Generation Of Cell Lines Research Articles

Abstract A145: CBFβ supports global protein translation in osteosarcoma and may provide a new therapeutic target

Abstract Background: Core binding factor beta (CBFβ) is a binding partner to the RUNX family of DNA binding transcription factors (RUNX1-3) and acts as a transcriptional co-activator by allosterically increasing their affinity for DNA. RUNX2 is the master regulator of bone growth and differentiation, and its binding to CBFβ is of particular interest to osteosarcoma (OS) research. Notably, increased expression of each is correlated with poor disease-free and overall survival in numerous sarcomas. CBFβ’s transcriptional role is well-understood but recent research in breast cancer cells proposes a non-canonical role in the regulation of protein translation, influencing translation of hundreds of mRNA transcripts via binding with heterogenous nuclear ribonucleoprotein K (hnRNPK). The binding of CBFβ to hnRNPK or RUNX1 is reportedly mutually exclusive, suggesting possible interplay between the two roles. We hypothesize that CBFβ regulates protein translation in OS, participating in the translation of RUNX2 and other oncoproteins, promoting a malignant phenotype. Furthermore, we propose that disrupting its translational role may result in an antitumor effect. While CBFβ’s transcriptional activities are well-characterized, we endeavored to isolate its translational role and investigate its contribution to OS. Methods: CRISPR/Cas9 was used to generate a CBFβ knockout (KO) U2OS cell line, while site-directed mutagenesis of CBFβ and lentiviral transduction of U2OS CBFβ KO cells was used to generate cell lines expressing FLAG-tagged wild type (WT) mutant CBFβ. Western Blotting (WB) was used to assess changes in protein expression and subcellular localization while RUNX2 mRNA expression was measured via qPCR and RNAseq. CBFβ’s interacting partners were identified by Immunoprecipitation Mass Spectrometry (IP-MS). Cellular electro-thermal shift assay was used to evaluate influences of CBFβ mutations on RUNX2 and hnRNPK binding. The Click-IT system followed by WB and IP-MS were used to assess global protein translation and synthesis rates of specific proteins, respectively. Results: CBFβ and hnRNPK interact in U2OS cells and loss of CBFβ leads to a decrease in global protein translation. This results in decreased RUNX2 protein, but not mRNA, expression. Re-introduction of WT CBFβ caused RUNX2 protein levels to recover while expression of CBFβ with key mutations in the binding interface abrogated this effect. Importantly, we observed this was not due to direct protection of RUNX2 from proteasomal degradation by WT CBFβ. We identified a cohort of proteins that appear to be translationally regulated by CBFβ and investigated the impact of CBFβ mutations on its translational activities and RUNX2 binding. We also identified a list of putative CBFβ protein-protein interactions in human OS cells that are altered by these mutations. Conclusions: CBFβ appears to participate in protein translation in OS, regulating the expression of numerous oncoproteins including RUNX2. Key mutations in CBFβ designed to interrupt RUNX2 binding also affect this non-canonical activity of CBFβ. Citation Format: Nicholas A Oldberg, Dayn R Godinez, Luke A Wittenburg. CBFβ supports global protein translation in osteosarcoma and may provide a new therapeutic target [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A145.

NAMPT Haploinsufficiency Is a Therapeutic Vulnerability in High-Risk Myeloid Malignancies

Monosomy 7 (−7) and del7q are the most common high-risk cytogenetic abnormalities and occur across the spectrum of myeloid disorders. -7/del(7q) also co-occur with other high-risk factors such as mutations or deletion of TP53. Standard, non-specific chemotherapy drugs are less effective in these high-risk patients, resulting in a median survival rate of approximately one year. To identify novel, targeted agents for these neoplasms, we sought “collateral lethal” genes, i.e. essential, druggable genes encoded on chromosome 7 that are haploinsufficient upon their loss of heterozygosity. To this end, we first identified essential genes located on chromosome 7. We mined genome-wide CRISPR/Cas9 screen data from 27 human acute myeloid leukemia (AML) cell lines within the DepMap database and identified 65 chromosome 7-encoded, candidate essential genes in AML. To determine those essential genes with known inhibitors, we intersected these 65 candidates with the Drug-Gene Interaction and canSAR.ai databases. We found that nicotinamide phosphoribosyltransferase ( NAMPT), the rate-limiting enzyme that catalyzes the first step of NAD + biosynthesis from nicotinamide, was one of four essential and druggable targets on chromosome 7. Notably, NAMPT was the only essential gene on chromosome 7 with a first-in-class orally bioavailable inhibitor, KPT 9274, currently in clinical trials (NCT04914845). Moreover, NAMPT DNA copy number, mRNA, and protein levels all negatively correlated with cell line sensitivity to NAMPT loss, implicating NAMPT as a collateral lethal candidate gene. We confirmed that isogenic human AML cell lines CRISPR-engineered to partially reduce NAMPT DNA copy led to reduced NAMPT protein levels, indicating NAMPT is a haploinsufficient gene. Cells with ~50% NAMPT levels were significantly more sensitive to the KPT 9274 treatment, and became less viable and more apoptotic, compared to control locus edited cells. To determine whether TP53 status could alter this vulnerability, we generated cell lines with both TP53 loss and 50% NAMPT loss. We found TP53 mutational status did not attenuate the observed effects of NAMPT inhibition on cell survival. Viability assays with primary patient AML samples confirmed that -7/del(7q) status imparts significantly elevated sensitivity to KPT 9274 treatment than samples with diploid chromosome 7 alleles. In summary, our findings reveal NAMPT heterozygosity as a therapeutic vulnerability in high-risk myeloid neoplasms that warrants clinical follow-up. Further, we provide a framework centered on data-mining for uncovering collateral lethal genes in other cancers with recurrent chromosomal arm level deletions.

