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To prospectively determine whether brain tumors will respond to immune checkpoint inhibitors (ICIs), we developed a novel mRNA vaccine as a viral mimic to elucidate cytokine release from brain cancer cells in vitro. Our results indicate that cytokine signatures following mRNA challenge differ substantially from ICI responsive versus non-responsive murine tumors. These findings allow for creation of a diagnostic assay to quickly assess brain tumor immunogenicity, allowing for informed treatment with ICI or lack thereof in poorly immunogenic settings.

BACKGROUND Recurrent PCNSBLs represent a therapeutic challenge. Up to 60% of PCNSBL patients relapse to later face survival rates as low as 22%. Unfortunately, tumor heterogeneity and off-target effects have limited the success of immunotherapy against PCNSBL. METHODS We propose a novel immunotherapy to overcome PCNSBL heterogeneity and off-target effects in an exquisitely tumor specific manner using nanoparticle vaccination, capable of delivering personalized tumor derived mRNAs, that induces systemic orchestration of innate and adaptive immunity. We target tumor antigens derived from the B cell receptor (i.e., heavy chain immunoglobulin - IgH) clonotypes. IgH clonotypes are hypervariable gene rearrangements clonally generated by B cells. Tumor IgH clonotypes are unique for each malignant B cell clone and hence attractive immune targets, not shared by normal B cell clones avoiding undesirable off-target effects. RESULTS RNA-NPs can reprogram tumor microenvironment while activating the innate immunity via IFN type I (i.e., IFNα) and priming of hypervariable region clonotype specific T cell responses in naïve mice. We determined the rearranged IgH sequences (predominant clone 99% and nine additional clones with frequencies < 1%) of clinically relevant inbred murine PCNSBL models (BAL17 and A20) by PCR. The number of identified clonotypes confirmed the IgH variability observed in human B cell hematological malignancies. In preliminary experiments targeting lymphoma derived single clonotypes with RNA-NPs, we showed the feasibility of priming in-vivo T cells specific against hypervariable regions after 3 weekly i.v. RNA-NPs (median IFNγ: 58 pg/ml; range: 50-70 pg/ml vs controls < 30 pg/ml; p=0.008). Targeting of clonotype RNA-NPs was associated with decreased tumor growth (p=0.04). Interestingly, we have observed tumor reactive lymphangiogenesis that communicates with regional skull bone marrow observed in 3D microscopy that might direct future routes of RNA-NP administration. CONCLUSION Our RNA-NP systemic vaccination platform can induce PCNSBL clonotype specific T cell responses, sparing normal tissues.

BACKGROUND Although mRNA vaccines have been deployed with great success against COVID-19, unlocking this technology against glioblastoma will necessitate new lipid-nanoparticle formulations that overcome cancer tolerance and immunosuppression. OBJECTIVE/METHODS We sought to develop a novel mRNA vaccine system to make tolerogenic tumor antigens appear more dangerous through use of unmodified nucleosides (pathogen associated molecular patterns, PAMPs) and highly cationic lipid shells that elicit a systemic damage response against cancer antigens. RESULTS We developed a novel vaccine formulation that increases payload packaging of tumor amplified mRNA into multilamellar (onion-shaped) particles for systemic (intravenous) administration. We demonstrate significant immunogenicity and efficacy of multilamellar RNA-NPs in syngeneic murine models for high-grade glioma (KR158b-pp65), and diffuse midline glioma (H3K27M DMG). Remarkably, RNA-NPs significantly improve median survival outcomes of DMG bearing mice beginning therapy at endpoint (Day 35 after midline intracranial implantation). Unlike prototypical mRNA vaccines that activate endosomal toll-like receptors (i.e. TLR7), multilamellar RNA-NPs elicit immunologic response predominantly through intracellular pathogen recognition receptors (RIG-I); long-term survival benefits from RNA-NPs were completely abrogated in RIG-I knockout mice. In canines (pet dogs) with spontaneous gliomas, RNA-NPs elicit massive recruitment/activation of peripheral blood mononuclear cells (PBMCs) which correlate with their trafficking into lymphoreticular organs (in follow-up murine studies). In canines receiving neoadjuvant RNA-NPs, prior to glioma biopsy, we see significant reprogramming of the glioma microenvironment with increased gene signatures for antigen processing/presentation, interferon signaling and cytotoxicity. Upon translation into human clinical trials for glioblastoma patients (NCT04573140), RNA-NPs elicit rapid (within hours) release of cytokines (e.g. IL-1, IL-6, IL-12 TNF-α, interferons) and chemokines (e.g. MIP1α, MCP-1, IP-10), which correlate with mobilization of PBMCs and activation of dendritic cells/CD8 lymphocytes. CONCLUSION First-in-human application of systemic multilamellar RNA-NP vaccines results in significant biologic effects and rapid immunologic reprogramming.

