title: Transcriptomic analysis of rps6 mutants in Arabidopsis thaliana

city: Philadelphia

first: Aman

middle: Yebio

last: Husbands

state: PA

address: 103B Caroline Lynch Bldg, 433 S University Ave

department: Biology

institute: The University of Pennsylvania

summary: The eukaryote-specific ribosomal protein of the small subunit eS6 is a target of phosphorylation for the Target of rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been known and studied for about 50 years, its biochemical and physiological significance remains controversial and poorly understood. To explore the role of eS6 and its phosphorylation we performed RNA-seq on the shoots of 12-day-old seedlings in five Arabidopsis thaliana genotypes. eS6 protein is encoded by two paralogous genes, RPS6A and RPS6B. Our data describe mRNA transcript levels in wild type (ecotype Columbia), two single mutants (rps6a and rps6b), an HA-epitope-tagged transgenic complementation line (rps6a rps6b; eS6A-HA) and a 'phosphonull' transgenic complementation line (rps6a rps6b; eS6A-Δ6SA) with six phosphorylatable residues mutated to alanine. Single mutants showed broad, but moderate changes to mRNA levels with the primary effects encompassing increases in translation and ribosome biogenesis genes and down regulation of photosynthesis. The rps6a rps6b; eS6A-HA plant almost fully complemented defects observed in the single mutants highlighting that the eS6 paralogs are functionally equivalent. Residual mRNA expression defects of the phospho-deficient seedlings could be understood as an incomplete rescue of the rps6 mutant defects, with little or no evidence for gain-of function defects. Our data also yield new insights into how plants cope with mutations in essential, duplicated ribosomal protein isoforms.

overall_design: Pairwise comparisons between 5 RPS6 genotypes: WT, rps6a, rps6b, rps6a rps6b; eS6A-HA, rps6a rps6b; eS6A-Δ6SA

first: Albrecht

last: von Arnim

first: Ramya

last: Enganti

first: Ricardo

middle: A

last: Urquidi Camacho

first: Anwesha

last: Dasgupta


title: Transcriptome analysis in brown adipose tissue of mice lacking ATF4 in thermogenic adipocytes.

status: Public on Jan 24 2024

city: Iowa City

first: Renata

middle: O

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

country: USA

institute: University of Iowa

type: Expression profiling by high throughput sequencing

summary: mRNA expression profiles from interscapular brown adipose (iBAT) tissue male ATF4 BAT KO mice and their WT counterparts after 3 days of cold exposure.

overall_design: Samples were collected from ad libitum fed ATF4 BAT KO male mice and their WT counterparts after 3 days of cold expoure.

first: Eric

middle: T

last: Weatherford


title: Effect of Shiga toxin (Stx) and glucosylceramide synthase inhibitor (Gb3i) treatments on SV40 transformed human kidney endothelial cells

city: Seattle

first: Russell

last: Whelan

state: Washington

address: 850 Republican St

department: Bioengineering

institute: University of Washington

summary: To investigate the transcriptional changes caused by Stx1 and Stx2 in human kidney microvascular cells (HKMECs), and the effects of GCSi pre-treatment on Stx-mediated effects

overall_design: SV40-transformed HKMECs were grown to confluency in cell culture plates, with subsequent treatment with GCSi or vehicle, and then treated with either Stx1, Stx2 or vehicle.

middle: S

first: Jun

last: Xue

first: Ying

last: Zheng

first: Jonathan

last: Himmelfarb


title: Proliferative Receptor Binding Domain (RBD)-specific CD4+ T cells correlate with neutralizing antibody levels after natural SARS-CoV-2 infection and are induced following vaccination

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

country: Australia

institute: Garvan Insititute of Medical Research

summary: Long-term immunity to SARS-CoV-2 infection, comprising neutralizing antibodies and T cell-mediated immunity, in a very large majority of the population, is required to reduce the current pandemic. We have investigated in detail the association between memory CD4 and CD8 T cells in recovered COVID-19 subjects, and their levels of neutralizing antibodies.The results show that RBD-specific memory CD4 T cells were particularly variable, and up to half of recovered individuals lacked these CD4 T cells and had much lower neutralizing antibody titres. Conversely, study of additional subjects identified as having low neutralizing antibody titres had very low levels of RBD-specific CD4 T cells. Furthermore, at both the protein and transcriptomic levels, these low antibody subjects had spike-specific CD4 T cells with a higher proportion of an inhibitory phenotype, including Foxp3 and CTLA-4, and less effector phenotype with T-bet and cytotoxic granzymes and perforin. Vaccination led to an improvement in RBD-specific memory CD4 T cells and neutralizing antibody titres in these at-risk subjects. Our results suggest that epitopes within the RBD-region should be the particular target of booster vaccines.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: scRNA seq of PBMC collected from 4 convalescent donor samples at 3 months post SARS-CoV-2 infection

first: Chansavath

last: Phetsouphanh

first: Weng

middle: H

last: Khoo

first: Katherine

last: Jackson

first: Vera

last: Klemm

first: Annett

last: Howe

first: Anupriya

last: Aggarwal

first: Anouschka

last: Akerman

first: Vanessa

last: Milogiannakis

first: Alberto

last: Stella

first: Romain

last: Rouet

last: Schofield

first: Megan

middle: L

last: Faulks

first: Hannah

last: Law

first: Thidarat

last: Danwilai

first: Mitchell

last: Starr

first: Stuart

last: Turville

first: Greg

middle: J

last: Dore

first: David

last: Darley

first: Philip

last: Cunningham

first: Gail

middle: V

last: Matthews

first: Anthony

middle: D

last: Kelleher

first: John

last: Zaunders


title: Id3 is required for the maintenance of tissue-infiltrating alloreactive T cells in GVHD but not anti-leukemia responses [ATAC-Seq]

city: Nutley

first: Ying

last: Wang

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health Center for Discovery and Innovation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate whether Id3 alters chromasome accessibility during CD4 T cell activation and Th1 differentiation.

overall_design: Differential chromatin accessiblity analysis of ATAC-seq data from Id3-KO and WT CD4 Th1 cells.

first: Shan

last: He

first: Gennaro

last: Calendo

first: Tien

last: Bui

first: Yuanyuan

last: Tian

first: Che

last: Lee

first: Xin

last: Zhao

first: Ciril

last: Abraham

first: Wenbin

last: Mo

first: Mimi

last: Chen

first: Ruqayyah

last: Sanders Braggs

first: Jozef

last: Madzo

first: Jean-Pierre

last: Issa

first: Elizabeth

middle: E

last: Hexner

last: Wiest

first: Ran

last: Reshef

first: Haihui

last: Xue

first: Yi

last: Zhang


title: Signaling modality within gp130 receptor enhances tissue regeneration [R805 treatment]

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Adult mammals are incapable of multi-tissue regeneration and augmentation of this potential may drastically shift current therapeutic paradigms. Here, we found that a common co-receptor of IL-6 cytokines, glycoprotein 130 (gp130), serves as a major nexus integrating various context-specific signaling inputs to either promote regenerative outcomes or aggravate disease progression. Via genetic and pharmacological experiments in vitro and in vivo, we demonstrated that a signaling tyrosine 814 (Y814) within gp130 serves as a major cellular stress sensor. Mice with constitutively inactivated Y814 (F814) exhibit regenerative, not reparative, responses after wounding in skin and anti-degenerative responses in the synovial joint. In addition, pharmacological inhibition of gp130 Y814 results in regeneration of multiple tissues in several species as well as disease modification in animal models of osteoarthritis. Our study characterizes a novel molecular mechanism that, if selectively manipulated, enhances the intrinsic regenerative capacity while preventing pathological outcomes in injury and disease.

overall_design: Single-cell mRNA sequencing for wild type (WT) mouse skin wound treated with or without R805 using 10x Genomics.

first: Ben

last: Van Handel


title: Epigenetically-regulated RNA-binding proteins signify malaria hypnozoite dormancy [ChIP-seq]

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

country: China

institute: GIBH

summary: Dormancy enables pathogens to survive unfavorable conditions and maximize their chance for transmission. Relapsing malaria parasites, such as Plasmodium vivax, ovale and cynomolgi employ this strategy. After inoculation by the bite of an infected mosquito, the so-called hypnozoites stay quiescent inside liver cells before reactivating, proliferating and establishing blood stage infection. Despite recent advances in molecular characterization of hypnozoites the mechanisms leading to hypnozoite formation and reactivation remain a mystery. Here we integrate various omics approaches to explore the involvement of gene regulatory mechanisms in these processes. By profiling the genome-wide distribution of repressive and activating epigenetic marks we identify a small set of genes that gets epigenetically silenced during liver stage development, a process that is conserved amongst relapsing parasites. Furthermore, by combining single-cell transcriptomics, chromatin accessibility profiling and fluorescent in situ RNA hybridization we show that these genes are expressed in hypnozoites and their silencing coincides with parasite development. Intriguingly, genes with clear hypnozoite-specific expression are almost exclusively encoding for proteins with RNA-binding domains. Overall, these findings support a model in which repressive RNA-binding proteins keep hypnozoites in a developmentally competent, but dormant state and heterochromatin-mediated silencing of these genes enables hypnozoite reactivation. Further testing of this hypothesis could provide decisive clues for targeted reactivation and killing of these vicious pathogens.

overall_design: ChIP-seq analysis of P. cynomolgy sprozoites and blood stage parasites for one heterochromatic (H3K9me2) and one euchromatic (H3K9/14ac) mark. Input samples are included to correct for any biases during sequencing.

first: Christa

middle: G

last: Toenhake

first: Annemarie

last: Voorberg-van der Wel

first: Roel

last: Cooijmans

first: Ivonne

last: Nieuwenhuis

first: Nicole

middle: M

last: van der Werff

first: Sam

last: Hofman

first: Anne-Marie

last: Zeeman

first: Clemens

last: Kocken

first: Richárd

last: Bártfai


title: Epigenetically-regulated RNA-binding proteins signify malaria hypnozoite dormancy [ATAC-seq]

sample_organism:
Plasmodium cynomolgi
Mus musculus

platform_organism:
Plasmodium cynomolgi
Mus musculus

overall_design: ATAC-seq analysis of three bulk populations of 3300-5000 day 6 hypnozoites (GFP+/mCherry-) and schizonts (GFP++/mCherry++) infected hepatocytes


title: Epigenetically-regulated RNA-binding proteins signify malaria hypnozoite dormancy [single-cell RNA-seq]

overall_design: scRNA-seq


title: RNA-sequencing (RNAseq) based transcriptomic profiling of aortae from C57BL/6 mouse by control or 24-hr fasting

