Progenitor-like State Research Articles

TMIC-33. MICROENVIRONMENT-DRIVEN CHANGES IN GLIOBLASTOMA CELL STATE SIGNATURES EXAMINED USING REGION-SPECIFIC HUMAN BRAIN ORGANOIDS

Abstract Cell state plasticity is retained by all stem-like and differentiated cells within glioblastoma (GBM) tumors. GBM cells can exploit these state-shifting capacities to evade and resist therapeutics. Thus, there is a need to identify and target the regulators of GBM cell state transitions. To address this question, we use a fully human platform where hiSPC-derived organoids serve as a recipient environment to host cells engrafted directly from surgically resected GBMs. This allows us to precisely examine how microenvironmental variables impact the molecular signatures of GBM cells. We acutely isolate GBM cells from surgical resections, label cells with a GFP-lentivirus for 4 hours, and then engraft these tumor cells into parallelly patterned region-specific organoids that mimic dorsal forebrain, ventral forebrain, midbrain, and hindbrain identities. These regions were chosen as they capture derivatives of the three primary brain vesicles and because these regions contain unique cell types and signaling molecules. We performed paired single-cell RNA sequencing on tumor cells pre-engraftment and 14 days post-engraftment. Universal to all regional organoids, we find that GBM cells shift towards a neural progenitor-like and neuron-like signature within organoids, regardless of the cell state of the parent tumor prior to engraftment. To support our findings, we also observed that patient-derived glioma cell lines converge on a neural progenitor-like state within organoids. Thus, the dominance of this shared GBM cell state within organoids implies the existence of shared extrinsic factors in these immature (neurogenic) organoids that favor a progenitor-like or neuron-like identity across all four regions. We are now asking whether this bias towards neuronal and/or neural progenitor identity is a result of engrafting into young neurogenic organoids, or if the same phenomenon could be true in late-stage (post-gliogenic) mature organoids. We are also using this valuable platform and data to identify the extrinsic signals that GBM cells rely on to fulfill their plastic potential, adapt to the microenvironment, and resist therapeutics.

The transcription factor foxo3 regulates cardiac remodeling after myocardial infarction

Abstract Background Myofibroblast and myeloid cell differentiation following acute myocardial infarction (MI) are important for myocardial fibrosis but also cause adverse remodeling leading to cardiac dysfunction and heart failure. The transcription factor forkhead box O 3 (Foxo3) inhibits hypertrophic cardiac remodeling. We hypothesized that Foxo3, a key regulator of cell differentiation and immunity might inhibit differentiation of fibroblasts and myoloid cells and therefore cardiac fibrosis after MI. Methods MI was induced in Foxo3-/- and wild-type mice by permanent LAD ligation. Cardiac function was determined by transthoracic echocardiography. Cell differentiation was investigated by single nucleus RNA-sequencing (snRNA-seq). Moreover, transdifferentiation assays ex vivo were performed. Results Foxo3-/- mice showed significantly improved survival post- MI (p<0.01) that was in part due to reduced cardiac ruptures (p<0.05). TTE showed reduced LV function, cardiac output, and global strain 4 days post-MI in both groups of animals. However, LV function was significantly attenuated in Foxo3-/- mice 14 d post-MI while diastolic parameters indicated enhanced wall stiffness. snRNA-seq on day 4 post-MI revealed significantly increased numbers of myofibroblasts (p<0.05) transdifferentiating from Progenitor-like state fibroblasts and epicardial derived fibroblasts in Foxo3-/- mice. Myofibroblasts upregulated genes important for extracellular matrix structure and cell migration. Moreover, an upregulation of pro-fibrotic genes was observed in other fibroblast clusters in Foxo3-/- mice and corroborated by significantly elevated collagen type 1 and 3 as well as periostin protein expression. Mechanistically, fibroblasts from Foxo3a-/- mice exhibited enhanced Smad3 dependent myofibroblast marker expression after TGF-ß stimulation. Cell chat analysis indicated enhanced number of interactions and interaction strength of myeloid cells with fibroblasts in Foxo3-/- animals. In line with these observations, differences in cardiac myeloid cell differentiation characterized by reduced center-log ratios of cardiac resident macrophages (Lyve1hiMHCIIlo and Lyve1loMHCIIhi) and increase in monocyte-derived macrophages (Ccr2hi MΦ and Trem2hi MΦ) on day 4 post-MI that was enhanced in Foxo3-/- mice were determined. Differential gene expression patterns on day 4 in pro-inflammatory macrophages (Ccr2hi MΦ) showed upregulation of genes in the interleukin-12 pathway while reparative macrophages (Trem2hi MΦ) revealed an increased expression of genes for extracellular matrix proteins and ECM-collagen interactions in Foxo3-/- mice. Conclusion Our data identify Foxo3 as a master regulator of cardiac remodeling inhibiting myofibroblast and myeloid cell differentiation after acute MI, and suggesting that deficiency of Foxo3 promotes early scar formation but also contributes to adverse matricellular remodeling resulting in impaired cardiac function and enhanced fibrosis.

Generation of human expandable limb-bud-like progenitors via chemically induced dedifferentiation.