Brain tumors remain especially challenging to treat due to the presence of the blood–brain barrier. The unique biophysical properties of nanomaterials enable access to the tumor environment with minimally invasive injection methods such as intranasal and systemic delivery. In this review, we will discuss approaches taken in NP delivery to brain tumors in preclinical neuro-oncology studies and ongoing clinical studies. Despite recent development of many promising nanoparticle systems to modulate immunologic function in the preclinical realm, clinical work with nanoparticles in malignant brain tumors has largely focused on imaging, chemotherapy, thermotherapy and radiation. Review of early preclinical studies and clinical trials provides foundational safety, feasibility and toxicology data that can usher a new wave of nanotherapeutics in application of immunotherapy and translational oncology for patients with brain tumors.

BACKGROUND Diffuse Intrinsic Pontine Glioma (DIPG) is uniformly fatal. Upon diagnosis, DIPG cannot be safely debulked and systemic therapies have unproven benefit. Immunotherapy can overcome these obstacles, but objective responses are rare; and cancer antigens, even when tumor specific (i.e. H3K27M), are usually poorly immunogenic. OBJECTIVE We sought to develop a murine model of diffuse midline glioma (DMG) that better recapitulates human disease. In these models, we tested different iterations of mRNA loaded nanoparticle (NP) vaccines for their therapeutic effect. APPROACH: We implanted murine gliomas (expressing H3K27M mutation) midline into developing neonatal brains. We manufactured different mRNA constructs encoding for foreign proteins (e.g. GFP), H3K27M or wildtype H3K27 and evaluated immunogenicity and anti-tumor efficacy. These mRNA vaccines were layered into lipid particles (RNA-NP) and administered intravenously when animals became acutely symptomatic (similar to when patients are diagnosed). RESULTS Surprisingly, all mRNA constructs tested were sufficient to elicit anti-tumor efficacy against DMGs. This was true for both antigen specific (H3K27M) and non-antigen specific constructs (GFP, H3K27 wildtype). While H3K27M encoding RNA-NPs were superior to H3K27 wildtype encoding RNA-NPs (p=0.057), the adaptive immune effects appear marginal relative to the innate immune responses generated by all RNA-NP constructs. These innate responses are characterized by induction of type I interferon response from plasmacytoid DCs. Interestingly, these effects could not be recapitulated in murine models of adult type glioblastoma (KR158b) which required antigen specificity for induction of anti-tumor efficacy. CONCLUSION These data suggest that pediatric gliomas may be particularly sensitive to innate immunity. We have optimized development of a target H3K27M mRNA construct that balances innate and adaptive bi-directional immune induction. We are completing FDA-IND enabling data to support translation of H3K27M loaded RNA-NPs into human clinical trials.

Brain tumors remain especially challenging to treat due to the presence of the blood-brain barrier. The unique biophysical properties of nanomaterials enable access to the tumor environment with minimally invasive injection methods such as intranasal and systemic delivery.In this review, we will discuss approaches taken in NP delivery to brain tumors in preclinical neuro-oncology studies and ongoing clinical studies.Despite recent development of many promising nanoparticle systems to modulate immunologic function in the preclinical realm, clinical work with nanoparticles in malignant brain tumors has largely focused on imaging, chemotherapy, thermotherapy and radiation.Review of early preclinical studies and clinical trials provides foundational safety, feasibility and toxicology data that can usher a new wave of nanotherapeutics in application of immunotherapy and translational oncology for patients with brain tumors.

Objective Non-invasive prenatal testing (NIPT) based on fetal cells in maternal blood has the advantage over NIPT based on circulating cell-free fetal DNA in that there is no contamination with maternal DNA. This will most likely result in better detection of chromosomal aberrations including subchromosomal defects. The objective of this study was to test whether fetal cells enriched from maternal blood can be used for cell-based NIPT. Methods We present a method for enriching fetal cells from maternal blood, subsequent amplification of the fetal genome and detection of chromosomal and subchromosomal variations in the genome. Results An average of 12.8 fetal cells from 30 mL of maternal blood were recovered using our method. Subsequently, whole genome amplification on fetal cells resulted in amplified fetal DNA in amounts and quality high enough to generate array comparative genomic hybridization as well as next-generation sequencing profiles. From one to two fetal cells, we were able to demonstrate copy number differences of whole chromosomes (21, X−, and Y) as well as subchromosomal aberrations (ring X). Conclusion Intact fetal cells can be isolated from every maternal blood sample. Amplified DNA from isolated fetal cells enabled genetic analysis by array comparative genomic hybridization and next-generation sequencing. © 2016 John Wiley & Sons, Ltd.

