Biology subjects

Wallace, K.

Publications and source records attributed to Wallace, K..

7 recordsLinked to original sources

bioRxiv2026

Differences in T-cell counts and neighborhood patterns in human colorectal adenomas and sessile serrated lesions

BackgroundT-cell responses influence recurrence and survival in colorectal cancer. T-cell subset distributions vary by molecular phenotype and location, shaping cytotoxic or immune-cold tumor immune microenvironments (TiMEs). However, the T-cell contexture and their spatial proximities within preinvasive lesions are not well characterized. MethodsWe analyzed sessile serrated lesions (SSLs), tubulovillous/villous adenomas (TVs), and tubular adenomas (TAs) from three completed studies (N=120). Whole-slide multiplex immunofluorescence was used to quantify eight T-cell subsets (CD4, CD8, Th1, Th17, Treg, Tc1, Tc17, TcTreg). Counts were compared by histology using a generalized linear mixed model with a negative binomial distribution, including an offset for total cell counts and adjusting for age, sex, anatomic location, and lesion size. Nearest-neighbor (NN) analyses assessed proximities of T-cell pairs across lesion types. ResultsTAs and SSLs had higher CD4 and CD8 T-cell counts compared with TVs (q<0.05). SSLs had lower Th17 counts than TAs (q<0.05) and compared with TVs leaned toward fewer Tregs (q=0.07). NN analysis showed that TVs, compared with SSLs and TAs, had increased Treg clustering. In contrast, TA versus SSL comparisons revealed predominant CD4 clustering with Th17, Th1, and CD8 subsets. ConclusionTVs are characterized by lower T-cell infiltration and a greater tendency for regulatory T-cell clustering, consistent with an immune-cold TiME relative to TAs. SSLs and TAs were both more immune-infiltrated than TVs, but SSLs appeared less inflamed and less dominated by regulatory subsets. In contrast, CD4dominant clustering in TAs suggested stronger helper coordination. Preinvasive lesions therefore demonstrate immune and spatial heterogeneity by lesion types.

pathology↗

bioRxiv2025

Notch receptors involved in the choice between intestinal secretory and enterocytes and differentiation of Bestrophin 4 cells.

During the first half of embryogenesis, the intestinal epithelium is a simple layer of cuboidal cells surrounded by lateral plate splanchnic mesoderm. As embryogenesis proceeds, the epithelium differentiates to include a variety of enterocytes and secretory cells. During the period of epithelial cell differentiation a number of signaling pathways are used to generate the full complement of cell types. Notch signaling is important for the choice between enterocytes and secretory cells. Following the initial choice, both enterocytes and secretory cells continue differentiating into a number of different subtypes of each cell type. In the zebrafish embryo, Notch signaling is utilized at least three times during development of the intestinal epithelium. The first two Notch signaling events are involved in the choice between enterocytes and secretory cells, while the third involves differentiation of a unique cell type that we previously called Notch Receiving Secretory Cells (NRSCs). While we have identified the times when Notch signaling is active, the individual Notch receptors used in each signaling event have not been previously identified. Here we use loss of function mutants in the four Notch receptors (notch 1a, 1b, 2, and 3) to identify which are used in the each of the Notch signaling events. We find redundant use of Notch receptors in the choice between enterocytes and secretory cells with loss of combinations of either notch 2 and notch 3 or notch 2 and notch 1b but not loss of individual receptors resulting in changes to secretory cell numbers. During the Notch signaling event following the choice between secretory and enterocytes, we identify NRSCs as Bestrophin 4 (BEST4+) cells. In contrast to the choice between secretory and enterocyte cells, we find that loss of individual Notch receptors result in differing numbers of BEST4+ cells. Even though loss of individual receptors affect BEST4+ numbers we suggest that combinations of Notch receptors play a role in differentiation of different BEST4+ subtypes. HighlightsO_LIRequirements for the choice between secretory and enterocytes within the intestinal epithelium require Notch2/Notch3 and Notch2/Notch1b combinations. C_LIO_LINotch 2 and Notch1b are required for Bestropin 4 (BEST4+) cell development. C_LIO_LICombinations of Notch2, Notch1b, and Notch3 may play roles in formation of different BEST4+ subtypes. C_LI

developmental biology↗

bioRxiv2023

SpaceANOVA: Spatial co-occurrence analysis of cell types in multiplex imaging data using point process and functional ANOVA