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

summary: We performed RNA sequencing (RNA-Seq) based transcriptomic profiling of aortae from C57BL/6 mice by control or 24-hr fasting.  Our RNA-Seq analysis revealed 529 altered genes (1.5 fold change, p<0.05), of which 278 genes were significantly up-regualted and  251 genes were significantly down-regulated in aortae isolated from mice by 24-hr fasting.Gene ontology and pathway analysis of the up-regulated genes indicated that multiple biological processes were enriched including regulation_of_cellular_metabolic_process, while the down-regulated genes were enriched in the biological processes such as sterol_biosynthetic_process.

overall_design: Examination of differentially expressed genes between aortae isolated from control mice and 24 hr-fasting mice

first: Vicky

last: Macrae

first: Kanchan

last: Phadwal

first: Jun

last: Gao


title: Signaling modality within gp130 receptor enhances tissue regeneration (Canine scRNA-seq)

overall_design: Single-cell mRNA sequencing for dog synovium treated with or without R805 using 10x Genomics.


title: Dyna-vivo-seq characterizes the heterogeneity of single-cell RNA dynamics in living tissues

status: Public on Jan 23 2024

city: Xiamen

first: Guo

last: Ye

state: Fujian

address: 422 Siming South Road, Siming District

institute: Xiamen university

summary: A fundamental objective of genomics is to track variations in gene expression programs that define cell state progression during development, differentiation, and response to stimuli. While metabolic RNA labeling-based single-cell RNA sequencing offers insights into temporal biological processes, its limited applicability to in vitro models challenges the study of in vivo gene expression dynamics. Herein, we introduce Dyna-vivo-seq, a strategy that enables time-resolved dynamic transcription profiling in vivo at the single-cell level by simultaneously examining new and old RNAs. Leveraging Dyna-vivo-seq, we characterized the heterogeneity of RNA dynamics and quantified turnover rates of 21, 231 genes in 24, 237 single cells. The new RNAs can offer an additional dimension to facilitate the discernment of cellular heterogeneity. Based on new RNAs, we discerned two distinct high and low metabolic labeling populations among proximal tubular (PT) cells. Leveraging the enhanced sensitivity of new RNA-based analysis, we identified 90 rapidly responded transcription factors (TFs) and explored the heterogeneous response of PT cells for the AKI, highlighting that PT cells with high RNA metabolic activity exhibit heightened susceptibility to injury. Dyna-vivo-seq has introduced a temporal dimension to traditional otherwise static measurements in vivo, providing a powerful tool to the characterization of dynamic transcriptome changes at single cell leveles in living organisms and holding great promise for a wide range of biomedical applications.

overall_design:
As a control, single cells of mice kidney tissues were cultured in vitro in medium containing 4sU and analyzed by scRNA-seq.
The experimental group labeled live mice by injection and removed kidney tissue for scRNA-seq analysis.
Ischemia-reperfusion-treated mice kidneys were injection-labeled and analyzed by scRNA-seq.

first: Kun

last: Yin

first: Yiling

last: Xu

first: Ye

last: Guo

first: Zhong

last: Zheng

first: Chaoyong

last: Yang

first: Jia

last: Song

first: Shichao

last: Lin

first: Junhua


title: Signaling modality within gp130 receptor enhances tissue regeneration [WT vs Y814]

first: Denis

last: Evseenko

overall_design: Single-cell mRNA sequencing for wild type (WT) mouse skin wound and Y814 mutated mouse skin wound from wound-induced hair neogenesis (WIHN) assay using 10x Genomics.

first: Ben

last: Van Handel


title: Signaling modality within gp130 receptor enhances tissue regeneration (bulkRNA-seq)

overall_design: Bulk RNA-sequencing for wild type (WT) mouse periarticular stromal cells stimulated with or without oncostatin M(OSM) and Y814 mutated mouse periarticular stromal cells stimulated with or without oncostatin M(OSM).


title: The effect of LAIR-1 ligation on naïve CD8 T cells

city: Utrecht

first: Akashdip

last: Singh

address: Lundlaan 6

country: Netherlands

institute: UMC Utrecht

summary: To assess the role of LAIR-1 signalling on CD3 stimulated CD8 T cells, we ligated LAIR-1 on CD8 T cells during CD3 mediated CD8 T cell stimulation

overall_design: naïve CD8 T cells were isolated and cultured for 6 hours in the presence of anti-CD3, or corresponding isotype antibody, and anti-LAIR-1 (or isotype control)

first: Saskia

last: Vijver

first: Ines

last: Pascoal Ramos

first: Linde

last: Meyaard


title: Epigenetically-regulated RNA-binding proteins signify malaria hypnozoite dormancy

first: Haoyu

last: Wu

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Treg cells from human blood differentiate into non-lymphoid tissue-resident effector cells upon TNFR2 costimulation

city: Leiden

first: Mark

last: Mensink

address: Albinusdreef 2

department: Immunology

institute: Leiden University Medical Center

summary: Regulatory T (Treg) cells can facilitate transplant tolerance and attenuate autoimmune- and inflammatory diseases. Therefore, it is clinically relevant to stimulate Treg cell expansion and function in vivo and to create therapeutic Treg cell products in vitro. We report that TNF receptor 2 (TNFR2) is a unique costimulus for naïve, thymus-derived (t)Treg cells from human blood that promotes their differentiation into non-lymphoid tissue (NLT)-resident effector Treg cells, without Th-like polarization. In contrast, CD28 costimulation maintains a lymphoid tissue (LT)-resident Treg cell phenotype. We base this conclusion on transcriptome and proteome analysis of TNFR2- and CD28-costimulated CD4+ tTreg cells and conventional T (Tconv) cells, followed by bioinformatic comparison with published transcriptomic Treg cell signatures from NLT and LT in health and disease, including autoimmunity and cancer. These analyses illuminated that TNFR2 costimulation promotes tTreg cell capacity for survival, migration, immunosuppression and tissue regeneration. Functional studies confirmed improved migratory ability of TNFR2-costimulated tTreg cells. Flow cytometry validated the presence of the TNFR2-driven tTreg cell signature in effector/memory Treg cells from the human placenta as opposed to blood. Thus, TNFR2 can be exploited as driver of NLT-resident tTreg cell differentiation for adoptive cell therapy or antibody-based immunomodulation in human disease.

overall_design: Whole transcriptome analysis of human naïve conventional and thymus-derived regulatory CD4 T cells that were stimulated with recombinant human IL-2 and anti-CD3 agonistic mAb and costimulated with either anti-CD28 or anti-TNFR2 agonistic mAb for 7 days. Samples are derived from 5 healthy blood donors.

first: Jannie

last: Borst


title: DNA hypomethylation ameliorates erosive inflammatory arthritis by modulating interferon regulatory factor-8

city: SaintLouis

first: Gaurav

last: Swarnkar

state: MO

address: 425 South Euclid Ave BJCIH Room 11406

department: Orthopedic Surgery

institute: Washington University in School of Medicine

summary: Epigenetic regulation plays a crucial role in the pathogenesis of autoimmune diseases such as inflammatory arthritis. DNA hypomethylating agents, such as decitabine (DAC), have been shown to dampen inflammation and restore immune homeostasis. In the present study, we demonstrate that DAC elicits potent anti-inflammatory effects and attenuates disease symptoms in several animal models of arthritis.

overall_design: For sc-RNA-seq, synovial cells were isolated from paw and ankle joints. Samples were collected from each experimental condition (i.e., Control, DAC, KBxN and DAC_KBxN groups). Three replicates were hashtagged and pooled for each group.

first: Yousef

last: Abu-Amer

first: Chia-Lung


title: Dual role of IL-27 in Epstein-Barr virus infection revealed by IL27RA deficiency

city: Paris

first: Sylvain

last: Latour

address: 24 bd du Montparnasse

country: France

institute: Institut Imagine

summary: Epstein-Barr virus (EBV) infection can engender severe B-cell lymphoproliferative diseases. The primary infection is often asymptomatic or causes infectious mononucleosis (IM), a self-limiting lymphoproliferative disorder. Selective vulnerability to EBV has been reported in association with inherited mutations impairing T cell immunity to EBV.  Herein, we report bi-allelic loss-of-function mutations variants in IL27RA that underlie an acute and severe primary EBV infection with a nevertheless favorable outcome requiring a minimal treatment. One mutant allele (rs201107107) was enriched in the Finnish population (MAF=0.0068) and carried a high risk of severe IM when homozygous. IL27RA codes for the a subunit of the receptor of IL-27. In the absence of IL27RA, phosphorylation of STAT1 and STAT3 in response to IL-27 is abolished in T cells. In in vitro studies, IL-27 exerts a synergistic effect on TCR-dependent T cell proliferation that is abolished in cells from the patients, leading to impaired expansion of potent anti-EBV effector cytotoxic CD8+ T cells. IL-27 is produced by EBV- infected B lymphocytes and an IL27RA-IL-27 autocrine loop is required for maintenance of EBV-transformed B cells. This potentially explains the eventual favorable outcome of the EBV-induced viral disease in IL27RA-deficient patients. Furthermore, we identified neutralizing anti-IL-27 autoantibodies in most individuals who developed sporadic IM and chronic EBV infection. Collectively, these results demonstrate the critical role of IL27RA-IL-27 axis in T cell immunity to EBV, but also the hijacking of this defense by EBV to promote expansion of infected B cells.

overall_design: To investigate transcriptomic impact associated with IL27RA-deficiency, gene expression (including EBV genes) of two control LCLs and two IL27RA-deficient LCLs issued from two patients P1.1 and P.2 were analysed in response to IL-27 (Stim_IL27) compared to non-stimulated cells (Basal).

first: Mathieu

last: Simonin


title: Signaling modality within gp130 receptor enhances tissue regeneration

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus


title: Id3 is required for the maintenance of tissue-infiltrating alloreactive T cells in GVHD but not anti-leukemia responses [RNA-Seq]

first: Ying

last: Wang

summary: To comprehensively identify the transcriptional regulatory pathways by Id3 during CD4 T cell activation and Th1 differentiation.

