Biology subjects

Arora, R.

Publications and source records attributed to Arora, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Yes Associated Transcriptional Regulator 1 (YAP1) and WW Domain Containing Transcription Regulator (WWTR1) are required for murine pregnancy initiation

Endometrial stromal cell decidualization is required for pregnancy success. Although this process is integral to fertility, many of the intricate molecular mechanisms contributing to decidualization remain undefined. One pathway that has been implicated in endometrial stromal cell decidualization in humans in vitro is the Hippo signaling pathway. Two previously conducted studies showed that the effectors of the Hippo signaling pathway, YAP1 and WWTR1, were required for decidualization of primary stromal cells in culture. To investigate the in vivo role of YAP1 and WWTR1 in decidualization and pregnancy initiation, we generated a Progesterone Cre mediated partial double knockout (pdKO) of Yap1 and Wwtr1. Female pdKOs exhibited subfertility, a compromised decidualization response, partial interruption in embryo transport, blunted endometrial receptivity, delayed implantation and subsequent embryonic development, and a unique transcriptional profile. Bulk mRNA sequencing revealed aberrant maternal remodeling evidenced by significant alterations in extracellular matrix proteins at 7.5 days post-coitus in pdKO dams and enrichment for terms associated with fertility-compromising diseases like pre-eclampsia and endometriosis. Our results indicate a required role for YAP1 and WWTR1 for successful mammalian uterine function and pregnancy success.

molecular biology↗

bioRxiv2024

Analysis Pipeline to Quantify Uterine Gland Structural Variations

Technical advances in whole tissue imaging and clearing have allowed 3D reconstruction of exocrine uterine glands deep seated in the endometrium. However, there are limited gland structure analysis platforms to analyze these imaging data sets. Here we present a pipeline for segmenting and analyzing uterine gland shape. Using this segmentation methodology, we derive individual metrics to describe gland length, shape, and branching patterns. These metrics are applied to quantify gland behavior with respect to organization around the embryo and proximity of each individual unit to the uterine lumen. Using this image analysis pipeline we evaluate uterine glands at the peri-implantation time points of a mouse pregnancy. Our analysis reveals that upon embryo entry into the uterus glands show changes in length, tortuosity, and proximity to the uterine lumen while gland branch number stays the same. These shape changes aid in reorganization of the glands around the site of embryo implantation. We further apply our analysis pipeline to human and guinea pig uterine glands, extending feasibility to other mammalian species. This work serves as a resource for researchers to extract quantitative, reproducible morphological features from three-dimensional uterine gland images in order to reveal insights about functional and structural patterns.

developmental biology↗

bioRxiv2024

A novel LysinB from an F2 sub-cluster mycobacteriophage RitSun

With the growing antibiotic resistance in mycobacterial species posing a significant threat globally, there is an urgent need to find alternative solutions. Bacteriophage-derived endolysins aid in releasing phage progeny from the host bacteria by attacking the cell wall at the end of their life cycle. Endolysins are attractive antibacterial candidates due to their rapid lytic action, specificity and low risk of resistance development. In mycobacteria, owing to the complex, hydrophobic cell wall, mycobacteriophages usually synthesize two endolysins: LysinA, which hydrolyzes peptidoglycan; LysinB, which delinks mycolylarabinogalactan from peptidoglycan and releases mycolic acid. In this study, we conducted domain analysis and functional characterization of a recombinant LysinB from RitSun, an F2 sub-cluster mycobacteriophage. Several properties of RitSun LysinB are important as an antimycobacterial agent: its ability to lyse Mycobacterium smegmatis from without, a specific activity of 1.36 U/mg, higher than the reported ones and its inhibitory effect on biofilm formation. Given the impervious nature of the mycobacterial cell envelope, native endolysins ability to damage cells on exogenous applications warrants further investigation. A molecular dissection of RitSun LysinB to identify its cell wall destabilizing sequence could be utilized to engineer other native lysins as fusion proteins and expand their activity profile.

molecular biology↗

bioRxiv2024

Genome announcement and analysis of five new mycobacteriophages belonging to the F, G, K, and P clusters

Mycobacterial infections are accountable for some of the most challenging to treat diseases in humans and animals. With the rise in drug-resistant clinical isolates of Mycobacterium spp., phage therapy is emerging as a promising alternative to antibiotic therapy. Isolation of genetically diverse phages that can infect pathogenic mycobacterium species is an important exercise. Here, we present the complete genome sequences of five mycobacteriophages isolated from environmental samples using Mycobacterium smegmatis Mc2 155 as the bacterial host. These phages belong to different clusters, including F, G, K and P and contribute to the diversity of sequenced mycobacteriophages.

