title: Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response [human]

summary: Regulatory T cells (Treg) are conventionally viewed to suppress endogenous and therapy-induced anti-tumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNAseq/TCRseq of >73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment naive non-small cell lung cancers (NSCLC) with single cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Notably, only one subset selectively expresses high levels of OX40 and GITR, whose engangement by cognate ligand mediated proliferative programs and NF-kB activation, as well as multiple genes involved in Treg suppression, including LAG3. Functionally, the OX40hiGITRhi subset is the most highly suppressive ex vivo and its higher representation among total TIL-Treg correlated with resistance to PD-1 blockade. Surprisingly, in the murine tumor model, we found that virtually all TIL-Treg expressing T cell receptors that are specific for TAA fully develop a distinct Th1-like signature over a two-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFN and certain pro-inflammatory granzymes. Transfer learning of a gene score from the murine TAA-specific Th1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1 responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally-defined subsets with potentially opposing effects on ICB-induced anti-tumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to anti-tumor responses.

overall_design:
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1).
NOTE FROM SUBMITTER: Our data includes human patient data, the human raw data will be deposit to EGA.

UPDATE: [08-15-2024] The Sample titles and processed data files were renamed, but the processed data associated with each Sample (GSM) did not change.

first: Arbor

middle: G

last: Dykema

first: Jiajia

last: Zhang


title: Unraveling the Mechanism of Thermotolerance in Cryptococcus neoformans by Set3C Complex

status: Public on Sep 05 2023

city: Shenyang City, Liaoning Province

first: XinDi

last: Gao

state: Liaoning

address: 89, North WenHua Road

country: China

institute: Northeastern university

type: Expression profiling by high throughput sequencing

summary: Thermotolerance, a key factor essential for the virulence of pathogenic fungi including Cryptococcus neoformans, remains largely unexplored in terms of its underlying mechanism. In this study, our findings demonstrate that Set3C, a widely distributed and conserved histone deacetylase complex, is required for thermotolerance in Cryptococcus neoformans. Specifically, the deletion of the core subunit Set302, responsible for the integrity of the complex, results in a significant reduction in the growth ability under high stress and the viability at extreme temperature. Moreover, the absence of Set302 leads to a decrease in the production of capsule and melanin. Transcriptomics analysis revealed that Set302 regulates a large number of genes compared to normal condition, and their expression is responsive to heat stress. Notably, we observed that Set302 positively influences the expression of genes related to ubiquitin-proteasome system (UPS) at high temperature. Using GFP-α-synuclein overexpression model, we observed a pronounced accumulation of misfolded proteins under heat stress, consequently inhibiting the thermotolerance of Cryptococcus neoformans. Furthermore, the loss of Set302 exacerbates this inhibition of thermotolerance. Interestingly, set302∆ strain exhibits a similar phenotype under proteasome stress as it does under high temperature. We also found that set302∆ strain displayed significantly reduced pathogenicity and colonization ability compared to the wild-type strain in the murine infection model. Collectively, our findings indicate that Set302 modulates the degradation of misfolded proteins through the UPS pathway, thereby affecting the thermotolerance and pathogenicity of Cryptococcus neoformans.

overall_design: performed paired-end RNA-seq of Cryptococcus neoformans H99s as Control group and set302∆ strains as in 100ml YPD broth  at OD600=1 at 30°C or 39°C, respectively in biological triplicates.


title: Overexpression of CLK and wild-type CPSF6 and mutant CPSF6 in HEK293T cells to verify the effect of CLK2 phosphorylation CPSF6 on APA

status: Public on Sep 07 2023

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

institute: SUN YAT-SEN UNIVERSITY

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

overall_design: Refer to individual Series


title: Impact of Age and Sex on neuroinflammation due to SARS-CoV2 infection in a murine model.

status: Public on Sep 06 2023

city: Minneapolis

first: Ling

last: Li

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

country: USA

institute: University of Minnesota

summary:
Objectives: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes the worldwide COVID-19 pandemic. While SARS-CoV-2 can infect people of all ages and both sexes, senior populations are at greatest risk of severe disease and worse outcomes, and sexual dimorphism has been reported in COVID-19. COVID-19 causes damage to multiple organ systems, including the brain. Neurological symptoms are widely observed in patients with Covid-19, with many survivors suffering from persistent neurological impairment, potentially accelerating Alzheimer’s disease (AD). This study aims to investigate the mechanisms underlying the impact of age, and sex on neuroinflammation due to SARS-CoV-2 infection using mouse models.
Methods: Wild-type C57BL/6 mice were subjected to intranasal inoculation of SARS-CoV-2 lineage B.1.351, followed by daily body weight monitoring. At 7 dpi, viral burden and inflammatory cytokine/chemokine responses in the lung and brain were determined by quantitative RT-PCR, followed by immunohistochemical and transcriptomic analyses.
Results: Older age, male sex, showed increased lung viral loads and severity of SARS-CoV-2 infection in mice. No viral RNA was detected in the brains of infected mice; however, IL-6 and CCL2 mRNA increased significantly, particularly in brains of old and APOE4 mice. Unbiased brain RNA-seq/transcriptomic analysis showed that SARS-CoV-2 infection caused significant changes in gene expression profiles, and pathway analysis identified innate immunity and defense response to virus and other organisms as the major molecular networks affected in the brain by SARS-CoV-2 infection.
Conclusions: Our findings demonstrate that age, and sex, modify the progression and outcome of SARS-CoV-2 infection. SARS-CoV-2 infection triggers neuroinflammatory responses despite the lack of detectable virus in the brain. Changes in molecular networks of innate immunity and defense response to microorganisms underlie the impact of SARS-CoV-2 infection in the brain. These findings in mice mimic epidemiological and clinical observations in humans with Covid-19.

overall_design: We performed bulk mRNA-seq to examine the transcriptomic changes associated with SARS-CoV-2 infection in wild-type mice. RNA-Seq data was collected from 12 mice (6 males & 6 female)  at 10 months of age at 7 days post-infection. Sequencing was performed using Illumina NovaSeq 6000 platform, generating 20 million reads per sample on a 150-bp paired-end run.

first: Venkatramana

middle: D

last: Krishna

first: Allison

last: Chang

first: Holly

last: Korthas

first: Susanna

middle: R

last: Var

first: Walter

middle: C

last: Low

first: Maxim

last: Cheeran


title: ATAC-seq Reveals Global Changes in Transcription Factor Activity Upon Perturbation of Cellular Zinc

status: Public on Sep 01 2023

city: Boulder

first: Amy

last: Palmer

state: Colorado

address: 596 UCB

department: BioFrontiers

institute: University of Colorado Boulder

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Zinc (Zn2+) is an essential metal required in approximately 10% of the human proteome. Of this, nearly half of these proteins are involved in transcription. Little is known on how these proteins get their Zn2+, but it is becoming increasingly clear in the literature that Zn2+ may function in some capability as an intracellular messenger. Here, we sought to profile the effect that Zn2+ has on global transcription. Using ATAC-seq, we observed broad changes in chromatin accessibility when Zn2+ was both increased and depleted. These changes in chromatin accessibility correlated with changes in the enrichment of hundreds of transcription factors, many of which are Zn2+ finger transcription factors. To validate whether these changes in motif enrichment correlate with changes in transcription factor occupancy, we selected p53 as a candidate to follow up on. Using previously published p53 ChIP-seq datasets and new nascent transcription datasets, we identified high-probability p53 binding sites to validate using ChIP-qPCR. We found that the global changes in p53 motif enrichment correlated with our ChIP-qPCR results but some targets yielded     local accessibility differences, a reminder that genomics datasets require experimental follow-ups before generalizations can be made. We believe that the experimental and computational workflow presented here will allow researchers to use ATAC-seq in conjunction with publicly available datasets as a relative starting point for studying transcription factor occupancy in the future.

overall_design: ATAC-seq on MCF10A cells exposed to the Zn2+ chelator TPA, excess Zn in the form of ZnCl2, or an untreated control

first: Leah

middle: J

last: Damon

first: Lynn

last: Sanford

first: Taylor

last: Jones

first: Mary

middle: A

last: Allen

first: Robin

last: Dowell

middle: E


title: Paneth cell scRNA-seq analysis of un-infected and Salmonella Typhimurium infected mice

city: Newark

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers University

summary: Paneth cells consist of heterogeous phenotypes. How Paneth cells respond to infection by invasive pathogenic bacteria at single cell level remains uncharacterized. We used a flow cytometry based method to isolate Paneth cells from uninfected and Salmonella-infected Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). These highly pure Paneth cell populations were used for single cell RNA sequencing analysis.

overall_design: Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER; R26R-tdTomato) were intraperitoneally injected with a single dose of tamoxifen to activate the tdTomato reporter. One day after, mice were orally administered with 15mg of streptomycin. One day after, mice were divided into two groups (uninfected and infected), which were orally inoculated with sterile PBS (as control) or 10^8 CFU Salmonella. Four days after infection, tdTomato+ Paneth cells were isoated from ilea of uninfected and infected mice, and processed for single cell RNA sequencing by 10xGenomics. S. Typhimurium orally administered with 15mg of streptomycin, followed by oral infection of PBS (ABX) or 108 CFU S. Typhimurium (SAL) 24 h later.,  Salmonella-infected mouse (4 days infection) and analyzed by scRNA-seq

first: Iyshwarya

last: Balasubramanian

first: Sheila

last: Bandyopadhyay

first: Juan

last: Flores


title: The impact of DNA-PKcs in V(D)J recombination of mouse IgK antigen locus

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

summary: DNA-PKcs is a critical component of the non-homologous end joining (NHEJ) pathway, playing a role in the re-ligation of DNA double-strand breaks (DSBs) generated by RAG1/2 during V(D)J recombination in antigen loci. When NHEJ is deficient, DSBs can be repaired through alternative end joining (A-EJ). In this study, we investigated the consequences of DNA-PKcs deletion on V-J recombination at the IgK antigen locus. Our results reveal that DNA-PKcs deletion leads to inefficient V-J recombination, exhibiting phenotypes such as reduced efficiency, increased end resection, and decreased micro-insertions in the repair pattern. These findings are consistent with previously reported functions of Ku70, another key player in NHEJ. However, unlike Ku70, additional deletion of DNA-PKcs does not restore the efficiency of repair in the absence of Lig4. Instead, it reduces both end resection and microhomology-mediated repair. These observations highlight the context-dependent role of DNA-PKcs in end processing. The presence or absence of Lig4 appears to influence the function of DNA-PKcs, further emphasizing the intricate interplay between repair factors in the DNA damage response. Overall, our findings provide insights into the distinct functions of DNA-PKcs and Ku70 in V(D)J recombination and underscore the complex regulatory mechanisms underlying repair efficiency in different genetic backgrounds.