overall_design: Differential expression analysis of RNA-seq data for Id3-KO and WT CD4 Th1 cells.

first: Shan

last: He

first: Gennaro

last: Calendo

first: Tien

last: Bui

first: Yuanyuan

last: Tian

first: Che

last: Lee

first: Xin

last: Zhao

first: Ciril

last: Abraham

first: Wenbin

last: Mo

first: Mimi

last: Chen

first: Ruqayyah

last: Sanders Braggs

first: Jozef

last: Madzo

first: Jean-Pierre

last: Issa

first: Elizabeth

last: Hexner

first: David

last: Wiest

first: Ran

last: Reshef

first: Haihui

last: Xue

first: Yi

last: Zhang


title: Protein language models-assisted optimization of a Uracil-N glycosylase variant enables programmable T-to-S base editing

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

summary: Current base editors use DNA deaminases, including cytidine deaminase in cytidine base editor (CBE) or adenine deaminase in adenine base editor (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for base editors capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG). Notably, after two rounds of testing fewer than 50 top-ranking variants, more than 50% exhibited over 1.5-fold enhancement in enzymatic activities. When eTDG was fused with nCas9, it induced programmable T-to-S (G/C) substitutions and corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel base editors, but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data.

overall_design: To develop a novel transversion base editors, we harness UNG variants to create orthogonal transversion base editors (CGBE and TSBE) independent of deaminases. We also developed a strategy based on protein language models and optimized an enhanced Uracil N-glycosylase variant with specificities toward thymines (eTDG).

first: He

last: Yan

first: Li

last: Geng


title: miR-126 knockdown and Mycobacterium marinum infection

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

institute: Centenary Institute

summary: We identify a putative link between miR-126 knockdown and neuroactive ligand and notch signalling pathways in uninfected and Mycobacterium marinum infected zebrafish embryos.

overall_design: Whole zebrafish embryo RNAseq of scram and miR-126 antagomir-injected, with and without Mycobacterium marinum infection

first: Wright

last: Kathryn

first: Song

last: Renhua

first: Wong

last: Justin

first: Oehlers

last: Stefan


title: Crnic Institute Human Trisome Project - JAK inhibition in Down syndrome: PolyA RNAseq from whole blood

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

summary: Analysis of steady-state mRNA levels in whole blood of  subjects with Down syndrome (trisomy 21) and qualifying moderate-to-severe immune skin conditions. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison across 10 subjects with Down syndrome at baseline and after treament with the JAK inhibitor tofacitinib for 2, 8, and 16 weeks.

first: Angela

last: Rachubinski

first: Joaquin

last: Espinosa


title: The effects of mitochondrial damages under stress or during aging on osteocytes networks homeostasis

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Using oligomycin A-treated MLO-Y4 cells and primary murine aging osteocytes as a model of cells with mitochondrial dysfunction, it is demonstrated that when mitochondria are damaged, osteocytes tend to release signaling compounds including adenosine diphosphate. We identified that the nucleotide membrane receptors P2Y2 and P2Y6 transduced the ADP signal to Mfn2, a critical regulator of osteocyte mitochondrial transfer. Whole RNA sequencing (RNA-seq) analysis of mouse cortical bone showed that mitochondrial metabolism is impaired in aged osteocytes, and there are more extracellular nucleotides released into the matrix in cortical bone in aged mice as compared to that in young mice. Aging decreases expression levels of P2Y2/P2Y6 and Mfn2.

overall_design: This study profiled the transcriptional changes of osteocytes during aging or under stress conditions.

first: Hao

last: Li


title: Epigenetic regulation of NK cell-mediated immune response in multiple myeloma [RNA-Seq]

city: Boston

first: Jiye

last: Liu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Anti-CD38 monoclonal antibodies like Daratumumab (Dara) are effective in multiple myeloma (MM); however, drug resistance ultimately occurs and the mechanisms behind this are poorly understood. Here, we performed two in vitro genome-wide CRISPR screens to systematically discover the regulators of sensitivity to Dara-mediated antibody-dependent cellular cytotoxicity (ADCC) and identified KDM6A. The loss of KDM6A led to a marked downregulation in CD38 expression by increasing H3K27me3 on the CD38 promoter, resulting in resistance to Dara-mediated ADCC. Yet, adding back CD38 did not completely rescue this phenotype. In fact, KDM6A loss also downregulated CD48, which promoted Dara resistance by inhibiting natural killer cell activity. Lowering the H3K27me3 with an EZH2 inhibitor restored sensitivity to Dara through CD38 and CD48 upregulation. These findings suggest KDM6A loss as a mechanism of Dara resistance and explore the strategy of using an EZH2 inhibitor, one of which is already FDA-approved, to improve the response to Dara in MM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H929 cells and its KDM6A KO derivatives

first: Jiang

first: Kenneth

last: Anderson


title: Granulocytic myeloid-derived suppressor cell activity during biofilm infection is regulated by a glycolysis-HIF-1α axis (scRNA-Seq)

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

summary: Staphylococcus aureus is a leading cause of biofilm-associated prosthetic joint infection (PJI). A primary contributor to infection chronicity is an expansion of granulocytic myeloid-derived suppressor cells (G-MDSCs) that are critical for orchestrating the anti-inflammatory biofilm milieu. Single-cell sequencing and bioinformatic metabolic algorithms were used to explore the link between G-MDSC metabolism and S. aureus PJI outcome. Glycolysis and the hypoxic response through hypoxia-inducible factor-1 alpha (HIF-1α) were significantly enriched in G-MDSCs. Interfering with both pathways in vivo, using a 2-deoxyglucose nanopreparation and granulocyte-targeted HIF-1α conditional knockout mice, respectively, attenuated G-MDSC-mediated immunosuppression and reduced bacterial burden in a mouse model of S. aureus PJI. In addition, scRNA-seq analysis of granulocytes from PJI patients also showed an enrichment in glycolysis and hypoxic response genes. These findings support the importance of a glycolysis/HIF-1α axis in promoting G-MDSC anti-inflammatory activity and biofilm persistence during PJI.

overall_design: Live CD45+ cells were collected from the soft tissue adjacent to the knee joint of C57BL/6J mice at days 3, 7, and 14 post-infection by FACS and prepared for single-cell sequencing using the 10X Genomics platform.

first: Chris

last: Horn

first: Prabhakar

last: Arumugam

first: Cortney

last: Heim

first: Tammy

last: Kielian


title: Characterization of novel endothelial-specific and smooth-muscle specific Poldip2 knockout mice

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

summary:
Poldip2 is a multifunctional protein whose roles are only partially understood. The previous Poldip2 knockout mouse generated by the gene trap model suffers from two limitations: perinatal lethality in homozygotes and constitutive Poldip2 inactivation.
To overcome these limitations, we developed a new conditional floxed Poldip2 mouse. Here, we correctly targeted floxed Poldip2 mice to produce an endothelial-specific by crossing it with CDH5 ERT2 Cre mouse.
Additionally, we also produced smooth-muscle specific Poldip2 knockout mice by crossing the flox'ed Poldip2  mice with SM22A-Cre mice. The Poldip2_EC-/-  and Poldip2_SMC-/-mice were viable and showed remarkably reduced Poldip2 expression. To characterize the effect of Poldip2 ablation in the ECs and in the SMCs, we performed a RNA-seq study using the carotid arteries of these mice.

overall_design: The carotid arteries were harvested from the Poldip2 knockout mice (n=4) as well as from the littermate controls (n=4). The lumen of these arteries were quickly flushed with Qiazol to extract the endothelial-enriched RNAs. Also, RNAs were extracted from the leftover arteries (containing the media and adventitia, consisting of smooth muscle cells and other adventiatial cells). These RNAs were subjected to RNAseq to determine the effect of Poldip2 knockdown in endothelium and in the vascular smooth muscle fraction of the carotid arteries.

first: Bernard

last: Lassègue

first: Kathy

middle: K

last: Griendling


title: O6-Methylguanine DNA Methyltransferase Regulates Beta-glucan Trained Immunity of Macrophages

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: Trained immunity is the heightened state of innate immune memory that enhances immune response resulting in nonspecific protection. Epigenetic changes and metabolic reprogramming are critical steps that regulate trained immunity. In this study, we reported the involvement of O6-methylguanine DNA methyltransferase (MGMT), a DNA repair enzyme of lesion induced by alkylating agents, in regulation the trained immunity induced by β-glucan (BG). Pharmacological inhibition or silencing of MGMT expression altered LPS stimulated pro-inflammatory cytokine productions in BG-trained bone marrow derived macrophages (BMMs). Targeted deletion of Mgmt in BMMs resulted in reduction of the trained responses both in vitro and in vivo models. The transcriptomic analysis revealed that the dampening trained immunity in MGMT KO BMMs is partially mediated by ATM/FXR/AMPK axis affecting the MAPK/mTOR/HIF1α pathways and the reduction in glycolysis function. Taken together, a failure to resolve a DNA damage may have consequences for innate immune memory.

overall_design: Transcriptomic profile of unstimulated, BG-primed (BG24), BG-primed with LPS stimulation WT and MGMT KO macrophages.

first: Salisa

last: Benjaskulluecha

first: Atsadang

last: Boonmee

first: Fazlul

last: Haque

first: Benjawan

last: Wongprom

first: Thitiporn

last: Pattarakankul

first: Chitsuda

last: Pongma

first: Kittitach

last: Sri-ngern-ngam

first: Pornlapat

last: Kaewvilai

first: Thadaphong

last: Sukdee

last: Saechue

first: Patipak

last: Kueanjinda


title: Signaling in microglia during CAR Tcell induced Immune cell associated neurotoxicity syndrome (ICANS)

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Strasse 53

department: Inner Medicine 1

country: Germany

summary: In this experiment, we studied the effect of ICANS on microglial kinase signaling

overall_design: Murine Microglia isolated from B-NHL treated mice that received either NT (n=5 ) or CAR T cells (n=4)

first: Vinnakota

last: Janaki Manoja


title: Epigenetic regulation of NK cell-mediated immune response in multiple myeloma [ATAC-Seq]

first: Jiye

last: Liu

overall_design: ATAC-sequencing (ChIP-seq) for the chromatin accessibility in H929 control and KDM6A KO cells

first: Jiang

last: Li

first: Kenneth

last: Anderson


title: Next-generation sequencing analysis of tea plant cultivar transcriptomes in response to Colletotrichum camelliae infection

city: Changchun

first: Shouan

address: Xi-An-Da Road 5333

institute: Jilin University

summary: Next-generation sequencing (NGS) was performed to identify genes changed in tea plant cultivar Zhongcha 108 upon Colletotrichum camelliae infection. The goal of the work is to find interesting genes involved in tea plant in response to fungi infection. The object is to reveal the molecular mechanism of tea plant defense.

