with purine analogs such as cladribine (2-CdA) achieves excellent remissions in classic hairy cell leukemia (HCL), but up to 25% of patients relapse early and there is a non-diminishing risk of late relapse in complete responders. Even when targeting the recurrent genetic driver mutation BRAF V600E, HCL cells frequently persist in the bone marrow suggesting cooperating biologic alterations facilitating disease survival and persistence. Methods: Single-cell RNA sequencing (scRNA-Seq) was performed in primary HCL cells derived from three long-term (>10 years progression-free survival, PFS) and three short-term responders after 2-CdA treatment (SR, <3 years PFS) and from up to three time points (HCL diagnosis, first, and second relapse). Functional studies were performed using the BRAF D594E-mutated HAIR-M cell line after validating BRAF D594E as an activating mutation with similar downstream signaling and inhibitory potential with BRAF inhibitors as compared to BRAF V600E in primary HCL cells. Results: scRNA-Seq revealed distinct HCL cell clusters characterized by marked overexpression of DUSP1, FOS and JUND in all six patients that were outgrowing at first and second relapse in all three SR. In these DUSP1hi/FOShi/JUNDhi HCL cells, PROGENy cancer pathway analysis demonstrated induced activation of MAPK pathways and gene ontology analysis found negative regulation of the pro-apoptotic p38-MAPK-cascade as potential underlying biologic alteration. BRAF D594E-mutated HAIR-M cells were selected as substitute for primary HCL cells in cell culture due to comparable changes upon exposure to BRAF inhibitors in BRAF kinase activity conformation as assessed by the modular kinase conformation biosensor platform (KinCon) and similar reduction in ERK phosphorylation levels in HEK293T cells transiently overexpressing either flag-tagged BRAF D594E or BRAF V600E. In HAIR-M, we confirm stable expression levels of DUSP1, FOS and JUND, which were highly increased when co-cultured with HS5 stromal cells. Whereas increased expression of FOS and JUND was reversible upon exposure to BRAF inhibitors, expression of DUSP1, a direct target of BRAF-MEK-ERK signaling, and phosphorylation of p38 remained unaffected. As DUSP1 preferentially dephosphorylates/inactivates p38, we studied exposure of the DUSP1-inhibitor BCI in co-culture and found re-phosphorylated p38. Conclusion: DUSP1hi/FOShi/JUNDhi HCL cells may represent a distinct subset of HCL cells highly dependent on environmental cues with an inherently more resistant phenotype to treatment with 2-CdA or BRAF-inhibitors. Inhibition of DUSP1 may represent a novel therapeutic approach by effectively truncating HCL cells from extracellular pro-survival stimuli. Finally, our results suggest that BRAF D594E-mutated HAIR-M cells may serve as a representative disease model for functional studies. Keywords: bioinformatics, computational and systems biology, indolent non-Hodgkin lymphoma, tumor biology and heterogeneity No conflicts of interests pertinent to the abstract.

From the Editor’s Desk...

From the Editor’s Desk...

Interactive webtool for analyzing drug sensitivity and resistance associated with genetic signatures of cancer cell lines

PurposeA wide therapeutic repertoire has become available to oncologists including radio- and chemotherapy, small molecules and monoclonal antibodies. However, drug efficacy can be limited by genetic heterogeneity. Here, we designed a webtool that facilitates the data analysis of the in vitro drug sensitivity data on 265 approved compounds from the GDSC database in association with a plethora of genetic changes documented for 1001 cell lines in the CCLE data.MethodsThe webtool computes odds ratios of drug resistance for a queried set of genetic alterations. It provides results on the efficacy of single compounds or groups of compounds assigned to cellular signaling pathways. Webtool availability: https://tools.hornlab.org/GDSC/.ResultsWe first replicated established associations of genetic driver mutations in BRAF, RAS genes and EGFR with drug response. We then tested the ‘BRCAness’ hypothesis and did not find increased sensitivity to the assayed PARP inhibitors. Analyzing specific PIK3CA mutations related to cancer and mendelian overgrowth, we found support for the described sensitivity of H1047 mutants to GSK690693 targeting the AKT pathway. Testing a co-mutated gene pair, GATA3 activation abolished PTEN-related sensitivity to PI3K/mTOR inhibition. Finally, the pharmacogenomic modifier ABCB1 was associated with olaparib resistance.ConclusionsThis tool could identify potential drug candidates in the presence of custom sets of genetic changes and moreover, improve the understanding of signaling pathways. The underlying computer code can be adapted to larger drug response datasets to help structure and accommodate the increasingly large biomedical knowledge base.

