Biology subjects

Hamilton, M.

Publications and source records attributed to Hamilton, M..

11 recordsLinked to original sources

bioRxiv2026

No Effect of Exercise Timing on Daily Glycaemia Despite Shifts in Acute Glucose Dynamics in Participants with Normal Glucose Tolerance: A Randomised Crossover Trial

Exercise is a well-established modulator of glucose regulation, but whether the time of day it is performed matters for healthy, free-living adults remains unresolved. In a randomised crossover trial, 29 healthy adults completed a single 30-minute bout of moderate-intensity exercise in the morning (07:00-10:00) and in the evening (16:00-19:00), with continuous glucose monitoring and wrist-worn activity tracking used to capture responses over an 8-day free-living protocol. Evening exercise produced a significantly greater acute reduction in blood glucose (P < 0.001) compared to morning exercise, but this did not translate into consistent differences in overall daily mean glycaemic exposure, whether measured over the calendar day or over a window aligned with exercise onset. Evening exercise was linked to greater within-day glycaemic variability than morning exercise, with the clearest evidence coming from the circadian-aligned analysis (day x timing interaction, SD: P = 0.00939; CV: P = 0.00766). Appetite rose after exercise in both conditions, with no difference by time of day. Taken together, these results show that exercise timing does not change how much glucose exposure a healthy adult accumulates over a day, but it does change the shape of the glucose response around the exercise bout itself, a distinction only visible when glucose is examined at a finer temporal resolution than daily averages allow.

physiology↗

bioRxiv2026

Cue-Dependent Fear Learning Drives Nucleus Accumbens Spine Plasticity

Nucleus accumbens (NAc) dopamine 2 receptor expressing medium spiny neurons (D2-MSNs) are involved in stress and aversive learning, where repeated stress increases excitatory spine density. Whether this plasticity reflects cue-specific learning or generalized stress response remains unknown. Using Pavlovian fear conditioning in Tac1-Cre/Tdtomato mice, we dissociated associative plasticity from the effects of foot shock stress. Acute fear conditioning produced distinct physiological outcomes between stress in the presence or absence of a cue. Conditioning for 7 days consolidated cue learning and increased excitatory transmission frequency via an increase in the total spine density. However, repeated exposure to foot shock did not lead to this synaptic remodeling. Our results suggest that morphological changes supporting synaptic plasticity on NAc D2-MSNs are due to cue-dependent learning, but not foot shock stress alone. We propose that NAc D2-MSNs encode learning and response to threat cues, which may heighten later stress responsivity.

neuroscience↗

bioRxiv2025

The role of MICOS in modulating mitochondrial dynamics and structural changes in vulnerable regions of Alzheimer's Disease

Mitochondrial contact site and cristae organizing system (MICOS) complexes are critical for maintaining the mitochondrial architecture, cristae integrity, and organelle communication in neurons. MICOS disruption has been implicated in neurodegenerative disorders, including Alzheimers disease (AD), yet the spatiotemporal dynamics of MICOS-associated neuronal alterations during aging remain unclear. Using three-dimensional reconstructions of hypothalamic and cortical neurons, we observed age-dependent fragmentation of mitochondrial cristae, reduced intermitochondrial connectivity, and compartment-specific changes in mitochondrial size and morphology. Notably, these structural deficits were most pronounced in neurons vulnerable to AD-related pathology, suggesting a mechanistic link between MICOS disruption and the early mitochondrial dysfunction observed in patients with AD. Our findings indicate that the loss of MICOS integrity is a progressive feature of neuronal aging, contributing to impaired bioenergetics and reduced resilience to metabolic stress and potentially facilitating neurodegenerative processes. MICOS disruption reduced neuronal firing and synaptic responsiveness, with miclxin treatment decreasing mitochondrial connectivity and inducing cristae disorganization. These changes link MICOS structural deficits directly to impaired neuronal excitability, highlighting vulnerability to AD-related neurodegeneration. These results underscore the importance of MICOS as a critical determinant of neuronal mitochondrial health and as a potential target for interventions aimed at mitigating AD-related mitochondrial dysfunction.

neuroscience↗

bioRxiv2025

Specificity of Aberrant Exons in a Saturated Background of Differentially Expressed Exons

