title: Whole-genome transcriptomic analysis in Sorghum bicolor variety CSV24SS

summary: We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

overall_design: Examination of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum variety CSV24SS

first: Supriya

last: Mathur

first: Madan

last: Pal


title: Whole-genome transcriptomic analysis in Sorghum bicolor variety M35-1

status: Public on Dec 31 2023

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

country: India

institute: Jawaharlal Nehru University

type: Expression profiling by high throughput sequencing

summary: We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

overall_design: Examination of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum variety M35-1

middle: K


title: Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas

status: Public on Dec 30 2023

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

type: Methylation profiling by high throughput sequencing

summary: Background: The placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. Contrary to popular belief, the placenta forms mainly from fetal tissue; therefore, it has the same biological sex as the fetus it supports. However, while placental function is linked to increased risks of pregnancy complications and neurodevelopmental diseases in male offspring in particular, the sex-specific epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown.Methods: We collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex-specific differences in transcription and DNA methylation. Results: Our sex-specific analysis revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Sex-specific differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several sex-specific DEGs were correlated with sex-specific DMRs. A subset of the sex-specific DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas, while others were acquired later in placental development.Conclusion: Our study provides comprehensive lists of sex-specific DEGs and DMRs that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function.

overall_design: To investigate the DNA methylation differences in the mouse placenta at late gestation between males and females, we conducted SureSelect Methyl-Seq (Capture).

first: Lisa-Marie

last: Legault

first: Mélanie

last: Breton-Larrivée

first: Anthony

last: Lemieux

first: Alexandra

last: Langford-Avelar


title: RNA-seq of group 2 (TCRβintCD69hi) and group 3 (TCRβhiCD69hi) thymocytes in Uba3F/F and Uba3ΔT mice

city: Beijing

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

country: China

institute: Institute of Basic Medical Sciences

summary: To explore the underlying molecular mechanisms responsible for the defective T cell development in the absence of neddylation, we isolated group 2 (TCRβintCD69hi) and group 3 (TCRβhiCD69hi) thymocytes by Flow cytometry from Uba3F/F and Uba3ΔT mice and performed RNA-seq. Pathway enrichment analysis indicated the MAPK signaling pathway  were involved during the process. Besides, STAT5 target genes were also changed.

overall_design: Examination of gene expression of group 2 (TCRβintCD69hi) and group 3 (TCRβhiCD69hi) thymocytes in Uba3F/F and Uba3ΔT mice.

first: Yujun

last: Pei

first: Yaolin


overall_design: To investigate the gene expression differences in the mouse placenta at late gestation between males and females, we performed mRNA-sequencing (mRNA-Seq)


title: Transcriptome diversity among rice root types in salinity tolerant and sensitive varieties

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

summary: Differences in gene expression were compared among nodal roots, S-type lateral roots, and L-type lateral roots of salinity tolerant and sensitive rice varieties.

overall_design: Using RNA sequencing, the gene expression patterns of different root types were compared in both salinity tolerant and sensitive rice varieties.


title: Immune suppressive landscape in the human non-small cell lung cancer microenvironment

city: Shanghai

first: Liwen

last: Fan

address: No.241 West Huaihai Street

institute: Shanghai Chest Hospital

summary:
Background: Lung cancer is the one of the malignant tumors with the highest morbidity and mortality in China and even the world. The overall five-year survival rate is about 20%, and most patients die of tumor metastasis. Non-small cell lung cancer (NSCLC) is the main pathologic type of lung cancer. The development and metastasis of tumor cells is influenced by the interaction with other cells in the environment. To explore the molecular expression spectrum of tumor and tumor microenvironment can provide clues for the mechanism of tumor progression, drug resistance and metastasis. The emergence of single cell ribonucleic acid sequencing (scRNA-seq) technology can explore the genomic and transcriptional characteristics of different tumor cells at the single cell resolution, which can reveal the molecular characteristics of individual cells and the relationship between individuals and the environment, thus making it possible to further understand the genesis and progression of NSCLC.
Methods: ScRNA-seq (10X genomics) was used to detect single-cell transcriptomes in 2 patients with NSCLC, aiming to more accurately explore the effects of the transcriptome in a single cell on its function and the progression of NSCLC, and to find new cell subtypes or molecular targets for drug therapy.
Results: The tumor tissue, distant normal tissue, and lymph node tissue of 2 patients with NSCLC were analyzed. A total of 43779 cells were analyzed, which were classified into epithelial cells, T lymphocytes, natural killer cells (NK cells), B lymphocytes, myeloid cells, endothelial cells, fibroblasts, and MAST cells. Tumor cells showed signature markers of epithelial (EPCAM, KRT7, KRT8, KRT18, CDH1, etc.) and tumor (KRT19, ENO2, SLC25A2, UBE2C, etc.) markers. Additionally, the acquired immunity is activated in the tumor microenvironment, while the innate immunity is exhausted. The proportion of B lymphocytes increases, and immunosuppressive tumor-infiltrating B cells (CD19+, MS4A1+, CD69+, CD27-, CR2-) are observed, which are capable of participating in the induction of exhausted regulatory T cells. The proportion of cytotoxic CD8+ T cells in T lymphocyte population decreases, and the number of exhausted regulatory T cells and exhausted follicular helper T cells increases. They all express LAG3+, TIGIT+, PDCD1+, CTLA4+, and other suppressive markers, showing a state of immunosuppression. High expression of WFDC2 in T cells has a significant effect on prognosis. NK cells show a state of depletion, not only in number, but also gradually transform into a less cytotoxic subtype (CD56+, CD16-). In addition, myeloid cells also play an important role in disrupting the anti-tumor immune response. Tumor associated macrophages (TAMs) and plasmacytoid dendritic cells (pDCs) are enriched in tumor tissue. TAMs highly express anti-inflammatory markers (APOE+, C1QA+, C1QB+) and proliferative markers (MKI67+, STMN1+, NUSAP1+), which are closely related to tumor progression and metastasis. TAMs show M2 type polarization of macrophages, which has a tumor promoting effect. At the same time, TAMs express monocyte markers, which may be transformed from monocyte derived macrophages. Macrophages highly express CXCL8, CCL2, and other genes, which participate in Toll-like receptor, NOD-like receptor signaling pathway, and have a significant impact on the prognosis. pDCs are immunosuppressive cells. The high expression of LILR family genes and GZMB in pDCs may lead to poor tumor antigen presentation of lung squamous cell carcinoma. Dendritic cells highly express NLRP3, IRF7, and other genes, which participate in C-type lectin receptor, Toll-like receptor, NOD-like receptor signaling pathway, and have a significant impact on the prognosis. In addition to the immune system, fibroblasts in the stroma also show characteristics of immunosuppressive cells. Enrichment of Cancer-associated fibroblasts (CAFs) in tumor can promote immunosuppression and tumor progression. Among them, a special subtype termed inflammatory CAFs is found, which participate in the process of extracellular matrix remodeling, angiogenesis, and cell migration, resulting in promoting tumor progression. Fibroblasts highly express FN1, TIMP1, and hub gene SPP1, which interact with macrophages, participate in PI3K-AKT pathway, and have a significant impact on the prognosis.
Conclusions: NSCLC shows heterogeneous tumor microenvironment. A variety of immune cells and stromal cells together lead to immunosuppressive environment and promote the progression of tumor. This study enhances our understanding of molecular and cellular dynamics of NSCLC, and reveals potential diagnostic and therapeutic targets in tumor microenvironment.

overall_design: Single-cell RNA sequencing (10X Genomics) of non-small cell lung cancer, including two tumor tissues, two paired adjacent normal lung tissues, and two lymph node tissues from two patinets.

first: Fan

last: Liwen

first: Yang

last: Haitang

first: Gao

last: Wen

first: Yao

last: Feng


title: Resistance to PRMT5 Inhibitor Targeted Therapy in MCL [WES]

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

country: USA

institute: Weill Cornell Medical College

summary: To identify the genomic changes underlying PRMT5 inhibitor resistance in MCL cell lines and MCL PDX

overall_design: Whole exome of MCL PDX cells (untreated (n=1), short-term treated (n=1), and resistant treated (n=2)) and resistant and sensitive MCL cell lines

first: Long

last: Mackenzie

first: Baiocchi

last: Robert

first: Alinari

last: Lapo

first: Blaser

last: Brad


first: Serge

last: McGraw

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

overall_design: Refer to individual Series


title: Resistance to PRMT5 Inhibitor Targeted Therapy in MCL [RNA-seq]

summary: To identify the transcriptomic changes underlying acquired PRMT5 inhibitor resistance in MCL cell lines (n=3/group) and MCL PDX

overall_design: RNA-sequencing of MCL PDX cells (untreated (n=3) short-term treated (n=3) and resistant treated (n=2)) and MCL cell lines resistant and sensitive treated (n=3) and untreated (n=3)


title: Resistance to PRMT5 Inhibitor Targeted Therapy in MCL


title: Synthetic reversed sequence reveals default chromatin states [Yeast_ChIP-seq]

first: Brendan

middle: R.

last: Camellato

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Langone Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Most of human genome may show evidence of transcription, yet annotated transcripts account for less than 5%. The basis for this major discrepancy is not clear, and it remains uncertain whether excess transcription is functional, or simply a byproduct of pervasive, non-specific RNA polymerase binding and transcription initiation. Understanding the default state of the genome would be informative in determining whether the observed pervasive activity is functional. The genome of any extant organism has undergone billions of years of evolution, making it unclear whether any observed genomic activity, or lack thereof, has been selected for. We sought to address this question by introducing a completely novel 101 kb locus into the genomes of two eukaryotic organisms, S. cerevisiae and M. musculus, and characterizing its genomic activity based on chromatin accessibility, chromatin states, and transcription. The locus was designed by reversing, but not complementing, the sequence of the human HPRT1 locus, including ~30 kb of both upstream and downstream regulatory regions, allowing retention of sequence features like repeat frequency and GC content but ablating coding information and transcription factor binding sites. We also compared this reversed locus with a synthetic version of the normal human HPRT1 locus in both organismal contexts. Neither the synthetic HPRT1 locus nor its reversed version evolved to harbor yeast promoters. Nevertheless, we observed widespread transcriptional activity of both loci in yeast, and this pervasive activity was observed both when the loci were present as episomes and when chromosomally integrated. In the latter case, it was obvious that the accessibility and level of transcription initiation substantially exceeded that of the flanking native yeast genome sequences. In contrast, when integrated in the mouse genome, the synthetic HPRT1 locus showed transcriptional activity corresponding precisely to the HPRT1 coding sequence, whereas the reverse locus displayed no activity at all, but was instead actively repressed by Polycomb machinery. Together, these results show that novel genomic sequences lacking coding information are active in yeast, but repressed in mouse stem cells, indicating a major difference in default genomic states between these two divergent eukaryotes, with implications for understanding pervasive transcription and the birth of new genes.

