title: Complementary HLH Susceptibility Factors Converge on CD8 T-cell Hyperactivation [TCR-seq]

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

summary: To determine the effects of excess IL-18 and perforin deficiency on CD8 T cell clonality toegther and separately under homeostatic conditions. These data support that together perforin deficiency and excess IL-18 promote hyperexpansion of CD8 T cell clones.

overall_design: FACS sorted CD8 T lymphocytes from Prfko, Il18tg, PrfHET18tg, and Prfko18tg mice under homeostatic conditions

first: Scott

last: Canna


title: Complementary HLH Susceptibility Factors Converge on CD8 T-cell Hyperactivation [bulk RNA-seq]

status: Public on Sep 28 2023

country: USA

type: Expression profiling by high throughput sequencing

summary: To determine the effects of excess IL-18 and perforin deficiency on CD8 T cells toegther and separately under homeostatic conditions. Mice harboring both excess IL-18 and perforin deficiency (DS) have increased activated (CD44+) CD8 t cells as well as a special CD44low/- CD62L- (DN) population of CD8 T cells. DS mice have CD8 T cells that have specifically upregulated inhibitory receptors Lag3, Havcr2, and Tigit, and the transcription factors Tox and Prdm1. Mice harboring excess IL-18 and partial perforin deficiency (DS-HET) as well as mice with only excess IL-18 (Il18tg) also have these signatures but only in the DN CD8 T cell population. These data support that IL-18 as a potent, independent, and modifiable driver of life-threatening innate nd adaptive hyperinflammation, and support the rationale for an IL-18-driven subclass of hyperinflammation.


title: IL-1B mediated adaptive reprogramming of endogenous human cardiac fibroblast to cells with immune features during fibrotic remodelling

city: Providence

first: Sharon

last: Rounds

state: RI

address: 830 Chalkstone Avenue,, Building 35, Room 216

institute: Brown University

summary: We profile the transcriptome of a unique sub-population of primary human ventricular cardiac fibroblast (hVCFs) cells expressing dual mesenchymal and lymphoidal features in response to cytokines specifically, IL-1B using next-generation sequencing (NGS). The goals of the project are to 1) compare and contrast novel CD4+ cells with CD4- human cardiac fibroblast cells; 2) identify and classify the novel subpopulation of cells from the heart based on the expression of   lineage specific markers, and markers associated with plasticity, morphogenesis, homeostasis, metabolism and signaling pathways. hVCFs were sorted based on the expression of CD4 markers classified as CD4+ and CD4- cell population. After initial samples QC analysis, RNA libraries were prepared with polyA selection and sequenced on Illumina in 2x150bp paired end configuration. About 35M paired reads per samples for 10 samples or 58M paired reads per samples for 6 samples were obtained for 3 biological replicates. This study provides genetic signatures of newly identified sub-population of human cardiac fibroblasts and response to pro-inflammatory cytokines critical to cardiac remodeling and heart failure.

overall_design: Transcriptomic signatures of primary adult CD4+ human cardiac fibroblasts

first: Jamila

middle: H

last: Siamwala


title: Olfactory receptor mRNAs act as selfish non-coding RNAs that enforce transcriptional singularity (Non-coding OR Hi-C & RNA-seq)

city: New York

first: Ariel

last: Pourmorady

state: NY

address: 3227 Broadway

department: Neurobiology and Behavior

institute: Columbia University

summary:
To investigate roles for olfactory receptor coding sequence mRNA in trans olfactory receptor gene silencing, and OR-gene enhancer recruitment.
Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, as every olfactory neuron stably transcribes one out of more than ~2,000 OR alleles1,2. OR gene choice is mediated by a multi-chromosomal enhancer hub that activates transcription at a single OR3,4, followed by ORtranslation dependent feedback that stabilizes this choice5,6. However, with more than one OR enhancer hub in each nucleus7, the mechanism by which only one OR allele is chosen for transcription remains enigmatic. Here, using single cell genomics, we show that only one of the OR enhancer hubs formed in each neuron retains euchromatic features and sustains transcriptional competence. Further, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, while OR RNA inhibits transcription in competing hubs over distance, promoting OR protein-independent transition to singularity. While OR RNA synthesis is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, revealing dual non-coding and coding mechanisms implemented by OR RNAs for transcriptional prevalence. We propose that coding mRNAs can function as “selfish” non-coding RNAs that influence nuclear architecture, enhance their own transcription, and inhibit their competitors, with generalizable implications in probabilistic cell fate decisions.

overall_design: CRISPR and transgene creation were used to generate inducible noncoding olfactory receptor genes to test the role of olfactory receptor RNA in olfactory receptor gene silencing and enhancer hub formation, which were assessed by performing RNA-seq and Hi-C.

first: Stavros

last: Lomvardas


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [DNA-seq]

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

country: China

institute: Tsinghua University

summary: We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

overall_design: DNA-seq of Homo sapiens: patient's plasma from colorectal and stomach cancer and healthy controls; Provided by Peking University First Affiliated Hospital.

first: Shaozhen

last: Xing

first: Yuhuan

last: Tao

first: Pengfei

last: Bao


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: INPP5D/SHIP1 regulates inflammasome activation in human microglia

status: Public on Sep 27 2023

city: Boston

first: Richard

middle: VanDyke

last: Pearse

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Womens Hospital

summary: Microglia and neuroinflammation are implicated in the development and progression of Alzheimer’s disease (AD). To better understand microglia-mediated processes in AD, we studied the function of INPP5D/SHIP1, a gene linked to AD through GWAS. Immunostaining and single nucleus RNA sequencing confirmed that INPP5D expression in the adult human brain is enriched in microglia. Examination of prefrontal cortex across a large cohort revealed reduced full-length soluble INPP5D protein levels in AD patient brains compared to cognitively normal controls. However, elevated INPP5D immunostaining in microglia in the AD brain was observed, which was driven by elevations in plaque-associated microglia suggesting that these two methods quantify different pools of INPP5D. Examination of INPP5D overexpression and bi-allelic loss-of-function in induced pluripotent stem cell derived microglia (iMGs) revealed that INPP5D LOF most closely resemble microglia in the AD brain with respect to immune signaling alterations, supporting the hypothesis that INPP5D function is reduced in AD microglia. The functional consequences of reduced INPP5D activity were evaluated in human iMGs, using both pharmacological inhibition of the phosphatase activity of INPP5D and genetic reduction in copy number. Unbiased transcriptional and proteomic profiling of these iMGs suggested an upregulation of innate immune signaling pathways, lower levels of scavenger receptors, reduced lysosomal proteins and altered inflammasome signaling with INPP5D reduction. INPP5D inhibition induced the secretion of IL-1ß and IL-18, further implicating inflammasome activation. Inflammasome activation was confirmed through visualization of inflammasome formation through ASC immunostaining in INPP5D-inhibited iMGs, increased cleaved caspase-1 and through rescue of elevated IL-1ß and IL-18 with caspase-1 and NLRP3 inhibitors. In accord, lower INPP5D is associated with higher IL-18 levels and an elevation in microglia with ASC specks in the AD brain. This work implicates INPP5D as a regulator of inflammasome signaling in human microglia.

overall_design: For INPP5D acute inhibition, samples include iMGs from 2 genetic backgrounds (BR01, BR33), treated with 3AC (1.25 uM 3AC, 6 hours) or vehicle. INPP5D HETs were in BR33 background. The INPP5D biallelic loss-of-function monoclones were in the BR24 iPSC line and the INPP5D overexpression samples were also collected from the BR24 iPSC line. For all samples 500ngs of total RNA input was pA selected and sequenced through the Genewiz polyA selection, HiSeq 2x150 single index sequencing platform. RNAseq reads were quality tested using fastqc, quality trimmed then quantified using the Kallisto pseudoalignment quantification program (v0.43.1)  running 50 bootstraps against a Kallisto index generated from GRCh38. Kallisto quantified samples were analyzed using the “Sleuth” package (v0.30.0) in R Studio (v3.6.1 of R; v1.2.5019 of R Studio). Expression values were exported from the Sleuth object as normalized TPM values. The final RNAseq master expression matrix has 16 samples and quantifies expression of 43,122 genes. To identify differentially expressed genes the above matrix was filtered to remove low expressers (greater than 5 TPM in at least 2 samples), leaving 13,532 quantified genes. Conditions were compared by linear modeling with empirical Bayesian analysis using the “limma” package.

first: Vicky

last: Chou

middle: V

last: Pearse II

first: Aimee

last: Aylward

first: Nancy

last: Ashour

first: Mariko

middle: F

last: Taga

first: Masashi

last: Fujita

first: Seeley

last: Fancher

first: Alina

last: Sigalov

first: Courtney

last: Benoit

first: Hyo

last: Lee

first: Matti

last: Lam

first: Nicholas

middle: T

last: Seyfried

first: David

middle: A

last: Bennett

first: Phillip

middle: L

last: De Jager

first: Vilan

last: Menon

first: Tracy

last: Young-Pearse


title: Lifelong dietary protein restriction accelerates skeletal muscle loss and reduces muscle fibre size by impairing proteostasis and mitochondrial homeostasis

city: Liverpool

first: Ufuk

last: Ersoy

address: William Henry Duncan Building

country: United Kingdom

institute: University of Liverpool

summary: To reveal the possible underlying mechanisms of protein restriction during lactation, we compared the transcriptomic profiles of GAS muscles from 21-day-old offsrping from mothers on a low protein diet during lactation and control group using RNAseq analysis.

overall_design:
Two weeks prior to mating, nulliparous female mice were fed either a low-protein diet (L, 8% crude protein) or a normal-protein diet (N, 20% crude protein), both fed ad libitum. Age-matched male mice on a normal-protein diet were used for mating. When the female mice were pregnant, they were kept on the same diet. The male offspring from mothers on normal-protein diet during gestation were used this study.
Within 24 hours of birth, the new-born male litters were cross-fostered to mothers fed either a normal-protein diet or a low-protein diet, in order to create Normal-Normal (NN) or Normal-Low (N-L) groups of mice, respectively

first: Gibran

last: Pedraza Vazquez

first: Moussira

last: Alameddine

first: Ioannis

last: Kanakis

first: Mandy

middle: J

last: Peffers

first: Susan

middle: E

last: Ozanne

first: Malcolm

last: Jackson

first: Katarzyna

last: Goljanek-Whysall

first: Aphrodite

last: Vasilaki


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [MeDIP-seq]

first: Zhi

last: Lu

summary: We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway  were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

overall_design: MeDIP-seq of Homo sapiens: patient's plasma from colorectal and stomach cancer and healthy controls; Provided by Peking University First Affiliated Hospital.

