Diffuse midline glioma (DMG) is a highly aggressive and untreatable pediatric cancer primarily arising in the pontine brainstem region, necessitating the development of representative models for treatment advance. Here we developed an FGF4-driven human brainstem organoid model, which we used to genetically engineer H3.3K27M-altered DMG. We demonstrated that brainstem pontine glial specification is critical for DMG tumorigenesis, yielding infiltrative tumors that recapitulate patient-representative intratumoral heterogeneity. Prolonged GD2 chimeric antigen receptor (CAR) T cell treatment mirrored clinical outcomes and revealed extensive transcriptional heterogeneity, from which both potent effector and dysfunctional CAR T cell populations could be identified. Furthermore, incorporation of myeloid cells generated DMG-specific microglia that reduced treatment efficacy and revealed CAR T cell functional states most vulnerable to microglia-mediated immunosuppression. Thus, we present a representative DMG model offering a months-long experimental window in vitro, which we leveraged to delineate CAR T cell functionality and microglial impact, aiding therapy development for this devastating disease. Bessler et al. developed a human organoid model for H3.3K27M-altered diffuse midline glioma that recapitulates key tumor features and demonstrated its utility for modeling CAR T cell and microglia functions.

This protocol details the transcriptomic analyses conducted to characterize a newly developed brainstem-regionalized organoid (BrO) and its corresponding diffuse midline glioma–bearing organoid (DMGO). Bulk RNA sequencing was used to evaluate media optimization and protocol standardization, focusing on the comparative effects of FGF4 versus FGF2 in hindbrain-pontine regionalization and assessing potential batch variability. Single-cell (sc) RNA sequencing provided a comprehensive cellular and molecular characterization of the BrO and the de novo DMG tumors arising within it, complemented by TrackerSeq-based genetic lineage tracing to investigate mechanisms of clonal expansion and tumor support. The protocol is expected to yield a robust transcriptional framework describing BrO patterning and DMG development, validate FGF4 as a key driver of pontine identity, andreveal pontine-glial lineage-specific dynamics underlying tumor growth within DMGO.

The genome duplication program is affected by multiple factors in vivo, including developmental cues, genotoxic stress, and aging. Here, we monitored DNA replication initiation dynamics in regenerating livers of young and old mice after partial hepatectomy to investigate the impact of aging. In young mice, the origin firing sites were well defined; the majority were located 10-50 kb upstream or downstream of expressed genes, and their position on the genome was conserved in human cells. Old mice displayed the same replication initiation sites, but origin firing was inefficient and accompanied by a replication stress response. Inhibitors of the ATR checkpoint kinase fully restored origin firing efficiency in the old mice but at the expense of an inflammatory response and without significantly enhancing the fraction of hepatocytes entering the cell cycle. These findings unveil aging-dependent replication stress and a crucial role of ATR in mitigating the stress-associated inflammation, a hallmark of aging.

Abstract Diffuse Midline Glioma (DMG) is a rare and aggressive pediatric cancer with no chance of survival, demonstrating a critical need for therapy development. Predictive preclinical models that take into account the unique developmental background and anatomical environment of DMG, are so far lacking. We developed a new regionally patterned brain organoid protocol based on a timely regulated sequence of morphogens. The patterned organoids give rise to pontine and medulla oblongata identity, as confirmed by transcriptomic profiling and immunofluorescence imaging. As the tissue matures, the complexity inherently takes shape and gives rise to pons-specific neurons and glial cells, offering the first human in vitro model for this region of the brain. Introducing H3K27M, including its partner mutations P53 and PDGFRA-D842V via electroporation forms de novo H3K27M diffuse midline glioma with a similar genetic make-up as found in patients. Indeed, contrary to common cell lines or PDX models, single cell sequencing and 3D imaging reveal that Organoid-DMG resembles WHO-defined primary patient cancer, including its diverse cell population heterogeneity and invasive nature. Utilizing barcode-based lineage tracing allows us to unravel and track the cancerous developmental evolution. Thus, we can now model early emerging populations and identify their transcriptomic signatures, which is conceptually impossible to conduct with patient-derived tumor tissue. In summary, we generated a bona fide DMG in vitro model which will give insights into tumorigenesis of DMG and ultimately contribute to pre-clinical drug- and immunotherapy development.

