Lineage-specific Gene Expression Research Articles

Abstract 1615: Balanced molecular feature selection unveils universally tumor-lineage informative methylation sites in colorectal cancer

Abstract In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step toward tailoring healthcare interventions. However, the critical aspect of equitably selecting molecular features across multiple patients is often overlooked. To address this challenge, we introduce FALAFL (FAir muLti-sAmple Feature seLection), a novel algorithmic approach based on integer linear programming. FALAFL is designed to bridge the gap between molecular feature selection and algorithmic fairness, ensuring a balanced selection of molecular features across different patient samples. We have applied FALAFL to the problem of selecting lineage-informative CpG sites within a cohort of 9 colorectal cancer patients subjected to low-coverage single-cell methylation sequencing. Our results demonstrate that FALAFL excels at rapidly determining the optimal set of CpG sites, which are well covered by cells across the vast majority of the patients, while ensuring that each patient contributes a similar number of sites to the final selection. An analysis of the FALAFL-selected CpG sites reveals that their lineage informativeness exhibits a strong association across diverse patient profiles, suggesting the non-stochasticity and universality of methylation changes in tumor evolution. Furthermore, these universally lineage-informative sites exhibit subclonal level alterations in the colorectal cancer primary tumors and are strongly associated with lineage-specific gene expression patterns. By integrating equity considerations into the molecular feature selection process, FALAFL is poised to propel equitable healthcare data science practices and advance our understanding of cancer and other complex diseases. Citation Format: Xuan Cindy Li, Yuelin Liu, Alejandro A. Schäffer, Stephen M. Mount, Süleyman C. Sahinalp. Balanced molecular feature selection unveils universally tumor-lineage informative methylation sites in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1615.

A neural network-based model framework for cell-fate decisions and development

Gene regulatory networks (GRNs) fulfill the essential function of maintaining the stability of cellular differentiation states by sustaining lineage-specific gene expression, while driving the progression of development. However, accounting for the relative stability of intermediate differentiation stages and their divergent trajectories remains a major challenge for models of developmental biology. Here, we develop an empirical data-based associative GRN model (AGRN) in which regulatory networks store multilineage stage-specific gene expression profiles as associative memory patterns. These networks are capable of responding to multiple instructive signals and, depending on signal timing and identity, can dynamically drive the differentiation of multipotent cells toward different cell state attractors. The AGRN dynamics can thus generate diverse lineage-committed cell populations in a robust yet flexible manner, providing an attractor-based explanation for signal-driven cell fate decisions during differentiation and offering a readily generalizable modelling tool that can be applied to a wide variety of cell specification systems.

Differential gene expression of Wharton's jelly-derived mesenchymal cells mediated by graphene oxide in basal and osteo-induced media.

Graphene oxide (GO) is widespread in scaffold engineering owing to its extraordinary properties such as multiple oxygen functional groups, high hydrophilicity ability and biocompatibility. It is known to promote differentiation in mesenchymal stem cells, but concomitant comparison of its modulation on the expression profiles of Wharton's jelly (WJ)-MSC surface markers, lineage differentiation, and epigenetic regulatory genes in basal and induced condition are still lacking. Unraveling the fundamental mechanisms is essential for the effective utilization of WJ-MSCs incorporated with GO in therapy. This study aims to explore the unique gene expression profiles and epigenetic characteristics of WJ-MSCs influenced by GO. The characterized GO-coated coverslip served as a substrate for culturing WJ-MSCs. In addition to investigating the impact of GO on cell proliferation and differentiation, we conducted a gene expression study using PCR array, while epigenetic control was assessed through bisulfite sequencing and Western blot analysis. Our findings indicate that the presence of GO maintained the proliferation and survival of WJ-MSCs. In the absence of induction, GO led to minor lipid and glycosaminoglycan deposition in WJ-MSCs. This was evidenced by the sustained expression of pluripotency and lineage-specific genes, demethylation at the OCT4 promoter, and a decrease in H3K9 methylation. In osteo-induced condition, the occurrence of osteogenesis appeared to be guided by BMP/TGF and ERK pathway activation, accompanied by the upregulation of osteogenic-related genes and downregulation of DNMT3b. GO in osteo-induced condition create a favorable microenvironment that promotes the osteogenesis of WJ-MSCs by influencing genetic and epigenetic controls. This helps in advancing our knowledge on the use of GO as priming platform and WJ-MSCs an alternate source for bone repair and regeneration.