first: Shaozhen

last: Xing

first: Yuhuan

last: Tao

first: Pengfei

last: Bao


title: USF1 modulates transcription and cellular functions by regulating multiple transcription factors in Huh7 cells [RNA-seq]

city: Zhengzhou

first: Yan-li

last: Zeng

state: Henan

address: No.7 of Weiwu Road

department: Department of Infectious Diseases

institute: Henan Provincial People’s Hospital

summary: Liver cancer, including hepatocellular carcinoma (HCC), is a malignant tumor type with high metastasis and mortality rate in worldwide. Upstream transcription factor 1 (USF1) is a canonical transcription factor (TF) and associated with the pathogenesis of several cancers, while its biological functions and molecular targets in HCC are not clear. In this study, we overexpressed USF1 in Huh7 cells and used whole transcriptome profile sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) methods to systematically investigate the downstream targets of USF1. Following polymerase chain reaction (PCR) was used to validate the downstream targets. Based on the results, we found USF1 significantly regulated 350 differentially expressed genes (DEGs). Up DEGs were mainly protein coding genes, and enriched in immune and inflammation response pathways; while down DEGs were mainly lncRNAs, indicating the regulatory feature of USF1. We also detected USF1 directly bound to the promoter region of 2492 genes, which may deeply participate in the viral progression and cell proliferation pathways. By integrating these two datasets, we detected 16 overlapped genes, including down lncRNA-NEAT1 and up TF-ETV5. Down lncRNA-NEAT1 showed reverse expression pattern and prognosis result to USF1 in liver cancer patients, while up TF-ETV5 showed consistent result to USF1. Promoter region motif analysis indicated that ETV5 had more binding motifs and genes than USF1 itself for USF1-regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. Finally, we validated the direct interaction between USF1 and the promoter of ETV5 using ChIP-qPCR. In summary, our results demonstrated that USF1 binds to the promoter region of thousands of genes, and affects large part of DEGs by indirectly manner. The downstream genes, including lncRNA-NEAT1 and TF-ETV5, may also tightly participate in the regulated network by USF1 and have potential functions in the progression of HCC. The USF1 and its downstream targets could be used as potential targets for HCC therapy in future.

overall_design: In order to explore the biological function and molecular mechanism of Upstream transcription factor 1 (USF1) in hepatocellular carcinoma (HCC),in this study, we overexpressed USF1 in Huh7 cells and used whole transcriptome profile sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) methods to systematically investigate the downstream targets of USF1.

first: Fei

last: Gao

first: Can

last: Zhang

first: Pei-pei

last: Ren

first: Li

last: Ma

first: Xin

last: Wang

first: Ru-zheng

first: Yi

last: Kang


title: Glycolytic shift during West Nile virus infection provides new therapeutic opportunities [Cerebellum]

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

summary:
To investigate the in vivo metabolic changes during WNV infection in a mouse model, we infected mice with WNV NY99 to compare to uninfected (mock) mice. We also use two compounds targeting energetic metabolism to analysed their effects on WNV infection
We then performed gene expression profiling analysis using data obtained from RNA-seq from infected vs uninfected mice and treated mice.

overall_design: Comparative gene expression profiling analysis of brain RNA-seq data for mice infected with WNV vs uninfected mice

first: Patricia

last: Mingo-Casas

first: Ana-Belén

last: Blázquez

first: Juan-Carlos

last: Saiz

first: Miguel


title: Glycolytic shift during West Nile virus infection provides new therapeutic opportunities [Brain]


title: LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2’-O methylation

first: Lihui

last: Liu

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: Glioblastoma (GBM) ranks among the most lethal of human cancers, containing glioma stem cells (GSCs) that display therapeutic resistance. Here, we report that the lncRNA INHEG is highly expressed in GSCs compared to differentiated glioma cells (DGCs) and promotes GSC self-renewal through control of rRNA 2’-O-methylation. INHEG induces the interaction between a novel SUMO E3 ligase TAF15 and NOP58, a core component of snoRNP that guides rRNA methylation, to regulate NOP58 sumoylation and accelerate the C/D box snoRNP assembly. INHEG activation enhances rRNA 2’-O-methylation, thereby increasing the translation of oncogenic proteins including EGFR and IGF1R in glioma cells. Taken together, this study identifies a lncRNA that connects snoRNP-guided rRNA 2’-O-methylation to upregulated protein translation in GSCs, supporting a new axis for potential therapeutic targeting of gliomas.

overall_design:
We report a lncRNA that connects snoRNP-guided rRNA 2’-O-methylation to upregulated protein translation in GSCs.  To interrogate the signaling pathways modulated by methyl transferase FBL, we performed RNA-seq of 3565 and MGG4 cells with FBL knockout compared to non-targeting control.  Furthermore, we explored the RNA interactome of NOP58 using ultraviolet cross-linked immunoprecipitation followed by RNA sequencing (uvRIP-seq).
We report a lncRNA that connects snoRNP-guided rRNA 2’-O-methylation to upregulated protein translation in GSCs. To investigate the role of rRNA methylation in the tumor hierarchy, we measured the rRNA 2'-O-Me levels in two matched patient-derived GSCs (3565, MGG4) and DGCs with RiboMethSeq. To interrogate the signaling pathways modulated by methyl transferase NOP58, we performed transcriptome sequencing of 3565 and MGG4 cells with NOP58 knockout compared to non-targeting control.  Furthermore, we conducted ribosome profiling (Ribo-seq) and RNA-seq  to identify the mRNA that lncRNA INHEG regulates.

first: Qinghua

first: Ziyang

first: Peng

last: Lin

first: Wei

last: Wu

first: Qi

last: Xie

first: Runsheng

last: Chen


title: Gene expression profile of uterine fibroblasts cocultured with epithelial cells infected with Chlamydia trachomatis [Coculture_scseq]

city: Omaha

first: Rey

last: Carabeo

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: To identify potential downstream effects of infection-associated expression of pro-fibrotic signal factors, we have cocultured infected epithelial cells with uninfected fibroblasts, using single-cell RNA-sequencing to identify changes in gene expression associated with infection-associated paracrine signaling.

overall_design: Immortalized endocervical epithelial cells (End1/E6E7) seeded at 35% of confluence in a 6-well plate were either mock-infected or infected with Chlamydia trachomatis serovar R2 at an MOI of 2. At 1 hpi, infected epithelial cells were washed with heparan sulfate to remove transiently adhered organisms. Immortalized uterine fibroblasts (KCO2s) were then added into the same well. Cells were harvested for library preparation at 24 hpi (23 hours of coculture).

first: Liam

last: Caven


title: Glycolytic shift during West Nile virus infection provides new therapeutic opportunities [2DG and DGA compounds]

summary:
To investigate the in vivo metabolic changes during WNV infection in a mouse model, we infected mice with WNV NY99 to compare to uninfected (mock) mice. We also use two compounds targeting energetic metabolism to analyze their effects on WNV infection
We then performed gene expression profiling analysis using data obtained from RNA-seq from infected vs uninfected mice and treated mice.


title: Glycolytic shift during West Nile virus infection provides new therapeutic opportunities


title: Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged Acute Lymphoblastic Leukemia’ [ATAC-seq]

city: Utrecht

first: Ronald

middle: W.

last: Stam

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

type: Genome binding/occupancy profiling by high throughput sequencing

summary: KMT2A-rearranged acute lymphoblastic leukemia (ALL) is an aggressive type of leukemia which represents the most common form diagnosed in infancy. Oncogenic KMT2A-fusion proteins recruit histone methyltransferase DOT1L which leads to misplaced H3K79 methylation inducing an abnormal transcriptomic landscape that favors leukemia development. Hence, inhibition of DOT1L represents an attractive therapeutic strategy. Unfortunately, the first-in-class DOT1L inhibitor pinometostat resulted in the development of resistance. To understand this resistance we established acquired resistance to DOT1L inhibition in a pediatric KMT2A::AFF1+ B-ALL cell line model that stably became ~35-fold more resistant to pinometostat. Interestingly, while becoming almost completely independent of DOT1L-mediated H3K79 methylation, these cells remained fully dependent on the physical presence of DOT1L, HOXA9, as well as the KMT2A::AFF1 fusion protein. Further characterization of these cells using RNA-, ChIP-, and ATAC-sequencing analyses revealed that acquired resistance to DOT1L inhibition leads to a selective loss of KMT2A-fusion driven epigenetic regulation and expression of genes such as PROM1 (encoding the hematopoietic/leukemia stem cell marker CD133) and its enhancer TAPT1, as well as other putative KMT2A::AFF1 target genes such as RUNX2, PRSS12, ZC3H12, and GNAQ. In contrast, the levels of H3K79me2 and expression of other KMT2A::AFF1 target genes, including HOXA9, MEIS1, and CDK6 remained unaffected. Concomitantly, pinometostat-resistant KMT2A::AFF1+ B-ALL cells showed upregulation of genes associated with a myeloid immunophenotype, including CD33, LILRB4/CD85k, MPEG1, CCL5, and LIMK1.  Taken together, we here present a valuable model to study the adaptive potential of KMT2A-rearranged ALL upon losing dependency on one of its main oncogenic properties.

overall_design: Acquired resistance to DOT1L inhibitor pinometostat was induced in the KMT2A::AFF1+ ALL cell line SEM, resulting in the pinometostat-resistant daughter line SEMPINO_RES. To characterize our SEMPINO_RES cells and gain insights into the underlying mechanisms of acquired resistance to DOT1L inhibition, we performed RNA-sequencing (RNA-seq), ChIP-sequencing for KMT2A, AFF1, H3K4me3, H3K79me2, and H3K27ac, as well as ATAC-sequencing on SEM and SEMPINO_RES cells cultured in both the absence and presence of 50 µM pinometostat for 7 days.

first: P

last: Schneider

first: RW

first: Nicholas

last: Crump

first: Alastair

last: Smith

first: Thomas

last: Milne


title: Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [long RNA]

first: Zhi

last: Lu

overall_design: RNA-seq of Homo sapiens: patient's plasma from colorectal and stomach cancer and healthy controls; Provided by Peking University First Affiliated Hospital.

first: Shaozhen

last: Xing

first: Yuhuan

last: Tao

first: Pengfei

last: Bao


title: CAG repeat expansion in the Huntington’s Disease gene correlates with defective linear and back-splicing

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento


title: Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged Acute Lymphoblastic Leukemia’


title: Activities, substrate specificity, and genetic interactions of fission yeast Siw14, a cysteinyl-phosphatase-type inositol pyrophosphatase

first: Ana

middle: M

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis compares gene expression of the siw14∆ mutant to the wild-type fission yeast (Schizosaccharomyces pombe).

overall_design: 1 test sample and 1 control sample were processed (each sample has 3 replicate experiments).

