Biology subjects

Grant, A.

Publications and source records attributed to Grant, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Contamination of widely used databases compromises rRNA based taxonomic assignment of metagenomes and metatranscriptomes

Taxonomic annotation of metagenomic and metatranscriptomic datasets frequently relies on aligning small subunit (SSU) rRNA reads to annotated reference databases. However, widely used SSU databases, including SILVA, GTDB, Eukaryome, and those distributed with SortMeRNA, are contaminated with large subunit (LSU) rRNA sequences. Low levels of LSU contamination can lead to large numbers of LSU reads being incorrectly identified as SSU and have serious consequences for downstream taxonomic assignments. The problem can be avoided by rigorously removing LSU sequences from databases used for taxonomic annotation, which we have done for KSGP 4.0. Alternatively, initial SSU read selection can be carried out with a carefully curated small SSU database that is free of LSU contamination. We illustrate these two approaches in combination using a metatranscriptomic dataset from an estuarine sediment. Without database cleaning, LSU-derived reads can make up half of supposed SSU sequences and are assigned to a small number of apparently dominant but artefactual taxa. Database cleaning removes this problem and we provide a script, total_rnaseq, to annotate total RNASeq or metagenomic data using this approach. The KSGP 4.0 database provides substantially improved annotation of Archaea compared to the SILVA database and moderate and small improvements for eukaryotes and bacteria respectively.

bioinformatics↗

bioRxiv2026

SNR Enhancement Considerations for Loop Receive Coils at Ultra-High Fields

PurposeTo quantify parasitic losses in ultra-high field (UHF) magnetic resonance imaging (MRI) receive coils and determine how they contribute to the mismatch between numerically predicted and experimentally realized signal-to-noise ratio (SNR), with the goal of guiding receive-array designs toward ultimate intrinsic SNR (uiSNR). MethodsSNR was measured across multiple field strengths (3T, 7T, 10.5T) using commercial and custom-built arrays. To quantify parasitic losses, unloaded-to-loaded quality factor ratio (QR) measurements were performed on representative loop resonators and practical RF coils. Measured losses were combined with single-loop electromagnetic simulations to separate conductor, radiation, and component losses. These bench-derived loss estimates were then incorporated into full-array electromagnetic simulations of a 128-channel receive array to evaluate their impact on predicted intrinsic SNR. ResultsMeasurements across field strengths supported the expected supralinear increase of SNR with B0. QR analysis showed that, at UHF, radiation loss must be excluded from unloaded-Q measurements to avoid overestimating electronic-noise penalties, and that multiple seemingly modest parasitic losses collectively impose substantial SNR degradation. In the 128-channel array, simulations including only conductor and radiation losses predicted 93% of central uiSNR, whereas inclusion of the full measured parasitic-loss budget reduced predicted performance to 78%, in close agreement with the experimentally measured 77%. ConclusionsThe gap between predicted and realized SNR performance of high-channel-count 10.5T loop arrays can be largely explained by parasitic losses that are not captured in conventional simulations. A bench-measurement-informed simulation framework enables more realistic prediction of coil performance and provides practical guidance for optimizing future UHF receive arrays.

bioengineering↗

bioRxiv2025

A Numerical Alternative to MR Thermometry for Safety Validation of Multi-Channel RF Transmit Coils

PurposeThis study proposes an alternative approach to MR thermometry (MRT) for the safety validation of multi-channel RF transmit coils and demonstrates its use to enable human studies at 10.5T. MethodsTo ensure patient safety, specific absorption rate (SAR) limits established under international guidelines must not be exceeded. Predicting SAR on state-of-the-art parallel transmit systems relies on electromagnetic simulations, which require extensive experimental validation. Despite a well-established validation workflow, SAR prediction errors are unavoidable and must be quantified as a safety margin. While MRT tests are commonly used for this purpose, their technical challenges necessitate an alternative. The proposed technique propagates the error between experimentally and numerically acquired B+distributions to the uncertainty in simulated peak local SAR using Monte-Carlo simulations without the need for MRT. This method was validated using a 16-channel transceiver coil for imaging the human torso (henceforth referred to as a "body" coil) at 10.5T with two excitation scenarios, as well as an 8-channel 10.5T head coil with four excitation scenarios. ResultsThe proposed numerical technique proved more conservative than existing MRT-based SAR error quantification methods across all tested scenarios. Its application to validate three state-of-the-art head coils (16Tx/32Rx, 16Tx/80Rx, and 16Tx/128Rx) led to regulatory approval for human head imaging and high-quality functional as well as diffusion MRI results at 10.5T. ConclusionA numerical alternative to MRT requires only the experimental acquisition of B+ maps for comparison with simulations, enabling the quantification of uncertainty in SAR prediction. This technique was applied to three 16-channel transmit arrays, each used in conjunction with high-channel-count receive arrays for in vivo imaging.