overall_design: mRNA profiling of tea plants in response to Colletotrichum camelliae infection.


title: Epigenetic regulation of NK cell-mediated immune response in multiple myeloma [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27me3 in H929 control and KDM6A KO cells


title: Expression profile comparing of sorted 4T1-Sca1+ and 4T1-Sca1- cells

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

first: Sanam

last: Peyvandi

first: Qiang

last: LAN

first: Curzio

last: Ruegg

first: Manon

last: Bulliard


title: Epigenetic regulation of NK cell-mediated immune response in multiple myeloma [CRISPR screening 1]

overall_design: Genome-wide CRISPR/cas9 screening in H929 cells for CD38 expression

first: Su

last: Wang


title: Effects of starvation on  physiology and liver transcriptome of yellowcheek carp (Elopichthys bambusa)

city: Changsha City

first: min

last: xie

address: No. 728 Shuanghe road

institute: Hunan Fisheries Science Institute

summary: In this study, we used transcriptome sequencing technology to analyze the effects of starvation for eight and 28 days on the liver transcriptome of yellowcheek carp

overall_design: In this experiment, two control group and two treatment group were set up. There were three replicates in each group. The treatment group was starved for 8 days and 28 days, respectively (F8 and F28). The two control groups were continuously fed with the above commercial diet (F8C and F28C), twice a day (8:00 and 18:00).

first: Min

last: Xie


title: Expression profile comparing tumor GR1+ educated 4T1 cells with spleen Gr1+ educated 4T1 cells


title: Chemotherapy selected 4T1 cells

summary: 10e6 tumor cells were plated in 10 cm cell cuture dish overnight before treatment. For methotrexate selection, cells were treated with the dosage around IC85 in culture medium. The medium with MTX were replaced in 2nd and 3rd day and then every 2-3 days. The treatment was continued for up to 2 weeks until single colonies os surviving cells were visible.

overall_design: Treated and untreated 4T1 cells, in triplicate.

last: Lan

first: Girieca

last: Lorusso

last: Rüegg


title: Effect of lncRNA MALAT1 knockdown on miRNA expression of EC109 cells

city: Nanjing

first: LiWen

last: Hu

address: 305 East Zhongshan Road

institute: Jinling Hospital, Medical School of Nanjing University

summary: Microarrays were used to characterize the global changes in miRNA expression in EC109 cells due to siRNA knockdown of long non-coding RNA MALAT1

overall_design: Negative Control or siRNAs specific for MALAT1 were transfected into human easophageal cancer cell line EC109. 48 hours later total RNAs were isolated and subjected with microarray analysis.

first: Liwen

first: Kai

first: Chao

last: Zheng

first: Yi

last: Shen


title: Stomatal Development and Gene Expression in Rice Florets

city: Sheffield

first: Julie

last: Gray

state: South Yorkshire

address: University of Sheffield, Firth Court, Western Bank

department: Plants, Photosynthesis and Soil, School of Biosciences

country: United Kingdom

institute: University of Sheffield

summary: Stomata play a fundamental role modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well-studied, little attention has been paid to the development or function of floral stomata. To characterise gene expression during the stomatal development in IR64 florets, as well as to identify potential gene expression differences in florets of transgenic plants with a reduction in stomatal density, a RNA-sequencing was carried out using floret samples from different developmental stages of IR64 (control) and transgenic plants overexpressing the gene OsEPF1. Differential expression analyses conducted on the RNA-seq dataset indicate that the cellular transitions during the development of floral stomata are regulated by the same genetic network used in rice leaves, and reveal alterations in global gene expression in florets of plants overexpressing OsEPF1.

overall_design: This dataset includes samples of florets in the developing stages 1 to 5 and mature from IR64 (control) and OsEPF1-oe-S (transgenic) rice plants. Three biological replicates per sample type were sequenced.

first: Lígia

last: Bertolino

first: Robert

last: Caine

first: Nicholas

last: Zoulias

first: Xiaojia

last: Yin

first: Caspar

middle: C

last: Chater

first: Akshaya

last: Biswal

first: William

middle: P

last: Quick


title: Tumor educated Gr1+CD11b+ myeloid cells instigate breast cancer cells plasticity, and trigger metastasis via OSM/IL6 JAK signaling

first: Nadine

last: Fournier

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Effect of lncRNA MALAT1 knockdown on gene expression of EC109 cells

summary: microarrays were used to characterize the global changes in gene expression in EC109 cells due to siRNA knockdown of long non-coding RNA MALAT1


title: IFN-γ stimulation induces immunosuppression in CRC

status: Public on Jan 22 2024

city: Guangzhou

first: Zhiliang

last: Jing

address: Nr. 1023–1063 Sha tai South Road

institute: Southern Medical University

summary: In the subcutaneous tumor tissue of the IFN-γ-stimulated group, pathways related to suppression, antigen presentation, and cell adhesion molecules were significantly upregulated.The corresponding differentially expressed genes, Gzmb, Cd274, Vtcn1, Irf1, Cd86 and Stat1 were also significantly activated.

overall_design: We explored the genetic alterations by which IFN-γ stimulation promoted the growth of subcutaneous tumors derived from implanted CT26.WT cells in Immunocompetent BALB/c mice.

first: Zhi-liang

first: Guang-long

last: Liu

first: Dong-yan

last: Xu

first: Min-shan

last: Tang


title: Single-nucleus RNA-Seq

city: Beijing

first: Wen

last: Zhang

address: 38 Xueyuan Rd

institute: Peking University

summary: Psilocybin is a psychedelic whose metabolite, psilocin, is a 5-HT2A receptor agonist. Nevertheless, the underlying mechanisms for the therapeutic effect of psilocybin are not fully illustrated, and cell-type-specific and circuit effects of it are not fully understood. Here, we combined single-nucleus RNA-seq with functional assays to study the long-term effects of psilocybin on the orbitofrontal cortex (OFC), a brain region vulnerable to brain disorders such as depression. We demonstrated that a single dose of psilocybin induced long-term genetic and functional changes in neurons in the OFC, and excitatory and inhibitory neurons jointly reduced circuit activity of the brain region.

overall_design: Samples of OFC of the brain were dissected and analyzed with single-nucleus RNA-seq

first: Zhang

last: Wen


title: The effect of CHRDL2 overexpression on gene expression in CACO2 CRC cells

city: Uxbridge

first: Annabelle

last: Lewis

address: Kingston Lane

institute: Brunel University London

summary: Chordin-like-2 (CHRDL2) is a secreted BMP antagonist, with overexpression and genomic variants associated with colorectal cancer (CRC) risk. BMP signalling in the normal intestinal epithelium operates in opposition to the WNT signalling pathway, which maintains stem-cells and self-renewal. Elevated WNT signalling leads to expansion of the stem cell compartment and hyperproliferation, defining characteristics of CRC. Here, we explored the impact of CHRDL2 overexpression on CRC cells to investigate whether CHRDL2's inhibition of BMP signalling intensified WNT signalling, and enhanced the cancer stem-cell phenotype. RNA-seq analysis revealed that CHRDL2 increased the expression of stem cell markers and well-established cancer-associated pathways. We suggest that CHRDL2 overexpression can augment the stem-cell potential of CRC and normal intestinal cells.

overall_design: To investigate the effect of CHRDL2 overexpression in CRC, Caco-2 cell lines were engineered to stably overexpress CHRDL2 cDNA upon addition of doxycyline. Doxycyline was administered in 3 levels of "low" "medium" and "high" to induce corresponding CHRDL2 gene expression. Cell were harvested for analysis at 3, 5, and 7 days post treatment. Differential expression was performed matching treatment type to a DMSO control at each time point.

first: Eloise

last: Clarkson


title: Essential Role of Mg2+ for Mouse Preimplantation Embryo Development Revealed by TRPM7 Chanzyme Deficient Gametes

city: Research Triangle Park

first: Paula

last: Stein

state: NC

address: 111 T.W. A;exander Dr.

department: Reproductive and Developmental Biology Laboratory

institute: NIEHS

summary: TRPM7 (transient receptor potential cation channel subfamily M member 7) is a chanzyme with channel and kinase domains essential for embryo development. Using gamete-specific Trpm7-null lines, we report that TRPM7-mediated Mg2+ influx is indispensable for reaching the blastocyst stage. TRPM7 was expressed dynamically from gametes to blastocysts, displaying stage-specific and distinct localizations on the plasma membrane, cytoplasm, and nucleus, and undergoes cleavage that produces C- terminal kinase fragments. TRPM7 underpinned Mg2+ homeostasis throughout this time, and excess Mg2+ but not Zn2+ or Ca2+ overcame the arrest of Trpm7-null embryos; expressing Trpm7 mRNA restored development, but mutant versions failed or were less effective. Transcriptomic analyses of embryos lacking Trpm7 revealed an abundance of oxidative stress-pathway genes, confirmed by mitochondrial dysfunction, and a reduction of transcription factor networks essential for proliferation; Mg2+ supplementation corrected these defects. Hence, TRPM7 underpins Mg2+ homeostasis in preimplantation embryos, prevents oxidative stress, and promotes gene expression patterns necessary for developmental progression and cell lineage specification.

overall_design: RNAseq was performed in control or Trpm7 knockout metaphase II eggs, 1-cell, 2-cell, 4-cell, and 8-cell embryos, morulas, and blastocysts, as well as embryos cultured for 24 or 48 hours from the 2-cell stage in the presence of 10 mM MgSO4.