Determining the maximal specificity of aberrant exons from multifactorial disease tissues in a whole body background could provide insights into the exon origin as well as potential targets of diagnosis or therapy, but it remains a challenging task. For this purpose, we obtained a saturated list of differentially expressed exons (DEXs) from our independent reference human exome extracted from 56 normal tissues by DEXSeq. We found that the DEXs comprised the majority of the reference exome and that 99.4% of cancer-specific exons relative to paired normal tissues fell within the DEX list, consistent with the ectopic expression of the majority of aberrant exons. We then screened over seven thousand pathogenic single nucleotide variants (SNVs) in the TCGA and COSMIC databases by SpliceAI. The analysis identified over three hundreds of highly confident, mostly somatic SNV-specific splicing events and/or novel exonic fragments in five types of adenocarcinomas. Interestingly, these events are all associated with cis-acting mutations in tumor suppressor genes, particularly in TP53 with an antigenic novel peptide. This revelation of the DEX exome dominance and non-specificity of nearly all aberrant exons not only reshapes our understanding of the normal human exome by highlighting its mainly variable over constitutive exons, but also illuminates the path through cis-acting somatic and pathogenic SNVs to identify genuine cancer-specific exonic fragments that are absent in any normal tissues, beyond neo-exon junctions. This path holds promise for identifying novel peptide fragments for antigens in holistic cancer treatments including vaccination and immunotherapies.

cancer biology↗

bioRxiv2024

Synthetic genomes unveil the effects of synonymous recoding

Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers1-4. Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement--recoding--is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organisms genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.

synthetic biology↗

bioRxiv2024

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

Multiple Myeloma (MM) remains incurable despite advances in treatment options. Although tumor subtypes and specific DNA abnormalities are linked to worse prognosis, the impact of immune dysfunction on disease emergence and/or treatment sensitivity remains unclear. We established a harmonized consortium to generate an Immune Atlas of MM aimed at informing disease etiology, risk stratification, and potential therapeutic strategies. We generated a transcriptome profile of 1,149,344 single cells from the bone marrow of 263 newly diagnosed patients enrolled in the CoMMpass study and characterized immune and hematopoietic cell populations. Associating cell abundances and gene expression with disease progression revealed the presence of a proinflammatory immune senescence-associated secretory phenotype in rapidly progressing patients. Furthermore, signaling analyses suggested active intercellular communication involving APRIL-BCMA, potentially promoting tumor growth and survival. Finally, we demonstrate that integrating immune cell levels with genetic information can significantly improve patient stratification.

genomics↗

bioRxiv2024

Regulation of lung cancer initiation and progression by the stem cell determinant Musashi

Despite advances in therapeutic approaches, lung cancer remains the leading cause of cancer-related deaths. To understand the molecular programs underlying lung cancer initiation and maintenance, we focused on stem cell programs that are normally extinguished with differentiation but can be reactivated during oncogenesis. Here we have used extensive genetic modeling and patient derived xenografts to identify a dual role for Msi2: as a signal that acts initially to sensitize cells to transformation, and subsequently to drive tumor propagation. Using Msi reporter mice, we found that Msi2-expressing cells were marked by a pro-oncogenic landscape and a preferential ability to respond to Ras and p53 mutations. Consistent with this, genetic deletion of Msi2 in an autochthonous Ras/p53 driven lung cancer model resulted in a marked reduction of tumor burden, delayed progression, and a doubling of median survival. Additionally, this dependency was conserved in human disease as inhibition of Msi2 impaired tumor growth in patient-derived xenografts. Mechanistically, Msi2 triggered a broad range of pathways critical for tumor growth, including several novel effectors of lung adenocarcinoma. Collectively, these findings reveal a critical role for Msi2 in aggressive lung adenocarcinoma, lend new insight into the biology of this disease, and identify potential new therapeutic targets.

cancer biology↗

bioRxiv2023

Identification of a Musashi2 translocation as a novel oncogene in myeloid leukemia

Myeloid leukemias, diseases marked by aggressiveness and poor outcomes, are frequently triggered by oncogenic translocations. In the case of chronic myelogenous leukemia (CML) the BCR-ABL fusion initiates chronic phase disease with second hits allowing progression to blast crisis. Although Gleevec has been transformative for CML, blast crisis CML remains relatively drug resistant. Here we show that MSI2-HOXA9, a translocation with an unknown role in cancer, can serve as a second hit in driving bcCML. Compared to BCR-ABL, BCR-ABL/MSI2-HOXA9 led to a more aggressive disease in vivo with decreased latency, increased lethality and a differentiation blockade that is a hallmark of blast crisis. Domain mapping revealed that the MSI2 RNA binding domain RRM1 had a preferential impact on growth and lethality of bcCML relative to RRM2 or the HOXA9 domain. Mechanistically, MSI2-HOXA9 triggered global downstream changes with a preferential upregulation of mitochondrial components. Consistent with this, BCR-ABL/MSI2-HOXA9 cells exhibited a significant increase in mitochondrial respiration. These data suggest that MSI2-HOXA9 acts, at least in part, by increasing expression of the mitochondrial polymerase Polrmt and augmenting mitochondrial function and basal respiration in blast crisis. Collectively, our findings demonstrate for the first time that translocations involving the stem and developmental signal MSI2 can be oncogenic, and suggest that MSI, which we found to be a frequent partner for an array of translocations, could also be a driver mutation across solid cancers.