MotivationMultiplex imaging platforms have enabled the identification of the spatial organization of different types of cells in complex tissue or tumor microenvironment (TME). Exploring the potential variations in the spatial co-occurrence or co-localization of different cell types across distinct tissue or disease classes can provide significant pathological insights, paving the way for intervention strategies. However, the existing methods in this context either rely on stringent statistical assumptions or suffer from a lack of generalizability. ResultsWe present a highly powerful method to study differential spatial co-occurrence of cell types across multiple tissue or disease groups, based on the theories of the Poisson point process (PPP) and functional analysis of variance (FANOVA). Notably, the method accommodates multiple images per subject and addresses the problem of missing tissue regions, commonly encountered in such a context due to the complex nature of the data-collection procedure. We demonstrate the superior statistical power and robustness of the method in comparison to existing approaches through realistic simulation studies. Furthermore, we apply the method to three real datasets on different diseases collected using different imaging platforms. In particular, one of these datasets reveals novel insights into the spatial characteristics of various types of precursor lesions associated with colorectal cancer. AvailabilityThe associated R package can be found here, https://github.com/sealx017/SpaceANOVA. Contactsealso@musc.edu Supplementary informationThe supplementary material is attached.

bioinformatics↗

bioRxiv2023

A dual MTOR/NAD+ acting gerotherapy

The geroscience hypothesis states that a therapy that prevents the underlying aging process should prevent multiple aging related diseases. The mTOR (mechanistic target of rapamycin)/insulin and NAD+ (nicotinamide adenine dinucleotide) pathways are two of the most validated aging pathways. Yet, its largely unclear how they might talk to each other in aging. In genome-wide CRISPRa screening with a novel class of N-O-Methyl-propanamide-containing compounds we named BIOIO-1001, we identified lipid metabolism centering on SIRT3 as a point of intersection of the mTOR/insulin and NAD+ pathways. In vivo testing indicated that BIOIO-1001 reduced high fat, high sugar diet-induced metabolic derangements, inflammation, and fibrosis, each being characteristic of non-alcoholic steatohepatitis (NASH). An unbiased screen of patient datasets suggested a potential link between the anti-inflammatory and anti-fibrotic effects of BIOIO-1001 in NASH models to those in amyotrophic lateral sclerosis (ALS). Directed experiments subsequently determined that BIOIO-1001 was protective in both sporadic and familial ALS models. Both NASH and ALS have no treatments and suffer from a lack of convenient biomarkers to monitor therapeutic efficacy. A potential strength in considering BIOIO-1001 as a therapy is that the blood biomarker that it modulates, namely plasma triglycerides, can be conveniently used to screen patients for responders. More conceptually, to our knowledge BIOIO-1001 is a first therapy that fits the geroscience hypothesis by acting on multiple core aging pathways and that can alleviate multiple conditions after they have set in. Brief SummaryThese studies characterize a novel gerotherapy, BIOIO-1001, that identifies lipid metabolism as an intersection of the mTOR and NAD+ pathways.

genomics↗

bioRxiv2022

Single molecule long-read real-time amplicon-based sequencing of CYP2D6: a proof-of-concept with hybrid haplotypes