In certain highly regenerative animals, cellular dedifferentiation occurs after injury, allowing specialized cells to become progenitor cells for regeneration. However, this capacity is restricted in human cells due to reduced plasticity. Here, we introduce a chemical-induced dedifferentiation approach that reverts the differentiated cells to a progenitor-like state, conferring the features of human limb bud cells from human adult somatic cells. These chemically induced human limb-bud-like progenitors (hCiLBP cells) show a high degree of transcriptomic similarity to human embryonic limb bud progenitors. Importantly, we established culture conditions that allow hCiLBP cells to undergo extensive expansion while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLBP cells exhibit increased osteochondrogenic differentiation ability, providing an innovative platform for generation of skeletal lineage cell types. These results highlight a potential therapeutic approach for repairing damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.

Tumor Protein D52 Regulates Paligenosis in Exocrine Pancreatic Acinar Cells

Background: Paligenosis is a conserved cellular plasticity program in which fully differentiated cells reenter the cell cycle in order to regenerate lost tissue during injury. This process is utilized by cells that have a slow turnover rate and lack dedicated stem cells, as is the case with exocrine pancreatic acinar cells. Acinar cells, which synthesize and secrete digestive enzymes necessary for macronutrient digestion, undergo paligenosis in response to damage induced by the inflammatory disease pancreatitis. During paligenosis, acinar cells first downscale their secretory apparatus by upregulating autophagy, and then take on a mucinous-ductal-progenitor-like identity in a process called acinar to ductal metaplasia (ADM) prior to proliferation. This phenomenon can be recapitulated in rodent models in vivo utilizing repeated episodes of cerulein-induced pancreatitis or in 18-hour suspension culture during which primary isolated acinar cells dedifferentiate to a progenitor-like state. We have previously reported that markers of the endolysosomal secretory pathway in acinar cells are rapidly lost during models of experimental pancreatitis and suspension culture. Tumor Protein D52, which regulates endolysosomal traffcking and secretion in acinar cells, undergoes lysosomal degradation at the onset of experimental pancreatitis; furthermore, restoring D52 expression by adenovirus in isolated acinar cells maintains secretion during experimental pancreatitis as well as maintains acinar differentiation in suspension culture. Hypothesis: Degradation of D52, and loss of the endolysosomal secretory pathway, are pivotal events during the initial stages of paligenosis. Methods: To study the role of D52 and the regulation of paligenosis, we generated tamoxifen-inducible, acinar specific D52 knockout mice (D52KOac), and markers of paligenosis (ADM, proliferation) were assessed by immunoblot, qPCR, and immunostaining. Mice were given tamoxifen at 2-3 months of age to ensure normal pancreatic development, and tissues were harvested 21 days after tamoxifen. Results: Compared to controls, D52KOac exhibited 2.5-fold upregulation of the ductal markers Sox9 and CK19, 50% reduction of Ptf1α, and a 5-fold increase in β-catenin; these markers signify the presence of ADM and cells with progenitor-like characteristics. Cell cycle regulation and proliferation were also observed in D52KOac by a nearly 3-fold increase in cyclin D and increased Ki67+ nuclei. Conclusions: These data support that loss of D52 in pancreatic acinar cells induces spontaneous paligenosis in the absence of cellular injury and inflammation. These findings point to a previously unrecognized role for D52 in the regulation of acinar cell differentiation and plasticity. Given that paligenosis is a key pathway involved in the development of pancreatic neoplasms and adenocarcinoma, studying D52-regulated paligenosis will reveal additional insights into this critical protective mechanism. American Pancreatic Association Foundation Young Investigator Award. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Abstract C094: Tff2 defines pancreatic TA progenitors that are protective against Kras-driven carcinogenesis

