title: A panel of TDP-43-regulated splicing events verifies loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue

status: Public on Feb 02 2023

city: Auckland

first: Maize

last: Cao

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

summary: To investigate differential exon usage/ cryptic exon events that occur with TDP-43 depletion using human brain-derived pericytes

overall_design: Differential exon usage analysis was performed on bulk RNA-seq data of 9 donor lines  (6 from motor cortex, 3 from middle temporal gyrus) treated with either scrambled siRNA (scr) or siRNA against TARDBP (siTDP)

first: Emma

last: Scotter


title: Single-cell RNAseq analysis (10X Genomics Chromium) of refilled lung interstium macrophages at the time points of 12h, 24h and 48h after depletion

status: Public on Feb 07 2023

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

type: Expression profiling by high throughput sequencing

summary: Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing.     The lung IMs and monocytes from the mice at 12 hours (DT12h), 24 hours (DT24h) and 48 hours (DT48h) after diphtheria toxin (DT)-induced IM depletion were analyzed and compared using single-cell RNA sequencing. A subpopulation was found to be a transit differentiating cells from monocytes to IMs. Transcription factor activity analysis and trajectory showed cMAF and MAFb transcription factors played important roles in monocyte-IM differentiation.

overall_design: The lung IMs and monocytes were sorted from three groups of mice:   Group “DT12h” contains 5 IM-DTR mice which were treated with 50 ng diphtheria toxin (DT) 12 hours before sacrifice.   Group “DT24h” contains 5 IM-DTR mice which were treated with 50 ng DT 24 hours before sacrifice.   Group “DT48h” contains 5 IM-DTR mice which were treated with 50 ng DT 48 hours before sacrifice.     Cells from each group were barcoded with different Biolegend anti-mouse Hastags before being pooled for library construction. Processed data then were analyzed with Bioconductor and Seurat package. The cells from different time points were demultiplexed with the barcode detected in each cell.

last: Bai

first: Shakir

last: Hasan

first: Domien

last: Vanneste

first: Thomas

last: Marichal


title: Single-cell RNAseq analysis (10X Genomics Chromium) of cMAF- and Mafb-deficent lung monocytes and interstium macrophages

summary: Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing.     The lung IMs and monocytes from either Lyz2-Cre Mafflox/flox mice (cMAF-KO), Lyz2-Cre Mafbflox/flox (MAFb-KO), Lyz2-Cre Mafflox/flox Mafbflox/flox (dKO) or control litermate mice without floxp locus (Control) were analyzed and compared using single-cell RNA sequencing. All the main substs, i.e. Ly6C+ classical monocytes, Ly6C- patrolling monocytes, CD206+ IMs, CD206- IMs were found in control sample, while IMs are absent in both MAFb-KO and dKO sample accompied by a new intermediate population independent of Mafb expression. CMAF-KO sample show less impact in cell population composition with a lower freqency of CD206+ IM population.

overall_design: The lung IMs and monocytes were sorted from four groups of mice:   Group “MAFb-KO” contains 3 Lyz2-Cre Mafbflox/flox (MAFb-KO) mice;   Group “cMAF-KO” contains 3 Lyz2-Cre Maflox/flox (cMAF-KO) mice;   Group “dKO” contains 3 Lyz2-Cre Mafflox/flox Mabflox/flox (dKO) mice.     Cells from each group were barcoded with different Biolegend anti-mouse Hastags before being pooled for library construction. Processed data then were analyzed with Bioconductor and Seurat package. The cells from different sample were demultiplexed with the barcode detected in each cell.


title: Effect of TET1/3 defiency on iTreg cell differentiation

status: Public on Jan 31 2023

city: Iowa City

first: Priya

middle: Darshinee

last: Issuree

state: IA

address: 431 Newton Road

department: Department of Internal Medicine

country: USA

institute: University of Iowa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the how TET1/3 remodels the chromatin landscape during iTreg cell differentiation and the role of autonomous IL-2 in this process, we performed ATAC-Seq on CD4 T cells that had been stimulated for 48hrs in the presence of TGF-b and in the presence or absence of exogenous IL-2.

overall_design: Comparative chromatin profiling analysis of ATAC-seq data for control and Tet1/3-deficient CD4 T cells that were stimulated for 48hrs in the presence of TGF-b and in the presence or absence of exogenous IL-2. Biological replicates were performed for each condition.


title: Investigating the effects of inflammatory cytokines associated with asthma on airway smooth muscle cell contractility

status: Public on Feb 01 2023

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins Dr

institute: NIBR

summary: Understanding the gene expression changes that are occuring with TGFb1 and IL-13 treatment that result in observed phenotypic changes in bronchial smooth muscle shortening/remodeling.

overall_design: Normal human bronchial smooth muscle cells (hBSMCs) were obtained from Lonza (CC-2576) and cultured using SmGMTM-2 BulletKitTM (Lonza CC-3182). To seed the microtissues: Cells were then suspended in a 2%1 mg/mL neutralized type 1 collagen solution then dispensed at a density of 50,000 cells per well into the plate over ice.  Cantilever arrays were immediately added to the well ensuring the ends of each cantilever were fully submerged and incubated at 37℃ for 15 min to allow for gelation.  Growth media was then added to the seeded wells and plates were incubated overnight to allow for initial tissue formation (Day 0).    Following 24h of incubation (Day 1) cantilever arrays were transferred into a fresh 96 well plate containing serum free mediahBSMC growth media with reduced serum (0.5% FBS) and the indicated recombinant cytokines at 10 ng/mL (see Supplementary Table X for catalog numbers). Microtissues were incubated for 3 days after which the media and cytokines were replenished (Day 4). After an additional three days of treatment (Day 7), microtissues were used for desired endpoint assessment, which includes brightfield imaging for contractility differences and lysing tissues in Qiagen Buffer RLT for RNA isolation, performed using the Qiagen RNEasy kit.

first: Pranjali

last: Beri

first: Christopher

last: Plunkett

first: Joshua

last: Barbara

first: Chien-Cheng

last: Shih

first: S

middle: W

last: Barnes

first: Olivia

last: Ross

first: Paula

last: Choconta

first: Ton

last: Trinh

first: Bella

last: Litvin

first: Minhua

last: Qiu

first: Scott

last: Hammack

first: Erin

last: Toyama


title: EGR4 is critical for cell-fate determination and maintenance of Geniculate Ganglion neurons underlying sweet and umami taste

city: Indianapolis

first: Brian

last: Pierchala

state: IN

department: Anatomy, Cell Biology & Physiology

institute: Indiana University School of Medicine

summary: The sense of taste starts with activation of receptor cells in taste buds by chemical stimuli which then communicate this signal via innervating oral sensory neurons to the CNS. The cell bodies of oral sensory neurons reside in the geniculate ganglion (GG) and nodose/petrosal/jugular ganglion. The geniculate ganglion contains two main neuronal populations, BRN3A+ somatosensory neurons that innervate the pinna, and PHOX2B+ sensory neurons that innervate the oral cavity. While much is known about the different taste bud cell subtypes, much less is known about the molecular identities of PHOX2B+ sensory subpopulations. In the GG as many as 12 different subpopulations have been predicted from electrophysiological studies, while transcriptional identities exist for only 3-6. Importantly, the cell fate pathways that diversify PHOX2B+ oral sensory neurons into these subpopulations are unknown. The transcription factor EGR4 was identified as being highly expressed in GG neurons. EGR4 deletion causes GG oral sensory neurons to lose their expression of PHOX2B and other oral sensory genes, and upregulate BRN3A. This is followed by a severe loss of chemosensory innervation of taste buds, a loss of Type II taste cells responsive to bitter, sweet, and umami stimuli, and a concomitant increase in Type I glial-like taste bud cells. These deficits culminate in a loss of nerve responses to sweet and umami taste qualities. Taken together, we identify a critical role of EGR4 in cell fate specification and maintenance of subpopulations of GG neurons, which in turn maintain the appropriate sweet and umami taste receptor cells.

overall_design: Differential gene expression analysis of RNAseq data from the geniculate ganglia of 4 wild type littermate mice and 4 Egr4-/- mice

first: Debarghya

middle: D

last: Banik


title: Cardiovascular progenitors regenerate infarcted swine hearts

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

summary: Stem cell-derived products could replace damaged heart muscle in regenerative cardiology. Here, human embryonic stem cells (hESCs) were differentiated on laminin 521+221 to cardiovascular progenitors (CVPs). The CVPs were transplanted into the infarcted region of 10 pigs and maintained for 4- and 12- weeks. Immunohistology analyses revealed in vivo engraftment and maturation of the CVPs into cardiomyocytes (CMs). Furthermore, heart function was analyzed by magnetic resonance imaging (MRI). We observed significant improvement in the left ventricular ejection fraction (DLVEF: 21.9 ± 1.6 %, at 12-weeks), ventricular wall thickness and wall motion, as well as a reduction in infarction size after CVP transplantation as compared to control pigs (p-value < 0.05). There are temporary episodes of ventricular tachyarrhythmia (VT) in four pigs and one pig had persistent VT. On the other hand, the remaining 5 pigs remained in normal sinus rhythm. Importantly, all pigs survived without any VT-related death, suggesting the potential for developing CVPs towards applications in regenerative cardiology.