The Role of over-Expressed β Globin in Driving Relapsed B - Cell Acute Lymphoblastic Leukemia (B-ALL)

Background: The prognosis for patients with relapsed acute lymphoblastic leukemia (ALL) remains suboptimal despite intensification of chemotherapy, immunotherapy and stem cell transplant. We and others have identified genetic and epigenetic alterations enriched at relapse that drive drug resistance and relapse. In our recent work mapping the epigenetic landscape of B-ALL, we discovered novel super-enhancers (SEs), or regions with increased H3K27 acetylation, enriched at relapse in a majority of patients, implicating a role in clonal evolution. One of these SEs was upstream of the β globin locus and lead to aberrant expression of hemoglobin beta subunit ( HBB) mRNA. HBB upregulation at relapse was also found in a large meta-analysis of gene expression data from pediatric diagnosis/relapse pairs. Of note, b globin is normally found in erythrocytes that interacts with other subunits to form functional hemoglobin. We hypothesized that HBB upregulation in blasts plays a role in relapse and aimed to determine whether it leads to drug tolerance, an early recovery phenotype and/or increased clonal potential. Methods: B-lineage REH, RS4;11 and 697 ALL cell lines were transduced with lentiviral vectors overexpressing either wild-type (WT) HBB or an empty vector (EV) control. Real time PCR was performed to confirm RNA expression and Western Blot analysis was performed to detect protein expression. We generated additional cell lines with a mutation in the translation start codon and another leading to a premature stop codon to unequivocally interrupt protein expression. The generated cell lines were then plated and evaluated for differences in apoptosis via Annexin V assay and proliferation, in response to chemotherapeutic agents commonly used in the treatment of ALL. Clonogenic growth in vitro was also assessed using MethoCult TM media. To test the possibility that HBB acted in generating a persistor cell phenotype, cell lines were placed in mercaptopurine and prednisone for 10-14 days at two different concentrations and counted throughout drug exposure and for an additional 10-14 days following removal of drug. Results: We did not observe significant differences in chemosensitivity to various chemotherapies used in the treatment of B-ALL. However, we did observe less cells undergoing apoptosis in HBB expressing cells compared to control following prolonged treatment with 6-mercaptopurine, suggesting an increase in a small population of drug tolerant cells. However, this did not result in a difference in recovery time following removal of the drug. We also demonstrated that β globin overexpression led to increased clonal growth in methylcellulose compared to control (Fig. 1A, REH) and this observation was replicated in a second cell line (Fig. 1B, RS4;11). While we confirmed mRNA expression, we were not able to confirm protein expression by Western blot or by immunoprecipitation. We therefore hypothesized that b globin mRNA, rather than protein, mediates the observed increase in clonal growth. Interestingly, we observed the same phenotype of increased clonal growth (Fig. 1) in mutated cell lines, suggesting a catalytic role for β globin RNA in expanding a leukemia stem cell population. Conclusions: The increased clonal potential upon overexpression of HBB could be indicative of the ability to reconstitute a tumor from a small subpopulation following treatment. Additionally, our data suggests that protein is not required for increased clonal growth leading us to hypothesize that catalytic RNA is responsible. We are also currently analyzing RNAseq data from the cell lines and will compare differential gene expression between the empty vector and HBB expressing cells to discover downstream pathways impacted by HBB. We will be testing this hypothesis further by performing limiting dilution analysis in an immunocompromised mouse model (with David Teachey, Children's Hospital of Philadelphia).

Novel Insights in TKI Resistance in BCR:: ABL1-Positive B-Cell Acute Lymphoblastic Leukemia Beyond Kinase Domain Mutations

