Biology subjects

McCullough, M.

Publications and source records attributed to McCullough, M..

6 recordsLinked to original sources

bioRxiv2026

Multidimensional mutational phenotypes of MMR deficiency in human cancer cells

Mismatch repair deficiency (MMRd) is a central driver of cancer genome evolution, yet it is commonly reduced to a binary MSI-high versus microsatellite-stable call. Here we combine multiplex CRISPR/Cas12a editing, long-term mutation accumulation experiments in human cells, and whole-genome sequencing to map the mutational consequences of single and pairwise perturbations across canonical and accessory MMR genes, together with selected base excision repair and direct-repair factors. Across 72 isogenic lineages representing 58 genotypes, we recover reproducible substitution, indel and short-tandem-repeat mutational states that distinguish MSH2, MSH6, MLH1, PMS2, MSH3 and MLH3 deficiencies. A dedicated STR spectrum reveals genome-wide evidence for MSH3-driven EMAST and enables design of compact loci panels for mechanism-aware MSI classification. Experimental spectra generalize across independent cell systems and to cancer whole genome sequences, where Elastic-net classifiers accurately identify causal MMR genes in Lynch tumors and uncover common occurrences of intermediate MMRd states. Pairwise perturbations further reveal repair crosstalk reflected in mutational spectra, including enhancement of MUTYH-associated oxidative mutagenesis by MMR loss. Together, these findings recast mismatch repair deficiency as a multidimensional genomic phenotype and provide a framework for interpreting DNA repair deficiencies by bridging mutational phenotypes from experimental systems and human cancers.

genomics↗

bioRxiv2025

Synthetic yeast genome SCRaMbLEing uncovers a new role for ribosomal proteins in genetic code expansion

The translation of proteins with non-canonical amino acids (ncAAs) has emerged as a powerful technology for embedding new functional elements into proteins, enabling the development of novel enzymes, materials, and biopharmaceuticals. However, the utility of this approach has been hindered by weak translation efficiencies. To address this challenge, we sought to substantially improve orthogonal translation in Saccharomyces cerevisiae. We first evaluated recently described {Delta}NPylRS-class pyrrolysyl-tRNA synthetase systems and identified a homolog with [~]5.4-fold higher activity than the best previously reported pyrrolysyl system. Building on this advance, we leveraged the SCRaMbLE system in the semi-synthetic yeast strain Syn6.5 to generate structural genomic variation, and identified strains with enhanced ncAA incorporation. Pooling genomic alterations across enhanced strains, we identified an association for the deletion of several ribosomal protein genes with the increased production of ncAA-containing protein. These findings demonstrate a previously unrecognized role for ribosomal proteins in enabling alternate genetic codes.

synthetic biology↗

bioRxiv2023

Cortical activity emerges in region-specific patterns during early brain development

The development of precise neural circuits in the brain requires spontaneous patterns of neural activity prior to functional maturation. In the rodent cerebral cortex patchwork and wave patterns of activity develop in somatosensory and visual regions, respectively, and are present at birth. However, whether such activity patterns occur in non-eutherian mammals, as well as when and how they arise during development remain open questions relevant to understand brain formation in health and disease. Since the onset of patterned cortical activity is challenging to study prenatally in eutherians, here we offer a new approach in a minimally invasive manner using marsupial dunnarts, whose cortex forms postnatally. We discovered similar patchwork and travelling waves in the dunnart somatosensory and visual cortices at stage 27 (equivalent to newborn mice), and examined progressively earlier stages of development to determine their onset and how they first emerge. We observed that these patterns of activity emerge in a region-specific and sequential manner, becoming evident as early as stage 24 in somatosensory and stage 25 in visual cortices (equivalent to embryonic day 16 and 17, respectively, in mice), as cortical layers establish and thalamic axons innervate the cortex. In addition to sculpting synaptic connections of existing circuits, evolutionarily conserved patterns of neural activity could therefore help regulate early events in cortical development. Significance StatementRegion-specific patterns of neural activity are present at birth in rodents and are thought to refine synaptic connections during critical periods of cerebral cortex development. Marsupials are born much more immature than rodents, allowing the investigation of how these patterns arise in vivo. We discovered that cortical activity patterns are remarkably similar in marsupial dunnarts and rodents, and that they emerge very early, before cortical neurogenesis is complete. Moreover, they arise from the outset in different patterns specific to somatosensory and visual areas (i.e., patchworks and waves) indicating they may also play evolutionarily conserved roles in cortical regionalization during development.

neuroscience↗

bioRxiv2021

fmr1 mutation interacts with sensory experience to alter the early development of behavior and sensory coding in zebrafish

While Autism Spectrum Disorders (ASDs) are developmental in origin little is known about how they affect the early development of behavior and sensory coding, or how this is modulated by the sensory environment. The most common inherited form of autism is Fragile X syndrome, caused by a mutation in FMR1. Here we show that zebrafish fmr1-/- mutant larvae raised in a naturalistic visual environment display early deficits in hunting behavior, tectal map development, tectal network properties and decoding of spatial stimuli. However when given a choice they preferred an environment with reduced visual stimulation, and rearing them in this environment improved these metrics. Older fmr1-/- fish showed differences in social behavior, spending more time observing a conspecific, but responding more slowly to social cues. Together these results help reveal how fmr1-/- changes the early development of vertebrate brain function, and how manipulating the environment could potentially help reduce these changes.

neuroscience↗

bioRxiv2021

Loss of HMCES is synthetic lethal with APOBEC activity in cancer cells

Analysis of cancer mutagenic signatures provides information about the origin of mutations and can inform the use of clinical therapies, including immunotherapy. In particular, APOBEC3A (A3A) has emerged as a major driver of mutagenesis in cancer cells and its expression results in DNA damage and susceptibility to treatment with inhibitors of the ATR and CHK1 checkpoint kinases. Here we report the implementation of CRISPR/Cas9 genetic screening to identify susceptibilities of multiple A3A-expressing lung adenocarcinoma cell lines. We identify HMCES, a protein recently linked to the protection of abasic sites, as a central protein for the tolerance of A3A expression. HMCES depletion results in synthetic lethality with A3A expression specifically in a TP53-mutant background. Analysis of previous screening data reveals a strong association between A3A mutational signatures and sensitivity to HMCES loss and indicates that HMCES is specialized in protecting against a narrow spectrum of DNA damaging agents in addition to A3A. We experimentally show that both HMCES disruption and A3A expression increase susceptibility of cancer cells to ionizing radiation, oxidative stress and ATR inhibition; strategies that are often applied in tumor therapies. Overall, our results suggest that HMCES is an attractive target for selective treatment of A3A expressing tumors.

cancer biology↗

bioRxiv2019

Behavioral signatures of a developing neural code

During early life neural codes must develop to appropriately transform sensory inputs into behavioral outputs. Here we demonstrate a direct link between the maturity of neural coding in the visual brain and developmental changes in visually-guided behavior. In zebrafish larvae we show that visually-driven hunting behavior improves from 4 to 15 days post-fertilization, becoming faster and more accurate. During the same period population activity in the optic tectum refines, leading to improved decoding and information transmission of spatial position, particularly in the representation of the frontal visual field. Remarkably, individual differences in decoding can predict each fishs hunting success. Together these results show how the neural codes required to subserve a natural behavior emerge during development.

neuroscience↗