overall_design: Various murine proB cells including WT, Lig4-/-, PKcs-/-, Ku70-/-, Lig4-/- PKcs-/- and Lig4-/- Ku70 (with/without DNA-PKcs inhibitors Nu7441 and Nu7026)  were arrested by STI-571 to induce V(D)J recombination, the V-J recombination in IgK locus were systematically captured using all four JK baits (JK1, JK2, JK4 and JK5) by HTGTS.

first: Richard

middle: L

last: Frock


title: Paneth cells

last: Gao


title: KAT2A and KAT2B prevent double-stranded RNA accumulation and interferon signaling to maintain intestinal stem cell renewal

status: Public on Aug 31 2023

city: Piscataway

first: Michael

last: Verzi

address: 145 Bevier Road

department: Genetics

institute: Rutgers, The State University of New Jersey


title: Exploring modulation in Staphylococcus aureus biofilm formation and virulence during platelet storage and its impact on platelet functionality

status: Public on Aug 28 2023

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

country: Canada

institute: University of Ottawa

summary: Staphylococcus aureus CBS2016-05 and PS/BAC/317/16/W were spiked (4E+06 CFU/ml) into platelet concentrates (PCs) and Trypticase soy broth (TSB) and allowed to grow until early stationary phase (6 days) at 22-24°C. Subsequently, the cells were pelleted at 4°C and subjected to RNA extraction using the miRNeasy Mini Kit, following the manufacturer's instructions. To eliminate genomic DNA, the RNA samples from three independent biological replicates were treated with TURBO™ DNase AmbionTM (Thermo Fisher Scientific).

overall_design: Staphylococcus aureus CBS2016-05 and PS/BAC/317/16/W were spiked in triplicate PC units and three flasks containing TSB. The strains were allowed to grow until stationary phase. Total RNA was extracted, DNAse treated and quality was analyzed using Fragment Analyzer™.

first: Sylvia

middle: I

last: Chi

first: Sandra

last: Ramirez-Arcos


title: Hepatic transcriptome profiling in beef cattle to determine the effects of fescue toxicity

status: Public on Aug 11 2023

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: The objective of our study was to assess the effect of fescue toxicosis on the overall transcriptomics profile of liver tissue on growing Angus × Simmental steers and heifers. The susceptibility was determined by the T-snip genetic tests for a total of 42 pregnant cows. At mid-gestation, these animals were randomly assigned to control group which received a based diet and fed endophyte free fescue seeds; a treatment group was fed endophyte-infected tall fescue seeds for 30 days. RNA-seq experiments were performed in liver biopsy samples, and a total of 828 differentially expressed genes were detected.

overall_design: Profile of transcriptome-wide gene expression changes in liver samples from Angus × Simmental cattle supplemented with endophyte-infected tall fescue seeds (n=3; data available under GSE206468) compared to control samples (n=3 susceptible and n=3 tolerant).

first: Sonia

last: Moisa


title: capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

city: Chengdu

first: keying

last: Lu

state: Sichuan

address: Wuhou

department: State Key Laboratory of Biotherapy

institute: Sichuan university

summary: Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression.

overall_design: We development a Cas9-assisted profiling TE expression sequencing (capTEs).We performed this technology to comparative TE and gene expression profiling analysis in cell lines.

first: Xumei

last: Li

first: Keying

first: Xiao

last: Chen


title: Transcriptomic changes in primary intestinal epithelium cells with Kat2a/Kat2b DKO.

summary: RNA-seq was conducted to determine differentially expressed genes in whole intestinal epithelial cells between Kat2a/Kat2b DKO and controls.

overall_design: Differential gene expression analysis from RNA-seq of whole intestinal epithelium from 4 KAT2A/KAT2B DKO and 4 control mice.

first: Mai-Uyen

last: Nguyen


title: Mutations of the selected strain growing in low levels of Vitamin B12  in Mycobacterium marinum

status: Public on Aug 14 2023

city: Amsterdam

first: Beatriz

last: Izquierdo Lafuente

address: De Boelelaan

country: Netherlands

institute: Vrije Universiteit

summary: Vitamin B12 (B12) is an important cofactor in mycobacterial metabolism, and some pathogenic mycobacteria need to obtain it from the host. In this study, we investigated the transport of vitamin B12 in Mycobacterium marinum. We identified a transcriptor regulator that could be potentially involved in the uptake process. RNA sequencing analysis were performed in order to elucidate the regulon of this new transcriptor.

overall_design:
The  strain used in the experimen is a metH mutant that is sensitive to vitamin B12  since it relies on MetE (B12 supressed) to produce methionine. It presents a frame-shift mutation for the transcription regulator. The control strain is the metH mutant strain.
The resulting mutants were grown on methionine and B12 before RNA extraction. Methonine chemically supplements the absence of MetH. Since the regulator is involved on the B12 uptake, to ensure a higher expression of the gene, we culture the strain with B12. RNA was extracted and transcriptomic analysis was performed.

last: Lafuente

first: Alexander

last: Speer

first: Wilbert

last: Bitter


title: Pharmacologic C5aR1 antagonism in the Arctic mouse model of Alzheimer’s disease modifies microglial polarization and astrocyte signaling

status: Public on Aug 22 2023

city: Irvine

first: Andrea

last: Tenner

state: CA

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UCI

summary: SC and SN RNA-seq reveal that pharmacologic inhibition of C5aR1 both suppresses disease enhancing processes and promotes disease mitigating pathways in an AD mouse model.

overall_design: The Arctic model of Alzheimer's disease and wildtype mice were treated with a C5aR1 antagonist (PMX205) or not for 12 weeks.  Hippocampi were dissect and processed for single cell and single nucleus RNA-sequencing

first: Nicole

last: Schartz

first: Heidi

middle: Y

last: Liang

first: S

last: Mortazavi


title: Co-occurrence of Beckwith-Wiedemann syndrome and Pseudohypoparathyroidism type 1B: coincidence or common molecular mechanism?

status: Public on Aug 01 2023

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

type: Methylation profiling by genome tiling array

summary: Imprinting disorders are congenital diseases caused by dysregulation of genomic imprinting, affecting growth, neurocognitive development, metabolism and cancer predisposition. Overlapping clinical features are often observed among this group of diseases. In rare cases, two fully expressed imprinting disorders may coexist in the same patient. A dozen cases of this type have been reported so far. Most of them are represented by individuals affected by Beckwith-Wiedemann spectrum (BWSp) and Transient Neonatal Diabetes Mellitus (TNDM) or BWSp and Pseudo-hypoparathyroidism type 1B (PHP1B). All these patients displayed multilocus imprinting disturbances (MLID). Here, we report the first case of co-occurrence of BWS and PHP1B in the same individual in absence of MLID. Genome-wide methylation and SNP-array analyses demonstrated loss of methylation of the KCNQ1OT1:TSS-DMR on chromosome 11p15.5 as molecular cause of BWSp, and upd(20)pat as cause of PHP1B. The absence of MLID and the heterodisomy of chromosome 20 suggests that BWSp and PHP1B arose through distinct and independent mechanism in our patient.

overall_design: DNA samples extracted from peripheral blood were subjected to methylation profile analysis using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. We analyzed 1 patient and 4 controls

first: Laura

last: Pignata

first: Fabio

last: Acquaviva

first: Emilia

last: D’Angelo

first: Daniela

last: Cioffi

first: Valeria

last: Pellino

first: Orazio

last: Palumbo

first: Pietro

first: Masimo

last: Carella

first: Angela

last: Sparago

first: Daniele

last: De Brasi

first: Flavia

last: Cerrato

last: Riccio


title: hictk: blazing fast toolkit to work with .hic and .cool files

status: Public on Sep 14 2023

city: Oslo

first: Roberto

last: Rossini

address: Blindernveien 31

country: Norway

institute: University of Oslo

type:
Other
Third-party reanalysis

summary: We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.

relation:
Reanalysis of: GSM1551550
Reanalysis of: GSM1551551
Reanalysis of: GSM1551552
Reanalysis of: GSM1551553
Reanalysis of: GSM1551554
Reanalysis of: GSM1551555
Reanalysis of: GSM1551556
Reanalysis of: GSM1551557
Reanalysis of: GSM1551558
Reanalysis of: GSM1551559
Reanalysis of: GSM1551560
Reanalysis of: GSM1551561
Reanalysis of: GSM1551562
Reanalysis of: GSM1551563
Reanalysis of: GSM1551564
Reanalysis of: GSM1551565
Reanalysis of: GSM1551566
Reanalysis of: GSM1551567
Reanalysis of: GSM1551568
Reanalysis of: GSM1551569
Reanalysis of: GSM1551570
Reanalysis of: GSM1551571
Reanalysis of: GSM1551572
Reanalysis of: GSM1551573
Reanalysis of: GSM1551574
Reanalysis of: GSM1551575
Reanalysis of: GSM1551576
Reanalysis of: GSM1551577
Reanalysis of: GSM1551578

overall_design: We reanalyzed data from ENCSR410MDC (GSE63525) to generate Hi-C matrices in .hic v8, .hic v9 and .mcool format for benchmarking purposes. Matrices in .hic v8 and v9 format were generated using JuicerTools and HiCTools respectively while .mcool files were generated using cooler. In all cases, pair-wise interactions from ENCFF447ERX were used as input. BEDPE files with cis and trans queries were generated by randomly sampling TADs from ENCFF301CUL.

first: Jonas

last: Paulsen


title: Single-cell-level gene expression and chromatin accessibility profiles of cells isolated from Drosophila embryonic gonads

status: Public on Aug 10 2023

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

department: Biomedical science

country: Taiwan

institute: Chang Gung University

summary: We use scRNA-seq and scATAC-seq to investigate the development of germ cells and somatic gonadal precursors during embryogenesis.