first: Brian

last: Papas

first: Virginia

last: Savy

first: Carmen

last: Williams


title: Single-cell RNA sequencing reveals dysregulated fibroblast subclusters in prurigo nodularis

city: Baltimore

first: Shawn

last: Kwatra MD

state: MD

address: 1550 Orleans Street

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: Prurigo nodularis (PN) is an intensely pruritic, inflammatory skin disease with a poorly understood pathogenesis. Thus, we performed single-cell transcriptomic profiling of 28,695 lesional and non-lesional PN cells. Lesional PN has increased dysregulated fibroblasts (FBs) and myofibroblasts. FBs in lesional PN were shifted towards a cancer-associated fibroblast (CAF)-like phenotype, with POSTN+WNT5A+ CAFs increased in PN, and similarly so in squamous cell carcinoma. A multi-center cohort study revealed an increased risk of SCC and CAF-associated malignancies (breast and colorectal) in PN patients. Systemic fibroproliferative diseases (renal sclerosis and idiopathic pulmonary fibrosis) were upregulated in PN patients. Ligand receptor analyses demonstrated a fibroblast neuronal axis with FB-derived WNT5A and periostin interactions with neuronal receptors MCAM and ITGAV. Compared to atopic dermatitis and psoriasis, mesenchymal dysregulation is unique to PN with an intermediate Th2/Th17 phenotype. These findings identify a pathogenic and  targetable POSTN+WNT5A+ fibroblast subpopulation that may predispose CAF-associated malignancies in PN patients.

overall_design: Single cell RNA sequencing and comparison was performed on six freshly obtained 6mm punch biopsies taken from lesional and adjacent non-lesional skin of patients with prurigo nodularis

first: Jay

middle: R

last: Patel

first: Marina

middle: Z

last: Joel

first: Kevin

last: Lee

first: Anusha

last: Kambala

first: Hannah

last: Cornman

first: Olusola

last: Oladipo

first: Matthew

last: Taylor

first: June

last: Deng

first: Varsha

last: Parthasarathy

first: Vito

last: Rebecca

first: Madan

last: Kwatra

first: Won

last: Ho

first: Xinhzhong

last: Dong

first: Sewon

last: Kang


title: Relation between TP53 GOF mutation and Osimertinib treatment in EGFR mutant lung cancer: ChIP-seq

city: Fukuoka

first: RITSU

last: IBUSUKI

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Respiratory Medicine

country: Japan

institute: Kyushu University

summary: Background: Although TP53 gain-of-function (GOF) mutations promote cancer survival, its effect on EGFR-TKI efficacy remains unclear. We established EGFR-mutant lung cancer cell lines expressing various TP53 genotypes using CRISPR-Cas9 technology and found that TP53-GOF mutant cells develop an early resistance to EGFR-TKI osimertinib.The goal of this study is to elucidate the mechanisms underlying resistance to osimertinib treatment in TP53 GOF mutations through comprehensive gene analysis using ChIP-seq.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for p53 in PC9 cells with p53-R248Q mutation which is gain-of-function mutaion, under osimertinib treatment

first: Ritsu

last: Ibusuki

first: Eiji

last: Iwama

first: Atsushi

last: Shimauchi

first: Isamu

last: Okamoto


title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons [RNA-Seq]

city: Innsbruck

first: Nico

last: Wahl

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

summary: The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on 3D epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal activity-regulated genes, thus influencing their expression. It also alters A/B compartments, Topologically Associating Domains and Frequently Interacting Regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence and schizophrenia. Our data establish SATB2 as a cell-type specific 3D genome modulator, which operates both independently and in cooperation with CTCF to set up the chromatin landscape of pyramidal neurons for cognitive processes.

overall_design: To explore a role of SATB2 in shaping 3D epigenome, cultured cortical neurons derived from Satb2flx/flx::Nes-Cre (cKO) and Satb2flx/flx (floxed) mice were used. On DIV14, Satb2 cKO and floxed cultures were treated with bicuculline, a GABA-A receptor antagonist, which stabilizes/increased neuronal activity in all neurons. To identify changes in chromatin accessibility and chromatin interactions, three ATAC-seq and six Hi-C libraries were prepared per genotype, respectively. To map SATB2 binding sites genome-wide, two CUT&RUN libraries were prepared from floxed cultures.

first: Sergio

last: Espeso-Gil

first: Georg

last: Dechant

first: Galina

last: Apostolova

first: Paola

last: Chietera


title: TOX3 drives hepatic gluconeogenesis and hyperglycemia by targeting FoxO1

city: jinan

first: congcong

last: liu

address: wenhua road

institute: Shandong university


title: Unravelling cell type specific response to Parkinson’s Disease at single cell resolution

city: Leuven

first: Araks

last: Martirosyan

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

summary: Parkinson’s Disease (PD) is the second most common neurodegenerative disorder. The pathological hallmark of PD is loss of dopaminergic neurons and the presence of aggregated α-synuclein, primarily in the substantia nigra pars compacta (SNpc) of the midbrain. However, the molecular mechanisms that underlie the pathology in different cell types is not currently understood. Here, we present a single nuclei transcriptomic analysis of human post-mortem in substantia nigra pars compacta (SNpc) tissue from 15 sporadic Parkinson’s Disease (PD) cases and 14 Controls. Our dataset comprised of ∼80K nuclei, representing all major cell types of the brain and allowed us to obtain a transcriptome-level characterization of these cell types. Importantly, we identified multiple subpopulations for each cell type and described subpopulation-specific gene sets that provide insights into the differing roles of these subpopulations. Our findings revealed a significant decrease in neuronal cells in PD samples, accompanied by an increase in glial cells and T cells. Subpopulation analyses demonstrated a significant depletion of tyrosine hydroxylase (TH)-positive astrocyte, microglia, and oligodendrocyte populations, along with the TH-expressing neurons in PD samples, which were also depleted. Moreover, marker gene analysis of the depleted subpopulations identified 28 overlapping genes including those associated with dopamine metabolism (e.g., ALDH1A1, SLC6A3 & SLC18A2). Overall, our study provides a valuable resource for understanding the molecular mechanisms involved in dopaminergic neuron degeneration and glial responses in PD, highlighting the existence of novel subpopulations and cell type-specific gene sets.

overall_design: We present a large-scale single nuclei RNA-seq dataset of 29 post-mortems human brains collected from substantia nigra pars compacta (SNpc) of 15 sporadic PD and 14 control samples obtained from Oregon Brain Bank. The Ethics Committee of UZ Leuven/KU Leuven approved the current study under the S-number S64182. H&E-guided 2 mm biopsy punches were collected from the SNpc of selected samples, nuclei were isolated and sequencing libraries were prepared using the Chromium Single Cell 3 Reagent Kits v.3 according to the manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced using a NovaSeq6000 system: 1% PhiX, paired-end sequencing with 10X v3 parameters (28-8-0-91 cycles). 13 libraries having a saturation rate lower than 60% were re-sequenced with the same 10x parameters to obtain more reads and improve the quality of the database. Combining reads from both runs giving a >40% saturation rate for all the samples was achieved. In total >170K nuclei was sequenced.

first: Rizwan

last: Ansari

first: Francisco

last: Pestana

first: Katja

last: Hebestreit

first: Hayk

last: Gasparyan

first: Razmik

last: Aleksanyan

first: Silvia

last: Hnatova

first: Suresh

last: Poovathingal

first: Catherine

last: Marneffe

first: Dietmar

last: Thal

first: Andrew

last: Kottick

first: Victor

last: Hanson-Smith

first: Sebastian

last: Guelfi

first: William

last: Plumbly

first: T

last: Grant Belgard

first: Emmanouil

last: Metzakopian

first: Matthew

last: Holt


title: TOX3 drives hepatic gluconeogenesis and hyperglycemia by targeting FoxO1 [ChIP-seq]

first: congcong

last: liu

summary:
Purpose: The goals of this study are to explore role of Tox3 in glucose homeostasis
Methods: Tox3-activation  was  generated  by adenovirus  from Genechem.Successful activation of Tox3 was determined by mRNA and protein expression.

overall_design: TOX3 ChIP-seq in primary hepatic cells

first: Congcong

last: Liu

first: Yuqing

last: Zhang


title: TOX3 drives hepatic gluconeogenesis and hyperglycemia by targeting FoxO1 [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control liver and its TOX3-activated liver


title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons [CUT&RUN]

first: Nico

last: Wahl

first: Sergio

last: Espeso-Gil

first: Georg

last: Dechant

first: Galina

last: Apostolova

first: Paola

last: Chietera


title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons [ATAC-seq]


title: Enhancement of the anticancer ability of natural killer cells through allogeneic mitochondrial transfer

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: Conventional natural killer (NK)-based anticancer immunotherapy has a limitation in that a culture period of approximately 2 weeks is required to increase the number and activity of NK cells. In addition, the anticancer activity of NK cells is closely associated with their mitochondrial function. In this study, we aimed to investigate whether the NK-anticancer activity increased after transferring allogeneic mitochondria into NK cells. Using this method, NK cells with enhanced anticancer activity can be produced without in vitro culture and can be used for anticancer treatment.

overall_design: Total RNA from NK-92MI cells was isolated and hybridized on Affymetrix microarrays.   The isolated mitochondria were transferred to the NK cells and compared to control NK cells.

first: Seong

first: Mi

first: Mina

last: Lim

first: Hyunmin

first: Chang-Koo

last: Yun

first: Yun-Joo

last: Yoo

first: Youngjun

last: Lee

first: Kyunghoon

last: Min

first: Yong-Soo

last: Choi


title: Role of neuroinflammation and skeletal muscle interaction in intermittent restraint stress

city: Chuo-ku, Kobe City, Hyogo

first: Kana

last: Uchiyama

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

institute: Kobe University Graduate School of Medicine

summary: We propose that neuroinflammation and skeletal muscle interaction in intermittent restraint stress regulate skeletal muscle mass through a defined mechanism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gastrocnemius muscle of intermittent restraint stress mice.

first: Wataru

last: Ogawa


title: Transcription factor Pbx4 regulates limb development and hematopoiesis in mice

first: Chunsheng

last: Han

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To characterize Pbx4-binding sites on the genome, we conducted ChIP-seq analyses by using testicular lysates from Pbx4-FLAG KI mice. We found Pbx4 preferentially binds to promoters of a large number of genes including other HD-containing protein and ribosomal protein genes, of which mutations are related to anemia. PBX4 binding sites are enriched in motifs similar to those of other HD-containing proteins indicating PBX4, like other PBX members, may act as a cofactor of other proteins. Together, these results show that PBX4 participates limb development and hematopoiesis although its expression in spermatogenic cells but not in other cell types in adult mice is detected.