overall_design: Human embryonic stem cells were cultured in wells coated with LN-521+LN-221 using nutristem medium. RNA is extracted when cells reached confluence. Bulk RNA-seq and single cell RNA-seq are performed on Day 0, 4, 9, 11, 20 of differentiation.

first: L

last: Yap

first: J

first: A

last: Swarnaseetha

first: E

last: Petretto

first: K

last: Tryggvason


title: Transcriptome analysis of PG0686 mutant in co-culture with Porphyromonas gingivalis II

status: Public on Jan 23 2023

city: Loma Linda

first: Yuetan

last: Dou

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

summary: We use high through put RNA sequenceing technology to study the genome-wide expression profile of a unknown-function gene PG0686 mutant, designated as FLL361,  in key-stone oral pathogen Porphyromonas gingivalis under anaerobic conditions and oxidative stress conditions.

overall_design: Comparison of PG0686 mutant (FLL361) to P. gingivalis under anaerobic conditions and oxidative stress conditions.

first: Hansel

middle: M

last: Fletcher


title: the mRNA expression quantitative Analysis of K562 and BaF3-T315I treated with JOA compared with control.

status: Public on Jan 19 2023

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

country: China

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in K562 and BaF3-T315I cell lines treated with JOA

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: There are 4 samples for K562 cell line ( control and JOA-treated) and 4 samples for BaF3-T315I cell line ( control and JOA-treated)

first: F

last: Li


title: In vivo CRISPR screens reveals SerpinB9 and Adam2 as regulators of immune therapy in lung cancer

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: We established a direct in vivo CRISPR/Cas9 gene editing methodology that allowed us to assess the immune-modulatory capabilities of 573 putative cancer genes associated with altered activity in mouse model of lung cancer. Using mouse models of of KrasG12D- and BrafV600E-driven lung cancer, we identified Serpinb9 as our top suppressive and Adam2 as our top enhancing gene. RNA seq analysis from tumors overexpressing Adam2 revealed that Adam2’s oncogenic function is dependent on modulating the tumor immune microenvironment by restraining productive type I and type II interferon responses as well as cytokine signaling, reducing presentation of tumor associated antigen, and modulating surface expression of several immunoregulatory receptors within Kras-driven lung tumors. Adam2 overexpression also led to reduction in expression of immune checkpoint inhibitors such as PD-L1, Lag3, Tigit, and Tim3.This less exhausted tumor microenvironment further induced enhanced cytotoxic efficacy against Adam2 overexpressing lung tumors, in vitro and in vivo. Together, our study highlights the power of integrating cancer genomic with in vivo CRISPR/Cas9 screens to uncover how cancer-associated genetic alterations control responses to immunotherapies.

overall_design: Profiling of Adam2, LLC-CTLR-OVA or LLC-Adam2-OVA cells transplanted in immunocompetent C57BL/6 mice followed by adoptive transfer of antigen primed OT-I cells at day 14 (=two days after tumor onset).

first: Dzana

last: Dervovic

first: Ahmad

last: Malik


title: Bone marrow progenitors and IL-2 signaling contribute to the strain differences of kidney innate lymphoid cells

city: Seoul

first: Hye Young

last: Kim

address: 103 Daehak-ro, Jongro-gu

country: South Korea

institute: Seoul National University

summary: Innate lymphoid cells (ILCs) are critical mediators of immune responses by their robust production of cytokines. ILCs are mainly present in mucosal tissues, but their regulatory function in the kidney is attracting attention. Nevertheless, the understanding of their unique biology, compared to other tissues, is largely unknown.Here, we aimed to examine the effect of BALB/c and C57BL/6 strains on the number and function of kidney ILCs and their underlying mechanisms. Although the BALB/c strain showed an increase in ILC2 frequency than that of C57BL/6 in most organs, the difference in ILC2 frequency between the two strains was most pronounced in the kidney. These results were derived from increased ILC precursors in the bone marrow, and levels of renal Il2 in BALB/c mice. Furthermore, IL-2 receptor (CD25) expression and STAT5 phosphorylation also exaggerated in BALB/c kidney ILC2s. However, similar IL-2-dependent proliferation and activation of ILC2s were observed upon IL-2C treatment in both strains. Thus, homeostatic differences in kidney ILC2 number and function derive from differences in IL-2 signaling resulting from intrinsic and extrinsic factors. Together, we demonstrate previously unknown properties of kidney ILC2s based on their mice strain background and contributing factors. All these factors should be considered critical for the successful translation of immune diseases in experimental mouse models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for kidney tissue from BALB/c mice (n=3), and C57BL/6 mice (n=3)

first: Seungwon

last: Ryu

first: Hye

middle: Y


title: Blood leukocyte transcriptional modules and differentially expressed genes associated with disease severity and age in COVID-19 patients

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: Since the molecular mechanisms determining COVID-19 severity are not yet well understood, there is a demand for biomarkers derived from comparative transcriptome analyses of mild and severe cases, combined with patients' clinico-demographic and laboratory data. Here the transcriptomic response of human leukocytes to SARS-CoV-2 infection was investigated by focusing on the differences between mild and severe cases and between age subgroups (younger and older adults). Three transcriptional modules correlated with these traits were functionally characterized, as well as 23 differentially expressed genes (DEGs) associated to disease severity. One module, correlated with severe cases and older patients, had an overrepresentation of genes involved in innate immune response and in neutrophil activation, whereas two other modules, correlated with disease severity and younger patients, harbored genes involved in the innate immune response to viral infections, and in the regulation of this response. This transcriptomic mechanism could be related to the better outcome observed in younger COVID-19 patients. The DEGs, all hyper-expressed in the group of severe cases, were mostly involved in neutrophil activation and in the p53 pathway, therefore related to inflammation and lymphopenia. These biomarkers may be useful for getting a better stratification of risk factors in COVID-19.

overall_design: A systems biology approach, integrating clinical and transcriptomic data - through WGCNA - to identify transcriptional modules highly correlated with clinical and demographic traits, in COVID-19.

first: Silvia

last: Bando

first: Fernanda

middle: B

last: Bertonha

first: Sandra

middle: E

last: Vieira

first: Danielle B

middle: L

last: Oliveira

first: Vanessa

middle: N

last: Chalup

first: Edison

last: Durigon

first: Patricia

last: Palmeira

first: Ana Cristina

middle: P

last: Curi

first: Caroline

middle: S

last: Faria

first: Leila

last: Antonangelo

first: Gerhard

last: Lauterbach

first: Fabiane

middle: A

last: Regalio

first: Roberto

last: Cesar Jr


title: Effect of systemic exposure of JAK1 Inhibition (AZ13748709) in C3H/HeJ Mice with Alopecia Areata In Vivo

status: Public on Jan 30 2023

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

summary: JAK inhibition by means of clinically available pan JAK inhibitors has recently demonstrated great efficacy in both restoring hair growth and resolving inflammation in the skin of patients with Alopecia Areata (AA). These effects are dose dependent and mainly efficacious at ranges close to a questionable risk profile. Given the great responses to JAK inhibition and the current lack of efficacious treatments in AA, it is exciting to explore the possibilities to separate the beneficial and adverse effects in order to provide a successful treatment option for these patients where the medical need is still vastly unmet. We have demonstrated that specific inhibition of JAK1 at relevant concentrations produces a fast resolution of inflammation and complete restoration of hair growth in the C3H/HeJ model of AA and importantly, that systemic exposure is essential for efficacy.

overall_design: 4 groups: Healthy, Alopecia, syst JAK1i, 8w off Tx. The aim of the present study is to evaluate hair growth as well as the skin ALADIN score and histopathological evaluation after 12 weeks of oral administration of the JAK1 selective antagonist AZ13748709 in C3H/HeJ mice with severe alopecia areata.

first: Annika

last: Åstrand

first: Lisa

last: Jinton

first: Kristofer

last: Thörn


title: JAK inhibition in human CD8+ T-cells and C3H/HeJ Mice with Alopecia Areata In Vivo

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

overall_design: Refer to individual Series


title: Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Firstly, we extracted bone marrow cells from AML mouse models in four different timepoints (T0, T1, T2 and T3). And we used droplet-based single cell RNA sequencing technology to reveal the early-MDS, late-MDS, MDS-AML and AML four-stage landscape in a mouse AML model initiated by Myc overexpression. Also, we extracted one AML patient bone marrow sample to sequence by constructing library following 10X genomics platform. And integrated this data with four AML patients data from 10X genomics database to explain the molecular mechanism of splicing events of TMEM134 in AML. To verify the alternative splicing results, we used smartseq2 to construct the single cell library in T3. And combined TCGA-LAML and TARGET-AML database and our mouse function data, we identify the alternative splicing events of TMEM134 could drive the proliferation function in acute myelogenous leukemogenesis.

