BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates

Cell fate decisions are achieved with gene expression changes driven by lineage-specific transcription factors (TFs). These TFs depend on chromatin remodelers including the Brahma-related gene 1 (BRG1)-associated factor (BAF) complex to activate target genes. BAF complex subunits are essential for development and frequently mutated in cancer. Thus, interrogating how BAF complexes contribute to cell fate decisions is critical for human health. We examined the requirement for the catalytic BAF subunit BRG1 in neural progenitor cell (NPC) specification from human embryonic stem cells. During the earliest stages of differentiation, BRG1 was required to establish chromatin accessibility at neuroectoderm-specific enhancers. Depletion of BRG1 dorsalized NPCs and promoted precocious neural crest specification and enhanced neuronal differentiation. These findings demonstrate that BRG1 mediates NPC specification by ensuring proper expression of lineage-specific TFs and appropriate activation of their transcriptional programs.

Abstract 3908: Universal genetic and transcriptomic concordance metrics to validate patient-derived tumor organoid models

Background

Patient derived tumor organoids (TOs) are emerging as potential models to elucidate mechanisms of tumor biology and therapeutic response. Here, we establish pan-cancer metrics for validation of genetic and transcriptomic recapitulation, and concordance of an organoid to its native tumor.

Methods/Results

We sequenced 50 tumor/TO pairs from 12 cancer types using the Tempus xT DNAseq panel and transcriptome RNAseq platforms. Concordance metrics between tumors and TOs were derived for genomic variants called by the DNA xT platform and comparative ratios were calculated for all detected somatic variants. Across all sequenced pairs, somatic variant detection concordance between any mutation identified in primary tissues and tumor organoids resulted in a mean value of 88.1%. Somatic primary tumor variant recapitulation, the percent of somatic variants identified in the primary tumors that were also detected in the TO, averaged 96.3%.

In addition to genetic concordance, DNAseq can identify and track clonal and subclonal diversity from source material to TO. In particular, we observed that >90% of source tumor/TO pairs harbor variants with allelic fractions <40% in both the sequenced TO and primary tumor tissue, suggesting intra-tumor heterogeneity in subclonal cell populations is maintained.

TOs and primary tumor transcriptomic profiles were compared by dimensionality reduction approaches (i.e. Uniform Manifold Approximation and Projection (UMAP), and Principal Components Analysis (PCA)) as well as differential expression analysis between cancer types. Overall, TOs recapitulated expected transcriptional programs of their tumor type as evidenced by UMAP and PCA as well as upregulation of defining pathways, such as estrogen receptor pathways in breast cancer TOs (ssGSEA p-values ranging from 0.004 to 5 × 10−5 for 5 gene ontology estrogen response pathways when compared to non-breast cancer TOs).

Conclusion

Determining genomic and transcriptomic concordance of TOs to source tumors is essential to confirm the validity of a given patient derived model. Our approach establishes metrics through key genomic features identified from routine next-generation sequencing data and can be extended beyond model validation to tracking clonal evolution over time in the presence or absence of therapeutic selection pressures. Our metrics may also serve as a critical quality control step if TOs are utilized in the clinical setting for personalized medicine.

Citation Format: Brandon L. Mapes, Joshua SK Bell, Lee F. Langer, Robert Huether, Catherine Igartua, Veronica Sanchez-Freire, Robert Tell, Jeffrey A. Borgia, Ashiq Masood, Ameen A. Salahudeen. Universal genetic and transcriptomic concordance metrics to validate patient-derived tumor organoid models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3908.

Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination

The SWI/SNF complex is a critical regulator of pluripotency in human embryonic stem cells (hESCs), and individual subunits have varied and specific roles during development and in diseases. The core subunit SMARCB1 is required for early embryonic survival, and mutations can give rise to atypical teratoid/rhabdoid tumors (AT/RTs) in the pediatric central nervous system. We report that in contrast to other studied systems, SMARCB1 represses bivalent genes in hESCs and antagonizes chromatin accessibility at super-enhancers. Moreover, and consistent with its established role as a CNS tumor suppressor, we find that SMARCB1 is essential for neural induction but dispensable for mesodermal or endodermal differentiation. Mechanistically, we demonstrate that SMARCB1 is essential for hESC super-enhancer silencing in neural differentiation conditions. This genomic assessment of hESC chromatin regulation by SMARCB1 reveals a novel positive regulatory function at super-enhancers and a unique lineage-specific role in regulating hESC differentiation.

Our bodies contain trillions of cells that play a wide variety of roles. Despite looking and behaving very differently to one another, all of these ‘mature’ cells somehow descend from a single fertilized egg that contains just one set of genes. This process is partially controlled by how ‘accessible’ genetic material is to the cell machinery that switches genes on or off. For example, in immature brain cells, genes required for memory are accessible, but genes needed to produce bone are not.