The Performance of an Extended Next Generation Sequencing Panel Using Endobronchial Ultrasound-Guided Fine Needle Aspiration Samples in Non-Squamous Non-Small Cell Lung Cancer: A Pragmatic Study

Introduction/BackgroundSamples from endobronchial ultrasound-guided fine needle aspiration (EBUS-TBNA) are frequently used for next generation sequencing (NGS) in patients with non-small cell lung cancer (NSCLC) to look for genetic driver mutations. The objective of the current study was to evaluate the performance of extended NGS panels using EBUS-TBNA samples in a real-world setting and identify factors associated with the success of NGS. Materials and MethodsThis study included all patients who underwent EBUS and were diagnosed with non-squamous NSCLC with mediastinal metastasis from 2016 to 2019 at the University of Pennsylvania. We reviewed demographic information, imaging studies, procedure reports, pathology and NGS reports. Logistic regression was used to analyze factors associated with the success of NGS panels. ResultsThe success rates of NGS using EBUS-TBNA samples were 92.5%, and 91.5% for DNA and RNA NGS panels respectively. Samples from higher N stage (N2 and N3 lymph nodes) and with higher tumor cellularity (>25%) resulted in higher success rate for DNA NGS. The effect of tumor cellularity remained borderline significant after entering multivariable logistic regression. The short-axis diameter of the sampled lymph node on CT scan, FDG-avidity on PET CT and >3 EBUS passes per lymph node during the procedure were not associated with NGS success. ConclusionBoth DNA and RNA extended-panel NGS had high performance using EBUS-TBNA samples. Sampling more advanced nodal stations and obtaining samples with higher tumor cellularity were associated with higher success rate of DNA NGS. Other imaging or procedural factors did not affect NGS performance.

Common genetic driver mutation in NSCLC and their association with thromboembolic events: A retrospective study

This retrospective study aimed to estimate the incidence, risk factors of thromboembolism events (TEs) in non-small cell lung cancer patients harboring common gene mutation, and evaluate a genetic link between oncogenes and the risk of TEs in Asian patients with NSCLC. MethodsUnivariate and multivariate Cox’s proportional hazards regression models were used to identify the strongest predictors of TE development and evaluate the risk of TE in patients with different gene statuses of NSCLC patients. ResultsIn univariate and multivariate COX analysis, patient with squamous cell carcinoma (HR 3.01, 95% CI: [1.06,8.56]; p = 0.039), multi-site metastases (HR: 2.72; 95% CI: [1.08,6.92]; p = 0.032) or high white blood cell (WBC) (HR 3.24, 95% CI: [1.46,7.22]; p = 0.004), less hemoglobin (HGB) (HR 4.89, 95% CI: [1.90,12.64]; p = 0.001), are at higher risk of thrombosis. At the molecular level, ROS and ALK rearrangement is highly associated with TE development, with HR of 4.04 (95%CI: [1.54,10.58]; p = 0.005) and HR of 3.57 (95% CI: [1.01,12.66]; p = 0.049) in univariate analysis, and even higher in multivariate analysis. EGFR mutations seem to be a protective factor against TE in univariate analyses (HR:0.28, 95%CI [0.12,0.65], p = 0.003) but are not statistically significant in the multivariate model. No correlation between KRAS mutations and TE events in both models. Besides, a numerically higher cumulative incidence of thrombosis event was observed in patients who used TKI (HR 1.473; 95% CI: [0.682, 3.181]; p = 0.32). ConclusionOur study demonstrated that driver gene mutation may increase the risk of thrombosis in non-small cell lung cancer patients. The presence of ALK/ROS rearrangements in our study is associated with an approximately threefold to fourfold increase in thrombosis risk in NSCLC patients. For advanced-stage patients who used TKI, an increased incidence of thrombosis risk and shorter follow-up were observed.