neuroscience↗

bioRxiv2025

Mesoscopic whole-brain T2*-weighted and associated quantitative MRI in healthy humans at 10.5 T

PurposeTo demonstrate the feasibility and performance of mesoscopic whole brain T2*-weighted (T2*w) MRI at 10.5 T by combining a motion-robust multi-echo gradient-echo (GRE) method with high-density RF receive arrays. MethodsMulti-echo GRE data were collected in healthy adults at isotropic 0.5 mm resolution using a custom-built 16-channel transmit/80-channel receive (16Tx/80Rx) RF coil. Whole brain images were reconstructed with navigator-guided joint motion and field correction and were used for quantitative R2* and susceptibility ({chi}) mapping. Intrinsic signal-to-noise ratio (iSNR) and quantification precision for R2* and{chi} were also estimated. The results were compared with those obtained in the same subjects with matched resolution at 7 T using the commercial Nova 1Tx/32Rx coil, to demonstrate the iSNR and quantification precision gains at 10.5 T. G-factors were also calculated at each field strength to evaluate parallel imaging performances. To demonstrate the benefit of increased parallel imaging performances at 10.5 T, whole brain images with higher acceleration were also obtained using a custom-built 16Tx/128Rx coil. Resultsthe utilized motion robust GRE sequence and reconstruction effectively reduced artifacts from motion and field changes during scans, producing high-quality whole-brain T2*w images and multi-parametric maps at 10.5 T with delineation of fine-scale brain structures. Compared to 7 T, the 10.5 T approach led to gains in both iSNR and quantification precision of R2* and{chi} . Quantitatively, iSNR estimated in the peripheral cortical gray matter increased by 42%. Parallel imaging performances were also improved at 10.5 T owing to the utilized high-density coils compared to the commonly used commercially available coil at 7 T, allowing high-quality images with up to 12-fold combined acceleration when using the 128Rx coil. ConclusionIt is feasible to perform motion-robust whole-brain mesoscopic multi-echo gradient echo imaging of the human brain at 10.5 T. Intrinsic SNR and quantification precision of R2* and{chi} were estimated and compared with 7 T results. The results presented here may shed light on future optimal implementation of anatomic T2*w brain MRI at ultrahigh field beyond 7 T.

bioengineering↗

bioRxiv2024

Spanning spatial scales with functional imaging in the human brain; initial experiences at 10.5 Tesla

One of the most important frontiers in the efforts to improve functional imaging of brain activity (fMRI) is the recent push to increase the magnetic fields for human imaging beyond 10 Tesla. Having established safety, large gains in signal-to-noise-ratio (SNR), and novel radiofrequency arrays that capture the higher SNR, here we demonstrate major gains in the spatial resolution, sensitivity, and functional contrast of BOLD (Blood Oxygenation Level Dependent) based human fMRI at 10.5 Tesla. Using image reconstruction methods developed to minimize blurring, we also demonstrate that ultrahigh resolutions achieved at 10.5 Tesla suppress large-vein confounds in gradient-recalled-echo BOLD fMRI, thus improving the fidelity of functional signals relative to neuronal activity and yielding accurate cortical depth-profiles for layer-specific activation. Together, these multiplicative benefits deliver much needed increases in precision and resolution for meso-scale fMRI applications and illustrate the transformative potential of human functional imaging at magnetic fields that exceed 10 Tesla.

neuroscience↗

bioRxiv2024

A 128-channel receive array with enhanced SNR performance for 10.5 tesla brain imaging

