scholarly journals Lineage Tracing in Chronic Lymphocytic Leukemia Reveals Clones with Stable Gene Expression States That Differentially Respond to Therapy

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1229-1229
Author(s):  
Catherine Gutierrez ◽  
Aziz Al'Khafaji ◽  
Eric Brenner ◽  
Russell Durrett ◽  
Kaitlyn Johnson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Research Funding ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
Stable Gene ◽  
High Tolerance ◽  
Clonal Composition ◽  
Stable Gene Expression

Cancer's ability to evolve and adapt is a major challenge to therapeutic success. Fueling this evolution is vast tumor heterogeneity, with constituent clones varying in their genetics, epigenetics and response to therapy. As a field, however, we have yet to couple the genetic alterations present within individual clones to their transcriptional or functional outputs. Here, we applied a novel adaptation of clone tracing that integrates DNA barcoding with single-cell RNA sequencing (scRNA-seq) to HG3, a CLL cell line harboring del(13q) and no other known cancer drivers, to model in vitro responses to front-line chemotherapy with fludarabine and cyclophosphamide at clone-level resolution. To generate a high-diversity barcode library compatible with scRNA-seq, a random pool of 20 base pair DNA barcodes was introduced into the 3'UTR of a reporter gene in a lentiviral expression vector. This viral barcode library was transduced into HG3 cells (at MOI 0.1 to minimize multiple barcode-tagging of cells) and 1.2x106 barcoded cells were sorted and expanded to establish the parental barcoded HG3 population. We subsequently treated this barcoded population with an LD95 combined dose of fludarabine and mafosfamide (the in vitro analog of cyclophosphamide) in 8 parallel experiments. Cell barcodes were sequenced prior to treatment (TP1) and following outgrowth from treatment (TP2) for analysis of clonal composition. 10,000 cells each from TP1 and from 2 of 8 parallel replicates at TP2 were processed for scRNA-seq. We observed a massive decrease in viability across all 8 replicates, with regrowth occurring at 20 days post-treatment. Barcode analysis revealed a marked decrease in clonal diversity from TP1 to TP2 (11,827 to 2,622 ± 380, n=8; or ~78%), and clones that survived treatment did so consistently such that 94% of surviving cells in each replicate had a clonal identity that was present in all 8 replicates. Analysis of clonally-resolved transcriptional profiles revealed that clones consistently fell into one of two stable gene expression states (clusters) prior to treatment, with nominal intermixing between populations. Treatment predominantly selected for clones comprising the smaller of these two clusters (TP1-'high tolerance'), with only a minimal number of resistant clones originating from the larger cluster at TP1 (TP1-'low tolerance'). Pathway and gene set enrichment analysis of these two TP1 clusters demonstrated that TP1-high tolerance had a stark upregulation of common CLL signaling pathways (i.e. WNT and CXCR4, an inflammatory/migratory phenotype) and a reliance on chromatin modification pathways. TP1-low tolerance, on the other hand, exhibited upregulated type 2 antigen presentation and prostaglandin biosynthesis/metabolism which has a known role in driving inflammation and migration in adjacent cells (Wang et al, BMJ 2006). These gene expression states remained stable after treatment, but with the added upregulation of well-described mechanisms of resistance to cyclophosphamide, with TP1-high tolerance exhibiting upregulation of GSTP1, a glutathione S-transferase that is a main mediator of cyclophosphamide metabolism, and TP1-low tolerance exhibiting upregulation of members of the ALDH family thought to ameliorate toxicity from chemotherapy-induced ROS (Andersson et al, Acta Oncologica 1995). Through this work, we resolved the underlying clonal composition of a CLL cell line and observed that the constituent clones exhibit stable and discrete gene expression states that differentially respond to chemotherapy. We noted two different axes of resistance - a more successful avenue that relies on WNT and CXCR4 signaling as well as cyclophosphamide clearance for resistance, and a less-successful avenue that involves clearance of reactive oxygen species for survival. The intersection of these two critical CLL pathways in in vitro resistance to first-line CLL therapy is of particular interest given the FAT1 (WNT regulator) mutations and CXCR4 upregulation frequently seen in chemo-refractory CLL (Messina et al, Blood 2014; Burger et al, Blood 2006), and future efforts will assess the stability and interplay of these two pathways in patient samples collected upon relapse to fludarabine and cyclophosphamide. Further, our approach provides a template for the high-resolution study of tens of thousands of clones and their respective phenotypes in a mixed leukemic population. Disclosures Neuberg: Pharmacyclics: Research Funding; Madrigal Pharmaceuticals: Equity Ownership; Celgene: Research Funding. Wu:Pharmacyclics: Research Funding; Neon Therapeutics: Other: Member, Advisory Board.