genomics↗

bioRxiv2024

Unlocking prophage potential: In silico and experimental analysis of a novel Mycobacterium fortuitum LysinB containing a peptidoglycan-binding domain

Endolysins are highly evolved bacteriophage-encoded lytic enzymes produced to damage the bacterial cell wall for phage progeny release. They offer promising potential as highly specific lytic proteins with a low chance of bacterial resistance. The diversity in lysin sequences and domain organization can be staggering. In silico analysis of bacteriophage and prophage genomes can help identify endolysins exhibiting unique features and high antibacterial activity, hence feeding the pipeline of narrow-spectrum protein antibiotics. Mycobacteriophage lysis cassettes mostly have two lytic enzymes, LysinA and LysinB. The enzyme LysinA targets peptidoglycan in the cell wall and possesses a modular architecture. LysinB typically contains a single domain and acts upon the mycolyl ester linkages in mycolyl-arabinogalactan-peptidoglycan (Payne et al., 2010). This study aimed to find novel LysinBs against Mycobacterium fortuitum. After a detailed in silico characterization of lysis cassettes from three M. fortuitum prophages, we chose to work on a LysinB (hereafter described as LysinB_MF) found in an incomplete prophage (phiE1336, 9.4 kb in strain E1336). LysinB_MF showed low sequence similarity with any other endolysins in the database and formed a separate clade on phylogenetic analysis. LysinB_MFs structure, extracted from the AlphaFold Protein Structure Database, demonstrated a modular architecture with two structurally distinct domains: a peptidoglycan-binding domain (PGBD) at the N-terminal and the characteristic alpha/beta hydrolase domain connected via a linker peptide. We found the alpha/beta hydrolase domain, which is the enzyme-active domain (EAD), contains the conserved Ser-Asp-His catalytic triad with a tunnel-like topology and forms intermolecular hydrogen bonds. The PGBD shows structural similarity to the cell-wall binding domain of an amidase from Clostridium acetobutylicum, hinting at its acquisition due to domain mobility. Our in silico electrostatic potential analysis suggested that PGBD might be essential to the enzyme activity. Based on our analysis, PGBD emerged as an integral constituent of enzymes with diverse functional properties and is predicted to be conserved cross-kingdom. Overall, this study highlights the importance of mining mycobacterial prophages as a novel endolysin source. It also provides unique insights into the diverse architecture of mycobacteriophage-encoded endolysins and the importance of functional domains for their catalytic activities.

molecular biology↗

bioRxiv2023

Imaging the dynamics of uterine contractions in early pregnancy

The myometrium or smooth muscle of the uterus contracts throughout the life of the organ. Uterine muscle contractility is essential for reproductive processes including sperm and embryo transport, and during the uterine cycle to remove menstrual effluent or estrus debris. Even still, uterine contractions have primarily only been studied in the context of preterm labor. This is partly due to a lack of methods for studying the contractile characteristics of the uterine muscle in the intact organ. Here, we describe an imaging-based method to evaluate the contractility of both the longitudinal and circular muscles of the uterus in the cycling stages and in early pregnancy. By transforming the image-based data into 3D spatiotemporal contractility maps, we calculate waveform characteristics of muscle contractions, including amplitude, frequency, wavelength, and velocity. We report that the native organ is highly contractile during the progesterone-dominant diestrus stage of the cycle when compared to the estrogen-dominant proestrus and estrus stages. We also observed correlations between contractility during pre-implantation stages of pregnancy and observed embryo movement patterns. During the first phase of embryo movement when clustered embryos move towards the middle of the uterine horn, uterine contractions are dynamic and non-uniform between different segments of the uterine horn. In the second phase of embryo movement, contractions are more uniform and rhythmic throughout the uterine horn. Finally, when our method is applied to Lpar3 mutant uteri that display faster embryo movement, we observe global and regional increases in contractility. Our method provides a means to understand the wave characteristics of uterine smooth muscle in response to modulators and in genetic mutants. Better understanding uterine contractility in the early pregnancy stages is critical for the advancement of artificial reproductive technologies and a possibility of modulating embryo movement during clinical embryo transfers.

developmental biology↗

bioRxiv2023

Proteolytic degradation of atrial sarcomere proteins underlies contractile defects in atrial fibrillation