PurposeTo develop and characterize the performance of a 128-channel head array for brain imaging at 10.5 tesla and evaluate the potential of brain imaging at this unique, >10 tesla magnetic field. MethodsThe coil is composed of a 16-channel self-decoupled loop transmit/receive array with a 112-loop receive-only (Rx) insert. Interactions between the outer transmitter and the inner 112Rx insert were mitigated using coaxial cable traps placed every 1/16 of a wavelength on each feed cable, locating most preamplifier boards outside the transmitter field and miniaturizing those placed directly on individual coils. ResultsThe 128-channel array described herein achieved 77% of ultimate intrinsic SNR in the center of the brain. Transmit field maps obtained experimentally on a phantom with and without the receive array were similar and matched EM simulations, leading to FDA approval for human imaging. Anatomical and functional data, including with power demanding sequences, were acquired successfully on human volunteers. ConclusionsCounterintuitive to expectations based on magnetic fields [≤]7T, the higher channel counts provided SNR gains centrally, capturing [~]80% uiSNR. Fraction of uiSNR achieved centrally in 64Rx, 80Rx, and 128Rx arrays suggested that a plateau was being reached at 80%. At this plateau, linear to approximately quadratic B0 dependent SNR gains for the periphery and the center, respectively, were observed for 10.5T relative 7T.

neuroscience↗

bioRxiv2024

Syngeneic adipose-derived stromal cells modulate the immune response but have limited persistence within decellularized adipose tissue implants in C57BL/6 mice

The delivery of adipose-derived stromal cells (ASCs) on cell-instructive decellularized adipose tissue (DAT) scaffolds is a promising strategy for stimulating host-derived soft tissue regeneration. However, a better understanding of the mechanisms through which ASCs modulate regeneration in vivo is needed to harness these cells more effectively. In this study, DAT scaffolds, both with and without seeded syngeneic DsRED+ mouse ASCs, were implanted into immunocompetent C57BL/6 mice. Downstream analyses focused on assessing donor ASC persistence and phenotype, as well as the effects of ASC seeding on host macrophage polarization and the perfused host vascular network. Notably, most donor ASCs were cleared from the scaffolds by 2 weeks. Mass spectrometry-based proteomics indicated that the transplanted ASCs maintained their pre-implantation phenotype up to 1 week in vivo, suggesting that the cells were not undergoing programmed cell death. A higher fraction of the infiltrating host macrophages expressed CD68 and Arginase-1 in the ASC-seeded implants up to 1-week post-implantation. Interestingly, a small population of phagocytic macrophages, identified by uptake of DsRED protein, was present in the DAT implants in the first 2 weeks and showed enhanced expression of CD68, Arginase-1, and CD163, along with reduced expression of iNOS. MicroCT angiography revealed a similar perfused vessel network in the seeded and unseeded groups at 4- and 8-weeks post-implantation. Overall, seeding with syngeneic ASCs modulated the host macrophage response to the DAT bioscaffolds at early timepoints, but did not impact long-term regenerative outcomes, potentially due to the rapid clearance of the donor cell population in this model.

cell biology↗

bioRxiv2024

β-Glucan Reprograms Neutrophils to Induce Disease Tolerance Against Influenza A Virus

ABSTRACTDisease tolerance is an evolutionarily conserved host defence strategy that preserves tissue integrity and physiology without affecting pathogen load. Unlike host resistance, the mechanisms underlying disease tolerance remain poorly understood. In the present study, we investigated whether an adjuvant ({beta}-glucan) can reprogram innate immunity to provide protection against Influenza A virus (IAV) infection. Here we observe that {beta}-glucan treatment reduced the morbidity and mortality against IAV infection, independent of host resistance (viral load). Increased survival of {beta}-glucan treated mice against IAV is associated with the accumulation of neutrophils via RoR{gamma}t+ T cells in the lung tissue. Using gain-and-loss-of-function approaches, we demonstrate that {beta}- glucan reprogrammed neutrophils are essential for promoting disease tolerance, limiting pulmonary tissue damage, and enhancing survival against IAV infection. {beta}-glucan treatment promotes granulopoiesis in a type 1 interferon-dependent manner that leads to the generation of a unique subset of neutrophils, which are less mature with higher mitochondrial mass utilizing mitochondrial oxidative (OXPHOS) metabolism. Collectively, our data indicate that {beta}-glucan reprograms hematopoietic stem cells (HSCs) to generate neutrophils with a novel "regulatory" function, which is required for promoting disease tolerance and maintaining lung tissue integrity against viral infection.

immunology↗

bioRxiv2024

RF coil design strategies for improving SNR at theultrahigh magnetic field of 10.5 Tesla

