Biology subjects

Grimson, A.

Publications and source records attributed to Grimson, A..

14 recordsLinked to original sources

bioRxiv2026

Single cell analysis of neonatal naïve CD8α+ T cells reveals novel subsets bridging the innate-adaptive spectrum

There is growing evidence that neonates harbor innate-like CD8a+ T cell subsets that contribute to both protection and hyper-inflammatory states. It remains unclear, however, where these innate-like features are found among the many conventional and unconventional T cell populations that can upregulate the CD8 receptor. Further delineation of these unique populations and functions, with a focus on CD8ab co-expression, will enable studies that seek to understand the unique immune features in conventional T cell populations that are present during fetal and early postnatal life. We used cord blood from infants across the full viable gestational age range to examine phenotypic and transcriptional heterogeneity, with a particular focus on the naive T cell pool. We report a set of fetally-derived and innate-like naive CD8{beta}+ T cells ( FITs) that are marked by their KLRG1+CD161+ phenotype, unique transcriptomic features and which are sparsely detected in adult peripheral blood. Additionally, using T cell receptor repertoire profiling, we can distinguish FITs from well-described and semi-invariant unconventional T cell populations such as mucosa-associated invariant T cells. Our delineation of FITs unique features will enable future investigation into their ontogeny and tissue distribution, and ultimately their role in immune-related outcomes in preterm infants.

immunology↗

bioRxiv2025

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis-regulatory contribution of TEs to immune cell development is less characterized. Here, we analyzed hundreds of chromatin accessibility, gene expression, transcription factor occupancy and DNA-DNA contact datasets in diverse mouse and human immune cells. We identified two rodent-specific TE subfamilies, ORR1E and ORR1D2 (collectively, ODE) that have transformed into cell type-specific enhancers across the mouse immune system. ODE loci acquired mutations post-insertion that enable differential binding of lineage-specifying transcription factors. ODEs show evidence of evolutionary sequence constraint and contact promoters of hundreds of genes in immune cells. ODE-targeted genes show cell type-specific and mouse-specific increases in expression compared to concordant human cell types. Thus, a single TE family can undergo functionalization after its genomic spread to generate batteries of cell-specific enhancers supporting a complex developmental cascade.

genomics↗

bioRxiv2025

Single-cell multiomics reveals the distinct properties of neonatal and adult recent thymic emigrants

Following thymic egress, CD8+ T cells must undergo a post-thymic maturation process to transition from a recent thymic emigrant (RTE) to a mature naive T cell. Since the neonatal T cell pool is comprised of significantly more RTEs, the prevailing notion is that neonatal CD8+ T cells behave differently than their adult counterparts simply because they have undergone less post-thymic maturation. To test this theory, we leveraged a fate mapping mouse model and paired single cell transcriptome and TCR sequencing to compare neonatal and adult CD8+ RTEs that have undergone the same amount of post-thymic maturation. Interestingly, we found that neonatal and adult CD8+ RTEs exhibit distinct phenotypes, gene expression profiles, TCR usage, and functions. These data suggest that neonatal CD8+ T cells are not simply immature adult CD8+ T cells and that age-related changes in CD8+ T cell functions in early life cannot be attributed solely to differences in the amount of post-thymic maturation.

immunology↗

bioRxiv2025

Argonaute proteins regulate the timing of the spermatogenic transcriptional program

Argonaute proteins are best known for their role in microRNA-mediated post-transcriptional gene silencing. Here, we show that AGO3 and AGO4, but not AGO2, localize to the sex chromatin of pachytene spermatocytes where they are required for transcriptional silencing of XY-linked genes, known as Meiotic Sex Chromosome Inactivation (MSCI). Using an Ago413-/- mouse, we show that AGO3 and AGO4 are key regulators of spermatogenesis, orchestrating expression of meiosis-related genes during prophase I while maintaining silencing of spermiogenesis genes. Premature overexpression of spermiogenesis genes during prophase I in Ago413-/- mice results in subfertility, altered sperm morphology and reduced fertilization capability. We also identify BRG1, a BAF complex subunit, as an AGO3 interactor. Loss of AGO3 and AGO4 results in increased BRG1 in spermatocytes, suggesting that AGO3 aids in removing BRG1 from the XY chromatin to achieve MSCI and demonstrating a meiotic role for AGO3 in transcriptional control through the chromatin remodeling machinery.

developmental biology↗

bioRxiv2024

Deciphering gene regulatory programs underlying functionally divergent naive T cell subsets

