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result(s) for
"Confer, Thomas"
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An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
by
Chapple, Richard H.
,
Koo, Selene C.
,
Kim, Yuna
in
Adrenal glands
,
algorithms
,
Animal Genetics and Genomics
2024
Background
Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models.
Results
Here, we generate single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We develop an unsupervised machine learning approach (“automatic consensus nonnegative matrix factorization” (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirm a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly, however, this weak-mesenchymal-like program is maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 h, suggesting an uncharacterized therapy-escape mechanism.
Conclusions
Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
Journal Article
RBM39 degrader invigorates innate immunity to eradicate neuroblastoma despite cancer cell plasticity
2025
The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic and mesenchymal, which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown, and how to eradicate neuroblastoma regardless of its cell state is a clinical challenge. To better understand the cellular plasticity of neuroblastoma in chemoresistance, we define the transcriptomic and epigenetic map of adrenergic and mesenchymal types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We show that cancer cells not only undergo a bidirectional switch between adrenergic and mesenchymal states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. These cell state alterations are coupled with epigenetic reprogramming and dependency switching of cell state–specific transcription factors, epigenetic modifiers, and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances the anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
Cell state plasticity of neuroblastoma cells is linked to therapy resistance. Here, the authors develop a transcriptomic and epigenetic map of indisulam (RBM39 degrader) resistant neuroblastoma, demonstrating bidirectional cell state switching accompanied by increased NK cell activity, which they therapeutically enhance by the addition of an anti-GD2 antibody.
Journal Article
RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticity
2024
The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown and how to eradicate neuroblastoma regardless of their cell states is a clinical challenge. To better understand the lineage switch of neuroblastoma in chemoresistance, we comprehensively defined the transcriptomic and epigenetic map of ADRN and MES types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We showed that cancer cells not only undergo a bidirectional switch between ADRN and MES states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. The lineage alterations are coupled with epigenetic reprogramming and dependency switch of lineage-specific transcription factors, epigenetic modifiers and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
Journal Article
Maternal immunization with distinct influenza vaccine platforms elicits unique antibody profiles that impact the protection of offspring
2023
Pregnant women and infants are considered high-risk groups for increased influenza disease severity. While influenza virus vaccines are recommended during pregnancy, infants cannot be vaccinated until at least six months of age. Passive transfer of maternal antibodies (matAbs) becomes vital for the infant's protection. Here, we employed an ultrasound-based timed-pregnancy murine model and examined matAb responses to distinct influenza vaccine platforms and influenza A virus (IAV) infection in dams and their offspring. We demonstrate vaccinating dams with a live-attenuated influenza virus (LAIV) vaccine or recombinant hemagglutinin (rHA) proteins administered with adjuvant resulted in enhanced and long-lasting immunity and protection from influenza in offspring. In contrast, a trivalent split-inactivated vaccine (TIV) afforded limited protection in our model. By cross-fostering pups, we show the timing of antibody transfer from vaccinated dams to their offspring (prenatal versus postnatal) can shape the antibody profile depending on the vaccine platform. Our studies provide information on how distinct influenza vaccines lead to immunogenicity and efficacy during pregnancy, impact the protection of their offspring, and detail roles for IgG1 and IgG2c in the development of vaccine administration during pregnancy that stimulate and measure expression of both antibody subclasses.Pregnant women and infants are considered high-risk groups for increased influenza disease severity. While influenza virus vaccines are recommended during pregnancy, infants cannot be vaccinated until at least six months of age. Passive transfer of maternal antibodies (matAbs) becomes vital for the infant's protection. Here, we employed an ultrasound-based timed-pregnancy murine model and examined matAb responses to distinct influenza vaccine platforms and influenza A virus (IAV) infection in dams and their offspring. We demonstrate vaccinating dams with a live-attenuated influenza virus (LAIV) vaccine or recombinant hemagglutinin (rHA) proteins administered with adjuvant resulted in enhanced and long-lasting immunity and protection from influenza in offspring. In contrast, a trivalent split-inactivated vaccine (TIV) afforded limited protection in our model. By cross-fostering pups, we show the timing of antibody transfer from vaccinated dams to their offspring (prenatal versus postnatal) can shape the antibody profile depending on the vaccine platform. Our studies provide information on how distinct influenza vaccines lead to immunogenicity and efficacy during pregnancy, impact the protection of their offspring, and detail roles for IgG1 and IgG2c in the development of vaccine administration during pregnancy that stimulate and measure expression of both antibody subclasses.