Abstract Background: Progenitor or stem cells play a pivotal role in maintaining tissue homeostasis and are often the source of tumor progression. While genuine stem cells are absent in the pancreatic exocrine organ, a variety of progenitor cells are present that contribute to normal homeostasis and regeneration process post-injury. In a previous study, we identified a pancreatic facultative progenitor (FP) that was marked by the gene doublecortin kinase like-1 (Dclk1). These Dclk1+ FP are rare, long-lived, quiescent cells that are critical for regeneration following injury. In contrast, cells marked by Trefoil factor 2 (Tff2) are active progenitors within the gastrointestinal tract, playing a crucial role in homeostasis and tumor progression. However, the role of Tff2+ cells within the pancreas remains relatively underexplored. Method & Results: To explore the function of Tff2 cells, we developed a Tff2 BAC transgenic mouse line (Tff2-DTR-CreERT2), which was then crossed with report mice. Employing lineage tracing and single cell RNA sequencing, we uncovered a new type of progenitor, distinct from the FP - Tff2+ transit amplifying progenitors (TAP). Tff2+ acinar cells showed much greater proliferation (>100-fold) than all other acinar cells. Single cell RNA-seq of the Tff2-expressing lineage showed that one cluster (cluster 0) identified acinar cells with a low differentiated, progenitor-like state. These cells were found to contribute to tissue homeostasis, exhibiting expansion in the early stages, giving rise to more differentiated acinar cells, peaking around six months, and then gradually diminishing until they disappeared. To understand the role of Tff2 in PanIN lesions, we developed a compound mouse model: Tff2-DTR-CreERT; Mist1-CreERT; KrasG12D(TMK). When Tff2+ cells were then ablated using Diphtheria Toxin in the setting of caerulein-induced pancreatitis, the TMK mice developed significantly more PanIN lesions. Tff2-CreERT; KrasG12D mice were generally more resistant to developing advanced PanINs, but in the setting of caerulein pancreatitis, the Tff2; KrasG12D model developed more pancreatic ductal adenocarcinoma (PDAC). To explore the role of the TFF2 peptide in tumor progression, we used an adenovirus expressing TFF2 (Ad-TFF2), and introduced it through tail vein injections. We found that Ad-Tff2 helped prevent the development of advanced PanIN lesions. Conclusion: In summary, our research indicated that Tff2 cells play a significant role in maintaining pancreatic homeostasis and act in paracrine fashion to suppress the development of pancreatic adenocarcinoma. Citation Format: Feijing Wu, Zhengyu Jiang, Xiaofei Zhi, Yosuke Ochiai, Ruth A. White, Ermanno Malagola, Jin Qian, Biyun Zheng, Ruhong Tu, Hiroki Kobayashi, Quin Waterbury, Leah B. Zamechek, Timothy C. Wang. Tff2 defines pancreatic TA progenitors that are protective against Kras-driven carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C094.

The benign nature and rare occurrence of cardiac myxoma as a possible consequence of the limited cardiac proliferative/ regenerative potential: a systematic review

BackgroundCardiac Myxoma is a primary tumor of heart. Its origins, rarity of the occurrence of primary cardiac tumors and how it may be related to limited cardiac regenerative potential, are not yet entirely known. This study investigates the key cardiac genes/ transcription factors (TFs) and signaling pathways to understand these important questions.MethodsDatabases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving cardiac myxoma, cardiac genes/TFs/signaling pathways and their roles in cardiogenesis, proliferation, differentiation, key interactions and tumorigenesis, with focus on cardiomyocytes.ResultsThe cardiac genetic landscape is governed by a very tight control between proliferation and differentiation-related genes/TFs/pathways. Cardiac myxoma originates possibly as a consequence of dysregulations in the gene expression of differentiation regulators including Tbx5, GATA4, HAND1/2, MYOCD, HOPX, BMPs. Such dysregulations switch the expression of cardiomyocytes into progenitor-like state in cardiac myxoma development by dysregulating Isl1, Baf60 complex, Wnt, FGF, Notch, Mef2c and others.The Nkx2–5 and MSX2 contribute predominantly to both proliferation and differentiation of Cardiac Progenitor Cells (CPCs), may possibly serve roles based on the microenvironment and the direction of cell circuitry in cardiac tumorigenesis. The Nkx2–5 in cardiac myxoma may serve to limit progression of tumorigenesis as it has massive control over the proliferation of CPCs. The cardiac cell type-specific genetic programming plays governing role in controlling the tumorigenesis and regenerative potential.ConclusionThe cardiomyocytes have very limited proliferative and regenerative potential. They survive for long periods of time and tightly maintain the gene expression of differentiation genes such as Tbx5, GATA4 that interact with tumor suppressors (TS) and exert TS like effect. The total effect such gene expression exerts is responsible for the rare occurrence and benign nature of primary cardiac tumors. This prevents the progression of tumorigenesis. But this also limits the regenerative and proliferative potential of cardiomyocytes. Cardiac Myxoma develops as a consequence of dysregulations in these key genes which revert the cells towards progenitor-like state, hallmark of CM. The CM development in carney complex also signifies the role of TS in cardiac cells.

Making a new limb out of old cells: exploring endogenous cell reprogramming and its role during limb regeneration.

Cellular reprogramming is characterized by the induced dedifferentiation of mature cells into a more plastic and potent state. This process can occur through artificial reprogramming manipulations in the laboratory such as nuclear reprogramming and induced pluripotent stem cell (iPSC) generation, and endogenously in vivo during amphibian limb regeneration. In amphibians such as the Mexican axolotl, a regeneration permissive environment is formed by nerve-dependent signaling in the wounded limb tissue. When exposed to these signals, limb connective tissue cells dedifferentiate into a limb progenitor-like state. This state allows the cells to acquire new pattern information, a property called positional plasticity. Here, we review our current understanding of endogenous reprogramming and why it is important for successful regeneration. We will also explore how naturally induced dedifferentiation and plasticity were leveraged to study how the missing pattern is established in the regenerating limb tissue.