Naive CD8+ T cells are a heterogeneous population, with different subsets possessing distinct functions and kinetics upon activation. However, the gene regulatory circuits differentiating these naive subsets are not well studied. In this work, we analyzed a large collection of public and newly generated RNA-seq and ATAC-seq profiles of different subsets of naive CD8+ T cells, revealing significant differences in the gene regulatory landscapes between subsets. We leveraged these data by employing a network inference algorithm, Inferelator, to identify the transcriptional regulatory circuits active in each subset. The predicted transcriptional network of the naive CD8+ T cell pool was validated by multiple orthogonal approaches, including CUT&Tag and Micro-C. Interestingly, our network analysis revealed a novel role for Eomes in promoting effector cell differentiation in specific cell subsets. Moreover, we uncovered multiple novel regulators across a variety of subsets and discovered several modules of genes that were co-regulated by shared sets of transcription factors in distinct subsets. Collectively, our data defines the gene regulatory programs differentiating naive CD8+ T cells and facilitates the identification of novel transcription factors that may alter the propensity of naive CD8+ T cells to become effector or memory cells after infection.

systems biology↗

bioRxiv2024

A novel regulatory pathway recognizes and degrades transcripts with long 3' untranslated regions

Quantitative control of gene expression is fundamental to cellular function, and post-transcriptional regulation is a consequential, additional layer of control over protein output. Within mammalian mRNAs, the 3' untranslated region (3'UTR) acts as a hub of regulatory control, typically mediated by regulatory sequence elements within the 3'UTR. We have found that expression from transcripts with long 3'UTRs is strongly repressed compared to those with short 3'UTRs, and this phenomenon appears to be independent of sequence elements within the 3'UTR. The repression increases with 3'UTR length and is substantial; reporters with 2,000 nucleotide long 3'UTRs are repressed >10-fold compared to 400 nucleotide 3'UTRs. Conversely, increasing the length of the coding region has no effect on expression, demonstrating that it is 3'UTR length, not transcript length, that elicits repression. Reporters with different length 3'UTRs show no difference in transcription rates nor translation efficiency but have clear differences in mRNA half-lives and nucleocytoplasmic distribution, indicating repression of long-3'UTR transcripts is mediated by accelerated RNA decay. However, this transcript degradation does not involve the nonsense-mediated decay (NMD) pathway nor other canonical RNA decay pathways. In order to identify trans factors involved in 3'UTR-length-mediated decay, we quantified the differences in proteins bound to reporters with long and short 3'UTRs, and identified over 100 differentially associated factors. Knockdowns of two differentially associating proteins, the mRNA nuclear export factors DDX39B and ZC3H11A, indicate they play a role in repression of mRNAs with long 3'UTRs. This study establishes a novel length-dependent regulatory feature of 3'UTRs, which potentially regulates many genes.

genetics↗

bioRxiv2023

A TOPBP1 Allele Causing Male Infertility Uncouples XY Silencing Dynamics From Sex Body Formation

Meiotic sex chromosome inactivation (MSCI) is a critical feature of meiotic prophase I progression in males. While the ATR kinase and its activator TOPBP1 are key drivers of MSCI within the specialized sex body (SB) domain of the nucleus, how they promote silencing remains unclear given their multifaceted meiotic functions that also include DNA repair, chromosome synapsis and SB formation. Here we report a novel mutant mouse harboring mutations in the TOPBP1-BRCT5 domain. Topbp1B5/B5 males are infertile, with impaired MSCI despite displaying grossly normal events of early prophase I, including synapsis and SB formation. Specific ATR-dependent events are disrupted including phosphorylation and localization of the RNA:DNA helicase Senataxin. Topbp1B5/B5 spermatocytes initiate, but cannot maintain ongoing, MSCI. These findings reveal a non-canonical role for the ATR-TOPBP1 signaling axis in MSCI dynamics at advanced stages in pachynema and establish the first mouse mutant that separates ATR signaling and MSCI from SB formation.

cell biology↗

bioRxiv2022

Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation

ME/CFS is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we used single-cell RNA-seq (scRNA-seq) to examine immune cells in cohorts of patients and controls. Post-exertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. Thus, to detect changes coincident with PEM, we also performed scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients displayed dysregulation of classical monocytes suggestive of inappropriate differentiation and migration to tissue. We were able to identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlated with metrics of disease severity. Comparing the transcriptome at baseline and post-exercise challenge, we discovered patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation following exercise. HighlightsME/CFS is a debilitating disease with unknown causes. Here, we provide, for the first time, an extensive single cell resolution dataset detailing the gene expression programs of circulating immune cells of ME/CFS cases at baseline and after symptom provocation. We were able to detect robust dysregulation in certain immune cells from patients, with dysregulation of classical monocytes manifesting the strongest signal. Indeed, the fraction of aberrant monocytes in ME/CFS patients correlated with the degree of disease severity. Surprisingly, platelet transcriptomes were also altered in ME/CFS, and they were the only component of the immune system that showed large-scale changes following symptom provocation.

