Biology subjects

Ramachandran, K.

Publications and source records attributed to Ramachandran, K..

8 recordsLinked to original sources

bioRxiv2026

LNP Delivery of Prime Editors Enables Durable Correction of PAH R408W in Phenylketonuria Models

Phenylketonuria (PKU) is a monogenic metabolic disorder caused by mutations in the phenylalanine hydroxylase (PAH) gene, the most common of which is c.1222C>T (p.R408W). Current treatment options, including dietary restriction and enzyme substitution, can be effective but are often challenging for patients to maintain and do not address the underlying genetic defect. Gene editing represents a compelling one-time treatment approach for PKU. Herein, we demonstrate mRNA:LNP-mediated delivery of prime editors that enable therapeutically-relevant levels of correction of the R408W mutation in both in vitro and in vivo model systems. Further, we found that co-delivery of the DNA repair modulator RAD18 and engineering of the prime editor protein, enabled 2-fold and 3-fold increases in prime editing relative to PE3 respectively, resulting in ~50% correction efficiency in a humanized PKU mouse model. Collectively, this work identifies novel potential approaches to enhancing prime editing and establishes LNP-delivered prime editing as a mutation-specific, non-viral therapeutic strategy for PKU, as well as providing a framework for extending prime editing to other inherited liver diseases.

pharmacology and toxicology↗

bioRxiv2026

A bacterial nucleolus for cold adaptation

Compartmentalisation enables cells to spatially organise essential biochemical processes. This is exemplified by the eukaryotic nucleolus, which concentrates the machinery for ribosome biogenesis. Bacteria are generally thought to lack an equivalent compartment. Here we discover a nucleolus-like condensate in Escherichia coli that emerges at rDNA loci during cold adaptation to spatially organise and promote ribosome biogenesis. Low temperatures, which stabilise RNA secondary structures, induce accumulation of the RNA-remodelling enzyme CsdA. This raises the cellular CsdA concentration above its condensation threshold, driving condensate formation at rDNA loci when rRNA transcription is active. CsdA compartments enrich the rRNA transcription machinery and ribosome-biogenesis factors, spatially linking rRNA synthesis to downstream processing and assembly. Disrupting CsdA condensation impairs ribosome maturation and reduces bacterial adaptation to cold temperature, demonstrating functional importance of condensate formation. Comparative genomics suggests that analogous condensate-forming RNA remodelling enzymes have evolved repeatedly across diverse bacterial lineages. Our findings establish biomolecular condensates as a unifying organisational principle of ribosome biogenesis across the tree of life and suggest that adaptive compartmentalisation can emerge when environmental conditions challenge the efficiency of essential biochemical processes.

cell biology↗

bioRxiv2026

Spatially resolved, multimodal in vivo Perturb-seq using antibody-based cell hashing

Large-scale perturbation screens have begun to map cell intrinsic gene-function relationships, yet how genes shape tissue architecture remains largely unexplored. To address this gap, we developed PerturbSpace, a novel approach that integrates CRISPR perturbations with spatially hashed single-cell multiomics. This approach enables the first high-throughput, spatially resolved Perturb-seq analysis across complex tissue architecture in vivo. Notably, PerturbSpace enables spatial transcriptome-wide perturbation readouts at organ scale and can be seamlessly integrated with orthogonal modalities. We combine PerturbSpace with surface proteomics and expressed lineage tracing barcodes to demonstrate multimodal compatibility. We use PerturbSpace to study the genetic determinants of tissue architecture. First, we map how 40 transcriptional regulators determine the size and lineage composition of colonies in the spleen during regenerative hematopoiesis. Second, we characterize immune-niche interactions in the liver by dissecting the extrinsic effects mediated by cytokine-secreting immune cells on their neighboring cells. Collectively, our work establishes PerturbSpace as a scalable and cost-effective approach for transcriptome-wide spatial profiling of whole cells while remaining compatible with the single-cell multiomics workflows that the field has already adopted at scale.

genomics↗

bioRxiv2025

Dystonia-associated Torsins sustain CLCC1 function to promote membrane fusion of the nuclear envelope for NPC biogenesis

DYT1 early-onset dystonia is a severe, incurable disorder of the central nervous system caused by mutations in the gene encoding Torsin1A (Tor1A, DYT1). Torsins are ER-resident AAA+-ATPases implicated in lipid metabolism, nuclear pore complex (NPC) biogenesis, and lipoprotein secretion, yet their molecular function that underlies the disease pathology has remained incompletely understood. Here, we have utilized Drosophila melanogaster and human somatic cells as experimental models to shed light on their mode-of-action. Fly germ cells lacking dTorsin are arrested in development and display defects in the final steps of NPC biogenesis due to a failure in fusion of the inner and outer nuclear membranes. Using proximity labelling of Torsin1A in human cells, we identify the conserved membrane protein chloride channel CLIC-like protein 1 (CLCC1) as a novel Torsin binding partner. Absence of human CLCC1 or its Drosophila homolog dClcc1 phenocopied the membrane fusion defects at NPC assembly sites observed upon Torsin deletion. Furthermore, CLCC1 is enriched at arrested fusion sites, suggesting it to be a candidate for the elusive NE membrane fusogen. Importantly, CLCC1/dClcc1 overexpression is sufficient to rescue NPC biogenesis and developmental defects associated with Torsin-loss-of-function. Taken together, our data suggest that Torsin-regulated CLCC1 activity drives membrane fusion during NPC biogenesis and reveal that modulating CLCC1 expression is a promising therapeutic prospect for DYT1 dystonia.