PurposeTo develop multichannel transmit and receive arrays towards capturing the ultimate-intrinsic-SNR (uiSNR) at 10.5 Tesla (T) and to demonstrate the feasibility and potential of whole-brain, high-resolution human brain imaging at this high field strength. MethodsA dual row 16-channel self-decoupled transmit (Tx) array was converted to a 16Tx/Rx transceiver using custom transmit/receive switches. A 64-channel receive-only (64Rx) array was built to fit into the 16Tx/Rx array. Electromagnetic modeling and experiments were employed to define safe operation limits of the resulting 16Tx/80Rx array and obtain FDA approval for human use. ResultsThe 64Rx array alone captured approximately 50% of the central uiSNR at 10.5T while the identical 7T 64Rx array captured [~]76% of uiSNR at this lower field strength. The 16Tx/80Rx configuration brought the fraction of uiSNR captured at 10.5T to levels comparable to the performance of the 64Rx array at 7T. SNR data obtained at the two field strengths with these arrays displayed [Formula] dependent increases over a large central region. Whole-brain high resolution T2* and T1 weighted anatomical and gradient-recalled echo EPI BOLD fMRI images were obtained at 10.5T for the first time with such an advanced array, illustrating the promise of >10T fields in studying the human brain. ConclusionWe demonstrated the ability to approach the uiSNR at 10.5T over the human brain with a novel, high channel count array, achieving large SNR gains over 7T, currently the most commonly employed ultrahigh field platform, and demonstrate high resolution and high contrast anatomical and functional imaging at 10.5T.

neuroscience↗

bioRxiv2023

Improved taxonomic annotation of Archaea communities using LotuS2, the Genome Taxonomy Database and RNAseq data

Metabarcoding is increasingly used to uncover diversity and characterise communities of Archaea In various habitats, but taxonomic annotation of their sequences remains more challenging than for bacteria. Fewer reference sequences are available; widely used databases do not reflect recent revisions of higher level archaeal taxonomy and a substantial fraction of their phylogenetic diversity remains to be fully characterised. We address these gaps with a systematic and tractable approach based around the Genome Taxonomy Database (GTDB). GTDB provides a standardized taxonomy with normalized ranks based on protein coding genes, allowing us to identify and remove incongruent SSU sequences. We then use this in combination with the eukaryote PR2 database to annotate a collection of near full length rRNA sequences and the Archaea SSU sequences in SILVA, creating a new reference database, KSGP (Karst, Silva, GTDB and PR2). GTDB SSUs alone provides a small improvement in annotation of an example marine Archaea OTU data set over standardized SSU databases such as SILVA and Greengenes2, while KSGP increases Class and Order assignments by 145% and 280% respectively and is likely to provide some improvement in annotation of bacterial sequences too. We make the KSGP database and a cleaned and deduplicated subset of GTDB SSU sequences available at ksgp.earlham.ac.uk; integrate them into a metabarcoding pipeline, LotuS2 and outline rapid and robust strategies to generate a set of annotated Archaea OTUs and to determine the proportion of Archaea sequences in metatranscriptomic data. We also demonstrate simple tools to visualise the completeness of database coverage and outline strategies to further understand poorly characterised components of the archaeal community which will be equally applicable to bacteria.

microbiology↗

bioRxiv2022

A graph-embedded topic model enables characterization of diverse pain phenotypes among UK Biobank individuals

Large biobank repositories of clinical conditions and medications data open opportunities to investigate the phenotypic disease network. To enable systematic investigation of entire structured phenomes, we present graph embedded topic model (GETM). Our contributions are two folds in terms of method and applications. On the methodology side, we offer two main contributions in GETM. First, to aid topic inference, we integrate existing biomedical knowledge graph information in the form of pre-trained graph embedding into the embedded topic model. Second, leveraging deep learning techniques, we developed a variational autoencoder framework to infer patient phenotypic mixture by modeling multi-modal discrete patient medical records. In particular, for interpretability, we use a linear decoder to simultaneously infer the bi-modal distributions of the disease conditions and medications. On the application side, we applied GETM to UK Biobank (UKB) self-reported clinical phenotype data, which contains 443 self-reported medical conditions and 802 self-reported medications for 457,461 individuals. Compared to existing methods, GETM demonstrates overall superior performance in imputing missing conditions and medications. Here, we focused on characterizing pain phenotypes recorded in the questionnaire of the UKB individuals. GETM accurately predicts the status of chronic musculoskeletal (CMK) pain, chronic pain by body-site, and non-specific chronic pain using past conditions and medications. Our analyses revealed not only the known pain-related topics but also the surprising predominance of medications and conditions in the cardiovascular category among the most predictive topics across chronic pain phenotypes.