immunology↗

bioRxiv2022

Lin28b specifies an innate-like lineage of CD8+ T cells in early life

The immune system is stratified into layers of specialized cells with distinct functions. Recently, Lin28b was shown to serve as a master regulator of fetal lymphopoiesis, programming the development of more innate-like lymphocytes in early life. However, it remains unclear whether Lin28b specifies innate functions in more conventional adaptive lymphocytes. In this report, we discovered that Lin28b promotes the development of a more innate-like lineage of CD8+ T cells that is capable of protecting the host against a wide variety of pathogens in the absence of TCR stimulation. Using RNA-seq and ATAC-seq, we found that Lin28b transcriptionally and epigenetically programs CD8+ T cells to be highly responsive to innate cytokines. We also performed scRNAseq and found that the shift from innate-like CD8+ T cells in early life to adaptive CD8+ T cells in adulthood is mediated by changes in the abundance of distinct subsets of cells. Remarkably, the innate CD8+ T cell subset predominates in early life but is also present in adult mice and humans. Collectively, our findings demonstrate that neonatal CD8+ T cells are a distinct lineage of lymphocytes that provide the host with innate defense in early life. One sentence SummaryHigh-dimensional analysis reveals how Lin28b programs neonatal CD8+ T cells for innate defense.

immunology↗

bioRxiv2020

Robust partitioning of microRNA targets from downstream regulatory changes

The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high falsepositive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networks in vivo.

genomics↗

bioRxiv2019

Evolutionary Dynamics of microRNA target sites across vertebrate evolution

MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3' untranslated regions (3'UTRs) of mRNAs, and are amongst the most highly conserved motifs within 3'UTRs. However, little is known regarding the evolutionary pressures that lead to loss and gain of such target sites. Here, we quantify the selective pressures that act upon miRNA target sites. Notably, selective pressure extends beyond deeply conserved binding sites to those that have undergone recent substitutions. Our approach reveals that even amongst ancient animal miRNAs, which exert the strongest selective pressures on 3'UTR sequences, there are striking differences in patterns of target site evolution between miRNAs. Considering only ancient animal miRNAs, we find three distinct miRNA groups, each exhibiting characteristic rates of target site gain and loss during mammalian evolution. The first group both loses and gains sites rarely. The second group shows selection only against site loss, with site gains occurring at a neutral rate, whereas the third loses and gains sites at neutral or above expected rates. Furthermore, mutations that alter strength of existing target sites are disfavored. Applying our approach to individual transcripts reveals variation in the distribution of selective pressure across the transcriptome and between miRNAs, ranging from strong selection acting on a small subset of targets of some miRNAs, to weak selection on many targets for other miRNAs. miR-20 and miR-30, and many other miRNAs, exhibit broad, deeply conserved targeting, while several other comparably ancient miRNAs show a lack of selective constraint, and a small number, including mir-146, exhibit striking evidence of rapidly evolving target sites. Our approach adds valuable perspective on the evolution of miRNAs and their targets, and can also be applied to characterize other 3'UTR regulatory motifs.\n\nAUTHOR SUMMARYGene regulation typically involves two components; the first is a regulator, and the second is a target that the regulator acts on. Examining the evolution of both components allows us to make inferences regarding how gene regulation originated and how it is changing over time. One gene regulatory system, which is widespread in mammals and other animals, relies upon regulators known as microRNAs (miRNAs), which recognize target sites within mRNAs, leading to post-transcriptional repression of the targeted mRNAs. This system has been studied extensively from the perspective of the evolution of the miRNA regulators. Moreover, a subset of the target sites themselves are known to be deeply conserved. Here, we have systematically examined the rate at which target sites for individual miRNAs are created and destroyed across mammalian evolution. We find that mutations that strengthen or weaken existing target sites are strongly disfavored. For ancient microRNAs, even recently evolved target sites are under strong selective constraint, and as miRNAs age, they tend to initially experience selection only against loss of existing target sites, and later accumulate strong selection against gain of novel target sites.