overall_design: As a first step to understand the molecular mechanism of PBX4 function , we carried out ChIP-seq analysis of its binding site in the genome. Because it is only detected to be highly and specifically expressed in spermatogenic cells, we used total testicular cells to do the experiments. About 1400 binding sites (peaks) were identified from pooled analysis of 5 ChIP-seq datasets generated from five different PBX4-FLAG mice

first: Yan

last: Ning

first: Xiwen

last: Lin


title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons [Hi-C]

first: Nico

last: Wahl

first: Sergio

first: Georg

first: Galina


title: Microglia activation during CAR T cell induced neurotoxicity is dependent on TGF-β-activated kinase-1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Treatment with chimeric antigen receptor (CAR) T-cell therapy targeting CD19 (CAR19) can cause neurotoxicity in patients. The role of microglia in CAR19-induced neurotoxicity was unclear.  We observed morphological microglia alterations, increased production of GM-CSF, MCP-1 and TNF by microglia and neurocognitive deficits in B-cell lymphoma-bearing mice upon CAR19 transfer. Gene expression analysis was performed to determine the microglial activation and downstream signalling in response to CAR19 transfer.

overall_design: A20Luc+GFP+ Cells were transplanted to a sub-lethally irradiated BALB/c mice. On Day7, CD19 CAR Tc or NT T cells were transplanted intravenously. On day10, mice were perfused with ice cold PBS, brains were isolated and sorted for CD11b+ and CD45lo cells.

first: Janaki

last: Vinnakota

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: Identification of AgRP cells in the murine hindbrain that drive feeding [scRNA-seq]

city: San Francisco

first: Allison

middle: W

last: Xu

state: Caliofrnia

address: 513 Parnassus Ave., HS Building. Room S1222

department: Diabetes Center

institute: University of California San Francisco

summary:
Objective: The central melanocortin system is essential for the regulation of food intake and body weight. Agouti-related protein (AgRP) is the sole orexigenic component of the central melanocortin system and is conserved across mammalian species. AgRP is currently known to be expressed exclusively in the mediobasal hypothalamus, and hypothalamic AgRP-expressing neurons are essential for feeding. Here we characterized a previously unknown population of AgRP cells in the mouse hindbrain.
Methods: Expression of AgRP in the hindbrain was investigated using gene expression analysis, single-cell RNA sequencing, immunofluorescent analysis and multiple transgenic mice with reporter expressions.  Activation of AgRP neurons was achieved by Designer Receptors Exclusively Activated by Designer Drugs (DREADD) and by transcranial focal photo-stimulation using a step-function opsin with ultra-high light sensitivity (SOUL).
Results: AgRP expressing cells were present in the area postrema (AP) and the adjacent subpostrema area (SubP) and commissural nucleus of the solitary tract (cNTS) of the mouse hindbrain (termed AgRPHind herein).  AgRPHind cells consisted of locally projecting neurons as well as tanycyte-like cells. Food deprivation stimulated hindbrain Agrp expression as well as neuronal activity of subsets of AgRPHind cells. In adult mice that lacked hypothalamic AgRP neurons, chemogenetic activation of AgRP neurons resulted in hyperphagia and weight gain. In addition, transcranial focal photo-stimulation of hindbrain AgRP cells increased food intake in adult mice with or without hypothalamic AgRP neurons.
Conclusions: Our study indicates that the central melanocortin system in the hindbrain possesses an orexigenic component, and that AgRPHind neurons stimulate feeding independently of hypothalamic AgRP neurons.

overall_design: Single cell RNA Sequencing of murine Area Postrema/NTS region

first: Tomas

last: Bachor

first: Ernie

last: Yulyaningsih

first: Kush

last: Attal

first: Eirini

last: Vagena

first: Martin

last: Valdearcos

first: Christian

last: Vaisse

first: Paul

last: Emmerson

first: Viana

last: Pham

first: Kevin

last: Williams

first: Eunsang

last: Hwang

first: Renzo

last: Huarcaya


title: Epigenome analysis of parent and radioresistant oral cancer cells ( OCSL).

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling changes in parent and radioresistant oral cancer cells ( OCSL-P and OCSL-R ) by The Illumina Infinium WG Methylation27.

overall_design: Bisulphite converted DNA from parent and radioresistantoral cancer cells ( OCSL-P and OCSL-R )were hybridised to the Illumina Infinium 27k

first: Michael

last: Chan

first: Hon-Yi

last: Lin

first: Shih-Kai

last: Hung

first: Ru-Inn


title: Characterization of immune cells infiltrating pancreatic islets using scRNA-seq

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: T cells infiltrate pancreatic islets during the progression of type 1 diabetes (T1D) but their differentiation states have not been completely defined. We used unbiased single-cell RNA sequencing analyses to gain further insight into the phenotypic complexity of islet-infiltrating T cells in non-obese diabetic (NOD) mice.

overall_design: Two samples (7 week and 12 week) prepared using 10x Genomics Chromium platform

first: David

last: Schauder


title: Single-cell transcriptome analysis reveals phenotypically diverse islet-infiltrating T cell subsets in type 1 diabetes

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Single nuclei transcriptomics reveals altered endothelial cell function, permeability, and cognition in diabetic mice.

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary: Diabetes (DM) increases cardiovascular and cerebrovascular disease risk. However, the mechanism of DM-associated microvascular dysfunction and neuroinflammation remain unknown. We present a global assessment of endothelial cell-specific gene expression and integrated transcriptomics directly addressing hippocampal endothelium in diabetic mice, with the goal of determining the effect of DM in endothelial cell function and potential implications to vascular dementia. We observe for the first-time differential gene expression with strong signatures of cell signaling, activation of pathways for endothelial dysfunction, and neurodegeneration. Moreover, we identified that the integrated transcriptomic changes associate with blood brain barrier disruption by magnetic resonance imaging, and behavioral alterations, and correlate with the clinical gene profile of dementia patients, revealing opportunities for treatments with specificity for molecular pathology.

overall_design: Wild type (C57BL/6J) and db/db male mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and single nuclei RNA sequencing was performed. Brain hippocampal endothelial cells gene expression was analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors. Functional outcomes such as cognitive behavior and blood brain barrier permeability were also assessed.

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: Amparo

last: Villablanca


title: RNA-seq of islet-specific CD8 T cells in the spleen and pancreatic islets

summary: T cells infiltrate pancreatic islets during the progression of type 1 diabetes (T1D) but their differentiation states have not been completely defined. We used unbiased single-cell RNA sequencing analyses to gain further insight into the phenotypic complexity of islet-infiltrating T cells in non-obese diabetic (NOD) mice.  In the CD4 T cell compartment, we identified naïve, memory, and regulatory T cells, as well as multiple Il21 expressing effector subsets positive for markers indicative of Th1 and Tfh cells. In CD8 T cells, we identified two activated subsets in addition to naïve cells.  The two activated islet CD8 T cell subsets respectively resemble the self-renewing progenitor cells and the terminally differentiated/exhausted effectors during chronic lymphocytic choriomeningitis virus infection. We also identified a BATF-driven transcriptional signature promoting the diabetogenic activity of islet-infiltrating β cell autoreactive CD8 T effectors. Our results provide a useful resource for understanding T cell differentiation programs in T1D.

overall_design: 2 samples (spleen, pancreatic islets), 3-4 biological replicates per sample


title: Manassantin A inhibits tumour growth under hypoxia through the activation of chaperone-mediated autophagy by modulating Hsp90 activity

city: Durham

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary:
Background: Chaperon-mediated autophagy (CMA) has taken on a new emphasis in cancer biology. However, the roles of CMA in hypoxic tumours are poorly understood. We investigated the anti-tumour effects of the natural product ManA through the activation of CMA in tumour progression under hypoxia.

Methods: The effect of ManA on CMA activation was assessed in mouse xenograft models and cells. The gene expressions of HIF-1α, HSP90AA1, and transcription factor EB (TFEB) were analysed using The Cancer Genome Atlas (TCGA) datasets to assess the clinical relevance of CMA.

Results: ManA activates photoswitchable CMA reporter activity and inhibits Hsp90 chaperone function by disrupting the Hsp90/F1F0-ATP synthase complex. Hsp90 inhibition enhances the interaction between CMA substrates and LAMP-2A and TFEB nuclear localisation, suggesting CMA activation by ManA. ManA-activated CMA retards tumour growth and displays cooperative anti-tumour activity with anti-PD-1 antibody. TCGA datasets show that a combined expression of HSP90AA1High/HIF1AHigh or TFEBLow/HIF1AHigh is strongly correlated with poor prognosis in patients with lung cancer.

Conclusions: ManA-induced CMA activation by modulating Hsp90 under hypoxia induces HIF-1α degradation and reduces tumour growth. Thus, inducing CMA activity by targeting Hsp90 may be a promising therapeutic strategy against hypoxic tumours.

overall_design: RNA was extracted by RNAeasy kits (Qiagen) from the MDA_MB231 cells which exposed to the DMSO, Rotenone, Digitoxin, Manassantin A (three replicates in each condition).

first: Jiyong

last: Hong


title: RNA-seq of BATF-overexpressing CD8 T cells in vitro

overall_design: 2 samples (MIG, MIG-BATF), 2 biological replicates per sample


title: Time course of maternal circulating miRNA signatures associated to normal human pregnancy

city: Mexico City

first: Mariana

last: Flores Torres

address: Periferico Sur 4809

country: Mexico

institute: Instituto Nacional de Medicina Genomica

type: Non-coding RNA profiling by high throughput sequencing

summary: Emerging evidence has revealed alterations of microRNA (miRNA) profiles in peripheral blood associated to changes in a range of physiological conditions, suggesting that circulating miRNA profiles could be used as prognostic and/or diagnostic biomarkers for a wide variety of clinical conditions. Normal human pregnancy poses an extensive number of physiological challenges, affecting virtually every level of the pregnant woman’s biology, as well as changing contributions of the placenta and fetus. In this cohort study, using longitudinal large-scale profiling of circulating miRNAs at four defined stages during and after normal pregnancy, relative to non-pregnant controls, we investigate temporal changes in miRNA profiles as potential biomarkers of pregnancy evolution. By comparing the profiling of blood plasma miRNAs with available expression data, we found that miRNAs most prominently expressed in key reproductive tissues are collectively down regulated throughout pregnancy. Furthermore, we find a bias in the proportion of differentially expressed miRNAs associated with fetal sex right from the first trimester. Lastly, by combining circulating miRNAs expression with fetal growth indicators derived from the same women, we identify a robust miRNA signature associated to fetal growth during normal pregnancy. Our results demonstrate the existence of temporal changes of specific miRNAs associated to distinct aspects of pregnancy, including correlates of placental function, fetal gender, and fetal growth, as well as an early lactation related signature; strongly suggesting the potential of peripheral miRNAs as biomarkers of normal pregnancy.