overall_design: For the scRNA part, the vas-GFP cells were collected from 8-12 and 12-20 hr embryos using Fluorescence-activated cell sorting (FACS) and then pooled together to generate a scRNA sequencing library. For the scATAC part, vas-GFP nuclei were isolated from 0-4, 4-8, 8-12, 12-16 and 16-20 hr embryos using FACS and then pooled together to generate both ATAC and snRNA sequencing libraries. To get an overview of the expression profiles of germ cells from the beginning of embryogenesis, we included our previous 0-8 hr scRNA-seq data (SRX8341666) here.

first: Yi

last: Li

first: Shu


title: Transcriptome analysis of human natural killer cells derived from umbilical cord blood in response to the BCL-2 inhibitor venetoclax

status: Public on Jul 31 2023

city: Hefei

first: mingming

last: wu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District


title: Single-cell transcriptome analysis of human natural killer cells derived from umbilical cord blood in response to the BCL-2 inhibitor venetoclax

institute: University of Science and Technology of China

summary: Natural killer (NK) cell-based immunotherapy holds promise for cancer treatment, but its efficacy is still limited, necessitating the development of new strategies. Here, we report an unexpected discovery that venetoclax, the first FDA-approved BCL-2 inhibitor, acts as an immunometabolic modulator to potentiate adoptive NK cell immunotherapy against acute myeloid leukemia (AML). Venetoclax directly activates human NK cells, boosting their cytotoxicity against AML both in vitro and in vivo, independent of BCL-2 inhibition. Notably, we identify a distinct CD161low CD218b+ NK cell subpopulation exhibiting the most pronounced proportional increase and transcriptomic changes upon venetoclax treatment.Venetoclax enhances NK cell binding avidity and lytic granule polarization during immunological synapse (IS) formation.Furthermore, venetoclax promotes mitochondrial respiration and ATP synthesis via the NF-κB pathway, facilitating IS formation and effector function in human NK cells.Our findings establish venetoclax as a multifaceted immunometabolic modulator that enhances NK cell function, providing new insights for augmenting NK cell-mediated cytotoxicity in cancer immunotherapy.

overall_design: In order to explore the regulatory role of venetoclax in the killing function of NK cells, we isolated and purified NK cells derived from umbilical cord blood from 4 donors and treated them with venetoclax for 18 hours.For the scRNA-seq analysis of human cord blood NK ,pool 4 cells from the control group in one tube and 4 cells from the Venetoclax-treated group in another tube. We then counted and resuspended the pooled cells at a concentration of 1000 cells/µL, targeting an estimated 6000 cells per library, following the instructions of the Single Cell 3ʹ Solution v3 Kit (10X Genomics). Single-cell libraries were constructed strictly according to the manufacturer's standard protocol. Libraries were sequenced on the Illumina NovaSeq 6000 System.

first: Yan

last: Wang

first: BeiBei

last: Huang

first: Changcheng

last: Zheng

first: Haiming

last: Wei

first: Fang

last: Ni


title: Transcriptional changes in human natural killer cells derived from umbilical cord blood in response to the BCL-2 inhibitor Venetoclax

summary: Natural killer (NK) cell-based immunotherapy holds promise for cancer treatment, but its efficacy is still limited, necessitating the development of new strategies. Here, we report an unexpected discovery that venetoclax, the first FDA-approved BCL-2 inhibitor, acts as an immunometabolic modulator to potentiate adoptive NK cell immunotherapy against acute myeloid leukemia (AML). Venetoclax directly activates human NK cells, boosting their cytotoxicity against AML both in vitro and in vivo, independent of BCL-2 inhibition. Venetoclax enhances NK cell binding avidity and lytic granule polarization during immunological synapse (IS) formation.Furthermore, venetoclax promotes mitochondrial respiration and ATP synthesis via the NF-κB pathway, facilitating IS formation and effector function in human NK cells.Our findings establish venetoclax as a multifaceted immunometabolic modulator that enhances NK cell function, providing new insights for augmenting NK cell-mediated cytotoxicity in cancer immunotherapy.

overall_design: In order to explore the regulatory role of Venetoclax in the killing function of NK cells, we isolated and purified NK cells derived from umbilical cord blood and treated them with Venetoclax for 18 hours.We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors .Comparative gene expression profling analysis of RNA-seq data for freshly isolated NK cell  treat with or without Venetoclax.


title: Synergistic Effect of Ultrasound and Wirelessly Powered Electrical Stimulation on Piezoelectric Membranes for Enhanced Osteogenesis by Immunomodulation of Macrophage Polarization

city: Shanghai,

first: Ting

last: Jiang

address: Quxi Road No. 500

institute: Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Effect of Low-intensity pulsed ultrasound (LIPUS) assisted BT/MWCNTs/Col (BMC) membrane on gene expression during  immune response  of macrophages (Raw 264.7).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of Raw264.7 under different conditions (control, BMC, BMC+lipus)

first: Ningjuan

last: Ouyang


title: Enrichment of dsRNA in primary intestinal epithelium cells with Kat2a/Kat2b DKO.

first: Michael

last: Verzi

summary: dsRIP-seq was conducted to determine differential enrichment of dsRNA in whole intestinal epithelial cells between Kat2a/Kat2b DKO and controls.

overall_design: Differential enrichment analysis from dsRIP-seq of whole intestinal epithelium from 2 KAT2A/KAT2B DKO and 2 control mice.

first: Mai-Uyen

last: Nguyen

first: Christopher

last: Ellison


title: Impact of Tfrc deficiency on gut microbiome [16s rRNA-seq]

status: Public on Jul 10 2023

city: Gainesville

first: Liang

last: Zhou

state: Fl

address: 2015 SW 16th Ave

institute: University of Florida

summary: Iron metabolism is pivotal for cell fitness in the mammalian host. However, its role in group 3 innate lymphoid cells (ILC3s) is unknown. Here we show that transferrin receptor CD71-mediated iron metabolism cell-intrinsically controls ILC3 maintenance, cytokine production and host protection against Citrobacter rodentium infection, and metabolically affects mitochondrial respiration by switching of oxidative phosphorylation toward glycolysis. Iron deprivation or Tfrc deficiency reduces the expression and/or activity of the aryl hydrocarbon receptor (Ahr), a ligand-dependent transcription factor and a key ILC3 regulator. Furthermore, consistent with its role in generation of Ahr ligand, microbiome exerts a negative impact on CD71 expression in an Ahr-dependent manner. Genetic ablation or activation of Ahr in ILC3s leads to CD71 upregulation or downregulation, respectively, suggesting an active suppression of CD71 by Ahr. Iron overload partially restores defective ILC3 compartment in the small intestine of Ahr-deficient mice, representing compensatory action of CD71 upregulation during Ahr deficiency. Mechanistically, Ahr directly binds to the promoter region of the Tfrc locus to inhibit Tfrc transcription. These data collectively demonstrate an under-appreciated role of the Ahr-CD71-iron axis in regulation of ILC3 maintenance and function.

overall_design: For microbiome analyses, fecal DNA was isolated the Quick-DNA Fecal/Soil Microbe Miniprep Kit (ZYMO, 11-322), followed by amplification and library generation with the Quick-16S NGS Library Prep Kit (ZYMO, D6410) according to the manufacturer’s instructions. Sequencing was performed on the Illumina MiSeq (Illumina, Inc., San Diego, CA). Raw FASTQ sequences were filtered and analyzed using QIIME2 (v2022.2.0) and Dada2. Operational taxonomic units were defined based on sequence similarity threshold of 97%. Taxonomy was assigned based on the Silva 138 reference database.

first: Lifeng

last: Xiong

first: Eric

last: Helm


title: Genome wide binding of Ahr in ILC3 [ChIP-seq]

overall_design: ILC3s (Lin–CD90hiCD45lo) were FACS-sorted from the gut LPLs (combined LI and SI) of Rag1−/− mice. For ChIP of Ahr, cells were treated with FICZ (200 nM) for 4 hours before harvest. Cells were cross-linked with 1% formaldehyde for 15 min. Chromatin was sheared by sonication with Bioruptor Pico (30 s on and 30 s off for 25 cycles) and immunoprecipitated with anti-Ahr (Enzo Life Science, BML-SA210-0100) using iDeal ChIP-Seq Kit for transcription factors (Diagenode). Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Samples were sequenced as 50 bp single-end reads on the Illumina HiSeq 2500 instrument.


title: Effect of depletion of USP22 on gene expression of A375 melanoma cell line

status: Public on Jul 06 2023

city: Changsha

first: Huiyan

last: Sun

address: National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.

institute: Xiangya hospital Central South University

summary: To investigate the function USP22 in the regulation of tumor progression, we established A375 cell lines in which each target gene has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells and  3 repeated samples for each cell.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A375 cells and its KD derivative (shUSP22).

first: Guangtong

last: Deng


title: Transcriptional impact of iron in ILC3 [RNA-seq]

overall_design: ILC3 cells (Lin–CD90hiCD45lo) were FACS-sorted from the gut of indicated mice, and MNK-3 cells were collected after in vitro treatment. RNA was extracted using the RNAeasy Micro Kit (TaKaRa), followed by complementary DNA (cDNA) generation with the SMART-Seq® HT Kit (TaKaRa). Sequencing libraries were generated with the Nextera® XT DNA Library Preparation Kit (Illumina), and sequenced on the Illumina HiSeq 2500 instrument. FastQC (v0.11.5) was used to ensure high per-base sequence quality of reads. Sequenced reads were mapped and raw count values quantified with STAR78 to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (v1.2.25). Differentially expressed genes (max FPKM ≥ 1, fold change ≥ 1.5, q-value ≤ 0.05) were identified by DESeq2 (v1.26.0) analysis. Gene Set Enrichment Analysis (GSEA) was performed for Gene Ontology (GO) analysis. Log2 transformed FPKM values were used for principal component analysis in R (v3.6.2) with the prcomp function and then visualized using the factoextra package (v1.0.7). Heatmaps were created using the R package pheatmap (v1.0.12).


title: Single nuclei sequencing in wild-type and Cox10-/- regenerating liver.