overall_design: Single cell RNA sequencing (scRNA-seq) in leukemogenesis

first: Xiangyu

first: Xuelan

last: Chen

first: Baohong

last: Wu

first: Jian

last: Wang

first: Shujun

last: Li

first: Chong

first: Yu

last: Liu


title: Methylome from liquid biopsy cell-free DNA using enzymatic conversion of unmethylated cysteines

status: Public on Jan 25 2023

city: Valencia

first: Jaime

last: Font de Mora Sain

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Oncology

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

type: Methylation profiling by high throughput sequencing

summary: Methylome of tumor cell-free DNA (cfDNA) has emerged as a powerful non-invasive technique for cancer subtyping and prognosis. However, its application is frequently hampered by the quality and total cfDNA yield. Here we demonstrate the feasibility of very low-input cfDNA for whole-methylome and copy-number profiling studies using enzymatic conversion of unmethylated cysteines (EMSEQ) to better preserve DNA integrity. We demonstrate that cfDNA methylation of our cohort was comparable with in situ cohorts and built a model that accurately predict MYCN amplification or 11q deletion in validation cohorts. RASSF1A methylation precedes this divergent methylome signature, supporting common and different epigenetic origins. After stratification by 11q, eight CpG methylations show additional prognostic value and two reveal known preclinical targets (CSF1R, CCR7). Methylation in CSF1R and CCR7 associated with differential expression levels and poorer prognosis. Noteworthy, haploinsufficiency of genes located on 11q that repair DNA double-strand breaks display reduced expression by a mechanism independent of promoter methylation.  Conclusions: RASSF1A is an early hypermethylation defect that may predispose to later genetic and epigenetic alterations specific to MYCN-amplified or 11q-deleted high-risk neuroblastomas. CSF1R and CCR7 hypermethylation are a hallmark of high-risk 11q-deleted neuroblastomas that could be exploited therapeutically with immunomodulators to override immunosupression and relapse. Our novel findings provide support for use of liquid biopsy as an optimal strategy to assess methylomes of neuroblastoma patients for a precision medicine approach.

overall_design: To prepare libraries for comprehensive methylome representation within a cfcDNA we used the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, NEB), following manufacturer's recommendations with minor modification that the cfcDNA was not sheared. The method utilizes 10 ng starting material of cfcDNA and relies on two step conversion of the cytosines. The first step uses TET2 oxidation of 5-methylcytosine that provides protection to the modified cytosines from conversion by APOBEC deamination, so only cytosines but not 5-methylcytosines are converted to uracil. Ultimately, cytosines are sequenced as thymines and 5-methylcytosines are sequenced as cytosines. The final 8 cycles of PCR library amplification were carried out using the NEB Unique dual index primer pairs (NEBNext multiplex oligos for Illumina).  The libraries were sequenced on NovaSeq 6000 (Illumina) in paired-end with a read length of 2x151bp according to the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run are processed using the manufacturer’s software Real Time Analysis (RTA 3.3.3) and followed by generation of FASTQ sequence files.  The EMSEQ reads were processed using the gemBS pipeline v4.03 using as reference GRCh38[23]. Reads with MAPQ scores < 20 and read pairs mapping to the same start and end points on the genome were filtered out after the alignment step. The first 5 bases from each read were trimmed before the variant and methylation calling step to avoid artifacts due to end repair. For each sample, CpG sites were selected where both bases were called with a Phred score of at least 20, corresponding to an estimated genotype error level of <=1%, and where the total number of reads informative for methylation from both strands combined was >=6. Sites with >500x coverage depth were excluded to avoid centromeric/telomeric repetitive regions. Sequencing depth for the analysis of copy number was calculated using samtools v1.15.

last: Font de Mora

first: Eva

last: Trinidad

first: Simon

last: Heath

first: Anna

last: Esteve-Codina


title: Selective Janus kinase 1 inhibition resolves inflammation and restores hair growth offering a viable treatment option for alopecia areata

summary: JAK inhibition by means of clinically available pan JAK inhibitors has recently demonstrated great efficacy in both restoring hair growth and resolving inflammation in the skin of patients with Alopecia Areata (AA). These effects are dose dependent and mainly efficacious at ranges close to a questionable risk profile. Given the great responses to JAK inhibition and the current lack of efficacious treatments in AA, it is exciting to explore the possibilities to separate the beneficial and adverse effects in order to provide a successful treatment option for these patients where the medical need is still vastly unmet. Selective JAK1 inhibition mainly affects genes downstream of STAT1, STAT3 & STAT6 in human immune cells. Importantly, pathways like T-cell differentiation and lymphopoiesis are less affected by the selective JAK1 inhibitor versus less specific JAK inhibitors like tofacitinib and ruxolitinib. These findings indicate that it is feasible to develop more selective and specific JAK1 inhibitors that are as efficacious as pan-JAK inhibitors but with a better safety profile as systemic exposure is mandatory for efficacy in this disease.

overall_design: Peripheral blood CD8+ T-cells from 4 healthy donors were stimulated in vitro for 40hrs with plate bound anti-CD3 (OKT3) in complete media in the presence or absence of different JAK inhibitors: tofacitinib, ruxolitinib and a selective JAK1 inhibitor at 300 nM. Soluble anti-CD28 were added to the CD8+ cultures to facilitate co-stimulation.

first: Linda

last: Yrlid


title: Revealing the small proteome of Haloferax volcanii by ribosome profiling and small-protein optimised mass spectrometry

status: Public on Jan 18 2023

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

summary: We present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii.

overall_design: Ribo-seq and RNA-seq experiments to study the transcriptome and the translatome of H. volcanii

first: Lydia

last: Hadjeras

first: Jürgen

last: Bartel

first: Cynthia

last: Sharma

first: Anita

last: Marchfelder


title: Butyrate limits inflammatory macrophage niche in NASH [ChIP-seq]

status: Public on Jan 15 2023

city: Kolkata

first: Abhishake

last: Lahiri

address: 4, Raja S. C. Mullick Road

country: India

institute: CSIR-Indian Institute of Chemical Biology

summary: Lipid accumulation associated with immune cell infiltration leading to hepatocellular ballooning and lobular inflammation are the cardinal features of NASH. With onset and development of multi-omics approaches in the last decade, we have been able to comprehend the existence and functionality of gut microbial ecology. Apart from the compositional variation (dysbiosis), functional alteration of the microbial population i.e., the impact of the crosstalk between gut microbiota-derived metabolites with host cells also remains elusive in terms of regulation of immunometabolic homeostasis and overall human health and disease. Sodium butyrate (NaBu), a short chain fatty acid derived metabolite is known to modulate the inflammatory status of NASH pathogenesis; however, its mechanism of action is not clearly deciphered. To unveil the immunomodulatory activity of NaBu, we found robust anti-inflammatory effect of NaBu in diet induced NASH model with reduced macrophage infiltration. Mechanistically, independent of p65 nuclear translocation, by maintaining the enhanced acetylation status of p65 along with differential p65 recruitment to the proinflammatory gene promoter, NaBu suppressed the inflammatory milieu and resulted in better prognosis. Along with transcriptional rewiring, NaBu also altered the metabolic status, modified the functional outcome and exhibited differential secretome which ultimately resulted skewing of macrophages towards a prohealing phenotype and induced autocrine as well as paracrine death of proinflammatory macrophages to abrogate inflammation in both isolated LMs and in vivo model.

overall_design: We performed RNA-seq  and ChIP-seq NaBu pretreated LPS-stimulated RAW264.7 cell. Three biological replicates from each group were sequenced for RNA-sseq and two replicates were sequenced for ChIP-seq..

first: Partha

last: Chakrabarti


title: Butyrate limits inflammatory macrophage niche in NASH


title: Butyrate limits inflammatory macrophage niche in NASH [RNA-seq]

summary: To investigate differentially expressed genes and promoter recruitment of p65 in NaBu pretreated LPS-stimulated RAW264.7 cells

overall_design: We performed RNA-seq and ChIP-seq NaBu pretreated LPS-stimulated RAW264.7 cell. Three biological replicates from each group were sequenced for RNA-seq and two replicates were sequenced for ChIP-seq.


title: Interferon gamma-induction of TH1-like regulatory T cells controls anti-viral responses

city: Pittsburgh

last: Cui

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary: Regulatory T cells (Tregs) are an immunosuppressive population that are required to maintain peripheral tolerance and prevent tissue damage during immunopathology, via anti-inflammatory cytokines, inhibitor receptors and metabolic disruption. We report that Tregs acquire an effector-like state, yet remain stable and functional, when exposed to IFNγ during chronic infection with lymphocytic choriomeningitis (LCMV) and Influenza A virus (IAV). Mechanistically, Treg-restricted-deletion of the IFNγ receptor 1 (IFNGR1), but not the IL12 receptor, prevented TH1-like polarization (decreased expression of T-bet, CXCR3 and IFNγ) and promoted TH2-like polarization (increased expression of GATA-3, CCR4 and IL4). TH1-like Tregs limited CD8+ T cell effector function, proliferation and memory formation during chronic and acute infection. These findings provide fundamental insights into how Tregs sense inflammatory cues from the environment (IFNγ) during viral infection to provide immune guidance to the effector T cell response, to prevent prolonged immunoinflammatory responses and shape the quality of the memory response.