cell biology↗

bioRxiv2025

A conserved mechanism of membrane fusion in nuclear pore complex assembly

The nuclear pore complex (NPC) forms a large channel that spans the double lipid bilayer of the nuclear envelope and is the central gateway for macromolecular transport between the nucleus and cytoplasm in eukaryotes. NPC biogenesis requires the coordinated assembly of over 500 proteins culminating in the fusion of the inner and outer nuclear membranes. The molecular mechanism of this membrane fusion step that occurs in all eukaryotes is unknown. Here, we elucidate the mechanism by which two paralogous transmembrane proteins, Brl1 and Brr6, mediate membrane fusion in S. cerevisiae. Both proteins form multimeric, ring-shaped complexes with membrane remodeling activity. Brl1 is enriched at NPC assembly sites via a nuclear export sequence and then interacts with Brr6 across the nuclear envelope lumen through conserved hydrophobic loops. Disrupting this interaction blocks fusion and halts NPC assembly. Molecular dynamics simulations suggest that the Brl1-Brr6 complex drives membrane fusion by forming a channel across bilayers that enables lipid exchange. Phylogenetic analyses reveal that Brl1/Brr6 homologues are broadly distributed across eukaryotes, and functional experiments in human cells and D. melanogaster establish CLCC1 as an NPC fusogen in metazoans. Together, our results uncover a novel, conserved mechanism for membrane fusion in eukaryotes.

cell biology↗

bioRxiv2025

Centromeres evolve progressively through selection at the kinetochore interface

During mitosis, stable but dynamic interactions between the centromere DNA and kinetochore complex enable accurate and efficient chromosome segregation. Even though many proteins of the kinetochore are highly conserved, centromeres are among the fastest evolving regions within a genome, showing extensive variation even on short evolutionary timescales. Here, we sought to understand how new types of centromeres emerge and reach fixation by mapping centromere evolution across 138 budding yeast species and over 2,500 natural strain isolates. We show that new centromeres spread progressively via drift and subsequent selection, and that the kinetochore interface, which is evolving slowly in relative terms, determines which new centromere variants are tolerated. Together, our findings provide insight into the evolutionary constraints and trajectories shaping centromere evolution.

evolutionary biology↗

bioRxiv2022

Molecular signatures of proteostasis control in motor neurons with different sensitivity to Amyotrophic Lateral Sclerosis

Amyotrophic Lateral Sclerosis (ALS) is a fatal adult neurodegenerative disease characterized by proteostasis dysregulation, resulting in progressive loss of spinal and upper motor neurons. A subset of cranial motor neurons resistant to ALS-stress survive until late stages of the disease. To investigate these differences, we exploited a unique platform of induced cranial and spinal motor neurons (iCrMNs and iSpMNs, respectively). Exposing both cell types to proteotoxic stress, we quantified transcriptome and proteome changes over 36 hours for a core set of >8,200 genes. While mRNA and protein changes under stress were congruent for many genes, cell-type specific differences manifested at either the RNA or protein level, but less at both. At the protein level, iCrMNs and iSpMNs differed significantly with respect to abundance of many membrane proteins, including synaptic proteins, solute carriers, adhesion molecules, and signaling molecules suggesting that the superior stress survival of iCrMNs involve diverse pathways supporting neuronal function. Other differences included genes involved in ribosome biogenesis and subunits of the core proteasome. We investigated the role of proteasomal degradation in more detail. Our data showed that although stress reduces proteasome activity in both neuronal types, iCrMNs had significantly more abundant and active 26S proteasome than iSpMNs, which indicate a higher capacity for the degradation of ubiquitinated proteins. We identified a new regulator of this better performance, i.e. the nuclear proteasome activator Ublcp1, whose inhibition sensitized iCrMNs, but not iSpMNs, to stress and abolished their higher survival rates. The results suggest that the two neuronal cell types regulate and use the degradation machinery differently under normal and stress conditions. Overall, this work demonstrates the value of unbiased system-wide analyses in generating hypotheses on differential proteostasis regulation in cranial and spinal motor neurons.

systems biology↗

bioRxiv2022

Neuronal membrane proteasomes homeostatically regulate neural circuit activity in vivo and are required for learning-induced behavioral plasticity

Protein degradation is critical for brain function through processes that remain poorly understood. Here we investigated the in vivo function of a recently reported neuronal membrane-associated proteasome (NMP) in the brain of Xenopus laevis tadpoles. We demonstrated that NMPs are present in the tadpole brain with biochemistry and electron microscopy, and showed that they actively degrade neuronal activity-induced nascent proteins. Using in vivo calcium imaging in the optic tectum, we showed that acute inhibition of NMP function rapidly increased spontaneous neuronal activity, resulting in hyper-synchronization among tectal neurons. At the circuit level, inhibiting NMPs abolished learning-dependent improvement in a visuomotor behavior paradigm in live animals. Our data provide the first in vivo characterization of NMP functions in the vertebrate nervous system and suggest that NMP-mediated degradation of activity-induced nascent proteins may serve as a homeostatic modulatory mechanism in neurons that is critical for regulating neuronal activity and experience-dependent circuit plasticity.

neuroscience↗