first: Beate

last: Schwer

first: Stewart

last: Shuman

first: Henning

last: Jessen

first: Nikolaus

last: Jork


title: Cell type-intrinsic differences in the host transcriptome of Chlamydia trachomatis-infected primary human endocervical epithelial cells and vaginal epithelial cells [HVE_seq]

first: Rey

last: Carabeo

summary: To investigate the role of cell type-intrinsic gene expression to fibrotic sequelae of Chlamydia trachomatis (Ct) infection of the upper female genital tract, we compared the transcriptomic response of primary human endocervical epithelial cells (HCECs, see GSE198272) to that in vaginal epithelial cells (HVEs).

overall_design: Comparative gene expression profiling analysis of RNA-seq data between Ct serovar L2- and mock-infected endocervical epithelial cells and vaginal epithelial cells.

first: Liam


title: Microglia shape AgRP neuron postnatal development via regulating perineuronal net plasticity

status: Public on Sep 26 2023

city: Nanjing

first: Yuanqing

last: Gao

state: CHINA

address: nanjing medical university, jiangning, nanjing, china

institute: Nanjing Medical University

summary: Microglia, the resident immune cells in the brain, have been shown to significantly influence neurodevelopment. However, their role in shaping the postnatal development of hypothalamic neural circuits remains underexplored. In this study, we investigated the dynamic changes of microglia in the hypothalamic arcuate nucleus (ARC) during lactation and their impact on the maturation of AgRP and POMC neurons.

overall_design: to investigate the contribution of microglia to the hypothalamic postnatal development, we deplete microglia from P9-P15 which is a critical time window of ARC neurons development. Then we perfromed the gene expression profiling analysis from the data obtained from RNA-seq of 8 P19 hypothalami (4 vehicle group and 4 PLX3397 group). Each group contains 2 males and 2 females.

first: Jia

last: Sun


title: Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [ATAC-Seq]

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

institute: University of Cambridge

summary: The PIWI-interacting RNA (piRNA) pathway plays a crucial role in preventing endogenous genomic parasites, transposable elements (TEs), from damaging the genetic material of animal gonadal cells.  Specific regions in the genome, called piRNA clusters, define each species’ piRNA repertoire and therefore its capacity to recognize and silence transposons.  In the somatic cells of the Drosophila melanogaster ovary, the flamenco (flam) unistrand cluster is the main source of piRNAs and primarily regulates Gypsy family TEs that are able to form virus-like particles and infect neighbouring germ cells.  Disruption of the flam locus or failure to process flam precursor transcripts into piRNAs results in sterility, yet it remains unknown whether this silencing mechanism is employed widely across Drosophilidae.  Here, using both synteny-based analyses and de novo TE annotation, we identify candidate loci sharing both their organisation and TE targeting repertoire with flam in widely divergent Drosophila species groups. Small RNA-sequencing validated these loci as bona-fide unistrand piRNA clusters and revealed their predominant expression in somatic cells of the ovary, likely to counter TE mobilisation in this tissue.  This study provides compelling evidence of co-evolution between virus-like Gypsy family transposons and a host defence mechanism in form of soma-expressed, unistrand piRNA clusters.

sample_organism:
Drosophila erecta
Drosophila melanogaster
Drosophila persimilis
Drosophila pseudoobscura
Drosophila simulans
Drosophila yakuba
Drosophila suzukii
Drosophila ficusphila
Drosophila biarmipes

overall_design: ATAC-seq of the whole intact ovaries across multiple fly species (Drosophilidae) to characterize the conserved chromatin accessibility landscape

first: Jasper

last: van Lopik

first: Azad

last: Alizada

first: Maria-Anna

last: Trapotsi

first: Gregory

last: Hannon

first: Benjamin

last: Czech Nicholson


title: Themis2 regulates the differentiation and function of memory natural killer cells [TIM_002_RNAseq]

city: Tsukuba

first: Tsukasa

last: Nabekura

state: Ibaraki

address: 1-1-1 Tennodai

department: Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance

country: Japan

institute: University of Tsukuba

summary: To investigate the role of Themis2 in the regulation of the differentiation and function of memory natural killer cells

overall_design: We performed RNA-seq analysis of naïve, effector, and long-lived natural killer cell subsets expressing and not expressing Ly49H during MCMV infection

first: Akira

last: Shibuya

first: Saeko

last: Tahara

first: Yuya

last: Arai


title: Loss-of-function of the nucleoside transporter SLC29A3 drives ERK activation, establishing an alternative pathway for histiocytosis development

city: Petach Tikva

first: Ruth

last: Shiloh

address: Felsenstein Medical Research Center

country: Israel

institute: Schneider Children's Medical Center

summary: Histiocytoses are inflammatory myeloid neoplasms, driven by somatic activating mutations in mitogen-activated protein kinase (MAPK) genes. H syndrome is a genetic disorder caused by germline loss-of-function mutations in SLC29A3, encoding the lysosomal equilibrative nucleoside transporter 3 (ENT3). Patients with H syndrome are predisposed to develop histiocytosis, yet the mechanism is unclear. Here, we demonstrate that loss-of-function of ENT3 leads to MAPK signaling activation, via the nucleoside sensor Toll-like receptor (TLR). We show that H syndrome monocytes exhibit an inflammatory expression pattern, display elevated levels of phospho-ERK, and secrete enhanced amounts of inflammatory cytokines in a TLR8/MEK-dependent manner. Finally, MEK inhibitor therapy successfully eliminated a histiocytic tumor of a patient with H syndrome. These results demonstrate a yet-unrecognized link between a defect in a lysosomal transporter and pathological activation of MAPK signaling, a novel alternative pathway to histiocytosis development, and establish MEK inhibition as a promising new treatment for H syndrome.

overall_design: PBMCs were isolated from fresh whole blood and then monocytes were enriched using a pan-monocyte negative selection method. Cells were analyzed using 10X scRNAseq.


title: CAG repeat expansion in the Huntington’s Disease gene correlates with defective linear and back-splicing [smallRNA-seq]

first: Erik

last: Dassi

summary: small RNA profiling of mESC and NPC cells with various Htt genotypes

overall_design: 2 biological samples per condition and cell type are used. A total of 24 samples were used: 12 for mESC cells (2 Htt KO, 2 Htt WT,2 Q20 Htt, 2 Q50 Htt, 2 Q92 Htt, 2 Q111 Htt) and 12 for NPC cells (2 Htt KO, 2 Htt WT,2 Q20 Htt, 2 Q50 Htt, 2 Q92 Htt, 2 Q111 Htt)

first: Marta

last: Biagioli


title: CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion

city: Sydney

first: Fabio

last: Luciani

address: High St. Kensington

country: Australia

institute: UNSW

summary: Our understanding of cell fate decisions in hematopoietic stem cells is incomplete. Here, we show that the transcription factor Helios is highly expressed in murine hematopoietic stem and progenitor cells (HSPCs), where it is required to suppress the separation of the platelet/megakaryocyte lineage from the HSPC pool. Helios acts mainly in quiescent cells, where it directly represses the megakaryocyte gene expression program in cells as early as the stem cell stage. Helios binding promotes chromatin compaction, notably at the regulatory regions of platelet-specific genes recognized by the Gata2 and Runx1 transcriptional activators, implicated in megakaryocyte priming. Helios null HSPCs are biased toward the megakaryocyte lineage at the expense of the lymphoid and partially resemble cells of aging animals. We propose that Helios acts as a guardian of HSPC pluripotency by continuously repressing the megakaryocyte fate, which in turn allows downstream lymphoid priming to take place. These results highlight the importance of negative and positive priming events in lineage commitment.

overall_design: Longitudinally sampled PBMC and CAR T sorted samples

first: Luciani

last: Fabio

first: Louie

last: Raymond Hall Yip

first: Cai

last: Curtis


title: Malaria drives unique regulatory responses across multiple immune cells during human infection

city: Brisbane

first: Zuleima

last: Pava Imitola

state: Queensland

address: 300 Herston road

institute: QIMR Berghofer

summary: To investigate malaria driven transcriptional changes in specific immune cell subsets, we sorted live PBMCs from 6 malaria infected donors (day 0), and two subsequent time points after drug treatment (day 7 and 28), along with PBMCs from 2 healthy controls. We performed scRNAseq of these cells, and used clustering and sub-clustering to identify specific immune cell subsets. Differential gene analysis between day 0 and day 28 was performed for each cell cluster and sub-cluster. Key transcriptional changes were confirmed at the protein level with additional donor samples.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 6 individuals (age 6-24) with P. falciparum infection and 2 healthy adult endemic controls (ages 20 and 27) were collected before drug treatment (day 0) and at 7 and 28 days after treatment. PBMCs were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of XX signal, and analysed using droplet-based scRNAseq.”

first: Michelle

last: Boyle

first: Nick

last: Dooley

first: Tinashe

last: Chabikwa

first: Jessica

middle: R

last: Loughland

last: Pava

first: J

last: Hamelink

first: K

last: Berry

first: Dean

last: Andrew

first: Megan

last: Soon

first: A

last: SheelaNair

first: Kim

last: Piera

first: T

last: Williams

first: Bridget

last: Barber

first: Matt

last: Grigg

first: Chris

last: Engweda

last: Lopez

last: Anstey


title: Themis2 regulates the differentiation and function of memory natural killer cells

first: Tsukasa

last: Nabekura

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

overall_design: Refer to individual Series


title: HDAC8 mediated alterations in melanoma cell line gene expression

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: HDAC8 expression is causative for resistance to BRAF inhibiton and increased migration in BRAF mutant melanoma cell lines.  Changes in gene expression were determined upon forced HDAC8 expression in an isogenic cell line.

overall_design: 1 million HDAC8 and EV expressing melanoma cells were harvested from melanoma cells grown to 70% confluence in 175 cm2 flasks.  RNA was extracted and gene expression was determined to account for changes in gene expression upon HDAC8 expression.

first: Michael

last: Emmons

first: Richard

last: Bennett


title: CAG repeat expansion in the Huntington’s Disease gene correlates with defective linear and back-splicing [RNA-seq]

first: Erik

last: Dassi

summary: Total RNA profiling of mESC and NPC cells with various Htt genotypes

first: Marta

last: Biagioli


title: Aurora A Kinase Inhibition Induces Accumulation of Tumor Cells in Mitosis with Restored Interferon Signaling to Potentiate Response to PD-L1 Immune Checkpoint Blockade [single cell RNA-seq]

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: By arresting tumor cells in mitosis, aurora A kinase inhibition restores interferon signaling in small cell lung cancer tumor cells and cooperates with PD-L1 immune checkpoint blockade.