CTNI-23. SINGLE CELL TRANSCRIPTOMICS, PHARMACOKINETICS, AND PHARMACODYNAMICS OF COMBINED CDK4/6 AND MTOR INHIBITION IN A PHASE 0 TRIAL OF RECURRENT HIGH-GRADE GLIOMA

Abstract Adult High-grade gliomas (HGGs) often exhibit deregulation of RB-CDK4/6 and mTOR signaling pathways. This study investigated tumor single cell transcriptomics, pharmacokinetics, and pharmacodynamics immediately following combined CDK4/6 (ribociclib) and mTOR (everolimus) inhibition in recurrent HGG. 24 patients with recurrent gliomas harboring RB+, CDKN2A/B deletion or CDK4/6 amplification, and PTEN loss or PIK3CA mutations were enrolled in a phase 0 trial. Patients received ribociclib treatment for 5 days before surgery, including six who received ribociclib (400mg QD) plus everolimus (2.5mg QD), and six dose-escalation cohorts (n = 3 each) reaching ribociclib 600mg QD plus everolimus 70mg QW. No dose-limiting toxicities were observed. Validated LC-MS/MS methods determined total and unbound drug concentrations. Preoperative MRI revealed a marked decrease in gadolinium-enhancement in all patients. In gadolinium-nonenhancing tumor regions, the median unbound concentration of ribociclib was 561 nM, while no unbound everolimus concentrations were detected. Ribociclib’s pharmacodynamic effects in surgical specimens were compared with matched archival tissue using IHC. Across IDH-wild-type tumors, there was significant decrease in MIB1 levels between the matched archival and surgical specimens (p < 0.05) suggesting drug-associated cell cycle inhibition. Single nuclei RNAseq (snRNA) analyses were performed on 17 IDH-wild-type recurrent samples treated with ribociclib plus everolimus and 29 IDH-wild-type recurrences treated with standard therapies. Cellular state analysis based on snRNAseq data demonstrated a decreased neural progenitor-like (NPC-like) malignant cell state compared with standard therapies (p < 0.01), indicating inhibition of the CDK4-driven neural progenitor-like cell state. This observation was validated using snRNA and patient-derived glioma cell lines exposed to ribociclib, showing a consistent decrease in NPC-like proportions and cycling cells (p < 0.05). This study highlights the value of integrating pharmacokinetics/pharmacodynamics and snRNA data to assess treatment effects in phase 0 surgical tissues. These findings support further development of ribociclib, but not everolimus, for the treatment of glioma patients.

Foxo3a and cardiac myofibroblast transdifferentiation after myocardial infarction

Abstract Background Fibroblast/ myofibroblast differentiation following acute myocardial infarction (MI) is important for myocardial scar formation but also causes adverse remodeling and stiffening of the myocardium leading to cardiac dysfunction and heart failure. Transdifferentiation of myofibroblasts are characterized by periostin, and extracellular matrix protein expression. The transcription factor forkhead box O 3 (FOXO3a) has been recently shown to inhibit hypertrophic cardiac remodeling. Purpose We hypothesized that FOXO3a, a key regulator of cell size, immunity, and cell differentiation, might inhibit transdifferentiation of fibroblasts into myofibroblasts and therefore cardiac fibrosis after MI. Methods Acute MI was induced in Foxo3a-/- mice and wild-type littermates by permanent LAD ligation. Cardiac function was determined by transthoracic echocardiography (TTE) at baseline as well as on days 4 and 14 post-MI. Immune histochemistry was performed with collagen and periostin. Finally, fibroblast differentiation was investigated by single nucleus RNA-sequencing (snRNA-seq). Results Foxo3a-/- mice showed significantly improved survival despite similar infarct size post-MI (p<0.01). The survival advantage was in part due to reduced cardiac ruptures on autopsy. TTE showed reduced LV function, cardiac output, and global strain 4 days post-MI that did not differ between both groups of animals. However, systolic LV function was significantly attenuated in Foxo3a-/- mice 14 days post-MI indicating enhanced wall stiffness. In line with these findings, sn-RNAseq on day 4 post-MI revealed significantly increased numbers of periostin positive myofibroblasts (Myo) (p<0.05) important for stabilizing matrix interactions that transdifferentiated mainly from progenitor-like state fibroblasts (PLS) and homeostatic epicardial derived fibroblasts (HEpiD) in Foxo3a-/- mice. Myo differentially expressed, i.e. upregulated genes important for extracellular matrix structure and organization, cell migration and collagen organization. Moreover, an upregulation of pro-fibrotic genes was observed in other fibroblast clusters such as in HEpiD (i.e., Col1a1, Col1a2, Col3a1), PLS (i.e., fgf10, il1r1), late response fibroblasts (LR-F) (i.e., Col14a1, Rin2) and in activated fibroblasts (F-ACT) (i.e., Gpc6, Slt2) in Foxo3a-/- mice. These changes were corroborated by significantly elevated collagen type 1 and 3 as well as periostin protein expression in Foxo3a-/- mice. Cell chat analysis indicated enhanced number of interactions and interaction strength of myeloid cells with fibroblasts in Foxo3a-/- mice. Conclusion Our data identify Foxo3a as a master regulator of cardiac remodeling attenuating myofibroblast transdifferentiation after acute MI. These findings suggest that deficiency of Foxo3a promotes early scar formation preventing rupture but also contributes to adverse remodeling in later stages resulting in impaired cardiac function and enhanced fibrosis after MI.