status: Public on Jul 02 2023

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: We report single nuclei sequencing in wild-type and Cox10-/- regenerating mouse livers.

overall_design: Floxed alleles targeting Cox10 were combined with an AAV8-Cre adenoassociated virus delivery to induced recombination in the liver.

first: Xun

first: Yi

last: Xiao


title: MEMO1 is required for ameloblast maturation and functional enamel formation

status: Public on Aug 03 2023

city: Iowa City

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

summary: Coordinated mineralization of soft tissue is central to organismal form and function, while dysregulated mineralization underlies several human pathologies. Oral epithelial derived ameloblasts are polarized, secretory cells responsible for generating enamel, the most mineralized substance in the human body. Defects in ameloblast development result in enamel anomalies, including amelogenesis imperfecta. Identifying proteins critical in ameloblast development can provide insight into specific pathologies associated with enamel related disorders or more broadly, mechanisms of mineralization. Previous studies identified a role for MEMO1 in bone mineralization; however, whether MEMO1 functions in the generation of additional mineralized structures remains unknown. Here, we identify a critical role for MEMO1 in enamel mineralization. First, we identified that Memo1 is expressed in ameloblasts and that conditional deletion of Memo1 from ameloblasts results in enamel defects, characterized by a decline in mineral density and tooth integrity. Molecular profiling of ameloblasts and their progenitors in Memo1 oral epithelial mutants revealed a disruption to cytoskeletal associated genes and a reduction in late stage ameloblast markers, relative to controls. Histology revealed that the molecular defects correlated with a disruption of the apical Tome’s process and the basolateral interacting, papillary layer, in Memo1 mutant ameloblasts. Finally, deletion of Memo1 from an oral epithelial ameloblast cell line, followed by cellular and molecular analyses, revealed altered cytoskeletal networks, relative to control cells. Collectively, our findings integrate MEMO1 into an emerging network of molecules important for ameloblast development and provide both in vivo and in vitro systems to further interrogate the relationship of cytoskeletal and amelogenesis-related defects.

overall_design: single cell RNA-sequencing of Memo1 mutant mouse ameloblast lineages and control tissue

first: Kent

last: Riemondy


title: Differential Network Analysis Reveals the Key Role of the ECM-receptor Pathway in α-Particle-induced Malignant Transformation

city: Suzhou

first: Wanshi

last: Li

address: 苏州大学

institute: 苏州大学

summary: Space particle radiation is a major environmental factor in spaceflight, and it is known to cause body damage and even trigger cancer, but with unknown molecular etiologies. To examine these causes, we developed a systems biology analytical approach that included co-expression network analysis of transcriptomics profiles obtained using different α-particle radiation exposures of BEAS-2B human bronchial epithelial cells. These exposures employed either single high-dose irradiation of 0.5 Gy one time, or, multiple low-dose irradiations consisting of 25 exposures to 0.02 Gy once every three days. These exposures were then followed by differential network comparative analysis through the multiscale interactomes. Overall pathway analysis based on the global network and the core modules showed that genes in the multiple low-dose irradiation groups had higher significant enrichment for the extracellular matrix (ECM)-receptor interaction pathway. Then, collagen gene COL1A1 was screened as an important ECM-related gene in the multiple low-dose irradiation group assessed by network robustness parameters, and an expression study of lung adenocarcinoma samples from The Cancer Genome Atlas (TCGA) database and additional biological experiments was performed. COL1A1 was found to promote the emergence of the neoplastic characteristics of BEAS-2B cells by both in vitro experimental analyses and in vivo immunohistochemical staining. These findings suggested that the degree of malignant transformation of cells exposed to multiple low-dose irradiations was greater than that of a single high-dose irradiation, which may be caused by the dysregulation of the ECM-receptor pathway. This study provides information on the molecular mechanisms underlying multiple low-dose irradiations used to mimic spaceflight, with a combination of high-throughput RNA-seq-based transcriptomics and systems biology approaches.

overall_design: The α-irradiator that we used in this study consisted of an Am source, a rotating radiation source holder, a sample holder and other necessary parts. The Am source emitted α-particles at a dose rate of 0.14 Gy/min. The BEAS-2B cells were irradiated either with a single dose of 0.5 Gy one time or were irradiated with 0.02 Gy (9 seconds of irradiation time) once every three days for 25 exposures. Meanwhile, a blank control was set up, which was sub-cultured together with the irradiated group. Thus, the three groups of cells were labeled as the Ctrl (blank control) group, the single exposure (SE) group (0.5 Gy) and the multiple exposures (ME) group (25 single-dose exposures of 0.02 Gy). After all exposures were completed, the cells were continuously sub-cultured to the 10th passage (approximately 3 weeks), 30th passage (approximately 9 weeks) or 50th passage (approximately 15 weeks), and harvested for RNA-seq at various passages. Thus, the SE groups included R1_05_10, R1_05_30 and R1_05_50, and the ME group included R25_05_10, R25_05_30 and R25_05_50. In summary, this project includes a total of 21 sets of samples.

first: Wenying

last: Yan

first: Wentao

last: Hu

first: Yidan

last: Song

first: Xingyi

last: Liu

first: Ziyun

first: Zhifei

last: Cao

first: Weiwei

last: Pei

first: Gungming

first: Guang


title: Gene expression profile at the single cell level of wild type and Cbl and Cblb knock-out organoids isolated from mouse intestional crypts.

status: Public on Jul 01 2023

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

summary: Organoid grown from intestinal crypts of Cbl flox/flox; Cbl-bflox/flox; R26Cre ERT2 mice were in presence or absence of 4-hydroxy-tamoxifen to delete Cbl and Cblb. Single cell RNA sequencing were performed in these two conditions to undestand the change in cell populations due to Cbl and Cblb depeletion.

overall_design: Intestinal crypts were isolated from two 10-week-old Cbl flox/flox; Cbl-bflox/flox; R26Cre ERT2 mice and grown into intestinal organoids using our established protocol. The organoids were replated and grown in presence or absence of 4-hydroxy-tamoxifen (400 nM) for 3 days to delete Cbl and Cblb. Organoids were dissociated into single cells and analzed using scRNAseq.

first: Bhopal

last: Mohapatra

first: Pinaki

last: Mondal


title: Reversible internalization of cytoplasm into the nucleus in senescent cells

status: Public on Sep 12 2023

city: Heraklion

first: Dimitrios

last: Botskaris

address: Nikolaou Plastira 100

country: Greece

institute: IMBB FORTH

summary: Cellular senescence is a heterogeneous phenotype, driven by diverse effector programs, which result in irreversible growth arrest, DNA damage, production of complex secretome and metabolic reprogramming1,2. Here we show that in liver-specific Setd8-KO mice, after mitogen treatment, a significant number of hepatocytes become senescent, have enlarged nuclei and increased nuclear envelope plasticity. Despite cell cycle arrest, senescent cells in Setd8-deficient mice retain inherent capability to replicate DNA, resulting in endoreduplication-driven chromosomal hyperploidy. Remarkably, the enlarged nuclei had multiple nuclear engulfments progressing to the generation of large intranuclear vesicles surrounded by nuclear lamina. These vesicles had externally-positioned membrane-associated chromatin, contained glycogen, various cytoplasmic proteins, even whole organelles like ER or mitochondria. We term this process “endonucleosis”. Intranuclear vesicles were absent in hepatocytes of Setd8/Atg5 double knockout mice, suggesting that the process requires the canonical autophagy machinery. Endonucleosis and hyperploidization are temporary, early features of senescence. Larger vesicles were split into microvesicles over time and were eventually eliminated, while large nuclei were segregated into smaller ones without mitosis. The results reveal a unique senescence phenotype with several unusual features, such as hyperploidy, endonucleosis and nuclear segregation, all of which are anticipated to function as parts of survival mechanisms to escape necrotic death.

overall_design: RNA-Seq, CUT&Tag, ATAC-Seq, ChIP-Seq

first: Ourania

last: Galanoploulou

first: Evangelia

last: Tachmatzidi

first: Elena

last: Deligianni

first: Dimitris

first: Kostas

last: Nikolaou

first: Sofia

last: Gargani

first: Yiannis

last: Dalezios

first: George

last: Chalepakis

first: Iannis

last: Talianidis


title: Transcriptomic investigation of the modes of action of polymyxins and colistin/sulbactam combination against carbapenem-resistant Acinetobacter baumannii

city: Shanghai

first: Xingchen

last: Bian

state: Shanghai

address: Fudan university, Huashan hospital

institute: Huashan hospital, Fudan University

summary:
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a Priority 1 (Critical) pathogen urgently requiring new antibiotics. Polymyxins are a last-line option against CRAB-associated infections. This transcriptomic study utilized a CRAB strain to investigate mechanisms of bacterial killing with polymyxin B, colistin, colistin B and colistin/sulbactam combination therapy. After 4 h of 2 mg/L polymyxin monotherapy, all polymyxins exhibited common modes of action which primarily involved disruption to amino acid and fatty acid metabolism. Of the three monotherapies, polymyxin B induced the greatest number of differentially expressed genes (DEGs), including for genes involved with fatty acid metabolism. Gene disturbances with colistin and colistin B were highly similar (89% common genes for colistin B), though effects on gene expression were generally lower (0-1.5-fold in most cases) with colistin B. Colistin alone (2 mg/L) or combined with sulbactam (64 mg/L) resulted in rapid membrane disruption as early as 1 h. Transcriptomic analysis of this combination revealed the effects were driven by colistin and included disturbances in fatty acid synthesis and catabolism and inhibition of nutrient uptake. Combination therapy produced substantially higher fold changes in 72% of DEGs shared with monotherapy, resulting in substantially greater reductions in fatty acid biosynthesis and increases in biofilm, cell wall and phospholipid synthesis. This indicates synergistic bacterial killing with the colistin/sulbactam combination results from a systematic increase in perturbation of many genes associated with bacterial metabolism. These mechanistic insights enhance our understanding of bacterial responses to polymyxin mono- and combination therapy and will assist to optimize polymyxin use in patients.
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a Priority 1 (Critical) pathogen urgently requiring new antibiotics. Polymyxins are a last-line option against CRAB-associated infections. This transcriptomic study utilized a CRAB strain to investigate mechanisms of bacterial killing with polymyxin B, colistin, colistin B and colistin/sulbactam combination therapy. After 4 h of 2 mg/L polymyxin monotherapy, all polymyxins exhibited common modes of action which primarily involved disruption to amino acid and fatty acid metabolism. Of the three monotherapies, polymyxin B induced the greatest number of differentially expressed genes (DEGs), including for genes involved with fatty acid metabolism. Gene disturbances with colistin and colistin B were highly similar (89% common genes for colistin B), though effects on gene expression were generally lower (0-1.5-fold in most cases) with colistin B. Colistin alone (2 mg/L) or combined with sulbactam (64 mg/L) resulted in rapid membrane disruption as early as 1 h. Transcriptomic analysis of this combination revealed the effects were driven by colistin and included disturbances in fatty acid synthesis and catabolism and inhibition of nutrient uptake. Combination therapy produced substantially higher fold changes in 72% of DEGs shared with monotherapy, resulting in substantially greater reductions in fatty acid biosynthesis and increases in biofilm, cell wall and phospholipid synthesis. This indicates synergistic bacterial killing with the colistin/sulbactam combination results from a systematic increase in perturbation of many genes associated with bacterial metabolism. These mechanistic insights enhance our understanding of bacterial responses to polymyxin mono- and combination therapy and will assist to optimize polymyxin use in patients.

