Biology subjects

Hanna, R.

Publications and source records attributed to Hanna, R..

12 recordsLinked to original sources

bioRxiv2025

Bioengineering of the implantable vascularized endocrine constructs for insulin delivery suitable for clinical upscaling

Beta cell replacement therapy for type 1 diabetes is hindered by poor graft survival and suboptimal function, largely due to inadequate vascularization and lack of supportive microenvironment. To address these challenges, we developed a clinically scalable, extracellular matrix (ECM)-mimetic hydrogel, termed Amniogel, derived from human amniotic membrane via streamlined, clinically compliant process. Co-encapsulation of pancreatic islets with blood outgrowth endothelial cells (BOECs) within Amniogel facilitated the formation of prevascularized endocrine constructs (VECs). These constructs demonstrated enhanced {beta}-cell viability and function through ECM-bound pro-survival signals, rapid self-assembly of perfusable endothelial networks enabling efficient glucose sensing, and deposition of laminin-rich basement membranes enhancing {beta}-cell coupling and insulin secretion kinetics. In preclinical diabetic mouse models, VECs rapidly integrated with the host vasculature and provided sustained glycemic control when implanted subcutaneously. This integrative approach, combining a scalable, cost-effective biological scaffold with autologous vascularization potential, represents a significant advancement toward durable and clinically translatable {beta}-cell replacement therapies for T1DM. One Sentence SummaryA clinically scalable, biological hydrogel based vascularized endocrine constructs show sustained diabetes reversal.

bioengineering↗

bioRxiv2025

A multi-modal cell-free RNA language model for liquid biopsy applications

Cell-free RNA (cfRNA) profiling has emerged as a powerful tool for non-invasive disease detection, but its application is limited by data sparsity and complexity, especially in settings with constrained sample availability. We introduce Exai-1, a multi-modal, transformer-based generative foundation model that integrates RNA sequence embeddings with cfRNA abundance data to capture biologically meaningful representations of circulating RNAs. By leveraging both sequence and expression modalities, Exai-1 captures a biologically meaningful latent structure of cfRNA profiles. Pre-trained on over 306 billion tokens from 8,339 samples, Exai-1 enhances signal fidelity, reduces technical noise, and improves disease detection by generating synthetic cfRNA profiles. We show that self-attention and variational inference are particularly important for preservation of biological signals and contextual relationships. Additionally, Exai-1 facilitates cross-biofluid translation and assay compatibility through disentangling biological signals from confounders. By uniting sequence-informed embeddings with cfRNA expression patterns, Exai-1 establishes a transfer learning foundation for liquid biopsy, offering a scalable and adaptable framework for next-generation cfRNA-based diagnostics.

bioinformatics↗

bioRxiv2024

BMI1-mediated heterochromatinization represses G-quadruplex DNA formation to maintain genomic stability during replication

Single-stranded DNA secondary structures such as G-quadruplexes (G4s) can potentially disrupt transcription, replication, and repair. Using bio-informatic analysis, here we show that BMI1 is enriched at putative G4s flanked by heterochromatin domains, and that BMI1 knockdown in human dermal fibroblasts (HDFs) resulted in heterochromatin relaxation and G4 induction, followed by replication stress and genomic instability. In these cells, G4s co-localized with large 53BP1 and PCNA foci resembling replication catastrophes. Inhibiting transcription partly attenuated DNA damage, suggesting rescue of transcription-replication collisions at difficult-to-replicate sequences. In BMI1 knockdown or pyridostatin-exposed HDFs, the Werner helicase accumulated and co-localized with G4s. Acute WRN knockdown also resulted in G4 induction. In HDFs from Werner and Hutchinson-Gilford progeria syndromes, loss of heterochromatin and nuclear envelope anomalies were associated with G4 induction and DNA damage. Nuclear envelope anomalies were also prominent following BMI1 knockdown. These findings suggests that heterochromatin-mediated repression of G4s attenuates replication stress and genomic instability, and that this mechanism is shared across distinct progeroid models.