overall_design: Single cell RNA sequencing in primary mouse small cell lung cancer cells (SCLC) derived from SCLC genetically-engineered mouse models that are treated with Aurora A Kinase inhibitor and/or PD-L1 ICB.

first: Matthew

middle: G

last: Oser


title: Aurora A Kinase Inhibition Induces Accumulation of Tumor Cells in Mitosis with Restored Interferon Signaling to Potentiate Response to PD-L1 Immune Checkpoint Blockade


title: SARS-CoV-2 infection establishes an enhanced, stable, and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using highly restricted TCRs

city: Durham

first: Joseph

middle: Ruixin

last: Chen

state: North Carolina

address: R323  Pegram 1340 Campus Drive

department: National Institute of Aging

institute: National Institute of Health

summary: In vitro antigenic challenge identified N222-230 (LLLDRLNQL referred to as LLL) as a dominant epitope that elicited the greatest response (number of responders and magnitude of expansion) from both convalescent and uninfected donors.  Analysis of scTCRseq of LLL-specific CD8+ T cells using scTCRseq revealed highly restricted V-gene usage (TRAV12-2) with limited CDR3 motifs, which was supported by structural characterization of a TCR–LLL–HLA-A2 complex. Lastly, transcriptome analysis of CD8+ T cells between expanders and non-expanders identified increased gene expressions associated with differentiation of CD8+ T cells from non- expanders which are shared across the different subsets in a TCR-independent manner. These results show that SARS-CoV-2 infection resulted in significantly enhanced proliferation of LLL-specific CD8+ T cells and suggest that an altered transcriptome is the underlying mechanism controlling activation-induced expansion of LLL-specific CD8+ T cells.

overall_design: Single Cell sequencing of TCRs and Gene Expression

first: Nan-Ping

last: Weng

first: Jian

last: Lu

first: Cecily

last: Choy


title: Transcriptome analysis of rice max1-1400 mutant

city: Thuwal

first: Jian You

last: Wang

state: Not Specified

address: 4700 King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900, Kingdom of Saudi Arabia

country: Saudi Arabia

institute: KAUST

summary: To investigate the general effect under normal and low phosphate conditions when MAX1-1400 mutated in rice

overall_design: Plants were grown hydroponically in Normal (+Pi) or Low Phosphate (Low Pi) conditions for two weeks

middle: Y

first: Guan-Ting

first: Salim

last: Al-Babili


title: Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [RNA-Seq]

first: Susanne

last: Bornelöv

sample_organism:
Drosophila ananassae
Drosophila bifasciata
Drosophila erecta
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila simulans
Drosophila subobscura
Drosophila virilis
Drosophila yakuba
Drosophila azteca
Drosophila suzukii
Drosophila takahashii
Drosophila ficusphila
Drosophila biarmipes

overall_design: Total RNA-seq from dissected ovaries from 10 Drosophila species, 1-8 replicates per species.

first: Jasper

last: van Lopik

first: Azad

last: Alizada

first: Maria-Anna

last: Trapotsi

first: Gregory

last: Hannon

first: Benjamin

last: Czech Nicholson


title: Themis2 regulates the differentiation and function of memory natural killer cells [TIM_007_ChIPseq]

first: Tsukasa

last: Nabekura

overall_design: We performed H3K4me3 and H3K27ac ChIP-seq analysis of naïve and memory wild-type (WT) and Themis2-deficient (KO) Ly49H+ natural killer cell subsets during MCMV infection

first: Akira

last: Shibuya

first: Saeko

last: Tahara

first: Yuya

last: Arai


title: Themis2 regulates the differentiation and function of memory natural killer cells [TIM_006_RNAseq]

overall_design: We performed RNA-seq analysis of naïve and memory wild-type (WT) and Themis2-deficeint (KO) Ly49H+ natural killer cell subsets during MCMV infection


title: HDAC8-mediated inhibition of EP300 drives a neural crest-like transcriptional state that increases melanoma brain metastasis

first: Alberto

last: Riva

summary: Stress-induced HDAC8 activity has been determined to be a driver of a neural crest stem cell (NCSC)-like transcriptional state that increased the formation of melanoma brain metastases (MBM). RNA-Seq experiments were performed against forced HDAC8 expressing cells and empty vector containing melanoma cells to determine differences in gene expression for the HDAC8-induced NCSC-like transcriptional state.

overall_design: HDAC8 expressing and empty vector expressing WM164 cell lines were analyzed for differences in gene expression.

first: Michael

last: Emmons

first: Richard

last: Bennett

first: Jonathan

last: Licht

first: Keiran

last: Smalley


title: SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-g and NK cells [BALF_NK_SARSWu_NHP]

status: Public on Sep 25 2023

city: Paris

first: Nicolas

last: Huot

address: 28, rue du Dr Roux

country: France

institute: Institut Pasteur

summary:
SARS-CoV-2 RNA generally becomes undetectable in upper airways after a few days or weeks post-infection. It is unclear however if the virus persists in other parts of the body and which mechanism(s) regulate SARS-CoV-2 persistence. We addressed this question in the macaque model. Replication-competent virus was detected in bronchioalveolar lavages (BAL) macrophages beyond 6 months post-infection. SARS-CoV-2 propagated in BAL macrophages from cell-to-cell. IFN-γ inhibited this replication. IFN-γ production within BAL lymphocytes was strongest in NKG2r+CD8+ T and NKG2Alo NK cells and was further increased in NKG2Alo NK cells after Spike protein stimulation. However, IFN-γ production was impaired in NK cells from animals with persisting virus. IFN-γ also enhanced MHC-E expression on BAL macrophages, possibly inhibiting natural killer cell mediated killing. Animals with less persisting virus mounted adaptive NK cells escaping this MHC-E dependent inhibition. Our findings reveal an interplay between NK cells and macrophages mediated by IFN-γ, regulating SARS-CoV-2 persistence in macrophages.
Gene expression in bronchoalveolar lavage fluid (BALF) NK cells in SARS-CoV-2 convalescent monkeys.

overall_design: Gene expression profiles in NKG2a/c+ NK cells from BALF of 15 wuhan infected cynomolgus macaques and 5 healthy controls at ≥461 days post-infection, based on mRNA counts normalized via the nanoString nCounter System.

first: Cyril

last: Planchais

first: Pierre

last: Rosenbaum

first: Vanessa

last: Contreras

first: Beatrice

last: Jacquelin

first: Caroline

last: Petitdemange

first: Marie

last: Lazzerini

first: Emma

last: Beaumont

first: Aurelio

last: Orta-Resendiz

first: Félix

last: Rey

first: R

middle: K

last: Reeves

first: Roger

last: Le Grand

first: Hugo

last: Mouquet

first: Michaela

last: Müller-Trutwin


title: Transcriptional heterogeneity overcomes super-enhancer disrupting drug combinations in multiple myeloma

city: Atlanta

first: Benjamin

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University


title: Aurora A Kinase Inhibition Induces Accumulation of Tumor Cells in Mitosis with Restored Interferon Signaling to Potentiate Response to PD-L1 Immune Checkpoint Blockade [RNA-seq]

city: Boston

first: Yixiang

last: Li

overall_design: Bulk RNA sequencing in primary mouse small cell lung cancer cells (SCLC) derived from SCLC genetically-engineered mouse models that are treated with Aurora A Kinase inhibitor.

first: Matthew

last: Oser


title: A gain-of-function p53 mutant synergizes with oncogenic Nras to promote acute myeloid leukemia in mice

city: Madison

first: Jing

last: Zhang

state: Wisconsin

address: 7453 WI Institutes for Medical Research, 1111 Highland Ave

department: University of Wisconsin Carbone Cancer Center

institute: University of Wisconsin-Madison

summary: We previously demonstrated that a subset of acute myeloid leukemia (AML) patients with concurrent RAS pathway and TP53 mutations have extremely poor prognosis, and most of these TP53 mutations are missense mutations. Here, we report that in contrast to mixed AML and T-cell malignancy developed in NrasG12D/+; p53-/- (NP-/-) mice, NrasG12D/+; p53R172H/+ (NPmut) mice rapidly developed an inflammation-associated AML. Under the inflammatory conditions, NPmut hematopoietic stem and progenitor cells (HSPCs) displayed imbalanced myelopoiesis and lymphopoiesis and largely normal cell proliferation despite MEK/ERK hyperactivation.  RNA-Seq analysis revealed that NrasG12D signaling and p53mut synergize to establish an NPmut-AML transcriptome distinct from that of NA-/- cells. The NPmut-AML transcriptome showed GATA2 downregulation and elevated expression of inflammatory genes, including those linked to NFΚB signaling. NFΚB was also upregulated in human NRAS;TP53 AML. Exogenous expression of GATA2 in human NPmut KY821 AML cells downregulated inflammatory gene expression. Mouse and human NPmut AML cells were sensitive to MEK and NFΚB inhibition in vitro. The proteasome inhibitor bortezomib stabilized NFΚB inhibitory protein IΚBɑ mitigated inflammatory gene expression, and potentiated the survival benefit of a MEK inhibitor in NPmut mice. Our study demonstrates that a p53 structural mutant synergizes with NrasG12D to promote AML through mechanisms distinct from p53 loss.

overall_design: To investigate how mutant p53 cooperates with oncogenic Nras to promote leukemogenesis, we performed RNA-Seq with sorted Lin- cKit+ bone marrow HSPCs from moribund double mutant [NPmut] (n=4) as well as poly I:C treated, age-matched control (n=3), p53 mutant (n=3), and oncogenic Nras (n=3) mice.

first: Adhithi

last: Rajagopalan

first: Yubin

last: Feng


title: Dual agonistic and antagonistic roles of ZC3H18 provides for co-activation of distinct nuclear RNA decay pathways

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the Nuclear EXosome Targeting (NEXT) complex and the PolyA eXosome Targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome was considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this unprecedented organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.

overall_design: Total RNA sequencing was carried out on HeLa cells depleted of endogenous ZFC3H1 using siRNA and complemented with exogenously expressed WT or mutated ZFC3H1 variants. Additional samples were prepared following the overexpression of either WT or mutated ZFC3H1_1-209 fragments.

first: Patrik

last: Polák

first: Manfred

last: Schmid

first: Anna

last: Salerno-Kochan

first: Lis

last: Jakobsen

first: Om

last: Rathore

first: Piotr

last: Gerlach

first: Toomas

last: Silla

first: Jens

middle: S

last: Andersen

first: Elena

last: Conti

first: Torben

middle: H

last: Jensen


title: COSMOS: A Platform for real-time morphology-based, label-free cell sorting using deep learning (targeted RNA-Seq)

city: Menlo Park

first: Mahyar

last: Salek

state: CA

address: 4025 Bohannon Dr.