Driver gene combinations dictate cutaneous squamous cell carcinoma disease continuum progression

The molecular basis of disease progression from UV-induced precancerous actinic keratosis (AK) to malignant invasive cutaneous squamous cell carcinoma (cSCC) and potentially lethal metastatic disease remains unclear. DNA sequencing studies have revealed a massive mutational burden but have yet to illuminate mechanisms of disease progression. Here we perform RNAseq transcriptomic profiling of 110 patient samples representing normal sun-exposed skin, AK, primary and metastatic cSCC and reveal a disease continuum from a differentiated to a progenitor-like state. This is accompanied by the orchestrated suppression of master regulators of epidermal differentiation, dynamic modulation of the epidermal differentiation complex, remodelling of the immune landscape and an increase in the preponderance of tumour specific keratinocytes. Comparative systems analysis of human cSCC coupled with the generation of genetically engineered murine models reveal that combinatorial sequential inactivation of the tumour suppressor genes Tgfbr2, Trp53, and Notch1 coupled with activation of Ras signalling progressively drives cSCC progression along a differentiated to progenitor axis. Taken together we provide a comprehensive map of the cSCC disease continuum and reveal potentially actionable events that promote and accompany disease progression.

Photobiomodulation therapy activates YAP and triggers proliferation and dedifferentiation of Müller glia in mammalian retina

Photobiomodulation therapy has been proposed as a promising therapeutic approach for retinal degenerative diseases. However, its effect on the regenerative capacity in mammalian retina and its intracellular signaling mechanisms remain unknown. Here, we showed that photobiomodulation with 670 nm light stimulates Müller glia cell cycle re-entry and dedifferentiation into a progenitor-like state in both uninjured and injured retina. We also found that 670 nm light treatment inhibits the Hippo pathway, which is activated in Müller glia following NaIO3-induced retinal injury. YAP, a major downstream effector of the Hippo signaling pathway was translocated into nucleus of Müller glia along with YAP dephosphorylation in retina treated with 670 nm light. Deficiency of YAP attenuated Müller glia cell cycle re-entry and dedifferentiation. Our data reveal the Hippo-YAP signaling pathway is associated with the photostimulatory effect on regenerative response in mammalian retina and suggest a potential therapeutic strategy for retinal degenerative diseases.

AcrAB-TolC, a major efflux pump in Gram negative bacteria: toward understanding its operation mechanism

Photobiomodulation therapy has been proposed as a promising therapeutic approach for retinal degenerative diseases. However, its effect on the regenerative capacity in mammalian retina and its intracellular signaling mechanisms remain unknown. Here, we showed that photobiomodulation with 670 nm light stimulates Müller glia cell cycle re-entry and dedifferentiation into a progenitor-like state in both uninjured and injured retina. We also found that 670 nm light treatment inhibits the Hippo pathway, which is activated in Müller glia following NaIO3-induced retinal injury. YAP, a major downstream effector of the Hippo signaling pathway was translocated into nucleus of Müller glia along with YAP dephosphorylation in retina treated with 670 nm light. Deficiency of YAP attenuated Müller glia cell cycle re-entry and dedifferentiation. Our data reveal the Hippo-YAP signaling pathway is associated with the photostimulatory effect on regenerative response in mammalian retina and suggest a potential therapeutic strategy for retinal degenerative diseases.

Lung adenocarcinoma promotion by air pollutants.

A complete understanding of how exposure to environmental substances promotes cancer formation is lacking. More than 70 years ago, tumorigenesis was proposed to occur in a two-step process: an initiating step that induces mutations in healthy cells, followed by a promoter step that triggers cancer development1. Here we propose that environmental particulate matter measuring ≤2.5 μm (PM2.5), known to be associated with lung cancer risk, promotes lung cancer by acting on cells that harbour pre-existing oncogenic mutations in healthy lung tissue. Focusing on EGFR-driven lung cancer, which is more common in never-smokers or light smokers, we found a significant association between PM2.5 levels and the incidence of lung cancer for 32,957 EGFR-driven lung cancer cases in four within-country cohorts. Functional mouse models revealed that air pollutants cause an influx of macrophages into the lung and release of interleukin-1β. This process results in a progenitor-like cell state within EGFR mutant lung alveolar type II epithelial cells that fuels tumorigenesis. Ultradeep mutational profiling of histologically normal lung tissue from 295 individuals across 3 clinical cohorts revealed oncogenic EGFR and KRAS driver mutations in 18% and 53% of healthy tissue samples, respectively. These findings collectively support a tumour-promoting role for PM2.5 air pollutants and provide impetus for public health policy initiatives to address air pollution to reduce disease burden.