Inorganic Ions Activate Lineage-Specific Gene Regulatory Networks

Inorganic biomaterials have been shown to direct cellular responses, including cell-cell and cell-matrix interactions. Notably, ions released from these inorganic biomaterials play a vital role in defining cell identity, and promoting tissue-specific functions. However, the effect of inorganic ions on cellular functions have yet to be investigated at the transcriptomic level, representing a critical knowledge gap in the development of next-generation of bioactive materials. To address this gap, we investigated the impact of various inorganic ions including silver, copper, titanium, and platinum on human mesenchymal stem cells (hMSCs). Our finding showed that silver and copper induce osteogenic and chondrogenic differentiation respectively, through enrichment of lineage-specific gene expression program. In particular, silver effectively induced Wingless/Integrated (Wnt) and mitogen-activated protein kinase (MAPK) signaling, which are vital for osteogenesis. On the other hand, copper specifically stimulated Transforming growth factor beta (TGFβ) signaling, while suppressing Janus kinase/signal transducers and activators of transcription (JAK-STAT) signaling, thereby promoting chondrogenesis. In contrast, platinum, tantalum, and titanium ions didn't stimulate regenerative responses. Together, our findings highlight the potential of inorganic biomaterials in tissue regeneration strategies, which currently rely largely on growth factors and small molecule therapeutics. STATEMENT OF SIGNIFICANCE: This research emphasizes the critical role of bioactive inorganic ions in controlling lineage-specific gene expression patterns in mesenchymal stem cells, effectively modulating the transcriptome landscape and directing cell fate. The study lays the foundation for a systematic database of biomaterial candidates and their effects on cellular functions, which will ultimately streamline the translation of new biomaterials into clinical applications.

Dynamic and distinct histone modifications facilitate human trophoblast lineage differentiation

The placenta serves as an essential organ for fetal growth throughout pregnancy. Histone modification is a crucial regulatory mechanism involved in numerous biological processes and development. Nevertheless, there remains a significant gap in our understanding regarding the epigenetic regulations that influence trophoblast lineage differentiation, a fundamental aspect of placental development. Here, through comprehensive mapping of H3K4me3, H3K27me3, H3K9me3, and H3K27ac loci during the differentiation of trophoblast stem cells (TSCs) into syncytiotrophoblasts (STs) and extravillous trophoblasts (EVTs), we reveal dynamic reconfiguration in H3K4me3 and H3K27ac patterns that establish an epigenetic landscape conducive to proper trophoblast lineage differentiation. We observe that broad H3K4me3 domains are associated with trophoblast lineage-specific gene expression. Unlike embryonic stem cells, TSCs lack robust bivalent domains. Notably, the repression of ST- and EVT-active genes in TSCs is primarily attributed to the weak H3K4me3 signal rather than bivalent domains. We also unveil the inactivation of TSC enhancers precedes the activation of ST enhancers during ST formation. Our results provide a comprehensive global map of diverse histone modifications, elucidating the dynamic histone modifications during trophoblast lineage differentiation.

Cellular development and evolution of the mammalian cerebellum

The expansion of the neocortex, a hallmark of mammalian evolution1,2, was accompanied by an increase in cerebellar neuron numbers3. However, little is known about the evolution of the cellular programmes underlying the development of the cerebellum in mammals. In this study we generated single-nucleus RNA-sequencing data for around 400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse and the marsupial opossum. We established a consensus classification of the cellular diversity in the developing mammalian cerebellum and validated it by spatial mapping in the fetal human cerebellum. Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Global transcriptome profiles, conserved cell-state markers and gene-expression trajectories across neuronal differentiation show that cerebellar cell-type-defining programmes have been overall preserved for at least 160 million years. However, we also identified many orthologous genes that gained or lost expression in cerebellar neural cell types in one of the species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level. In sum, our study unveils shared and lineage-specific gene-expression programmes governing the development of cerebellar cells and expands our understanding of mammalian brain evolution.

IL-33 Induces Paneth Cell Production of EGF and Soluble ST2, Regulating Epithelial Regeneration after Intestinal Injury