institute: Deepcell, Inc

summary: Cells are the singular building blocks of life, and comprehensive understanding of morphology among other properties is crucial to assessment of underlying heterogeneity. We developed Computational Sorting and Mapping of Single Cells (COSMOS), a platform based on Artificial Intelligence (AI) and microfluidics to characterize and sort single cells based on real-time deep learning interpretation of high-resolution brightfield images. Supervised deep learning models were applied to characterize and sort cell lines and dissociated primary tissue based on high-dimensional embedding vectors of morphology without need for biomarker labels and stains/dyes. We demonstrate COSMOS capabilities with multiple human cell lines and tissue samples. These early results suggest that our neural networks embedding space can capture and recapitulate deep visual characteristics and can be used to efficiently purify unlabeled viable cells with desired morphological traits. Our approach resolves a technical gap in ability to perform real-time deep learning assessment and sorting of cells based on high-resolution brightfield images.

overall_design: Transcriptome profiling by single cell target immune response panel with the BD Rhapsody system on pre-sorted and COSMOS-sorted peripheral blood mononuclear cells (PBMCs).

first: Nianzhen

first: Hou-Pu

last: Chou

first: Kiran

last: Saini

first: Andreja

last: Jovic

first: Kevin

middle: B

last: Jacobs

first: Chassidy

last: Johnson

first: Vivian

last: Lu

first: Esther

last: Lee

first: Christina

last: Chang

first: Phuc

last: Nguyen

first: Jeanette

last: Mei

first: Krishna

middle: P

last: Pant

first: Amy

last: Wong-Thai

first: Quillan

last: Smith

first: Stephanie

last: Huang

first: Ryan

last: Chow

first: Janifer

last: Cruz

first: Jeff

last: Walker

first: Bryan

last: Chan

first: Thomas

last: Musci

first: Euan

last: Ashley

first: Maddison

last: Masaeli


title: COSMOS: A Platform for real-time morphology-based, label-free cell sorting using deep learning (scRNA-Seq)

first: Mahyar

last: Salek

overall_design: Transcriptome profiling by single cell whole transcriptome workflow with the BD Rhapsody system on pre-sorted and COSMOS-sorted dissociated tumor cells (DTC) and peripheral blood mononuclear cells (PBMCs)

first: Nianzhen

last: Li

first: Hou-Pu

last: Chou

first: Kiran

last: Saini

first: Andreja

last: Jovic

first: Kevin

last: Jacobs

first: Chassidy

last: Johnson

middle: F


title: Transcriptome analysis of mouse heart under different intermittent fasting conditions

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

summary: Various intermittent fasting regimes are popularly being practiced but the scientific understanding for the mechanisms of intermittent fasting remains unclear. Observing the overall transcriptomic changes in specific organs, including heart, may contribute substantially in understanding the diverse effects of intermittent fasting. Our current study further investigate the differential transcriptomic changes in the heart among the different regimes of intermittent fasting as well.

overall_design: Male C57BL/6 mice were exposed to 6 months of intermittent fasting regimes starting from at the age of 3 months-old. Experimental groups were daily intermittent fasting for 12 h (IF12), 16 h (IF16), and every-other-day fasting (EOD) groups with ad libitum feeding (AL) group as a control. On the last fasting day, mice were sacrificed and hearts were surgically collected to extract the total RNA samples. Collected total RNA samples were used for mRNA sequencing using Illumina HiSeq 4000 system.

first: Thiruma

middle: V

last: Arumugam


title: SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-g and NK cells [BALF_BloodNK_SARSWu_NHP]

first: Nicolas

last: Huot

overall_design: Gene expression profiles in NKG2a/c+ NK cells from BALF of 12 wuhan infected cynomolgus macaques and their blood counterparts at ≥461 days post-infection, based on mRNA counts normalized via the nanoString nCounter System.

first: Cyril

last: Planchais

first: Pierre

last: Rosenbaum

first: Vanessa

last: Contreras

first: Beatrice

last: Jacquelin

first: Caroline

last: Petitdemange

first: Marie

last: Lazzerini

first: Emma

last: Beaumont

first: Aurelio

last: Orta-Resendiz

first: Félix

middle: A

last: Rey

first: R

last: Reeves

first: Roger

last: Le Grand

first: Hugo

last: Mouquet

first: Michaela

last: Müller-Trutwin


title: SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-g and NK cells

overall_design: Refer to individual Series


title: Total RNA profiles of brain tissue in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology

city: Baltimore

first: Kenneth

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Antiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Regulatory RNAs have emerged as important participants in HIV disease pathogenesis. Using brain tissue  from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs) and circular RNAs (circRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation.

overall_design: Postmortem occipital cortex tissue were collected from pigtailed macaques: uninfected controls and SIV-infected subjects (acute phase and chronic phase with or without CNS pathology). RNAs from  tissue were used for total RNA sequencing to detect mRNA and circRNA levels.

middle: W

first: Yiyao

last: Huang

first: Andrey

last: Turchinovich


title: Small RNA profiles of brain tissue and brain tissue-derived extracellular vesicles in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology

summary: Antiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Brain tissue-derived extracellular vesicles (bdEVs) act locally in the source tissue and may indicate molecular mechanisms in HIV CNS pathology. Regulatory RNAs from EVs have emerged as important participants in HIV disease pathogenesis. Using brain tissue and bdEVs from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs) and microRNAs (miRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation.

overall_design: Postmortem occipital cortex tissue were collected from pigtailed macaques: uninfected controls and SIV-infected subjects (acute phase and chronic phase with or without CNS pathology). bdEVs were separated and characterized in accordance with international consensus standards. RNAs from bdEVs and source tissue were used for small RNA sequencing to detect mRNA and miRNA levels.


title: Characterization of the genes that were regulated by feeding with Lactococcus lactis strains

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the effect of Lactobacillus lactis on healthspan using Caenorhabditis elegans as a model animal. The healthspan of the adult C. elegans fed the mixture of E. coli OP50 and Lactobacillus lactis NBRC 100913 or NBRC 12007 strains was significantly longer than that of animals fed sole OP50 (control). Transcriptional profiling comparing Lactobacillus lactis- and control-fed animals suggested that genes related to “locomotion” were upregulated by Lactobacillus lactis.

overall_design: Transcriptional profiling of three-day-old worms that were fed OP50 or the mixture of OP50 and Lactobacillus lactis NBRC 100913 or NBRC 12007 for five days, by deep sequencing, using Illumina HiSeq.


title: Modulation of insulin secretion through RBFOX2-mediated alternative splicing [eCLIP-Seq MIN6]

city: Aurora

first: Nicole

middle: D

last: Moss

address: 1775 Aurora Ct

institute: University of Colorado

summary: Recent studies have identified dysregulation of RNA-binding proteins (RBPs) and aberrant mRNA splicing in the onset of diseases including diabetes. Here we investigated the role of RBFOX2 in the pancreatic β cell through the conditional mutation of Rbfox2 in the mouse pancreas (Pdx1:Cre; Rbfox2fl/lf) and RNAi experiments in the mouse insulinoma cell line, MIN6. We then identified the direct targets of RBFOX2 in the mouse β cell transcriptome my eCLIP-Seq in MIN6 cells.

overall_design: Identify RBFOX2 bound regions of the transcriptome in MIN6 cells by comparing RBFOX2-eCLIP to its size matched input (SMI) and an IgG-eCLIP with related SMI.

first: Moss

last: Nicole

first: Sussel

last: Lori


title: Dars2 is involved in mRNA splicing in mouse bone marrow hematopoietic stem and progenitor cells

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

summary: Deletion of Dars2 in HSPCs largely impairs spliceosome function and suppresses the protein expression of Srsf3.We performed high-coverage mRNA-seq on lin- ckit+ (LK) cells from both WT and Dars2-KO mice, respectively, to characterize genome-wide alternative splicing (AS) events affected in Dars2-KO HSPCs. Globally, 3970 AS events were significantly changed by loss of Dars2 in HSPCs, including 2431 events in skipped exons (SEs), 516 events in retained introns (RIs), 375 events in mutually exclusive exons (MXEs), 340 events in alternative 3’ splice sites (A3SSs) and 308 events in alternative 5’ splice sites (A5SSs)

overall_design: Comparative gene expression profiling analysis  and alternative splicing analysis of RNA-seq data for Dars2 WT and Dars2 KO lineage negative and ckit positive cells.

first: Xuan

last: Gu

first: Kailing

last: Li

first: Jun

last: Wan


title: Mouse modeling of pediatric glioma, MYCN reveals intratumoral heterogeneity including neuronal and oligodendroglial lineage signatures (scRNA, set 2)

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

summary: Pediatric glioma of the subclass MYCN are highly aggressive tumors frequently carrying MYCN amplifications, TP53 mutations, or both alterations. In order to understand the biology of these tumors better and to improve treatment options, we generated a genetically engineered model by breeding hGFAP-cre::TP53Fl/Fl::lsl-MYCN mice. All such mice developed aggressive forebrain tumors early in lifetime that mimic their human counterparts regarding histology, DNA methylation, and gene expression.

overall_design: A mouse model, hGFAP-cre::TP53Fl/Fl::lsl-MYCNFl/wt, for pediatric high-grade glioma, MYCN was generated. Tumors of four additional tumor-bearing mice were isolated and subsequently analyzed by droplet-based single-cell RNA-seq technology (10X Genomics).

first: Ulrich

last: Schüller

first: Melanie

last: Schoof

first: Julia

middle: E

last: Neumann

first: Kornelius

last: Kerl

first: Thomas

last: Albert


title: Mouse modeling of pediatric glioma, MYCN reveals intratumoral heterogeneity including neuronal and oligodendroglial lineage signatures.