Background and Aim Despite the introduction of tyrosine kinase inhibitors (TKIs), approximately 30% of newly diagnosed pediatric and adult BCR:: ABL1-positive B-cell acute lymphoblastic leukemia (B-ALL) patients experience relapsed or refractory disease (Biondi et al, Lancet Haematology 2018; Bassan et al, Journal of Clinical Oncology 2010). ABL1 kinase domain mutations, hindering TKI binding, explain part of the relapses and are acquired during TKI therapy but are rarely detected in newly diagnosed BCR:: ABL1-positive B-ALL patients (Baer et al, Haematologica 2022). Intrinsic TKI resistance mechanisms in BCR:: ABL1-positive B-ALL present prior to TKI treatment are less well documented. Therefore, we aimed to identify potential biomarkers for TKI sensitivity at diagnosis using primary patient samples and newly generated cell lines made from patient-derived xenografts (PDX cell lines). Patients and Methods Leukemic cells from diagnosis of BCR:: ABL1-positive B-ALL patients without ABL1-kinase domain mutations were used to measure cell survival in an ex vivo co-culture assay after imatinib (1.95-125 μM), dasatinib (1.95-125 nM), or bosutinib (0.016-2 μM) exposure. TKI sensitivity was assessed using the area under the dose-response curve (AUC), with <80 arbitrary units (AU) classified as imatinib-sensitive, 80-120 AU as intermediate, and >120 AU as resistant. Multiplex ligation-dependent probe amplification, whole exome sequencing, and RNA sequencing were performed on diagnostic material if available. ABL1 phosphorylation and expression levels were measured using (phospho)flow cytometry in patient-derived xenografts from diagnostic samples and (PDX) cell lines. Results We determined ex vivo sensitivity to imatinib, dasatinib, and bosutinib in 32 pediatric and 19 adult BCR:: ABL1-positive B-ALL patient samples. We observed a substantial variability in ex vivo imatinib response in pediatric and adult patient samples (median AUC: 98 AU; range: 16 to 281 AU). The sensitivity towards imatinib strongly correlated with the sensitivity towards second-generation TKIs dasatinib and bosutinib (rho = 0.84; p < 0.001 and rho= 0.89; p <0.001). Moreover, imatinib's AUC of samples derived from newly diagnosed patients who relapsed after TKI treatment was higher compared with those derived from patients who did not suffer from a relapse (median AUC 123 vs 84 AU; p = 0.03). We observed that an increase in ex vivo imatinib resistance was correlated with a decreased amount of phosphorylated ABL1 protein (rho=-0.92; p=0.0013) and total ABL1 protein (rho=-0.82; p=0.01) in untreated, newly diagnosed samples. Ex vivo exposure to imatinib reduced the ABL1 phosphorylation levels in both sensitive and resistant samples but resistant cells exhibited lower levels of (p)ABL1 protein, indicating reduced dependence on BCR-ABL1 signaling. The ex vivo imatinib resistance in samples carrying deletions in B-cell development genes IKZF1 and/or PAX5 was higher than in samples without these deletions (median AUC: 122 versus 80 AU; p=0.01). In addition, one imatinib-resistant patient had a p.His1038Arg mutation in ZEB2, which is recurrent in B-ALL and this gene has also been described as B-cell development gene (Studd et al, Blood Cancer Journal 2021). Interestingly, another resistant patient had a mutation in SETD2,a gene previously associated with ex vivo TKI resistance in chronic myeloid leukemia cell lines (Sheng et al, Cell Proliferation 2019). Other secondary lesions included SH2B3 inactivation lesions and CRLF2 rearrangements. These lesions were present in intermediately sensitive and resistant BCR:: ABL1-positive samples and are expected to lead to increased JAK/STAT signaling, potentially serving as a resistance mechanism for TKI. Conclusion Our study revealed that the amount of total and phosphorylated ABL1 protein was correlated with ex vivo TKI sensitivity. Newly diagnosed TKI-resistant BCR:: ABL1 samples were further characterized by somatic lesions in B-cell development genes including IKZF1. These results link the known poor prognostic value of IKZF1 deletions in BCR:: ABL1-positive B-ALL patients (van der Veer et al. Blood 2014; Fedullo et al, Haematologica 2019) with intrinsic mechanisms of TKI resistance other than tyrosine kinase domain mutations.

Functional Characterization of GPRC5D alteration and Its Impact on Talquetamab Resistance in Relapsed/ Refractory Multiple Myeloma

Background T-cell engaging (TCE) antibodies show unprecedented efficacy in heavily pretreated penta-refractory multiple myeloma (MM). Responses however are often not durable as resistance mechanisms can arise despite the initial absence of resistance-conferring mutations. Biallelic loss of GPRC5D on chr.12p is a rare, yet well-established mechanism of acquired resistance to the first-in-class anti-GPRC5D directed TCE talquetamab (Lee et al., 2022). At the same time, monoallelic GPRC5D frameshift and missense mutations are much more common and occur in up to 15% of MM patients (Truger et al., 2021). In this study, we investigated the functional relevance of monoallelic GPRC5D alterations and their impact on talquetamab resistance. Methods GPRC5D alterations were modeled in vitro by using CRISPR-Cas9 editing in the OPM-2 MM cell line. The bioluminescence-based cytotoxic assay was performed using PBMCs as effector cells to measure the resistance to talquetamab. Quantitative PCR (qPCR), immunohistochemistry, bulk whole genome sequencing (WGS), and whole genome bisulfite sequencing (WGBS) were performed for molecular, genomic, and epigenetic characterization in a patient with acquired talquetamab resistance. Results Using CRISPR-Cas9, we generated cell line models with mono- vs. biallelic deletions in the GPRC5D gene. Clones with biallelic alterations (OPM-2 Del/Del) displayed a 96.4%, reduced expression of GPRC5D ( p < .0001), leading to in vitro resistance to talquetamab. GPRC5D expression levels in monoallelic models (OPM-2 Wt/Del) decreased by 57.4% ( p = .0004) compared to the wild type. Sensitivity to talquetamab in these clones was equally impaired, however, less pronounced than in the biallelic knock-outs. To assess the impact of monoallelic GPRC5D deletions in the clinic, we next investigated the case of a heavily pretreated 58-year-old patient with lambda light-chain MM treated at our institution with talquetamab in his 7th line of therapy. qPCR was used to measure GPRC5D expression in CD138+ MM cells from the bone marrow of this patient before and at the time of relapse to talquetamab after 15 months of treatment (best response: CR). At the time of relapse, we observed a 94.0% ( p < .0001) decrease in GPRC5D expression upon qPCR assessment as compared to the pre-treatment time point which was confirmed by immunohistochemistry. WGS revealed a novel monoallelic loss of chr.12p encompassing GPRC5D in talquetamab-resistant CD138+ MM cells. Since monoallelic alterations seem unlikely as the sole drivers of resistance, we hypothesized that epigenetic modifications may have contributed to talquetamab resistance in this patient. To this end, WGBS was performed and uncovered a significant shift towards hypermethylation of two regulatory regions of GPRC5D, most likely resulting in the silencing of the second GPRC5D allele. Time-course experiments are currently ongoing to explore the methylation landscape of our CRISPR-Cas9-generated clones with monoallelic GPRC5D deletions. Data for these validation experiments will be presented at the meeting. Conclusions Our study provides the first evidence of the functional impact of monoallelic GPRC5D alterations resulting in relative resistance to talquetamab in vitro. We further report on epigenetic regulation as a potential second-hit mechanism conferring clinical resistance to anti-GPRC5D-directed TCE therapy. This data suggests that patients with monoallelic GPRC5D deletions may be at particular risk for developing resistance to talquetamab.