bioinformatics↗

bioRxiv2021

Molecular Drivers of Tumor Progression in Microsatellite Stable APC Mutation-Negative Colorectal Cancers

BackgroundThe tumor suppressor gene adenomatous polyposis coli (APC) is the initiating mutation in approximately 80% of all colorectal cancers (CRC), underscoring the importance of aberrant regulation of intracellular WNT signaling in CRC development. Recent studies have found that early-onset CRC exhibits an increased proportion of tumors lacking an APC mutation. We set out to identify mechanisms underlying APC mutation-negative (APCmut-) CRCs. MethodsWe analyzed data from The Cancer Genome Atlas to compare clinical phenotypes, somatic mutations, copy number variations, gene fusions, RNA expression, and DNA methylation profiles between APCmut- and APC mutation-positive (APCmut+) microsatellite stable CRCs. ResultsTranscriptionally, APCmut- CRCs clustered into two approximately equal groups. Cluster One was associated with enhanced mitochondrial activation. Cluster Two was strikingly associated with genetic inactivation or decreased RNA expression of the WNT antagonist RNF43, increased expression of the WNT agonist RSPO3, activating mutation of BRAF, or increased methylation and decreased expression of AXIN2. APCmut- CRCs exhibited evidence of increased immune cell infiltration, with significant correlation between M2 macrophages and RSPO3. ConclusionsAPCmut- CRCs comprise two groups of tumors characterized by enhanced mitochondrial activation or increased sensitivity to extracellular WNT, suggesting that they could be respectively susceptible to inhibition of these pathways.

cancer biology↗

bioRxiv2021

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. Author SummaryAntimicrobial resistance (AMR) is one of the biggest global health threats humanity is facing. Understanding the emergence and spread of AMR between different bacterial species is crucial for the development of effective countermeasures. In this paper we describe a user-friendly, affordable and comprehensive (laboratory and bioinformatics) workflow that is able to identify, associate and track AMR genes in bacteria. We demonstrate the efficiency and reliability of the method by comparing 50 faecal microbiomes from pig farms with high-antibiotic use (conventional farms), and 50 faecal microbiomes from pig farms with low-antibiotic use (organic farms). Our method provides a novel approach to resistance gene tracking, that also leads to the generation of high quality metagenomic assembled genomes that includes genes on mobile genetic elements, such as plasmids, that would not otherwise be included in these assembled genomes.

bioinformatics↗

bioRxiv2020

Detection of a bedaquiline / clofazimine resistance reservoir in Mycobacterium tuberculosis predating the antibiotic era

Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. We compiled a dataset of 3,682 Mtb genomes, including 150 carrying variants in mmpR5 that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade of isolates where the RAV Ile67fs is estimated to have emerged prior to the antibiotic era, co-occurrence of mutations in mmpL5 are found to neutralise bedaquiline resistance. The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.

genomics↗

bioRxiv2020

An 8 Dipole Transceive and 24 Loop Receive Array for Non-Human Primate Head Imaging at 10.5T

A 32-channel RF coil was developed for brain imaging of anesthetized non-human primates (Rhesus Macaque) at 10.5 tesla. The coil is composed of an 8-channel dipole transmit/receive array, close-fitting 16-channel loop receive array headcap, and 8-channel loop receive array lower insert. The transceiver dipole array is composed of eight end-loaded dipole elements self-resonant at the 10.5 tesla proton Larmor frequency. These dipole elements were arranged on a plastic cylindrical former which was split in two to allow for convenient animal positioning. Nested into the bottom of the dipole array former is located an 8-channel loop receive array which contains 5x10 cm2 square loops arranged in two rows of four loops. Arranged in a close-fitting plastic headcap is located a high-density 16-channel loop receive array. This array is composed of 14 round loops 37 mm in diameter and two partially detachable, irregularly shaped loops that encircle the ears. Imaging experiments were performed on anesthetized non-human primates on a 10.5 tesla MRI system equipped with body gradients with a 60 cm open bore. The coil enabled submillimeter (0.58 mm isotropic) high resolution anatomical and functional imaging as well as tractography of fasciculated axonal bundles. The combination of a close-fitting loop receive array and dipole transceiver array allowed for a higher channel count receiver and consequent higher SNR and parallel imaging gains. Parallel imaging performance supports high resolution fMRI and dMRI with a factor of three reduction in sampling. The transceive array elements during reception contributed approximately one quarter of SNR in the lower half of the brain which was farthest from the close-fitting headcap receive array.