overall_design:
Exploratory RNA-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are transcribed in yeast, and to compare to the rest of the respective genome.
the records are duplicated by GSE252472

middle: R

first: Ran

last: Brosh

first: Hannah

middle: J

last: Ashe

first: Matthew

middle: T

last: Maurano

first: Jef

middle: D

last: Boeke


title: scRNAseq of Cd45+ cells from brains of Aducanumab-treated ApoE-variant Alzheimer's mice

status: Public on Dec 29 2023

first: Alon

last: Millet

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Here we perform single cell sequencing to examine the impact of aducanumab treatment on the transcriptome of immune cells of aged AD mice bearing knock-in of human APOE variants in the murine APOE locus, treated either with aducanumab or an IgG control.

overall_design: We isolated Cd45+ cells from the hippocampal and cortical regions of 60-week-old 5XFAD-hemizygous mice bearing homozygous knock-in of APOE2, APOE3, or APOE4 in the murine Apoe allele after 7d treatment with either aducanumab or an IgG control i.p. Cells were hashed and sequenced as a single library by 10X 5'v2 single cell sequencing.


title: Regulation of respiratory complex I assembly by FMN cofactor targeting

city: Madrid

first: Jose

middle: Luis

last: Cabrera

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: The main objective of this study is to answer whether the stability of mammalian complex I is regulated by its flavin cofactor. For this purpose, diphenyleneiodonium (DPI) was used as inhibitor of N-module, to evaluate stability in  in CI

overall_design: Expression profiling by high-throughput sequencing, to reveal the effect of DPI treatment at 24 and 72.

first: Andrea

last: Curtabbi

first: Adela

last: Guaras

first: José

middle: L

first: Rivero

last: Marivel

first: Erique

last: Calvo

first: Marina

last: Rosa

first: Jesús

last: Váquez

first: Milagros

last: Medina

middle: A

last: Enríquez


title: Pericyte loss initiates microvascular dysfunction in the development of diastolic dysfunction

city: Leuven

first: Elizabeth

last: Jones

address: Herestraat 49

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

summary: Microvascular dysfunction has been proposed to drive heart failure with preserved ejection fraction (HFpEF), but the initiating molecular and cellular events are largely unknown. Our objective was to determine when microvascular alterations in HFpEF begin, how they contribute to disease progression, and how pericyte dysfunction plays a role herein. We aimed to assess microvascular dysfunction with respect to the development of cardiac dysfunction, in the Zucker fatty and spontaneously hypertensive (ZSF1) obese rat model of HFpEF at three time points: 6, 14, and 21 weeks of age. We found that pericyte loss was the earliest and strongest microvascular change, occurring before prominent echocardiographic signs of diastolic dysfunction were present. Pericytes were shown to be less proliferative and had a disrupted morphology at 14 weeks in the obese ZSF1 animals, who also exhibited an increased capillary luminal diameter and disrupted endothelial junctions. Pericytes exposed to oxidative stress in vitro showed downregulation of cell cycle associated pathways, and induced a pro-inflammatory state in endothelial cells upon co-culture. We propose pericytes are important for maintaining endothelial cell function, where loss of pericytes enhances the reactivity of endothelial cells to inflammatory signals and promotes microvascular dysfunction, thereby accelerating the development of HFpEF.

overall_design: To identify the underlying mechanisms of pericyte dysfunction, we exposed human immortalised pericytes to oxidative stress for 24h and compared their gene expression profile to non-treated cells. DEG analysis erroneously used oxidative stress (OX) as control condition and non-oxidative stress (NOX) as experimental condition.

first: Ilona

last: Cuijpers

first: Mandy

last: Grootaert

first: Steven

last: Simmonds


title: Synthetic reversed sequence reveals default chromatin states [Yeast_CAGE-seq]

first: Brendan

last: Camellato

overall_design:
Exploratory RNA-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are transcribed in yeast, and to compare to the rest of the respective genome.
the records are duplicated by GSE252471

first: Ran

last: Brosh

first: Hannah

last: Ashe


title: scRNAseq of Cd45+ cells from brains of ApoE-variant Alzheimer's mice sorted by ex-vivo amyloid beta uptake

first: Alon

last: Millet

summary: Here we perform single cell sequencing of immune cells of aged AD mice bearing knock-in of human APOE variants in the murine APOE locus, sorted into high-uptake and low-uptake pools after incubation with fluorescently labeled amyloid beta.

overall_design: We produced single cell suspensions from the hippocampal and cortical regions of 60-week-old 5XFAD-hemizygous mice bearing homozygous knock-in of APOE2, APOE3, or APOE4 in the murine Apoe allele. Cells were incubated with fluorescently labeled amyloid beta before being sorted for Cd45+ and split into a high- and low-uptake pool. Cells were hashed post-sort and sequenced as a single library by 10X 5'v2 single cell sequencing.


title: An Exhausted-Like Microglial Population Accumulates in Aged and APOE4 Genotype Alzheimer’s Brains


title: Comparative analysis of the transcriptional response to bulky DNA damages

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

summary: A systematic RNA-seq study comparing the transcriptional response to three independent bulky DNA damage inducing agents: UV, the chemotherapy cisplatin and benzo[a]pyrene, a component of cigarette smoke. It was performed in 2 different cell lines - GM12878 immortalized lymphoblast cell line and A549 lung cancer cell line.

overall_design: We performed RNA-Seq in untreated GM12878 and A549 cells, as well as 6h after being treated with 5μM of BPDE, 200μM of cisplatin, 20J/m2 of UVC. For each condition there were 3 replicates: A549 control, A549 + cisplatin, A549 + BPDE , A549 + UV , GM12878 control, GM12878 + cisplatin, GM12878 + BPDE , GM12878 + UV.

first: May

last: Merav

first: Elnatan

middle: M

last: Bitensky

first: Elisheva

last: Heilbrun

first: Tamar

last: Hacohen

first: Ayala

last: Kirshenbaum

first: Hadar

last: Golan-Berman

first: Yuval

last: Cohen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ADAR1-/- mouse Transcriptomes

city: Shenzhen, Guangdong

first: Wenjing

last: Chen

address: XueYuan Road

institute: SUSTech

summary:
Purpose: The goals of this study are to compare WT and ADAR1 knockout mouse B cell transcriptome profiling (RNA-seq)
Methods: Cells are sorted from bone marrow of WT and ADAR1 KO mice and mRNA profiles were generated by deep sequencing using Illumina Hiseq.
Results: Using an optimized data analysis workflow, we confirmed over hundrad differential expressed genes by KEGG pathway analysis with 185 up-regulated genes and 136 down-regulated genes.
Conclusions: Our study represents the first detailed analysis of B cell mRNA profile from WT and ADAR1 KO mice using RNA-Seq.   We conclude that ADAR1 plays important roles during early B cell development.

overall_design: Early B cell mRNA profiles of  wild type (WT) and ADAR1 KO mice

first: Xijun

last: Ou


title: TEA domain transcription factor 1(TEAD1) induces cardiac fibroblasts cells remodeling through BRD4/Wnt4 pathway [RNA-Seq]

status: Public on Dec 28 2023

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

institute: Zhongshan  Hospital, Fudan University

summary: Cardiac fibroblasts (CFs) are the primary cells tasked with depositing and remodeling collagen and significantly associated with heart failure (HF). TEAD1 has been shown to be essential for heart development and homeostasis. However, endogenous fibroblast TEAD1 in cardiac remodeling remains incompletely understood. Transcriptomic analyses revealed consistently upregulated cardiac TEAD1 expression in mice 4 weeks after transverse aortic constriction (TAC) and Ang-II infusion. Further investigation revealed that CFs were the primary cell type expressing elevated TEAD1 levels in response to pressure overload. Conditional TEAD1 knockout was achieved by crossing TEAD1-floxed mice with CFs- and myofibroblasts-specific Cre mice. Echocardiographic and histological analyses demonstrated that CFs- and myofibroblasts-specific TEAD1 deficiency and treatment with TEAD1 inhibitor, VT103, ameliorated TAC-induced cardiac remodeling. Mechanistically, RNA-seq analysis identified Wnt4 as a novel TEAD1 target. TEAD1 has been shown to promote the fibroblast-to-myofibroblast transition through the Wnt signalling pathway, and genetic Wnt4 knockdown inhibited the pro-transformation phenotype in CFs with TEAD1 overexpression. Furthermore, co-immunoprecipitation combined with mass spectrometry, chromatin immunoprecipitation, and luciferase assays demonstrated interaction between TEAD1 and BET protein BRD4, leading to the binding and activation of the Wnt4 promoter. In conclusion, TEAD1 is an essential regulator of the pro-fibrotic CFs phenotype associated with pathological cardiac remodeling via the BRD4/Wnt4 signalling pathway.

overall_design: To fully understand the molecular mechanisms underlying TEAD1-mediated cardiac remodeling, we next performed genome-wide RNA-seq to identify the transcriptomic changes in response to TEAD1 knockdown and overexpression in NMCFs. RNA samples were collected from NMCFs in different experimental groups, including si-NC (negative control), si-TEAD1 (TEAD1 knockdown), Ang-II (angiotensin II stimulation), si-TEAD1+Ang-II (combined TEAD1 knockdown and angiotensin II stimulation), OE-NC (overexpression negative control), and OE-TEAD1 (TEAD1 overexpression).


title: Circulating NK cells establish tissue-residency upon acute infection of skin and mediate accelerated effector responses to secondary infection

city: Wuerzburg

first: Georg

last: Gasteiger

address: Versbacher Strasse 9

department: Institute of Systems Immunology

country: Germany

institute: University Wuerzburg

summary:
Natural killer (NK) cells are present in the circulation and can also be found residing in
tissues; these populations exhibit distinct developmental requirements and are thought
to differ in terms of ontogeny. Here, we investigated whether circulating conventional
NK (cNK) cells can develop into long-lived, tissue-resident cells following acute
infections. We found that viral and bacterial infections of the skin triggered the
recruitment of cNK cells and their differentiation into Tcf1hiCD69hi tissue-resident (trNK)
cells that share transcriptional similarity with CD56brightTCF1hi NK cells in human
tissues. Skin trNK arose from IFN--producing effector cells and required restricted
expression of the transcriptional regulator Blimp1 to optimize Tcf1-dependent trNK
formation. Upon secondary infection, trNK cells rapidly gained effector function and
mediated an accelerated NK cell response. Thus, cNK cells redistribute and
permanently position at sites of previous infection via a mechanism promoting tissueresidency
that is distinct from Hobit-dependent developmental paths of NK cells and
ILC1 seeding tissues during ontogeny.

