Academic literature on the topic 'Isogenic cellular models'

Neutrophils with immunosuppressive activity are polymorphonuclear myeloid-derived suppressor cells (MDSCs) and may contribute to the resistance to cancer immunotherapy. A major gap for understanding and targeting these cells is the paucity of cell line models with cardinal features of human immunosuppressive neutrophils and their normal counterparts, especially in an isogenic manner. To address this issue, we employ the human promyelocytic cell line HL60 and use DMSO and cytokines (granulocyte macrophage-colony stimulating factor (GM-CSF) and interleukin 6 (IL6)) to induce the formation of either neutrophils or MDSCs. The induced MDSCs are CD11b+ CD33+ HLA-DR−/low and are heterogeneous for CD15 and CD14 expression. The induced MDSCs abrogate IL2 production and activation-induced cell death of the human T cell line Jurkat stimulated by CD3/CD28 antibodies, whereas the induced neutrophils enhance IL2 production from Jurkat cells. The induced MDSCs upregulate the expression of C/EBPβ, STAT3, VEGFR1, FATP2 and S100A8. Lastly, the immunosuppressive activity of the induced MDSCs is inhibited by all-trans retinoic acid and STAT3 inhibitor BP-1-102 through cellular differentiation and dedifferentiation mechanisms, respectively. Together, our study establishes a human isogenic cell line system for neutrophils and MDSCs and this system is expected to facilitate future studies on the biology and therapeutics of human immunosuppressive neutrophils.

The ability to recapitulate muscle differentiation in vitro enables the exploration of mechanisms underlying myogenesis and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases or from healthy subjects poses ethical and procedural challenges that limit such investigations. An alternative consists in converting skin fibroblasts into myogenic cells by forcing the expression of the myogenic regulator MYOD. Here, we directly compared cellular phenotype, transcriptome, and nuclear lamina-associated domains (LADs) in myo-converted human fibroblasts and myotubes differentiated from myoblasts. We used isogenic cells from a 16-year-old donor, ruling out, for the first time to our knowledge, genetic factors as a source of variations between the two myogenic models. We show that myo-conversion of fibroblasts upregulates genes controlling myogenic pathways leading to multinucleated cells expressing muscle cell markers. However, myotubes are more advanced in myogenesis than myo-converted fibroblasts at the phenotypic and transcriptomic levels. While most LADs are shared between the two cell types, each also displays unique domains of lamin A/C interactions. Furthermore, myotube-specific LADs are more gene-rich and less heterochromatic than shared LADs or LADs unique to myo-converted fibroblasts, and they uniquely sequester developmental genes. Thus, myo-converted fibroblasts and myotubes retain cell type-specific features of radial and functional genome organization. Our results favor a view of myo-converted fibroblasts as a practical model to investigate the phenotypic and genomic properties of muscle cell differentiation in normal and pathological contexts, but also highlight current limitations in using fibroblasts as a source of myogenic cells.

Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder caused by mutations in the acid β-glucosidase gene (GBA1). Besides causing GD, GBA1 mutations constitute the main genetic risk factor for developing Parkinson’s disease. The molecular basis of neurological manifestations in GD remain elusive. However, neuroinflammation has been proposed as a key player in this process. We exploited CRISPR/Cas9 technology to edit GBA1 in the human monocytic THP-1 cell line to develop an isogenic GD model of monocytes and in glioblastoma U87 cell lines to generate an isogenic GD model of glial cells. Both edited (GBA1 mutant) cell lines presented low levels of mutant acid β-glucosidase expression, less than 1% of residual activity and massive accumulation of substrate. Moreover, U87 GBA1 mutant cells showed that the mutant enzyme was retained in the ER and subjected to proteasomal degradation, triggering unfolded protein response (UPR). U87 GBA1 mutant cells displayed an increased production of interleukin-1β, both with and without inflammosome activation, α-syn accumulation and a higher rate of cell death in comparison with wild-type cells. In conclusion, we developed reliable, isogenic, and easy-to-handle cellular models of GD obtained from commercially accessible cells to be employed in GD pathophysiology studies and high-throughput drug screenings.

Polyglutamine (polyQ) diseases, including Huntington’s disease, are a group of late-onset progressive neurological disorders caused by CAG repeat expansions. Although recently, many studies have investigated the pathological features and development of polyQ diseases, many questions remain unanswered. The advancement of new gene-editing technologies, especially the CRISPR-Cas9 technique, has undeniable value for the generation of relevant polyQ models, which substantially support the research process. Here, we review how these tools have been used to correct disease-causing mutations or create isogenic cell lines with different numbers of CAG repeats. We characterize various cellular models such as HEK 293 cells, patient-derived fibroblasts, human embryonic stem cells (hESCs), induced pluripotent stem cells (iPSCs) and animal models generated with the use of genome-editing technology.