Crypt base intestinal stem cells (ISCs) maintain the epithelial lining of the intestines, but their frequencies are reduced in experimental models of graft vs. host disease (GVHD). Paneth cells provide an epithelial contribution to the stem cell niche, but their frequencies are also reduced in GVHD mouse models and in patients with GVHD. Mechanisms regulating ISCs and their niche after damage remain poorly understood. Interleukin-33 (IL-33) is an immunomodulatory alarmin typically thought to target lymphocytes such as T cells and innate lymphoid cells. In experimental models of allogeneic bone marrow transplantation, IL-33 can promote or attenuate GVHD, depending on the cellular target and the timing of the exposure. A secreted isoform of the IL-33 receptor, termed soluble ST2 (sST2), acts as a negative regulator by blocking IL-33 from binding to the membrane-bound isoform that mediates intracellular signaling. sST2 also has diagnostic and prognostic utility, serving as a biomarker for GVHD severity. While IL-33 has well-described effects on lymphocytes populations, there is limited understanding of the role of IL-33 signaling within the intestinal mucosa after damage. Utilizing experimental radiation injury to model conditioning-related intestinal pathology, we investigated the role of the IL-33/ST2 axis in epithelial damage and regeneration. Wild-type (WT) mice increased IL-33 mRNA and protein expression in the small intestine within days after 10 Gy total body irradiation (TBI). Intestinal sST2 expression also increased quickly in WT mice after TBI, but not in IL-33 -/- mice, suggesting that IL-33 itself was a regulator of sST2. While the ileal mucosa appeared similar at baseline in wild-type and IL-33 -/- mice, the IL-33 -/- mice demonstrated more severe radiation injury 5 days after 10 Gy TBI, with more crypt loss, loss of ISCs and Paneth cells, and an attenuated regenerative response with smaller crypts post-TBI containing fewer Ki67 + cells. 3-D whole-mount confocal microscopy of ileal tissue from IL-33-GFP reporter mice indicated that the crypt epithelium did not express IL-33 at baseline, but Olfm4 + ISCs adjacent to Paneth cells began to express IL-33 following radiation injury (Fig 1). Anti-Thy1-mediated lymphocyte depletion prior to irradiation of WT and IL-33 -/- mice did not abrogate the increased radiation sensitivity of IL-33 -/- mice, indicating a role for IL-33 beyond immunomodulation and suggesting that IL-33 could have direct effects within the epithelium. Intestinal organoid cultures confirmed epithelial expression of IL-33, confirmed increased radiation sensitivity of IL-33 -/- epithelium, and identified impaired epidermal growth factor (EGF) expression in the absence of IL-33. Furthermore, treatment of intestinal organoids with IL-33 induced EGF mRNA and protein expression, both of which were abrogated by the p38 inhibitor SB202190. Treatment of purified Lysozyme-DsRed + Paneth cells indicated that IL-33 directly promoted their production of EGF. In vivo, TBI-induced EGF upregulation was absent in IL-33 -/- mice. To further investigate this newly identified epithelial IL-33/ST2/EGF pathway in the ISC compartment, RiboTag mice, which facilitate analysis of lineage-specific proteome-relevant gene expression with minimal tissue processing and artifact introduction, were crossed to Olfm4-Cre and Lysozyme-Cre transgenics. Lineage-specific ribosome targeting was confirmed by immunostains and qPCR, and this approach also confirmed ISC upregulation of IL-33 following radiation injury and Paneth cell upregulation of EGF and sST2. Finally, to investigate the importance of this radiation-induced EGF upregulation, WT mice were treated with the EGFR inhibitor gefitinib following irradiation, which resulted in more severe radiation-induced ISC loss, similar to IL-33 deficiency. Furthermore, epithelial regeneration and ISC recovery were augmented in IL-33 -/- mice after TBI by treatment with exogenous EGF (Fig 2). These findings reveal an unknown pathway of stem cell niche regulation and crypt regeneration whereby the Paneth cell niche responds dynamically upon injury by upregulating EGF and the stem cells orchestrate regeneration by regulating their niche with IL-33. This regenerative circuit also highlights the breadth of IL-33 activity beyond immunomodulation and the therapeutic potential of EGF administration for treatment of intestinal injury.

Α-Globin Lentiviral Vectors for Hematopoietic Stem Cell Gene Therapy of α-Thalassemia