overall_design: RNA isolated from pregnant women plasma samples at 1st, 2nd and 3rd trimester (same women for each trimester) was used for library preparation (NextFLEX small RNA-Seq kit v3, Bioo Scientific) and miRNA sequencing (NextSeq 500, Illumina). Data quality control analysis was performed using FastQC and adaptors were trimmed with Cudadapt. Sequences were aligned to the human genome (Hg38p12) with  BWA, miRNA profile was determined using miRDeep2 and miRBase v.22 as miRNA reference. Reads were tallied to generate total counts for each miRNA.

first: Erika

last: Chavira-Suarez

first: Alma

last: Hernandez-Olvera

last: Flores-Torres

first: Karen

last: Celaya-Cruz

first: Sofia

last: Gitler

first: Juan

last: De la Cerda-Angeles

last: Maldonado-Espinosa

last: Flores-Jasso

first: Humberto

last: Gutierrez

first: Felipe

last: Vadillo-Ortega


title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons

first: Nico

last: Wahl

overall_design: To explore a role of SATB2 in shaping 3D epigenome, cultured cortical neurons derived from Satb2flx/flx::Nes-Cre (cKO) and Satb2flx/flx (floxed) mice were used. On DIV14, Satb2 cKO and floxed cultures were treated with bicuculline, a GABA-A receptor antagonist, which stabilizes/increased neuronal activity in all neurons. To identify changes in chromatin accessibility and chromatin interactions, three ATAC-seq and six Hi-C libraries were prepared per genotype, respectively. To map SATB2 binding sites genome-wide, two CUT&RUN libraries were prepared from floxed cultures.


title: Influence of nine days of physical inactivity on the expression of miRNAs and their predicted target genes in human skeletal muscle

city: Copenhagen

first: Malene

middle: Maag

last: Kristensen

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

summary: miRNA profiles were investigated in healthy young males before and after bed rest and subsequently after retraining.

overall_design: We examined miRNA expression profiles in skeletal muscle from 56 healthy young males before and after nine days of bed rest and again after a four-week endurance-training program. We identified deregulated miRNAs in skeletal muscle samples from individuals born with normal birth weight (NBW, n=20) and two groups with predisposition to type 2 diabetes mellitus (T2DM); individuals born with low birth weight (LBW, n=19) and first degree relatives (REL, n=11) to patients with Type 2 Diabetes

first: Jette

last: Bork-jensen

first: Lars

last: Jensen

first: Christina

middle: N

last: Hansen

first: Joern

last: Helge

first: Allan

middle: A

last: Vaag

first: Flemming

last: Dela


title: Weight loss following Roux-en-Y gastric bypass surgery leads to changes in the expression of several miRNAs and their predicted target genes in skeletal muscle

summary: miRNA profiles were investigated in skeletal muscle in severely obese individuals with or without diabetes before and after Roux-en-Y gastric bypass surgery.

overall_design: 16 severely obese patients without type 2 diabetes mellitus (OB) and nine severely obese patients with type 2 diabetes mellitus (T2DM) were elected for Roux-en-Y gastric bypass surgery. We examined the participants after a diet-induced weight loss (B) and approximately 4 months post-surgery (C). 50 samples were included in this screen.

first: Jørn


title: Annual transcriptome dynamics of Japanese cedar (Cryptomeria japonica) in three regions

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

institute: Forest Tree Breeding Center

summary: Investigation of annual transcriptome dynamics of Japanese cedar cuttings planted in three regions (Yamagata, Ibaraki and Kumamoto, Japan).

overall_design: The 10-cm portion of lateral branch apexes was collected from two different cuttings (2 biological repeats) every month from February 2014 to February 2015  (13 time points) in each region (total 78 samples).

first: Atsushi

last: Watanabe


title: RNA sequencing of three dimensional endothelial spheroids seeded in an artificial collagen matrix with or without VEGF stimulation

status: Public on Jan 21 2024

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

institute: University Medical Center Freiburg

summary: This study investigates the influence of VEGF on the transcriptome of Human umbilical vein endothelial cells (HUVECs) formed to a spheroid and seeded in a 3D collagen matrix in a standard spheroid sprouting assay as one of the most commen angiogenesis assay.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVEC spheroids from a spheroid sprouting assay with n=5 VEGF stimulated samples and n=5 spheroids treated with just basel medium

first: Jan

last: Neß

first: Felicitas

last: Bucher

first: Clemens

last: Lange


title: KIF2C is a critical regulator for malignant progression of head and neck squamous cell carcinoma

city: Chongqing

first: Haiyue

last: Zhu

address: No.1 Medical College Road, Yuzhong District, Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Head and neck squamous cell carcinoma(HNSCC) is a significant cause of mortality, while the underlying mechanism remains unclear. Recent studies indicate that KIF2C could play a vital role in tumor proliferation and metastasis. Our results demonstrate that KIF2C is highly expressed at both the mRNA and protein levels in HNSCC samples compared to normal samples. Gene ontol-ogy and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that differentially expressed genes were enriched in processes or pathways related to cell adhesion and cell mitosis in HNSCC. Additionally, a protein-protein interaction network was established, identifying KIF2C as a potential hub gene in HNSCC. Cell phenotype assays showed that KIF2C knockdown reduces cell migration and invasion ability and exhibited cell cycle arrest, high proportion of abnormal cell apoptosis and cell chromosome division mismatches in HNSCC cell line. RNA-seq and RT-PCR assay results revealed that KIF2C knockdown influenced the expression levels of PDGFA, CCNA1, RRM1, CCND2, CAV1, EGFR, SNAI2, KRT5, KRT14, NID1, TP63. TGFBR2, TGFB2, ICAM1, ITGB2, CDH2, CDH5, FN1. And KIF2C knockdown also decreased the phos-phorylation of mTOR, AKT, and ERK. Furthermore, in vivo studies have demonstrated that KIF2C knockdown significantly inhibits tumor proliferation in nude mice. As such, our study highlights the potential therapeutic role of KIF2C for HNSCC treatment.

overall_design: To investigate the regulatory role played by KIF2C in head and neck cancer proliferation and motility, we established a FaDu cell line in which the target genes were knocked down by shRNA, and then we performed gene expression profiling using RNA-seq data from FaDu cells transfected with blank vectors and KIF2C-knocked-down cells at the same time point.

first: Yuxin

last: Bao


title: Effect of the  Foxp3 inhibitory peptide P60  on gene array  expression of Karpas cell line

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: By using a phage displayed peptide library we  identified  peptide P60 as able to bind Foxp3 and inhibit Treg activity. To gain insight into the effect of P60 in Foxp3+ve cells  we used Karpas 299 human cell line derived from a human lymphoma with a regulatory T cell profile. Microarray analysis of Karpas cell line incubated with or without  P60 peptide was carried out using the Affymetrix human U133 Plus 2.0 array.

overall_design: Two culture condition (absence or presence of P60 peptide in the culture) were studied in two replicates


title: Transcriptional profiling of intestinal tissue from mice with and without Eif3h deficiency and Kras G12D mutation.

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

institute: Cancer Research UK Scotland Institute

summary: A profile of gene expression differences in mouse small intestine with and without short term induction of Kras G12D mutation and Eif3h deficiency.

overall_design: Expression data from intestine with and without Eif3h deficiency and Kras mutation.

first: Nikola

last: Vlahov

first: Owen

last: Sansom


title: Evidence of small interfering RNA in the fungus Fusarium fujikuroi (RNA-Seq)

city: Sevilla

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetica

institute: Universidad de Sevilla

summary: RNA interference (RNAi) mechanisms play key regulatory roles in many biological systems, and components of the RNAi pathway are conserved in a wide range of eukaryotic genomes, including those of filamentous fungi. The biotechnological fungus Fusarium fujikuroi, widely used in secondary metabolism studies, contains the complete set of genes expected for RNAi pathways, including dcl1 and dcl2 dicer genes. We have analyzed by means of a high-throughput sequencing technology the content of sRNAs in F. fujikuroi grown in the dark or after one hour of illumination. For comparative purposes, the study was extended to the phytopathogenesis model Fusarium oxysporum, grown under the same conditions. Total RNA samples from each species and growth condition were used to construct RNA libraries, which were subjected to massive sequencing. sRNA preparations included a size cut-off below 150 nt, which covered sRNAs and their precursors. The size distributions and 5' nucleotide preferences of the sRNA reads showed a higher proportion of 5' uracil in the RNA samples of the expected sizes in both species, more noticeable in F. fujikuroi, indicating the occurrence of genuine sRNAs. Consistently, the number of sRNAs mapped at CDS loci was significantly higher in F. fujikuroi compared to F. oxysporum. F. fujikuroi carries at least one transcriptionally expressed copy of a Ty1/copia-like retrotransposable element, in which sRNAs were found in both sense and antisense DNA strands, whereas in F. oxysporum Skippy-like elements are expressed and show siRNA formation. The finding of sRNA in these mobile elements is an indication of an active siRNA-based RNAi pathway. The dcl2 deletion mutants did not show phenotypic alterations or changes in their global transcriptome, while no dcl1 deletion mutants could be obtained.

overall_design: This RNA-seq data set investigates the function of the Dicer gene dcl2 in the fungus Fusarium fujikuroi through the effect of its the deletion on the whole transcriptome . The results are presented in a manuscript that provide evidence of the occurrence of smalRNAs in Fusarium and the role of the dcl2 gene by targeted deletion.

last: Pardo-Medina

first: Tim

last: Dahlmann

first: Minou

last: Nowrousian

first: M

last: Limón


title: Next Generation Sequencing Facilitates Quantitative Analysis of Luc976, shVHL61, shKIM1-A1 and shVHL61-KIM1-A1 kidney tubular cell line transcriptomes