Multiple endocrine neoplasia type 1 (MEN1) is a rare tumor syndrome that manifests differently among various patients. Despite the mutations in the MEN1 gene that commonly predispose tumor development, there are no obvious phenotype–genotype correlations. The existing animal and in vitro models do not allow for studies of the molecular genetics of the disease in a human-specific context. We aimed to create a new human cell-based model, which would consider the variability in genetic or environmental factors that cause the complexity of MEN1 syndrome. Here, we generated patient-specific induced pluripotent stem cell lines carrying the mutation c.1252G>T, D418Y in the MEN1 gene. To reduce the genetically determined variability of the existing cellular models, we created an isogenic cell system by modifying the target allele through CRISPR/Cas9 editing with great specificity and efficiency. The high potential of these cell lines to differentiate into the endodermal lineage in defined conditions ensures the next steps in the development of more specialized cells that are commonly affected in MEN1 patients, such as parathyroid or pancreatic islet cells. We anticipate that this isogenic system will be broadly useful to comprehensively study MEN1 gene function across different contexts, including in vitro modeling of MEN1 syndrome.

Abstract Abstract 174 Myelodysplastic syndromes (MDS) are clonal hematologic disorders characterized by peripheral blood cytopenias and a dysplastic bone marrow (BM). Despite their relatively high incidence, these syndromes remain poorly understood and poorly studied, largely due to the unavailability of good animal models and the challenges of the ex vivo culture of primary MDS BM cells: their scarcity, poor proliferative potential and cellular heterogeneity. MDS BM cells exhibit poor growth and clonogenic capacity in culture, suggestive of a cell-intrinsic defect, but the cellular processes that are abnormal (e.g. proliferation, differentiation, cell death) remain elusive. We set to establish an in vitro system of pure clonal MDS hematopoiesis as a new platform to investigate the pathophysiology of MDS. We used reprogramming technology to derive induced pluripotent stem cells (iPSCs) from BM mononuclear cells of 3 MDS patients (RAEB by FAB) using our excisable polycistronic lentiviral vector (Papapetrou et al. Nat Biotech, 2009) or Sendai viruses. We derived 4 iPSC lines from a del(20q)-MDS patient (MDS-0), one line from a del(7q)-MDS patient (MDS-206), as well as 10 normal (wt-) iPSC lines derived in parallel in one reprogramming experiment from the same starting BM sample (MDS-206). We also derived 9 iPSC lines with chromosome 7 uniparental disomy (UPD) from a third patient (MDS-L1). Karyotyping and aCGH analyses confirmed that the MDS-iPSC lines harbored typical chromosomal deletions (20q12-q13.2 and 7q21.3-qter, respectively), identical to the starting cells. The wt- iPSCs had a normal karyotype and were confirmed to be isogenic to the del(7q) MDS-206.13 line by DNA fingerprinting. All wt- and MDS-iPSC lines display characteristic morphology and pluripotency marker expression. 6 selected lines were shown to fulfill all criteria of pluripotency, including teratoma formation. One del(7q)- and two del(20q)- iPSC lines so far studied show a 2- to 6- fold reduced proliferation rate (quantified by CFSE dilution and growth curves) compared to that of isogenic and non-isogenic wt-iPSCs, a phenotype much more pronounced in the del(7q) MDS-206.13 line, but absent from all 3 MDS-L1 UPD lines. Cell cycle analysis showed a relative accumulation in G0-G1 phase (40% in MDS-206.13 vs 23–25% in controls). Annexin V staining showed no differences in the percentage of apoptotic cells. Microarray analysis revealed 675 and 780 significantly differentially expressed genes in del(7q) MDS-206.13 and del(20q) MDS-0.12 iPSCs, respectively, compared to the wt MDS-206.12 line. In both cases, these were most enriched in the Gene Ontology categories of cellular growth and proliferation, cellular development and cell death. Ingenuity pathway analysis identified activation of p53 and FOS-JUN (AP1 transcription factor) among predominant potential regulators. Out of ∼1150 protein-coding genes residing in chromosome 7, 102 genes in 7q had reduced expression by at least 1.5-fold (23 of which by 2-fold) in the del(7q) iPSC line MDS-206.13 compared to its isogenic diploid line MDS-206.12. The hematopoietic potential of the MDS-206.13 line and its normal isogenic control MDS-206.12 was assessed in embryoid body differentiation culture with cytokine supplementation. Strikingly, after mesoderm specification for 3 days followed by 10 days of hematopoietic differentiation, less than 1% of MDS-206.13 vs 48% of MDS-206.12 cells became committed to the hematopoietic lineage (CD34+/CD45+co-expression). Consistent with this, hematopoietic colony formation in methylcellulose and further differentiation in erythroid culture of del(7q)-iPSCs was altogether absent, in contrast to the robust clonogenic and erythroid differentiation potential of the isogenic control line. Our data suggest that impaired cell proliferation may be integral to the pathophysiology of del(7q)-MDS. Since this phenotype is predominant in del(7q)-iPSCs, but absent from UPD7-iPSCs, it may be caused by reduced dosage of one or more genes on chromosome 7 (haploinsufficiency). Further studies with additional iPSC lines patient-derived and genetically engineered to harbor artificial 7/7q deletions are underway. In summary, we have developed a novel MDS model of patient-derived and isogenic normal iPSCs. This model should prove useful to study the cellular, molecular and genetic pathogenesis of MDS, identify critical genes and test therapeutic compounds. Disclosures: No relevant conflicts of interest to declare.