overall_design: Our goal was to determine how Tregs become specialized in response to inflammation in vivo and the consequential impact on primary and secondary responses to viral infection. We report that viral infection promotes TH1-like differentiation of Tregs in vivo. Since TH1 cells produce IFNγ, we asked if IFNγ promoted TH1-like polarization in Tregs. Surprisingly, Ddeletion of the IFNγ receptor (IFNGR1), but not the IL12 receptor (IL12RB2), from Tregs robustly prevented TH1 polarization and consequently induced TH2 polarization. TH2-like Ifngr1-deficient Tregs were unable to adequately limit the T cell anti-viral response and CD8+ T cell effector memory, and central memory, formation. Our study uncovers a unique mechanism underlaying how Tregs respond to inflammation to program their immunosuppressive function appropriately and limit excessive immunoinflammatory responses.

first: Angela

last: Gocher-Demske

first: Dario

last: Vignali


title: Single-cell sequencing of PBMCs from myasthenia crisis patients

status: Public on Jan 13 2023

city: Shanghai

first: Sushan

last: Luo

state: Shanghai

address: 12 Wulumuqi Rd (M), Jing'An, Shanghai

institute: Huashan Hospital

summary: This project contains pre-processed single-cell sequencing data of the human peripheral blood mononuclear cells (PBMCs) from three myasthenia crisis patinets.

overall_design:
This is a self-control study, and every patients were sampled twice (at the most acute stage and at three months after discharge). The patients are composed of 2 AChR+ and 1 MuSK+ myasthenia patients (2 males and 1 female, 66.67±17.10 years old).

***The submitters delares that the raw sequence data generated in this study will been deposited in the National Omics Data Encyclopedia database of Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences due to data privacy laws and access can be obtained by reasonable request to the corresponding authors.

first: Huahua

last: Zhong

first: Xiao

last: Huan

first: Chongbo

last: Zhao


title: Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

status: Public on Jan 14 2023

city: Cambridge

first: Lee

last: Rubin

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors.

overall_design: Total of 56 mouse brains with raw and processed data for 158,767 cells and filtered data for 50 mouse brains and 105,329 cells.

first: Methodios

last: Ximerakis

first: Kristina

last: Holton

first: Joshua

middle: Z

last: Levin


title: Defining Inflammatory Cell States in Acute and Chronic Pulmonary Infection with Pseudomonas aeruginosa by Single-Cell Transcriptomics

status: Public on Jan 06 2023

city: sichuan

first: Xue

middle: li

last: Hu

address: Section 3 renmin South Road

institute: sichuan university

summary: Using mouse models of acute and chronic Pseudomonas aeruginosa (P. aeruginosa) pulmonary infection, combined with single-cell RNA sequencing (scRNA-seq), flow cytometry and fluorescent multiplex immunohistochemistry (mIHC) and other experimental strategies, we map immune changes and particular immune cell subtypes during acute and chronic infection.This integrated method profiled extensive cell atlas of healthy and infected mouse lungs and defined subpopulations of main immune cells not further subdivided before. We found that the proportions and status of several kinds of pulmonary immune cells were changed a lot after P. aeruginosa pulmonary infection.In particular, the percentage of neutrophils and CD200+ B cells increased significantly after acute infection, while interstitial macrophages (IMs) expanded distinctly during chronic infections, respectively. By analyzing public datasets, we have also found consistent findings of the changes of myeloid subpopulations in other bacterial and SARS-CoV-2 infections, thus arising a hypothesis that CD200+ B cells and IMs may play an unanticipated role in progression of infection diseases. Therefore, our findings provide novel perspectives for P. aeruginosa infection and have potential impact on the development of vaccines, antibiotics, and immunotherapeutic strategies when facing with pathogen challenges.

overall_design:
Single-cell RNA sequencing of lung tissues from wild type, acute and chronic Pseudomonas aeruginosa (P. aeruginosa) pulmonary infected mice (n=2), combined with bulk-RNA seq.

Please note that the matrix.mtx file has been updated on Mar 7, 2023.

first: Xueli

first: Mingbo

last: Wu

first: Teng

last: Ma

first: Yige

last: Zhang

first: Chaoyu

last: Zou

first: Ruihuan

last: Wang

first: Yongxin

first: Yuan

last: Ren

first: Qianqian

last: Li

first: Huan

last: Liu

first: Heyue

first: Taolin

first: Xiaolong

last: Sun

first: Yang

last: Yang

first: Miao

last: Tang

first: Jing

first: Xiang

last: Gao

first: Taiwen

first: Xikun

last: Zhou


title: Neuronal APOE4 removal strongly protects against Tau-mediated gliosis, neurodegeneration, and myelin deficits

city: San Francisco

first: Ayushi

last: Agrawal

address: 1650 Owens St

institute: Gladstone Institutes

summary: Apolipoprotein E4 (APOE4) is the strongest known genetic risk factor for late-onset Alzheimer’s disease (AD). Conditions of stress or injury induce APOE expression within neurons, but the exact roles of neuronal APOE4 in AD pathogenesis are still unclear. Here we report a rigorous characterization of neuronal APOE4 effects on prominent AD-related pathologies by selectively removing APOE4 from neurons in an APOE4-expressing tauopathy mouse model. We found that the removal of neuronal APOE4 led to a drastic reduction in Tau pathology accumulation and spread, gliosis, neurodegeneration, neurodysfunction, and myelin deficits in this tauopathy mouse model. Single-nucleus RNA-sequencing revealed that the removal of neuronal APOE4 greatly diminished neurodegenerative disease-associated subpopulations of neurons, oligodendrocytes, astrocytes, and microglia that were enriched in APOE4-expressing tauopathy mice and whose accumulation correlated to the severity of Tau pathology, neurodegeneration, and myelin deficits. Thus, neuronal APOE4 plays a central role in promoting the development of major AD pathologies and its removal can effectively combat APOE4-driven effects in AD and other tauopathies.

overall_design: Single-nucleus RNA sequencing on isolated hippocampi from 10-month-old PS19-fE4 mice with or without Syn1-Cre and PS19-fE3 mice.

first: Nicole

last: Koutsodendris

first: Jessica

last: Blumenfeld

first: Michela

last: Traglia

first: Brian

last: Grone

first: Reuben

last: Thomas

first: Yadong

last: Huang


title: RELMα provides sex-specific protection from obesity through macrophages and eosinophils

status: Public on Jan 12 2023

city: Riverside

first: Djurdjica

last: Coss

address: 109 Picnic Hill Rd

department: Biomedical Sciences

institute: University of California Riverside

summary: The obesity incidence is increasing worldwide with the urgent need to identify new therapeutics. Sex differences in immune cell activation drive obesity-mediated pathologies where males are more susceptible to comorbidities with exacerbated inflammation, and females are protected. The focus of this study was to identify sex-specific immune effectors that regulate obesity pathogenesis, focusing on the M2 macrophage signature gene, Resistin-like molecule α (RELMα). Here we performed single cell RNA-sequencing (scRNA-seq) on visceral adipose tissue stromal vascular fraction on wildtype and RELMα knock-out animals, both males and females, on high fat diet. We utilized the 10x Genomics 3’ CellPlex platform, to label cells with cell multiplexing oligos (CMOs) per sample in each group prior to pooling for downstream barcoding and library construction. This study revealed sex-specific and RELMα-dependent cellular targets and population differences of female and RELMα-mediated protection.

overall_design: For multiplexing prior to generation of single-cell gel bead-in emulsions (GEMs), we took stromal vascular fractions for three animals per group (WT female, WT male, KO female, KO male) on high fat diet and labeled them with a lipid-containing CMO prior to pooling. Each group contained a pool of three animals to achieve a targeted cell recovery of 30,000 cells per group. After GEM creation, we sent the samples for sequencing, using the 10x Genomics 3’ Gene expression and cell multiplexing library preparation method for each group. Per group in the gene expression library preparation, we sequenced an estimated number of 15,350 cells (WT females), 15,556 cells (WT males), 14,481 cells (KO females) and 16,642 cells (KO males). For the multiplexing library preparation, we sequenced the following of number of cells with positive CMO labeling animal per group: WT female (3,949, 4,676 and 4,360 cells), WT male (3,861, 3,190 and 3,105 cells), KO female (4,240, 4,342 and 3,710 cells) and KO male (4,025, 3,681 and 3,593 cells).

first: Jiang

first: Rebecca

last: Ruggiero-Ruff

first: Meera

middle: G

last: Nair


title: Elucidation of HHEX in pancreatic endoderm differentiation using a human iPSC differentiation model

status: Public on Jan 05 2023

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

country: Japan

institute: Kyoto University

summary:
To investigate the role of HHEX in regulating human pancreatic endoderm differentiation, we knocked down the HHEX gene in 585A1 cell line-derived pancreatic endoderm cells by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the 3 cell samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 585A1 cell line-derived posterior foregut cells and pancreatic endoderm cells (siHHEX and siControl).