(ii) ABSTRACTO_ST_ABSAimsC_ST_ABSAtrial fibrillation (AFib) is the most common cardiac rhythm disturbance. Treatment of AFib involves restoration of the atrial electrical rhythm. Following rhythm restoration, a period of depressed mechanical function known as atrial stunning occurs that involves decreased blood flow velocity and reduced atrial contractility. This suggests that defects in contractility occur in AFib and are revealed upon restoration of rhythm. The aim of this project is to define the contractile remodeling that occurs in AFib Methods and ResultsTo assess contractile function, we used a canine atrial tachypacing model of induced AFib. Mass spectrometry analysis showed dysregulation of contractile proteins in samples from AFib compared to sinus rhythm atria. Atrial cardiomyocytes showed reduced force of contraction in skinned single cardiomyocyte calcium-force studies. There were no significant differences in myosin heavy chain isoform expression. Resting tension is decreased in the AFib samples correlating with reduced full-length titin in the sarcomere. We measured degradation of other myofilament proteins including cMyBP-C, actinin, and cTnI, showing significant degradation in the AFib samples compared to sinus rhythm atria. Many of the protein degradation products appeared as discrete cleavage products that are generated by calpain proteolysis. We assessed calpain activity and found it to be significantly increased. Skinned cardiomyocytes from AFib atria showed decreased troponin I phosphorylation, consistent with the increased calcium sensitivity that was found within these cardiomyocytes. ConclusionsWith these results it can be concluded that AFib causes alterations in contraction that can be explained by both molecular changes occurring in myofilament proteins and overall myofilament protein degradation. These results provide an understanding of the contractile remodeling that occurs in AFib and provides insight into the molecular explanation for atrial stunning and the increased risk of atrial thrombus and stroke in AFib.

cell biology↗

bioRxiv2023

Murine uterine gland branching is necessary for gland function in implantation

Uterine glands are branched, tubular structures whose secretions are essential for pregnancy success. It is known that pre-implantation glandular expression of leukemia inhibitory factor (LIF) is crucial for embryo implantation, however contribution of uterine gland structure to gland secretions such as LIF is not known. Here we use mice deficient in estrogen receptor 1 (ESR1) signaling to uncover the role of ESR1 signaling in gland branching and the role of a branched structure in LIF secretion and embryo implantation. We observed that deletion of ESR1 in neonatal uterine epithelium, stroma and muscle using the progesterone receptor PgrCre causes a block in uterine gland development at the gland bud stage. Embryonic epithelial deletion of ESR1 using a mullerian duct Cre line - Pax2Cre, displays gland bud elongation but a failure in gland branching. Surprisingly, adult uterine epithelial deletion of ESR1 using the lactoferrin-Cre (LtfCre) displays normally branched uterine glands. Intriguingly, unbranched glands from Pax2Cre Esr1flox/flox uteri fail to express glandular pre-implantation Lif, preventing implantation chamber formation and embryo alignment along the uterine mesometrial-antimesometrial axis. In contrast, branched glands from LtfCre Esr1flox/flox uteri display reduced expression of glandular Lif resulting in delayed implantation chamber formation and embryo-uterine axes alignment but deliver a normal number of pups. Finally, pre-pubertal unbranched glands in control mice express Lif in the luminal epithelium but fail to express Lif in the glandular epithelium even in the presence of estrogen. These data strongly suggest that branched glands are necessary for pre-implantation glandular Lif expression for implantation success. Our study is the first to identify a relationship between the branched structure and secretory function of uterine glands and provides a framework for understanding how uterine gland structure-function contributes to pregnancy success.

developmental biology↗

bioRxiv2023

Revealing Molecular Mechanisms of Early-Onset Tongue Cancer by Spatial Transcriptomics

Tongue cancer at a young age demonstrates an increase in incidence, aggressiveness, and poor response to therapy. Classic etiological factors for head and neck tumors such as tobacco, alcohol, and human papillomavirus are not related to early-onset tongue cancer. Mechanisms of development and progression of this cancer remain unclear. In this study, we performed spatial whole-transcriptome profiling of tongue cancer in young adults compared with elderly patients. Oxidative stress, vascular mimicry, and MAPK and JAK-STAT pathways were enriched in early-onset tongue cancer. Tumor microenvironment demonstrated increased gene signatures corresponding to myeloid-derived suppressor cells, tumor-associated macrophages, and plasma cells. The invasive front was accompanied by vascular mimicry with arrangement of tumor-associated macrophages and aggregations of plasma cells and lymphocytes organized into tertiary lymphoid structures. Taken together, these results indicate that early-onset tongue cancer has distinct spatial transcriptomic features and molecular mechanisms compared to older patients. HIGHLIGHTSO_LIEarly-onset tongue cancer demonstrates extremely downregulated oxidative phosphorylation and upregulated glycolysis. C_LIO_LIMAPK pathway is the key player in the pathogenesis of tongue cancer in young adults. C_LIO_LIEarly-onset tongue cancer is characterized by JAK-STAT dependent vascular mimicry supported by tumor-associated macrophages at the invasive edge. C_LIO_LITongue cancer microenvironment in young adults enriches for immunosuppressive myeloid derived suppressor cells and demonstrates reduced antigen presentation function. C_LIO_LIThe tumor border in early-onset tongue cancer is enriched with plasma cells and lymphocytes in tertiary lymphoid structures. C_LI

cancer biology↗

bioRxiv2023

Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale

Ever-increasing volumes of sequencing data offer potential for large-scale meta-analyses to address significant biological questions. However, challenges such as insufficient data processing information, data quality concerns, and issues related to accessibility and curation often present obstacles. Additionally, most experimental biologists lack the time and expertise needed to independently analyse, manage and share their own data. To overcome these hurdles, we present Flow, a web-based platform that links bioinformatic analysis and database solutions with a user-friendly interface and web API. Flow currently accommodates a range of genomics methods and further DSL2-compliant Nextflow pipelines can be added via a simple JSON schema file. Deployable on local systems or cloud services, an instance is freely accessible to academic researchers at https://flow.bio.

bioinformatics↗

bioRxiv2023

Insights into the genomic features, lifestyle and therapeutic potential of B1 sub-cluster mycobacteriophages

BackgroundA large number (about 1200) of mycobacteriophages (phages) have been isolated on Mycobacterium smegmatis mc2155. Their genome analysis shows high sequence diversity; therefore, based on nucleotide sequence similarity and genomic architecture, the related phages have been grouped in clusters and sub-clusters. However, a deeper study of mycobacteriophages has been conducted only for a few clusters. This study explores the traits of phages belonging to the B1 sub-cluster. We have attempted to functionally annotate and experimentally characterize B1 phages to get an insight into their biology and explore their therapeutic potential. MethodsAnalysis of B1 sub-cluster phage genomes to understand their key characteristics & lifestyle and to determine the putative function of hypothetical proteins (HPs), we developed a framework with a specific set of computational tools available online. For the experimental characterization, mycobacteriophages were isolated from environmental samples and were examined for their morphology, lysogeny status, effect on biofilm and activity against drug-resistant M. smegmatis. The B1 sub-cluster phages were identified by PCR using the specific primers. ResultsWe have predicted the function of about 55% of the 77 representative proteins in B1 phages, which were previously deemed hypothetical. We studied ten B1 phages (Phages 1-10) which included their morphological characteristics, lysogeny status and antibiofilm activity. TEM analysis, showing an average head & tail size of 65 nm and 202.12 nm, respectively. The turbid morphology of several plaques suggested these phages to be temperate. To verify, we tested their potential to lysogenize M. smegmatis and later found the spontaneous release from the putative lysogens. Interestingly, a putative RepA-like protein was identified in B1 phage genomes, indicating a possibility of extrachromosomal replication of prophages. Further, the impact of Phages 1-10 on M. smegmatis biofilm was found to be potent; the highest inhibitory and disruptive effect of phages (at a fixed titre of 108 pfu/ml) was 64% and 46%, respectively. Also, all ten phages could kill 4XR1 (the isoniazid-resistant M. smegmatis strain). ConclusionWe believe this combination of experimental analysis and exploration of genomic features of mycobacteriophages belonging to a sub-cluster can provide deeper insights into mycobacteriophage biology and also help in understanding their therapeutic potential.

microbiology↗

bioRxiv2023

Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells.

Myometrial stem/progenitor cells (MyoSPCs) have been proposed as the cells of origin for uterine fibroids, which are benign tumors that develop in the myometrium of most reproductive age women, but the identity of the MyoSPC has not been well established. We previously identified SUSD2 as a possible MyoSPC marker, but the relatively poor enrichment in stem cell characteristics of SUSD2+ over SUSD2- cells compelled us to find better discerning markers for more rigorous downstream analyses. We combined bulk RNA-seq of SUSD2+/- cells with single cell RNA-seq to identify markers capable of further enriching for MyoSPCs. We observed seven distinct cell clusters within the myometrium, with the vascular myocyte cluster most highly enriched for MyoSPC characteristics and markers, including SUSD2. CRIP1 expression was found highly upregulated in both techniques and was used as a marker to sort CRIP1+/PECAM1- cells that were both enriched for colony forming potential and able to differentiate into mesenchymal lineages, suggesting that CRIP1+/PECAM1- cells could be used to better study the etiology of uterine fibroids.

developmental biology↗

bioRxiv2022

Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response

We performed the first integrative single-cell and spatial transcriptomic analysis on HPV-negative oral squamous cell carcinoma (OSCC) to comprehensively characterize tumor core (TC) and leading edge (LE) transcriptional architectures. We show that the TC and LE are characterized by unique transcriptional profiles, cellular compositions, and ligand-receptor interactions. We demonstrate that LE regions are conserved across multiple cancers while TC states are more tissue specific. Additionally, we found our LE gene signature is associated with worse clinical outcomes while the TC gene signature is associated with improved prognosis across multiple cancer types. Finally, using an in silico modeling approach, we describe spatially-regulated patterns of cell development in OSCC that are predictably associated with drug response. Our work provides pan-cancer insights into TC and LE biologies, a platform for data exploration (http://www.pboselab.ca/spatial_OSCC/) and is foundational for developing novel targeted therapies.

cancer biology↗

bioRxiv2022

Analysis of Inbred Mouse strains' High-Impact Genotype-phenotype Hypotheses (AIMHIGH) reveals novel disease-causing candidate genes

Inbred mouse strains reveal the molecular basis of mammalian traits and diseases, particularly recessive ones. We utilized mouse community curated resources to set up an automated screen to discover novel testable gene function hypotheses. Using 11,832 community contributed strain-differentiating experiments and trait presence/absence scoring, we searched for all experiments where strains can be split by their phenotypic values (e.g., high vs. low responders). Then, using 48 sequenced strains, we found one or more candidate gene for each experiment where homozygous high-impact variants (such as stopgain, frameshifts) segregate strains into these same binary grouping. Our approach rediscovered 212 known gene-phenotype relationships, almost always highlighting potentially novel causal variants, as well as thousands of gene function hypotheses. To help find the most exciting hypotheses, we improved the state of the art in machine learning driven literature-based discovery (LBD). Reading on our top 3 ranked candidate genes per experiment reveals 80% of rediscovered relationships, compared to 5% reading at random. We proposed 1,842 novel gene-phenotype testable hypotheses using our approach. We built a web portal at aimhigh.stanford.edu to allow researchers to view all our testable hypotheses in detail. Our open-source code can be rerun as more sequenced strains and phenotyping experiments become available.

genomics↗

bioRxiv2022

Repertoire-Scale Measures of Antigen Binding

Antibodies and T-cell receptors (TCRs) are the fundamental building blocks of adaptive immunity. Repertoire-scale functionality derives from their epitope-binding properties, just as macroscopic properties like temperature derive from microscopic molecular properties. However, most approaches to repertoire-scale measurement, including sequence diversity and entropy, are not based on antibody or TCR function in this way. Thus, they potentially overlook key features of immunological function. Here we present a framework that describes repertoires in terms of the epitope-binding properties of their constituent antibodies and TCRs, based on analysis of thousands of antibody-antigen and TCR-peptide-major-histocompatibility-complex binding interactions and over 400 high-throughput repertoires. We show that repertoires consist of loose overlapping classes of antibodies and TCRs with similar binding properties. We demonstrate the potential of this framework to distinguish specific responses vs. bystander activation in influenza vaccinees, stratify CMV-infected cohorts, and identify potential immunological "super-agers." Classes add a new dimension to assessment of immune function.

immunology↗

bioRxiv2022

Ventral forebrain organoids derived from individuals with schizophrenia recapitulate perturbed striatal gene expression dynamics of the donor's brains

Schizophrenia (SCZ) is a brain disorder originating during neurodevelopment with complex genetic and environmental etiologies. Despite decades of clinical evidence of altered striatal function in affected patients, its cellular and molecular underpinnings remain unclear. Here, to explore neurodevelopmental alterations in the striatum associated with SCZ, we established a method for the differentiation of iPS cells into ventral forebrain organoids. Given substantial genetic heterogeneity among individuals, which can obscure disease-associated phenotypes, we generated organoids from postmortem dural fibroblast-derived iPS cells of 3 patients and 4 healthy control individuals with nonoverlapping polygenic risk score (PRS) for SCZ and whose genotype and postmortem caudate transcriptomic data were profiled in the Brainseq neurogenomics consortium. Single cell RNA sequencing (scRNA-seq) analyses of the organoids revealed differences in developmental trajectory between SCZ cases and controls in which inhibitory neurons from patients exhibited accelerated maturation. Furthermore, we found a significant overlap of genes upregulated in the inhibitory neurons in SCZ organoids with upregulated genes in postmortem caudate tissues from patients with SCZ compared with control individuals, including the donors of our iPS cell cohort. Our findings suggest that striatal neurons in the patients with SCZ carry abnormalities that originated during early brain development and a ventral forebrain striatal organoid model can recapitulate those neurodevelopmental phenotypes in a dish.

neuroscience↗

bioRxiv2022

Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism

X-linked Dystonia-Parkinsonism (XDP) is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. The mechanisms underlying regional differences in degeneration and age of onset are unknown. Developing therapeutics that target XDP-related mechanisms requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is due, in part, to either a partial loss of TAF1 function and/or a SVA-driven pathological gain of function. A disease-specific SINE-VNTR-Alu (SVA) retrotransposon insertion occurs within intron 32 of TAF1, a subunit of TFIID involved in transcription initiation. While all XDP males are usually clinically affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight iPSC lines from XDP female carrier individuals, and identified isogenic lines where one clonal iPSC line expressed the wild-type X, and the two other clonal iPSC lines expressed the XDP haplotype. Furthermore, we characterized XDP-relevant transcript expression variation in humans, and found that SVA-F expression decreases slightly after 30 years of age in the neurotypical human brain and that TAF1 is modestly decreased in the majority of female samples. Uniquely in the caudate nucleus, TAF1 expression is not sexually dymorphic and decreased after 15 years of age. These findings indicate that regional-, age- and sex-specific mechanisms regulate TAF1, highlighting the importance of disease-relevant models and postmortem tissue analysis. We propose that the decreased TAF1 expression in the adult caudate may synergize with the XDP-specific partial loss of TAF1 function in patients, thereby passing a minimum threshold of TAF1 function, and triggering degeneration in the neostriatum. Significance StatementXDP is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due to a partial loss of TAF1 function. While all XDP males are usually affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight stem cell lines from XDP female carrier individuals. Furthermore, we found that, uniquely in the caudate nucleus, TAF1 expression decreases after adolescence in healthy humans. We hypothesize that the decrease of TAF1 after adolescence in human caudate, in general, may underlie the vulnerability of the adult neostriatum in XDP.

neuroscience↗

bioRxiv2022

Endometriotic Organoids as an In Vitro Model of Endometriotic Lesion Development.

The development and progression of endometriotic lesions are poorly understood, but immune cell dysfunction and inflammation are closely associated with the pathophysiology of endometriosis. A lack of suitable 3D in vitro models permitting the study of interactions between cell types and the microenvironment is a contributing factor. To address this limitation, we developed endometriotic organoids (EO) to explore the role of epithelial-stromal interactions and model peritoneal cell invasion associated with lesion development. Using a non-adherent microwell culture system, spherical organoids were generated with endometriotic epithelial cells (12Z) combined with immortalized endometriotic stromal cells (iEc-ESC) or immortalized uterine stromal cells (iHUF). Organoids self-organized with stromal cells occupying the center and epithelial cells on the periphery of the organoid. Endometriotic organoids (EO), containing iEc-ESC, resulted in the development of stratified 12Z epithelial cells compared to those with iHUF where the 12Z cells developed as a single layered epithelium. Transcriptomic analysis found 4,522 differentially expressed genes (DEG) between EO and 12Z/iHUF organoids, and the top DEG included increased expression of interleukins and prostaglandin synthase enzymes. An overlap of the EO DEG with baboon endometriotic lesions was highly significant. Finally, to mimic invasion of endometrial tissue into the peritoneum, a model was developed using EO and extracellular matrix containing human peritoneal mesothelial cells (LP9). Invasion of EO into the extracellular matrix-LP9 layer was increased in presence of estrogen or THP1-derived proinflammatory macrophages. Taken together, our results strongly support the concept that EO are an appropriate model for dissecting mechanisms that contribute to endometriotic lesion development. One Sentence SummaryEndometriotic organoids are an appropriate model to study epithelial-stromal interactions and model cell invasion associated with lesion development.

cell biology↗