Abstract 3404: Single nuclei RNAseq analysis of recurrent high-grade glioma tumors from patients in the phase 0/1 ‘trigger’ trial of ribociclib plus everolimus

Abstract Background: The RB-CDK4/6 and mTOR signaling pathways are deregulated in high-grade glioma (HGG) and mTOR activation is a potential mechanism of resistance to CDK4/6 inhibition. This study evaluates the tumor pharmacokinetics (PK) and pharmacodynamics (PD) of combined CDK4/6 and mTOR inhibition in recurrent HGG patients. Furthermore, single nuclei RNA sequencing (snRNAseq) provides further insight on the transcriptomic and cell state change in all patients enrolled in the Phase 0 trial. Methods: Eligible patients had recurrent HGG with (1) RB+, (2) CDKN2A/B deletion or CDK4/6 amplification, and (3) PTEN loss or PIK3CA mutations. Six patients received five days of ribociclib (400mg QD) plus everolimus (2.5mg QD) and underwent tumor resection at 2, 8 or 24 hours following the last dose. Six dose-escalation cohorts (n=3 each) reached a dose-level of ribociclib (600mg QD) plus everolimus (70mg QW). Tumor tissue, CSF, and plasma were collected. Total and unbound drug concentrations were determined using validated LC-MS/MS methods. Tumor PD effects were compared to matched archival tissue. A PK ‘trigger’ (i.e., unbound concentration > 5-fold biochemical IC50) and a PD ‘trigger’ (>30% decrease in both pRB and pS6) in Gd-nonenhancing tissue were set to qualify patients for expansion. Single nuclei cell analysis was performed on 21 fresh frozen surgical tumor samples to capture transcriptional and cell state changes. Results: 24 patients with WHO Grade III (n=2) and Grade IV (n=22) gliomas were enrolled. No dose-limiting toxicities were observed. Following presurgical drug, all patients demonstrated marked decrease in Gd-enhancement on preoperative MRI. In Gd-nonenhancing tumor regions, the median unbound concentration of ribociclib was 561 nM whereas no unbound everolimus concentrations were detected. Across all dose-levels, 57% (13/23) and 43% (10/23) of tumors demonstrated RB and S6 phosphorylation decrease, respectively. snRNAseq analysis revealed significant downregulation of mTOR signaling only in endothelial cells at higher dose levels of everolimus. Amongst the tumor cells, the neural progenitor-like cell state was decreased whereas oligodendrocyte progenitor-like cell state was increased compared to standard-of-care cohort, suggesting a possible inhibition of CDK4-driven neural progenitor-like cell state. Conclusion: In adult HGG, ribociclib achieves pharmacologically-relevant concentrations in Gd-nonenhancing tumor. Everolimus exhibits limited penetration into human glioma tissue. Phase 0 surgical tumor tissue is shown to be great resource for identifying pharmacodynamic treatment effect at the single nuclei level. Our study supports further development of ribociclib, but not everolimus, for the treatment of glioma patients. Citation Format: Nader Sanai, An-Chi Tien, Kevin Johnson, Jun Jiang, Yu-Wei Chang, Chelsea Montgomery, Anita DeSantis, Yoko Fujita, Seongho Kim, Jing Li, Roel Verhaak, Shwetal Mehta. Single nuclei RNAseq analysis of recurrent high-grade glioma tumors from patients in the phase 0/1 ‘trigger’ trial of ribociclib plus everolimus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3404.

EPCO-25. MULTI-OMIC ANALYSIS OF THE GLIOBLASTOMA EPIGENOME AND TRANSCRIPTOME INFORMS OF MIGRATORY INTERNEURON-LIKE DEVELOPMENTAL REGULATORS

Abstract Recent studies have demonstrated that, despite their nomenclature, gliomas recapitulate an interneuron progenitor-like state that drives tumor progression. During human neurodevelopment, interneurons arise from the subcortical ganglionic eminences and migrate tangentially into the neocortex, settling in the cortical plate where they integrate local neurocircuitry. Analogously, malignant glioblastoma (GBM) cells migrate from the tumor core into the surrounding healthy tissue. This innate infiltrative property renders these malignant cells elusive to surgical resection, leading to tumor recurrence. To understand the regulatory networks that drive tumor infiltration from a neurodevelopmental perspective, we generated a single-nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) dataset of 41,000 nuclei from the core and infiltrative edge of surgically resected GBM specimens (n = 4). Concurrently, we sequenced 46,000 nuclei from non-pathological, postmortem samples of second- and third-trimester neocortices (n = 17). We integrated these datasets with paired single-nucleus RNA sequencing (snRNA-seq) data and identified candidate regulatory TFs that exhibit high correlation between motif enrichment and TF expression. Using single-trajectory inference and pseudo-time analyses, we identified TCF12 as a potential driver of interneuron lineage fate in developing cortical progenitors. Given its implication in projection neuron migration, we were intrigued to find that TCF12 activity is highest in GBM cells with a migratory interneuron signature, hinting at its putative role in tumor infiltration. To understand the significance of these findings, we will interrogate other genes in the TCF12 regulatory network with the ultimate goal of identifying therapeutic targets that inhibit GBM infiltration.