cancer biology↗

bioRxiv2019

3D-printing Enabled Micro-assembly of Microfluidic Electroporation System for 3D Tissue Engineering

Electro-transfection is an essential workhorse tool for regulating cellular responses and engineering cellular materials in tissue engineering. However, existing approaches, including microfluidic platforms and bench top methods, are only able to study monolayer cell suspensions in vitro, and are incapable of clinical translation within in vivo tissue microenvironment. Knowledge regarding the three-dimensional (3D) electric field distribution and mass transport in a tissue microenvironment is lacking. However, building a 3D electro-transfection system that is compatible with 3D cell culture for mimicking in vivo tissue microenvironment is challenging, due to the substantial difficulties in control of 3D electric field distribution as well as the cellular growth. To address such challenges, we introduce a novel 3D micro-assembling strategy assisted by 3D printing, which enables the molding of 3D microstructures as LEGO(R) parts from 3D-printed molds. The molded PDMS LEGO(R) bricks are then assembled into a 3D-cell culture chamber interconnected with vertical and horizontal perfusion microchannels as a 3D channel network. Such 3D perfusion microchannel network is unattainable by direct 3D printing or other microfabrication approaches, which can facilitate the high-efficient exchange of nutrition and waste for 3D cell growth. Four flat electrodes are mounted into the 3D culture chamber via a 3D-printed holder and controlled by a programmable power sequencer for multi-directional electric frequency scanning (3D -electro-transfection). This multi-directional scanning not only can create transient pores all over the cell membrane, but also can generate local oscillation for enhancing mass transport and improving cell transfection efficiency. As a proof-of-concept, we electro-delivered pAcGFP1-C1 vector to 3D cultured HeLa cells within peptide hydrogel scaffolding. The expressed GFP level from transfected HeLa cells reflects the transfection efficiency. We found two key parameters including electric field strength and plasmid concentration playing more important roles than manipulating pulse duration and duty cycles. The results showed an effective transfection efficiency of ~15% with ~85% cell viability, which is a 3-fold increase compared to the conventional benchtop 3D cell transfection. This 3D -electrotransfection system was further used for genetically editing 3D-cultured Hek-293 cells via direct delivery of CRISPR/Cas9 plasmid which showed successful transfection with GFP expressed in the cytoplasm as the reporter. The 3D-printing enabled micro-assembly allows facile creation of novel 3D culture system for electro-transfection which can be employed for versatile gene delivery and cellular engineering, as well as building in-vivo like tissue models for fundamentally studying cellular regulatory mechanisms.

bioengineering↗

bioRxiv2017

Ultrasound Produces Extensive Brain Activation via a Cochlear Pathway

Ultrasound (US) can noninvasively activate intact brain circuits, making it a promising neuromodulation technique. However, little is known about the underlying mechanism. Here, we apply transcranial US and perform brain mapping studies in guinea pigs using extracellular electrophysiology. We find that US elicits extensive activation across cortical and subcortical brain regions. However, transection of the auditory nerves or removal of cochlear fluids eliminates the US-induced activity, revealing an indirect auditory mechanism for US neural activation. US likely vibrates the cerebrospinal fluid in the brain, which is continuous with the fluid in the cochlea via cochlear aqueducts; thus, US can activate the ascending auditory pathways and other non-auditory regions through cross-modal projections. This finding of a cochlear fluid-induced vibration mechanism challenges the idea that US can directly activate neurons in the intact brain, suggesting that future US stimulation studies will need to control for this effect to reach reliable conclusions.

neuroscience↗

bioRxiv2017

Early Detection of Apathetic Phenotypes in Huntington’s Disease Knock-in Mice Using Open Source Tools

Apathy is one of the most prevalent and progressive psychiatric symptom in Huntingtons disease (HD) patients. However, preclinical work in HD mouse models tend to focus on molecular and motor, rather than affective, phenotypes. Measuring behavior in mice often produces noisy data and requires large cohorts to detect phenotypic rescue with appropriate power. The operant equipment necessary for measuring affective phenotypes is typically expensive, proprietary to commercial entities, and bulky which can render adequately sized mouse cohorts as cost-prohibitive. Thus, we describe here a home-built open-source alternative to commercial hardware that is reliable, scalable, and reproducible. Using off-the-shelf hardware, we adapted and built several of the rodent operant buckets (ROBucket) designed to test HttQ111/+ mice for attention deficits in fixed ratio (FR) and progressive ratio (PR) tasks. We find that, despite normal performance in reward attainment in the FR task, HttQ111/+ mice exhibit reduced PR performance at 9-11 months of age, suggesting motivational deficits. We replicated this in two independent cohorts, which demonstrates the reliability and utility of both the apathetic phenotype, and these ROBuckets, for preclinical HD studies.

animal behavior and cognition↗