Abstract Background The maintenance of genome stability is a key process to slow aging. One of the mechanisms ensuring this stability is the correct coordination of origins of replication (ORI), resulting in the successful transmission of DNA. Previously, we mapped and compared ORI firing between young and aged mice in vivo, using a regenerating liver mouse model. We confirmed a decreased hepatocyte ORI efficiency in aged mice, known to have impaired liver regeneration. ORI firing proved to be fully rescued when blocking the aged mice's ATR serine/threonine-protein kinase, suggesting that the DNA replication checkpoint actively mediates ORI firing impairment upon DNA damage detection. Aims To explore DNA damage differences between young and aged mice regenerating livers. Methods To induce proliferation, mice were subjected to partial hepatectomy (PH) and liver sections were harvested at different timepoints. Immunohistochemistry staining (IHC) were used to address proliferation and DNA damage, using Ki67 and serine 139 phosphorylated histone H2AX (g-H2AX) as markers, respectively. Results We confirmed a lack of Ki67 signal in young and aged mice prior to PH. The signal takes off at 24-28h post-PH and reaches its peak at 36-48h, which is significantly lower in aged mice. After 48h post-PH, young hepatocytes’ Ki67 reaches its basal level 120h post-PH. However, aged hepatocytes’ Ki67 is maintained at low levels overtime. Next, we compared DNA damage kinetics between young and aged mice livers. Both mouse groups present an increase of g-H2AX upon PH, higher in young mice. The g-H2AX signal decreases in young hepatocytes after 48h post-PH until disappearing 120h post PH. Aged mice hepatocytes maintain the g-H2AX rates overtime after 48h post-PH. Conclusions Our data suggests that hepatocytes develop DNA damage upon proliferation, which is able to be resolved in young mice hepatocytes but remains present in aged livers, ultimately leading to impaired liver regeneration.

Abstract BACKGROUND Diffuse Midline Glioma (DMG) is a rare and aggressive pediatric brain cancer with no chance of survival, highlighting a critical need for therapy development. Disease representative models can aid the search for effective treatments, but human preclinical models that reflect the unique developmental features and anatomical environment of DMG, are so far lacking. Latest research on DMG suggest a fetal neurodevelopmental origin with a stem cell-like cellular profile. Here, we developed a novel pontine hindbrain model to create de novo H3K27M DMG and applied it to study early tumorigenesis and immunotherapy response. MATERIAL AND METHODS Timely sequenced morphogens were applied to developing cerebral organoids, to create a new pontine patterned brain organoid model. Bulk sequencing and 3D imaging over a period of 16 weeks were used to determine ideal patterning conditions, confirm the correct brain regionality and reconstruct cellular developmental dynamics. Introducing H3K27M with common pontine mutations P53 and PDGFRA-D842V via electroporation resulted in de novo H3K27M DMG, which subsequently was characterized based on WHO-histopathological criteria and single cell sequencing. Exploiting this new human DMG model, we applied barcode-based genetic lineage tracing paired with single cell sequencing, to delineate tumorigenesis, and anti-GD2 chimeric antigen receptor (CAR) T cell therapy to investigate CAR T cell responses. RESULTS Our novel pontine hindbrain organoid model inherently gives rise to all relevant macroglia and pons-specific neurons, resembling the same developmental dynamics as seen in humans. Moreover, de novo DMG introduced in these pontine organoids strongly resembles patient cancer, including its cellular human-specific heterogeneity and invasive nature, outperforming existing gold standard PDX and cell line models. As a first model for investigating DMG, the applied barcoded lineage-tracing delineates cancerous transforming precursor states and how they contribute to the diverse lineage among known DMG cancer cell populations. Finally, administration of CAR T cells recreates treatment outcomes observed in patients and demonstrates a high level of CAR T cell heterogeneity. CONCLUSION We generated a bona fide DMG pontine hindbrain organoid model, the first human in vitro model for this specific region of the brain. The matching resemblance to patient tumor paired with the relevant healthy brain environment gives this model the potential for new insights into DMG early tumorigenesis and microenvironmental impact, as well as next generation therapy development.

The LIM-domain protein Ajuba is associated with cell proliferation, a fundamental process of tissue regeneration and cancer. We report that in the liver, Ajuba expression is increased during regeneration and in tumour cells and tissues. Knockout of Ajuba using CRISPR/Cas9 is embryonic lethal in mice. shRNA targeting of Ajuba reduces cell proliferation, delays cell entry into S-phase, reduces cell survival and tumour growth in vivo and increases expression of the DNA damage marker gamma H2AX. Ajuba binding partners include proteins involved in DNA replication and damage, such as SKP2, MCM2, MCM7 and RPA70. Taken together, our data support that Ajuba promotes liver cell proliferation associated with development, regeneration and tumour growth and is involved in DNA replication and damage repair.