overall_design: 15 samples

first: Tommaso

last: Torcellan

first: Christin

last: Friedrich

first: Rémi

last: Doucet-Ladevèze

first: Thomas

last: Ossner

first: Virgínia

last: Visaconill Solé

first: Sofie

last: Riedmann

first: Milas

last: Ugur

first: Fabian

last: Imdahl

first: Stephan

middle: P

last: Rosshart

first: Sebastian

last: Arnold

first: Mercedes

last: Gomez de Agüero

first: Nicola

last: Gagliani

first: Richard

last: Flavell

first: Simone

last: Backes

first: Wolfgang

last: Kastenmueller


title: scRNAseq and scATACseq of Cd45+ cells from brains of 5XFAD mice bearing distinct APOE alleles and across age

first: Alon

last: Millet

summary: Here we analyze the gene expression and chromatin accessibility landscape of immune cells in the brains of 5XFAD mice, a common model of Alzheimer's disease, bearing knock-in of human APOE variants in the mouse APOE locus, and aged to 10, 20, 60, or 96 weeks of age.

overall_design: Cd45+ cells were isolated from hippocampal and cortical regions of brains from 5XFAD APOE-hu/hu mice by fluorescence activated cell sorting (FACS) and analyzed using either scRNAseq or 10X multiome.


title: Molecular mechanisms underlying the high mortality of hypervirulent Klebsiella pneumoniae and its effective therapy development

status: Public on Dec 26 2023

city: Hong Kong

first: QI

last: XU

address: B2530, Yeung Kin Man Academic Building, City University of Hong Kong, Hong Kong

department: Department of Infectious Disease and Public Health

institute: City University of Hong Kong

summary: High-resolution single-cell RNA-seq reveals the immune landscape of hvKp-infected lungs

overall_design: Lung cells of the C57B/L6 mice were isolated and analyzed using scRNAseq.

first: Qi

first: Xiaoxuan

last: LIU

first: Heng

last: HENG

first: Sheng

last: CHEN


title: nCounter mouse immune exhaustion panel in 4t1 breast cancer treated with repeat intratumoral influenza vaccine

status: Public on Dec 25 2023

city: Chicago

first: Amanda

last: Marzo

state: IL

address: 1620 W Harrison St

institute: Rush University

summary: Murine 4T1 breast cancer was grown in vivo and treated with repeat intratumoral influenza vaccine. Flash frozen tissue evaluated by nCounter mouse immune exhaustion panel.

overall_design: Murine 4T1 breast cancer was established in vivo and upon palpable size was treated with repeat intratumoral influenza vaccine. Mice sacrificed 20 days later and tumor tissue taken to examine tumor microenviroment by nanostring murine immune exhaustion panel.

first: Preston

last: Daniels


title: Single cell RNA seq analysis of LPS-stimulated PBMCs pre-treated with JRD-SIK1/2i-3

city: Spring House

first: Luvena

last: Ong

state: PA

address: 1400 McKean Rd

institute: Johnson & Johnson Innovative Medicine

summary: The Salt-Inducible Kinases (SIK) 1-3 are key regulators of pro- versus anti-inflammatory cytokine responses during innate immune activation. The lack of highly SIK-family or SIK isoform-selective inhibitors suitable for repeat, oral dosing has limited the study of which SIK isoforms need to be targeted to suppress inflammation in vivo. To overcome this challenge, we devised a structure-based design strategy for developing potent SIK inhibitors that are highly selective against other kinases by engaging two differentiating features of the SIK catalytic site. This effort resulted in SIK1/2-selective probes that inhibit key intracellular proximal signaling events including reducing phosphorylation of the SIK substrate cAMP response element binding protein (CREB) regulated transcription coactivator 3 (CRTC3) 3 as detected with a newly generated phospho-Ser329-specific antibody. These inhibitors also suppress production of pro-inflammatory cytokines while inducing anti-inflammatory interleukin-10 in activated human and murine myeloid cells as well as in mice following a lipopolysaccharide challenge. To define the functional effects of SIK1/2 inhibitors in primary human immune cells, we profiled the transcriptional responses elicited by SIK1/2-selective probe JRD-SIK1/2i-3 in peripheral blood mononuclear cells (PBMCs) isolated from healthy donors responding to TLR4 activation at single cell resolution.

overall_design: single-cell RNAseq of human PBMCs from two donors pre-treated with 0, 1 uM, or 10 uM JRD-SIK1/2i-3 for 1 hr, followed by 5 ng/mL LPS stimulation for 1, 4, or 24 hours.

first: Holger

last: Babbe

first: Thomas

middle: B

last: Sundberg

first: Ashok

last: Mathur

first: Prerak

last: Desai


title: Transcriptome Profiling for Escherichia coli K12 wild type and ΔcsdA mutant before and after rifampicin-treatment

city: Hohhot

first: Xiaoli

last: Lv

address: NO.24 Zhao jun Street

institute: Inner Mongolia Universtiy

summary: The cell cycle coordinates with growth to ensure suitable genome inheritance. The CsdA protein is a highly conserved, DEAD-box RNA helicase and assists RNA structural remodeling at low temperature. The absence of CsdA yields a severe growth defect manifested by increased doubling time, more extensive cell size, or slower colony growth at low temperature. Nevertheless, it is unknown how the lack of CsdA at low temperature affects the cell cycle and the causes of the yield of severe growth defect phenotypes. This work shows that the lack of CsdA results in incoordination of the cell cycle to growth at low temperature. We performed microarray analyses to compare the transcriptome profiles of ΔcsdA mutant with WT cell before and after rifampicin-treatment in LB to understand how the lack of CsdA at low temperature affects the cell cycle and the causes of the yield of severe growth defect phenotypes.

overall_design: Wild-type cells and ΔcsdA mutant were treated with or without rifampicin, respectively. Transcriptome analysis using transcriptome microarrays.

first: Morigen

last: Morigen


title: Longitudinal Transcription Profiling of Bladder Cancers Dictate the Response to BCG Treatment and Disease Progression

city: Seoul

first: Seo

middle: Young

last: Lee

state: Goyang-si,Gyeonggi-do

address: Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

summary: Although the intravesical instillation of Bacillus Calmette-Guerin (BCG) is widely used as adjuvant treatment for nonmuscle-invasive bladder cancers, the clinical benefit is variable across patients, and the molecular mechanisms underlying the sensitivity to BCG administration and disease progression are poorly understood. To establish the molecular signatures that predict the responsiveness and disease progression of bladder cancers treated with BCG, we performed transcriptome sequencing (RNA-seq) for 13 treatment-naïve and 22 post-treatment specimens obtained from 14 bladder cancer patients. To overcome disease heterogeneity, we used non-negative matrix factorization to identify the latent molecular features associated with drug responsiveness and disease progression. At least 12 molecular features were present, among which the immune-related feature was associated with drug responsiveness, indicating that pre-treatment anti-cancer immunity might dictate BCG responsiveness. We also identified disease progression-associated molecular features indicative of elevated cellular proliferation in post-treatment specimens. The progression-associated molecular features were validated in an extended cohort of BCG-treated bladder cancers. Our study advances understanding of the molecular mechanisms of BCG activity in bladder cancers and provides clinically relevant gene markers for evaluating and monitoring patients.

overall_design: To predict progressed patients who were treated BCG, we discovered NMF features that related progression with clinical features.

first: U-Syn

last: Ha

first: Tae-Min

last: Kim

first: Yun-Hee

first: Seo-Young


title: Bulk RNA sequencing of Cd45+ cells from brains of aged Alzheimer's mice bearing human APOE knockin

first: Alon

last: Millet

summary: Here we perform bulk RNA sequencing of immune cells of aged AD mice bearing knock-in of human APOE variants in the murine APOE locus.

overall_design: We produced single cell suspensions from the hippocampal and cortical regions of 60-week-old 5XFAD-hemizygous mice bearing homozygous knock-in of APOE2, APOE3, or APOE4 in the murine Apoe allele. Cells were sorted for Cd45+ directly into lysis buffer for RNA isolation. RNA was purified and used as input for SMARTseq low input library preparation.


title: PAX3-FOXO1 directs CBP/P300 via its activation domain to build RNA Pol2 clusters

city: Cleveland

first: Hyunmin

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Activation of oncogenic gene expression from long-range enhancers is initiated by the assembly of DNA-binding transcription factors (TF), leading to recruitment of co-activators such as CBP/p300 to modify the local genomic context and facilitate RNA-Polymerase 2 (Pol2) binding. Yet, most TF-to-coactivator recruitment relationships remain unmapped. Here, studying the oncogenic fusion TF PAX3-FOXO1 (P3F) from alveolar rhabdomyosarcoma (aRMS), we show that a single cysteine in the activation domain (AD) of PAX3-FOXO1 forms a small alpha helical hook that recruits CBP/p300 to chromatin. P3F driven transcription requires both this single cysteine, and also CBP/p300. Furthermore, we discover a profound dependence on CBP/p300 for clustering of Pol2 loops that connect P3F to its target genes. In the absence of CBP/p300, Pol2 long range enhancer loops collapse, Pol2 accumulates in CpG islands and fails to exit the gene body. These results reveal a potential novel axis for therapeutic interference with P3F in aRMS and clarify the molecular relationship of P3F and CBP/p300 in sustaining active Pol2 clusters essential for oncogenic transcription.

overall_design:
RNA-seq and Pol2 HiChIP in RMS cells treated with HAT inhibitors and degraders.
Pol2 ChIP-seq in ABE RMS cells with wt P3F or C793R mutant P3F and H3K27ac ChIP-seq in RMS cells treated with HAT degraders.
Pol2 HiChIP in RMS cells with P3F-FKBP12 treated with DMSO or dTAG.

first: Gryder

first: Issra

last: Osman


title: Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways

status: Public on Dec 22 2023

city: Philadelphia

first: Daniel

last: Xu

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Alzheimer’s Disease (AD) is a disorder characterized by cognitive decline, neurodegeneration, and accumulation of amyloid plaques and tau neurofibrillary tangles in the brain. Dysregulation of epigenetic histone modifications may lead to expression of transcriptional programs that play a role either in protecting against disease genesis or in worsening of disease pathology. One such histone modification, acetylation of histone H3 lysine residue 27 (H3K27ac), is primarily localized to genomic enhancer regions and promotes active gene transcription. We previously discovered H3K27ac to be more abundant in AD patient brain tissue compared to the brains of age-matched non-demented controls. In this study, we use iPSC-neurons derived from familial AD patients with an amyloid precursor protein (APP) duplication (APPDup neurons) as a model to study the functional effect of lowering CBP/P300 enzymes that catalyze H3K27ac. We found that homeostatic amyloid-reducing genes were upregulated in the APPDup neurons compared to non-demented controls. We lowered CBP/P300 to reduce H3K27ac, which led to decreased expression of numerous of these homeostatic amyloid-reducing genes, along with increased extracellular secretion of a toxic amyloid-β species, Aβ(1-42). Our findings suggest that epigenomic histone acetylation, including H3K27ac, drives expression of compensatory genetic programs in response to AD-associated insults, specifically those resulting from APP duplication, and thus may play a role in mitigating AD pathology in neurons.