Generation of an NCS1 gene knockout human induced pluripotent stem cell line using CRISPR/Cas9

NCS1 (Neuronal calcium sensor protein 1) encodes a highly conserved calcium binding protein abundantly expressed in neurons. It modulates intracellular calcium homeostasis, calcium-dependent signaling pathways as well as neuronal transmission and plasticity. Here, we generated a NCS1 knockout human induced pluripotent stem cell (hiPSC) line using CRISPR-Cas9 genome editing. It shows regular expression of pluripotent markers, normal iPSC morphology and karyotype as well as no detectable off-target effects on top 6 potentially affected genes. This newly generated cell line constitutes a valuable tool for studying the role of NCS1 in the pathophysiology of various neuropsychiatric disorders and non-neurological disease.

EXTH-20. A MOUSE MODEL REVEALS VULNERABILITY OF IDH1-MUTATED GLIOMA TO FERROPTOSIS

Abstract The molecular classification of gliomas is currently based on the presence of IDH1 mutation, which is associated with better prognosis and longer survival. The hallmark of the IDH1 mutation is the production of D-2-Hydroxyglutarate with subsequent effects that are not fully understood. Ferroptosis, an iron-dependent mechanism of non-apoptotic cell death, is mostly triggered through blocking system Xc- or suppressing the antioxidant enzyme glutathione peroxidase 4 (GPX-4). In this study, we generated a mouse model of glioma harboring the IDH1(R132H) mutation in heterozygous condition, in combination with p53-deletion induced by the expression of PDGFA. We show that IDH1(R132H)-expressing mice survive longer compared to their wild-type counterparts, while histological analysis reveals characteristics of low-grade diffuse gliomas. We generated cell lines from primary tumors and analyzed their metabolic profile and response to mitochondrial stress and Ferroptosis. We treated them in vitro with RSL3, a GPX-4 inhibitor, alone or in combination with Cysteine and Methionine restriction. We show that IDH1(R132H)-expressing cells are far more sensitive to Ferroptosis in vitro. Finally, we show that convection-enhanced delivery of RSL3 in combination with dietary Cysteine and Methionine restriction in vivo, significantly prolongs survival of the IDH1(R132H)-expressing mice. Our findings suggest that Ferroptosis provides promising therapeutic potential worth exploring further and our mouse model could be used to test the efficacy of different treatments for IDH1(R132H) gliomas.

BIOM-58. ZERO-WASTE MOLECULAR DIAGNOSTICS FROM BIOPSY NEEDLE WASHES

Abstract BACKGROUND Brain tumor classification has increasingly integrated molecular diagnostics into official criteria. However, biopsy tissue is limited due to the small quantity acquired in eloquent areas of the brain and is, therefore, usually earmarked for histology. We have identified that the fluid used to wash biopsy needles contains excess tumor material that can be diagnostically useful. Characterization of this non-zero-sum waste material provides an opportunity for improvement in the diagnosis and treatment for brain tumor patients. METHODS For suspected or established high grade brain tumor biopsies (n = 37 across a multi-institutional cohort at submission), neurosurgeons were instructed to save fluid used to wash biopsy needles. Samples were processed and characterized in a variety of methods to establish diagnostic utility including (1) cell-free DNA isolation and targeted panel sequencing (n = 13), (2) isothermal amplification of cell-free DNA from raw wash water for rapid diagnostics (n = 2), (3) cell-line generation (n = 24) and, (4) cell-free mutant protein capture and quantification (n = 9). RESULTS (1) 13 wash samples were considered for cf-tDNA extraction and Illumina TruSight Oncology 500 panel sequencing (with extracted DNA ranging from 20ng-40ug). In 2 returned cases (11 pending), concordance was 100% with clinical targeted panel sequencing where panels overlapped. (2) One case suspected of harboring H3K27M was subjected to targeted, loop-mediated isothermal amplification and Oxford Nanopore real-time sequencing, confirming an H3.3K27M diagnosis (11.8% allele fraction) within 1hr35min of receipt of sample from the operating room. (3) 5 cases resulted in primary cell culture generation (4) A novel single-molecule mutant protein quantification technique was performed on 9 cases. RESULTS from all analyses and concordance with outstanding sequencing will be presented. CONCLUSION We demonstrate that biopsy byproducts contain enough high-quality tumor-derived material to perform a variety of useful diagnostics with the potential to have immediate translational impact on standard of care.