overall_design: We have six groups including colistin, polymyxin B, colistin B, sulbactam, colistin combined with sulbactam and control. Each group have three replicates.

first: Mengyao

last: Li

first: Xiaofen

first: Yan

last: Zhu

first: Jian

first: Phillip

last: Bergen

first: Wanzhen

first: Xin

first: Meiqing

last: Feng

first: Jing

last: Zhang


title: RNA-sequencing analysis of oncospheres from control and SNORD88B-deficient HCC cells

status: Public on Jun 30 2023

city: Beijing

first: Yang

last: gu

address: 15 Datun Road

institute: institute of biophysics

summary: To explore the role of small nucleolar RNA, SNORD88B on self-renewal of liver cancer stem cells (CSCs), we enriched contorl or SNORD88B-deficient HCC oncospheres.

overall_design:
Then RNA-sequencing analysis were performed and differentially expressed genes were identified.
Total RNAs were extracted from oncospheres and subjected to RNA-sequencing analysis  through BGISEQ-500 platform

last: Gu

first: Zusen

last: Fan


title: Gene expression data from biological replicates of imatinib and nilotinib resistant K-562 cells.

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

country: Germany

institute: University Hospital Schleswig-Holstein, Campus Kiel

summary:
Resistant cells were generated by stepwise exposure to increasing concentrations of imatinib or nilotinib to establish 0.5 and 2 µM imatinib and 0.05 µM nilotinib resistant cells. This procedure was performed twice independently to establish biological replicates of TKI resistance.
We performed microarrays (Clariom S) to analyze the changes in gene expression during the development of TKI resistance.

overall_design: RNA from cells was isolated and microarrays were run using two biological replicates of each resistance as well as four technical replicates. In addition, 4 controls were analyzed.


title: Role of the Ahr-CD71-iron axis in regulation of ILC3 maintenance and function

first: Liang

last: Zhou

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

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome

overall_design: Refer to individual Series


title: snoRNA-sequencing analysis of liver cancer stem cells from human samples

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore the role of small nucleolar RNA (snoRNA) on self-renewal of liver cancer stem cells (CSCs), we isolated liver CSCs (CD133+CD13+) and Non-CSCs (CD133-CD13-) from huamn liver tumor tissues.

overall_design: Then snoRNA-sequencing analysis were performed and differentially expressed snoRNAs were identified.  Total RNAs were extracted from liver cancer stem cells and subjected to snoRNA-sequencing analysis


title: Ropinirole hydrochloride identified by iPSC drug discovery for amyotrophic lateral sclerosis: a single-centered, randomized, double-blind, placebo-controlled phase 1/2a trial

city: Kanagawa

first: Satoru

last: Morimoto

address: 3－25－10, Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Keio Regenerative Medicine Research Center (KRM)

country: Japan

institute: Keio University

summary: We assessed the safety and efficacy of ropinirole, a candidate drug for amyotrophic lateral sclerosis (ALS) identified using induced pluripotent stem cells (iPSCs) technology, by a randomized controlled trial (UMIN000034954). Twenty participants were randomly assigned to ropinirole or placebo for 24 weeks in the double-blind period, followed by a 24-week open-label active extension period. Primary outcomes were safety and tolerability. Secondary outcomes evaluated the therapeutic effects of ropinirole. Adverse events were mostly those previously reported, with similar rates in both groups. Participants in the ropinirole group had lived an additional 27.9 weeks without disease progression compared with the placebo group at 12 months. We validated and confirmed the efficacy of ropinirole in patients with ALS using the largest publicly available real-world registry database of ALS (PRO-ACT). The iPSCs-derived motor neurons from the participants showed the D2R expression and the potential involvement of the SREBP2-cholesterol synthetic pathway in the therapeutic effects.

overall_design: Motor neurons were differenciated from iPS cells derived from sporadic ALS patients and performed total RNA-sequencing under the conditions of cell culture with and without ropinirole hydrochloride.

first: Shinichi

last: Takahashi

first: Daisuke

last: Ito

first: Yugaku

last: Daté

first: Kensuke

last: Okada

first: Chris

last: Kato

first: Shiho

last: Nakamura

first: Fumiko

last: Ozawa

first: Chai

middle: M

last: Chyi

first: Ayumi

last: Nishiyama

first: Naoki

last: Suzuki

first: Koki

last: Fujimori

first: Masaki

last: Takao

first: Miwa

last: Hirai

first: Yasuaki

last: Kabe

first: Makoto

last: Suematsu

first: Masahiro

last: Jinzaki

first: Masashi

last: Aoki

first: Yuto

last: Fujiki

first: Yasunori

last: Sato

first: Norihiro

first: Jin

last: Nakahara

first: Hideyuki

last: Okano


title: H3K27ac ChIP-seq in wild-type and Cox10-/- regenerating liver.

first: Prashant

last: Mishra

summary: We report here the genome-wide deposition of H3K27ac marks in wild-type and Cox10-/- regenerating mouse livers.

first: Xun

last: Wang


title: PIKfyve controls dendritic cell function and tumor immunity I

status: Public on Jun 26 2023

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: To understand the mechanism of Pikfyve loss in dendritic cells, we cultured conventional dendritic cells isolated from the bone marrow of Pikfyvef/f (“WT”) and mice with ItgaxTg/0 Pikfyvef/f (“KO”) mice and performed transcriptome profiling on RNA extracted from cells on Day 9 in culture. Taken together, these data demonstrate the PIKfyve mediates suppression of DC transcriptional maturation programs through the alternate/non-canonical NF-κB regulatory pathway.

overall_design: Comparative gene expression profiling of RNA-seq data from primary cultured conventional dendritic cells isolated from wild-type (WT) or Pikfyve-deficient (KO) mice (littermate pair-matched biological triplicates).

first: Jae

last: Choi

first: Yuping

last: Zhang

first: Weiping

last: Zou


title: A Single Trophoblast Layer Acts as the Gatekeeper at the Endothelial-Hematopoietic Crossroad in the Placenta

status: Public on Jun 25 2023

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: During embryonic development the placental vasculature acts as a major hematopoietic niche, where endolthelial to hematopoietic transition ensures emergence of hematopoietic stem cells (HSCs). However, the molecular mechanisms that regulate the placental hematoendothelial niche are poorly understood. Using a parietal trophoblast giant cell (TGC)-specific knockout mouse model and single-cell RNA-sequencing, we show that the paracrine factors secreted by this single layer of TGCs are critical in the development of this niche. Disruptions in the TGC specific paracrine signaling leads to the loss of HSC population and the concomitant expansion of a KDR+/DLL4+/PROM1+ hematoendothelial cell-population in the placenta. Combining single-cell transcriptomics and receptor-ligand pair analyses, we also define the parietal TGC-dependent paracrine signaling network and identify Integrin signaling as a fundamental regulator of this process. Our study elucidates novel mechanisms by which non autonomous signaling from the primary parietal TGCs maintains the delicate placental hematopoietic-angiogenic balance and ensures embryonic and extraembryonic development.

overall_design: Gata2f/f;Gata3f/f; Pl1Cre +/- males were crossed to Gata2f/f;Gata3f/f females and the embryos  were analyzed at E13.5. Single cell RNA sequencing of the placental samples were generated by deep sequencing using the 10x Genomics Chromium Single Cell Gene Expression Solution (10xgenomics.com).

first: Home

last: Pratik

first: Ghosh

last: Ananya

first: Ganguly

last: Avishek

first: Paul

last: Soumen

first: Gunewardena

last: Sumedha


title: Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS/AML

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Splicing modulation is a promising treatment strategy pursued to date only in splicing-factor mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer and are associated with poor outcomes in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Here, we show that cohesin mutations are biomarkers of sensitivity to drugs targeting splicing-factor SF3B1 (H3B-8800 and E-7107) and identify drug-induced alterations in splicing of DNA repair genes as the mechanism underlying this sensitivity. We demonstrate that treatment of cohesin-mutant cells with SF3B1 modulators results in impaired DNA damage response, accumulation of DNA damage, and increased sensitivity to a panel of chemotherapeutic agents in vitro and in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS/AML.

overall_design:
RNA-seq in wildtype or cohesin-mutant cells with or without treatment of splicing modulators. For all experiments at least two replicates were generated for each condition.