overall_design: The purpose of this experiment is to compare the gene expression changes of human iPSC-neurons treated with EP300 or CBP KD with human iPSC-neurons treated with CTRL RNAi KD, and to compare the responses to knockdown between neurons with an APP duplication familial AD background vs control, non-demented control background. iPSCs from APP duplication donors (APPDup1 and APPDup2) w as well as from NDC donors (NDC 1 and NDC2) were obtained as a generous gift from the laboratory of Lawrence Goldstein. Undifferentiated iPSCs were cultured and harvested and mRNA was extracted to yield the samples labled "iPSC". iPSCs were differentiated and treated with either EP300, CBP, or CTRL RNAi and cultured for 21 days to yield the samples labeled "neuron". mRNA was isolated from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) to prepare libraries with NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760L) following manufacture’s instruction. RNA libraries were pooled and sequenced with NextSeq 500/550 High Output Kit (75 cycles) v2.5 kit (illumina 20024906) on NextSeq 550 platform (illumina) using paired-end sequencing (42:6:0:42).

first: Shelley

last: Berger


title: CRISPR/Cas9-mediated Nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo

status: Public on Dec 20 2023

city: Ulm

first: Janessa

last: Hofeichner

address: Albert-Einstein-Allee 23

department: Internal Medicine II

institute: Uniklinik Ulm

summary: Nexilin (NEXN) plays a crucial role in stabilizing the sarcomeric Z-disk of striated muscle fibers and, when mutated,  leads to dilated cardiomyopathy in humans. Due to its early neonatal lethality in mice, the detailed impact of the  constitutive homozygous NEXN knockout on heart and skeletal muscle morphology and function is insufficiently investigated.  We characterized a constitutive homozygous CRISPR/Cas9-mediated nexn knockout zebrafish model. We found that Nexn deficient embryos developed significantly reduced cardiac contractility and under stressed conditions also impaired  skeletal muscle organization whereas skeletal muscle function seemed not to be affected. Remarkably, in contrast to nexn  morphants, CRISPR/Cas9 nexn-/- knockout embryos showed a milder phenotype without the development of a pronounced  pericardial edema or blood congestion. nexn-specific expression analysis as well as whole transcriptome profiling suggest  some degree of compensatory mechanisms. Transcripts of numerous essential sarcomeric proteins were massively induced  and may mediate a sarcomere stabilizing function in nexn-/- knockout embryos.

overall_design: To investigate the influence of nexn knockout on cardiac and skeletal muslce, we generated a CRISPR/Cas9-mediated nexn  knockout zebrafish model. We then performed gene expression profiling analysis using data obtained from RNA-seq.

first: Bernd

last: Gahr

first: Magdalena

last: Huber

first: Alena

last: Boos

first: Wolfgang

last: Rottbauer

first: Steffen

last: Just


title: Allopregnanolone Pleiotropic Action in Neurons and Astrocytes: Calcium Signaling Pathways as the Unifying Mechanism

city: Tucson

first: Tian

last: Wang

state: AZ

address: 1230 N Cherry Avenue

department: Center for innovation in brain science

institute: Univeristy of Arizona

summary: To investigated the mechanims of Allopreganolone in neurons and astrocytes, the RNAseq analysis were conducted.

overall_design: Comparative gene expression profilling analysis of RNA-seq data generated from Allo and Veh treated neurons and astrocytes.

first: Roberta

last: Brinton

first: Shuhua

last: Chen

first: Yuan

last: Shang

first: Zisu

last: Mao


title: Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle

status: Public on Dec 21 2023

city: SHANG HAI

first: XUETING

last: WANG

state: Not US or Canada

address: 100 Hai Ke ROAD, shanghai, china

institute: IRCBC

summary: Nicotinamide adenine dinucleotide (NAD), a nucleotide-containing metabolite, can be incorporated into the RNA 5’-terminus to result in NAD-capped RNA (NAD-RNA). Since NAD has been heightened as one of the most essential metabolites in cells, its attachment to RNA might indicate a yet-to-be discovered mechanism at the epitranscriptomic level. Here, we design a highly-sensitive method, DO-seq, to capture NAD-RNAs. Using Drosophila, we identify thousands of previously unexplored NAD-RNAs and their dynamics in the fly life cycle, from embryo to adult. We show the evidence that chromosomal clustering might be the structural basis by which co-expression can couple with NAD capping on physically and functionally-linked genes. Furthermore, we note that NAD capping of cuticle genes seems to inversely correlate with gene expression. Combined, we propose NAD-RNA epitranscriptome as a hidden layer of regulation that profoundly impacts biological processes. DO-seq empowers the identification of NAD-capped RNAs, facilitating functional investigation into this modification.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: DO-seq of total RNAs (2-month-old mouse livers) with spike-in RNA that had different ratios of NAD-RNA (0, 1, 5%); DO-seq with or without yDcpS treatment of mouse livers (18-month-old); NAD-RNA profiles and transcriptome profiles of Drosophila life cycle (embryo (14h-16h AEL), larva (4d AEL), pupa (7d AEL) and adult fly (3d)) were generated by deep sequencing, using Illumina Novaseq.To profile NAD-RNAs from Drosophila life cycle,  total RNAs from those samples were mixed with spike-in RNA from mouse livers, and two synthetic spike-in, of which one with 5% NAD-capped forms and another with 100% m7G-capped forms. The mixtures were then subjected to DO-seq.

first: Xueting

first: Shuwen

last: Ge

last: Liu


title: Single-cell RNA-seq investigation of skin and blood T cells from patients with cutaneous T-cell lymphoma

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

summary: Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)

first: Desislava

last: Ignatova

first: Emmanuella

last: Guenova


title: Gene expression in the placenta, and cerebral cortex of the brain of offspring mice; effect of maternal exposure to carbon black nanoparticle and ascorbic acid pre-treatment

city: Katsushika

first: Masakazu

last: Umezawa

state: Tokyo

address: 6-3-1 Niijuku

department: Department of Medical and Robotic Engineering Design, Faculty of Advanced Engineering

institute: Tokyo University of Science

summary:
To investigate the effects of administration of carbon black nanoparticle (CB-NP) to pregnant mice on the brain development in infantile mice, we have employed whole-genome microarray expression profiling to identify genes which show dose-dependent differential expression with astrogliosis in the frontal cortex of offspring mice. Some pregnant mice were pretreated with ascorbic acid to investigate the mechanism underlying the CB-NP effect. In addition to the frontal cortex of offspring mice who were exposed to CB-NP maternally, placenta was also subjected to the analysis to investigate the mechanism.
Pregnant mice were intranasally exposed to 0, 2.9, 15, 73, or 95 micro gram of CB-NP (Printex 90) per kg (body weight) on gestational days　(GDs) 5 and 9. Some pregnant mice were treated with intraperitoneal injection of ascorbic acid (500 mg/kg) at 1 h before the CB-NP instillation (95 μg/kg). Placentae were collected from pregnant dams on GD 13. Dissected cerebral cortex were collected from 6- and 12-week-old offspring mice.

overall_design: Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.

first: Atsuto

last: Onoda

first: Hiyori

last: Edo

first: Ryodai

last: Itano

first: Ken

last: Takeda


title: NELF Focuses Sites of Initiation and Maintains Promoter Architecture

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

institute: University of Iowa

summary: Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits of NELFB, PAF1 and RTF1 to probe the effects of depletion of the factors on nascent transcripts using PRO-Seq and on chromatin architecture using DFF-ChIP. Although NELF is involved in promoter proximal pausing, depletion of NELFB had only a minimal effect on the level of paused transcripts and almost no effect on control of productive elongation. Instead, NELF depletion increased the utilization of downstream transcription start sites and caused a dramatic, genome-wide loss of H3K4me3 marked nucleosomes. Depletion of PAF1 and RTF1 both had major effects on productive transcript elongation in gene bodies and also caused initiation site changes like those seen with NELFB depletion. Our study confirmed that the first nucleosome encountered during initiation and early elongation is highly positioned with respect to the major TSS. In contrast, the positions of H3K4me3 marked nucleosomes in promoter regions are heterogeneous and are influenced by transcription. We propose a model defining NELF function and a general role of the H3K4me3 modification in blocking transcription initiation.

overall_design: To investigate the function of NELFB, PAF1, and RTF1, we created individual cell lines in which the endogenous locus for each of these factors were tagged with FKBP12^F36V. This allowed us to deplete rapidly and selectively each of these factors upon the addition of 400 nM dTAGV-1. NELFB was depleted for 2h and 48h in the presence or absence of 1µM Flavopiridol, RTF1 was depleted for 2h, and PAF1 for 48h. We then performed PRO-Seq to quantitatively determine genome-wide levels of nascent transcripts. We also performed Pol-II and H3K4me3 DFF-ChIP-Seq on NELFB control and dTAGV-1 treated cells. For the Pol-II experiment, we depleted cells for 2h, while for the H3K4me3 experiment, we depleted cells for 2h and 48h. Finally, we profiled H3K36me3 genome-wide in control NELFB cells with DFF-ChIP-Seq. The Sf21 moth and 4T1 mouse cell lines were used for spike-in controls for PRO-Seq and DFF-Seq, respectively. Two biological replicates per sample were sequenced twice (two different runs).

first: Juan

middle: F

last: Santana

first: Ben

last: Spector

first: Gustavo

last: Suarez

first: Donal

middle: S

last: Luse


title: Gene expression profile in the mouse primary oligodendrocytes during the differentiation

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

institute: Takeda Pharmaceutical Company

summary: To characterize gene expression of mouse primary oligodendrocytes in the diffrentiation into oligodendendrocytes, we generated RNA-seq. data in a time-course manner.

overall_design: We then used RNA-seq data to assess gene expression profiling of interested genes.