CRISPR-Cas9 system: a novel and promising era of genotherapy for beta-hemoglobinopathies, hematological malignancy, and hemophilia.

Gene therapy represents a significant potential to revolutionize the field of hematology with applications in correcting genetic mutations, generating cell lines and animal models, and improving the feasibility and efficacy of cancer immunotherapy. Compared to different genetic engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated protein 9 (Cas9) emerged as an effective and versatile genetic editor with the ability to precisely modify the genome. The applications of genetic engineering in various hematological disorders have shown encouraging results. Monogenic hematological disorders can conceivably be corrected with single gene modification. Through the use of CRISPR-CAS9, restoration of functional red blood cells and hemostasis factors were successfully attained in sickle cell anemia, beta-thalassemia, and hemophilia disorders. Our understanding of hemato-oncology has been advanced via CRIPSR-CAS9 technology. CRISPR-CAS9 aided to build a platform of mutated genes responsible for cell survival and proliferation in leukemia. Therapeutic application of CRISPR-CAS9 when combined with chimeric antigen receptor (CAR) T cell therapy in multiple myeloma and acute lymphoblastic leukemia was feasible with attenuation of CAR T cell therapy pitfalls. Our review outlines the latest literature on the utilization of CRISPR-Cas9 in the treatment of beta-hemoglobinopathies and hemophilia disorders. We present the strategies that were employed and the findings of preclinical and clinical trials. Also, the review will discuss gene engineering in the field of hemato-oncology as a proper tool to facilitate and overcome the drawbacks of chimeric antigen receptor T cell therapy (CAR-T).

Stable Chinese Hamster Ovary Suspension Cell Lines Harboring Recombinant Human Cytochrome P450 Oxidoreductase and Human Cytochrome P450 Monooxygenases as Platform for In Vitro Biotransformation Studies.

In the liver, phase-1 biotransformation of drugs and other xenobiotics is largely facilitated by enzyme complexes consisting of cytochrome P450 oxidoreductase (CPR) and cytochrome P450 monooxygenases (CYPs). Generated from human liver-derived cell lines, recombinant in vitro cell systems with overexpression of defined phase-1 enzymes are widely used for pharmacological and toxicological drug assessment and laboratory-scale production of drug-specific reference metabolites. Most, if not all, of these cell lines, however, display some background activity of several CYPs, making it difficult to attribute effects to defined CYPs. The aim of this study was to generate cell lines with stable overexpression of human phase-1 enzymes based on Chinese hamster ovary (CHO) suspension cells. Cells were sequentially modified with cDNAs for human CPR in combination with CYP1A2, CYP2B6, or CYP3A4, using lentiviral gene transfer. In parallel, CYP-overexpressing cell lines without recombinant CPR were generated. Successful recombinant expression was demonstrated by mRNA and protein analyses. Using prototypical CYP-substrates, generated cell lines proved to display specific enzyme activities of each overexpressed CYP while we did not find any endogenous activity of those CYPs in parental CHO cells. Interestingly, cell lines revealed some evidence that the dependence of CYP activity on CPR could vary between CYPs. This needs to be confirmed in further studies. Recombinant expression of CPR was also shown to enhance CYP3A4-independent metabolisation of testosterone to androstenedione in CHO cells. We propose the novel serum-free CHO suspension cell lines with enhanced CPR and/or defined CYP activity as a promising "humanised" in vitro model to study the specific effects of those human CYPs. This could be relevant for toxicology and/or pharmacology studies in the pharmaceutical industry or medicine.

Amyloidogenic light chains impair plasma cell survival.

Systemic light chain amyloidosis (AL) is a clonal plasma cell disorder characterized by the deposition of misfolded immunoglobulin light chains (LC) as insoluble fibrils in organs. The lack of suitable models has hindered the investigation of the disease mechanisms. Our aim was to establish AL LC-producing plasma cell lines and use them to investigate the biology of the amyloidogenic clone. We used lentiviral vectors to generate cell lines expressing LC from patients suffering from AL amyloidosis. The AL LC-producing cell lines showed a significant decrease in proliferation, cell cycle arrest, and an increase in apoptosis and autophagy as compared with the multiple myeloma LC-producing cells. According to the results of RNA sequencing the AL LC-producing lines showed higher mitochondrial oxidative stress, and decreased activity of the Myc and cholesterol pathways. The neoplastic behavior of plasma cells is altered by the constitutive expression of amyloidogenic LC causing intracellular toxicity. This observation may explain the disparity in the malignant behavior of the amyloid clone compared to the myeloma clone. These findings should enable future in vitro studies and help delineate the unique cellular pathways of AL, thus expediting the development of specific treatments for patients with this disorder.