>>> Raw data not provided due to patient privacy concerns: PDX and patient RNA-seq samples <<<

first: Benjamin

last: Martin

first: Emily

last: Wheeler

first: Zuzana

last: Tothova


title: Effect of nano-hydroxyapatite and phosphate on thorium toxicity – Arabidopsis transcriptomic study

status: Public on Jun 24 2023

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: Thorium (Th) is a ubiquitous element but elevated concentrations caused by anthropogenic or natural activities pose health and environmental risks. Nowadays, Th is obtained mainly as by-product during the mining and extraction rare earth element. However, due to its abundance in nature, which is higher than the abundance of uranium, Th is considered as a potential fuel for the reactors. Therefore, in this study, we focused on the effect of thorium on Arabidopsis plants at the transcriptomic level. Since Th and phosphorus form insoluble phosphates, we focused on the effect of Th in the presence/absence of phosphate. Furthermore, we investigated the effect of hydroxyapatite nanoparticles, which are considered as material for in situ remediation, on Th toxicity. Not surprisingly, the highest number of DEGs was recorded in the combination of P absence and Th presence followed by the presence of Th in the standard hydroponic medium, the absence of P in the medium, the presence of nano-hydroxyapatite, and the presence of Th together with hydroxyapatite. Besides a high number of genes involved in stress response, Th also induced the transcription of genes involved in response to P starvation, indicating that Th decreased the availability of P. P deficiency caused by Th contributed to the phytotoxic effect of Th. Nano-hydroxyapatite significantly reduced Th toxicity. Nano-hydroxyapatite also served as a source of inorganic P for the plants, but caused deficiency of essential metals indicated by up-regulation of genes involved in their acquisition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from wild type and mutants N8507, N8508, and N9416. All mutants were exposed to 1) untreated control plants, 2) plants exposed to thorium (+Th variant), 3) plants on the phosphate-free medium (-P), 4) plants on the phosphate-free medium exposed to thorium (-P+Th), 5) plants on the phosphate-free medium exposed to nano-hydroxyapatite (NanoP) and, 6) plants on the phosphate-free medium exposed to nano-hydroxyapatite and thorium (NanoP+Th) for 14 days.

first: Přemysl

last: Landa

last: Müller

first: Sylva

last: Přerostová

first: Petr

last: Soudek


title: Loss of Lamin A leads to nuclear translocation of AGO2 mediated by EGFR signaling and inactivation of RNAi

status: Public on Jun 22 2023

city: Gothenburg

first: Aishe

last: Sarshad

address: Medicinaregatan 9C

department: Dept.of Biochemistry & Cell Biology

country: Sweden

institute: University of Gothenburg

summary: In mammals, RNA interference (RNAi) is mostly studied as a cytoplasmic event, however, numerous reports convincingly showed nuclear localization of AGO proteins. Nevertheless, the mechanism of the nuclear entry remains to be fully elucidated, and the extent of nuclear RNAi explored. The nuclear import of large proteins requires active transport through the nuclear envelope (NE). Therefore, we hypothesized that the NE, and its composition, is important for nuclear AGO2 translocation. Lamin A knockout significantly induced nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cells. We unravelled that the loss of Lamin A leads to EGFR and Src kinase activation, which regulates the turnover and stability of cytoplasmic specifically AGO2. Furthermore, EGFR mediated phosphorylation at Y393 inhibits the activity of nuclear RNAi. This was evident by AGO fPAR-CLIP in WT and KO cells, where we observed a decrease in RNAi potential. Mass spectrometry of AGO interactome, from the nuclear fraction, indicated that AGO2 is in complex with FAM120A, which may further reduced the activity of RNAi by competing with AGO2 transcript binding. Therefore, loss of Lamin A starts a signalling cascade that mediates nuclear AGO2 translocation to rapidly inhibit RNAi.

overall_design: We performed a gene expression profiling of A375 and SHSY5Y WT and Lamin A KO cells via RNA sequencing in 3 biological replicates, and carried out differential expression analysis between WT and Lamin A KO cells of respective cell line.

first: V

last: Lobo

first: I

last: Nowak

first: C

last: Fernandez

first: AIC

last: Muler

first: JO

last: Westholm

first: HC

last: Huang

last: Fabrik

first: HT

last: Huynh

first: M

last: Kanik

first: A

last: Härtlova

first: D

last: Benhalevy

last: Angeletti


title: PIKfyve controls dendritic cell function and tumor immunity II

first: Arul

last: Chinnaiyan

summary: To understand the mechanism of Pikfyve inhibition in dendritic cells, we cultured conventional dendritic cells isolated from the bone marrow of wild-type mice and performed transcriptome profiling on RNA extracted from cells treated with DMSO or apilimod for 3 or 8 hours on Day 6 in culture. Taken together, these data demonstrate the PIKfyve mediates suppression of DC transcriptional maturation programs through the alternate/non-canonical NF-κB regulatory pathway.

overall_design: Comparative gene expression profiling of RNA-seq data from primary cultured conventional dendritic cells isolated from wild-type mice treated with DMSO or the PIKfyve inhibitor, apilimod.

first: Jae

last: Choi

first: Yuping

last: Zhang

first: Weiping

last: Zou


title: Gene expression of subpopulations arising from a nitrogen down-shift with proline as a nitrogen source in S. cerevisiae

city: London

first: Kiyan

last: Shabestary

address: Exhibition Road

country: United Kingdom

institute: Imperial College London

summary: When S. cerevisiae cells growing exponentially in rich media (YPD) are shifted to nitrogen-limited media with proline (0.8 mM) as a nitrogen source, they differentiate into two subpopulations of different phenotypes including cell size, growth and survival capabilities. The RNA-seq data presented here are for each subpopulation (5 biological replicates per subpopulation) sampled 1 hour after the shift and separated by FACS.

overall_design: We compare 5 biological replicates for each subpopulation. Strain is a prototrophic version of BY4741 containing a subpopulation marker (pRPL28) identified by scRNAseq.

first: Rodrigo

last: Ledesma-Amaro


title: The hyperconnected 3D clique at the Ets1 locus is required for T cell function

status: Public on Jun 20 2023

city: Philadelphia

first: Golnaz

last: Vahedi

state: PA

address: 421 Curie Blvd

department: Department of Genetics

institute: University of Pennsylvania

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


status: Public on Jun 14 2023

city: San Francisco

first: William

last: Chen

address: 1450 3rd Street, HD 402

institute: UCSF

summary: RNA Nanostring from human meningioma samples This set of data pertains to RNA extracted from 2mm core punches from the representative FFPE blocks, on which a custom codeset was run.

overall_design: The study cohort consisted of 16 samples from 10 clinically aggressive meningiomas that were resected from 9 patients

first: Calixto-Hope

last: Lucas

first: David

last: Raleigh


title: The hyperconnected 3D clique at the Ets1 locus is required for T cell function (Hi-C)

summary: The spatiotemporal control of gene-expression programs relies on selection and nuclear organization of enhancers. Despite mounting evidence on the formation of multi-enhancer hubs with extensive spatial connectivity, the functional importance of these architectural units remains elusive. Here, we generated a new mouse model and genetically perturbed a genomic locus harboring the Ets1 gene which is hyperconnected in T cells and has strong association with immune-mediated diseases. Although T cell development was intact, competence towards CD4+ T helper 1 specialization was lost in vitro and in vivo after genetic perturbation of the Ets1 locus. Extensive high-resolution molecular mapping of 3D genome organization revealed that the hyperconnectivity of the Ets1 locus controlled the expression level of Ets1 which was required for the Th1-specific genome topology. Our work illustrates the functional relevance of multi-enhancer hub formation in T cells.

overall_design: Hi-C

first: Aditi

last: Chandra

first: Sora

last: Yoon

first: Michael

middle: F

last: Michieletto

first: Naomi

last: Goldman

first: Emily

middle: K

last: Ferrari

first: Leonel

last: Joannas

first: Jorge

last: Henao-Mejia


summary: DNA methylation from human meningioma samples that were also profiled for spatial heterogeneity analysis. Some samples represent spatially distinct regions, punched using a 2mm core punch from FFPE blocks in a given tumor. Other samples represent serial tumor samples at index treatment and then recurrence.

overall_design: The study cohort consisted of 16 samples from 10 clinically aggressive meningiomas that were resected from 9 patients.


title: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine

status: Public on Jun 19 2023

city: Ipswich

first: Bo

last: Yan

address: County Road

institute: New England Biolabs

type: Methylation profiling by high throughput sequencing

summary: Multi-omics requires concerted recording of independent information, ideally from a single experiment. In this study, we introduce RIMS-seq2, a high-throughput technique to simultaneously sequence genomes and overlay methylation information while requiring only a small modification of the experimental protocol for high throughput DNA sequencing to include a controlled deamination step. Importantly, the rate of deamination of 5mC is negligible and thus, do not interfere with standard DNA sequencing and data processing. Thus, RIMS-seq2 libraries from whole or targeted genome sequencing show the same germline variation calling accuracy and sensitivity as compared to standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.

overall_design: The Ultra II prepared ngs libraries are treated with heat alkaline before PCR amplification to increase the deamination rate of 5mC

first: Laurence

last: Ettwiller


title: Protocadherin 20 maintains intestinal barrier function to protect against Crohn’s disease by targeting ATF6

city: Guangzhou

first: Jing

last: Han

address: No.58 Zhongshan Er Road

department: Division of Gastroenterology

institute: The First Affiliated Hospital, Sun Yat-Sen University

summary: We identified cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in CD using transcriptome sequencing. Thus,we elucidated the function and mechanisms of PCDH20 in gut homeostasis, barrier integrity, and CD development.

overall_design: Mucosal biopsies were obtained at endoscopy from the colon of 10 Crohn's disease (CD) patients and 10 controls that matched in terms of gender, age, and location. The biopsies of CD patients were taken at the most affected sites but at a distance of ulcerations.

first: Shenghong

last: Zhang

first: Minhu

first: Shanshan

last: Huang


title: Herpesviruses mimic zygotic genome activation to promote viral replication

status: Public on Jun 11 2023

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary:
DUX4 is a germline transcription factor and a master regulator of zygotic genome activation. During early embryogenesis, DUX4 is crucial for maternal to zygotic transition at the 8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In adult somatic cells, DUX4 expression is silenced and its activation in adult muscle cells causes the genetic disorder Facioscapulohumeral Muscular Dystrophy (FSHD).
Here we show that herpesviruses actively induce DUX4 expression to promote viral transcription and replication. We demonstrate that HSV-1 immediate early proteins directly induce expression of DUX4 and its target genes including endogenous retroelements, which mimics zygotic genome activation. DUX4 directly binds to the viral genome, promotes viral transcription and genetic depletion of DUX4 by CRISPR/Cas9 abrogates viral replication.
Our results show that viruses from alpha-, beta- and gamma-herpesvirus subfamilies induce DUX4 expression and downstream germline-specific genes and retroelements. Herpesviruses activate DUX4 expression in order to induce an early embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for DUX4 in HSV-1 infected and mock HFF-1 cells. Harvesting timepoints were 2, 4, 6, 8, 10, and 12h post infection.