Abstract 2213: Generating a collection of isogenic lung adenocarcinoma cell lines to study RAS gene activation in black Americans

Abstract Lung cancer is a source of cancer health disparity among black Americans, especially men. Lung cancer incidence rates and mortality rates are higher in black Americans than in white Americans despite lower tobacco exposure among black men than white men. Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer in all ethnic/racial groups, including blacks. Genetic driver mutations differ among racial/ethnic groups. In addition, the same mutation could have different effects based on the genetic background arising from different racial/ethnic groups. Therefore, it is important to study appropriate driver mutations in the correct genetic background. Protooncogenes from the RAS family, KRAS, NRAS, and HRAS, play a crucial role in cell growth regulation, cell proliferation, and survival. KRAS is the most frequently mutated driver gene in black LUAD (~14%). NRAS mutations are also seen (1-2%). It is therefore important to study LUAD cell lines carrying different RAS mutations in black Americans’ genetic backgrounds. Unfortunately, to our knowledge, there is only one LUAD cell line from a black subject. The NCI-H23 cell line contains a heterozygous KRAS mutation at codon 12. We are generating a collection of isogenic cell lines derived from NCI-H23, tailored to study RAS gene activation in black Americans. We will correct the KRAS mutation to wildtype through CRISPR/Cas9 deletion with co-transfection of the wild-type sequence. However, we expect that the NCI-H23 cells may not tolerate the removal of the KRAS without simultaneous replacement with another driver mutation. Therefore, we will replace the KRAS mutation with either mutated NRAS, HRAS, or EGFR. EGFR functions as a receptor tyrosine kinase in the RAS-RAF-MEK-ERK pathway to control the activation of RAS oncogenes and is also frequently mutated in black LUAD (~8%). We have identified a heterozygous single nucleotide polymorphism, rs11047919, 839 nucleotides downstream from the KRAS mutation which we are using to differentiate between the wild-type and mutated KRAS alleles following CRISPR editing. We will use the new cell lines to test the efficacy of polyisoprenylated cysteinyl amide inhibitors (PCAIs). These agents have been shown to disrupt RAS-mediated signaling in ethnically/racially diverse cell lines. In the future, we will develop immortalized alveolar epithelial cell lines from black subjects to further address the lack of lung cancer models representing black Americans. Through our research, we intend to address one facet of the prominent lack of representation of black Americans in LUAD studies. Citation Format: Pablo E. Puente, Chunli Yan, Matthew Gregory, Nadine L. Belony, Nazarius Lamango, Yong Huang, Ite A. Offringa. Generating a collection of isogenic lung adenocarcinoma cell lines to study RAS gene activation in black Americans [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2213.

Clinical implications of germline variations for treatment outcome and drug resistance for small molecule kinase inhibitors in patients with non-small cell lung cancer.

Small-molecule kinase inhibitors (SMKIs) represent the cornerstone in the treatment of non-small cell lung cancer (NSCLC) patients harboring genetic driver mutations. Because of the introduction of SMKIs in the last decades, treatment outcomes have drastically improved. Their treatment efficacy, the development of drug resistance as well as untoward toxicity, all suffer from large patient variability. This variability can be explained, at least in part, by their oral route of administration, which leads to a large inter- and intra-patient variation in bioavailability based on differences in absorption. Additionally, drug-drug and food-drug interactions are frequently reported. These interactions could modulate SMKI efficacy and/or untoward toxicity. Furthermore, the large patient variability could be explained by the presence of germline variations in target receptor domains, metabolizing enzymes, and drug efflux transporters. Knowledge about these predictor variations is crucial for handling SMKIs in clinical practice, and for selecting the most optimal therapy. In the current review, the literature search included all SMKIs registered for locally-advanced and metastatic NSCLC by the US Food and Drug Administration (FDA) or European Medicines Agency (EMA) until March 24th, 2022. The BIM deletion showed a significantly decreased PFS and OS for East-Asian patients treated with gefitinib, and has the potential to be clinically relevant for other SMKIs as well. Furthermore, we expect most relevance from the ABCG2 34G>A and CYP1A1 variations during erlotinib and gefitinib treatment. Pre-emptive CYP2D6 testing before starting gefitinib treatment can also be considered to prevent severe drug-related toxicity. These and other germline variations are summarized and discussed, in order to provide clear recommendations for clinical practice.