Induced pluripotent stem cells (iPSCs) have been established as a reliable in vitro disease model system and represent a particularly informative tool when animal models are not available or do not recapitulate the human pathophenotype. The recognized limit in using this technology is linked to some degree of variability in the behavior of the individual patient-derived clones. The development of CRISPR/Cas9-based gene editing solves this drawback by obtaining isogenic iPSCs in which the genetic lesion is corrected, allowing a straightforward comparison with the parental patient-derived iPSC lines. Here, we report the generation of a footprint-free isogenic cell line of patient-derived TBCD-mutated iPSCs edited using the CRISPR/Cas9 and piggyBac technologies. The corrected iPSC line had no genetic footprint after the removal of the selection cassette and maintained its “stemness”. The correction of the disease-causing TBCD missense substitution restored proper protein levels of the chaperone and mitotic spindle organization, as well as reduced cellular death, which were used as read-outs of the TBCD KO-related endophenotype. The generated line represents an informative in vitro model to understand the impact of pathogenic TBCD mutations on nervous system development and physiology.

Deformability is shown to correlate with the invasiveness and metastasis of cancer cells. Recent studies suggest epithelial-to-mesenchymal transition (EMT) might enable cancer metastasis. However, the correlation of EMT with cancer cell deformability has not been well elucidated. Cellular deformability could also help evaluate the drug response of cancer cells. Here, we combine hydrodynamic stretching and microsieve filtration to study cellular deformability in several cellular models. Hydrodynamic stretching uses extensional flow to rapidly quantify cellular deformability and size with high throughput at the single cell level. Microsieve filtration can rapidly estimate relative deformability in cellular populations. We show that colorectal cancer cell line RKO with the mesenchymal-like feature is more flexible than the epithelial-like HCT116. In another model, the breast epithelial cells MCF10A with deletion of the TP53 gene are also significantly more deformable compared to their isogenic wildtype counterpart, indicating a potential genetic link to cellular deformability. We also find that the drug docetaxel leads to an increase in the size of A549 lung cancer cells. The ability to associate mechanical properties of cancer cells with their phenotypes and genetics using single cell hydrodynamic stretching or the microsieve may help to deepen our understanding of the basic properties of cancer progression.