Journal Article
Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma
2024
The MYC proto-oncogenes (c-MYC,
,
) are among the most deregulated oncogenic drivers in human malignancies including high-risk neuroblastoma, 50% of which are
-amplified. Genetically engineered mouse models (GEMMs) based on the
transgene have greatly expanded the understanding of neuroblastoma biology and are powerful tools for testing new therapies. However, a lack of c-MYC-driven GEMMs has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and therapy development given that c-MYC is also an important driver of many high-risk neuroblastomas. In this study, we report two transgenic murine neuroendocrine models driven by conditional c-MYC induction in tyrosine hydroxylase (Th) and dopamine β-hydroxylase (Dbh)-expressing cells. c-MYC induction in Th-expressing cells leads to a preponderance of Pdx1
somatostatinomas, a type of pancreatic neuroendocrine tumor (PNET), resembling human somatostatinoma with highly expressed gene signatures of δ cells and potassium channels. In contrast, c-MYC induction in Dbh-expressing cells leads to onset of neuroblastomas, showing a better transforming capacity than MYCN in a comparable C57BL/6 genetic background. The c-MYC murine neuroblastoma tumors recapitulate the pathologic and genetic features of human neuroblastoma, express GD2, and respond to anti-GD2 immunotherapy. This model also responds to DFMO, an FDA-approved inhibitor targeting ODC1, which is a known MYC transcriptional target. Thus, establishing c-MYC-overexpressing GEMMs resulted in different but related tumor types depending on the targeted cell and provide useful tools for testing immunotherapies and targeted therapies for these diseases.
Journal Article
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
2024
Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models. Here, we generated single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We developed an unsupervised machine learning approach ('automatic consensus nonnegative matrix factorization' (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirmed a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly however, this weak-mesenchymal-like program was maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 hours, suggesting an uncharacterized therapy-escape mechanism. Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
Journal Article
Partnership Key to Toxic Disclosure
1985
There were some nervous moments last month when the county's proposed toxic disclosure law came before the membership of the 7-month-old Indtustrial Environmental Coalition of Orange County
Newspaper Article
Comparison of model and ground observations finds snowpack and blowing snow aerosols both contribute to Arctic tropospheric reactive bromine
by
Swanson, William F.
,
Confer, Kaitlyn
,
Jaeglé, Lyatt
in
Absorption spectroscopy
,
Aerosol formation
,
Aerosols
2022
Reactive halogens play a prominent role in the atmospheric chemistry of the Arctic during springtime. Field measurements and modeling studies suggest that halogens are emitted into the atmosphere from snowpack and reactions on wind-blown snow-sourced aerosols. The relative importance of snowpack and blowing snow sources is still debated, both at local scales and regionally throughout the Arctic. To understand the implications of these halogen sources on a pan-Arctic scale, we simulate Arctic reactive bromine chemistry in the atmospheric chemical transport model GEOS-Chem. Two mechanisms are included: (1) a blowing snow sea salt aerosol formation mechanism and (2) a snowpack mechanism assuming uniform molecular bromine production from all snow surfaces. We compare simulations including neither mechanism, each mechanism individually, and both mechanisms to examine conditions where one process may dominate or the mechanisms may interact. We compare the models using these mechanisms to observations of bromine monoxide (BrO) derived from multiple-axis differential optical absorption spectroscopy (MAX-DOAS) instruments on O-Buoy platforms on the sea ice and at a coastal site in Utqiaġvik, Alaska, during spring 2015. Model estimations of hourly and monthly average BrO are improved by assuming a constant yield of 0.1 % molecular bromine from all snowpack surfaces on ozone deposition. The blowing snow aerosol mechanism increases modeled BrO by providing more bromide-rich aerosol surface area for reactive bromine recycling. The snowpack mechanism led to increased model BrO across the Arctic Ocean with maximum production in coastal regions, whereas the blowing snow aerosol mechanism increases BrO in specific areas due to high surface wind speeds. Our uniform snowpack source has a greater impact on BrO mixing ratios than the blowing snow source. Model results best replicate several features of BrO observations during spring 2015 when using both mechanisms in conjunction, adding evidence that these mechanisms are both active during the Arctic spring. Extending our transport model throughout the entire year leads to predictions of enhanced fall BrO that are not supported by observations.