Tau deficiency protects human neurons from Abeta‐induced reduction of network activity

AbstractBackgroundOne hallmark of many neurodegenerative diseases, such as Alzheimer’s disease (AD), is the formation of neurofibrillary tangles by hyperphosphorylated Tau in the brain, resulting in neuronal death and cognitive decline. In the adult human brain, six Tau‐isoforms are expressed, originating from alternative splicing of exons 2, 3, and 10 of the MAPT gene. The isoforms differ in the number of N‐terminal inserts (0, 1, or 2N) and the C‐terminal repeat number (3 or 4R). Recent results from murine neurons highlight that the six human‐specific isoforms are differentially localized within neurons and influence microtubule dynamics in an isoform‐specific manner. In this study, we generated a human neuronal model system to further characterize the human‐specific Tau‐isoforms under basic and pathological conditions.MethodWe successfully generated three Tau KO hiPSC cell lines derived from Ngn2‐WTC11 cells using CRISPR/Cas9 and characterized the generated cell lines using genetic, biochemical and microscopy‐based methods.ResultNo difference between Tau KO and WT hiPSCs was observed in the capability of neuronal differentiation or neuronal morphology. Interestingly, Tau KO neurons were shown to be resistant to an Abeta‐induced reduction of network activity. Initial results from re‐expressed Tau‐isoforms in these neurons support the differential localization of the isoforms observed previously. Further experiments will investigate the isoform‐specific role of Tau regarding microtubule dynamics, axonal branching, and synapse formation under basal and pathological conditions.ConclusionTau KO hiPSCs are a versatile tool to study basic as well as pathological functions of Tau. Expected results will provide a major understanding of Tau function and help identifying potential therapeutic targets for the treatment of AD and related neurodegenerative diseases.

A Recent SARS-CoV-2 Infection Enhances Antibody-Dependent Cellular Cytotoxicity against Several Omicron Subvariants following a Fourth mRNA Vaccine Dose.

Since the beginning of the SARS-CoV-2 pandemic, several variants of concern (VOCs), such as the Alpha, Beta, Gamma, Delta and Omicron variants, have arisen and spread worldwide. Today, the predominant circulating subvariants are sublineages of the Omicron variant, which have more than 30 mutations in their Spike glycoprotein compared to the ancestral strain. The Omicron subvariants were significantly less recognized and neutralized by antibodies from vaccinated individuals. This resulted in a surge in the number of infections, and booster shots were recommended to improve responses against these variants. While most studies mainly measured the neutralizing activity against variants, we and others previously reported that Fc-effector functions, including antibody-dependent cellular cytotoxicity (ADCC), play an important role in humoral responses against SARS-CoV-2. In this study, we analyzed Spike recognition and ADCC activity against several Omicron subvariants by generating cell lines expressing different Omicron subvariant Spikes. We tested these responses in a cohort of donors, who were recently infected or not, before and after a fourth dose of mRNA vaccine. We showed that ADCC activity is less affected than neutralization by the antigenic shift of the tested Omicron subvariant Spikes. Moreover, we found that individuals with a history of recent infection have higher antibody binding and ADCC activity against all Omicron subvariants than people who were not recently infected. With an increase in the number of reinfections, this study helps better understand Fc-effector responses in the context of hybrid immunity.

Assessing Reuse of Hypodermic Needles in Mice by means of Digital Imaging, Photomicrography, Bacterial Culture, Analysis of Nest Building, and Animal Vocalization.

Hypodermic needles are sometimes reused in animal research settings to preserve the viability of and to conserve limited quantities of injected material. However, the reuse of needles is strongly discouraged in human medicine to prevent inju- ries and the spread of infectious disease. No official guidelines prohibit needle reuse in veterinary medicine, although the practice may be discouraged. We hypothesized that reused needles would be significantly more blunt than unused needles and that reuse for additional injections would cause more animal stress. To test these ideas, we evaluated mice that were injected subcutaneously in the flank or mammary fat pad to generate cell line xenograft and mouse allograft models. Needles were reused up to 20 times, based on an IACUC-approved protocol. A subset of reused needles was digitally imaged to determine needle dullness based on the area of deformation from the secondary bevel angle; this parameter was not different between new needles and needles that had been reused 20 times. In addition, the number of times a needle was reused was not significantly related to audible mouse vocalization during injection. Finally, nest building scores for mice that were injected with a needle used 0 through 5 times were similar to those of mice injected with a needle had been used 16 through 20 times. Among the 37 reused needles that were tested, 4 were positive for bacterial growth; the only organisms cultured were Staphylococcus spp. Contrary to our hypothesis, reusing needles for subcutaneous injections did not increase animal stress based on analysis of vocalization or nest building.

Rapid cancer cell perineural invasion utilizes amoeboid migration

The invasion of nerves by cancer cells, or perineural invasion (PNI), is potentiated by the nerve microenvironment and is associated with adverse clinical outcomes. However, the cancer cell characteristics that enable PNI are poorly defined. Here, we generated cell lines enriched for a rapid neuroinvasive phenotype by serially passaging pancreatic cancer cells in a murine sciatic nerve model of PNI. Cancer cells isolated from the leading edge of nerve invasion showed a progressively increasing nerve invasion velocity with higher passage number. Transcriptome analysis revealed an upregulation of proteins involving the plasma membrane, cell leading edge, and cell movement in the leading neuroinvasive cells. Leading cells progressively became round and blebbed, lost focal adhesions and filipodia, and transitioned from a mesenchymal to amoeboid phenotype. Leading cells acquired an increased ability to migrate through microchannel constrictions and associated more with dorsal root ganglia than nonleading cells. ROCK inhibition reverted leading cells from an amoeboid to mesenchymal phenotype, reduced migration through microchannel constrictions, reduced neurite association, and reduced PNI in a murine sciatic nerve model. Cancer cells with rapid PNI exhibit an amoeboid phenotype, highlighting the plasticity of cancer migration mode in enabling rapid nerve invasion.