first: Walter

last: Stephanie

first: Neugebauer

last: Eva

first: Tan

last: Jiang

first: Drayman

last: Nir

first: Franke

last: Vedran

first: Tay

last: Savas

first: Landthaler

last: Markus

first: Akalin

last: Altuna

first: Ensser

last: Armin

first: Wyler

last: Emanuel

first: Full

last: Florian


title: Monocyte-derived macrophages orchestrate multiple cell-type interactions to repair necrotic liver lesions

status: Public on Jun 06 2023

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: The liver can fully regenerate after partial resection and its underlying mechanisms have been extensively studied. The liver can also rapidly regenerate after injury with most studies focusing on hepatocyte proliferation; however, how hepatic necrotic lesions during acute or chronic liver diseases are eliminated and repaired remains obscure. Here we demonstrate that monocyte-derived macrophages (MoMFs) are rapidly recruited to and encapsulate necrotic areas during immune-mediated liver injury, and this feature is essential in repairing necrotic lesions. At the early stage of injury, infiltrating MoMFs activate the JAG1-NOTCH2 axis to induce cell death-resistant SOX9+ hepatocytes near the necrotic lesions, which acts as a barrier from further injury. Subsequently, necrotic environment (hypoxia and dead cells) induces a cluster of C1q+MoMFs that promote necrotic removal and liver repair, while Pdgfb+MoMFs activate hepatic stellate cells (HSCs) to express a-smooth muscle actin and induce a strong contraction signal (YAP, pMLC) to squeeze and finally eliminate the necrotic lesions. In conclusion, MoMFs play a key role in repairing the necrotic lesions not only by removing necrotic tissues but also by inducing cell death resistant hepatocytes to form a perinecrotic capsule and by activating a-smooth actin expressing HSCs to facilitate necrotic lesion resolution.

overall_design: The liver samples were homogenized with a gentleMACS Dissociator (Miltenyi), filtered through 70-μm cell strainers, and then centrifuged through a Percoll density gradient (40% and 70%), immune cells were collected and further sorted with BD FACSMelody to isolate CD45+ CD11b+ Ccr2+ Ly6G- liver MoMFs. These Liver MoMFs were subjected to scRNA seq.

first: Dechun

last: Feng

first: Chingwen

last: Chang

first: Bin

last: Gao


title: FOXO3 Deficiency in Neutrophils Drives Colonic Inflammation and Tumorigenesis

status: Public on Jun 05 2023

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1430 Tulane Ave.

department: Pathology and Laboratory Medicine

institute: Tulane University

summary: Inflammatory bowel disease (IBD), characterized by infiltration of polymorphonuclear neutrophils (PMNs), increases the risk of colon cancer. PMN activation corresponds to accumulation of their intracellular Lipid Droplets (LDs). As increased LDs are negatively regulated by transcription factor FOXO3, our aim is to determine the significance of this regulatory network in PMN-mediated IBD and tumorigenesis. Affected tissue of IBD and colon cancer patients, colonic and infiltrated immune cells, have increased LDs’ coat protein, PLIN2. Mouse peritoneal PMNs with increased LDs and FOXO3 deficiency have elevated transmigratory activity. Transcriptomic analysis of these FOXO3-deficient PMNs showed differentially expressed genes (DEGs; FDR < 0.05) involved in metabolism, inflammation, and tumorigenesis. Upstream regulators of these DEGs, similar to colonic inflammation and dysplasia in mice, were linked to IBD and human colon cancer. Additionally, a transcriptional signature representing FOXO3-deficient PMNs (PMN-FOXO3389) separated transcriptomes of affected tissue in IBD (p=0.00018) and colon cancer (p=0.0037) from control. PMN-FOXO3389 predicted colon cancer invasion (lymphovascular p= 0.015; vascular p= 0.046; perineural p=0.03), and poor survival. Validated DEGs from PMN-FOXO3389 (P2RX1, MGLL, MCAM, CDKN1A, RALBP1, CCPG1, PLA2G7) are involved in metabolism, inflammation, and tumorigenesis (p<0.05). These findings highlight the significance of LDs and FOXO3-mediated PMN functions that promote colonic pathobiology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FOXO3 KO Neutrophils (PMNs) compared to WT.

first: Jenisha

last: Ghimire

first: Rida

last: Iftikhar

first: Harrison

last: Penrose

first: Patricia

last: Snarski

first: Emmanuelle

last: Ruiz


title: Pre-determined diversity in resistant fates emerges from homogenous cells after anti-cancer drug treatment (single-cell data)

status: Public on Jun 03 2023

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: Even amongst genetically identical cancer cells, therapy resistance often only emerges from a very small subset of those cells. Much effort has gone into uncovering the molecular differences in rare individual cells in the initial population that may allow certain cells to become therapy resistant; however, comparatively little is known about variability in the resistant outcomes themselves. Here, we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically, and functionally distinct fate types. These different resistant types are largely predetermined by molecular differences between cells before addition of drug and not by extrinsic cell-specific microenvironmental factors. Changes in dose and kind of drug can, however, switch the resistant fate type of an initial cell, even resulting in the generation and elimination of certain fate types. Diversity in resistant fates was observed across several single-cell-derived cancer cell lines and types treated with a variety of drugs. Cell fate diversity as a result of variability in intrinsic cell states may be a generic feature of response to external cues.

overall_design: RNA was extracted as per the manufacter's protocol using a 10x Genomics v3 kit. We generated gel beads-in-emulsion (GEMs) using the 10X Chromium system and a Chromium Next GEM Single Cell 3' Reagent Kit v3.1 as per the manufecturer's protocol, aiming for 10,000 cells for recovery. We used the 10X Genomics single-cell RNA-seq kit v3 to sequence cells. We resuspended the cells (targeting ~10,000 cells for recovery/ sample) in PBS and followed the protocol for the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 as per manufacturer directions (10X Genomics, Pleasanton, CA). Briefly, we generated gel beads-in-emulsion (GEMs) using the 10X Chromium system, and subsequently extracted and amplified (11 cycles) barcoded cDNA as per post-GEM RT-cleanup instructions. We then used a fraction of this amplified cDNA (25%) and proceeded with fragmentation, end-repair, poly A-tailing, adapter ligation, and 10X sample indexing per the manufacturer’s protocol.

first: Arjun

last: Raj


title: Dystrophin deficiency hampers cell state transitions during somite development

status: Public on Jun 01 2023

city: Nantes

first: Jean-Baptiste

last: Dupont

address: 22 boulevard Benoni Goullin

department: INSERM

country: France

institute: Nantes Université

summary: This dataset describes human induced pluripotent stem cells as they differentiate into somite progenitors, and the consequences of dystrophin deficiency on the transcriptome of these single cells

overall_design: hiPSCs from three cell lines (Healthy, DMD, CRISPR) were collected at Day 10 of a myogenic differentiation protocol and subjected to single-cell RNA-Seq using a commercial split-pool barcoding kit provided by Parse Biosciences

first: Elise

last: Mozin


title: DMD hiPSCs bifurcate to an alternative branch of the myogenic trajectory

summary: This dataset describes the myogenic trajectory followed by human induced pluripotent stem cells, and the consequences of dystrophin deficiency on the outcome of differentiation

overall_design: hiPSCs from two cell lines (Healthy, DMD) were collected at 10 successive time points of the myogenic differentiation and subjected to single-cell combinatorial indexing RNA-Seq  (sci-RNA-Seq)

first: Dana

last: Jackson

first: Jonathan

last: Packer

first: David

last: Mack

first: Cole

last: Trapnell


title: Dystrophin deficiency dysregulates cell junctions during somite formation from pluripotent stem cells

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

overall_design: Refer to individual Series


title: scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

status: Public on May 23 2023

city: Bethesda

first: Welles

last: Robinson

state: Maryland

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: We profiled cell lines (HCT116, THP1 and Jurkat T) exposed to heat-killed and live Fusobacterium nucleatum using multiple scRNA-seq technologies

first: Joshua

last: Stone

first: Alejandro

last: Schaffer

first: Eytan

last: Ruppin


title: Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section

status: Public on May 21 2023

city: Solna

first: Marco

last: Vicari

address: Tomtebodavägen 23

department: Gene Technology

institute: KTH, SciLifeLab

summary: We present a spatial omics approach that merges and expands the capabilities of independently performedin situassays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinson’s disease.

overall_design:
Tissue sections processed with MALDI-MSI were eventually analyzed using Visium. Controls for some of the samples are included.
*** From Submitter:  We are restricted to deposit raw sequencing from humans to SRA. Those will be deposited on the Swedish federated EGA node and we will link when it became available to us. ***

first: Reza

last: Mirzazadeh

first: Anna

last: Nilsson

last: Shariatgorji

first: Patrik

last: Bjärterot

first: Ludvig

last: Larsson

first: Hower

last: Lee

first: Mats

first: Julia

last: Foyer

first: Markus

last: Ekvall

first: Paulo

last: Czarnewski

first: Xiaoqun

last: Zhang

first: Per

last: Svenningsson

last: Andrén

first: Joakim

last: Lundeberg


title: Next-generation RNA sequencing of human astrocyte cultures to study the comparative levels of transmembrane proteins and their transcriptional variants

status: Public on May 25 2023

city: Daejeon

first: C Justin

address: 55, Expo-ro, Doryong-dong, Yuseong-gu

department: Center for Cognition and Sociality

country: South Korea

institute: Institute for Basic Science

summary: The aim of this study was to perform Next-generation RNA sequencing to analyse the expression of transmembrane proteins in human astrocytes and compare the prevalance of transcriptional variants thereof.

overall_design: Human astrocyte cell cultures were allowed to grow to 70% confluence in DMEM supplemented with 10% FBS and 1% antibiotics. RNA was isolated from the cultured cells and processed to prepare cDNA libraries compatible with Illumina HiSeq NEXT Generation high-throughput sequencer. After the 2 x 100bp Illumina HiSeq paired-end sequencing run was complete, data in the form of BCL files was procured and processed to obtain relevant findings.