Summary The liver is exemplar to study tissue regeneration due to its inherent ability of repair and regrowth. It replaces its lost or injured tissue by the proliferation, interaction and temporal coordination of multiple residential cell types. Until now we lacked a detailed description of the specific contributions of each cell type to the regenerative process, and therefore analyzed mouse livers 0, 3, 6, and 24 hours following two-thirds partial hepatectomy (PHx) by single cell RNA-sequencing (scRNA-seq) and mass cytometry. Our resulting genome wide temporal atlas contains the time dependent transcriptional changes in hepatocytes, endothelial cells, bone marrow-derived macrophages (BMDM) and Kupffer cells. In addition, it describes the cell specific contribution of mitogenic growth factors from biliary epithelial, endothelial and stellate cells as well as chemokines and cytokines from BMDM and granulocytes. And interestingly, Kupffer cells as opposed to hepatocytes emerged as the first cell to proliferate presenting a new dynamic in the liver following PHx. Here, we provide a robust data set at cellular resolution to uncover new elements and revisit current dogmas on the mechanisms underlying liver regeneration. To facilitate access to the data, we have launched the portal www.phxatlas.ch in which the scRNA-seq data can be visualized.

Assessing similarity is highly important for bioinformatics algorithms to determine correlations between biological information. A common problem is that similarity can appear by chance, particularly for low expressed entities. This is especially relevant in single-cell RNA-seq (scRNA-seq) data because read counts are much lower compared to bulk RNA-seq. Recently, a Bayesian correlation scheme that assigns low similarity to genes that have low confidence expression estimates has been proposed to assess similarity for bulk RNA-seq. Our goal is to extend the properties of the Bayesian correlation in scRNA-seq data by considering three ways to compute similarity. First, we compute the similarity of pairs of genes over all cells. Second, we identify specific cell populations and compute the correlation in those populations. Third, we compute the similarity of pairs of genes over all clusters, by considering the total mRNA expression. We demonstrate that Bayesian correlations are more reproducible than Pearson correlations. Compared to Pearson correlations, Bayesian correlations have a smaller dependence on the number of input cells. We show that the Bayesian correlation algorithm assigns high similarity values to genes with a biological relevance in a specific population. We conclude that Bayesian correlation is a robust similarity measure in scRNA-seq data.

Colorectal cancer, along with its high potential for recurrence and metastasis, is a major health burden. Uncovering proteins and pathways required for tumor cell growth is necessary for the development of novel targeted therapies. Ajuba is a member of the LIM domain family of proteins whose expression is positively associated with numerous cancers. Our data shows that Ajuba is highly expressed in human colon cancer tissue and cell lines. Publicly available data from The Cancer Genome Atlas shows a negative correlation between survival and Ajuba expression in patients with colon cancer. To investigate its function, we transduced SW480 human colon cancer cells, with lentiviral constructs to knockdown or overexpress Ajuba protein. The transcriptome of the modified cell lines was analyzed by RNA sequencing. Among the pathways enriched in the differentially expressed genes, were cell proliferation, migration and differentiation. We confirmed our sequencing data with biological assays; cells depleted of Ajuba were less proliferative, more sensitive to irradiation, migrated less and were less efficient in colony formation. In addition, loss of Ajuba expression decreased the tumor burden in a murine model of colorectal metastasis to the liver. Taken together, our data supports that Ajuba promotes colon cancer growth, migration and metastasis and therefore is a potential candidate for targeted therapy.

Lysosomal sequestration of anti-cancer compounds reduces drug availability at intracellular target sites, thereby limiting drug-sensitivity and inducing chemoresistance. For hepatocellular carcinoma (HCC), sorafenib (SF) is the first line systemic treatment, as well as a simultaneous activator of autophagy-induced drug resistance. The purpose of this study is to elucidate how combination therapy with the FDA-approved photosensitizer verteporfin (VP) can potentiate the antitumor effect of SF, overcoming its acquired resistance mechanisms. HCC cell lines and patient-derived in vitro and in vivo preclinical models were used to identify the molecular mechanism of action of VP alone and in combination with SF. We demonstrate that SF is lysosomotropic and increases the total number of lysosomes in HCC cells and patient-derived xenograft model. Contrary to the effect on lysosomal stability by SF, VP is not only sequestered in lysosomes, but induces lysosomal pH alkalinization, lysosomal membrane permeabilization (LMP) and tumor-selective proteotoxicity. In combination, VP-induced LMP potentiates the antitumor effect of SF, further decreasing tumor proliferation and progression in HCC cell lines and patient-derived samples in vitro and in vivo. Our data suggest that combination of lysosome-targeting compounds, such as VP, in combination with already approved chemotherapeutic agents could open a new avenue to overcome chemo-insensitivity caused by passive lysosomal sequestration of anti-cancer drugs in the context of HCC.