title: Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis

city: San Francisco

first: Martin

last: Kampmann

state: CA

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute of Neurodegenerative Disease

institute: University of California, San Francisco

summary: Recent studies have identified a large number of high confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses have consistently implicated excitatory neurogenesis. However, the extent to which hcASD genes are involved in this process has not been explored systematically nor have the underlying biological pathways. Here, we leveraged CROP-Seq to repress 87 hcASD genes in an in vitro model of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cell state characterized by disruptions in proliferation and differentiation, cell cycle occupancy, mitotic spindle and microtubule biology, and RNA-binding proteins (RBPs). We also identified over 3,000 differentially expressed genes, 286 of which have expression profiles correlated with changes in developmental trajectory. Collectively, these genes again highlight microtubule biology and RBPs. Overall, we uncover transcriptional disruptions downstream of hcASD gene perturbations and correlate these disruptions with distinct differentiation phenotypes, while reinforcing neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD.

overall_design: iPSC derived neural progenitor cells and neurons expressing the CRISPRi machinery were sequenced using 10X Chromium v3 using a CROP-seq protocol at three timepoints during differentiation (D0, D2, D4). The 10X labeled sequencing reads are the transcriptomic data and the PCR labeled reads are the sgRNA enrichment PCR reads used to assign sgRNAs to cell barcodes.

first: Sun

last: Nawei

first: Teyssier

last: Noam

first: Tian

last: Ruilin

first: Kampmann

last: Martin

first: Willsey

last: A Jeremy


title: Daily Patterns of Retinal and Choroidal Gene Expression and Circadian Biology in Myopia Pathogenesis

city: Boston

first: Debora

last: Nickla

state: MA

address: 424 Beacon St

department: Dept. of Biosciences and Disease

institute: New England College of Optometry

summary: We investigated diurnal changes in gene expression in the retina and choroid at the onset of experimental myopia. We induced visual form deprivation myopia in young chicks, and isolated retinal and choroidal tissues separately in form- deprived and contralateral control eyes every 4 hours over a single 24-hour period.

overall_design: After applying RNA-Seq separately to each tissue extract, we used various bioinformatics analyses and gene expression profiling analyses to assess the retinas and choroids of experimental and control eyes at each time point.

first: Richard

last: Stone

first: John

middle: W

last: Tobias

first: Jonathan

last: Shrug

first: P

last: Iuvone


title: Effect of knockdown of Secisbp2l in primary oligodendrocyte precursor cells

summary:
To investigate the function of  Secibp2l which we identified as an oligodendrocyte-specific RNA binding protein, we performced transcriptome profiling of primary oligodnedrocytes with Secisbp2l knockdown by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse primary oligodendrocytes and its KD derivatives (siSbp2l, siPdgfra, siNegativeControls).


title: Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [methylation]

status: Public on Dec 19 2023

city: Lyon

first: Thomas

last: Diot

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary:
Rhabdomyosarcoma (RMS) is the main form of pediatric soft-tissue sarcoma. Its cure rate has not improved in the last 20 years notably following relapse, and the lack of reliable preclinical models has so far hampered the design of new therapies. This is particularly true for highly heterogeneous fusion-negative RMS (FNRMS). Although methods have been proposed to establish FNRMS organoids, their efficiency remains limited to date, both in terms of derivation rate and ability to accurately mimic the original tumor.
Here, we present the development of a next-generation 3D-organoid model derived from relapsed adult and pediatric FNRMS. This model preserves the molecular features of the patients’ tumors and is expandable for several months in 3D, reinforcing its interest to drug combination screening with longitudinal efficacy monitoring.
As a proof-of-concept, we demonstrated its preclinical relevance by reevaluating the therapeutic opportunities of targeting apoptosis in FNRMS from a streamlined approach based on transcriptomic data exploitation.

overall_design: We generated the methylation profile of rhabdomyosarcoma tissue samples coming from 4 patients (7 samples) and their associated in vitro models (18 samples)

first: Laura

last: Broutier


title: Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [Exome panel]

overall_design: We performed exome sequencing for a panel of genes on rhabdomyosarcoma tissue samples coming from 2 patients (2 samples) and their associated in vitro models (13 samples)


title: Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [RNAseq]

overall_design: We generated the transcriptome profile of rhabdomyosarcoma tissue samples coming from 2 patients (4 samples) and their associated in vitro models (25 samples)


title: Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations

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

overall_design: Refer to individual Series


title: Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration

city: Würzburg

first: Yanying

last: Yu

state: DE Deutschland

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: CRISPR interference (CRISPRi), the targeting of a catalytically dead Cas protein to block transcription, is the leading technique to silence gene expression in bacteria. However, design rules for CRISPRi remain poorly defined, limiting predictable design for gene interrogation, pathway manipulation, and high-throughput screens. Here we develop a best-in-class prediction algorithm for guide silencing efficiency by systematically investigating factors influencing guide depletion in multiple genome-wide essentiality screens, with the surprising discovery that gene-specific features such as transcriptional activity substantially impact prediction of guide activity.  Accounting for these features as part of algorithm development allowed us to develop a mixed-effect random forest regression model that provides better estimates of guide efficiency than existing methods, as demonstrated in an independent saturating screen. We further applied methods from explainable AI to extract interpretable design rules from the model, such as sequence preferences in the vicinity of the PAM distinct from those previously described for genome engineering applications. Our approach provides a blueprint for the development of predictive models for CRISPR technologies where only indirect measurements of guide activity are available.

overall_design: 750 gRNAs were designed to target 9 purine biosynthesis  genes, with between 35 and 233 guides per gene. Duplicate samples were then collected at three time points during growth in M9 minimal media, and gRNA depletion was measured with reference to input samples, normalized using a set of 50 gRNAs designed not to target any E. coli sequence.

first: Sandra

last: Gawlitt

first: Chase

last: Beisel

first: Lars

last: Barquist


title: Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [scRNAseq]

overall_design: We performed single-cell RNAseq transcriptome profiling of 1 rhabdomyosarcoma patient-derived in vitro model (2 samples)


title: Transcriptional profiling of Gastrocnemius Muscle in Pompe's disease

status: Public on Jan 01 2024

city: South San Francisco

first: Russell

last: Bainer

address: 171 Oyster Point Blvd

department: Data Sciences

institute: Maze Therapeutics

summary:
Study identifying transcriptional differences present between C57BL/6J and B6;129-Gaatm1Rabn/J mice, or driven by Enzyme Replacement Therapy (ERT), Substrate Reduction Therapy (SRT), or Both, administered to the mutant strain.
All expression profiles were assessed in bulk gastrocnemius muscle collected from 18-21 week-old mice that had been provided with chow formulated with vehicle (veh.), MZ-101 (SRT), or alglucosidase alfa 20mg/kg biweekly (ERT) for 12 weeks.

overall_design: Comparative gene expression profiling analysis of RNA-seq data derived from mouse models of Pompe's disease treated with vehicle, SRT, ERT, or Combo, versus wildtype strain

first: Julie

last: Ullman


title: Host-response Transcriptional Biomarkers Accurately Discriminate Bacterial and Viral Infections by Global Pathogens

city: Durham

first: Emily

last: Ko

state: NC

address: 4103 Graceview Way

department: Medicine

institute: Duke University

summary: Global endemic infections, such as leptospirosis, rickettsial diseases, and dengue infections present diagnostic challenges, posing a dilemma for antibiotic stewardship worldwide. The goal of this project was to identify accurate transcriptional classifiers able to discriminate between bacterial and viral illness of global pathogens.

overall_design: Whole transcriptome RNA sequencing was performed on 294 human whole blood PAXgene RNA tubes from the U.S. and Sri Lanka. A variety of bacterial and viral infections from global pathogens were included. Noninfectious illness was included as a control category.

first: Christopher

last: Woods

first: Sunil

last: Suchindran

first: Micah

last: McClain

first: Ricardo

last: Henao

last: Burke

first: L

middle: G

last: Tillekeratne

first: Megan

last: Reller

first: Champica

middle: K

last: Bodinayake


title: Gene expression profiling of skin and blood in human acute Graft-versus host disease (GVHD) of the skin

city: Vienna

first: Johanna

last: Strobl

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary: GVHD following allogneeic hematopoietic stem cell transplantation is described as a T cell mediated disease. We analyze mononuclear phagocyte subsets and other leukocyte populations in blood and skin from patients with acyte cutaneous GVHD

overall_design:
Single cell suspensions were obtained from skin and blood of GVHD patients, FACS-sorted and sequenced using the 10XGenomics platform as previously described (Saluzzo et al. STAR Protoc. 2022 Jun 17;3(3):101470. doi: 10.1016/j.xpro.2022.101470. PMID: 35769924; PMCID: PMC9234085.
>>>Raw data not provided due to patient confidentiality.<<<

last: Gail

first: Ruth

last: Dingelmaier-Hovorka

first: Georg

last: Stary


title: Spatiotemporal insight into early pregnancy governed by immune-featured stromal cells [Spatial Transcriptomics]

status: Public on Dec 18 2023

city: Beijing

first: Min

last: Yang

state: Beijing

address: No. 5, yiheyuan road, haidian district,

institute: Peking University

summary: Endometrial decidualization connecting embryo implantation and placentation is transient but essential for successful pregnancy, which, however, is not systematically investigated. Here, we use a scStereo-seq technology to spatially visualize and deﬁne the dynamic functional decidual hubs assembled by distinct immune, endothelial, trophoblast, and decidual stromal cells (DSCs) in early pregnant mice. We unravel the DSC transdifferentiation trajectory and surprisingly discover a dual-featured type of immune-featured DSCs (iDSCs). We ﬁnd that immature DSCs attract immune cells and induce decidual angiogenesis at the mesenchymalepithelial transition hub during decidualization initiation. iDSCs enable immune cell recruitment and suppression, govern vascularization, and promote cytolysis at immune cell assembling and vascular hubs, respectively, to establish decidual homeostasis at a later stage. Interestingly, dysfunctional and spatially disordered iDSCs cause abnormal accumulation of immune cells in the vascular hub, which disrupts decidual hub speciﬁcation and eventually leads to pregnancy complications in DBA/2-mated CBA/J mice.

overall_design: E6.5-E9.5 implantation sites of normal pregnant ICR mice and E8.5 and E9.5 implantation sites of DBA/2-mated CBA/J mice.

first: Yang

last: Min

first: Ong

last: Jennie

first: Du

last: Peng


title: Analysis of differential gene expression in HPV+ and HPV- HNSCC cell lines

city: Liverpool

first: Lekh

last: Dahal

address: Sherrington Building, Ashton Street

country: United Kingdom

institute: University of Liverpool

summary: HPV+ and HPV- HNSCCs are defined as two aetiologically distinct diseases that are driven by unique risk factors. RNA-seq was used to investigate transcriptional differences based on HPV phenotype.

overall_design: Comparative gene expression profling analysis of RNA-seq data from total RNA samples of wildtype HPV+ and HPV- HNSCC cell lines.