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


title: COSMOS: A Platform for real-time morphology-based, label-free cell sorting using deep learning (bulk RNA-Seq)

first: Mahyar

last: Salek

overall_design: Transcriptome profiling by bulk RNA-Sequencing on pre-sorted and COSMOS-sorted neutrophil samples.

first: Nianzhen

first: Hou-Pu

last: Chou

first: Kiran

last: Saini

first: Andreja

last: Jovic

first: Kevin

last: Jacobs

first: Chassidy

last: Johnson

first: Vivian

last: Lu

first: Esther

middle: J

last: Lee

first: Christina

last: Chang

first: Phuc

last: Nguyen

first: Jeanette

last: Mei

first: Krishna

last: Pant

first: Amy

last: Wong-Thai

first: Quillan

last: Smith

first: Stephanie

first: Ryan

last: Chow

first: Janifer

last: Cruz

first: Jeff

last: Walker

first: Bryan

last: Chan

last: Musci

first: Euan

last: Ashley

first: Maddison

last: Masaeli


title: SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-g and NK cells [BALF_Macro_SARS_NHP]

first: Nicolas

last: Huot

summary:
SARS-CoV-2 RNA generally becomes undetectable in upper airways after a few days or weeks post-infection. It is unclear however if the virus persists in other parts of the body and which mechanism(s) regulate SARS-CoV-2 persistence. We addressed this question in the macaque model. Replication-competent virus was detected in bronchioalveolar lavages (BAL) macrophages beyond 6 months post-infection. SARS-CoV-2 propagated in BAL macrophages from cell-to-cell. IFN-γ inhibited this replication. IFN-γ production within BAL lymphocytes was strongest in NKG2r+CD8+ T and NKG2Alo NK cells and was further increased in NKG2Alo NK cells after Spike protein stimulation. However, IFN-γ production was impaired in NK cells from animals with persisting virus. IFN-γ also enhanced MHC-E expression on BAL macrophages, possibly inhibiting natural killer cell mediated killing. Animals with less persisting virus mounted adaptive NK cells escaping this MHC-E dependent inhibition. Our findings reveal an interplay between NK cells and macrophages mediated by IFN-γ, regulating SARS-CoV-2 persistence in macrophages.
Gene expression in bronchoalveolar lavage fluid (BALF) CD64+ Macrophages isolated from 6 healthy donors, 5 randomly chosen wuhan- and 10 omicron infected cynomolgus macaques at least 221 days post-infection, cultured for 8h and profiled with the NanoString nCounter System.

overall_design: SARS-CoV-2 replication alter the transcriptome of Simian Macrophage isolated from bronchoalveolar lavages in culture

first: Cyril

last: Planchais

first: Pierre

last: Rosenbaum

first: Vanessa

last: Contreras

first: Beatrice

last: Jacquelin

first: Caroline

last: Petitdemange

first: Marie

last: Lazzerini

first: Emma

last: Beaumont

first: Aurelio

last: Orta-Resendiz

first: Félix

last: Rey

first: R

last: Reeves

first: Roger

last: Le Grand

first: Hugo

last: Mouquet

first: Michaela

last: Müller-Trutwin


title: Activation of the pentose phosphate pathway in macrophages is crucial for granuloma formation in sarcoidosis

first: Satoshi

last: NAKAMIZO

address: 54 Shogoin-Kawahara, Sakyo

institute: Kyoto University

summary: Sarcoidosis is a granulomatous disease of unknown cause. We performed single-cell RNA sequencing to identify the macrophages that comprise sarcoidosis granulomas.

overall_design:
Skin samples were obtained from healthy subjects and patients with sarcoidosis by skin biopsy.  Skin samples were digested with collagenase and single-cell suspensions were prepared.  Cell suspensions were analyzed by single-cell RNA sequencing.

>>>Submitter states: Raw data are unavailable due to patient privacy concerns.<<<

last: Nakamizo

first: Kenji

last: Kabashima


title: Targeting of Th17-related cytokines in patients with Darier Disease

city: Lausanne

first: Emmanuella

last: Guenova-Hoetzenecker

state: Vaud

address: 49 rue Bugnon

department: Dermatology

country: Switzerland

institute: CHUV

summary: Darier disease (DD) is a rare, inherited multi-organ disorder associated with mutations in the ATP2A2 gene. In DD patients, the skin is frequently affected, characterized by malodorous, inflamed skin and recurrent, severe infections. Therapeutic options are limited and inadequate for the long-term management of this chronic disease. Using immunoprofiling with NanoString technology, qPCR and immunohistochemistry, we demonstrate enhanced expression of Th-17-related genes and cytokines in six DD patients. We prove that targeting the IL-23/-17 axis in DD with monoclonal antibodies is an effective and safe therapy in DD patients, leading to significant clinical improvement. As DD is a chronic, relapsing disease, our findings provide new options for the long-term management of skin inflammation in patients with DD.

overall_design: Four Darier patients had their lesion skin biopsy sampled an processed by single-cell RNA-seq

first: Monika

last: Ettinger

first: Teresa

last: Burner

first: Anshu

last: Sharma

first: Yun-Tsan

last: Chang

first: Angelika

last: Lackner

first: Yi-Chien

last: Tsai

first: Isabella

last: Pospischil

first: Judith

last: Traxler

first: Gerald

last: Wahl

first: Sabine

last: Altrichter

first: Pacôme

last: Prompsy

first: Leonie

last: Schoeftner

first: Christoph

last: Iselin

first: Iris

last: Gratz

first: Susanne

last: Kimeswenger

last: Guenova

first: Wolfram

last: Hoetzenecker


title: Endoplasmic reticulum stress leads to pancreatic beta-cell desensitization to incretin and beta-cell dysfunction via ATF4-mediated PDE4D expression

city: Daegu

first: Jaemin

last: Lee

state: Select One

address: 333 Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun

department: New Biology

country: South Korea

institute: DGIST

summary: Pancreatic beta-cell dysfunction and eventual beta-cell loss are key steps in the course of type 2 diabetes (T2D). Endoplasmic reticulum (ER) stress, in particular the PERK-ATF4 pathway, has been implicated in promoting these beta-cell pathologies. However, the exact molecular events surrounding the PERK-ATF4 pathway in beta-cell dysfunction remain unknown. Here, we discovered that ATF4 transcriptionally promotes expression of PDE4D, which results in beta-cell dysfunction via downregulation of cAMP signaling. Beta-cell-specific transgenic expression of ATF4 resulted in early beta-cell dysfunction and loss, resembling accelerated T2D. ATF4 expression, rather than CHOP, promoted PDE4D expression, decreased cAMP signaling, and attenuated responses to incretins and elevated glucose. Further, beta-cells of leptin receptor-deficient diabetic (db/db) mice expressed increased levels of ATF4 and PDE4D, accompanying impaired beta-cell function. Moreover, inhibiting PDE4D activity with selective pharmacological inhibitors significantly ameliorated beta-cell dysfunction in both db/db mice and beta-cell-specific ATF4 transgenic mice. In summary, our findings support that ER stress causes beta-cell failure via ATF4-mediated PDE4D production, and this is a highly promising therapeutic target for protecting beta-cell function during progression of T2D.

overall_design: Islet mRNA profiles of 5-wk-old wild type (WT) and beta-cell-specific ATF4 transgenic mice

first: Ji-Hye

first: Hanguk

last: Ryu


title: Comprehensive immune profile changes to human interferon stimulation in normal and HBV-infected conditions in a humanized mouse

status: Public on Sep 24 2023

city: Guangzhou

first: Feng

last: Li

address: No.8, Huaying Road, Baiyun District.

department: Infectious Diseases Institute

institute: Guangzhou Eighth People's Hospital, Guangzhou Medical University


title: The phage-encoded PIT4 protein impacts the Pseudomonas aeruginosa type IV pili by affecting different two-component systems

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

summary: Two component systems (TCSs) control a large proportion of virulence factors in Pseudomonas aeruginosa. Yet, investigations on inhibitors of regulatory pathways of TCS remain scare, despite their potential in anti-virulence strategies. This work encompasses the working mechanism of PIT4, a protein derived from the lytic P. aeruginosa phage LSL4. This viral protein inhibits bacterial motility and in particular twitching motility, while reducing the virulence of P. aeruginosa towards HeLa cells. Via differential gene expression and a yeast two-hybrid screen, PIT4 was shown to interact with components of different two component systems. In one-on-one interaction assays, it was confirmed that PIT4 interacts with the histidine kinases FleS, PilS and PA2882, through interaction with the histidine kinase domain. As such, this work highlights the potential of previously unknown phage proteins in virulence regulation of multidrug resistant pathogens that might be exploited for anti-virulence strategies and biotechnological applications.

overall_design: The transcriptional landscape of cells expressing pit4 was compared to a control, a PAO1 strain harboring an empty construct.

first: Kaat

last: Schroven

first: Leena

last: Putzeys

first: Alison

last: Kerremans

first: Pieter-Jan

last: Ceyssens

first: Marta

last: Vallino

first: Jan

last: Paeshuyse


title: Mouse modeling of pediatric glioma, MYCN reveals intratumoral heterogeneity including neuronal and oligodendroglial lineage signatures (scRNA, set 1)

first: Carolin

last: Walter

overall_design: A mouse model, hGFAP-cre::TP53Fl/Fl::lsl-MYCNFl/wt, for pediatric high-grade glioma, MYCN was generated. Tumors of three tumor-bearing mice were isolated and subsequently analyzed by droplet-based single-cell RNA-seq technology (10X Genomics).

first: Ulrich

last: Schüller

first: Melanie

last: Schoof

first: Julia

last: Neumann

first: Kornelius

last: Kerl

first: Thomas

last: Albert


title: Spliceosome component Usp39 contributes to hepatic lipid homeostasis by sustaining HSF1-lipophagy axis

city: Jinan

first: Zixiang

last: Wang

state: Shandong

address: No.44 Wenhuaxi Road

department: Cheeloo College of Medicine

institute: Shandong University


title: Mouse modeling of pediatric glioma, MYCN reveals intratumoral heterogeneity including neuronal and oligodendroglial lineage signatures [array]

city: Hamburg

address: Martinistr. 52

institute: Research Institute Childrens Cancer Center Hamburg

overall_design: Mouse tumors were dissected and fresh frozen. The DNA was extracted and analyzed by the MM285 mouse methylation array (Illumina).


title: Comprehensive immune profile changes to human interferon stimulation in normal and HBV-infected conditions in a humanized mouse I

summary: The underlying mechanism of chronic hepatitis B virus (HBV) functional cure by interferon (IFN), especially in patients with low HBsAg or/and young ages, is still unresolved for lacking surrogate models. Here, we generated a type I interferon receptor humanized mouse (huIFNAR mouse) through a CRISPR/Cas9-based knock-in strategy. Then, we demonstrated that human IFN stimulated a similar gene expression profile of huIFNAR peripheral blood mononuclear cells (PBMC) to what in human PBMCs, supporting the representativeness of the novel mouse model in functionally analyzing human IFN in vivo. Next, we revealed a markedly tissue-specific gene expression atlas against human IFN treatment in the multiple organs less appreciated in healthy humans in vivo. Finally, using the AAV-HBV model, we test the antiviral effects of human interferon in this mouse. Fifteen-week human PEG-IFNα2 treatment significantly reduced HBsAg and HBeAg and even achieved HBsAg seroconversion. We observed that activation of intrahepatic monocytes and effector memory CD8 T cells by human interferon might be critical for HBsAg suppression. In conclusion, our novel huIFNAR mouse can authentically respond to human Interferon stimulation, providing a novel platform to study interferon function in vivo. The PEG-IFNα2 treatment successfully suppresses intrahepatic HBV replication and achieved HBsAg seroconversion in some mice.