Abstract LB158: Rapid cancer cell perineural invasion utilizes amoeboid migration

Abstract The invasion of nerves by cancer cells, or perineural invasion (PNI), is potentiated by the nerve microenvironment and is associated with adverse clinical outcomes. However, the cancer cell characteristics that enable PNI are poorly defined. Here, we generated cell lines enriched for a rapid neural invasive phenotype by serially passaging pancreatic cancer cells in a murine sciatic nerve model of PNI. Cancer cells isolated from the leading edge of nerve invasion showed a progressively increasing nerve invasion velocity with higher passage number. Transcriptome analysis revealed an upregulation of proteins involving the plasma membrane, cell leading edge, and cell movement in the leading neural-invasive cells. Leading cells progressively became round and blebbed, lost focal adhesions and filipodia, and transitioned from mesenchymal to amoeboid phenotype. Leading cells acquired an increased ability to migrate through microchannel constrictions and associate with dorsal root ganglia than non-leading cells. ROCK inhibition reverted leading cells from an amoeboid to mesenchymal phenotype, reduced migration through microchannel constrictions, reduced neurite association, and reduced PNI in a murine sciatic nerve model. Cancer cells with rapid PNI exhibit an amoeboid phenotype, highlighting the plasticity of cancer migration mode in enabling rapid nerve invasion. Citation Format: Qi Wang, Andrea Marcadis, Elizabeth Kao, Chun-Hao Chen, Laxmi Gusain, Ann Powers, Richard Bakst, Sylvie Deborde, Richard J. Wong. Rapid cancer cell perineural invasion utilizes amoeboid migration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB158.

Abstract 104: The role of APOBEC3A in ovarian cancer progression

Abstract Cancer progression is enabled by the accumulation of somatic mutations and genomic aberrations, leading to metastasis, treatment resistance, and poor clinical outcomes. The analysis of cancer genomes has identified APOBEC3A (A3A) cytidine deaminase activity as a cause of somatic mutagenesis in over 20 tumor types. In particular, A3A mutational signatures are found in a large proportion of ovarian tumors, ranging from 2-26% depending on subtype. Furthermore, genomic analyses of ovarian tumors suggest that A3A mutagenesis occurred during early metastatic progression, indicating the potential for A3A activity to promote clonal evolution. In non-ovarian tumors, A3A activity is associated with metastatic progression through the identification of A3A mutational patterns enriched in or unique to metastatic sites. Therefore, we hypothesized that aberrant A3A activity on OC genomes would increase mutagenesis, promote clonal diversity, and enable tumor progression. To examine the impact of aberrant A3A activity during OC progression, we developed a model system of inducible A3A expression in OC cell lines. We treated cells for 45 days with doxycycline to induce A3A expression (long-term, LT-A3A) and generated three biological replicates by treating individual wells of the parental lines independently. A3A is known to mutate the genome stochastically. Despite this, all versions of LT-A3A cells exhibited similar phenotypes compared to non-treated isogenic controls (NT). LT-A3A cells demonstrated increased colony formation relative to NT cells, indicating improved cell survival. We assessed cellular migration by scratch-wound assays and found that LT-A3A cells exhibited accelerated wound closure rates compared to NT controls, despite similar proliferation rates. In addition, cellular invasion was assessed by spheroid Matrigel invasion assays in which the invasive distance was significantly greater in LT-A3A cells relative to NT controls. By generating cell lines with a catalytically inactive doxycycline-inducible A3A transgene, we determined that the observed A3A-mediated cellular phenotypes were deaminase-dependent. To assess the molecular alterations driving these phenotypic differences, we performed RNA-seq on LT-A3A and NT cell lines. Gene set enrichment analysis of differentially expressed genes identified significant overlap between the Epithelial-Mesenchymal Transition (EMT) and WNT/Beta Catenin, Hedgehog, and TGFβ signaling gene sets. These related signaling pathways converge on the promotion of metastasis and cancer progression. These data suggest that aberrant A3A activity promotes the survival, migration, and invasion of OC cells by altering intracellular signaling pathways that promote EMT. Our ongoing experimental investigation will assess how long-term A3A mutagenesis impacts genomic heterogeneity and how A3A affects tumor behavior in animal models. Citation Format: Jessica Merritt Devenport, Mary Mullen, Katherine Fuh, Abby Green. The role of APOBEC3A in ovarian cancer progression [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 104.