first: Ryo

last: Ito

first: Azuma

last: Kimura

first: Yurie

last: Hirose

first: Yu

last: Hatano

first: Atsushi

last: Mima

first: Shin-Ichi

last: Mae

first: Yamato

last: Keidai

first: Toshihiro

last: Nakamura

first: Junji

last: Fujikura

first: Yohei

last: Nishi

first: Akira

last: Ohta

first: Taro

last: Toyoda

first: Nobuya

last: Inagaki


title: Stress resilience is established during development and is regulated by complement factors

city: Rehovot

first: Gil

last: Levkowitz

state: Israel

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently, others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development, we established a new paradigm to identify resilience in zebrafish larvae. Using this assay, we identified resilient and susceptible subsets of zebrafish larvae at 6 days post fertilization and performed gene expression analysis on whole larvae.

overall_design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates (1 larva per sample) were subjected to next-generation sequencing.

first: Amrutha

last: Swaminathan

first: Noa

last: Wigoda


title: Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae anchor-away Sth1, Swi2 and/of TBP cells in raffinose and galactose-rich media in rapamycin or DMSO

status: Public on Jan 11 2023

city: Amsterdam

first: Ineke

last: Brouwer

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease on yeast strains that were grown in raffinose or galactose containing media (synthetic complete). Strains contained FRB-tags to Sth1, Swi2, Sth1 & Swi2 or Sth1 and TBP, where TBP was tagged on one of two alleles in a diploid strain. Cells were treated for 60 min either with 7.5 uM rapamycin or the same volume of DMSO.

overall_design: Mnase-seq of 4 strains grown in galactose-rich media after treatment with rapamyin or DMSO. Mnase-seq of 1 strain grown in raffinose-rich media after treatment with DMSO.

first: Tineke

last: Lenstra


title: A Transcription Factor Atlas of Directed Differentiation [SHAREseq_210715_combinatorial]

first: Julia

last: Joung

address: 75 Ames St

institute: Broad Institute

summary: SHARE-seq single-cell RNA-seq data profiling hESCs overexpressing combinations of transcription factors

overall_design: hESCs were transduced with a library of 10 transcription factor ORFs in combinations and cultured for 7 days before single-cell RNA-seq

first: Feng

last: Zhang


title: Functional partitioning of transcriptional regulators by patterned charge blocks

status: Public on Jan 03 2023

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Components of the transcriptional machinery are dynamically compartmentalized by weak multivalent interactions, yet we know little about how specificity or selectivity of partitioning is achieved. Here we show that condensates composed of the intrinsically disordered region (IDR) of MED1 (MED1_IDR) selectively partition positive regulators of transcription(SPT6, CTR9, IWS1) with RNA Pol II while excluding negative regulators of transcription (NELF and HP1a).This selective compartmentalization by MED1_IDR is sufficient to activate transcription and is required for gene activation during a cell state transition. Surprisingly, the IDRs of partitioned proteins are sufficient to recapitulate selective compartmentalization. We find that IDR-mediated selective partitioning requires multivalent blocks of positive and negative charge on MED1_IDR and IDRs of partitioned proteins. The charge patterns required for partitioning are also required for gene activation. These findings demonstrate that proteins can be functionally compartmentalized by specific multivalent interactions driven by the charge patterning within disordered regions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3T3-L1 cells and mutants during  adipocyte differentiation.

first: Heankel

last: Lyons

first: Reshma

middle: T

last: Veettil

first: Prashant

last: Pradhan

first: Christy

last: Fornero

first: Nancy

last: De La Cruz

first: Keiichi

last: Ito

first: Mikayla

last: Eppert

first: Robert

last: Roeder

middle: R


title: Human BATF overexpression PRO-cap

status: Public on Jan 02 2023

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline as targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. However, the fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal that aberrant transcription initiation inside genes is widespread in senescence and aging. It co-occurs with changes in the chromatin landscape and formation of non-canonical transcription start sites. Interventions that alter spurious transcripts have dramatic consequences on cellular health primarily affecting intracellular signal transduction pathways. We propose that spurious transcription is a conserved hallmark of aging that promotes a noisy transcriptome and a degradation of coherent transcriptional networks.

overall_design: Includes one replicate each of PRO-CAP run-on transcription data from IMR90 fibroblasts overexpressing one of BATF, CD27, or CD70.

first: Payel

last: Sen

first: Greg

first: Catherine

last: Li

first: Yemin

last: Lan

first: Gabor

last: Egervari

first: Neil

last: Robertson

first: Parisha

last: Shah

first: Erik

last: Kerkhoven

first: David

middle: C

last: Schultz

first: Peter

last: Adams

first: Shelley

last: Berger


title: Human senescence ATAC-seq [II]

overall_design: Includes two replicates each of ATAC-seq from proliferating (PD35 and PD43) and replicative senescent (PD80) fibroblasts

middle: D


title: Gene expression of cardiomyocytes isolated from vehicle and Doxorubicin challenged mice

status: Public on Jan 29 2023

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: The goal of this study was to identify differentially expressed genes in cardiomyocytes isolated from vehicle and Doxorubicin treated mice

overall_design: MX1gfp mice (Jackson Laboratory strain 033219, n = 3 per group) were intraperitoneally (i.p.) injected with vehicle (PBS) or one dose of 25 mg/kg of Doxorubicin. Forty eight hours (48 h) post injection, hearts were perfused, digested, and cardiomyocytes were isolated. Total RNA was isolated from cardiomyocytes using the Direct-zol RNA miniprep kit (Zymo Research) and subjected to library preparation and RNA sequencing at the Experimental Genomics Core of the Texas A&M Institute for Genome Sciences and Society. FASTQ files were normalized, processed, and analyzed using BaseSpace Sequence Hub (Illumina). The STAR algorithm of RNAseq Alignment V2.0.2 software was utilized to align the results to the Mus musculus/mm10 (RefSeq) reference genome, then RNA-seq Differential Expression V1.0.1 software was used to obtain differential gene expression values and determine statistically significant changes in gene expression via pairwise comparison of experimental groups.

first: Yuanjiu

last: Lei

first: Yi-Fan

last: Chen


title: Human senescence ChIP-seq

overall_design: Includes one replicate each of H3K79me1 and H3K79me2 from proliferating and replicative senescent IMR90 fibroblasts. Includes two replicates of H2A.z, H3K36me3, three replicates of histone subunit H3, and four replicates of input from the same cells in the same conditions. H2A.z replicates and H3K36me3 replicates were pooled after alignment in the analysis; H3 samples are matched to each of the H3 histone PTM chIPs while input is matched to the H2A.z chIP (see "Matching Background" characteristic).


title: Regulatory T cells underlies resistance to radio-immunotherapy, prevent the formation of tertiary lymphoid structures and impair CD8 T cell activation in glioblastoma

status: Public on Dec 31 2022

first: Daan

middle: Juri

last: Kloosterman

department: Tumor Biology & Immunology

institute: The Netherlands Cancer

summary: Glioblastomas (GBM) are aggressive primary brain tumors with an inherent resistance to T cell-centric immunotherapy imparted to their low mutational burden and immunosuppressive tumor microenvironment (TME). Examination of the GBM TME dynamics following fractionated RT revealed a 10-fold increase in T cell content, an enrichment also observed by spatial imaging mass cytometry in matched primary and recurrent human GBM. Implementation of a-PD-1 treatment at the peak of T cell infiltration results in a modest, albeit distinct survival benefit compared to concurrent a-PD-1 administration in GBM-bearing mice. CD103+ Tregs presenting increased cholesterol pathway activity are recruited to the GBM TME in response to a-PD-1 therapy, suggestive of their ability to restrain the response to immune checkpoint blockade. Targeting of Tregs elicits the formation of tertiary lymphoid structures, enhanced CD8 T cell content and activation and enables the therapeutic efficacy of radio-immunotherapy. These results support the rational design of therapeutic regimens limiting the induction of immunosuppressive feedback pathways in order to unleash the efficacy of T-cell centric immunotherapy in glioblastoma.

overall_design: In light of recent studies underlining that not only the content of T cells but also their education profiles segregate ICB responders and non-responders, we performed in-depth investigation of the T cells transcriptional changes occurring in response to radio-immunotherapy in the concurrent or adjuvant setting. We FACS-purified CD8+ and CD4+ T cells from PDG-Ink4a GBM at day 12 post treatment initiation, a timepoint where T cell infiltration is at its peak, and subjected these cells to RNA sequencing.

first: Luuk

last: van Hooren

first: Shanna

middle: M

last: Handgraaf

middle: J

first: Awa

last: Gassama

first: Beatriz

last: Gomez Solsona

first: Marnix

middle: H

last: de Groot

first: Dieta

last: Brandsma

first: Daniela

middle: F

last: Quail

first: Logan

last: Walsh

first: Gerben

last: Borst

first: Leila

last: Akkari


title: ATAC-Seq of  wild type and Terc-/-  ESCs

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

summary: We aimed to see if the short telomere could affect the chromatin accessibility  profiles.

overall_design: The ATAC-Seq of the wild type and short telomere (Terc-/-) in ESCs.

first: Lin

last: Liu

first: Xinyi

last: Lv

first: Nannan

last: Zhao

first: Chun

first: Guoxing

last: Yin


title: IL-4 induced non-canonical trained immunity in murine BMDMs

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: The canonical role IL-4 is to induce M2 macrophage polarization. Herein we report that in addition to its canonical role, IL-4 also induces non-canonical pro-inflammatory response via epigenetic memory. Although IL-4 stimulated macrophages do not produce classic proinflammatory cytokines such as IL-6 and IL-1b, they produce heightened proinflammatory cytokine upon LPS stimulation.