CYP2D6 is a widely expressed human xenobiotic metabolizing enzyme, best known for its role in the hepatic phase I cytochrome P450 enzyme system, where it metabolizes [~]20% of medications. It is also expressed in other organs including the brain, where its potential role in physiology and mental health traits and disorders is under further investigation. Owing to the presence of homologous pseudogenes in the CYP2D locus and transposable repeat elements in the intergenic regions, the gene encoding the CYP2D6 enzyme, CYP2D6, is one of the most hypervariable known human genes - with more than 165 core haplotypes. Haplotypes include structural variants, with a subtype of these known as hybrid haplotypes or fusion genes comprising part of CYP2D6 and part of its adjacent pseudogene, CYP2D7. The fusion genes are particularly challenging to identify. High fidelity (HiFi) single molecule real-time (SMRT) long-read sequencing can cover whole CYP2D6 haplotypes in a single continuous sequence, and is therefore ideal for structural variant detection. In addition, it is highly accurate and suitable for novel haplotype identification, which is necessary as new CYP2D6 haplotypes are continuously being discovered, and many more likely remain to be identified in relatively understudied populations such as Indigenous Peoples. The aim of the present work was to develop an efficient and accurate HiFi SMRT amplicon-based method capable of detecting the full range of CYP2D6 haplotypes including fusion genes. We report proof-of-concept for 24 amplicons including three positive controls, aligned to fusion gene haplotypes, with prior cross-validation data. Amplicons with CYP2D7-D6 fusion genes, including positive controls, aligned to the *13 subhaplotypes predicted (*13F, *13A2) with 100% accuracy, with the exception of one that aligned at 99.9%. Alignment of the *68 was 100% and above 99.9% to the CYP2D6*68 partial sequences EU5300606 and JF307779, respectively. The best alignments for the remaining CYP2D6-2D7 fusion genes were [≥]99.7% (to 3 significant figures). Lower percentage alignment for CYP2D6-2D7 fusion genes may reflect imperfect PCR optimization and/or the possibility that we may have haplotypes not yet in public databases. Further work on these is in progress. Moreover, we have adapted this method for non-hybrid haplotypes. This technique could therefore suffice for the characterization of the full range of CYP2D6 haplotypes. The method that we have developed could be extended to other complex loci and to other species in a multiplexed high throughput assay.

genomics↗

bioRxiv2021

Focused Ultrasound Modulation of Hepatic Neural Plexus Restores Glucose Homeostasis in Diabetes

While peripheral glucose sensors are known to relay signals of substrate availability to integrative nuclei in the brain, the importance of these pathways in maintaining energy homeostasis and their contribution to disease remain unknown. Herein, we demonstrate that selective activation of the hepatoportal neural plexus via transient peripheral focused ultrasound (pFUS) induces glucose homeostasis in models of well-established insulin resistant diabetes. pFUS modulates sensory projections to the hindbrain and alters hypothalamic concentrations of neurotransmitters that regulate metabolism, resulting in potentiation of hypothalamic insulin signaling, leptin-independent inhibition of the orexigenic neuropeptide Y system, and therapeutic alteration in autonomic output to peripheral effector organs. Multiomic profiling confirms pFUS-induced modifications of key metabolic functions in liver, pancreas, muscle, adipose, kidney, and intestines. Activation of the hepatic nutrient sensing pathway not only restores nervous system coordination of peripheral metabolism in three different species but does so across these organ systems; several of which are current targets of antidiabetic drug classes. These results demonstrate the potential of hepatic pFUS as a novel/non-pharmacologic therapeutic modality to restore glucose homeostasis in metabolic diseases, including type II diabetes. One Sentence SummaryWe utilize a non-invasive ultrasound technique to activate a liver-brain sensory pathway and demonstrate its potential to induce durable normalization of glucose homeostasis in models of well-established insulin resistant diabetes.

biophysics↗

bioRxiv2018

Wd*-test: Robust Distance-Based Multivariate Analysis of Variance

BackgroundCommunity-wide analyses provide an essential means for evaluation of the effect of interventions or design variables on the composition of the microbiome. Applications of these analyses are omnipresent in microbiome literature, yet some of their statistical properties have not been tested for robustness towards common features of microbiome data. Recently, it has been reported that PERMANOVA can yield wrong results in the presence of heteroscedasticity and unbalanced sample sizes.\n\nFindingsWe develop a method for multivariate analysis of variance, [Formula], based on Welch MANOVA that is robust to heteroscedasticity in the data. We do so by extending a previously reported method that does the same for two-level independent factor variables. Our approach can accommodate multi-level factors, stratification, and multiple post hoc testing scenarios. An R language implementation of the method is available at https://github.com/alekseyenko/WdStar.\n\nConclusionOur method resolves potential for confounding of location and dispersion effects in multivariate analyses by explicitly accounting for the differences in multivariate dispersion in the data tested. The methods based on [Formula] have general applicability in microbiome and other omics data analyses.

bioinformatics↗