first: Emma

last: Saulters


title: Human herpesvirus 6B (HHV-6B) detection and genome-wide host expression profiles implicate HHV-6B as a pulmonary pathogen after hematopoietic cell transplantation

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

summary: Limited understanding of the immunopathogenesis of human herpesvirus 6B (HHV-6B) has prevented its acceptance as a pulmonary pathogen after hematopoietic cell transplantation (HCT). We conducted a prospective multicenter study of patients undergoing bronchoalveolar lavage (BAL) for pneumonia after allogeneic HCT. We tested blood and BAL fluid (BALF) for HHV-6B DNA and mRNA transcripts associated with lytic infection and performed RNA-seq on paired blood. Among 116 participants, HHV-6B DNA was detected in 37% of BALs, 49% of which had HHV-6B mRNA detection. We established an HHV-6B DNA threshold (≥2.3 log10copies/ml in BALF) that was highly predictive of HHV-6B mRNA detection and increased risk for death from respiratory failure (adjusted HR, 2.35; 95% CI, 1.08-5.11). Participants with HHV-6B DNA in BALF exhibited distinct host gene expression signatures, notable for enriched interferon signaling pathways in participants clinically diagnosed with idiopathic pneumonia. These data implicate HHV-6B as a pulmonary pathogen after allogeneic HCT.

overall_design: In this study, we prospectively enrolled adult allogeneic HCT recipients undergoing a BAL for evaluation of LRTD within 120 days of HCT from three centers and followed outcomes for up to 60 days after the BAL. We collected and tested paired blood and BALF samples with multiple molecular diagnostic techniques to comprehensively investigate the role of HHV-6B as a pulmonary pathogen after allogeneic HCT and determine the utility of whole blood gene expression signatures as a complement to pathogen-directed diagnostic testing.

first: Joshua

last: Hill


title: Alterations in leukocyte DNA methylome are associated to immunosuppression in severe clinical phenotypes of septic patients

city: València

first: José Luis

last: García-Giménez

state: València

address: Avenida Blasco Ibáñez, 15

department: Departamento de Fisiología. Facultad de Medicina y Odontología

institute: Universitat de València

type: Methylation profiling by genome tiling array

summary:
Sepsis patients experience a complex interplay of host pro- and anti-inflammatory processes which can compromise outcome. Even taking the latest clinical and scientific research data into account, the immunosuppressive events occurring during a septic episode are incompletely understood. Moreover, there is a lack of data on the way epigenetics can modulate immunosuppression, which in turn affects patient survival.

To advance current understanding of the mechanisms underlying immunosuppression, in this study we explored DNA methylation changes using the Infinium MethylationEPIC v1.0 BeadChip Kit in leukocytes from patients suffering from sepsis, septic shock, and critically ill patients as controls, within the first 24 h after admission in the Intensive Care Unit of a tertiary hospital.

The top 100 differentially methylated positions (DMPs) between septic shock and critically ill patients enabled us to clearly distinguish between the 3 groups of patients. Interestingly, the top 6,657 DMPs were associated with organ dysfunction and lactate levels. Two different analysis approaches (based on the use of DMRcate and mCSEA) comparing septic shock and critically ill patients revealed a total of 1,256 differentially methylated regions (DMRs) involved in critical immune system-related pathways. Among the individual genes exhibiting significant differential methylation, IL10, TREM1, IL1B, and TNFAIP8 showed the largest methylation differences among the different groups when analyzing their methylation levels by DNA bisulfite pyrosequencing.

Our findings indicate that DNA methylation profile undergoes the most substantial changes in patients with septic shock, and that these changes are linked to disease severity. Importantly, IL10 and S100A8, which are closely related to immunosuppression, were hypomethylated in septic shock patients.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip v1.0

first: Jesús

last: Beltrán-García

first: Germán

last: Casabó-Vallés

first: Rebeca

last: Osca-Verdegal

first: Paula

last: Navarrete-López

first: María

last: Rodríguez-Gimillo

first: Elena

last: Nácher-Sendra

first: Carolina

last: Ferrando-Sánchez

first: Eva

last: García-López

first: Federico

middle: V

last: Pallardó

first: Nieves

last: Carbonell

first: Salvador

last: Mena-Mollá


title: VGLL1 regulates extraembryonic lineage specification in human [RNA-seq II]

city: guangzhou

first: Wenjuan

last: Li

state: 广东

address: UCAS

department: GIBH

institute: UCAS

summary: Placenta abnormality is one of the key reasons for early pregnancy loss but the regulatory mechanisms underlying placenta formation are largely unknown. Here, we applied a human naïve pluripotent stem cell (PSC) derived TE model to explore the driven regulatory machinery. We demonstrate that VGLL1 (vestigiallikefamilymember1) is crucial for TE self-renewal and TE-specific gene expression, thus suppressing VGLL1 leads to severely impaired cell proliferation and skewed TE induction. VGLL1 exerts its function through interacting with TEAD4 (TEA domain transcription factor 4) and colocalize at target gene promoters and enhancers. Further investigation uncovers the enrichment of H3K27ac active histone marks at genomic regions occupied by VGLL1-TEAD4 complex, indicates a close association between them. Overall, our data reveals the critical function model of VGLL1-TEAD4 in human TE derivation, highlighting a potential interspecies difference between human and mouse TE induction.

overall_design: Human naïve PSCs were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express and plated at a density of 100,000 cell/well of 6-well plate on Geltrex in TE induction medium (1:1 mix of Neurobasal medium (Gibco) and DMEM/F12 (HyClone) supplemented with N2 (Gibco) and B27 (Gibco), penicillin-streptomycin (HyClone), Glutamax (Gibco), β-mercaptoethanol (Sigma), 1 µM PD0325901 (Axon) and 1 µM A83-01 (Selleck)) for five days. TELCs at day 5 were used for downstream analysis throughout this study. For generating expandable TSCs, TELCs at day 5 were dissociated into single cells with TrypLE and plated on Geltrex-coated six-well plates at a 1:4-1:8 split ratio in TSC medium (DMEM/F12 supplemented with N2 and B27, penicillin-streptomycin, Glutamax, β-mercaptoethanol, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF (PeproTech), 0.5 µM A83-01 (Selleck), 1 µM SB431542 (Selleck), 2 µM CHIR99021 (Axon), 0.8 mM VPA (Vetec) and 5 µM Y-27632 (Axon)) supplemented with 10 µM Y-27632.

first: Yueli

last: Yang


title: MicroRNA-148a-3p in pericyte-derived extracellular vesicles improves erectile function in diabetic mice by promoting cavernous neurovascular regeneration

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: To investigate the regulatory role of microRNA (miR)-148a-3p in mouse corpus cavernous pericyte (MCPs)-derived extracellular vesicles (EVs) in the treatment of diabetes-induced erectile dysfunction (ED).  Materials and Methods: Mouse corpus cavernous tissue was used for MCPs primary culture and EVs isolation. Small RNA sequencing analysis was performed to assess the type and content of miRs in MCPs-EVs. Four groups of mice were used: control nondiabetic mice and streptozotocin-induced diabetic mice receiving two intracavernous injections (days -3 and 0) of phosphate buffered saline, MCPs-EVs transfected with regent control, or MCPs-EVs transfected with miR-148a-3p inhibitor. The function of miR-148a-3p in MCPs-EVs was evaluated by tube formation assay, migration assay, TUNEL assay, intracavernous pressure, immunofluorescence staining, and western blot experiments.   Results: We extracted EVs from MCPs and by small RNA sequencing analysis we found that miR-148a-3p is enriched in MCPs-EVs. Exogenous administration of MCPs-EVs can effectively promote mouse cavernous endothelial cell (MCECs) tube formation, migration, proliferation, and reduce MCECs apoptosis under high-glucose conditions. However, these effects are significantly attenuated in miR-148a-3p-depleted MCPs-EVs, which is extracted after inhibiting miR-148a-3p expression in MCPs. Repeated intracavernous injections of MCPs-EVs improves erectile function by inducing cavernous neurovascular regeneration in diabetic mice. Through online bioinformatics databases and luciferase report assays, we predict Pyruvate dehydrogenase kinase-4 (PDK4) is a potential target gene of miR-148a-3p.  Conclusions: Our findings provide new and reliable evidence that miR-148a-3p in MCPs-EVs significantly enhances cavernous neurovascular regeneration by inhibiting PDK4 in diabetic mice.

overall_design: MCPs-derived EVs (MCPs-EVs) were isolated from MCPs cultured medium by using a Commercials EV isolation kit (ExoQuick-TC, System Biosciences, LLC., Palo Alto, CA, USA) following manufacturers’ instructions.

first: Guo

middle: N

last: Yin


title: Immunomodulatory response to neoadjuvant nivolumab in non-metastatic clear cell renal cell carcinoma

city: Baltimore

first: Roy

last: Elias

state: Maryland

address: 201 N Broadway

institute: Johns Hopkins University

summary: Novel perioperative strategies are needed to reduce recurrence rates in patients undergoing nephrectomy for high-risk, non-metastatic clear cell renal cell carcinoma (ccRCC).  We conducted a prospective, phase I trial of neoadjuvant nivolumab prior to nephrectomy in 15 evaluable patients with non-metastatic ccRCC. We leveraged tissue from that cohort to elucidate the effects of PD-1 inhibition on immune cell populations in ccRCC and correlate the evolving immune milieu with anti-PD-1 response.  We found that nivolumab durably induces a pro-inflammatory state within the primary tumor, and baseline immune infiltration within the primary tumor correlates with nivolumab responsiveness.  Nivolumab increases CTLA-4 expression in the primary tumor, and subsequent nephrectomy increases circulating concentrations of sPD-L1, sPD-L3 (sB7-H3), and s4-1BB. These findings form the basis to consider neoadjuvant immune checkpoint inhibition (ICI) for high-risk ccRCC while the tumor remains in situ and provide the rationale for perioperative strategies of novel ICI combinations.

overall_design:
Bulk RNAseq data from treatment-naïve biopsy and post-treatment nephrectomy from patients with non-metastatic ccRCC.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Nirmish

last: Singla

first: Thomas

middle: R

last: Nirschl

first: Aleksandar

middle: Z

last: Obradovic

first: Eugene

last: Shenderov

first: Kara

last: Lombardo

first: Xiaopu

last: Liu

first: Alice

last: Pons

first: Jelani

middle: C

last: Zarif

first: Steven

last: Rowe

first: Bruce

middle: J

last: Trock

first: Hans

last: Hammers

first: Trinity

last: Bivalacqua

first: Phillip

last: Pierorazio

first: Julie

last: Deutsch

first: Tamara

last: Lotan

first: Janis

last: Taube

first: Yasser

last: Ged

first: Michael

last: Gorin

first: Mohamad

middle: E

last: Allaf

first: Charles

last: Drake


title: Global blood miRNA profiling unravels early signatures of immunogenicity of Ebola vaccine rVSVΔG-ZEBOV-GP

city: Göteborg

first: Björn

last: Andersson

address: Sahlgrenska akademin, Core Facilities, Box 413

department: Boinformatics and Data center

country: Sweden

institute: Univeristy of Gothenburg

summary:
We characterized the extracellular miRNAs, isolated from serum-derived extracellular vesicles (EV), induced by vaccination against Ebola.
We identified early miRNA signatures associated with the ZEBOV-specific IgG antibody responses at day 28 or 360 post-vaccination.