α-thalassemia is an inherited blood disorder caused by mutations in α-globin genes (HBA1 and HBA2) resulting in the reduction of α-globin chains, the subunit, along with β-globin chain, constituting adult hemoglobin (α 2β 2). While a reduction of α-globin expression of 40% presents asymptomatic phenotypes, expression levels decreasing to <20% or an α/β-globin mRNA ratio of <0.2, causes severe anima. Treatment for severe cases of α-thalassemia entails lifelong, biweekly blood transfusions with daily chelation therapy. While these therapies enable patients to live into mid- to late-adulthood, they continue to engender serious clinical manifestations, such as iron toxicity. To answer this clinical need, our laboratory has developed a stem cell gene therapy in which functional copies of α-globin gene integrate into the genome of patient's hematopoietic and progenitor stem cells (HSPCs) by lentiviral vectors (LVs) to normalize the globin chain imbalance and restore hemoglobin function in derived red blood cells (RBCs). The design of our α-globin LVs (AGLVs) is based on GLOBE β-globin LV utilized in a clinical trial for β-thalassemia (NCT02453477), which has achieved transfusion reduction and independence in patients with transfusion-dependence β-thalassemia major. We have constructed a series of short proviral length AGLVs for optimized titer production, HSPC infectivity, and lineage-specific α-globin gene expression. Twelve AGLVs varying in gene and regulatory element compositions were constructed and assessed for raw titer yields and characterized for gene transfer efficiency, mRNA expression and hemoglobin production in a α-globin knockout (KO) human erythroid cell line. Successfully, all AGLVs confer high raw titers ~ 1e7 TU/mL and enabled the production of adult hemoglobin (HbA). We identified two optimal AGLVs for further characterization in human primary HSPCs: 1) A2-UV for yielding highest raw titers and gene transfer efficiency, and 2) A2-Globe for producing the most α-globin mRNA. Both A2-UV and A2-Globe LVsharbor HBA2, are regulated by the β-globin promoter and enhanced by the core or large β-LCR enhancer region, respectively. To assess candidate AGLVs in human HSPCs, AGLVs were tagged at the transcription level to enable identification and quantification of vector-derived α-globin mRNA proceeding HSPCs transduction anderythroid differentiation. A2-UV demonstrated optimum CD34 + infectivity and gene transfer, and A2-Globe expressed a high ~30% of α-globin mRNA per total β-globin per vector copy number (VCN), achieving levels of one endogenous α-globin gene (~25% per total β-globin). Current studies examined A2-UV and A2-Globe in α-thalassemia major patient HSPCs - lacking all four α-globin genes - harboring a lethal homozygous 20kb deletion of HBA1 and HBA2, known as SEA –/– mutation. Patient HSPCs were transduced and differentiated into RBCs. A high CD34+ infectivity and gene transfer was obtained by both candidate vectors, without utilization of transduction enhancers. Furthermore, a correction of α/β-globin mRNA ratio of ~0.7 was obtained while retaining a low VCN (<3).RBCs were then analyzed at the protein level . Chromatograms of hemoglobin tetramers revealed that HbA represented 98% of all hemoglobin, compared to 0% in non-transduced patient RBCs. Single globin chain chromatograms successfully demonstrated α/β-globin chain ratio of ~0.4 or higher and successfully demonstrated that a low average of copies per cell (~3) restored 60% of adult hemoglobin when normalized to healthy donor RBCs. These data demonstrate α/β-globin correction and hemoglobin restoration in α-thalassemia patient cells with the most severe mutation. Three assays were conducted on patient cells, all with similar and highly encouraging results for disease amelioration in severe cases of α-thalassemia. Overall, this project is paving the way for the first development of a curative gene therapy approach for α-thalassemia.

Uncovering the Cis-Regulatory Program of Early Human B-Cell Commitment and Its Implications in the Pathogenesis of B-Cell Acute Lymphoblastic Leukemia

The early stages of the B-cell system are key for cellular immunity development. The development of functional B cells requires appropriate regulation of dynamic transcription-factor networks. These regulatory networks are responsible for lineage-specific gene expression activation and lineage commitment. Thus, understanding the gene regulatory network (GRN) of this system is essential for studying healthy development and malignant transformations. To this end, in the present study, we aim to uncover the complete chart of the cis-regulatory elements and their dynamic activity over early B-cell commitment in healthy humans. We generated matched human data for chromatin accessibility (ATAC-Seq) and transcriptome (RNA-Seq) in eight sorted B-cell subpopulations (HSCs, CLPs, pro-B cells, pre-B cells, Immature B cells, and Transitional B cells as well as CD5+ and CD5- Naive B cells) isolated from bone marrow and peripheral blood from the same healthy donors (n=13). These comprehensive profiles of the stepwise progression of B-cell precursors and the combined analysis of both omics allowed us to infer the regulatory elements of B-cell differentiation and the resulting GRNs. Our data identified 169 TFs, 7,310 genes, and 16,074 OCRs governing the early B-cell differentiation, resulting in a GRN with 377,268 TF-OCR-gene interactions. The inferred GRN included genes and OCRs able to draw the entire regulatory dynamics over differentiation behaving in accordance with established knowledge. As example, we identified genes and TFs related to homeostasis and stemness, such as MEIS1, CD34, and CDH2, and antiapoptotic genes such as BCL2, highly expressed in HSC, CLP, and pro-B cells. We identified surface marker genes and TFs involved in the commitment and differentiation of B cell lineage, including CD79A/B, PAX5, TCF3, EBF1, and FOXO1, to become upregulated in pro-B cells, as well as down-regulation in pre-B cells of genes linked to T cell development such as NOTCH1. To identify the key regulatory elements along B cell differentiation, we generated a snapshot of the GRN for each cell subpopulation. As a result, the networks' node hub architectures revealed those TFs with relevant transcriptional activity per subpopulation (Figure 1). In the analysis we recovered the primary TFs involved in B cell commitment, differentiation, maintenance, and class-switch recombination: TCF3, BCL11A, IRF8, PAX5, REL, IRF4, EBF1, POU2F2, FOXO1, and LEF1; but also identified ELK3 as a novel TF critical in pro-B cells. Interestingly, this ETS-factor, recently defined as a novel oncogene, has been reported to increase in ETV6-RUNX1+ acute lymphoblastic leukemia cases and other carcinogenic processes. Moreover, it has been associated with pro-B cell expansion. In a deeper approach, our GRNs allowed the exploration of upstream regulators of specific genes. In the case of ELK3, the TFs ERG, STAT5A/B, E2F3, ETS2, ETV6, SPIB, and POU2F2 were uncovered as putative regulators. As a positive control, we explored the upstream regulation of EBF1 gene, a well-known and key TF of B cell fate. Besides the already described regulators (PAX5, TCF3, FOXO1, RUNX1, etc.), we identified new candidates such as MLXIP. Finally, we translated our findings into a disease context using public data. Our resource facilitated the identification of triggers for specific B-cell acute lymphoblastic leukemia (B-ALL) subtypes, pinpointing the inflection point of malignant transformation. We found ETV6-RUNX1 fusions significantly enriched in pro-B cells, MEF2D fusions and TCF3-PBX1 mutations in pre-B cells, DUX4 fusions in HSCs, and KMT2A fusions in CLPs. Moreover, our data shed light on the functional implications of B-ALL susceptibility loci. The susceptibility locus rs17481869, associated with ETV6-RUNX1 patients, was identified within a small OCR specific to pro-B cells. The ALL-associated rs4762284 locus was observed in a closed chromatin region, but we could identify two proxies (rs2268508 and rs17736737) in open regions. Furthermore, from the list of SNPs associated with BCP ALL-related traits from the GWAS catalog (NHGRI-EBI), we identified 11 SNPs overlapping some of our OCRs. In summary, we are presenting the most comprehensive publicly available atlas of early B cell regulation (B-rex; https://brex.shinyapps.io/brex/), and therefore a powerful resource for understanding early B cell differentiation in health and disease.

Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS

A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

Histological Evaluation of A unilateral Critical-Sized Mandibular Defect Reconstruction using human dental pulp stem cells by Light Microscope and Real-Time Quantitative PCR

Objective: To evaluate the osteogenic differentiation potential of human dental pulp stem cells (DPSCs) isolated from the dental pulp of third molar teeth in vitro cultures, and to evaluate the bone regenerative capacity of human dental pulp stem cells (DPSCs) when transplanted into a unilateral critical-sized bone defect in the mandibular bone in vivo after receiving a hydroxyapatite matrix and polylactic-polyglycolic acid (HA/PLGA) scaffold. Material and methods: A total of 18 mandibular defects were made, and three groups (each n = 6) were created. The first group: the transplanted DPSCs implanted in the critical-sized bone defect after receiving (HA/PLGA) scaffold. The second group received only (HA/PLGA) scaffold. The third group, which served as the control, had a critical-sized defect left empty. After characterization, Von Kossa [VK] and Alizarin red staining were employed to identify differentiated osteoblasts at the 14th and 21st days, and histological analyses, as well as polymerase chain reactions (PCR), were also used. Results: It showed that DPSCs had high proliferation potential and typical fibroblastic shape. Additionally, osteogenic differentiation of DPSCs was validated by morphological alterations, histological examination, and the expression of lineage-specific genes confirmed osteogenic differentiation of DPSCs. Conclusion: High proliferation potential and the capacity to differentiate into osteoblasts are two characteristics of DPSCs taken from impacted third molars.

MLL1 inhibits the neurogenic potential of SCAPs by interacting with WDR5 and repressing HES1

Mesenchymal stem cell (MSC)-based therapy has emerged as a promising treatment for spinal cord injury (SCI), but improving the neurogenic potential of MSCs remains a challenge. Mixed lineage leukemia 1 (MLL1), an H3K4me3 methyltransferases, plays a critical role in regulating lineage-specific gene expression and influences neurogenesis. In this study, we investigated the role and mechanism of MLL1 in the neurogenesis of stem cells from apical papilla (SCAPs). We examined the expression of neural markers, and the nerve repair and regeneration ability of SCAPs using dynamic changes in neuron-like cells, immunofluorescence staining, and a SCI model. We employed a coimmunoprecipitation (Co-IP) assay, real-time RT-PCR, microarray analysis, and chromatin immunoprecipitation (ChIP) assay to investigate the molecular mechanism. The results showed that MLL1 knock-down increased the expression of neural markers, including neurogenic differentiation factor (NeuroD), neural cell adhesion molecule (NCAM), tyrosine hydroxylase (TH), βIII-tubulin and Nestin, and promoted neuron-like cell formation in SCAPs. In vivo, a transplantation experiment showed that depletion of MLL 1 in SCAPs can restore motor function in a rat SCI model. MLL1 can combine with WD repeat domain 5 (WDR5) and WDR5 inhibit the expression of neural markers in SCAPs. MLL1 regulates Hairy and enhancer of split 1 (HES1) expression by directly binds to HES1 promoters via regulating H3K4me3 methylation by interacting with WDR5. Additionally, HES1 enhances the expression of neural markers in SCAPs. Our findings demonstrate that MLL1 inhibits the neurogenic potential of SCAPs by interacting with WDR5 and repressing HES1. These results provide a potential therapeutic target for promoting the recovery of motor function in SCI patients.

