Biomedical subjects

Sean Hackett

Publications and source records attributed to Sean Hackett.

5 recordsLinked to original sources

PubMed2025

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.

Predicting gene expression from DNA sequence remains challenging due to complex regulatory codes. We introduce a masked DNA language model pretrained on 165 fungal genomes closely related to budding yeast that captures conserved regulatory grammar. Fine-tuning the LM on yeast RNA-seq data-including high-resolution transcriptional regulator induction time courses generated in this study-yielded Shorkie, a model that substantially improves gene expression prediction compared to baselines trained without self-supervision. Shorkie identified canonical transcription factor (TF) binding motifs and tracked their usage across induction experiments. Furthermore, Shorkie accurately predicted variant effects, outperforming leading sequence-to-expression models in cis-eQTL classification and achieving high concordance with massively parallel reporter assays. Interpretability analyses revealed Shorkie's ability to resolve promoter dynamics, splicing signals, and temporal changes in regulatory motif usage. This framework demonstrates that evolutionary-scale pretraining combined with transfer learning substantially improves our ability to decode gene regulation from sequence, providing insights into noncoding variants and regulatory networks.

Journal Article↗

PubMed2003

Increased expression of brain-derived neurotrophic factor preserves retinal function and slows cell death from rhodopsin mutation or oxidative damage.

There are no effective treatments for inherited retinal degenerations, which are prevalent causes of visual disability. Several proteins promote the survival of various types of neurons, and increasing expression of one or more of these survival factors is a promising strategy for a new treatment. Studies examining the effects of intravitreous injections of brain-derived neurotrophic factor (BDNF) in models of inherited retinal degenerations have suggested that BDNF has little survival-promoting activity for photoreceptors. In this study, we generated double transgenic mice with doxycycline-inducible expression of BDNF in the retina. In a model of primary rod photoreceptor degeneration, expression of BDNF resulted in significant delay in photoreceptor cell death and maintenance of retinal function assessed by electroretinogram recordings. Expression of BDNF also caused strong protection of photoreceptors from oxidative damage-induced cell death. These data suggest that continuous expression of BDNF, unlike intravitreous injections, results in morphologic and functional benefit in animal models of inherited retinal degeneration. Double transgenic mice with inducible expression of survival factors provide valuable tools for selection of survival factor candidates for gene therapy.

Animals↗

PubMed2002

Sustained transduction of ocular cells with a bovine immunodeficiency viral vector.

Human immunodeficiency viral (HIV) vectors mediate long-term transduction of many types of nondividing cells in vivo. Bovine immunodeficiency virus (BIV) is a lentivirus that shares many characteristics with HIV, but does not cause human disease. In this study, we investigated the potential of BIV vectors for ocular gene therapy. An enhanced green fluorescent protein (eGFP)-encoding reporter gene was packaged in recombinant BIV vector (BIV.eGFP). Adult C57BL/6 mice were given an intravitreous (5 x 10(4) or 5 x 10(5) transducing units [TU]) or subretinal (5 x 10(5) TU) injection of BIV.eGFP and then GFP expression was assessed at several time points. In vivo examinations of mice showed that subretinal injection of BIV.eGFP resulted in strong expression of GFP from the first examination at 1 week through the final examination at 20 weeks. Only a few mice that received intravitreous injection of BIV.eGFP showed GFP expression by ocular examinations until 11-12 weeks, when most showed small areas of expression. Postmortem examinations showed prominent GFP expression in retinal pigmented epithelial (RPE) cells throughout the region of subretinal injection of vector, although occasional negatively staining RPE cells were scattered among the much more numerous, brilliantly staining cells. Ciliary epithelial cells frequently expressed GFP, as did occasional Müller cells and rarely other retinal cells. The expression was stable from the first time point (2 weeks) to the last (20 weeks). Postmortem examination of eyes given an intravitreous injection of BIV.eGFP showed transduction of cells in the corneal endothelium and a few scattered retinal cells. There was no evidence of inflammation or toxicity in any eyes. These data show that BIV vectors mediate rapid and sustained transduction of RPE cells, suggesting that they may be useful for ocular gene therapy targeting RPE cells.

Animals↗

PubMed2002

Inducible expression of vascular endothelial growth factor in adult mice causes severe proliferative retinopathy and retinal detachment.

Transgenic mice with vascular endothelial growth factor (VEGF) driven by the rhodopsin promoter (rho/VEGF mice) develop neovascularization that originates from the deep capillary bed of the retina and grows into the subretinal space. In rho/VEGF mice, VEGF expression in photoreceptors begins between postnatal days 5 and 7, the period when the deep capillary bed is developing. An important question is whether or not the developmental stage of the deep capillary bed is critical for occurrence of neovascularization. Also, although rho/VEGF mice are extremely useful for the study of ocular neovascularization, there are some applications for which the early onset of VEGF expression is a disadvantage. In this study, we used the reverse tetracycline transactivator (rtTA) inducible promoter system coupled to either the rhodopsin or interphotoreceptor retinoid-binding protein (IRBP) promoter to control the time of onset of VEGF transgene expression in photoreceptors. In the absence of doxycycline, adult double-transgenic rho/rtTA-TRE/VEGF or IRBP/rtTA-TRE/VEGF mice showed little VEGF transgene expression and no phenotype. The addition of doxycycline to the drinking water resulted in prominent transgene expression and evidence of neovascularization within 3 to 4 days. Like rho/VEGF mice, the neovascularization originated from the deep capillary bed of the retina, but it was more extensive and caused outer retinal folds followed by total retinal detachment. Real-time polymerase chain reaction and enzyme-linked immunosorbent assay demonstrated that the mice with inducible expression of VEGF that developed retinal detachment had much higher ocular levels of VEGF mRNA and protein compared to rho/VEGF mice that manifest a much milder phenotype. These data demonstrate that regardless of developmental stage of the vascular bed, increased expression of VEGF in the retina is sufficient to cause neovascularization, and high levels of expression cause severe neovascularization and traction retinal detachment. Mice with inducible expression of VEGF in the retina provide a valuable new model of ocular neovascularization.

Animals↗

PubMedDate not supplied

Deficiency of neuropilin 2 suppresses VEGF-induced retinal neovascularization.

Vascular endothelial growth factor (VEGF) plays a central role in the development of ocular neovascularization (NV) and is an excellent target for therapeutic intervention. VEGF acts through several receptors, including VEGF receptor 1, VEGF receptor 2, neuropilin-1 (Npn1), and Npn2, but the exact role of these receptors in the development of retinal NV is unknown. In this study, we investigated the expression of npn2 mRNA during new blood vessel growth in the retina and used npn2 knockout mice to assess the impact of deficiency of Npn2 on retinal NV. The level of npn2 mRNA in the retina increased during retinal vascular development, after exposure to hyperoxia, and after the onset of retinal ischemia. Immunohistochemistry showed colocalization of Npn2 with a vascular marker in retinal NV. Compared with littermate controls, mice deficient in Npn2 had significantly less ischemia-induced retinal NV and very little subretinal NV due to expression of a Vegf transgene. These data suggest that Npn2 facilitates VEGF-induced retinal NV and may constitute a useful target for therapeutic intervention in ocular diseases complicated by NV.

Animals↗