Deregulated Apoptotic Pathways Point to Effectiveness of IAP Inhibitor Therapy in Acute Myeloid Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1275-1275
Author(s):  
Sonja C Lück ◽  
Annika C Russ ◽  
Konstanze Döhner ◽  
Ursula Botzenhardt ◽  
Domagoj Vucic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Cell Line ◽  
Cell Lines ◽  
Myeloid Leukemia ◽  
Gene Set Enrichment Analysis ◽  
Core Binding Factor ◽  
Binding Factor ◽  
Acute Myeloid

Abstract Abstract 1275 Poster Board I-297 Core binding factor (CBF) leukemias, characterized by translocations t(8;21) or inv(16)/t(16;16) targeting the core binding factor, constitute acute myeloid leukemia (AML) subgroups with favorable prognosis. However, 40-50% of patients relapse, and the current classification system does not fully reflect the heterogeneity existing within the cytogenetic subgroups. Therefore, illuminating the biological mechanisms underlying these differences is important for an optimization of therapy. Previously, gene expression profiling (GEP) revealed two distinct CBF leukemia subgroups displaying significant outcome differences (Bullinger et al., Blood 2007). In order to further characterize these GEP defined CBF subgroups, we again used gene expression profiles to identify cell line models similar to the respective CBF cohorts. Treatment of these cell lines with cytarabine (araC) revealed a differential response to the drug as expected based on the expression patterns reflecting the CBF subgroups. In accordance, the cell lines resembling the inferior outcome CBF cohort (ME-1, MONO-MAC-1, OCI-AML2) were less sensitive to araC than those modeling the good prognostic subgroup (Kasumi-1, HEL, MV4-11). A previous gene set enrichment analysis had identified the pathways Caspase cascade in apoptosis and Role of mitochondria in apoptotic signaling among the most significant differentially regulated BioCarta pathways distinguishing the two CBF leukemia subgroups. Thus, we concluded that those pathways might be interesting targets for specific intervention, as deregulated apoptosis underlying the distinct subgroups should also result in a subgroup specific sensitivity to apoptotic stimuli. Therefore, we treated our model cell lines with the Smac mimetic BV6, which antagonizes inhibitor of apoptosis (IAP) proteins that are differentially expressed among our CBF cohorts. In general, sensitivity to BV6 treatment was higher in the cell lines corresponding to the subgroup with good outcome. Time-course experiments with the CBF leukemia cell line Kasumi-1 suggested a role for caspases in this response. Interestingly, combination treatment of araC and BV6 in Kasumi-1 showed a synergistic effect of these drugs, with the underlying mechanisms being currently further investigated. Based on the promising sensitivity to BV6 treatment in some cell lines, we next treated mononuclear cells (mostly leukemic blasts) derived from newly diagnosed AML patients with BV6 in vitro to evaluate BV6 potency in primary leukemia samples. Interestingly, in vitro BV6 treatment also discriminated AML cases into two distinct populations. Most patient samples were sensitive to BV6 monotherapy, but about one-third of cases were resistant even at higher BV6 dosage. GEP of BV6 sensitive patients (at 24h following either BV6 or DMSO treatment) provided insights into BV6-induced pathway alterations in the primary AML patient samples, which included apoptosis-related pathways. In contrast to the BV6 sensitive patients, GEP analyses of BV6 resistant cases revealed no differential regulation of apoptosis-related pathways in this cohort. These results provide evidence that targeting deregulated apoptosis pathways by Smac mimetics might represent a promising new therapeutic approach in AML and that GEP might be used to predict response to therapy, thereby enabling novel individual risk-adapted therapeutic approaches. Disclosures Vucic: Genentech, Inc.: Employment. Deshayes:Genentech, Inc.: Employment.

Connecting gene expression subtypes of colorectal cancer (CRC) with cell lines and drug resistance.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e14544-e14544
Author(s):  
Eva Budinska ◽  
Jenny Wilding ◽  
Vlad Calin Popovici ◽  
Edoardo Missiaglia ◽  
Arnaud Roth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Clinical Significance ◽  
Cell Lines ◽  
Drug Response ◽  
Drug Sensitivity ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis

e14544 Background: We identified CRC gene expression subtypes (ASCO 2012, #3511), which associate with established parameters of outcome as well as relevant biological motifs. We now substantiate their biological and potentially clinical significance by linking them with cell line data and drug sensitivity, primarily attempting to identify models for the poor prognosis subtypes Mesenchymal and CIMP-H like (characterized by EMT/stroma and immune-associated gene modules, respectively). Methods: We analyzed gene expression profiles of 35 publicly available cell lines with sensitivity data for 82 drug compounds, and our 94 cell lines with data on sensitivity for 7 compounds and colony morphology. As in vitro, stromal and immune-associated genes loose their relevance, we trained a new classifier based on genes expressed in both systems, which identifies the subtypes in both tissue and cell cultures. Cell line subtypes were validated by comparing their enrichment for molecular markers with that of our CRC subtypes. Drug sensitivity was assessed by linking original subtypes with 92 drug response signatures (MsigDB) via gene set enrichment analysis, and by screening drug sensitivity of cell line panels against our subtypes (Kruskal-Wallis test). Results: Of the cell lines 70% could be assigned to a subtype with a probability as high as 0.95. The cell line subtypes were significantly associated with their KRAS, BRAF and MSI status and corresponded to our CRC subtypes. Interestingly, the cell lines which in matrigel created a network of undifferentiated cells were assigned to the Mesenchymal subtype. Drug response studies revealed potential sensitivity of subtypes to multiple compounds, in addition to what could be predicted based on their mutational profile (e.g. sensitivity of the CIMP-H subtype to Dasatinib, p<0.01). Conclusions: Our data support the biological and potentially clinical significance of the CRC subtypes in their association with cell line models, including results of drug sensitivity analysis. Our subtypes might not only have prognostic value but might also be predictive for response to drugs. Subtyping cell lines further substantiates their significance as relevant model for functional studies.

scholarly journals Unleashing Cell-Intrinsic Inflammation As a Strategy to Kill AML Blasts

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3305-3305
Author(s):  
Jana M Ellegast ◽  
Gabriela Alexe ◽  
Amanda Hamze ◽  
Shan Lin ◽  
Maxim Pimkin ◽  
...  
Keyword(s):  
Cell Death ◽  
Inflammatory Response ◽  
Cell Line ◽  
Research Funding ◽  
Gene Set Enrichment Analysis ◽  
Luciferase Reporter ◽  
Inflammatory Signaling ◽  
Inflammatory Pathways

Abstract Leukemic blasts are immune cells gone awry. We hypothesized that dysregulation of inflammatory pathways contributes to the maintenance of their leukemic state and can be exploited as cell-intrinsic, self-directed immunotherapy. To test the hypothesis, we analyzed three large, independent data collections from primary acute myeloid leukemia (AML) samples and identified an AML subgroup of approximately 40% of all samples enriched for immune and inflammatory pathways. Moreover, we observed a positive correlation between the enrichment of inflammatory response and a monocytic lineage signature in these primary AML samples. To discover genetic vulnerabilities in AML cells implicated in inflammatory pathways, we integrated data from the Cancer Dependency Map on 789 cancer cell lines with two independent genome-wide screens. We identified the immune modulator interferon regulatory factor 2 binding protein 2 (IRF2BP2) as a selective dependency in AML. We validated AML cell dependency on IRF2BP2 with orthogonal genetic and degradation approaches in vitro and in vivo. Genetic perturbation and degradation of IRF2BP2 translated into a reduction of AML cell line viability and decreased colony formation capacity in vitro and impaired leukemia progression in vivo in AML cell line xenografts. Moreover, inducible knock-out of IRF2BP2 significantly attenuated disease burden in multiple patient-derived xenograft models of AML and prolonged survival. Mechanistically, IRF2BP2 repression induced cell death with hallmarks of apoptosis, evidenced by an increase in annexin V/PI-positive cells and induction of cleaved caspase 3 and 8. To decipher the role of IRF2BP2 in inflammatory signaling, we studied its localization on chromatin and its relationship to histone marks and RNA polymerase II binding in AML cells. We determined that IRF2BP2 binds at both enhancers and promotors. Global gene expression profiling, performed six hours after degradation of IRF2BP2, identified significantly more genes increased than decreased in expression. Most upregulated genes were bound by IRF2BP2 at baseline and gained H3K27ac at enhancers with IRF2BP2 degradation. All told, our data support a role for IRF2BP2 as a transcriptional repressor in AML. Gene set enrichment analysis of the genes directly regulated by IRF2BP2 identified immune response signatures as the top enriched gene sets, with genes regulated by NF-kB in response to TNFa being the most significantly enriched. We thus hypothesized that IRF2BP2 is a repressor of NF-kB mediated TNFa signaling that, when acutely perturbed, leads to leukemia cell death. Indeed, we observed an activation of NF-κB signaling in a luciferase reporter assay, an increase in nuclear NF-kB (RELA) protein levels, and a gain in NF-κB chromatin binding following degradation of IRF2BP2 in AML cells. Moreover, a mutant "super-repressor" allele of IkBa rescued the impaired cell growth upon IRF2BP2 perturbation in AML cells, supporting cell death associated with IRF2BP2 loss being mediated through activation of NF-kB signaling. In addition, we identified IL-1ß as an enhancer of the inflammatory response repressed by IRF2BP2. In summary, we have demonstrated that IRF2BP2 represses IL-1ß/TNFα signaling via NF-κB, and IRF2BP2 perturbation results in an acute inflammatory state leading to AML cell death. These findings elucidate a hitherto unexplored AML dependency, reveal cell-intrinsic inflammatory signaling as a mechanism priming leukemic blasts for regulated cell death, and establish IRF2BP2-mediated transcriptional repression as a mechanism for blast survival. Disclosures Dharia: Genentech: Current Employment. Benajiba: Gilead: Research Funding; Pfizer: Research Funding. Gray: Gatekeeper, Syros, Petra, C4, Allorion, Jengu, B2S, Inception and Soltego: Consultancy, Research Funding. Stegmaier: Auron Therapeutics, Kronos Bio, AstraZeneca, Novartis Institute of Biomedical Research: Consultancy, Research Funding.