Transforming growth factor-β signaling modifies the hematopoietic acute inflammatory response to drive bone marrow failure.

Bone marrow failure syndromes are characterized by ineffective hematopoiesis due to impaired fitness of hematopoietic stem cells. They can be acquired during bone marrow stress or innate and are associated with driver genetic mutations. Patients with a bone marrow failure syndrome are at higher risk of developing secondary neoplasms, including myelodysplastic syndromes and leukemia. Despite the identification of genetic driver mutations, the hematopoietic presentation of the disease is quite heterogeneous, raising the possibility that non-genetic factors contribute to the pathogenesis of the disease. The role of inflammation has emerged as an important contributing factor, but remains to be understood in detail. In this study, we examined the effect of increased transforming growth factor-b (TGFb) signaling, in combination or not with an acute innate immune challenge using polyinosinc:polycytidilic acid (pIC), on the hematopoietic system without genetic mutations. We show that acute rounds of pIC alone drive a benign age-related myeloid cell expansion and increased TGFb signaling alone causes a modest anemia in old mice. In sharp contrast, increased TGFb signaling plus acute pIC challenge result in chronic pancytopenia, expanded hematopoietic stem and progenitor cell pools, and increased bone marrow dysplasia 3-4 months after stress, which are phenotypes similar to human bone marrow failure syndromes. Mechanistically, this disease phenotype is uniquely associated with increased mitochondrial content, increased reactive oxygen species and enhanced caspase-1 activity. Our results suggest that chronic increased TGFb signaling modifies the memory of an acute immune response to drive bone marrow failure without the need for a preexisting genetic insult. Hence, non-genetic factors in combination are sufficient to drive bone marrow failure.

Increased levels of NETosis in myeloproliferative neoplasms are not linked to thrombotic events

Morbidity and mortality of Philadelphia chromosome–negative myeloproliferative neoplasms (MPNs) are mainly determined by thromboembolic complications. Thrombus formation is facilitated by a neutrophil-specific form of cell death linked to neutrophil extracellular trap (NET) formation (NETosis). Preclinical and clinical data suggested a potential link between NETosis and thrombosis in MPNs. In this study, we aimed to define the impact of NETosis on clinical end points in a large MPN cohort. NETosis was induced in vitro by ionomycin and quantified by enzyme-linked immunosorbent assay–based nucleosome release assays as well as fluorescent staining of free DNA in samples from 103 MPN patients and 28 healthy donors. NETosis rate was correlated with a broad set of clinical data, such as MPN subtype, mutational status, laboratory variables, history of thrombotic events, and treatment types. Triggered NETosis levels were clearly higher in MPN patients than in healthy donors. Positivity for JAK2 V617F or exon 12 as well as CALR mutations correlate with increased NET formation. However, neither JAK2 allelic burden nor history of thromboembolic complication nor the presence of other risk factors for thrombosis (eg, leukocytosis) were associated with the rate of NETosis. In addition, none of the analyzed laboratory parameters nor the type of treatment significantly impacted the rate of NETosis formation. The biology of MPNs has an impact on NET formation because genetic driver mutations favor induction of NETosis, but this does not seems to translate into important clinical end points such as thromboembolic complications. Therefore, NETosis may play a role in facilitating thrombosis, but it is not a sole causative determinant in MPN-associated thrombophilia.