Single-cell analysis of prenatal and postnatal human cortical development.

We analyzed >700,000 single-nucleus RNA sequencing profiles from 106 donors during prenatal and postnatal developmental stages and identified lineage-specific programs that underlie the development of specific subtypes of excitatory cortical neurons, interneurons, glial cell types, and brain vasculature. By leveraging single-nucleus chromatin accessibility data, we delineated enhancer gene regulatory networks and transcription factors that control commitment of specific cortical lineages. By intersecting our results with genetic risk factors for human brain diseases, we identified the cortical cell types and lineages most vulnerable to genetic insults of different brain disorders, especially autism. We find that lineage-specific gene expression programs up-regulated in female cells are especially enriched for the genetic risk factors of autism. Our study captures the molecular progression of cortical lineages across human development.

Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome.

The human brain is a complex organ comprised of distinct cell types, and the contribution of the 3D genome to lineage specific gene expression remains poorly understood. To decipher cell type specific genome architecture, and characterize fine scale changes in the chromatin interactome across neural development, we compared the 3D genome of the human fetal cortical plate to that of neurons and glia isolated from the adult prefrontal cortex. We found that neurons have weaker genome compartmentalization compared to glia, but stronger TADs, which emerge during fetal development. Furthermore, relative to glia, the neuronal genome shifts more strongly towards repressive compartments. Neurons have differential TAD boundaries that are proximal to active promoters involved in neurodevelopmental processes. CRISPRi on CNTNAP2 in hIPSC-derived neurons reveals that transcriptional inactivation correlates with loss of insulation at the differential boundary. Finally, re-wiring of chromatin loops during neural development is associated with transcriptional and functional changes. Importantly, differential loops in the fetal cortex are associated with autism GWAS loci, suggesting a neuropsychiatric disease mechanism affecting the chromatin interactome. Furthermore, neural development involves gaining enhancer-promoter loops that upregulate genes that control synaptic activity. Altogether, our study provides multi-scale insights on the 3D genome in the human brain.

Mesenchymal stem cells derived from the fibrotic tissue of atrophic nonunion or the bone marrow of iliac crest: A donor-matched comparison

PurposeAtrophic nonunion is one of the most difficult complications of fracture. The cellular factors that contribute to atrophic nonunion are poorly understood, and mesenchymal stem cells (MSCs) are recognized as the key contributor to bone formation. This study aimed to characterize the MSCs isolated from the fibrotic tissue of atrophic nonunion (AN-MSCs) from the perspective of proliferation, differentiation potential, senescence, and paracrine function. MethodsHuman atrophic fibrotic tissue was obtained from four donors aged 29–37 for isolating AN-MSCs, and donor-matched bone marrow acquired from the iliac crest for isolating MSCs (IC-MSCs) as control. The AN-MSCs or IC-MSCs in passage 3 were applied for the following evaluations. The surface markers expressed on the two cells were evaluated using flow cytometry. The proliferation of the two cells for up to 11 days was comparatively investigated. After osteogenic, chondrogenic, or adipogenic induction, multi-lineage differentiation of AN-MSCs or IC-MSCs was comparatively evaluated using lineage-specific stains and lineage-specific gene expression. Enzyme-linked immunosorbent assay (ELISA) assessment was applied to evaluate the paracrine function of AN-MSCs or IC-MSCs. Cellular senescence of AN-MSCs or IC-MSCs was evaluated using senescence-associated β-galactosidase (SA-β-gal) staining. ResultsAN-MSCs or IC-MSCs from the four donors showed morphologic and immunophenotypic characteristics of MSCs, with the expression of MSCs markers and negative expression of hematopoietic markers. In general, AN-MSCs showed similar proliferation and adipogenic capacity with IC-MSCs. In contrast, IC-MSCs showed significantly higher osteogenic and chondrogenic capacity compared to AN-MSCs. Moreover, the culture medium of IC-MSCs contains significantly higher levels of VEGF, TGF-β1, PDGF-BB, and IGF-1 than the culture medium of AN-MSCs. Lastly, the AN-MSCs are more prone to cellular senescence than the IC-MSCs. ConclusionsIn-vitro, AN-MSCs were similar to IC-MSCs in proliferation and adipogenic capacity, but inferior to IC-MSCs in osteogenic and chondrogenic capacity, paracrine function, and anti-senescence.

ARID4B loss leads to activated STAT1-dependent interferon pathway in mouse embryonic stem cells and during meso/endodermal differentiation.