overall_design: BMDMs were isolated from bone marrow, treated with 20ng/ml IL4 or/with 100ng/ml LPS.

first: Buyun

last: Dang

first: Jia

last: Zhang

first: Shih-chin

last: Cheng


title: Anti-proliferative effect of selexipag active metabolite MRE-269 on pulmonary arterial smooth muscle cells from patients with chronic thromboembolic pulmonary hypertension

status: Public on Dec 27 2022

first: Kazuya

last: Kuramoto

address: 14, Nishinosho-Monguchi-cho, Kisshoin, Minami-ku

department: R&D Administration Dept.

institute: Nippon Shinyaku Co., Ltd.

summary: Chronic thromboembolic pulmonary hypertension (CTEPH) is a group 4 pulmonary hypertension (PH) characterized by non-resolving thromboembolism in the central pulmonary artery and vascular occlusion in the proximal and distal pulmonary artery. Medical therapy is chosen for patients who are ineligible for pulmonary endarterectomy or balloon pulmonary angioplasty or who have symptomatic residual PH after surgery or intervention. Selexipag, an oral prostacyclin receptor agonist and potent vasodilator, was approved for CTEPH in Japan in 2021. To evaluate the pharmacological effect of selexipag on vascular occlusion in CTEPH, we examined how its active metabolite MRE-269 affects platelet-derived growth factor-stimulated pulmonary arterial smooth muscle cells (PASMCs) from CTEPH patients. MRE-269 showed a more potent anti-proliferative effect on PASMCs from CTEPH patients than on those from normal subjects. DNA-binding protein inhibitor genes ID1 and ID3 were found by RNA sequencing and real-time quantitative polymerase chain reaction to be expressed at lower levels in PASMCs from CTEPH patients than in those from normal subjects and were upregulated by MRE-269 treatment. ID1 and ID3 upregulation by MRE-269 was blocked by co-incubation with a prostacyclin receptor antagonist, and ID1 knockdown by small interfering RNA transfection attenuated the anti-proliferative effect of MRE-269. ID signaling may be involved in the anti-proliferative effect of MRE-269 on PASMCs. This is the first study to demonstrate the pharmacological effects on PASMCs from CTEPH patients of a drug approved for the treatment of CTEPH. Both the vasodilatory and the anti-proliferative effect of MRE-269 may contribute to the efficacy of selexipag in CTEPH.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pulmonary arterial smooth muscel cells from normal subjects or patients with CTEPH, and the effect of MRE-269 treatment on pulmonary arterial smooth muscel cells from patients with CTEPH.

first: Aiko

last: Ogawa

first: Kazuko

last: Kiyama

first: Hiromi

last: Matsubara

first: Yuji

last: Ohno

first: Chiaki

last: Fuchikami

first: Kyota

last: Hayashi

first: Keiji

last: Kosugi

first: Keiichi

last: Kuwano


title: IL-4 induced non-canonical trained immunity via epigenetic modification

summary: The canonical role of IL-4 is to induce M2 macrophage polarization. Herein we report that in addition to its canonical role, IL-4 also induces non-canonical pro-inflammatory response via epigenetic memory. Although IL-4 stimulated macrophages do not produce classic proinflammatory cytokines such as IL-6 and IL-1β, they produce heightened proinflammatory cytokine upon LPS stimulation.

overall_design: BMDMs were isolated from bone marrow, treated with 20ng/ml IL4.


title: Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging V

status: Public on Dec 24 2022

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

institute: Stanford University

summary: To gain insight into the mechanisms by which exercise affects the neural stem cell compartment, we subjected young and old mice to aerobic exercise and performed single cell transcriptome analysis of cells from the subventricular zone of the brain of these animals.

overall_design: Single cells were isolated from the brain subventricular zone of exercised or control young (4-month old) and old (22-month old) mice and processed for single cell RNA-seq.

first: Thomas

last: Rando


title: Transcription Analysis of yZSJ025

status: Public on Dec 30 2022

city: Tianjin

first: Zhou

last: Sijie

address: No.135 Yaguan road

institute: Tianjin Unversity

summary: We carried out RNA-seq to compare gene expression and recombination frequency of yZSJ025. The transcriptome data allowed us to analyze the expression levels and the rearrangement frequencies at different loci across the synthetic chromosomes.

overall_design: PCRTags were used to distinguish the transcription of wild-type genes from the transcription of synthetic genes.

first: Sijie

last: Zhou

first: Yi

last: Wu


title: RNAseq analysis of DPSC-derived neurons from Neurotypical control, ROHHAD, and CCHS subjects

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: A major challenge to the study and treatment of neurogenetic syndromes is the difficulty in gaining access to live neurons from individuals with these disorders. Although other sources of stem cells are currently available for differentiation into neurons, these can involve invasive procedures and be difficult or expensive to generate limiting their use on a broad scale, especially for rare syndromes which may not be well represented in the local population.  Dental pulp stem cells (DPSC) are neural crest derived multipotent stem cells that reside deep the pulp of shed (baby) teeth and have the potential for broad use in the study of neurogenetic disease. Here, we use DPSC-derived neurons to investigate the transcriptional differences between neurotypical controls, Rapid-onset obesity with hypothalamic dysfunction, hypoventilation, and autonomic dysfunction (ROHHAD) and Central congenital hypoventilation syndrome (CCHS) subjects.

overall_design: RNA-seq Analysis of DPSC derived neurons; 3 individuals per group of the following: neurotypical control, ROHHAD and 2 individuals for CCHS

first: A

middle: K

last: Victor

first: Tayler

last: Hedgecock

first: Martin

last: Donaldson

first: Casey

last: Rand

first: Debra

last: Weese-Mayer

first: Lawrence

last: Reiter


title: Telomeres suppress the activity of retrotransposons in pluripotent stem cells [exp1]

status: Public on Dec 25 2022

first: Xinyi

last: Lu

address: 94 Weijin Road

institute: Nankai University

summary: Telomeres, which locate at the end of chromosomes protect chromosomes from fusion and deterioration. This is essential for cells to maintain genome staibility. Hee, we applied RNA-seq, to identify the impact of Terc knockout on the expression of retrotransposons in embryonic stem cells. In addition, we performed ChIP-seq to identify changes of histone mark H3K9me3 after telomere shortening.

overall_design: RNA-seq and H3K9me3 ChIP-seq analysis of wild type, Terc knockout, and Terc rescued ESCs.

first: Yang

last: Shen


title: Oral administration of engineered yeast produced H5HA-based vaccines

status: Public on Jan 01 2023

first: Zexing

last: Li

address: No.92 Weijin road

department: School of Life Sciences

institute: Tianjin University

summary: H5N8 influenza virus is a highly pathogenic pathogen for the poultry and human. Vaccination is the most effective method to control the spread of the virus right now. The traditional inactivated vaccine, though well developed and used widely, is laborious during application and more interests are stimulated in developing alternative approaches. In this study, we developed three HA gene-based yeast vaccines and our experimental results demonstrated that all of these vaccines elicited the humoral immunity, inhibited viral load in the chicken tissues, and provided protective efficacy partially due to the high dose of H5N8 virus. Molecular mechanism studies suggested that, compared to the traditional inactivated vaccine, our engineered yeast vaccines reshaped the immune cell microenvironment in bursa of Fabriciu to promote the defense and immune responses. Analysis of gut microbiota further suggested that oral administration of engineered ST1814G/H5HA yeast vaccines increased the diversity of gut microbiota and the increasement of Reuteri and Muciniphila might benefit the recovery from influenza virus infection. These results provide strong evidences for further clinical use of these engineered yeast vaccines in poultry.

overall_design: At the 6th day after the third vaccination, three immunized chickens were randomly selected in each group. The total RNA of bursa of Fabricius were isolated and sent to RNA-seq. The genes expression of chickens bursa of Fabricius with ST1814G treat, ST1814G/H5HA treat, and Inactivated vaccine treated were examined, respectively.

first: Jinhai

last: Huang

first: Ruyu

last: Xie


title: Effect of culture system on gene expression during traditional 2D culture and 3D culture of mouse mesothelioma cells

status: Public on Dec 22 2022

city: Baltimore

first: Fumiya

last: Ito

state: MARYLAND

address: 725 N. Wolfe Street, 119 Hunterian

department: Cell Biology

institute: Johns Hopkins University

summary:
To investigate the differences between mesothelioma- organoid culture and 2D traditional culture, we established 7 mesothelioma lines and 3 normal mesothelial cells from model mouse.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 20 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mesothelioma cells and its culture system between 2D and 3D.