Abstract IA020: Reprogramming of myogenic transcription factors in rhabdomyosarcoma

Abstract Rhabdomyosarcoma, a pediatric malignancy with partial resemblance to undifferentiated skeletal muscle, is characterized by high expression of myogenic-lineage transcription factors such as MYOD1 and MYOG. Despite high expression of these transcription factors, which in normal muscle result in differentiation, RMS cells fail to differentiate, suggesting the presence of factors that inhibit their normal differentiation-promoting functions. In this talk, I will present data that the key muscle transcriptional regulator, SIX1, which in development activates the myogenic regulatory factors (MRFs) and promotes muscle differentiation, in fact inhibits differentiation in fusion-negative (FN) RMS. SIX1 holds FN-RMS cells in a progenitor-like state by altering the chromatin landscape and causing MYOD1, a key MRF, to preferentially bind to regulatory regions of genes permissive to growth rather than differentiation. Loss of SIX1 results in re-localization of MYOD1 to promoters/enhancers of genes associated with differentiation, and further results in increased binding of MYOG at such loci. Altered binding of MYOD1 and MYOG in response to SIX1 loss results in marked inhibition of RMS growth in vivo, via induction of differentiation. These data suggest that SIX1 acts as a master regulatory factor controlling the fate of RMS cells. Data will be presented that suggest dynamic actions of SIX1 and its co-factors throughout normal muscle differentiation, whereby high levels of SIX1 expressed in early muscle differentiation may mimic a transcriptional state seen in RMS. We hypothesize that the specific levels of SIX1, combined with a unique combination of transcriptional co-factors, reprogram genome-wide binding of MRFs to different promoter/enhancer sites at specific developmental time points, and that RMS is trapped in an early developmental state where SIX1 represses differentiation via genome-wide alterations in MRF binding that favor growth. Understanding the co-factors that work with SIX1 to alter chromatin state and MRF binding may enable the discovery of novel targets whose inhibition could serve as a relatively non-toxic treatment to restore normal developmental processes and inhibit RMS progression. Citation Format: Heide L. Ford, Jessica Y. Hsu, Etienne P. Danis, Stephanie Nance, Jenean H. O’Brien, Annika L. Gustafson, Veronica M. Wessells, Andrew E. Goodspeed, Jared C. Talbot, Sharon L. Amacher, Paul Jedlicka, Joshua C. Black, James C. Costello, Adam D. Durbin, Kristin B. Artinger. Reprogramming of myogenic transcription factors in rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA020.

LBA1 Mechanism of action and an actionable inflammatory axis for air pollution induced non-small cell lung cancer: Towards molecular cancer prevention

A mechanistic basis for non-small cell lung cancer (NSCLC) initiation in never smokers, a disease with a high frequency of EGFR mutations (EGFRm), is unknown. The air pollutant, particulate matter (PM), is known to be associated with the risk of NSCLC, however a direct cause and mechanism remain elusive. We analysed 463,679 individuals to address the associations of increasing 2.5um PM (PM2.5) concentrations with cancer risk. We performed ultra-deep profiling of 247 normal lung tissue samples, analysed normal lung tissue from humans and mice following exposures to PM, and investigated the consequences of PM on tumour promotion in mouse lung cancer models. Increasing PM2.5 levels were associated with increased risk of EGFRm NSCLC in England, S.Korea and Taiwan and with increased risk of mesothelioma (HR=1.19), lung (HR=1.16), anal (HR=1.23), small intestine (HR=1.30), GBM (HR=1.19), lip, oral cavity and pharynx (HR: 1.15) and laryngeal carcinomas (HR=1.26) in UK Biobank; HR for each 1ug/m3 PM2.5 increment. 18-33% of normal lung tissue samples harbour driver mutations in EGFR and KRAS in the absence of malignancy. PM promotes a macrophage response and a progenitor-like state in lung epithelium harbouring mutant EGFR. Consistent with PM promoting NSCLC in at-risk epithelium harbouring driver mutations, PM increased tumour burden in three EGFR or KRAS driven lung cancer models in a dose-dependent manner. Finally, we uncover an actionable inflammatory axis driven by IL1B in response to PM, with anti-IL1B therapy preventing PM-induced mouse tumour formation, consistent with reductions in human lung cancer incidence with anti-IL1B therapy. These results shed light on the aetiology of EGFRm lung cancer, particularly in never-smokers, and suggest that oncogenic mutations may be necessary but insufficient for tumour formation. These data reveal a mechanistic basis for PM driven lung cancer in the absence of classical carcinogen-driven mutagenesis, reminiscent of models of tumour initiation and promotion proposed 70 years ago, providing evidence to limit air pollution and opportunities for molecular targeted cancer prevention.

Heterogeneity and altered β-cell identity in the TallyHo model of early-onset type 2 diabetes

A primary underlying defect makes β-cells "susceptible" to no longer compensate for the peripheral insulin resistance and to trigger the onset of type 2 diabetes (T2D). New evidence suggests that in T2D, β-cells are not destroyed but experience a loss of identity, reverting to a progenitor-like state and largely losing the ability to sense glucose and produce insulin. We assessed (using fluorescence microscopy and histomorphometry correlated with the glycaemic status) the main β-cell identity modifications as diabetes progresses in the TallyHo/JngJ (TH) male mice, a polygenic model of spontaneous T2D, akin to the human phenotype. We found that: 1) conversion to overt diabetes is paralleled by a progressive reduction of insulin-expressing cells and expansion of a glucagon-positive population, together with alteration of islet size and shape; 2) the β-cell population is highly heterogeneous in terms of insulin content and specific transcription factors like PDX1 and NKX6.1, that are gradually lost during diabetes progression; 3) GLUT2 expression is altered early and strongly reduced at late stages of diabetes; 4) an endocrine developmental program dependent on NGN3-expressing progenitors is revived when hyperglycaemia becomes severe; and 5) the re-expression of the EMT-associated factor vimentin occurs as diabetes worsens, representing a possible regenerative response to β-cell loss. Based on these results, we formulated additional hypotheses for the β-cell identity alteration in the TH model, together with several limitations of the study, that constitute future research directions.