Proper deactivation of the pluripotency network and activation of a lineage-specific gene expression program are critical for mouse embryonic stem cell (mESC) differentiation. This is achieved by the coordinated action of transcription and chromatin factors. Our previous work identified ARID4B as a critical chromatin factor for mesoderm and endoderm differentiation. As part of a histone deacetylase complex, ARID4B plays a role in transcriptional suppression of its direct targets. Here, we investigated the mechanism of ARID4B function in mESC differentiation by focusing on genes and pathways that are upregulated in its absence. We analyzed transcriptomic results of wild-type and arid4bΔ endoderm or mesoderm differentiated cells through integrative genomics viewer and ingenuity pathway analysis. We performed real-time quantitative polymerase chain reaction for selected genes. To understand pathway activation, we performed Western blot for candidate proteins during the time-course of differentiation. We also analyzed H3K4me3, H3K27me3 and H3K27Ac ChIP-seq results to understand changes in the chromatin environment. Interferon-related genes were activated in arid4bΔ mESCs and endoderm or mesoderm directed cells. Consistent with this, higher phosphorylated STAT1 levels were found in arid4bΔ mESCs while a related phosphorylated STAT3 was unchanged. Finally, we observed a significant increase in H3K4me3 around interferon-related distal gene regulatory regions with a combination of either upregulation of H3K27Ac level or downregulation of H3K27me3 level. These results provide evidence that ARID4B is involved in the suppression of interferon-related genes in mESCs and during meso/endoderm differentiation through modulation, mainly of H3K4me3. This regulation might be important for successful mESC differentiation.

First-in-human phase 1 dose escalation study of the KAT6 inhibitor PF-07248144 in patients with advanced solid tumors.

1054 Background: KAT6A and KAT6B regulate gene transcription via acetylation of histone H3K23 and their dysregulation drives lineage-specific gene expression in cancer. We report dose escalation data from the first-in-human phase 1 (Part 1A and 1B; NCT04606446) study of the KAT6-selective inhibitor PF-07248144. Methods: Part 1A (monotherapy dose escalation) enrolled patients (pts) with advanced/metastatic ER+/HER2− breast cancer (mBC), CRPC, or NSCLC, resistant/intolerant to standard therapy. Part 1B (PF-07248144 + fulvestrant combination dose escalation) enrolled pts with advanced/metastatic ER+/HER2- mBC with disease progression after ≥1 line of CDK4/6 inhibitor and endocrine therapy (ET). PF-07248144 (1-15 mg in Part 1A) was administered orally once per day (QD) in 28-day cycles following Bayesian design with overdose control. Study objectives: primary - assess PF-07248144 safety and tolerability, including dose limiting toxicities (DLT); secondary - evaluate PF-07248144 pharmacokinetics (PK); and exploratory - evaluate pharmacodynamics (PD; peripheral blood mononuclear cells [PBMC] and tumor H3K23Ac inhibition) and antitumor activity (using RECIST 1.1 by investigator assessment). Results: At data cut off (30 Sep 2022), 29 pts were enrolled: 25 in Part 1A (12 mBC, 11 CRPC, 2 NSCLC) and 4 in Part 1B (mBC). Part 1A evaluated 5 dose levels (1-15 mg QD) and Part 1B evaluated 5 mg PF-07248144 QD + 500 mg fulvestrant. Median age across Part 1A and 1B was 67 yrs (range 48-90). A total of 83% (Part 1A) and 75% (Part 1B) of pts with mBC had received > 3 prior lines of systemic anticancer therapy. Three DLTs (Grade 3 [G3] neutropenia) were observed: 2 in Part 1A (8 mg and 2 mg QD) and 1 in Part 1B (5 mg QD). A maximum tolerated dose was not identified; 5 mg QD was identified as the recommended dose for expansion for both monotherapy and fulvestrant combination. Across Parts 1A and 1B, treatment-related AEs (TRAEs; any grade) in ≥20% pts were dysgeusia (72%), anemia (52%), neutropenia (48%), thrombocytopenia (31%), diarrhea (31%), white blood cells (WBC) decreased (28%), fatigue (24%), and aspartate aminotransferase increased (21%); the majority of TRAEs were G1-2. TRAEs ≥G3 seen in > 1 pt were neutropenia (6/29; 21%), anemia (5/29; 17%), and WBC decreased (2/29; 7%). PF-07248144 PK was linear between 1 and 15 mg. H3K23Ac inhibition (≥70%) in PBMCs was achieved at steady state at doses of ≥1 mg. Tumor H3K23Ac levels were reduced by > 50% in 4 paired tumor biopsies at exposures associated with preclinical anti-tumor activity. Confirmed and durable partial responses were observed in 1/8 (Part 1A) and 2/4 (Part 1B) response-evaluable pts with ER+/HER2- mBC who progressed on prior ET+CDK4/6 inhibitor treatment. Conclusions: PF-07248144 was well tolerated and associated with strong KAT6 inhibition in PBMCs and tumors and confirmed partial responses in pts with heavily treated ER+/HER2- mBC during dose escalation. Clinical trial information: NCT04606446 .