Stable gene expression in vitro

Nature ◽  
1982 ◽  
Vol 297 (5866) ◽  
pp. 457-458 ◽  
Author(s):  
H.R. Woodland
Keyword(s):  
Gene Expression ◽  
Stable Gene ◽  
Stable Gene Expression

scholarly journals Transcriptional Regulation of Hematopoietic Stem Cells in Aging and Myelodysplastic Syndrome Reveals DDIT3 As a Potential Driver of Transformation

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3764-3764
Author(s):  
Teresa Ezponda ◽  
Juan P. Romero ◽  
Marina Ainciburu ◽  
Ana Alfonso ◽  
Nerea Berastegui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Board Of Directors ◽  
Research Funding ◽  
Expression Profiles ◽  
Genetic Alterations ◽  
Transcriptional Profile ◽  
Gene Set Enrichment Analysis ◽  
Advisory Committees ◽  
Hematopoietic Stem ◽  
Transcriptional Changes

Myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell (HSC) malignancies characterized by ineffective hematopoiesis. Genetic alterations do not fully explain the molecular pathogenesis of the disease, indicating that other types of lesions, such as transcriptional aberrations, may play a role in its development. Moreover, MDS prevalence is almost exclusive to older patients, suggesting that elderly-related alterations may predispose to the development of this clinical entity. Thus, study of the transcriptional lesions occurring in the aging-MDS axis could shed some light of the molecular bases of the disease. To characterize the transcriptional profile of HSCs in aging and MDS, we isolated CD34+, CD38-, CD90+, CD45RA- cells from 11 untreated MDS patients with unilineage and multilineage dysplasia (median of 75 y/o), as well as from 16 young and 8 elderly healthy donors (median of 21 and 70 y/o, respectively), and their expression profile was analyzed using MARS-seq. Unsupervised principal component analysis demonstrated that the three groups of HSCs clustered separately, indicating that different expression profiles characterize healthy young and elderly, and MDS-associated HSCs. To better understand the gene expression deregulation of HSCs, we analyzed the transcriptional dynamisms along the aging-MDS axis, detecting groups of genes following different patterns of expression. Some gene clusters showed exclusive alteration either in aging or in the progression from elderly HSCs to MDS-HSCs, other groups of genes presented a continuous alteration along the axis, and some displayed opposite regulation in aging and in the transition to MDS (Figure 1). Genes showing specific downregulation in aging were involved in DNA damage sensing and repair, and in cell cycle regulation, whereas genes overexpressed in this process were enriched in apoptosis regulators and in cancer-associated genes, including AML-related factors. These findings indicate that transcriptional changes in aging may predispose for MDS and AML, and potentially other malignancies. Interestingly, we detected a group of genes in which the age-mediated upregulation of gene expression was reversed to that of young HSCs in MDS, indicating a "rejuvenation" profile of malignant HSCs. These genes were involved in response to inflammation, to different types of stress conditions such as hypoxia or radiation, and to cytokines. Elderly HSCs may upregulate such genes in response to the known inflammatory microenvironment of elderly bone marrow. Intriguingly, the decrease in expression detected in MDS suggests that malignant HSCs lose the ability of reacting to such stimuli, possibly favoring their survival in a hostile microenvironment. Finally, the analyses performed allowed for the identification of genes showing MDS-specific deregulation. Genes specifically overexpressed in MDS compared to normal (both young and elderly) HSCs, we enriched in transcriptional and epigenetic regulators, and among them, we detected the presence of DDIT3/CHOP, a member of the CCAAT/enhancer-binding protein (C/EBP) family of transcription factors. To determine its potential effects on hematopoietic deregulation, DDIT3 was exogenously overexpressed in healthy HSCs. Notably, its upregulation produced an erythroid bias in an ex-vivo differentiation system, with an increase in the percentage of erythroblasts and a decrease in granulocytes and monocytes compared to HSCs transduced with the empty vector. Transcriptomic analysis of transduced HSCs not subjected to differentiation demonstrated how DDIT3 overexpression produced an erythroid-prone state of HSCs, suggesting it may act as a pioneer factor in MDS-HSCs. Furthermore, gene set enrichment analysis showed that DDIT3 overexpression produced an MDS-like transcriptional profile, suggesting this factor may be key in the acquisition of the disease. Altogether, our results demonstrate that HSCs undergo transcriptional changes in the aging-MDS axis that may alter their intrinsic functions as well as their response to the microenvironment, ultimately contributing to the acquisition of the disease. In particular, our data show that DDIT3 may be a potential driver of MDS transformation. Disclosures Paiva: Amgen, Bristol-Myers Squibb, Celgene, Janssen, Merck, Novartis, Roche, and Sanofi; unrestricted grants from Celgene, EngMab, Sanofi, and Takeda; and consultancy for Celgene, Janssen, and Sanofi: Consultancy, Honoraria, Research Funding, Speakers Bureau. Díez-Campelo:Celgene Corporation: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding.