Abstract 1339: Targeting specific extracellular matrix proteins to reactivate T cell trafficking in triple-negative breast cancer

Abstract It is now widely recognised that the tumour microenvironment (TME) is playing a crucial role in promoting tumour immune evasion by modulating the local immune infiltration. A growing body of evidence highlights the crucial role of the tumour extracellular matrix (ECM) in limiting trafficking of newly activated T cells in solid cancers, thus restricting their access to tumour and preventing the success of cancer immunotherapies. Accordingly, we are investigating whether targeting specific tumour ECM components may enhance T cell infiltration in triple-negative breast cancer (TNBC). Matrisome profiling of patient-derived fibroblasts and patient tumour tissues allowed us to identify two matrix proteins overexpressed in tumours and associated with T cell signatures, the matrix proteoglycan, versican (VCAN) and the glycoprotein, fibronectin (FN1). As there are currently no specific inhibitors of matrix proteins, we have modelled their loss-of-function using the clustered, regularly interspaced, short palindromic repeats-associated nuclease Cas9 (CRISPR-Cas9) technology with the goal of engineering cell-editable matrisomes which are enriched, reduced, or absent for specific matrix proteins. First, we constituted a panel of human and murine mammary fibroblast and TNBC cancer cell lines, which we have introduced with an inducible Cas9 protein expression. We measured VCAN and FN1 expression in the panel which showed distinct VCAN levels. Therefore, depending on VCAN basal levels, we have generated cell lines with VCAN overexpression, transient knockdown or stable knockout. Proteomic matrisome profiling of transient VCAN knockdown cells revealed that reducing VCAN may impact ECM abundance by decreasing VCAN direct binding partners. Finally, we used the edited cells to build 2D and 3D in vitro TME models to evaluate the impact of modulating VCAN expression on chimeric antigen receptor (CAR) T cell cytotoxicity and location. In parallel, we built in vivo mouse models of TNBC with controlled ECM deposition. Specifically, we have targeted mVcan and mFn1 in tumours and investigated the impact of their removal on tumour growth and immune cell infiltration. Overall, this work aims to identify immunomodulating features of the ECM which could be targeted to boost response to immunotherapies in solid cancers. Citation Format: Valentine Gauthier, Elly Tyler, Ying Liu, Tyson V. Sharp, Oliver MT Pearce. Targeting specific extracellular matrix proteins to reactivate T cell trafficking in triple-negative breast cancer [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 1339.

Abstract 5380: Systematic evaluation and comparison of drug response prediction models: a case study of prediction generalization across cell lines datasets

Abstract Predictive modeling holds great promise for improving personalized cancer treatment and efficiency of drug development. In recent years, deep learning (DL) has been extensively explored for drug response prediction (DRP), outperforming classical machine learning in prediction generalization to new data. Despite the considerable interest in DRP, no agreed-upon methodology for evaluating and comparing the diverse DL models yet exists. Existing papers generally demonstrate the performance of proposed models using cross-validation within a single cell line dataset and compare with baseline models of their choice, substantially limiting the scope and validity of model evaluation and comparison. In this work, we investigate the ability of DRP models for generalizing predictions across datasets of multiple drug screening studies, a more challenging scenario mimicking practical applications of DRP models. Five cell line datasets and six community DRP models with advanced DL architectures have been explored. Public cell line drug screening datasets have been curated and processed for this analysis, including CCLE, CTRP, GDSC1, GDSC2, and GCSI. For each dataset, the same preprocessing pipeline was used to generate cell line gene expressions, drug representations, and drug response values. The six DRP models include advanced architectures and feature engineering methods such as transformer, graph neural network, and image representation of tabular data. Systematic model curation and training have been applied, including consistent training and testing data splits across models and hyperparameter optimization (HPO). To cope with the large-scale model training and HPO, automatic workflows have been implemented and executed on high-performance computing systems. A 5-by-5 matrix of prediction scores, corresponding to the five datasets in both row and column dimensions, has been generated for each model, with off-diagonal values representing the cross-dataset generalization. Despite the advanced DL techniques, all models exhibit substantially inferior performance in cross-dataset analysis as compared with cross-validation within a single dataset. This result demonstrates the challenge of cross-dataset generalization for DRP and motivates the need for rigorous and systematic evaluation of DRP models, which simulates real-world applications. Citation Format: Alexander Partin, Thomas S. Brettin, Yitan Zhu, Jamie Overbeek, Oleksandr Narykov, Priyanka Vasanthakumari, Austin Clyde, Sara E. Jones, Satishkumar Ranganathan Ganakammal, Justin M. Wozniak, Andreas Wilke, Jamaludin Mohd-Yusof, Michael R. Weil, Alexander T. Pearson, Rick L. Stevens. Systematic evaluation and comparison of drug response prediction models: a case study of prediction generalization across cell lines datasets. [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 5380.

Establishment of cell lines from individual zebrafish embryos.

With the increasing use of fish as model species for research, cell cultures derived from caudal fin explants as well as pre-hatching stage embryos have provided powerful in vitro tools that can complement or serve as an ethically more acceptable alternative to live animal experiments. The widely-used protocols to establish these lines require, as a starting point, homogeneous pools of embryos or viable adult fish which are large enough for collecting sufficient fin tissue. This excludes the use of fish lines with adverse phenotypes or lines that exhibit mortality at early developmental stages and so can only be propagated as heterozygotes. Specifically, when no visually overt mutant phenotype is detectable for identifying homozygous mutants at early embryonic stages, it is then impossible to sort pools of embryos with the same genotypes to generate cell lines from the progeny of a heterozygote in-cross. Here, we describe a simple protocol to generate cell lines on a large scale starting from individual early embryos that can subsequently be genotyped by polymerase chain reaction. This protocol should help to establish fish cell culture models as a routine approach for the functional characterization of genetic changes in fish models such as the zebrafish. Furthermore, it should contribute to a reduction of experiments which are ethically discouraged to avoid pain and distress.