first: Katsuhiro

last: Kato

first: Shinya

last: Toyokuni


title: Mouse aged liver PRO-cap

first: Gregory

last: Donahue

overall_design: Includes two replicates each of PRO-CAP run-on transcription data from young and old mouse liver from male and female mice, for eight samples total

first: Payel

last: Sen

first: Greg

first: Catherine

first: Yemin

last: Lan

first: Gabor

last: Egervari

first: Neil

last: Robertson

first: Parisha

middle: P

last: Shah

first: Erik

last: Kerkhoven

first: David

last: Schultz

first: Peter

last: Adams

first: Shelley

middle: L

last: Berger


title: RNA-Seq of CD19+ B-cell, CD14+ monocyte, CD4+ and CD8+ T cell populations from patients with juvenile dermatomyositis and controls

city: London

first: Meredyth

middle: G Ll

last: Wilkinson

state: London

address: 30 Guilford Street

country: United Kingdom

institute: UCL GOS Institute of Child Health

summary: RNA sequencing was used to compare the transcriptional state of ex-vivo B-cells, moncytes and T-cells from children with Juvenile dermatomyositis (JDM) pre- and on-treatment and age-matched healthy controls. RNA was extracted from blood samples that were taken from juvenile dermatomyositis patients at diagnosis (before they received treatment) and approximately a year into treatment. The treatment included oral prednisolone, methotrexate, azathioprine, cyclophosphamide and other drugs.

overall_design: Case control

first: Restuadi

last: Restuadi

first: Claire

last: Deakin

first: Georg

last: Otto

first: Daniel

last: Kelberman

first: Sergi

last: Castellano

first: Lucy

last: Wedderburn


title: Clonal hematopoiesis is driven by aberrant activation of TCL1A [ATAC-seq]

status: Public on Dec 20 2022

first: Jayakrishnan (Jk)

last: Gopakumar

state: CA

address: 240 Pasteur Dr Rm 4600

institute: Stanford

summary: We used OMNI-ATAC to analyze the chromatin accessibility of TCL1A in TET2 edited HSPCs.

overall_design: Lin- CD34+ CD38- CD45RA- GFP+ were cultured in HSPC expansion media for 5 days before OMNI-ATAC was performed.

first: Joshua

last: Weinstock

first: Jk

first: Alex

last: Bick

first: Siddhartha

last: Jaiswal


title: Clonal hematopoiesis is driven by aberrant activation of TCL1A

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

overall_design: Refer to individual Series


title: Human senescence ATAC-seq [I]

first: Gregory

last: Donahue

overall_design: Includes one replicate each of ATAC-seq from proliferating (PD33) and replicative senescent (PD75) fibroblasts

first: Payel

last: Sen

first: Greg

first: Catherine

last: Li

first: Yemin

last: Lan

first: Gabor

last: Egervari

first: Neil

last: Robertson

first: Parisha


title: Mononuclear phagocytes in neonatal Peyer's patches

city: Aachen

first: Mathias

middle: W.

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

institute: RWTH Áachen University

summary: The small intestine contains lymph node-like structures termed Peyer’s patches (PP). In adult mice they contain active germinal centers reminiscent of active crosstalk with microbiota. In neonatal mice, however, homeostatic immune activation does not take place. We wanted to test whether immune maturation in neonatal mice is stalled due to a reduced presence or function of antigen presenting mononuclear phagocytes (MNP). Thus we subjected PP MNP of postnatal day (PND) 11 and adult mice to scRNAseq in steady state or after immune activation with the TLR7 agonist R848 that induces type I interferon and TNFa after oral gavage. Our results show an altered subset distribution of MNP in neonatal mice (predominance of cDC1 and cDC2b, reduced proportion of cDC2a) and a reduced potential to take up microorganisms and process/present antigen as well as decreased type I interferon mediated gene expresseion. R848 administration could partly overcome this maturation defect of neonatal MNP by increasing the proportion of CCR7+ mature cDC as well as upregulation of interferon I dependent genes.

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to investigate to investigate the landscape of mononuclear phagocytes in neonatal Peyer's patches in steady state and after oral R848 (TLR7 agonist) treatment

first: Natalia

last: Torow

first: Ronghui

first: Ivan

last: Costa

middle: W

first: Narasimha

last: Gubbi


title: Expression data from whole blood sample of eight kinds of TCM syndromes of rheumatoid arthritis patients.

city: Beijing

first: chen

middle: wen

last: jia

address: Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences

institute: institute

summary:
To explore the biological connotation of eight syndromes of Rheumatoid Arthritis (RA) from the syndrome-symptom association network, and the relationship between the clinical characteristics of various syndromes and their key network target genes and pathways, which may offer clinicians auxiliary tools for diagnosis and treatment of RA patients with various traditional Chinese medicine (TCM)  syndromes and promoting the developments of TCM Syndrome Theory.
We used microarrays to detail the biological connotation of five syndromes (D-H, N) of Rheumatoid Arthritis (RA) and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Three to four RA patients cases per syndrome group respectively with Damp Heat Obstruction Syndrome (A), Phlegm Stasis Obstruction Syndrome (B), Qi-Yin Deficiency Syndrome (C), Blood Stasis Syndrome (D), Qi-Blood Deficiency Syndrome (E), Liver and Kidney Deficiency Syndrome (F), Wind-dampness Obstruction Syndrome (G) and Cold-dampness obstruction syndrome  (H) were collected as RA group, and seven healthy people were collected as normal control group (N).

first: Yanqiong

last: Zhang

last: Lin


title: Integrated long- and short-read single-cell RNA-sequencing

city: NORWICH

first: Laura

last: mincarelli

state: County (optional)

address: Norwich Research Park, Colney Lane, Colney

institute: Earlham Institute

summary: Single-cell RNA sequencing analysis has recently provided snapshots of gene expression of specific cell types and enabled cell types classification within an heterogenous population. As well as transcriptional changes, alternative splicing events and modifications of components of splicing machinery actively contributes in shaping cellular phenotype as well as ageing process and diseases occurence. Current high-throughput single-cell RNA sequencing methods may lack information on cell-specific isoform expression, missing key aspects of cell biology. In the present work we introduce a novel approach using the 10X Genomics Chromium to generate short-read (Illumina) and long-read (Pacific Biosciences Sequel II) RNA-sequencing libraries from the same single cells. This approach produced single cell parallel transcriptional and splicing profiling that demonstrates for the first time cell-type specific isoform expression and alterations at transcriptional levels associated with ageing in haematopoietic stem and progenitor cells

overall_design:
We generated single cell full length cDNA libraries using 10x Genomics platform from young and aged murine bone marrow. cDNA library has been then used to produce short read Illumina library following 10x protocol instructions, and simultanosly as an input for long read SMRT bell library preparation (PacBio). That approach enables sequencing of the full-length of the transcript and detection of alternative splicing or recombination events in addition to quantify gene expression changes
Mouse 1 ( M26_....._fastq file for Illumina raw data, one PB Sequel I raw file and one PacBio Sequenl II raw file) Mouse 2 ( M27_...._fastq file for Illumina raw data, one PB Sequel I raw file and one PacBio Sequenl II raw file) Mouse 3 (M28_...._fastq file for Illumina raw data, one PB Sequel I raw file and one PacBio Sequenl II raw file) Mouse 4 (M29_...._fastq file for Illumina raw data, one PB Sequel I raw file and one PacBio Sequenl II raw file) Mouse 5 (M 30_...._fastq file for Illumina raw data, one PB Sequel I raw file and one PacBio Sequenl II raw file) Mouse 6 (M31_...._fastq file for Illumina raw data, one PB Sequel I raw file and one PacBio Sequenl II raw file)

last: Mincarelli

first: Vladimir

last: Uzun

first: David

last: Wright

first: Stuart

middle: A

last: Rushworth

first: Wilfried

last: Haerty

first: Iain

last: Macaulay


title: Next generation sequencing discovers alternative splicing pattern among mouse embryonic stem cells, mouse embryonic fibroblasts and Dppa5a knockdown mouse embryonic stem cells and Dppa5a target RNAs

status: Public on Dec 28 2022

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

summary: Purpose: The goals of this study are to reveal the alternative splicing pattern between mouse embryonic stem cells and mouse embryonic fibroblasts, to identify alternative splicing events regulated by Dppa5a and to discover the direct targets of Dppa5a.

overall_design: Comparative gene alternative splicing pattern of RNA-seq data for mouse embryonic stem cells, mouse embryonic fibroblasts and Dppa5a knockdown mouse embryonic stem cells. Examination of Dppa5a target RNAs in HU-treated or untreated mouse embryonic stem cells.

first: Fangjie

last: Jiang

first: Lin

last: Wang


title: Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging

first: Ling

last: Liu


title: Human senescence PRO-cap

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

institute: The University of Pennsylvania

summary: Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline as targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. However, the fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal that aberrant transcription initiation inside genes is widespread in senescence and aging. It co-occurs with changes in the chromatin landscape and formation of non-canonical transcription start sites. Interventions that alter spurious transcripts have dramatic consequences on cellular health primarily affecting intracellular signal transduction pathways. We propose that spurious transcription is a conserved hallmark of aging that promotes a noisy transcriptome and a degradation of coherent transcriptional networks.

overall_design: Includes one replicate each of PRO-seq and three of PRO-CAP run-on transcription data from proliferating (PD20, PD23, PD26) and replicative senescent (PD67, PD76) fibroblasts.

