Biology subjects

Marin, V.

Publications and source records attributed to Marin, V..

3 recordsLinked to original sources

bioRxiv2025

ZIP editors for efficient and versatile CRISPR-Cas9 precise genome editing

Precise genome editing technologies create the potential for genetic studies and innovative gene therapies. Here we present new CRISPR-Cas9 tools, named ZIP CRISPR, loaded with a single-stranded oligodeoxynucleotide (ssODN) template on the Cas ribonucleoprotein complex. The ssODN template is annealed to an extended guide RNA (gRNA) allowing its nuclear delivery at the right place, i.e. the targeted DNA cut, and at the right time. This new template import system is easy-to-design, easy-to-use, inexpensive and versatile. It increases homology-directed repair (HDR) editing efficiency using Cas9 nuclease up to 12-fold with a mean increase of 5-fold as demonstrated at many loci in many cell types. Based on a heteroduplex gRNA-ssODN, it can also be used with the Cas9 nickase, resulting in HDR editing with minimal InDels, and preventing double-strand break (DSB)-mediated genotoxicity. ZIP CRISPR is a non-viral platform adaptable to targeted DSB (higher HDR editing efficiency) or nick (higher safety) to precisely model and correct a wide range of edits. It is suitable for many biological applications and could be considered for HDR-based gene therapies.

bioengineering↗

bioRxiv2024

An in-cell approach to evaluate E3 ligases for use in targeted protein degradation.

One of the major challenges in evaluating the suitability of potential [~]700 E3 ligases for target protein degradation (TPD) is the lack of binders specific to each E3 ligase. Here we apply genetic code expansion (GCE) to encode a tetrazine-containing non-canonical amino acid (Tet-ncAA) site-specifically into the E3 ligase, which can be conjugated with strained trans-cyclooctene (sTCO) tethered to a neo-substrate protein binder by click chemistry within living cells. The resulting E3 ligase minimally modified and functionalized in an E3-ligand free (ELF) manner, can be evaluated for TPD of the neo-substrate. We demonstrate that CRBN encoded with clickable Tet-ncAA, either in the known immunomodulatory drug (IMiD)-binding pocket or across surface, can be covalently tethered to sTCO-linker-JQ1 and recruit BRD2/4 for CRBN mediated degradation, indicating the high plasticity of CRBN for TPD. The degradation efficiency is dependent on location of the Tet-ncAA encoding on CRBN as well as the length of the linker, showing the capability of this approach to map the surface of E3 ligase for identifying optimal TPD pockets. This ELF-degrader approach has the advantages of not only maintaining the native state of E3 ligase, but also allowing the interrogation of E3 ligases and target protein partners under intracellular conditions and can be applied to any known E3 ligase.

cell biology↗

bioRxiv2021

A study of the neuronal injury biomarkers pNF-H and UCHL1 in serum, CSF and urine in a cohort of thoracic endovascular aortic repair (TEVAR) patients.

A collection of longitudinal serum, cerebrospinal fluid (CSF) and urine samples were collected from a cohort of 50 patients undergoing thoracic endovascular aortic repairs (TEVAR). Samples were taken multiple time per day out to 5 days post operation and were probed with novel electrochemiluminescent assays specific for the phosphorylated axonal form of the major neurofilament subunit NF-H (pNF-H) and for ubiquitin C-terminal hydrolase 1 (UCHL1). Control blood samples showed small signals for pNF-H and in some cases rather larger signals for UCHL1. The presence of UCHL1 in these control blood samples was convincingly verified by western blotting with multiple well characterized UCHL1 antibodies and by mass spectroscopy. Elevated levels of both pNF-H and UCHL1 in blood and CSF in recovering TEVAR patients were associated with poorer outcomes. In particular release of UCHL1 into blood over several hours following TEVAR and peaking at any time over 1 ng/ml was a very strong predictor of patient death and was associated with renal failure and spinal cord ischemia (SCI). An unexpected finding was that high levels of UCHL1 were detected in certain urine samples, again in association with SCI, renal failure and poor patient outcome. We also present epitope mapping data on the UCHL1 monoclonal antibodies used including data on the widely used commercially available MCA-BH7. These studies suggest that measurement of the levels of both proteins in the blood, CSF and urine of TEVAR patients may be of clinical utility. However this study also raises questions about the origin and significance of UCHL1 both in control blood, in patient blood samples and in urine.

neuroscience↗