overall_design:
We isolated total RNA including miRNA from serum-derived extracellular vesicles (EV) from 48 healthy individuals receiving the rVSVΔG-ZEBOV-GP vaccine or placebo. Timepoints day 0 (baseline before vaccination), and days 1, 2, 3, 4 and 7 post-vaccination have been considered. We performed miRNA-seq. We then identified differentially expressed miRNAs by comparing rVSVΔG-ZEBOV-GP vaccines vs placebo controls. Next, we correlated baseline and early miRNAs with the ZEBOV-specific IgG antibody titer measured at day 28 and day 360 by performing Pearson Correlation. We used Machine Learning algorithms to identify the best early miRNA signatures able to discriminate high and low antibody levels at day 28 and day 360. Finally, we identified a miRNA antibody predictive signature associated with immune-related target mRNAs and corresponding pathways.
VEBCON Consortium
VSV-EBOVAC Consortium
VSV-EBOPLUS Consortium

first: Eleonora

last: Vianello

first: Josefine

last: Persson

first: Suzanne

last: van Veen

first: Thomaz

last: Lüscher Dias

first: Francesco

last: Santoro

first: Malin

last: Östensson

first: Ogonna

last: Obudulu

first: Christopher

last: Agbajogu

first: Sara

last: Torkzadeh

first: Helder

last: Nakaya

first: Donata

last: Medaglini

first: Claire-Anne

last: Siegrist

first: Tom

middle: M

last: Ottenhoff

first: Ali

last: Harandi


title: VGLL1 regulates extraembryonic lineage specification in human [RNA-Seq]

first: Wenjuan

last: Li

summary: Placenta abnormality is one of the key reasons for early pregnancy loss but the regulatory mechanisms underlying placenta formation are largely unknown. Here, we applied a human naïve pluripotent stem cell (PSC) derived TE model to explore the driven regulatory machinery. We demonstrate that VGLL1 (vestigial like family member 1) is crucial for TE self-renewal and TE-specific gene expression, thus suppressing VGLL1 leads to severely impaired cell proliferation and skewed TE induction. VGLL1 exerts its function through interacting with TEAD4 (TEA domain transcription factor 4) and colocalize at target gene promoters and enhancers. Further investigation uncovers the enrichment of H3K27ac active histone marks at genomic regions occupied by VGLL1-TEAD4 complex, indicates a close association between them. Overall, our data reveals the critical function model of VGLL1-TEAD4 in human TE derivation, highlighting a potential interspecies difference between human and mouse TE induction.

overall_design: Human naïve PSC were plated at a density of 100000 cells per well onextracellular matrix (ECM; Geltrex™)-coated 6-well plates and cultured with TE medium. Cells were collected for sequencing on day 5. For human TSC cells, cells cultured in TS-1 medium for five or six days were plated on Collagen IV coated 6-well plates and cultured with TSC medium. Cells cultured in TSC medium became morphologically stable after 2-3 passages.

first: Yueli

last: Yang


title: Disrupted extracellular matrix and cell cycle genes in autism-associated Shank3 deficiency can be rescued with Lithium

city: Ulm

first: Valentin

last: Ioannidis

address: Albert-Einstein-Allee 11

department: Institut for Anatomy and Cell Biology

institute: Ulm University

summary: The Shank3 gene encodes the major postsynaptic scaffolding protein SHANK3. Its mutation causes a syndromic form of autism spectrum disorder (ASD): Phelan-McDermid Syndrome (PMDS). It is characterized by global developmental delay, intellectual disorders (ID), ASD behavior, affective symptoms, as well as extra-cerebral symptoms. Although Shank3 deficiency causes a variety of molecular alterations, they do not suffice to explain all clinical aspects of this heterogenic syndrome. Since global gene expression alterations in Shank3 deficiency remain inadequately studied, we explored the transcriptome in vitro in primary hippocampal cells from Shank3∆11(-/-) mice, under control and lithium (Li) treatment conditions, and confirmed the findings in vivo. The Shank3∆11(-/-) genotype affected the overall transcriptome. Remarkably, extracellular matrix (ECM) and cell cycle transcriptional programs were disrupted. Accordingly, in the hippocampi of adolescent Shank3∆11(-/-) mice we found proteins of the collagen family and core cell cycle proteins downregulated. In vitro Li treatment of Shank3∆11(-/-) cells had a rescue-like effect on the ECM and cell cycle gene sets. Reversed ECM gene sets were part of a network, regulated by common transcription factors (TF) such as cAMP responsive element binding protein 1 (CREB1) and β-Catenin (CTNNB1), which are known downstream effectors of synaptic activity and targets of Li. These TFs were less abundant and/or hypo-phosphorylated in hippocampi of Shank3∆11(-/-) mice and could be rescued with Li in vitro and in vivo. Our investigations suggest the ECM compartment and cell cycle genes as new players in the pathophysiology of Shank3 deficiency, and imply involvement of transcriptional regulators, which can be modulated by Li. This work supports Li as potential drug in the management of PMDS symptoms, where a Phase II study is ongoing.

overall_design: Primary hippocampal cells from P1-2 mice of WT and KO genotype were culutered for 14 days and received either vehicle or lithium treatment at day 9. The experiment was replicated 4 times. Sequencing was performed in 2 batches.


title: VGLL1 regulates extraembryonic lineage specification in human [ATAC-Seq]


title: Microglia

status: Public on Dec 15 2023

city: Solna

first: Rasmus

middle: Par Arild Oskar

last: Berglund

state: Sweden

address: CMM L8:04, Neuroimmunology

department: Clinical neuroscience

institute: Karolinska institute

summary: Microglia from aged mice

overall_design: Aged mice


title: scRNA-seq of myeloid cells from subcutaneous MC38-Ova tumours and draining lymph nodes (LN) in photoconvertible Kaede mice

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

institute: Molecular Immunity Unit

summary: We combined scRNA-seq and a photoconvertible mouse model to study the spatiotemporal dynamics of macrophages and dendritic cells (DCs) in murine tumours including their migration to the lymph node, including the effects of immune checkpoint therapy (anti-PD-L1).

overall_design: Myeloid cells in tumours were isolated by fluorescence-activated cell sort (FACS) using LiveCD45+TER119-Kaede+CD11b+NK1.1- signal, followed by separation of Kaede-green or Kaede-red fractions for analysis with scRNA-seq. Kaede-red immune cells in the tumour-dLN (representing cells that have migrated from the tumour) were isolated using LiveCD45+TER119-Kaede-red+ signal.

first: Menna

last: Clatworthy

first: David

last: Withers

middle: Y


title: scRNA-seq reveals the temporal dynamics of NK cells in subcutaneous MC38-Ova murine tumours

summary: We combined scRNA-seq and a photoconvertible Kaede transgenic mouse tumour model to study the temporal dynamics of NK cells in murine tumours.

overall_design: Tumour-infiltrating lymphocytes were isolated by FACS using LiveCD45+TER119-Kaede+ signal followed by exclusion of CD11b+NK1.1- (myeloid) cells. Thereafter, Kaede-green and Kaede-red fractions were separated for analysis with scRNA-seq.

first: Isaac

last: Dean


title: The Mosquito Effect: Regulatory and effector T cells acquire cytoplasmic material from tumor cells through intercellular transfer

city: Amherst

first: Leonid

last: Pobezinsky

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

summary: The phenomenon of intercellular transfer of cellular material, including membranes, cytoplasm, and even organelles, has been observed for decades. The functional impact and molecular mechanisms of such transfer in the immune system remain largely elusive due to the absence of a robust in vivo model. Here, we introduce a new tumor mouse model, where tumor cells express the soluble ultra-bright fluorescent protein ZsGreen, which allows detection and measurement of intercellular transfer of cytoplasm from tumor cells to infiltrating immune cells. We found that in addition to various types of myeloid lineage cells, a large fraction of T regulatory cells and effector CD8 T cells acquire tumor material. Based on the distribution of tumor-derived ZsGreen, the majority of T cells integrate captured cytoplasm into their own, while most myeloid cells store tumor material in granules. Furthermore, scRNA-seq analysis revealed significant alterations in transcriptomes of T cells that acquired tumor cell cytoplasm, suggesting potential impact on T cell function. We identified that the participation of T cells in intercellular transfer requires cell-cell contact and is strictly dependent on the activation status of T lymphocytes. Finally, we propose to name the described phenomenon of intercellular transfer for tumor infiltrating T cells the “mosquito effect”.

overall_design: Single cell RNA sequencing of tumor infiltrating lymphocytes (TILs), collected from a B16 ZsGreen+ tumor and sorted into "ZsGreen- TILs (CD45+ZsG-)",  "ZsGreen+ TILs (CD45+ZsG+)". A separate sequencing experiment was performed on TILs sorted as "ZsGreen- Tumor Infiltrating T cells (CD45+TCR+ZsG-)", or  "ZsGreen+ Tumor Infiltrating T cells (CD45+TCR+ZsG+)".

first: Kaito

middle: A

last: Hioki

first: Elena

middle: L

last: Pobezinskaya


title: β-cell responses to high fat feeding in mice: A role and mechanism for redox sensing by SENP1

city: Dallas

first: Xi

address: 2929 N Stemmons Fwy

institute: UT Southwestern Medical Center

summary: Pancreatic β-cells respond to metabolic stress by upregulating insulin secretion, however the underlying mechanisms remain unclear. In β-cells from overweight humans without diabetes, and mice fed a high-fat diet for 2 days, insulin exocytosis and secretion are enhanced without increased Ca2+ influx. β-cell RNA-seq suggests altered metabolic pathways early following HFD, where we find increased basal oxygen consumption, proton leak, but a more reduced cytosolic redox state. Increased β-cell exocytosis after 2-day HFD is dependent on this reduced intracellular redox, and requires the sentrin-specific SUMO-protease-1 (SENP1). Mice with either pancreas- or β-cell-specific SENP1 deletion fail to up-regulate exocytosis and become rapidly glucose intolerant after 2-day HFD. Mechanistically, redox-sensing by SENP1 requires a thiol group at C535 which together with Zn+-binding suppresses basal protease activity and unrestrained β-cell exocytosis, and increases SENP1 sensitivity to regulation by redox signals.