scholarly journals Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kornphimol Kulthong ◽  
Guido J. E. J. Hooiveld ◽  
Loes Duivenvoorde ◽  
Ignacio Miro Estruch ◽  
Victor Marin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Culture Conditions ◽  
Gene Set Enrichment Analysis ◽  
Shear Stresses ◽  
Static Culture ◽  
Dynamic Culture ◽  
Intestinal Segments ◽  
On Chip

AbstractGut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. For this we applied whole genome transcriptomics. Dynamic culture conditions led to a total of 5927 differentially expressed genes (3280 upregulated and 2647 downregulated genes) compared to static culture conditions. Gene set enrichment analysis revealed upregulated pathways associated with the immune system, signal transduction and cell growth and death, and downregulated pathways associated with drug metabolism, compound digestion and absorption under dynamic culture conditions. Comparison of the in vitro gene expression data with transcriptome profiles of human in vivo duodenum, jejunum, ileum and colon tissue samples showed similarities in gene expression profiles with intestinal segments. It is concluded that both the static and the dynamic gut-on-chip model are suitable to study human intestinal epithelial responses as an alternative for animal models.

Electric field-mediated DNA transfer: transient and stable gene expression in human and mouse lymphoid cells

1986 ◽  
Vol 6 (2) ◽  
pp. 703-706
Author(s):  
F Toneguzzo ◽  
A C Hayday ◽  
A Keating
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Lymphoid Cell ◽  
Simian Virus 40 ◽  
Lymphoid Cells ◽  
Dna Transfer ◽  
Stable Gene ◽  
Regulatory Sequences ◽  
Stable Gene Expression ◽  
Lymphoid Cell Lines

The technique of DNA transfer by electroporation was investigated in an effort to evaluate its utility for the identification of developmentally controlled regulatory sequences. Transient and stable gene expression was detected in a variety of lymphoid cell lines subjected to electroporation. No correlation existed between the levels of chloramphenicol acetyltransferase (acetyl-CoA; chloramphenicol 3-O-acetyltransferase, EC 2.3.1.28) expression and stable transfection frequency. In all lymphoid cell lines tested, the simian virus 40 early region was a better promoter than was the Rous sarcoma virus long terminal repeat.

scholarly journals Downregulation of Prdm16 mRNA is a specific antileukemic mechanism during HOXB4-mediated HSC expansion in vivo

Blood ◽  
2014 ◽  
Vol 124 (11) ◽  
pp. 1737-1747 ◽  
Author(s):  
Hui Yu ◽  
Geoffrey Neale ◽  
Hui Zhang ◽  
Han M. Lee ◽  
Zhijun Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stable Gene ◽  
Self Renewal ◽  
Key Points ◽  
Stable Gene Expression

Key Points HOXB4 induces stable gene expression changes in transplanted HSCs that drive balanced self-renewal and differentiation divisions. Marked downregulation of Prdm16 occurs concurrently with HOXB4-mediated HSC expansion and functions to prevent leukemia in vivo.

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