cell biology↗

bioRxiv2024

Oceanic photosynthesis is directly affected by cyanophage NblA proteins

Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages, viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phages benefit1-5. One such gene is nblA which is present in multiple cyanophage families2,6-8. Under nutrient deprivation the cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome9-11, the large cyanobacterial photosynthetic light harvesting complex. This increases the pool of amino acids available for essential tasks11, serving as a survival mechanism12. Ectopic expression of different cyanophage nblA genes results in host pigment protein degradation9,6. However, the benefit of the cyanophage-encoded NblA for the cyanophage and the broader impact on the host are unknown. Here, using a recently developed genetic manipulation system for marine cyanophages14, we reveal that cyanophage NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins and reduces host photosynthetic light harvesting efficiency. Metagenomic analysis revealed that cyanophages carrying nblA are widespread in the oceans and compose 35% and 65% of oceanic T7-like cyanophages in the surface and deep photic zones, respectively. Our results show a large benefit of the nblA gene to the cyanophage while exerting a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest that cyanophage nblA has an adverse global impact on light harvesting by oceanic picocyanobacteria.

microbiology↗

bioRxiv2024

Epigenomic anomalies in induced pluripotent stem cells from Alzheimer disease cases

Reprogramming of adult somatic cells into induced pluripotent stem cells (iPSCs) resets the aging clock. However, primed iPSCs can retain cell-of-origin epigenomic marks, especially those linked to heterochromatin and lamina-associated regions. Here we show that iPSCs produced from dermal fibroblasts of late-onset sporadic Alzheimers disease (AD) cases retain epigenomic anomalies that supersede developmental defects and neurodegeneration. When compared to iPSCs from elderly controls, AD iPSCs show reduced BMI1 expression, lower H3K9me3 levels, and an altered DNA methylome. Gene Ontology analysis of differentially methylated DNA regions (DMRs) reveals terms linked to cell-cell adhesion and synapse, with the cognitive resilience-associated MEF2 family of transcription factors being the most enriched at DMRs. Upon noggin exposure, AD iPSCs show lesser efficient neural induction and forebrain specification, together with increased ZIC2, ZIC5 and WNT-related gene expression. Long-term AD neuronal cultures present a dedifferentiation and loss-of-cell identity phenotype. Despite these epigenomic anomalies, AD iPSCs generate cortical neurons in normal proportion and readily form cerebral organoids developing amyloid and Tau pathology. BMI1 overexpression in AD neurons mitigates amyloid and tau accumulation, heterochromatin fragmentation, and G4 DNA induction. These findings implicate reprogramming resistant epigenomic anomalies or uncharacterized genetic alterations working in trans on the epigenome in AD pathophysiology.

neuroscience↗

bioRxiv2024

Proteomic Analysis of Dorsal Root Ganglia in a Mouse Model of Paclitaxel-Induced Neuropathic Pain

Paclitaxel is a chemotherapy drug widely used for the treatment of various cancers based on its ability to potently stabilize cellular microtubules and block division in cancer cells. Paclitaxel-based treatment, however, accumulates in peripheral system sensory neurons and leads to a high incidence rate (over 60%) of chemotherapy induced peripheral neuropathy. Using an established preclinical model of paclitaxel-induced peripheral neuropathy (PIPN), we examined proteomic changes in dorsal root ganglia (DRG) of adult male mice that were treated with paclitaxel (8 mg/kg, at 4 injections every other day) relative to vehicle-treated mice. High throughput proteomics based on liquid chromatography electrospray ionization mass spectrometry identified 165 significantly altered proteins in lumbar DRG. Gene ontology enrichment and bioinformatic analysis revealed an effect of paclitaxel on pathways for mitochondrial regulation, axonal function, and inflammatory purinergic signaling as well as microtubule activity. These findings provide insight into molecular mechanisms that can contribute to PIPN in patients.

neuroscience↗

bioRxiv2024

The high-light-tolerant desert alga Chlorella ohadii is protected from oxidative stress by a non-photochemical quenching-independent mechanism