Objective The goal was to develop methods for detection of chromosomal and subchromosomal abnormalities in fetal cells in the mother's circulation at 10–16 weeks' gestation using analysis by array comparative genomic hybridization (CGH) and/or next‐generation sequencing (NGS). Method Nucleated cells from 30 mL of blood collected at 10–16 weeks' gestation were separated from red cells by density fractionation and then immunostained to identify cytokeratin positive and CD45 negative trophoblasts. Individual cells were picked and subjected to whole genome amplification, genotyping, and analysis by array CGH and NGS. Results Fetal cells were recovered from most samples as documented by Y chromosome PCR, short tandem repeat analysis, array CGH, and NGS including over 30 normal male cells, one 47,XXY cell from an affected fetus, one trisomy 18 cell from an affected fetus, nine cells from a trisomy 21 case, three normal cells and one trisomy 13 cell from a case with confined placental mosaicism, and two chromosome 15 deletion cells from a case known by CVS to have a 2.7 Mb de novo deletion. Conclusion We believe that this is the first report of using array CGH and NGS whole genome sequencing to detect chromosomal abnormalities in fetal trophoblastic cells from maternal blood. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd., What's already known about this topic? Analysis of cell‐free DNA for noninvasive prenatal testing (NIPT) is widely practiced, and the frequency of amniocentesis and CVS has decreased.However, cell‐free NIPT is not adequate for detecting smaller deletions and duplications with high specificity, sensitivity, and positive predictive value.Although fetal nucleated red blood cells and trophoblastic cells are known to be present in the maternal circulation, it has not been possible to develop a reliable cytogenetic cell‐based form of NIPT. What does this study add? Fetal cytotrophoblasts were successfully recovered from maternal blood.Although a clinical test has not been validated, for the first time, the feasibility of using array comparative genomic hybridization and next generation sequencing to detect chromosomal and subchromosomal abnormalities is demonstrated.The results suggest the possibility of developing a cell‐based form of NIPT with ability to detect abnormalities with a similar accuracy as can currently be obtained with amniocentesis and CVS.

Objective Detection of genomic copy number abnormalities in a single cell using array comparative genomic hybridization (CGH) offers a promising non-invasive alternative for prenatal diagnosis. Our objective was to compare three commercially available whole-genome amplification (WGA) kits for their capacity to produce high quality DNA from single cells that is suitable for both molecular genotyping and array CGH. Methods We examined kit performance on unfixed, fixed and fixed/permeabilized lymphoblastoid cells. Molecular genotyping methods were used to evaluate the fidelity of amplified DNA for genomic profiling, while array CGH was used to assess copy number from single cells harboring trisomy 21, a DiGeorge syndrome deletion, a CMT1A duplication or a MECP2 duplication. Results Molecular genotyping was achieved from single cells but performance varied between WGA kits. Furthermore, we consistently detected a dosage difference in sex chromosomes for gender mismatched hybridizations and for chromosome 21 in trisomy 21 cells. The 2.5 Mb DiGeorge syndrome deletion was also detected using all three WGA platforms, whereas the 1.3 Mb CMT1A and the 0.6 Mb MECP2 duplications were not consistently detected. Conclusion These data suggest that single cell molecular genotyping and copy number analysis can be accomplished when WGA conditions are optimized. © 2016 John Wiley & Sons, Ltd.