first: Hyunji

last: Kang

first: Mridula

last: Bhalla

first: C


title: Remodeling of the Immune and Stromal Cell Compartment by PD-1 Blockade in Mismatch Repair-Deficient Colorectal Cancer

status: Public on May 11 2023

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

summary: Immune checkpoint inhibitor (ICI) therapy can induce complete responses in mismatch repair-deficient and microsatellite instability-high (d-MMR/MSI-H) colorectal cancers (CRCs). However, the mechanism responsible for pathological complete response (pCR) to immunotherapy has not been completely understood. We utilize single-cell RNA sequencing to examine the immune and stromal cell dynamics in 19 patients with d-MMR/MSI-H CRC treated with the neoadjuvant PD-1 blockade. In tumors with a pCR, the proportions of CD8+ Trm-mitotic, CD4+ Tregs, proinflammatory IL1B monocyte and CCL2+Fibroblast concertedly decrease following treatment, while those of CD8+ Tem, CD4+ Th, CD20+ B and HLA-DRA+ Endothelial cells increase. Proinflammatory features in tumor microenvironment mediate the persistence of residual tumors by modulating CD8+ T cells and other response-associated immune cell populations. Our study provides rich resources and biological insights into the mechanism of successful ICI therapy and potential targets to improve treatment efficacy.

overall_design:
Illumina BCL files were converted to fastq files by using 10X Genomics Cell Ranger pipeline mkfastq function ( https://support.10xgenomics.com/). Next, cellranger count function was used to generate Gene-Barcode matrices from the fastq files, which uses the STAR algorithm to map high-quality reads to the human reference genome (GRCh38), followed by UMI counting.
The raw FASTQ files in this study will be provided for scientific research upon request complying with the law due to human patient privacy concerns.

first: Yanhong

last: Deng

first: Zhi

last: Xie

first: Jianxia

last: Li


title: pre-GC and GC B cell scRNAseq

city: New York

first: Ryan

last: Smolkin

state: NY

address: 408 E 69th St

institute: MSKCC

summary: Following infection or vaccination, activated B cells at extrafollicular sites or within germinal centers (GCs) undergo vigorous clonal proliferation. Proliferating lymphocytes have been shown to undertake lactate dehydrogenase A (LDHA)-dependent aerobic glycolysis; however, the specific role of this metabolic pathway in a B cell transitioning from a naïve to a highly proliferative, activated state remains poorly defined. Here, we deleted LDHA in a stage- and cell-specific manner. We find that ablation of LDHA in a naïve B cell did not profoundly affect its ability to undergo a T cell-independent extrafollicular B cell response. On the other hand, LDHA-deleted naïve B cells had a severe defect in the capacities to form GCs and mount GC-dependent antibody responses. In addition, loss of LDHA in T cells severely compromised B cell-dependent immune responses. Strikingly, when LDHA was deleted in activated, as opposed to naïve, B cells, there were only minimal effects on the GC reaction and in the generation of high-affinity antibodies. These findings strongly suggest that naïve and activated B cells have distinct metabolic requirements that are further regulated by niche and cellular interactions.

overall_design: We performed scRNA sequencing to understand role of LDHA in the activation and proliferation of germinal center (GC) B cells. We combined this technology to HASH-sequencing in order to measure analyze LDHA-sufficient and -deficient GCs in triplicate and BCR sequencing to detect clonality and validate hypermutation in the early potential GC cells.

first: Rahul

last: Sharma

first: Jayanta

last: Chaudhuri


title: Distinct Metabolic Requirements Regulate B Cell Activation and Germinal Center Responses


title: High-throughput JH4 sequencing of germinal centers of LDHA-suffiicient and -deficient B cells

overall_design: JH4 sequencing of LDHA-sufficient and -deficient splenocytes

first: Keith

last: Fernandez


title: GC B cell RNAseq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LDHA-sufficient and -deficient GC B cells.


title: DRMY1 promotes robust morphogenesis by sustaining translation of a hormone signaling protein

status: Public on Apr 24 2023

city: Ithaca

first: Adrienne

last: Roeder

address: 239 Weill Hall, 526 Campus Road

department: Weill Institute of Cell and Molecular Biology and Plant Biology Section, School of Integrative Plant Science

institute: Cornell University

summary: Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals initiate at robust positions and times and grow to equal size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 (drmy1), where 3-5 sepals initiate at irregular positions and variable times and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7), a rapidly synthesized and degraded cytokinin signaling inhibitor. The resultant upregulation of cytokinin signaling disrupts the robust positioning of auxin signaling, causing variable sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.

overall_design: Inflorescences of ap1 cal AP1-GR and drmy1 ap1 cal AP1-GR were induced with dexamethasone for three days and collected on the fourth day since the first induction (when sepals are emerging from the floral meristems). Three biological replicates were collected for each genotype.

first: Mingyuan

last: Zhu


title: Gene expression data of mRNA from mesenchymal stem cells derived from two different sorts of synovial membrane of German Landrace (DL) and Angeln Saddleback (AS) pigs II

status: Public on Apr 30 2023

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: 47,845 probe-sets were screened, This study compared expression profiles of mesenchymal stem cells derived from the two breed DL and AS and then analyzed the expression profile genes between two different sorts of synovial membrane in each breed.

overall_design: RNAs of mesenchymal stem cells derived from two different sorts of synovial membrane of DL and AS were hybridized to Affymetrix Porcine Snowball Array


title: Spatial Transcriptomics of Liver tissue with Bcatenin exon3 genetic mutations.

status: Public on Apr 28 2023

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: Gene expression was profiled in different regions of mouse liver with either Bcatenin exon3 mutation or Bcatenin exon3/Myc mutation at the noted time points.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Spatial transcriptomic data of the noted regions in mouse liver with the noted genetic mutations.

first: Alexander

last: Raven

first: Nigel

last: Jamieson

first: Owen

last: Sansom


title: Clariom S Microarray Expression Data from Mouse Colonic Lesion and Healthy Tissue following AOM/DSS Chemical Induction of Colitis-associated Colorectal Cancer to Assess NF-κB Mediated Intestinal Epithelial Cell Regeneration

status: Public on Apr 23 2023

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 205 Duck Pond Dr.

department: Biomedical Sciences and Pathobiology

institute: Virginia-Maryland College of Veterinary Medicine

summary:
This study sought to evaluate the diffferential gene expression following the conditional knockout of either the canonical (p65) or non-canonical (NIK) NF-κB signaling pathway in myeloid (LysMCre)  or intestinal epithelial (VillinCre) cell deletions in a murine model. Genetic susceptibility to colitis-associated colorectal cancer via the chemical induction of AOM/DSS was evaluated on colonic lesion (LT) and healthy tissue (HT) using microarray to assess implicated genes/pathways downstream of NF-kappaB.
Abstract from associated publication: Dysregulation of intestinal epithelial cell proliferation is a critical feature in the development of colorectal cancer. This malignancy is typically driven by loss of stem cell regulation in the crypts. Here, we show that NF-κB-inducing kinase (NIK) attenuates colorectal cancer through the regulation of intestinal epithelial cell regeneration and differentiation mediated by noncanonical NF-κB signaling. We observed increased tumor burden in mice lacking NIK either systemically or specifically in intestinal epithelial cells in a model of inflammation-induced tumorigenesis in the colon. Mechanistic studies using crypts and organoids revealed that loss of NIK results in the accumulation of mature, non-dividing colonic epithelial cells, which are more susceptible to mutations and eventual transformation. These findings are consistent with our observations in human colorectal cancer patients revealing a significant decrease in NIK and noncanonical NF-κB signaling. Our work extends previous findings for NIK in attenuating sepsis and gastrointestinal inflammation and defines a critical role for this kinase in colorectal cancer.

overall_design: RNA extractions were collected from each lesion tissue (LT) and healthy tissue (HT) sample using a Qiagen AllPrep Kit. Groups include Nikfl/fl x VillinCre mice (n=3), Nikfl/fl mice (n=3), RelAfl/fl x LysMCre mice (n=3), RelAfl/fl mice (n=3). 4 mouse strains (groups) x3 replicates of LT and HT was collected and assessed for each group totaling n=24. 1 MRSL, provided by the manufacturer, was included.

first: Holly

last: Morrison


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (scRNA-Seq)

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.

overall_design: scRNA-seq of WT and Meteor promoter KO mESCs

first: Noa

last: Gil


title: Transcriptome of GCKR-P446L-EMI-B6N on a high-fat high-sugar diet

status: Public on Apr 19 2023

city: Newcastle upon Tyne

first: Loranne

last: Agius

address: Framlington Place

department: Biosciences Institute

institute: Newcastle University

overall_design:
Mice were maintained on a diet (HFHSD) of high-fat (45%fat, 20% protein, 35% carbohydrate) and high sugar (10% glucose, 5% fructose) for 20 weeks; mice were culled and livers harvested for RNA extraction and sequencing.  A sub-group of mice of each genotype was additionally given a GKA in the HFHSD
Male mice: N=10 446PP genotype (HFHSD); N=10 446PP (HFHSD + GKA);  N=8 446PL genotype (HFHSD); N=8 446PL (HFHSD + GKA); N=10 446LL (HFHSD); N=10 446LL(HFHSD + GKA)

first: Brian

last: Ford


title: Atlas of nascent RNA transcripts reveals high confidence enhancer associated bidirectionals linked with genes across different tissue types

status: Public on Apr 20 2023

city: Boulder

first: Taylor

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

summary: Gene transcription is controlled and modulated by enhancers and promoters. These regions are abundant in non-coding bidirectional RNA transcripts which have been used as a read-out of enhancer and promoter activity. Using nascent RNA transcription data across hundreds of samples, we identified 500,000 regions of bidirectional transcription and linked the transcripts to gene targets. The identified bidirectional and gene pairs are associated with diseases associated SNPs and these pairs are links in 3D genome space. We present these resources as an SQL database which allows for further investigation and understanding of how gene transcription is regulated.

overall_design: WT or p53 -/- MCF10A cells were treated with 10uM nutlin3a and 0.01% DMSO (control) for 3 hours with a total of 2 biological replicates. Nuclei were isolated and PRO-seq libraries were constructed and sequenced.