Abstract 1300: Identification of efficacious treatment for glioblastoma (GBM) by applying computational drug sensitivity imputation to novel GBM avatars and GBM clinical datasets

Abstract Glioblastoma (GBM) is a debilitating disease associated with poor prognosis and a limited response to therapies. At present, patients receive chemotherapy with temozolomide, following radiation therapy and surgery; however, none of the treatments are curative, and clinical trials are recommended as the preferred option for eligible patients. Regrettably, only 3-5% of GBM patients survive 3 years or more. Therefore, it is imperative to develop efficacious therapies. To achieve this goal, we have developed a computation method that allows us to impute drug sensitivity when transcriptome data is available. We have applied this imputation method to several publicly available normal brain tissue, low grade glioma (LGG), and GBM patient datasets to identify compounds of interest. We also compared the leads from these patient/in vivo data analyses with those generated from previous imputations made using a novel GBM avatar model; this model was created by introducing different genetic driver mutations using CRISPR-Cas9 into human induced pluripotent stem cells, followed by differentiation to GBM-associated mutations containing neural progenitor cells (NPC) and animal engraftment to develop human adult GBM models. We applied the drug imputation to over 1200 human normal brain, LGG and GBM samples as well as 18 NPC, tumor sphere and engrafted GBM tumor avatar samples. For each sample, we imputed over 700 drug sensitivity scores. Our model was trained independently using one of two separate high throughput in vitro drug screening datasets (GDSC and CTRP). To identify drugs showing higher sensitivity in GBM than in normal tissues, we compared the imputed drug sensitivity for each compound between samples belonging to the precancerous or the non-high grade glioma state (represented by the normal tissue and LGG data) and samples representing the cancerous or high grade glioma state (GBM). We identified a number of compounds showing higher imputed sensitivity in samples belonging to the cancerous state when compared to those in the precancerous or LGG state. We were also able to cross check compounds of interest with our avatar data. Among them, some agents have been used in the clinic to treat GBM, supporting the validity of integration of our computational tool with novel ex vivo GBM avatars and GBM clinical data in the development of new therapeutic strategy for GBM. More importantly, we have identified other compounds with various mechanism of action that show higher efficacy in GBM and will be further evaluated with the goal to quickly translate into clinic. Therefore, we can successfully integrate ovel experimental and computational models to speed up drug discovery with the goal of finding new therapeutics for GBM. Citation Format: Danielle Maeser, Robert Gruener, Robert Galvin, Tomoyuki Koga, Frank B. Furnari, David Largaespada, Clark C. Chen, Stephanie R. Huang. Identification of efficacious treatment for glioblastoma (GBM) by applying computational drug sensitivity imputation to novel GBM avatars and GBM clinical datasets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1300.

Rhabdomyosarcoma: How Advanced Molecular Methods Are Shaping the Diagnostic and Therapeutic Paradigm.

For the past 40 years, progress in rhabdomyosarcoma (RMS) has been focused on understanding its molecular basis and characterizing the mutations that drive its tumorigenesis and progression. Genetic predisposition to RMS has allowed discovery of key genetic pathways and driver mutations. Subclassification of RMS into embryonal (ERMS) and alveolar (ARMS) subtypes has shifted from histology to PAX-FOXO1 fusion status, and new driver mutations have been found in spindle cell RMS. Comprehensive molecular profiling leveraging genome-scale next-generation sequencing (NGS) indicates that the RAS/RAF/PI3K axis is mutated in the majority of ERMS and modulated by downstream effects of PAX-FOXO1 fusions in ARMS. Because of the continued poor outcome of high-risk RMS, a variety of molecular targets have been or are now being tested in current or recent therapy trials. New techniques such as single cell sequencing, spatial multi-omics, and CRISPR/Cas9 genome editing offer potential for further discovery, but a need for clinically annotated specimens persists.

48-Year-Old Woman With Dyspnea and Chest Pain

48-Year-Old Woman With Dyspnea and Chest Pain

Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours

Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies.