Biology subjects

Patel, D.

Publications and source records attributed to Patel, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Transcriptional Landscape of THAP9 across Oligodendrocyte Developmental Stages: Molecular Mechanisms and Network Analysis

Oligodendrocyte maturation and myelination are critical processes in human neurodevelopment, and their dysregulation is linked to numerous neurological disorders. While model organisms have provided insight into these processes, human-specific regulatory mechanisms remain poorly understood. This study investigated human THAP9, a protein homologous to the Drosophila P-element transposase, whose function in oligodendrocytes remains unknown. An analysis of publicly available RNA-sequencing data and H3K27ac ChIP-sequencing data from oligodendrocyte progenitor cells (OPCs) and mature oligodendrocytes (MOs) revealed significant upregulation of THAP9 during oligodendrocyte maturation. Co-expression analysis demonstrated a strong correlation with established markers of oligodendrocyte development, including myelin-associated genes (MOG, MBP) and key transcriptional regulators (PDGFRA, SOX5, SOX6, SOX11). THAP9 lacks homologues in mice, highlighting potential human-specific mechanisms in oligodendrocyte development and emphasising the importance of studying species-specific factors in neurodevelopment. Our findings suggest that THAP9 is a novel human-specific regulator of oligodendrocyte maturation and opens new avenues for studying myelination disorders.

genomics↗

bioRxiv2024

The N-terminus of the Chlamydia trachomatis effector Tarp engages the host Hippo pathway

Chlamydia trachomatis is an obligate, intracellular Gram-negative bacteria and the leading bacterial STI in the United States. Chlamydias developmental cycle involves host cell entry, replication within a parasitophorous vacuole called an inclusion, and induction of host cell lysis to release new infectious particles. During development, Chlamydia manipulates the host cell biology using various secreted bacterial effectors. The early effector Tarp is important for Chlamydia entry via its well-characterized C-terminal region which can polymerize and bundle F-actin. In contrast, not much is known about the function of Tarps N-terminus (N-Tarp), though this N-terminal region is present in many Chlamydia species. To address this, we use Drosophila melanogaster as an in vivo cell biology platform to study N-Tarp-host interactions. Drosophila development is well-characterized such that developmental phenotypes can be traced back to the perturbed molecular pathway. Transgenic expression of N-Tarp in Drosophila tissues results in phenotypes consistent with altered host Hippo signaling. The Salvador-Warts-Hippo pathway is a conserved signaling cascade that regulates host cell proliferation and survival during normal animal development. We studied N-Tarp function in larval imaginal wing discs, which are sensitive to perturbations in Hippo signaling. N-Tarp causes wing disc overgrowth and a concomitant increase in adult wing size, phenocopying overexpression of the Hippo co-activator Yorkie. N-Tarp also causes upregulation of Hippo target genes. Last, N-Tarp-induced phenotypes can be rescued by reducing the levels of Yorkie, or the Hippo target genes CycE and Diap1. Thus, we provide the first evidence that the N-terminal region of the Chlamydia effector Tarp is sufficient to alter host Hippo signaling and acts upstream of the co-activator Yorkie. Chlamydia alters host cell apoptosis during infection, though the exact mechanism remains unknown. Our findings implicate the N-terminal region of Tarp as a way to manipulate the host Hippo signaling pathway, which directly influences cell survival. Author SummaryChlamydia-infected cells are known to be resistant to apoptotic cues, facilitating the successful completion of its infectious cycle. The exact molecular mechanism of apoptosis inhibition is unknown and the search for secreted effectors that mediate this is ongoing. We developed Drosophila melanogaster as a platform to study Chlamydia effector function in vivo without the confounding influence of actual infection. Genetic tools make it easy to generate transgenic flies and express bacterial effectors of interest in any tissue, allowing for discovery of new function based on observed developmental phenotypes. Using this platform, we showed that the N-terminal region of the early effector Tarp intersects with the host Hippo pathway, causing upregulation of Hippo target genes. Interestingly, the Hippo pathway directly controls the expression of potent inhibitors of apoptosis (IAPs). Our findings support a possible link between a secreted effector, Tarp and its N-terminal region, and the Hippo pathway to block apoptosis during infection.

microbiology↗

bioRxiv2024

DOCK8 regulates a mechanosensitive actin redistribution that maintains immune cell cohesion and protects the nucleus during migration

Immune cells navigate through complex 3-dimensional tissue architectures, utilizing an amoeboid mode of migration, characterized by extensive cellular deformation, low adhesion, and high cell velocities. In the absence of expression of Dedicator of Cytokinesis 8 (Dock8), a gene identified with loss-of-function mutations in immunodeficiency, cells become entangled during migration through dense, confined environments and consequently undergo catastrophic cell rupturing, while migration on 2D surfaces remains entirely intact. Here we investigated the specific cytoskeletal defect of Dock8-deficient activated T cells, showing that even prior to entanglement they display a striking difference in F-actin distribution compared to wild type (WT) cells. We describe a central pool of F-actin in WT murine and human T cells which is absent in Dock8 KO T cells, and determine that the relocalization of F-actin is a mechanoresponsive circuit, emerging only when cells are very confined. Our works shows that the central actin pool is nucleo-protective, reducing nuclear deformation and DNA damage during confined migration. We identify the Hippo-pathway kinase Mst1 as a co-mediator of this mechanosensitive pathway in conjunction with Dock8, allowing for cell cohesion and survival during migration through complex environments.

immunology↗

bioRxiv2024

Antiviral insulin signaling during West Nile virus infection results in viral mutations

Arthropod-borne viruses or arboviruses, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV) pose significant threats to public health. It is imperative to develop novel methods to control these mosquito-borne viral infections. We previously showed that insulin/insulin-like growth factor-1 signaling (IIS)-dependent activation of ERK and JAK-STAT signaling has significant antiviral activity. Continuous immune pressure can lead to adaptive mutations of viruses during infection. We aim to elucidate how IIS-signaling in mosquitoes selects for West Nile virus escape variants, to help formulate future transmission blocking strategies. We hypothesize that passage of WNV under activation of IIS will induce adaptive mutations or escape variants in the infecting virus. To test our hypothesis, WNV was serially passaged through Culex quinquefasciatus Hsu cells in the presence or absence of bovine insulin to activate IIS antiviral pressure. We sequenced WNV genes encoding for E, NS2B, NS3, and NS5 and identified variants in E and NS5 arising from IIS antiviral pressure. In parallel to the genetic analyses, we also report differences in the levels of virus replication and Akt activation in human cells using virus passaged in the presence or absence of insulin. Finally, using adult Culex quinquefasciatus, we demonstrated the enhancement of immune response gene expression in virus-infected mosquitoes fed on insulin, compared to control. Notably, virus collected from insulin-fed mosquitoes contained a non-synonymous mutation in NS3. These results contribute towards achieving our long-term goal of manipulating mosquito IIS-dependent antiviral immunity to reduce WNV or other flavivirus transmission to mammalian hosts.

immunology↗

bioRxiv2024

Subcellular visualization of the distribution of atmospheric dinitrogen fixed by Gluconacetobacter diazotrophicus bacteria in maize

Plants normally obtain the nitrogen required for growth through their roots, often after application of synthetic fertilizer to the soil, at great cost to the environment and climate. Inoculation of plant seeds with nitrogen-fixing bacteria is a promising alternative means of supplying plants the nitrogen they require in an environmentally friendly manner. When maize seeds inoculated with nitrogen-fixing Gluconacetobacter diazotrophicus (Gd) are grown for two weeks in a 15N2 air environment, nanoscale secondary ion mass spectrometry (NanoSIMS) imaging shows the distribution of fixed nitrogen with subcellular resolution, with the majority being incorporated heterogeneously into chloroplasts. Chloroplasts, as the chief energy source that drives plant growth via photosynthesis, are vital for healthy plant growth and these results help explain the observations of enhanced growth rates in plants containing this nitrogen fixing bacteria. The methodology provides a template upon which more powerful, correlative studies combining genomic and/or spatial transcriptomic methods may be based.

plant biology↗

bioRxiv2024

Light-induced Extracellular Vesicle Adsorption

The role of extracellular vesicles (EVs) in human health and disease has garnered considerable attention over the past two decades. However, while several types of EVs are known to interact dynamically with the extracellular matrix and there is great potential value in producing high-fidelity EV micropatterns, there are currently no label-free, high-resolution, and tunable platform technologies with this capability. We introduce Light-induced Extracellular Vesicle Adsorption (LEVA) as a powerful solution to rapidly advance the study of matrix- and surface-bound EVs and other particles. The versatility of LEVA is demonstrated using commercial GFP-EV standards, EVs from glioblastoma bioreactors, and E. coli outer membrane vesicles (OMVs), with the resulting patterns used for single EV characterization, single cell migration on migrasome-mimetic trails, and OMV-mediated neutrophil swarming. LEVA will enable rapid advancements in the study of matrix- and surface-bound EVs and other particles, and should encourage researchers from many disciplines to create novel diagnostic, biomimetic, immunoengineering, and therapeutic screening assays.

bioengineering↗

bioRxiv2024

Effect of Emoji on Autonomic Nervous System: Evidence from EDA and RSA studies

BackgroundFacial expression, gesture, and posture play an important role in perceiving emotions during communication. In virtual communication platforms, users have devised and learned to use a variety of expressive emojis along with text messages to express certain emotions. The effect of emojis on human psychology and associated autonomic responses is still vague. MethodsA total of 100 healthy individuals (50 males and 50 females) aged between 18-40 years were recruited. Electrodermal activity (skin conductance level (SCL) and skin conductance response (SCR) amplitude) and Respiratory Sinus Arrhythmia (RSA) were assessed during the Emotional Stroop Task (EST). EST having expressive emojis superimposed with the congruent and incongruent words was used. ResultMean SCL and SCR amplitude was significantly increased during EST in incongruent and congruent blocks as compared to neutral block (respectively: 14.64 {+/-} 6.73, 12.99 {+/-} 6.26 vs. 7.75 {+/-} 4.93 S, p < 0.001 and 0.182 {+/-} 0.168, 0.158 {+/-} 0.134 vs. 0.021 {+/-} 0.015 S, p < 0.001). RSA was significantly decreased in incongruent and congruent blocks as compared to neutral blocks (respectively: 36.47 {+/-} 10.53, 39.40 {+/-} 10.15 vs. 48.66 {+/-} 10.27 msec2, p < 0.001). We found an increased sympathetic activity and parasympathetic withdrawal while performing the task. ConclusionThe results of this study suggested that emojis are adequate stimuli to elicit autonomic responses and change both sympathetic (EDA) as well as parasympathetic responses (RSA). Males and females showed similar autonomic arousal for emoji but the baseline emotional status was different for both genders.

physiology↗

bioRxiv2024

Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes

The combination of immunotherapy and epigenetic therapy is emerging as a promising approach for cancer therapy. Epigenetic therapy can induce derepression of transposable elements (TEs) that play a major role in activation of immune response against cancer cells. However, the molecular mechanism of TE regulation by distinct chromatin modifier enzymes (CME) and in the context of p53 is still elusive. Here, we used epigenetic drugs to inhibit distinct CMEs in p53 wild-type and p53-mutant colorectal and esophageal cancer cells. We show that distinct TEs subfamilies are derepressed by inhibition of different CMEs in a cell-type specific manner with loss of p53 resulting in stronger TE derepression. We show that KAP1, a known repressor of TEs, associates with stronger derepression of specific TE subfamilies such as LTR12C, indicating that KAP1 also has an activating role in TE regulation in cancer cells upon co-inhibition of DNMT and HDAC. Co-inhibition of DNMT and HDAC activates immune response by inducing inverted repeat Alu expression, reducing ADAR1-mediated Alu RNA editing and inducing cell type-specific TE-chimeric transcript expression. Collectively, our study demonstrates that inhibition of different CMEs results in derepression of distinct TEs in cell type-specific manner and by utilizing distinct mechanistic pathways, providing insights for epigenetic therapies that could selectively enhance anti-tumor immunity in distinct cancer types.

cancer biology↗

bioRxiv2023

Transcriptome-wide analysis of primary human endothelial cell responses to 1 hour of protein translation inhibition identify nonsense mediated decay targets and a non-coding SLC11A2 exon as an acute biomarker

Nonsense mediated decay (NMD) lowers the cellular concentration of spliced RNAs harboring premature termination codons (PTC), and inhibition has been proposed as a potential therapeutic method. Conversely, NMD plays regulatory roles throughout the eukaryotic kingdom, including when protein translation is inhibited acutely as part of the integrated stress response. To define tools for endothelial evaluations of therapeutic NMD inhibition, and quantification of subtle cellular stress states, natural endothelial-expressed targets were examined via whole transcriptome RNA sequencing of primary human microvascular endothelial cells (HMECs) treated for 1h with cycloheximide, a protein translation and NMD inhibitor. Genes differentially expressed after 1h cycloheximide overlapped with genes differentially expressed many days after NMD-specific knockdown in other cell types. For endothelial cells, customized novel scripts used 255,500 exons in media-treated HMEC and 261,725 exons in cycloheximide-treated HMEC to predict 1h cycloheximide-stabilized exons. RT-PCR and RNASeq validations in other endothelial cells highlighted exon 3B of the iron transporter SLC11A2 (also known as NRAMP2/DMT1) as a novel exon in a transcript most consistently stabilized. Exact junctional alignments to SLC11A2 exon 3B were confirmed in blood outgrowth endothelial cells (BOECs) from 3 donors at mean 5.9% (standard deviation 2.0%) of adjacent constitutive exon expression, increasing 3.7-fold following 1h treatment with cycloheximide. Relevance beyond endothelial cells is supported by SLC11A2s wide expression profiles, genome-wide associations with microcytic anemia, biomarker status for poor prognosis ovarian cancer, and exon 3B sequence in RefSeq non-coding transcript NR_183176.1. The studies contribute understanding to functions affected acutely by NMD/translation inhibition and provide a stimulus for further studies in experimental, stress, and therapeutic settings.

molecular biology↗

bioRxiv2023

Rab35 is required for embryonic development and kidney and ureter homeostasis through regulation of epithelial cell junctions

Structured AbstractO_ST_ABSBackgroundC_ST_ABSRab35 is a member of a GTPase family of endocytic trafficking proteins. Studies in cell lines have indicated that Rab35 participates in cell adhesion, polarity, cytokinesis, and primary cilia length and composition. Additionally, sea urchin Rab35 regulates actin organization and is required for gastrulation. In mice, loss of Rab35 in the CNS disrupts hippocampal development and neuronal organization. Outside of the CNS, the functions of mammalian Rab35 in vivo are unknown. MethodsWe generated and analyzed the consequences of both congenital and conditional null Rab35 mutations in mice. Using a LacZ reporter allele, we assessed Rab35 expression during development and postnatally. We assessed Rab35 loss in the kidney and ureter using histology, immunofluorescence microscopy, and western blotting. ResultsCongenital Rab35 loss of function caused embryonic lethality: homozygous mutants arrested at E7.5 with cardiac edema. Conditional loss of Rab35, either during gestation or postnatally, caused hydronephrosis. The kidney and ureter phenotype were associated with disrupted actin cytoskeletal architecture, altered Arf6 epithelial polarity, reduced adherens junctions, loss of tight junction formation, defects in EGFR expression and localization, disrupted cell differentiation, and shortened primary cilia. ConclusionRab35 is essential for mammalian development and the maintenance of kidney and ureter architecture. Loss of Rab35 leads to non-obstructive hydronephrosis, making the Rab35 mutant mouse a novel mammalian model to study mechanisms underlying this disease. Significance StatementHydronephrosis, distention of the renal calyces and pelvis, affects 1 in 100 infants. Most cases of hydronephrosis are associated with obstruction. Non-obstructive hydronephrosis is typically associated with impaired ureter development, and requires surgical intervention. Here, we describe a mouse model of non-obstructive hydronephrosis caused by mutations in Rab35. Hydronephrosis in Rab35 mutants is associated with the inability to maintain epithelial cell junctions, defects in EGFR expression, and altered urothelium and smooth muscle integrity of the ureter. The Rab35 mutant mouse is a novel model to study mechanisms and treatment strategies for non-obstructive hydronephrosis.

cell biology↗

bioRxiv2023

Identifying novel links between cardiovascular disease and insomnia by Drosophila modeling of genes from a pleiotropic GWAS locus

Insomnia symptoms have been associated with cardiovascular disease (CVD), doubling the risk of incident CVD, but specific shared pathways remain poorly understood. Recently, genome-wide association studies (GWAS) identified genetic loci significantly associated with insomnia symptoms, including one locus (near ATP5G1, UBE2Z, SNF8, IGF2BP1, and GIP) that was previously linked with CVD in an independent GWAS. To evaluate the cell-autonomous role of genes within the 17q21 insomnia and CVD locus, we used Drosophila melanogaster models to perform tissue-specific RNAi knockdown of four conserved orthologues (ATPSynC, Lsn, Bruce, and Imp) in neurons and in the heart. To identify non-cell-autonomous mechanisms, we also assessed heart function in flies with neuronal-specific knockdown and sleep in flies with heart-specific knockdown. Neuronal and cardiac-specific RNAi knockdown of several of the genes conserved in Drosophila led to compromised sleep quality and impaired cardiac performance. Neuronal-specific knockdown of ATPSynC, Imp, and Lsn led to disruptions in sleep quantity and quality. Knockdown of ATPSynC and Lsn in the heart led to significantly reduced cardiac performance without and with cardiac dilation, respectively. Furthermore, Lsn and ATPSynC-suppressed hearts showed disruption in the actin-containing myofibrillar organization and led to a significantly shortened lifespan. Non-cell-autonomous effects were seen both from neurons to heart (Imp), and heart to neurons (ATPSynC and Lsn). Specifically, Imp neuronal knockdown led to a significantly compromised cardiac function, whereas knockdown of ATPSynC and Lsn in the heart led to compromised sleep characterized by increased sleep fragmentation, both accompanied by an increase in inflammation through Upd3, an inflammatory cytokine, in the heart or head, respectively. We also demonstrate disrupted cardiac function or sleep upon cardiac-specific or neuronal-specific overexpression of Upd3, respectively, showing a direct link between cardiac dysfunction and sleep disruption through inflammation. Our study reveals tissue-specific and cross-tissue consequences of Drosophila knockdown of multiple genes at this locus, providing novel insights into potential genetic mechanisms linking CVD and insomnia. Our study also highlights the key role of these four conserved genes in both sleep and cardiac function.

physiology↗

bioRxiv2023

Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication

Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.

evolutionary biology↗

bioRxiv2023

Evaluating Study Design Rigor in Preclinical Cardiovascular Research: A Replication Study

BackgroundMethodological rigor remains a priority in preclinical cardiovascular research to ensure experimental reproducibility and high-quality research. Limited reproducibility diminishes the translation of preclinical discoveries into medical practice. In addition, lack of reproducibility fosters uncertainty in the publics acceptance of reported research results. MethodsWe evaluated the reporting of methodological practices in preclinical cardiovascular research studies published in leading scientific journals by screening articles for the inclusion of the following study design elements (SDEs): considering sex as a biological variable, randomization, blinding, and sample size power estimation. We screened for these SDEs across articles regarding preclinical cardiovascular research studies published between 2011 and 2021. We replicated and extended a study published in 2017 by Ramirez et al. We hypothesized a higher SDE inclusion across preclinical studies over time, that preclinical studies that include human and animal substudies within the same study will exhibit greater SDE inclusion than animal-only preclinical studies, and that a difference exists in SDE usage between large and small animal models. ResultsSDE inclusion was low; with 15.2% of animal-only studies including both sexes as a biological variable, 30.4% including randomization, 32.1% including blinding, and 8.2% including sample size estimation. The incorporation of SDEs did not significantly increase over the ten-year timeframe in the screened articles. Randomization and sample size estimation differed significantly between animal and human substudies (corrected p=1.85e-05 and corrected p=3.81e-07, respectively.) ConclusionsEvidence of methodological rigor varies depending on the study type and model organisms used. From 2011-2021, SDE reporting within preclinical studies has not increased, suggesting more work is needed to foster the inclusion of rigorous study design elements in cardiovascular research.

systems biology↗

bioRxiv2023

The Neurochemical Mechanisms Underlying the Enhancing Effects of Rewards and Punishments on Motor Performance

Monetary rewards and punishments enhance motor performance and are associated with corticospinal excitability (CSE) increases within the motor cortex (M1) during movement preparation. However, such CSE changes have unclear origins; they could stem from increased glutamatergic (GLUTergic) facilitation and/or decreased type A gamma-aminobutyric acid (GABAA)-mediated inhibition within M1. To investigate this, paired-pulse transcranial magnetic stimulation was used to assess GLUTergic facilitation and GABAA inhibition within M1 whilst participants prepared to execute 4-element finger-press sequences. Behaviourally, rewards and punishments enhanced both reaction and movement times. Neurochemically, regardless of rewards or punishments, a digit-specific increase in GLUTergic facilitation and digit-unspecific decrease in GABAA inhibition occurred during preparation as movement onset approached. In parallel, both rewards and punishments non-specifically increased GLUTergic facilitation, but only rewards non-specifically decreased GABAA inhibition during preparation. This suggests that, to enhance performance, rewards both increase GLUTergic facilitation and decrease GABAA inhibition whilst punishments selectively increase GLUTergic facilitation. A control experiment revealed that such changes were not observed post-movement as participants processed reward and punishment feedback, indicating they were selective to movement preparation. Collectively, these results map the neurochemical changes in M1 by which incentives enhance motor performance.