bioengineering↗

bioRxiv2019

Breast tumor stiffness instructs bone metastasis via mechanical memory

The mechanical microenvironment of primary breast tumors plays a substantial role in promoting tumor progression. While the transitory response of cancer cells to pathological stiffness in their native microenvironment has been well described, it is still unclear how mechanical stimuli in the primary tumor influence distant, late-stage metastatic phenotypes across time and space in absentia. Here, we show that primary tumor stiffness promotes stable, non-genetically heritable phenotypes in breast cancer cells. This mechanical memory instructs cancer cells to adopt and maintain increased cytoskeletal dynamics, traction force, and 3D invasion in vitro, in addition to promoting osteolytic bone metastasis in vivo. Furthermore, we established a mechanical conditioning (MeCo) score comprised of mechanically-regulated genes as a global gene expression measurement of tumor stiffness response. Clinically, we show that a high MeCo score is strongly associated with bone metastasis in patients. Using a discovery approach, we mechanistically traced mechanical memory in part to ERK-mediated mechanotransductive activation of RUNX2, an osteogenic gene bookmarker and bone metastasis driver. The combination of these RUNX2 traits permits the stable transactivation of osteolytic target genes that remain upregulated after cancer cells disseminate from their activating microenvironment in order to modify a distant microenvironment. Using genetic, epigenetic, and functional approaches, we were able to simulate, repress, select and extend RUNX2-mediated mechanical memory and alter cancer cell behavior accordingly. In concert with previous studies detailing the influence of biochemical properties of the primary tumor stroma on distinct metastatic phenotypes, our findings detailing the influence of biomechanical properties support a generalized model of cancer progression in which the integrated properties of the primary tumor microenvironment govern the secondary tumor microenvironment, i.e., soil instructs soil.

cancer biology↗

bioRxiv2018

Consensus interpretation of the Met34Thr and Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel

PURPOSEPathogenic variants in GJB2 are the most common cause of autosomal recessive sensorineural hearing loss. The classification of c.101T>C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants.\n\nMETHODSThe ClinGen Hearing Loss Expert Panel (HL-EP) collected published data and shared unpublished information from participating laboratories regarding the two variants. Functional, computational, allelic, and segregation data were also obtained.\n\nRESULTSThe panel reviewed the synthesized information, and classified the Met34Thr and Val37Ile variants according to professional variant interpretation guidelines. We found that Met34Thr and Val37Ile are significantly overrepresented in hearing loss patients, compared to the general population. Met34Thr or Val37Ile homozygotes or compound heterozygotes typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for those two variants.\n\nCONCLUSIONResolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification rules, review evidence, and reach a consensus. The ClinGen HL-EP concluded that Met34Thr and Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and age-dependent penetrance.

genetics↗

bioRxiv2018

Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations

Genetic alterations are essential for cancer initiation and progression. However, differentiating mutations that drive the tumor phenotype from mutations that do not affect tumor fitness remains a fundamental challenge in cancer biology. To better understand the impact of a given mutation within cancer, RNA-sequencing data was used to categorize mutations based on their allelic expression. For this purpose, we developed the MAXX (Mutation Allelic Expression Extractor) software, which is highly effective at delineating the allelic expression of both single nucleotide variants and small insertions and deletions. Results from MAXX demonstrated that mutations can be separated into three groups based on their expression of the mutant allele, lack of expression from both alleles, or expression of only the wild-type allele. By taking into consideration the allelic expression patterns of genes that are mutated in PDAC, it was possible to increase the sensitivity of widely used driver mutation detection methods, as well as identify subtypes that have prognostic significance and are associated with sensitivity to select classes of therapeutic agents in cell culture. Thus, differentiating mutations based on their mutant allele expression via MAXX represents a means to parse somatic variants in tumor genomes, helping to elucidate of a genes respective role in cancer.

cancer biology↗