Biology subjects

Goldenberg, D.

Publications and source records attributed to Goldenberg, D..

4 recordsLinked to original sources

bioRxiv2026

Rational mRNA Structure -guided Attenuation Enables Embryo-safe in-ovo NDV Vaccination and Protection

Newcastle disease virus (NDV) continues to cause major economic losses in poultry, driving many recent virulent outbreaks. Maternally derived antibodies (MDA) can interfere with the development of active immunity following vaccination in young chicks. NDV vaccine strains that are safe for day-old chicks are not safe for administration to embryos. Here, we combined a computationally guided attenuation strategy with an in-ovo vaccination and challenge study to develop and evaluate an embryo-safe NDV vaccine candidate. Using a large NDV sequence compendium, we applied a local RNA folding energy based algorithm to identify folding selected clusters within the NDV fusion protein; we introduced targeted synonymous substitutions within the first ~900 nucleotides to modulate local RNA structure while preserving the encoded protein sequence. The recombinant attenuated variant was propagated in embryonated chicken eggs to generate vaccine stocks for in-ovo vaccination. After 18 days of embryonation, the synthetic variants were well tolerated, achieving more than 97% hatchability, with no pre-challenge morbidity or mortality, while unvaccinated challenge controls showed complete mortality. Together, these data support a model in which structure-aware synonymous modifications can yield an embryo-safe NDV backbone suitable for in-ovo delivery, with protective efficacy exhibiting a clear dose window under high MDA conditions.

synthetic biology↗

bioRxiv2024

Genome Instability Precedes Viral Integration in Human Papilloma Virus Transformed Tonsillar Keratinocytes

Approximately 70% of oropharyngeal squamous carcinomas (OPSCC) are associated with human papillomavirus (HPV). While HPV-positive (HPV+) OPSCC responds better to standard therapies and patients with HPV+ tumor generally have better outcomes than those with HPV-negative (HPV-) tumors, a subset of HPV+ patients do have poor outcomes. Our previous work suggested that tumors with integrated virus exhibit significantly greater genome wide genomic instability than those with only episomal viral genomes and patients with HPV+ OPSCC with episomal viral genomes had better outcomes. To explore the causal relation between viral integration and genomic instability, we have examined the time course of viral integration and genetic instability in tonsillar keratinocytes transformed with HPV16. HPV-infected human tonsil keratinocyte cell lines were continuously passaged and every fifth passage some cells were retained for genomic analysis. Whole genome sequencing and optical genomic mapping confirmed that virus integrated in five of six cell lines while remaining episomal in the sixth. In all lines genome instability occurred during early passages, but essentially ceased following viral integration but continued to occur later passages in the episomal line. To test tumorigenicity of the cell lines, cells were injected subcutaneously into the flanks of nude mice. A cell line with the integrated virus induced tumors following injection in the nude mouse while that with the episomal virus did not. We conclude that genomic instability is not the result of viral integration but likely promotes integration. Moreover, those transformants with episomal virus appear to be less tumorigenic than those with integrated virus.

cancer biology↗

bioRxiv2019

Runx3 prevents spontaneous colitis by directingdifferentiation of anti-inflammatory mononuclear phagocytes

RUNX3 is one of three mammalian Runt-domain transcription factors (TFs) that regulate gene expression in several types of immune cells. Runx3-deficiency in mice is associated with a multitude of defects in the adaptive and innate immunity systems, including the development of early onset colitis. Our study reveals that conditional deletion of Runx3 specifically in mononuclear phagocytes (MNP) (MNPRunx3-/-) but not in T cells, recapitulates the early onset spontaneous colitis seen in Runx3-/- mice.\n\nWe show that Runx3 is expressed in colonic MNP, including resident macrophages (RM) and the dendritic cell cDC2 subsets and its loss results in impaired differentiation/maturation of both cell types. At the transcriptome level, loss of Runx3 in RM and cDC2 was associated with upregulation of pro-inflammatory genes similar to those in the early onset IBD murine model of RMIl10r-/-. The impaired RM maturation in the absence of Runx3 was associated with a marked decrease in expression of anti-inflammatory and TGF{beta}-regulated genes. Similarly, the decreased expression of {beta}-catenin signaling associated genes in Runx3-deficient cDC2 indicates their impaired differentiation/maturation. Analysis of ChIP-seq data suggests that in both MNP cell types a significant fraction of these differentially expressed genes are high confidence Runx3 directly regulated genes. Interestingly, several of these putative Runx3 target genes harbor SNPs associated with IBD susceptibility in humans. Remarkably, the impaired maturation and pro-inflammatory phenotype of MNP lacking Runx3 was associated with a substantial reduction in the prevalence of colonic lamina propria Foxp3+ regulatory T cells and an increase in IFN{gamma}-producing CD4+ T cells, underscoring Runx3 critical role in establishing tolerogenic MNP.\n\nTogether, these data emphasize the dual role of Runx3 in colonic MNP, as a transcriptional repressor of pro-inflammatory genes and an activator of maturation-associated genes including anti-inflammatory genes. Our study highlights the significance of the current MNPRunx3-/- model for understanding of human MNP-associated colitis. It provides new insights into the crucial involvement of Runx3 in intestinal immune tolerance by regulating colonic MNP maturation through TGF{beta}R signaling and anti-inflammatory functions by Il10R signaling, befitting the identification of RUNX3 as a genome-wide associated risk gene for various immune-related diseases in humans including gastrointestinal tract diseases such as celiac and Crohns disease.

genetics↗

bioRxiv2019

An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients' Samples

While genomic analysis of tumors has stimulated major advances in cancer diagnosis, prognosis and treatment, current methods fail to identify a large fraction of somatic structural variants in tumors. We have applied a combination of whole genome sequencing and optical genome mapping to a number of adult and pediatric leukemia samples, which revealed in each of these samples a large number of structural variants not recognizable by current tools of genomic analyses. We developed computational methods to determine which of those variants likely arose as somatic mutations. The method identified 97% of the structural variants previously reported by karyotype analysis of these samples and revealed an additional fivefold more such somatic rearrangements. The method identified on average tens of previously unrecognizable inversions and duplications and hundreds of previously unrecognizable insertions and deletions. These structural variants recurrently affected a number of leukemia associated genes as well as cancer driver genes not previously associated with leukemia and genes not previously associated with cancer. A number of variants only affected intergenic regions but caused cis-acting alterations in expression of neighboring genes. Analysis of TCGA data indicates that the status of several of the recurrently mutated genes identified in this study significantly affect survival of AML patients. Our results suggest that current genomic analysis methods fail to identify a majority of structural variants in leukemia samples and this lacunae may hamper diagnostic and prognostic efforts.

genomics↗