overall_design:
In an effort to explore the mechanism underlying the functional cure of Hepatitis B Virus (HBV) by interferon (IFN), we developed a humanized mouse model expressing the type I interferon receptor (huIFNAR mouse) via a CRISPR/Cas9-based knock-in technique.
Further, we unveiled a remarkably tissue-specific gene expression atlas in response to human IFN treatment across several organs; these findings highlight the potential underappreciated effects of IFN in healthy human tissues in vivo, thereby expanding the scope of our understanding of IFN action.

first: Yaping

first: Liliangzi

last: Guo

first: Jingrong

last: Shi


title: Mouse modeling of pediatric glioma, MYCN reveals intratumoral heterogeneity including neuronal and oligodendroglial lineage signatures [RNA-Seq]

overall_design: Mouse tumors were dissected and fresh frozen. The RNA was extracted with the TRIZOL method and RNA was sequences by Illumina HiSeq sequencing. 11 mouse tumors of hGFAP-cre::TP53 Fl/Fl::lsl-MYCN and 6 mouse tumors of Math1-cre::SmoM2 Fl/wt tumors as well as 3 samples of healthy control cerebellum and 3 olfactory bulbs were analyzed.


title: RIP-seq analysis of Usp39 binding sites in mouse AML12 cell line

summary: Regulation of alternative splicing (AS) is crucial for gene expression and enables a single transcript to yield multiple isoforms that increase transcriptome and proteome diversity. Dysregulated AS has been linked to the development of non-alcoholic fatty liver diseases (NAFLD). However, the splicing factors involved in hepatic homeostasis and their functional mechanisms remain to be further characterized. Here, we report that spliceosome component Usp39 plays a critical role in the regulation of hepatocyte lipid homeostasis. We found that Usp39 expression is downregulated in hepatic tissues of NAFLD and non-alcoholic steatohepatitis (NASH) subjects. We observed increased lipid accumulation, spontaneous steatosis and impaired autophagy, lipophagy in particular, in mice with hepatocyte-specific Usp39 deletion. Combined analysis of RIP-seq and RNA-seq data revealed that Usp39 regulates AS of several autophagy-related genes including Hsf1. More specifically, deletion of Usp39 resulted in alternative 5’ splice site selection of exon 6 in Hsf1 and consequently reduced expression. Hsf1 was also found to be downregulated in NAFLD/NASH mice and patients. Importantly, overexpression of Hsf1 restored lipophagy, attenuated lipid accumulation and alleviated NASH caused by Usp39 deficiency. Taken together, our findings indicate that Usp39-mediated AS is crucial for sustaining lipophagy and lipid homeostasis in the liver.

overall_design: RNA immunoprecipitation sequencing (RIP-seq) for splicing factor Usp39 in mouse AML12 cells.

first: Donghai

last: Cui

first: Changshun

last: Shao

first: Xiyu

last: Zhang

first: Zhaojian

last: Liu


title: RNA sequencing of liver tissues from liver-specific Usp39 knockout (Usp39-HKO) mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 5-week-old Usp39-HKO and control littermates liver


title: Modulation of insulin secretion through RBFOX2-mediated alternative splicing

first: Nicole

last: Moss

country: USA

overall_design: Refer to individual Series


title: Response of the amnion to intrauterine inflammation and effects of inhibition of TNF signaling in preterm Rhesus macaque

status: Public on Sep 23 2023

city: Los Angeles

first: Suhas

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

summary: We demonstrate that during chorioamnionitis the amnion transcriptome is dominated by immune and inflammation related genes, largely driven by the NF-kB pathway. The amnion mesenchymal cells expressing We demonstrated that during chorioamnionitis the amnion transcriptome is dominated by immune and inflammation related genes, largely driven by the NF-kB pathway. CD14 and other myeloid cell markers increase in number with increased expression of innate immune activation markers during intrauterine infections.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: We compared transcriptomics of the amnion in a preterm rhesus macaque model of IUI-induced by lypopolysaccharide with human cohorts of chorioamnionitis.

first: Pietro

last: Presicce

first: Monica

last: Cappelletti

first: Marco

last: Morselli

first: Faiyang

last: Ma

first: Paranthaman

last: Senthamaraikannan

first: Giulia

last: Protti

first: Brian

last: Nadel

first: Laila

last: Aryan

first: Mansoureh

last: Eghbali

first: Salwinski

last: Lukasz

first: Neema

last: Pithia

first: Emily

last: De Franco

first: Lisa

last: Miller

first: Matteo

last: Pellegrini

first: Alan

last: Jobe

first: Claire

last: Chougnet


title: RNA profiles of brain tissue

first: Kenneth

middle: W.

last: Witwer


title: Modulation of insulin secretion through RBFOX2-mediated alternative splicing [RNA-seq Mouse Iselt]

first: Nicole

last: Moss

overall_design: To investigate alternative splicing sensitive genes in the presence and absence of RBFOX2, we generated Rbfox2 conditional mutant mice by combining a single Pdx1:CRE allele (B6.FVB-Tg(Pdx1-cre)6Tuv) (Hingorani et al., 2003) with one or two Rbfox2flox/flox alleles (B6.129S2-Rbfox2tm1.1Dblk/J) (Gehman et al., 2012). We then performed gene expression profiling analysis using data obtained from RNA-seq. Three biological replicates for each genotype. Comparative gene expression profiling analysis of RNA-seq data form non-cre control islets and Rbfox2-mutant islets.

first: Moss

last: Nicole

first: Sussel

last: Lori


title: Modulation of insulin secretion through RBFOX2-mediated alternative splicing [RNA-seq MIN6]

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 replicates each for the NT and Rbfox2-KD conditions.


title: The environmentally-regulated interplay between three-dimensional chromatin organisation and transcription of the Escherichia coli proVWX operon

city: Leiden

first: Remus

last: Dame

state: Zuid-Holland

address: Einsteinweg 55

department: Leiden Institute of Chemistry

institute: Leiden University

summary: Nucleoid associated proteins maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-modelling. Here, we provide the first in vivo evidence supporting this hypothesis. Using RT-qPCR and 3C-qPCR, we show that activation of the H-NS-regulated, osmosensitive proVWX operon of Escherichia coli in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges in cells adapted to hyperosmolarity represses the operon. While the DRE—H-NS—URE bridge is disrupted by hyperosmolarity, the DRE—H-NS—ygaY bridge weakens and requires active transcription to be dismantled. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that structural regulation of expression may be a typical feature of transcriptional control in bacteria.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Chromosome conformation capture experiments to test how various cell fixation techniques, and the enrichment of DNA-protein complexes impact the signal-to-noise ratio in chromosome contact maps.

first: Fatema-Zahra

middle: M

last: Rashid

first: Andreas

last: Hofmann

first: Dieter

last: Heermann

first: Frédéric

last: Crémazy

middle: T

first: David

middle: C

last: Grainger

last: Forrest


title: scRNA-seq of aged Drosophila midgut under methionine restriction

city: Kobe

first: Fumiaki

last: Obata

address: 2-2-3 Minatojima-minamimachi

institute: RIKEN BDR

summary: Methionine restriction is known to extend lifespan in various model organisms including Drosophila melanogaster. In this analysis, we performed scRNAseq of Drosophila female midgut samples to understand the cell type specific response to methionine restriction.

overall_design: The midgut samples were obtained from young (day5), aged (5 weeks old), or aged flies fed with methionine-restricted diet for four weeks. Methionine restriction was achieved by reducing 90% of dietary methionine using the chemically defined diet, which has 40% of all amino acids compared to the original recipe. This resulted in the 1.6 mM methionine in the control, which 0.16mM methionine in the restricted diet.

first: Hina

last: Kosakamoto

first: Hide

last: Aikawa

first: Masayuki

last: Miura


title: Comprehensive immune profile changes to human interferon stimulation in normal and HBV-infected conditions in a humanized mouse II

first: Feng

last: Li

country: China

summary: As IFNs do not directly act on the intracellular HBV viral genome, the intrahepatic microenvironment alteration is postulated to be vital for HBV functional cure, and its characteristics at the termination would be informative. We used scRNA-seq to analyze the intrahepatic immune cell population alliteration after 15-week PEG-IFNα2 treatment.

overall_design:
Immune cells isolated from the liver tissues of mock- and PEG-IFNα2-treated type I interferon receptor humanized mouse were subjected to single-cell sequencing
Due to insufficient numbers, intrahepatic immune cells isolated from 2-3 mice in each group were pooled. We compiled genes express data from 8856 cells for clustering analysis and revealed eight main distinct large cell clusters visualized as Uniform Manifold Approximation and Projection (UMAP) embedding, consisting of Lymphoid cells such as B, T, CD8+ T, CD4+ T, regulatory T, and myeloid cells such as natural killer (NK) cells, neutrophils, and macrophages

first: Yaping

last: Wang

first: Liliangzi

last: Guo

first: Jingrong

last: Shi


title: The smooth muscle-specific lncRNA Carmn is required for visceral smooth muscle contractile function

city: Augusta

first: Jiliang

last: Zhou

address: 1120 15th street

institute: Augusta University

summary: Altered gastrointestinal (GI) motility is associated with significant morbidity and mortality. Here, we aimed at delineating the functional role of Carmn (Cardiac mesoderm enhancer-associated noncoding RNA), a SMC-specific lncRNA, in GI motility. In this study, we observed that Carmn global knockout (gKO) or inducible smooth muscle cell-specific KO (iKO) mice exhibited premature lethality owing to colonic pseudo-obstruction, characterized by severe distension of the cecum and colon.  Bulk RNA-seq and snRNA-seq of colonic muscularis showed that Carmn deficiency impairs the contraction of the colonic muscularis and disrupts the colon homeostasis, which closely related with the down-regulation of the genes maintain the SMC contraction, especially the Mylk. Overall, our data suggest that Carmn is indispensable for maintaining GI contractile function.

overall_design: The colonic muscularis were isolated from Carmn KO and control mice for bulk RNA-sequecing or single-nucleus RNA-sequencing.

first: Xiangqin

last: He

first: Kunzhe

last: Dong


title: RNA-seq  analysis of functionally distinct HLADR+CD38+ CD8 T cells from acute dengue febrile patients

status: Public on Sep 22 2023

city: New Delhi

first: Anmol

last: Chandele

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: International Center for Genetic Engineering and Biotechnology

summary:
A discrete population of the CD8 T population with HLADR+ CD38+ phenotype expand massively during the acute febrile phase of natural infection with dengue virus. Although about a third of these massively expanding HLADR+ CD38+ CD8 T cells were also CD69high when examined ex vivo, only a small fraction made IFNg upon in vitro peptide stimulation.
Here we analyse the transcriptional profile of CD69+IFNg+, CD69+IFNg-, CD69-IFNg-, unstimulated HLADR+ CD38+ and HLADR-CD38- subsets upon peptide stimulation using RNA seq.