overall_design: Mice were fed chow diet (n=4) or high fat diet (n=3) for 2 days. Pancreatic islet β-cells were sorted by FACS and then used for RNA-sequenicng.


title: The Mediator Subunit MED20 Organizes the Early Adipogenic Complex to Promote Development of Adipose Tissues and Diet-Induced Obesity

city: xiamen

first: Guosheng

last: Hu

state: fujian

address: Xiang'an South Road, Xiang'an District

department: school of life sciences

institute: xiamen university

summary: MED20 is a non-essential subunit of the transcriptional coactivator Mediator complex, but its physiological function remains largely unknown. Here we show that MED20 plays a key role in the development of adipose tissue and diet-induced obesity. Through affinity purification and candidate screening, we demonstrate that MED20 is targeted for degradation by the anti-obesity CRL4-WDTC1 E3 complex. Depleting MED20 in either 3T3-L1 cells or primary preadipocytes inhibits adipogenesis. Mice with MED20 knocked out in preadipocytes show dramatic defect in the development of brown adipose tissue. Furthermore, removing one allele of Med20 in preadipocytes protects mice from diet-induced obesity, and reverses weight gain in Cul4a- or Cul4b-depleted mice. Mechanistically, MED20 plays a key role in organizing the early adipogenic complex by bridging C/EBPβ and RNA polymerase II and thereby stimulating the transcription of PPARγ. Our study has thus identified MED20 as a potential target for obesity treatment.

overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying MED20 in gene transcription regulation.

first: Wen-Shuai

last: Tang

first: Li

last: Weng

first: Xu

last: Wang

first: Guo-Sheng

first: Wen

last: Liu

first: Tong-Jin

last: Zhao


title: VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification

status: Public on Dec 16 2023

first: Wenjuan

last: Li

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

overall_design: Refer to individual Series


title: Genome-wide map of FOXO1-bound chromatin in pituitary somatotropes

status: Public on Dec 14 2023

city: Carbondale

first: Buffy

middle: Sue

last: Ellsworth

state: IL

address: 1135 Lincoln Dr

department: Department of Physiology

institute: Southern Illinois University

summary: Pituitary gland function is regulated by the activity of various transcription factors which control cell fate decisions leading to cellular differentiation and hormone production. FOXO1 is necessary for the proper timing of somatotrope differentiation and for somatotrope function, but the exact mechanism of action has yet to be elucidated. Recent data implicate FOXO1 in the regulation of genes important for somatotrope differentiation including Gh1, Neurod4, and Pou1f1. Previously, a mouse model with conditional deletion of Foxo1 from the developing pituitary gland displayed reduced Gh1 and Neurod4 transcripts as early as embryonic day 18.5. Additional data from adult animals with conditional deletion of both Foxo1 and Foxo3 from the pituitary gland have a similar reduction in Neurod4 and Gh1, as well as Pou1f1. To investigate the mechanism by which FOXO1 regulates pituitary gland gene expression and confirm in vivo findings, the somatotrope-like cell line, GH3, was treated with the FOXO1 inhibitor, AS1842856, for 24 hours at various concentrations. Neurod4 was the most severely affected genes with a dose-dependent reduction in transcript at inhibitor concentrations as low as 30 nM. Gh1 transcripts were significantly reduced at 300 nM. Pou1f1 expression was trending down at 3 microM inhibitor (p=0.066). Consistent with these findings, CRISPR/Cas9-mediated deletion of Foxo1 in GH3 cells significantly reduced expression of Gh1, Neurod4, but not Pou1f1. To elucidate the molecular mechanisms underlying the role of FOXO1 in somatotropes, ChIPseq was performed for FOXO1 in the GH3 cell line. This study identified novel FOXO1 binding sites associated with the Neurod4, Gh1, and Pou1f1 genes. The FOXO1 binding site in the Neurod4 gene exhibits enhancer activity in somatotrope-like cells, but not in gonadotrope-like or heterologous cells. These data strongly suggest FOXO1 directly contributes to the transcriptional control of genes important for somatotrope differentiation. These novel findings contribute to the much-needed understanding of pituitary cell fate decisions.

overall_design:
ChIPseq was performed using GH3 cells and anti-FOXO1 (FKHR H-128 sc-11350, Santa Cruz Biotechnology, Santa Cruz, CA, USA) at Active Motif (Carlsbad, CA, USA). Three separate passages were pooled. Active Motif performed the ChIPseq and generated approximately 33 x 107 reads. These reads were aligned to rat genome rn6 and compared to input control.
1 sample with FOXO1 Antibody and 1 input sample were sequenced

middle: S


title: Sex-dimorphic neuroprotective effect of CD163 in an alpha-synuclein mouse model of Parkinson’s disease

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

summary: Alpha-synuclein (α-syn) aggregation and immune activation represent hallmark pathological events in Parkinson’s disease (PD). The PD-associated immune response encompasses both brain and peripheral immune cells, although little is known about the immune proteins relevant for such response. We propose that the upregulation of CD163 observed in blood monocytes and in the responsive microglia in the PD patients is a protective mechanism in the disease.  To investigate this, we used the PD model based on intrastriatal injections of murine α-syn pre-formed fibrils (PFF) in CD163 knockout (KO) mice and wild-type littermates. CD163KO females revealed an impaired and differential early immune response to α-syn pathology as revealed by immunohistochemical and transcriptomic analysis. After 6 months, CD163KO females showed an exacerbated immune response and α-syn pathology, which ultimately led to a dopaminergic neurodegeneration of greater magnitude. These findings support a novel, sex-dimorphic neuroprotective role for CD163 during α-syn-induced neurodegeneration.

overall_design: To generate a PD model, murine alpha-synuclein pre-formed fibrils (α-syn PFF) were used due to their higher seeding efficiency in mice compared to human α-syn PFF. In parallel, phosphate buffered saline (PBS) was used as an absolute control, and murine monomeric α-syn (MONO) was used as a control for α-syn pathology, based on its reported lack of seeding capacity in vitro and in vivo. For whole population RNA sequencing, a third and fourth group of mice (batch 1 and batch 2) received bilateral intrastriatal injection of α-syn MONO (Males WT n=7 & CD163KO n=4*; Females WT n=7 &CD163KO n=5), and α-syn PFF (Males WT n=7, & CD163KO n =5; Females WT n=7 & CD163KO n=5). Triplicates were used for sequencing. Mice were sacrificed 2 months post-surgery, their brains dissected and the immune cells (microglia & macrophages) isolated and FACS sorted for RNA purification and subsequent SMART-seq2 sequencing. *CD163KO-MONO males were excluded from the analysis due to inconsistencies in the technical replicates. For the in vitro experiment, bone-marrow derived macrophages (BMDM) were isolated from CD163KO and WT C57BL/6N male and female mice, aged 6-12 weeks (n=5 per group).

first: Sara

last: Ferreira

first: Conghui

first: Ida

middle: H

last: Klæstrup

first: Zagorka

last: Vitic

first: Rikke

last: Rasmussen

first: Asger

last: Kirkegaard

first: Gitte

middle: U

last: Toft

first: Cristine

last: Betzer

first: Pia

last: Svendsen

first: Poul

last: Jensen

first: Anders

last: Etzerodt

first: Søren

last: Moestrup

first: Marina

last: Romero-Ramos


title: Soluble CD83 modulates human-monocyte-derived macrophages towards alternative phenotype, function and metabolism

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: Alterations in macrophage (Mφ) polarization, function and metabolic signature can foster development of chronic diseases, such as autoimmunity, or fibrotic tissue remodeling. Thus, identification of novel therapeutic agents that modulate human Mφ biology is crucial for treatment of such conditions. Herein we demonstrate that the soluble CD83 (sCD83) protein induces pro-resolving features in human monocyte-derived Mφ biology. We show that sCD83 strikingly increases the expression of inhibitory molecules including ILT-2 (immunoglobulin-like transcript 2), ILT-4, ILT-5 and CD163, whilst activation markers, such as MHC-II and MSR-1 were significantly downregulated. This goes along with a decreased capacity to stimulate alloreactive T cells in mixed lymphocyte reaction (MLR) assays. Bulk RNA sequencing and pathway analyses revealed that sCD83 downregulates pathways associated with pro-inflammatory, classically-activated Mφ (CAM) differentiation including HIF-1A, IL-6 as well as cytokine storm, whilst pathways related to alternative Mφ activation and Liver X receptor were significantly induced. By using the LXR pathway antagonist GSK2033, we show that transcription of specific genes (e.g. PPARG, ABCA1, ABCG1, CD36) induced by sCD83 are dependent on LXR activation. In summary, we herein reveal for the first time mechanistic insights into the modulation of human Mφ biology by sCD83, which is a further crucial pre-clinical study for the establishment of sCD83 as a new therapeutical agent to treat inflammatory conditions.

overall_design: RNA sequencing analyses of human monocyte-derived Macrophages, which were treated with sCD83 (25 µg/ml) or the corresponding amount of PBS as control on day 0 as well as day 3 during differentiation process. In detail, PBMCs from three different healthy donors were isolated via density gradient centrifugation and subsequently monocytes were seeded for adherence. Monocytes were differentiated into Mφ in the presence of M-CSF (20 ng/ml), +/- sCD83 (25 µg/ml). sCD83 was added on day 0 as well as day 3 during the differentiation process - or the corresponding amount of PBS as control. Subsequently, Mφ were harvested on day 6 of differentiation and RNA isolation was performed using the RNAeasy Mini Kit (Qiagen). 1 µg RNA was subsequently send for RNA sequencing performed by Novogene.

first: Katrin

last: Peckert-Maier

first: Andreas

middle: B

last: Wild

first: Dmytro

last: Royzman


title: IDR-Targeting Compounds Suppress HPV Genome Replication via Disruption of Phospho-BRD4 Association with DNA Damage Response Factors

first: Cheng-Ming

last: Chiang

state: Texas

address: 6001 Forest Park Road

department: Simmons Comprehensive Cancer Center

summary: Perturbation of genome-wide expression profiles and BRD4 isoform (BRD4-L and BRD4-S) binding by phospho-BRD4-targeting compounds (pNPS14, pNPS90, or pNPS145) or BET bromodomain inhibitor JQ1 in proliferating and differentiated W12E human cervical keratinocytes

overall_design: RNA-seq, PRO-seq, and CUT&RUN-seq were performed in extrachromosomal HPV16 (ecHPV16)-containing W12E cells with or without phospho-BRD4 inhibitor (pNPS14/90/145) or BET bromodomain inhibitor JQ1 treatment.

first: Shwu-Yuan

last: Wu