Harnessing spatial transcriptomics to study fate decisions and lineage specification in T cell development

Abstract T cells are critical components of the adaptive immune system; they develop from bone-marrow derived precursors that migrate to the thymus. There, precursors undergo a sequence of lineage specification and commitment steps that give rise to multiple T cell lineages serving essential functions in defenses against infection and immune homeostasis. The diversity of thymocytes, and their complex interactions with the thymic stroma, including epithelial cells and other hematopoietic compartments, have hampered our understanding of T cell development. For greater insight into intrathymic developmental trajectories and their transcriptional control, we and others have utilized single cell RNA- and ATAC-sequencing (scRNA-seq and scATAC-seq). However, single-cell approaches do not assess contextual cell-cell interactions. To address this limitation, we used in-situ transcriptomics, specifically the 10× Genomics “Visium” technology, which assays in-situ gene expression in 55-micron spots spanning whole mouse thymus lobes. We will present initial results of these experiments, including mapping of thymocyte differentiation stages, location of developmental bifurcations, and the spatial progression of lineage specific gene expression. Briefly, we use statistical models informed by scRNA-seq data to infer the location, relative to the thymic architecture, of lineage decisions. Additionally, we combine positional information of thymocytes and stromal cells to infer cell-cell interactions that direct lineage decisions. Collectively, this analysis sheds light on the interactions that guide development of the diverse T cell family from a common precursor and characterizes the journey of these cells to reach maturity.

Effect of Xenogeneic Substances on the Glycan Profiles and Electrophysiological Properties of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes.

Human induced pluripotent stem cell (hiPSC)-derived cardiomyocyte (CM) hold great promise as a cellular source of CM for cardiac function restoration in ischemic heart disease. However, the use of animal-derived xenogeneic substances during the biomanufacturing of hiPSC-CM can induce inadvertent immune responses or chronic inflammation, followed by tumorigenicity. In this study, we aimed to reveal the effects of xenogeneic substances on the functional properties and potential immunogenicity of hiPSC-CM during differentiation, demonstrating the quality and safety of hiPSC-based cell therapy. We successfully generated hiPSC-CM in the presence and absence of xenogeneic substances (xeno-containing (XC) and xeno-free (XF) conditions, respectively), and compared their characteristics, including the contractile functions and glycan profiles. Compared to XC-hiPSC-CM, XF-hiPSC-CM showed early onset of myocyte contractile beating and maturation, with a high expression of cardiac lineage-specific genes (ACTC1, TNNT2, and RYR2) by using MEA and RT-qPCR. We quantified N-glycolylneuraminic acid (Neu5Gc), a xenogeneic sialic acid, in hiPSC-CM using an indirect enzyme-linked immunosorbent assay and liquid chromatography-multiple reaction monitoring- mass spectrometry. Neu5Gc was incorporated into the glycans of hiPSC-CM during xeno-containing differentiation, whereas it was barely detected in XF-hiPSC-CM. To the best of our knowledge, this is the first study to show that the electrophysiological function and glycan profiles of hiPSC-CM can be affected by the presence of xenogeneic substances during their differentiation and maturation. To ensure quality control and safety in hiPSC-based cell therapy, xenogeneic substances should be excluded from the biomanufacturing process.

CRL4B complex-mediated H2AK119 monoubiquitination restrains Th1 and Th2 cell differentiation.

CD4+ T helper (Th) cell differentiation is regulated by lineage-specific expression of transcription factors, which is tightly associated with epigenetic modifications, including histone acetylation and methylation. However, the factors regulating histone modifications involved in Th cell differentiation remain largely unknown. We herein demonstrated a critical role of Cullin 4B (CUL4B) in restricting Th1 and Th2 cell differentiation. CUL4B, which is assembled into the CUL4B-RING E3 ligase (CRL4B) complex, participates in various physiological and developmental processes through epigenetic repression of transcription. Depletion of Cul4b in CD4+ T cells enhanced Th1 and Th2 cell differentiation. In vivo, an aggravated Th2 response caused by the absence of CUL4B was observed in a murine asthma model. Mechanistically, the CRL4B complex promoted monoubiquitination at H2AK119 (H2AK119ub1) and polycomb repressive complex 2 (PRC2)-mediated trimethylation at H3K27 (H3K27me3) at Tbx21 and Maf and consequently repressed their expression during Th cell differentiation. Our study suggests that CRL4B complex-mediated H2AK119ub1 deposition functions to prevent the aberrant expression of Th1 and Th2 lineage-specific genes.