Non-photochemical quenching (NPQ) mechanisms are crucial for protecting photosynthesis from photoinhibition in plants, algae, and cyanobacteria, and their modulation is a long-standing goal for improving photosynthesis and crop yields. The current work demonstrates that Chlorella ohadii, a green micro-alga that thrives in the desert under high light intensities which are fatal to many photosynthetic organisms, does not perform nor require NPQ to protect photosynthesis under constant high light. Instead of dissipating excess energy, it minimizes its uptake by eliminating the photosynthetic antenna of photosystem II. In addition it accumulates antioxidants that neutralize harmful reactive oxygen species (ROS) and ramps up cyclic electron flow around PSI. These NPQ-independent responses proved efficient in preventing ROS accumulation and reducing oxidative damage to proteins in high-light-grown cells.

plant biology↗

bioRxiv2023

CLIPPER 2.0: Peptide level annotation and data analysis for positional proteomics

Positional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, such progress has not been observed to the same extent in data analysis and post-processing steps, which arguably constitute the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms, and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/569335v1_ufig1.gif" ALT="Figure 1"> View larger version (83K): org.highwire.dtl.DTLVardef@16d603borg.highwire.dtl.DTLVardef@1c8d9d0org.highwire.dtl.DTLVardef@1540246org.highwire.dtl.DTLVardef@614c9a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Sub-retinal transplantation of human iPSC-derived retinal sheets: A promising approach for the treatment of macular degeneration

Retinal degenerative diseases affect millions of people worldwide, and legal blindness is generally associated with the loss of cone photoreceptors located in the retinas central region called the macula. Currently, there is no treatment to replace the macula. Addressing this unmet need, we employed control isogenic and hypoimmunogenic induced pluripotent stem cell (iPSC) lines to generate spontaneously polarized retinal sheets (RSs). They presented the advantage of facile customization and large-scale production, exhibiting a polarized 3D architecture within a 2D cell culture environment, thus readily adaptable for clinical applications. RSs were enriched in retinal progenitor and cone precursor cells, which could differentiate into mature S- and M/L-cones in long-term cultures. Single-cell RNA-seq analysis showed that RSs recapitulate the ontogeny of the developing human retina and are devoid of pluripotent stem cells. Isolation of neural rosettes for sub-retinal transplantation effectively eliminated unwanted cells such as RPE cells. In a porcine model of chemically induced retinal degeneration, grafts integrated the host retina and formed a new, yet immature, photoreceptor layer, exhibiting viability for up to 2 months. In one transplanted animal that met all criteria, including correct apicobasal orientation and seamless graft integration, functional and immunohistochemical assays suggest that grafts exhibited responsiveness to light stimuli and established putative synaptic connections with host bipolar neurons. This study underscores the potential and challenges of iPSC-derived RS for clinical applications while establishing the optimal methodology and conditions for RS transplantation, thus paving the path for future long-term functional investigations using RS grafts.

bioengineering↗

bioRxiv2023

Age-Related Differences in Alpha Power for Distractor Inhibition During Visual Working Memory

As visual working memory (WM) is limited in capacity, it is important to direct neural resources towards task-relevant information and away from task-irrelevant information. Neural oscillations in the alpha frequency band (8-12 Hz) have been suggested to play a role in the inhibition of distracting information during WM retention in younger adults, but it is unclear if alpha power modulation also supports distractor inhibition in older adults. Here, we recorded electroencephalography (EEG) while 24 younger (aged 18-35) and 24 older (aged 60-86) adults completed a modified delay match-to-sample task in which distractors of varying strength appeared during the retention period. We found: (1) strong distractors impaired WM performance compared with weak and no distractors in both age groups, but there were no age-differences in WM performance; (2) while younger adults demonstrated significant increases in alpha power prior to the onset of the distractor in all conditions, decreases in alpha power were seen in all distractor conditions in older adults; (3) there was no difference in alpha power between the strong and no distractor conditions; and (4) alpha power in anticipation of the distractor was only associated with task performance in younger adults. Our results suggest that younger adults, but not older adults, modulate alpha power in anticipation of distractors during the visual WM retention period.

neuroscience↗

bioRxiv2022

In-depth characterization of apoptosis N-terminome reveals a link between caspase-3 cleavage and post-translational N-terminal acetylation

The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of -amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.

biochemistry↗

bioRxiv2020

Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-{beta} signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.

genetics↗