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

institute: China Medical University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: mRNA profiles of Luc976, shVHL61, shKIM-1, shVHL61-KIM1A1 human proximal kidney cell line (HK-2) were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: RNA-seq data analyzed the differentially expressed genes (DEGs) comparing control, VHL knockdown, KIM-1 knockdown, and VHL-KIM1 double knockdown.  Many genes were found and 20 of these were validated with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. There are four distint groups of genes that show different express patterns in different gene knockdown background, with a fold change ≥1.5 and p value <0.05. The functional relationship between VHL and KIM-1 is not likely a simple linear pathway. Some functions are VHL dominant and others are KIM-1 dominants. A majority appears to be independent of each other.
Conclusions: Our study represents the detailed analysis transcriptomes in proximal tubule epithelial cell line with different gene knockdown background, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Rebecca

last: Smith

first: David

last: Doe


title: Immunogenicity of autologous and allogeneic human primary cholangiocyte organoids

status: Public on Jan 20 2024

city: Cambridge

first: Sandra

last: Petrus-Reurer

address: Box 202, Level E9 Addenbrooke’s Hospital, Hills Road

department: Department of Surgery

institute: University of Cambridge

summary: Primary human cells cultured in 3D organoid format have great promise as potential regenerative cellular therapies, but their immunogenicity has not yet been fully characterized. In this study, we use in vitro co-cultures and in vivo humanized mouse experimental models to examine the human immune response to autologous and allogeneic primary cholangiocyte organoids (PCOs). Our data demonstrate that PCOs upregulate the expression of HLA-I and HLA-II in inflammatory conditions. The immune response to allogeneic PCOs is driven by both HLA-I and HLA-II and is substantially ameliorated by donor-recipient HLA matching. Autologous PCOs induce a low-level immune infiltration into the graft site, while allogeneic cells display evolving stages of immune rejection in vivo. Our findings have important implications for the design and clinical translation of autologous and allogeneic organoid cellular therapies.

overall_design: Examination of the human immune response to autologous versus allogeneic primary cholangiocyte organoids (PCOs).

first: Olivia

last: Tysoe

first: Winnie

last: Lei

first: Maelle

last: Mairesse

first: Thomas

last: Tan

first: Sylvia

last: Rehakova

first: Krishnnaa

last: Mahbubani

first: Julia

last: Jones

first: Cara

last: Brodie

first: Namshik

last: Han

first: Catherine

last: Betts

first: Ludovic

last: Vallier

first: Kourosh

last: Saeb-Parsy


title: Synergistic immunochemotherapy exerts efficiently anti-hepatocellular carcinoma effect to induce SAMD4B-APOA2 axis for inhibition of tumor immune evasion [NM-seq]

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: RNA modifications are a type of post-transcriptional modification and involved in many biological processes of immune cells, thus regulating immune response and participating in immune related diseases. 2'-O-methylation is one of the most common modifications. However, whether 2’-O-methylation is involved in immune evasion via regulating programmed death ligand 1 (PD-L1) is unclear. Here, we were the first to propose a new treatment strategy for patients with advanced hepatocellular carcinoma (HCC), provided evidence that synergistic immunochemotherapy had a better prognosis, and revealing the mechanism of immune regulation through 2'-O-methylation modification mediated by SAMD4B, as a tumor suppressor gene.

overall_design: We transfected SAMD4B and APOA2 plasmids into 6 HEK293T cell line, and observed the mRNA instability and expression of APOA2 by overexpression and knockout of SAMD4B, respectively.The control group overexpressed APOA2, and the treatment group overexpressed both SAMD4B and APOA2.

first: Feng

last: Qi

first: Jian

last: Zhang

first: Jia

last: Li

first: Donghe

last: Gao

first: Zhuoran

first: Xiuyan

last: Kong

first: Zhijie

last: Yu

first: Biwei

last: Yang

first: Jinglin

last: Xia


title: Phytochrome C And Low Temperature Promote The Expression And Red Light Signaling Of Phytochrome D

status: Public on Jan 19 2024

city: Szeged

first: Gabor

last: Grezal

state: Csongrád

address: Temesvári krt. 62.

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre

summary: Light is an ever-changing environmental parameter affecting almost every aspects of plant growth and development. It is perceived by photoreceptors, among them phytochromes (PHY) are responsible for monitoring the red and far-red part of the spectrum. Arabidopsis thaliana possesses five phytochromes genes, named through phyA-phyE. Whereas the function of phyA and phyB – that mediate most of the phytochrome responses – is extensively studied, our knowledge on other phytochromes are still rudimentary. To analyze phyD function we expressed it at high levels in different phytochrome deficient genetic backgrounds. We found that overexpressed phyD governs effective light signaling at low temperatures but only in cooperation with functional phyC. Under these conditions, opposite to phyB, phyD accumulates to high levels and this pool is stable under light illumination. Furthermore, the detectable photoconvertible phyD amount is proportional with the available protein amount indicating that the phyD pool contains fully functional photoreceptors. The thermal reversion of phyD is very fast suggesting that the thermosensing of phyD is based on its protein amount and not on its Pfr conformer stability, which was described for phyB. We also found that phyD and phyB associate to identical genomic locations and mediate similar gene expression changes, however the efficiency of phyD is lower. Taken together our data suggest that under certain conditions synergistic interaction of phyD and phyC substitutes phyB function thus increases the ability of plants to respond more flexible to environmental changes.

overall_design: 4-day-old seedlings were grown on half-strength MS plates at 17 or 27°C in the dark and illuminated for 1 or 24 h. 0.1 g plant material was snap frozen in liquid nitrogen from etiolated or 1 h or 24 h red light (50 µmol m-2 s-1) illuminated seedlings. Total RNA was extracted using RNeasy Miniprep Kits (Qiagen) according to the manufacturer's instructions. RNA sequencing was done by Novogene, Cambridge, United Kingdom.

first: Gábor

last: Grézal

first: Csaba

last: Péter

first: Dániel

last: Silhavy

first: Ferenc

last: Nagy

first: Éva

last: Ádám

first: András

last: Viczián


title: Autologous transplantation of P63+ lung progenitor cells for chronic obstructive pulmonary disease therapy

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: Adult lung resident stem/progenitor cells, including P63+ progenitor cells, have demonstrated the capacity for regeneration of lung epithelium in precinical models. Here we report a clinical trial of intra-pulmonary P63+ progenitor cell transplantation which included 28 participants with chronic obstructive pulmonary disease (COPD) (stage II~IV). For control group, standard of care (SOC) for COPD treatment was given. For intervention group, in addition to SOC, autologous P63+ progenitor cells were isolated from the airway basal layer via bronchoscopic brushing, cultured for 3~5 weeks, and then transplanted into the lungs via bronchoscopy with 0.7-5.2x10^6 cells per kilogram bodyweight. Eventually 20 patients were evaluated (intervention group n=17; control group n=3). No grade 3~5 adverse events (AE) or serious adverse events occurred in any group. Bronchoscopy-associated AEs were recorded only in intervention groups, while the other AEs were recorded in both groups without showing significant difference. Participants in intervention group displayed significant improvement in diffusing capacity of the lung for carbon monoxide (DLCO) (change from baseline, 24 weeks: +18.2%), showing significant difference comparing to control group (change from baseline, 24 weeks: -17.4%)(p-value=0.008). Furthermore, more participants in intervention group showed > 30 m increase in walking distance within 6 minutes, demonstrating significant difference comparing to control group (p-value=0.036). Transcriptomic analysis of cells isolated from responding and non-responding individuals in the intervention group showed that higher expression of P63 and Nkx homeobox-1 was associated with better efficacy. In conclusion, transplantation of cultured P63+ lung progenitor cells was safe and represented a potential treatment strategy for COPD.

overall_design: To investigate whether the status of donor cells affects the therapeutic outcome, we analyzed basal progenitor cells isolated from seven donors who were recruited most recently. Among them, four donors showed “responsiveness” to autologous cell transplantation treatment as defined by DLCO increase to MCID after therapy (R-Patient #8009, #8004, #8001, and #2301), while three donors showed no responsiveness to cell therapy (NR-Patient #8002, #8007, and #2104). We conducted whole-genome RNA sequencing to analyze the transcriptome of progenitor cells derived from these seven donors.

first: Yu

last: Zhao


title: Paternal starvation affects metabolic gene expression during zebrafish offspring development and life-long fitness

city: Birmingham

first: Ada

last: Jimenez-Gonzalez

address: 1, Vincent Drive

institute: University of Birmingham

summary: Dietary restriction in the form of fasting is a putative key to a healthier and longer life, but these benefits may come at a trade-off with reproductive fitness and may affect the following generation(s). The potential inter- and transgenerational effects of long-term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split-egg clutch design to explore the male-specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected, we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hours post fertilization in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra-embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism-associated genes. These similarities suggest a physiologically relevant, directed and potentially adaptive response transmitted by the father, independently from the offspring’s nutritional state, which was defined by the mother.

overall_design: Sperm from fed and starved males was used for in vitro fertilization of fed wildtype females. The resulting embryos were raised until 24 hours postfertilization and collected to study their transcriptome by 3'RNA-seq (lexogen). We analyzed the differences in gene expression between embryos from several fed fathers and embryos from several starved fathers.


title: Transcriptome sequencing revealed a set of differentially expressed related genes between systemic lupus  erythematosus (SLE) patients with and without pulmonary fibrosis (PF)

city: shiyan

first: Xueyan

last: Xi

state: Hubei Province

address: Renmin Nanlu #30

department: Immunology

institute: Hubei University of Medicine

summary: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by abnormal immune responses that include aberrant activation of autoreactive T and B lymphocytes, with subsequent production of pathogenic autoantibodies and formation of immune complexes leading to organ injury. Pulmonary involvement in SLE is common and protean with different clinical manifestations ranging from acute pneumonitis, pulmonary hemorrhage to pulmonary fibrosis (PF). The health status of SLE patients with pulmonary disease is relatively poor, and the mortality rate is high, but research on SLE pulmonary domain is still lacking. In order to further explore the difference between  SLE with PF and SLE without PF, we perform transcriptome sequencing analysis. The PBMCs from 3 SLE patients with PF and 3 SLE without PF were drawn, and RNA-seq was performed with subsequent bioinformatics analysis. Compared with the SLE patients without PF, the genes that changed in all three SLE patients with PF included 647 significantly up-regulated and 1364 significantly down-regulated differentially expressed genes.

overall_design: Include 6 samples, 3 are Systemic lupus erythematosus patients with pulmonary fibrosis,another 3 are Systemic lupus erythematosus patients without pulmonary fibrosis.

first: Fen

last: Qiu

first: Boyu

last: Du

first: Youling