BACKGROUND Molecular drivers of cancer immunogenicity in brain tumors are still being unraveled. While BATF3 expression, STING, and interferon response factors (IRFs) are necessary for cancer immunogenicity, the presence of type I interferon (IFN-I) is contextual having been reported to elicit both anti-tumoral and pro-tumoral effects. A better understanding of IFN-I signaling mechanisms is necessary to elucidate drivers of brain cancer immunogenicity and resistance. OBJECTIVE We sought to assess the role of IFN-I signaling in brain tumor immunogenicity and response to immune checkpoint inhibitors (ICIs) in ICI sensitive brain tumor models (i.e. GL261). We then sought to develop strategies to reset IFN-I signaling in ICI resistant brain tumor models (i.e. KR158b). METHODS To reset IFN-I signaling in immunologically ‘cold’ tumors unresponsive to ICIs, we developed lipid-nanoparticles (NPs) to deliver mRNA payloads to the brain tumor microenvironment (TME). RESULTS In immune-sensitive GL261 tumors, we showed that early release of IFN-I unlocks cancer immunogenicity and ICI response. Blockade of IFN-I during tumorigenesis (within 24h, but not days later) increases tumorigenicity and abrogates ICI activity in sensitive tumors. In ICI resistant KR158b tumors, we show that systemic administration of tumor-derived RNA-NPs localize to myeloid cells within the TME for simultaneous activation of multiple innate pathways including BATF3 (necessary for effector DCs), IRF5 (necessary for M2 to M1 macrophage reprograming), and IRF7 (necessary for IFN-I production). These RNA-NPs induce near-immediate release of IFN-I (within hours), reprogram the brain TME in an IFNAR1 (IFN-I receptor) dependent manner, and elicit significant anti-KR158b efficacy as a monotherapy. Following IFNAR1 blockade, RNA-NP mediated anti-tumor efficacy was abrogated. We demonstrated safety of tumor-specific RNA-NPs (derived from KR158b) in acute/chronic GLP toxicity studies without normal-brain cross-reactivity, and confirmed feasibility/safety and immunologic activity in large-animal studies. FUTURE DIRECTIONS We have since received FDA-IND approval for first-in-human trials (IND#BB-19304) in glioblastoma patients.

BACKGROUND Glioblastoma (GBM) can be an effective teacher in the war on COVID-19, as an operative vaccine for either must elicit near-immediate protective responses that overcomes disease heterogeneity and immune suppression. Current prophylactic strategies against COVID-19 utilize mRNA vaccines targeting small fragments of the SARS-CoV-2 genome, but these may not induce robust T cell responses or elicit immunity quickly enough. OBJECTIVE We sought to adapt an FDA-IND approved mRNA vaccine in GBM against COVID-19 for: 1) activation of near immediate immune responses, 2) targeting of full-length SARS-CoV-2 structural proteins, and 3) induction of bidirectional (B and T cell) adaptive immunity. METHODS We utilized a novel engineering design that layers mRNA into a lipid-nanoparticle (NP) shell (much like an onion); this allows greater packaging of mRNA per particle to quickly boost innate/adaptive immune responses against full-length glioblastoma antigens or SARS-CoV-2 structural proteins. RESULTS In small and large animal models, RNA-NPs safely mimic viremia activating the quiescent immune system in only a few hours for induction of protective immunity against its mRNA payload. RNA-NPs activate dendritic cells (DCs), upregulate critical innate gene signatures, and induce antigen-specific cellular and humoral immunity. We found that mice receiving SARS-CoV-2 spike RNA-NPs had more effector T cells after vaccination with significant memory recall expansion after in vitro re-stimulation with overlapping SARS-CoV-2 spike peptide mix. We also found increased release of MIP-1-alpha (i.e. CCL3) previously shown by our group (Mitchell et al. Nature 2015) to be responsible for Th1 mediated memory recall to infectious vaccine antigens in GBM patients. CONCLUSION SARS-CoV-2 RNA-NPs elicit memory recall response after vaccination. We have obtained FDA-IND approval (BB-19304, Sayour) in GBM with SARS-CoV-2 specific amendment (BB-20871) underway to support first-in-human trials of RNA-NPs targeting both GBM and COVID-19.

Non-invasive prenatal testing (NIPT) based on fetal cells in maternal blood has the advantage over NIPT based on circulating cell-free fetal DNA in that there is no contamination with maternal DNA. This will most likely result in better detection of chromosomal aberrations including subchromosomal defects. The objective of this study was to test whether fetal cells enriched from maternal blood can be used for cell-based NIPT.We present a method for enriching fetal cells from maternal blood, subsequent amplification of the fetal genome and detection of chromosomal and subchromosomal variations in the genome.An average of 12.8 fetal cells from 30 mL of maternal blood were recovered using our method. Subsequently, whole genome amplification on fetal cells resulted in amplified fetal DNA in amounts and quality high enough to generate array comparative genomic hybridization as well as next-generation sequencing profiles. From one to two fetal cells, we were able to demonstrate copy number differences of whole chromosomes (21, X-, and Y) as well as subchromosomal aberrations (ring X).Intact fetal cells can be isolated from every maternal blood sample. Amplified DNA from isolated fetal cells enabled genetic analysis by array comparative genomic hybridization and next-generation sequencing. © 2016 John WileySons, Ltd.