evolutionary biology↗

bioRxiv2019

CDK2 kinase activity is a regulator of male germ cell fate

The ability of men to remain fertile throughout their lives depends upon establishment of a spermatogonial stem cell (SSC) pool from gonocyte progenitors, and also maintaining the proper balance between SSC renewal and spermatogenic differentiation throughout life. Depletion of SSCs causes infertility with a Sertoli Cell Only Syndrome (SCOS) phenotype. We previously created a mouse strain in which an inhibitory phosphorylation site (Tyr15) of Cyclin-dependent kinase 2 (Cdk2) was altered. Juvenile males homozygous for this allele (Cdk2Y15S) initiate the first round of spermatogenesis, which originates from prospermatogonia, but meiocytes arrest due to chromosomal defects resembling those in Cdk2-/- mice. Subsequent waves of spermatogonial differentiation and meiosis were largely absent, leading to an SCOS-like phenotype. Here, we demonstrate that Cdk2Y15S/Y15S mice possess mitotically active GFRa1+ SSC-like cells, but they are impaired in their ability to differentiate. Marker analysis and single cell RNA-seq revealed defective differentiation of gonocytes into SSCs. Biochemical and genetic data demonstrated that Cdk2Y15S is a gain-of-function allele causing deregulated kinase activity, and its phenotypic effects could be reversed by mutating the Thr160 positive regulatory site in cis. These results demonstrate that precise temporal regulation of CDK2 activity in male germ cell development and in the cell cycle is critical for long-term spermatogenic homeostasis.

genetics↗

bioRxiv2018

MiR-146a wild-type 3’ sequence identity is dispensable for proper innate immune function in vivo

The prevailing model of microRNA function is that the \"seed\" region (nucleotides 2-8) is typically sufficient to mediate target recognition and repression. However, numerous recent studies have challenged this model, either by demonstrating extensive 3 pairing between physically defined miRNA-mRNA pairs or by showing in C. elegans that disrupted 3 pairing can result in impaired function in vivo. To test the importance of miRNA 3 pairing in a mammalian system in vivo, we engineered a mutant murine mir-146a allele in which the 5 half of the mature microRNA retains its wild-type sequence, but the 3 half has been altered to be anti-complementary. Mice homozygous or hemizygous for this mutant allele are phenotypically indistinguishable from wild-type controls and do not recapitulate any of the immunopathology previously described for mir-146a-null mice. Our results indicate that 3 pairing is dispensable for the established myeloid function of this key mammalian microRNA.\n\nSummary Blurb3 sequence identity is dispensable for the established function of a mammalian miRNA in vivo.

genetics↗

bioRxiv2018

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

Spermatogenesis is the process by which male gametes are formed from a self-renewing population of spermatogonial stem cells (SSCs) residing in the testis. SSCs represent less than 1% of the total testicular cell population, but must achieve a stable balance between self-renewal and differentiation. Once differentiation has occurred, the newly formed and highly proliferative spermatogonia must then enter the meiotic program in which DNA content is doubled, then halved twice to create haploid gametes. While much is known about the critical cellular processes that take place during the specialized cell division that is meiosis, much less is known about how the spermatocytes in the \"first-wave\" compare to those that contribute to long-term, \"steady-state\" spermatogenesis. Given the strictly-defined developmental process of spermatogenesis, this study was aimed at exploring the transcriptional profiles of developmental cell stages over the age of the animal. Using a combination of comprehensive germ cell sampling with high-resolution, single-cell-mRNA-sequencing, we have generated a reference dataset of germ cell gene expression. We show that discrete developmental stages possess significant differences in the transcriptional profiles from neonates compared to juveniles and adults. Importantly, these gene expression dynamics are also reflected at the protein level in their respective cell types. We also show differential utilization of many biological pathways with age in both spermatogonia and spermatocytes, demonstrating significantly different underlying gene regulatory programs in these cell types over the course of testis development and spermatogenic waves. This dataset represents the first unbiased sampling of spermatogonia and spermatocytes in the developing testis over developmental age, at high-resolution, single-cell depth. Not only does this analysis reveal previously unknown transcriptional dynamics of a highly transitional cell population, it has also begun to reveal critical differences in biological pathway utilization in developing spermatogonia and spermatocytes, including response to DNA damage and double-strand breaks.\n\nAuthor SummarySpermatogenesis is the process by which male gametes - mature spermatozoa - are produced in the testis. This process requires exquisite control over many developmental transitions, including the self-renewal of the germline stem cell population, commitment to meiosis, and ultimately, spermiogenesis. While much is known about molecular mechanisms regulating single transitions at single time points in the mouse, much less is understood about how the spermatogenic progenitor cells, spermatogonia, or the meiotic cells, spermatocytes, of the testis change over developmental age.\n\nOur single-cell-mRNA-sequencing analysis is the first to profile both spermatogonia and spermatocytes from neonatal mice through adulthood, revealing novel gene expression dynamics and differential utilization of biological pathways. These discoveries help us to understand how the spermatogenic progenitors of this population modulate their activity to adapt to a changing testicular environment. Furthermore, they also begin to explain previously-observed differences - and deficiencies - in spermatocytes that are derived from the first \"wave\" of spermatogenesis. Overall, this dataset is the first of its kind to comprehensively profile gene expression dynamics in male germ cell populations over time, enriching our understanding of the complex and highly-orchestrated process of spermatogenesis.

genomics↗