Abstract 679: Inhibition of Notch signaling causes progenitor-to-hepatocyte differentiation and regressions in a subset of hepatocellular carcinoma by controlling C/EBPα expression and HNF4α activity

Abstract ​​Notch signaling regulates cell fate decisions during development and maintenance of many organs. During hepatogenesis, an active NOTCH2 signal is required for specification of the cholangiocyte lineage, while hepatoblasts remaining in a Notch-off state contribute to the default hepatocyte lineage. Notch pathway activation has been reported in liver tumors, although Notch-related liver cancer mutations are rare. We identified a subset of hepatocellular carcinoma that is exceptionally sensitive to the inhibition of a JAG1-NOTCH2 signal in a mouse preclinical trial using 47 liver cancer PDX models. Transcriptional profiling revealed that the sensitive models resemble a progenitor-like state. Highly selective therapeutic antibodies targeting either the JAG1 ligand or the NOTCH2 receptor triggered hepatocyte differentiation programs and tumor regressions.Single cell analyses revealed heterogeneous transcriptional states at baseline, some of which were profoundly perturbed upon Notch inhibition. Topic modeling combined with inference of transcription factor activities suggested the involvement of HNF4α and C/EBPα in treatment induced changes. Through its target HES1, Notch signaling directly represses C/EBPα expression. Notch inhibition derepresses C/EBPα which then binds chromatin in cooperation with HNF4α. We found that this cooperative binding results in expression of genes associated with mature hepatocyte activity, which was incompatible with tumor maintenance. Importantly, we identify hallmarks to aid the identification of this relatively rare tumor type. We suggest that inducing cell states towards differentiated, less aggressive states, especially using targeted single-agent therapeutics, holds great promise for the treatment of certain tumors in the liver and, by extension, possibly in other progenitor-like cancers. Citation Format: Kerstin Seidel, Robert Piskol, Thi Thu Thao Nguyen, Charisa Cottonham, Mark Merchant, Christian Siebel. Inhibition of Notch signaling causes progenitor-to-hepatocyte differentiation and regressions in a subset of hepatocellular carcinoma by controlling C/EBPα expression and HNF4α activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 679.

Elucidating the Role of the Electron Transport Chain in Retinal Progenitor Cells and Neuro‐ regeneration

In the retinas of non‐mammalian vertebrates, such as zebrafish, neural regeneration is mediated by the molecular reprogramming of MGs into progenitor‐like cells. While mammalian MGs do not exhibit the regenerative potential of the zebrafish, it has been shown that MGs of mammals display limited‐ and transient‐entry into the cell cycle in response to damage. Therefore, an intrinsic proliferative and/or regenerative block likely prevents mammalian MGs from undergoing sustained cell cycle re‐entry and acquiring a multipotential retinal progenitor‐like state. Using a gain‐of‐function strategy we bypassed the Hippo signaling pathway and induced expression of a mutant version of YAP (YAP5SA) in MGs. Lineage tracing and histological analyses of these YAP5SA‐mutant retinas showed that MGs that expressed YAP5SA entered the cell cycle and formed radial clusters of proliferative cells strikingly similar to clonally expanding MG‐derived progenitors of the regenerating zebrafish retina. This finding indicated that YAP5SA is capable of spontaneously driving MGs into the cell cycle. Whether this YAP‐mediated reprogramming of MGs is sufficient to induce differentiation of MGs into fully functional neurons is undetermined. Subsequent single cell RNA sequencing analysis of the YAP5SA‐mutant retinas revealed that the proliferative event of YAP5SA‐positive cells occurred coincident with a dramatic downregulation of genes required for mitochondrial metabolic processes indicating that a metabolic shift is part of the MG reprogramming event. In a variety of cellular contexts, mitochondrial function and the electron transport chain (ETC) activity have emerged as integral regulators of the cell cycle and cell fate. The factors regulating a mitochondrial metabolic reprogramming and cell cycle are coupled but unknown. We generated a mouse line to conditionally knock out (CKO) the mitochondrial transcription factor A (Tfam) to target the ETC. In the CKO developing retinas, loss of Tfam results in loss of ETC activity. Preliminary histological analysis of CKO developing retinas show that loss of Tfam delays progenitor cell cycle exit and reduces neurogenesis resulting in a hypoplastic adult retina. Our findings so far indicate that unless retinal progenitor cells have a functional ETC‐driven oxidative activity, they remain within the cell cycle compromising the normal neural developmental program. The overall goal of this studies will be to determine how the RPC cell cycle machinery interfaces with ETC to drive cell cycle exit and neural differentiation. A better understanding of these requirements will have broad implications for the entire field of neural regeneration.