neuroscience↗

bioRxiv2023

Dynamic Bayesian modeling of the social behavior of Drosophila melanogaster

Organismal behavior has always been a challenge to understand. Insects are one of the amenable systems used to understand behavior. A striking variety of insect behaviors gain support from genetic and physiological studies. Drosophila, a widely studied model organism due to its known molecular pathways, has also been popular in behavioral studies. Several behavioral traits in Drosophila including mating, locomotion, and oviposition choice have been traced to the neuronal level. Yet, the results of behavioral analyses are equivocal since they often overlook the external milieu, such as social context, which evidentially influences behavior. There have been many attempts to model Drosophila behavior, however, all have some fundamental issues like lack of complexity, limitation to isolated organisms, and lack of explainability. Here, we model the behavior of a pair of Drosophila melanogaster flies using a novel Dynamic Bayesian Network based approach to better understand behavior in a social context. Two models are proposed, each of which is further used as a predictor for predicting the behavior of both the flies in the pair. They are evaluated on an existing dataset and achieve a remarkable performance: 98.22% and 98.32% accuracy on the two models. Our modeling approach could be applied in predicting animal behaviors in a wide variety of contexts to support existing behavioral studies.

animal behavior and cognition↗

bioRxiv2023

Brain-localized CD4 and CD8 T cells perform correlated random walks and not Levy walks

For survival of the organism T cells must efficiently control pathogens invading different peripheral tissues but whether such control (and lack of thereof) is achieved by utilizing different movement strategies remains poorly understood. Liver-localized CD8 T cells perform correlated random walks -- a type of a Brownian walk - in liver sinusoids but in some condition these T cells may also perform Levy flights - rapid and large displacements by floating with the blood flow. CD8 T cells in lymph nodes or skin also undergo Brownian walks. A recent study suggested that brain-localized CD8 T cells, specific to Toxoplasma gondii, perform generalized Levy walks - a walk type in which T cells alternate pausing and displacing long distances -- which may indicate that brain is a unique organ where T cells exhibit movement strategies different from other tissues. We quantified movement patterns of brain-localized Plasmodium berghei-specific CD4 and CD8 T cells by using well-established statistical and computational methods. Interestingly, we found that T cells change their movement pattern with time since infection and that CD4 T cells move faster and turn less than CD8 T cells. Importantly, both CD4 and CD8 T cells move in the brain by correlated random walks without long displacements challenging previous observations. We have also re-analyzed the movement data of brain-localized CD8 T cells in T. gondii -infected mice and found no evidence of Levy walks. We hypothesize that the previous conclusion of Levy walks of T. gondii-specific CD8 T cells in the brain was reached due to missing time-frames in the data that create an impression of large displacements between assumed-to-be-sequential movements. Taken together, our results suggests that movement strategies of CD8 T cells are largely similar between LNs, liver, and the brain and consistent with correlated random walks and not Levy walks.

immunology↗

bioRxiv2022

Transposable elements as tissue-specific enhancers in cancers of endodermal lineage

Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we have utilized unbiased massively parallel reporter assay data using whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identified distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.

genomics↗

bioRxiv2022

Genomic variations drive phenotypic heterogeneity in pancreatic cancer cells

ObjectivesTo evaluate the suitability of the MIA PaCa-2 cell line for studying pancreatic cancer intratumor heterogeneity, we aim to further characterize the nature of MIA PaCa-2 cells phenotypic, genomic, and transcriptomic heterogeneity. MethodsMIA PaCa-2 single-cell clones were established through flow cytometry. For the phenotypic study, we quantified the cellular morphology, proliferation rate, migration potential, and drug sensitivity of the clones. The chromosome copy number and transcriptomic profiles were quantified using SNPa and RNA-seq, respectively. ResultsFour MIA PaCa-2 clones showed distinctive phenotypes, with differences in cellular morphology, proliferation rate, migration potential, and drug sensitivity. We also observed a degree of genomic variations between these clones in form of chromosome copy number alterations and single nucleotide variations, suggesting the genomic heterogeneity of the population, and the intrinsic genomic instability of MIA PaCa-2 cells. Lastly, transcriptomic analysis of the clones also revealed gene expression profile differences between the clones, including the uniquely regulated ITGAV, which dictates the morphology of MIA PaCa-2 clones. ConclusionsMIA PaCa-2 is comprised of cells with distinctive phenotypes, heterogeneous genomes, and differential transcriptomic profiles, suggesting its suitability as a model to study the underlying mechanisms behind pancreatic cancer heterogeneity.

cancer biology↗