The developing embryo needs to control gene accessibility carefully to ensure that the right genes become available at the right time, and that crucial genes are not incorrectly ‘hidden’. In humans, the protein SMARCB1 plays an important role in this process: if damaged or deleted, development will be severely disrupted, sometimes causing brain cancer early in life. However, it remains unclear how exactly SMARCB1 regulates the accessibility of its ‘target’ genes. Now, Langer et al. set out to answer this question, and also to determine which parts of the body need SMARCB1 to develop properly.

Human stem cells can develop into multiple mature cell types if given the right signals. Langer et al. found reducing levels of SMARCB1 prevented stem cells from maturing into brain cells, but not other kinds of cells. This suggests that SMARCB1 has a specific role in brain development, which is consistent with its devastating effect on brain health when damaged.

A detailed analysis of genetic activity and DNA accessibility showed that SMARCB1 was doing this by switching off specific regions of DNA, called stem cell super-enhancers. These regions normally enhance the activity of genes that maintain stem cells in their immature state: when certain super-enhancers are turned off by SMARCB1, this allows stem cells to progress towards a brain cell fate.

These results help us understand why damage to SMARCB1 during development causes brain cancer more often than other kinds of cancer. In the future, they could also help explain how certain types of cancer form, which would be the first step towards knowing how to treat them.

MiRNA-Mediated Regulation of the SWI/SNF Chromatin Remodeling Complex Controls Pluripotency and Endodermal Differentiation in Human ESCs

MicroRNAs and chromatin remodeling complexes represent powerful epigenetic mechanisms that regulate the pluripotent state. miR-302 is a strong inducer of pluripotency, which is characterized by a distinct chromatin architecture. This suggests that miR-302 regulates global chromatin structure; however, a direct relationship between miR-302 and chromatin remodelers has not been established. Here, we provide data to show that miR-302 regulates Brg1 chromatin remodeling complex composition in human embryonic stem cells (hESCs) through direct repression of the BAF53a and BAF170 subunits. With the subsequent overexpression of BAF170 in hESCs, we show that miR-302's inhibition of BAF170 protein levels can affect the expression of genes involved in cell proliferation. Furthermore, miR-302-mediated repression of BAF170 regulates pluripotency by positively influencing mesendodermal differentiation. Overexpression of BAF170 in hESCs led to biased differentiation toward the ectoderm lineage during EB formation and severely hindered directed definitive endoderm differentiation. Taken together, these data uncover a direct regulatory relationship between miR-302 and the Brg1 chromatin remodeling complex that controls gene expression and cell fate decisions in hESCs and suggests that similar mechanisms are at play during early human development.

Update on anti-CTLA-4 antibodies in clinical trials

Breaking immune tolerance against tumor self-antigens is presently an area of intense research in the design of cancer therapies. One possible method to enhance immune system activation against tumor antigens is by blocking the inhibitory co-stimulatory signals mediated by cytotoxic T lymphocyte antigen 4, (CTLA-4) expressed on activated T cells. The fully human monoclonal antibodies that are directed against human CTLA-4, ipilimumab (Medarex/Bristol-Myers Squibb) and CP-675,206 (Pfizer/Abgenix, now Amgen), have demonstrated activity against metastatic melanoma, hormone refractory prostate cancer and other malignancies. They have also uncovered unusual immune-related adverse events manifesting as self-limiting inflammatory reactions of the bowel, skin and pituitary. This article reviews preclinical development and data generated from Phase I, II and III studies with regard to the end points reported and immune-related adverse events.

Distinct nigrostriatal projection systems innervate striosomes and matrix in the primate striatum

Mesostriatal projections were labeled in 11 squirrel monkeys by injecting the anterograde tracer, [35S]methionine, into different parts of the dopamine-containing A8-A9-A10 cell complex of the midbrain. Two strikingly different compartmental patterns of mesostriatal projection were found. Fields of dense labeling in both the caudate nucleus and the putamen, interrupted by pockets of sparse labeling, were observed with deposits involving cell group A8, cell group A10 and/or the dorsally situated 'pars mixta' of the substantia nigra. Where striosomes could be identified as such in adjoining histochemically stained sections, the sparsely labeled zones were aligned with them. By contrast, a pattern of focally dense labeling in the caudate nucleus and putamen, with much weaker labeling surrounding the densely labeled zones, was found with injection sites centered in the horizontal band and associated ventrally extending fingers of the substantia nigra pars compacta. Many of the pockets of heightened labeling could be shown to correspond to histochemically defined striosomes. These compartmental patterns were identified both in the caudate nucleus and in the putamen. We conclude that the A8-A9-A10 cell complex of the primate contains spatially distinct subdivisions with preferential projections directed, respectively, toward the striosome and matrix compartments of the striatum.

New directions in CNS drug delivery

This commentary expands on the above article in 2 ways. First, it provides more recent information on polymer-based drug delivery systems. Second, it discusses experimental systems that may be clinically viable in the future such as prodrugs, cell-polymer transplants and gene transplants.