Journal Article
Medical Management of the Acute Radiation Syndrome: Recommendations of the Strategic National Stockpile Radiation Working Group
by
Armitage, James O.
,
Waselenko, Jamie K.
,
Pesik, Nicki
in
Animals
,
Biological and medical sciences
,
Disaster Planning
2004
Physicians, hospitals, and other health care facilities will assume the responsibility for aiding individuals injured by a terrorist act involving radioactive material. Scenarios have been developed for such acts that include a range of exposures resulting in few to many casualties. This consensus document was developed by the Strategic National Stockpile Radiation Working Group to provide a framework for physicians in internal medicine and the medical subspecialties to evaluate and manage large-scale radiation injuries. Individual radiation dose is assessed by determining the time to onset and severity of nausea and vomiting, decline in absolute lymphocyte count over several hours or days after exposure, and appearance of chromosome aberrations (including dicentrics and ring forms) in peripheral blood lymphocytes. Documentation of clinical signs and symptoms (affecting the hematopoietic, gastrointestinal, cerebrovascular, and cutaneous systems) over time is essential for triage of victims, selection of therapy, and assignment of prognosis. Recommendations based on radiation dose and physiologic response are made for treatment of the hematopoietic syndrome. Therapy includes treatment with hematopoietic cytokines; blood transfusion; and, in selected cases, stem-cell transplantation. Additional medical management based on the evolution of clinical signs and symptoms includes the use of antimicrobial agents (quinolones, antiviral therapy, and antifungal agents), antiemetic agents, and analgesic agents. Because of the strong psychological impact of a possible radiation exposure, psychosocial support will be required for those exposed, regardless of the dose, as well as for family and friends. Treatment of pregnant women must account for risk to the fetus. For terrorist or accidental events involving exposure to radioiodines, prophylaxis against malignant disease of the thyroid is also recommended, particularly for children and adolescents.
Journal Article
Anthropogenic Influence on Tropospheric Reactive Bromine Since the Pre‐industrial: Implications for Arctic Ice‐Core Bromine Trends
2024
Tropospheric reactive bromine (Bry) influences the oxidation capacity of the atmosphere by acting as a sink for ozone and nitrogen oxides. Aerosol acidity plays a crucial role in Bry abundances through acid‐catalyzed debromination from sea‐salt‐aerosol, the largest global source. Bromine concentrations in a Russian Arctic ice‐core, Akademii Nauk, show a 3.5‐fold increase from pre‐industrial (PI) to the 1970s (peak acidity, PA), and decreased by half to 1999 (present day, PD). Ice‐core acidity mirrors this trend, showing robust correlation with bromine, especially after 1940 (r = 0.9). Model simulations considering anthropogenic emission changes alone show that atmospheric acidity is the main driver of Bry changes, consistent with the observed relationship between acidity and bromine. The influence of atmospheric acidity on Bry should be considered in interpretation of ice‐core bromine trends. Plain Language Summary Reactive bromine in the air impacts major oxidants in our atmosphere, which remove pollutants and greenhouse gases and has changed over time in the Russian Arctic. Ice‐core bromine and acidity show a significant increase from pre‐industrial to the 1970s followed by a decrease. Our study suggests that human activities caused changes in bromine through the emissions of acidic gases from fossil fuel combustion. Considering relationships between atmospheric acidity and bromine is crucial to interpreting bromine variations in ice cores. Key Points Bromine (Br) concentrations increased 3.5‐fold from pre‐industrial to 1975 and declined 50% by 1999 in a Russian Arctic ice‐core A robust correlation between ice‐core Br and acidity highlights acidity’s key role in influencing the atmospheric Br budget Model shows acid‐catalyzed sea‐salt debromination is the largest source of reactive Br and drives ice‐core Br trends
Journal Article