Le traitement des DMG altérés H3 K27, n’ayant pas connu d’amélioration au cours de ces 50 dernières années, figure parmi les plus grands défis de la neuro-oncologie pédiatrique. En 2012, a été découverte une mutation spécifique de l’histone 3 (oncohistone), dite H3.3 K27M, présentant une prévalence très élevée (70-80% des cas) dans les DMG. Bien que l’impact épigénétique de cette mutation ait été décrit, des études demeurent nécessaires afin de mieux comprendre son rôle dans le phénotype agressif et la réponse aux thérapies des cellules DMG. Afin d’étudier précisément l’impact de la mutation H3.3 K27M sur le phénotype des cellules de DMG,nous avons développé et caractérisé des modèles cellulaires isogéniques complémentaires de gliome pédiatrique de haut grade induits et invalidés pour l’oncohistone. À l’aide de ces modèles, nous souhaitions élucider l’impact de H3.3 K27M sur la biologie des cellules de DMG et leur réponse aux traitements anti-cancéreux, notamment la radiothérapie, unique traitement de référence actuel pour la prise en charge des DMG. Par la caractérisation de nos lignées cellulaires de gliomes pédiatriques sustentoriels induites pourH3.3 K27M, nous avons montré que l’oncohistone impacte la réponse aux radiations ionisantes et à certaines thérapies ciblées de manière dépendante du contexte cellulaire.Sur la base de ce constat, nous avons pris le parti de caractériser les impacts biologiques de l’oncohistone dans un contexte cellulaire plus pertinent de DMG. En ce sens, nous avons établi des modèles cellulaires knock-out pour H3.3 K27M et les avons caractérisés comparativement à leurs lignées cellulaires parentales mutées. Par des caractérisations omiques (transcriptomique et protéomique) et du métabolisme cellulaire de ces modèles, nous avons notamment identifié un impact de la mutation H3.3 K27M sur le métabolisme lipidique des cellules DMG. De surcroit, dans des modèles de sphéroïdes 3D, cette modification du métabolisme lipidique associée à l’oncohistone semblait conditionnée par des facteurs du microenvironnement encore à l’étude.D’autre part, une approche fonctionnelle par criblage pharmacologique nous a permis d’identifier des dépendances à certaines voies de réparation des dommages à l’ADN spécifiquement associées à la mutationH3.3 K27M. De plus, la caractérisation radiobiologique de nos modèles, actuellement en cours, indique une radiosensibilité associée à H3.3 K27M, corrélant avec une diminution de l’efficacité de réparation de l’ADN postirradiation. Au-delà de cet impact sur la réparation des dommages à l’ADN, notre criblage pharmacologique a également révélé une sensibilité exacerbée à certains composés de la famille des glycosides cardiaques induite par H3.3 K27M. Ce résultat apparaît particulièrement intéressant au regard de nos données transcriptomiques montrant un enrichissement en gènes impliqués dans les cardiomyopathies et l’homéostasie ionique parmi les gènes différentiellement exprimés en présence de l’oncohistone. Dans ce contexte, nous avons entrepris l’étude des processus moléculaires et biologiques sous-jacents à cette différence de sensibilité gouvernée parH3.3 K27M.In fine, nous avons utilisé nos modèles cellulaires isogéniques pour montrer que l’oncohistoneH3.3 K27M entraîne des modifications du métabolisme lipidique des cellules de DMG. Ces changements métaboliques pourraient rendre les cellules de DMG altérés H3 K27 plus susceptibles au déclenchement de certaines voies de morts cellulaires (e.g. ferroptose) et affecter la réponse à certaines thérapies. De plus, H3.3K27M semble induire des sensibilités spécifiques, notamment à la radiothérapie et aux glycosides cardiaques [...]
H3K27-altered DMG treatment is one of the most significant challenges in pediatric neuro-oncology,with no improvement in patient survival over the past 50 years. In 2012, it was shown that DMGs harbor a specific histone 3 mutation (oncohistone) called H3.3 K27M with a very high prevalence (70-80% of cases). Although theH3.3 K27M impact on the epigenetic landscape has been well described, studies are needed to understand betterits role in DMG cells’ aggressiveness and response to therapies.To study the H3.3 K27M mutation impact on DMG cell phenotypes precisely, we developed andcharacterized pediatric high-grade glioma isogenic cellular models induced and knock-out for the oncohistone.Using these models, we aimed to decipher the oncohistone impact on DMG cell biology and response to anticancertherapies, including radiation therapy, the only current standard of care for DMGs. Characterization of our H3.3 K27M-induced pediatric supratentorial glioma cell lines reveals that the oncohistone affects the response to ionizing radiations and specific targeted therapies in a cellular context-dependentway. Based on these results, we settled to characterize oncohistone biological impacts in a more relevant cellular context of DMG. In that sense, we established H3.3 K27M knock-out cellular models and characterized them regarding their parental DMG H3.3 K27M mutated cell lines. Through omic (transcriptomic and proteomic)and cell metabolism characterizations of these models, we notably showed the H3.3 K27M mutation impact on DMG cells’ lipid metabolism. In 3D spheroid models, this H3.3 K27M-induced lipid metabolism rewiring appeared conditioned by microenvironment factors still under investigation.On the other hand, a functional pharmacological screen identified H3.3 K27M-driven dependencies tospecific DNA repair pathways. In addition, ongoing radiobiological characterization of our models indicates anH3.3 K27M-associated radiosensitivity correlating with a decrease in DNA repair efficiency following ionizingradiations. Beyond this DNA repair impact, our pharmacological screen also revealed an H3.3 K27M-relatedsensitivity to cardiac glycoside drugs. This result makes sense with our transcriptomic data showing enrichmentin genes involved in cardiomyopathies and ion homeostasis among differentially expressed genes with theoncohistone. In this context, we began unraveling the molecular and biological processes underlying thisH3.3 K27M-driven effect.Finally, we used our isogenic cellular models to show that the H3.3 K27M oncohistone drives lipidmetabolism modifications. These metabolic changes could prime H3K27-altered DMG cells to specific regulatedcell death pathways (e.g., ferroptosis) and affect the response to certain therapies. Moreover, the H3.3 K27Mseems to drive specific sensitivities, notably to radiation therapy and cardiac glycoside drugs. Understanding the underlying molecular mechanisms governing these H3.3 K27M-associated Achille heels could highlight newinsights into the oncohistone role in DMG cells and provide rationales for developing new therapeutic strategies