overall_design: Expression analysis of HLADR+CD38+CD69+IFNg+, HLADR+ CD38+CD69+IFNg-, HLADR+ CD38+ CD69-IFNg-, unstimulated HLADR+ CD38+, HLADR-CD38- CD8 T cell subsets

first: Murali

last: Krishna Kaja

first: Naveet

last: Wig


title: Differential usage of DNA modifications in neurons, astrocytes and microglia [WGoxBS]

city: Oklahoma City

first: Kyla

last: Tooley

state: OK

address: 825 NE 13th St

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

summary: Cellular identity is determined, in part, by cell type-specific epigenomic profiles that govern gene expression. Isolation and epigenomic characterization of specific cell types is greatly needed in neuroscience. While single cell DNA modification studies offer promise to answer this question, these approaches suffer from limited genomic coverage and cannot differentiate between methylation and hydroxymethylation. Thus, approaches to isolate and analyze DNA from specific CNS cell populations are needed. Here we validate a temporally controlled in vivo nuclear tagging mouse model (NuTRAP) and isolation (INTACT) of neuronal nucleic acids. Analysis of differential DNA modifications (methylation and hydroxymethylation) and gene expression in neurons, astrocytes, and microglia demonstrates a common regulatory function for DNA modifications that transcends cell type. Insight into the normal function of DNA modifications in genomic regulation is crucial in order to better understand the epigenomic mechanisms underlying disease.

overall_design: Camk2a-cre/ERT2;NuTRAP; Nuclei isolated via INTACT method- Input, Negative, and Positive Fractions; 4 biological replicates

first: Ana

last: Chucair-Elliott

first: Sarah

middle: R

last: Ocanas

first: Kevin

last: Pham

first: Walker

last: Hoolehan

first: Adam

last: Kulpa

last: Standford

first: Willard

last: Freeman


title: Genome-wide Human Placenta Enhancer Identification and Association with Function, Differentiation, and Disease [RNA-seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Placental gene expression changes associated with advancing gestational age in weeks or by trimester were identified by differential expression analysis

overall_design: RNA-Seq was perfomed in human placenta tissue from first, second, and third trimester pregnancies

first: David

last: Owen

first: Xuan

last: Huang

first: Anusha

last: Nagari

first: Tulip

last: Nandu

first: W

middle: L


title: Differential usage of DNA modifications in neurons, astrocytes and microglia


title: Differential usage of DNA modifications in neurons, astrocytes and microglia [RNA-seq]

overall_design: Camk2a-cre/ERT2+;NuTRAP+ RNA isolated via TRAP method- Input, Negative, and Positive Fractions; 4 biological replicates

last: Stanford


title: Genome-wide Human Placenta Enhancer Identification and Association with Function, Differentiation, and Disease [CHIP-seq]

summary: Histone modifications associated with genomic enhancer regions (H3K27ac, H3K4me1) were assayed to identify dynamic changes in genomic regulatory regions in human placenta tissue across gestation

overall_design: ChIP-Seq was perfomed in human placenta tissue from first, second, and third trimester pregnancies


title: Mutations in AK9 impair male fertility by altering sperm motility in mice and cattle.

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

summary: Despite passing routine laboratory tests for semen quality, bulls used in artificial insemination (AI) can exhibit a significant variation in fertility. During fertility analysis, a subfertile bull with a low pregnancy rate of 10% was identified. To fully characterize the phenotype, a range of in vitro, in vivo and molecular assays were carried out. Additionally, knockout mice were generated to investigate the function of the identified mutated gene. Sperm from the subfertile bull exhibited reduced motility and severely reduced caffeine-induced hyperactivation compared to control bulls of proven fertility. Ability to penetrate the zona pellucida, cleavage rate, cleavage kinetics, and blastocyst yield after IVF or AI were significantly lower than in control bulls. Whole-genome sequencing and RNA sequencing of testis revealed a critical mutation in AK9 that affect splicing, shaping the majority of AK9 transcripts that leads to a premature termination codon and a severely truncated protein. Transgenic mice deficient in AK9 were generated, resulting in the production of immotile sperm that were unable to fertilize the oocyte. These sperm exhibited abnormalities, including a low ATP concentration. RNA-seq analysis of testis revealed differential gene expression of components of the axoneme and sperm flagella, as well as steroid metabolic processes. Sperm ultrastructural analysis showed a higher percentage of sperm with abnormal flagella. The infertility produced by AK9 mutant bull and in AK9 deficient mice indicates the essential metabolic role of AK9 in sperm motility and/or hyperactivation, which in turn affects sperm binding and penetration of the zona pellucida.

overall_design: Differential gene expression analysis in mice Ak9 knockout testis compared to wild-type testis.

first: Elena

last: O'Callaghan

first: Paula

last: Navarrete-López

first: Miriama

last: Stiavnicka

first: Jose

last: Sanchez

first: Maria

last: Maroto

first: Eva

last: Pericuesta

first: Raúl

last: Fernández-González

first: Ciara

last: O'Meara

first: Bernard

last: Eivers

first: Margaret

last: Kelleher

first: Ross

last: Evans

first: Xena

last: Mapel

first: Audald

last: Lloret-Villas

first: Hubert

last: Pausch

first: Miriam

last: Balastegui-Alarcón

first: Manuel

last: Avilés

last: Sanchez-Rodriguez

first: Eduardo

last: Roldan

first: Michael

last: McDonald

last: Kenny

first: Sean

last: Fair

first: Patrick

last: Lonergan


title: Nanostring gene expression data, comparison of response to subcutaneously implanted porcine-derived decellularized myocardial matrix hydrogels in mast cell deficient mice compared to deficient mice with mast cell engraftment and wild-type C57BL6/J mice

city: La Jolla

first: Raymond

middle: Ma

last: Wang

state: California

address: 2880 Torrey Pines Scenic Dr

department: Bioengineering

institute: University of California San Diego

summary: Nanostring gene expression count data from the Nanostring Mouse Immunology Panel  consisting of 546 genes with 15 internal controls from excised subcutaneous injections of porcine derived decellularized myocardial matrix hydrogels that were lysed and extracted for total RNA.  Data was then exported through the manufacturer nSolverTM Analysis Software 4.0 and analyzed through custom R scripts under R versions 4.04 with normalized counts determined by the NanostringDiff package and thresholding outside of one standard deivation from the mean signal from the negative control probes.

overall_design: In this study, porcine-derived decellularized myocardial matrix hydrogels were injected into the dorsal region of male 11-13 week old mast cell deficient mice (w-sh mice: B6.Cg-KitW-sh/HNihrJaeBsmJ, Jackson Laboratory, Sacramento, CA), mast cell engrafted mice and wild-type C57BL6/J.  Hydrogels were isolated at 11 days post-injection based on latest timepoint for discernible presence hydrogel degradation profile and analyzed for gene expression analysis by Nanostring Mouse Immunology Panel.  Mast cell-engrafted mice were created by delivering eight to ten 100 µL subcutaneous injections of bone marrow differentiated mast cells in DMEM totaling 4 million cells.  Injections were at evenly spaced intervals throughout the dorsal region of 4-6 week old deficient mice.

first: Karen

last: Christman


title: Genome-wide Human Placenta Enhancer Identification and Association with Function, Differentiation, and Disease.

first: W. Lee

last: Kraus

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


title: Biological sex divergence in transcriptomic profiles during the onset of hindlimb unloading-induced atrophy

status: Public on Sep 21 2023

city: Fayetteville

first: Stavroula

last: Tsitkanou

state: AR

address: 155 North Stadium Drive

institute: University of Arkansas

summary: Disuse-induced muscle atrophy is a common clinical problem observed mainly in older adults, intensive care units patients, or astronauts. Previous studies presented biological sex divergence in progression of disuse-induced atrophy along with differential changes in molecular mechanisms possibly underlying muscle atrophy. The aim of this study was to perform transcriptomic profiling of male and female mice during the onset and progression of unloading disuse-induced atrophy. Male and female mice underwent hindlimb unloading (HU) for 24, 48, 72 and 168h (n=8/group). Muscles were weighed for each cohort and gastrocnemius was used for RNA-sequencing analysis. Females exhibited muscle loss as early as 24h of HU, while males after 168h of HU. In males, pathways related to proteasome degradation were upregulated throughout 168-h HU, while in females these pathways were upregulated up to 72-h HU. Lcn2, a gene contributing to regulation of myogenesis, was upregulated by 6.46–19.86-fold across all time points in females only. A reverse expression of Fosb, a gene related to muscle degeneration, was observed between males (4.27-fold up) and females (4.57-fold down) at 24-h HU. Mitochondrial pathways related to TCA cycle were highly downregulated at 168h of HU in males, while in females this downregulation was less pronounced. Collagen-related pathways were consistently downregulated throughout 168-h HU only in females, suggesting a potential biological sex-specific protective mechanism against disuse-induced fibrosis. In conclusion, females may have protection against HU-induced skeletal muscle mitochondrial degeneration and fibrosis through transcriptional mechanisms, although they may be more vulnerable to HU-induced muscle wasting compared to males.

first: Nicholas

last: Greene

first: Megan

last: Rosa-Caldwell


title: Dietary trans-vaccenic acid promotes anti-tumor immunity

city: Chicago

first: fan

last: hao

state: IL

address: 5801 S Ellis Ave

institute: University of Chicago

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome


title: Immunoprofiling of Darier Disease patients

city: Linz

first: Susanne

last: Kimeswenger

address: Krankenhausstraße 5

department: Department of Dermatology and Venerology

country: Austria

institute: Johannes Kepler University Linz

summary: Darier disease (DD) is a rare, inherited multi-organ disorder associated with mutations in the ATP2A2 gene. In DD patients, the skin is frequently affected, characterized by malodorous, inflamed skin and recurrent, severe infections. Therapeutic options are limited and inadequate for the long-term management of this chronic disease. Using immunoprofiling with NanoString technology we demonstrate enhanced expression of Th-17-related genes and cytokines in five DD patients. We prove that targeting the IL-23/-17 axis in DD with monoclonal antibodies is an effective and safe therapy in DD patients, leading also to significant clinical improvement.

overall_design: We analyzed six samples from DD patients (one (DAR2) had to be excluded due to poor quality), two of them were also analyzed after treatment with monoclonal antibodies. As negative controls two normal skin samples were included, as positive controls two samples from lesional skin of psoriasis patients were included.

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