Detection of genomic copy number abnormalities in a single cell using array comparative genomic hybridization (CGH) offers a promising non-invasive alternative for prenatal diagnosis. Our objective was to compare three commercially available whole-genome amplification (WGA) kits for their capacity to produce high quality DNA from single cells that is suitable for both molecular genotyping and array CGH.We examined kit performance on unfixed, fixed and fixed/permeabilized lymphoblastoid cells. Molecular genotyping methods were used to evaluate the fidelity of amplified DNA for genomic profiling, while array CGH was used to assess copy number from single cells harboring trisomy 21, a DiGeorge syndrome deletion, a CMT1A duplication or a MECP2 duplication.Molecular genotyping was achieved from single cells but performance varied between WGA kits. Furthermore, we consistently detected a dosage difference in sex chromosomes for gender mismatched hybridizations and for chromosome 21 in trisomy 21 cells. The 2.5 Mb DiGeorge syndrome deletion was also detected using all three WGA platforms, whereas the 1.3 Mb CMT1A and the 0.6 Mb MECP2 duplications were not consistently detected.These data suggest that single cell molecular genotyping and copy number analysis can be accomplished when WGA conditions are optimized. © 2016 John WileySons, Ltd.

Chronic lymphocytic leukemia (CLL) is the most common leukemia in the United States. Metaphase-based cytogenetic tests, such as G-Band karyotyping, are among the most effective to detect CLL and provide significant prognostic information. However, the use of metaphase cytogenetics is currently problematic due to the low mitotic index of most CLL cells in vitro cultures. Even when metaphases can be generated in the presence of traditional B-cell mitogen LPS, the quality is often poor and aberrations escape detection.We hypothesized that immuno-stimulatory interleukin-2(IL-2) plus cytosine-phosphodiester-guanine oligodeoxynucleotide (CpG ODN) can work as a novel B-cell mitogen to stimulate bone marrow cultures which result in a higher mitotic index than regular standard bone marrow cultures stimulated with LPS. This will increase the clonal chromosomal aberration detection rate in patients with CLL.Bone marrow samples from CLL patients were divided and parallel cultures were set up using LPS and CpG Oligonucleotide/ IL-2 (IL-2/CpG) as mitogens, respectively. Mitotic index was read under the microscope blindly by three different readers (SQ, LV, RM). G-banding, and Spectral Karyotyping (SKY) were performed to confirm and compare abnormalities.The readings showed that mitotic index in IL-2/CpG stimulated bone marrow cultures was seven times higher than that of standard LPS bone marrow cultures with an average standard deviation of "0.92'" and CI of 95%, p less than 0.05. G-Banding and Spectral Karyotyping (SKY) showed the same abnormalities in IL-2/CpG found in LPS Bone marrow cultures.According to the results, IL-2/CpG cultures should be used in the cytogenetic lab for chromosomal analysis instead of LPS due to the higher mitotic index that helps in reducing false negative results. Further research should be done in order to lower false negative CLL detection results.

Objective The goal was to develop methods for detection of chromosomal and subchromosomal abnormalities in fetal cells in the mother's circulation at 10–16 weeks' gestation using analysis by array comparative genomic hybridization (CGH) and/or next-generation sequencing (NGS). Method Nucleated cells from 30 mL of blood collected at 10–16 weeks' gestation were separated from red cells by density fractionation and then immunostained to identify cytokeratin positive and CD45 negative trophoblasts. Individual cells were picked and subjected to whole genome amplification, genotyping, and analysis by array CGH and NGS. Results Fetal cells were recovered from most samples as documented by Y chromosome PCR, short tandem repeat analysis, array CGH, and NGS including over 30 normal male cells, one 47,XXY cell from an affected fetus, one trisomy 18 cell from an affected fetus, nine cells from a trisomy 21 case, three normal cells and one trisomy 13 cell from a case with confined placental mosaicism, and two chromosome 15 deletion cells from a case known by CVS to have a 2.7 Mb de novo deletion. Conclusion We believe that this is the first report of using array CGH and NGS whole genome sequencing to detect chromosomal abnormalities in fetal trophoblastic cells from maternal blood. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.