first: Payel

last: Sen

first: Greg

first: Catherine

last: Li

first: Yemin

last: Lan

first: Gabor

last: Egervari

first: Neil

last: Robertson

first: Parisha

last: Shah

first: Erik

last: Kerkhoven

last: Schultz

first: Peter

last: Adams

first: Shelley

last: Berger


title: Endothelial Arid1a Deletion Disrupts the Balance among Angiogenesis, Neurogenesis, and Astrogenesis in the Developing Brain

status: Public on Dec 21 2022

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose:To gain  futher insight into how endothelial Arid1a regulates the angiogenesis, neurogenesis, and astrogenesis,RNA-seq was used to analyze the genome-wide changes resulting from isolated endothelial cells of E15 Arid1a endothelial conditional knockout mice and littermate wild-type.
Methods:  mRNA from E15 isolated endothelial cells of Arid1afl/fl and Arid1acKO-Tie2 mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately  one six thousand transcripts showed differential expression between the Arid1afl/fl and Arid1acKO-Tie2 mice brain cortex, with a fold change ≥2 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development process and regulation of cell communication.The down-regulated genes exhibited enrichment of biological processes related to cell movement. These results reflected endothelial Arid1a plays a vital role in cortex development.
Conclusions:  Endothelial Arid1a RNA-seq would provide a overall understanding how endothelial Arid1a regulates the Balance among angiogenesis, neurogenesis, and astrogenesis in the developing Brain

overall_design: mRNA profiles of E15 Arid1afl/fl and Arid1acKO-Tie2 mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Yuanyuan


title: Small molecule-induced epigenomic reprogramming of APL blasts leading to antiviral-like response and c-MYC downregulation

status: Public on Dec 15 2022

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA


title: RNA-Seq of  wild type and Terc-/- in  G3 tail, G3 liver, G3 testis, G3 TTF, G3 ASC, G4 early ESC, G4 late ESC

first: nannan

last: zhao

address: nankai

institute: nankai university

summary: We aimed to see if the short telomere could affect the genome stability and the retrotransposon expression profiles.

overall_design: The mRNA profiles of the wild type and short telomere (Terc-/-) in seven cell types.

first: Xinyi

last: Lv

first: Nannan

last: Zhao

first: Chun

first: Guoxing

last: Yin


title: Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging

first: Gregory

last: Donahue


title: Small molecule-induced epigenomic reprogramming of APL blasts leading to antiviral-like response and c-MYC downregulation [RNA-seq]

summary: The epigenomic effects of maltonis, a novel maltol-derived molecule with promising antiproliferative activity against leukemic cells, have been characterized in the APL NB4 cell line. We demonstrate that maltonis treatments induce a profound remodulation of the histone code, reducing global H3K9me3 signal and modulating other histone post-translational modifications (HPTMs). Transcriptomic and epigenomic analyses revealed that maltonis exposure of NB4 cells induces changes in the expression of hundreds of genes (551 upregulated and 288 downregulated) in association with the modulation of the permissive HPTMs histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) at their gene promoters. The upregulation of interferon alpha and gamma and the downregulation of c-MYC target genes have been identified as most significant pathways modulated by maltonis. Most importantly, c-MYC is strongly downregulated by maltonis and represents the common denominator of the downregulated gene sets, suggesting a central role of this gene in the biological response of NB4 cells to maltonis.

overall_design: NB4 cells were treated for 24 hours with maltonis 10 μM in vitro and analysed

first: Stefano

last: Amatori

first: Giuseppe

last: Persico

first: Francesco

last: Cantatore

first: Martina

last: Rusin

first: Mauro

last: Formica

first: Luca

last: Giorgi

first: Eleonora

last: Macedi

first: Francesca

last: Casciaro

first: Alfredo

middle: E

last: Provenzano

last: Gambardella

first: Roberta

last: Noberini

first: Tiziana

last: Bonaldi

first: Vieri

last: Fusi

first: Marco

last: Giorgio

first: Mirco

last: Fanelli


title: p140Cap overexpression in Balb-neuT HER2 breast cancer transgenic mice

status: Public on Dec 19 2022

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: In HER2-positive breast cancer patients the adaptor protein p140Cap correlates with increased patient survival and decreased probability to develop metastasis. Causally, p140Cap negatively regulates in vitro and in vivo breast tumor properties. Here we show that p140Cap status correlates with a rewiring of the tumor immune microenvironment, with an increased presence of tumor-infiltrating lymphocytes (TILs) in human breast cancers and an inverse correlation with inflammatory hallmarks. Preclinical syngeneic p140Cap models show a significant increase of CD8+ T-Lymphocytes, NK cells and M1-macrophages in p140Cap tumors, a reduced mobilization and a decreased recruitment of G-CSF-dependent Myeloid-Derived Suppressor Cells (MDSC), with a specific reduction in G-CSF mRNA and protein levels. Indeed, p140Cap impacts on the G-CSF axis by reducing the fraction of Tumour-Initiating Cells (TICs) that exhibit an enhanced G-CSF production. Interestingly, p140Cap affects the TIC compartment by limiting the active β-Catenin intracellular pool, stabilizing the destruction complex. These findings identify a novel role of p140Cap in preventing the development of an immunosuppressive tumor promoting microenvironment in Breast Cancer.

overall_design: Three Balb-NeuT mice (Mock 1-3, Rovero et al. J. Immunol. 165, 5133–5142, 2000) were compared with respect to three Balb-NeuT mice overexpressing p140Cap (p140 1-3)

first: Paola

last: Defilippi

first: Vincenzo

last: Salemme


title: Small molecule-induced epigenomic reprogramming of APL blasts leading to antiviral-like response and c-MYC downregulation [ChIP-seq]

first: GIUSEPPE

last: PERSICO

first: Stefano

last: Amatori

last: Persico


title: Chronic kidney disease is characterized by expansion of pro-inflammatory, HLA-DR-high intermediate monocytes and by increased monocyte adhesion to endothelial cells

city: st louis

first: andrew

last: malone

state: MO

address: 4525 laclede ave

institute: Washington University

summary: We sequenced and analyzed the transcriptomes of PBMCs from the peripheral blood of 5 kidney transplant patients taken at the time of indicated biopsy. We filtered these data to focus on monocytes and compared these data with previously published monocytes/macrophage transcriptomes from paired biopsies.

overall_design: 10X Chromium and NGS used for scRNA-seq of peripheral blood of transplant patients and previously published scRNA-seq data from paired biopsies to study monocyte and macrophage transcriptomes.

first: Andrew

last: Malone


title: Telomere-to-mitochondria signaling by ZBP1 mediates replicative crisis

status: Public on Dec 12 2022

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies


title: Small RNA sequencing of hearts from female mice on high fat diet, from 85 strains

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

address: 10833 Le Conte Avenue

institute: UCLA

type: Non-coding RNA profiling by high throughput sequencing

summary: We used small RNA-Seq to characterize heart non-coding RNAs in 85 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits.

overall_design: miRNA expression of heart in 85 female inbred strains fed chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks

first: Aldons

last: Lusis

first: Karthickeyan

middle: C

last: Krishnan

first: Karolina

last: Kaczor-Urbanowicz


title: NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion

city: Epalinges

first: Grégory

last: Verdeil

state: Vaud

address: Chemin des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: University of Lausanne


title: Transcriptome of ZmPMP3g overexpressing maize inbred line Ye478, and wild type Ye478 under control, moderate drought, exogenous abscisic acid, or treatment combinations

status: Public on Dec 11 2022

city: Nanning

first: Ling

last: Lei

state: Guangxi

address: No.100, Daxue East Road

department: College of Life Science and Technology

institute: Guangxi University

summary: This study is to identify the role of maize ZmPMP3g (GenBank accession no. EC869579.1), a  proteolipid membrane potential modulator 3 (PMP3) domain gene, in drought tolerance of maize, and the genes and signaling pathways under over-expression of ZmPMP3g

overall_design:
The tillage soil from the experimental field of Guangxi University was collected, sun-dried, sieved, and then fully mixed with the local commercial organic fertilizer (8:2/w:w) as pot mix. The pot mix was loaded in pots (31 cm in diameter and 21 cm in height), 5 kg per pot. The pot mix of each pot was saturated with tap water and then monitored for moisture by using a Dong mei DT001 soil tester (Shanghai, China) equipped with a thin and long detector. When the moisture of the pot mix reached about 70%, pot experiment started.
The maize ZmPMP3g (GenBank accession no. EC869579.1) ranging from start codon to stop codon was cloned into NcoI and BamHI restriction sites downstream of the 3×CaMV35S (3×200) promoter of plasmid pGSA1252 of Basta resistance gene, generating an expression construct, pGSA1252::ZmPMP3g. The construct was introduced into mature embryos of Chinese maize inbred line Ye478 by Agrobacterium tumefaciens strain LBA4404 mediated infection. The LBA4404-infected maize embryos were transferred onto Murashige and Skoog medium plates containing 0.1 mg/L IAA, 250 mg/L cefotaxime, 20 ppm herbicide Basta and 30 g/L sucrose, and then allowed to grow for 7 d at 28 °C under a cycle of light/16 h and dark/8 h. The regenerated Basta-resistant maize plantlets were transplanted into sandy soil in trays and then grew for 10 d at room temperature followed by foliar-spraying 40 ppm Basta once. The maize seedlings that survived 7 d after spraying Basta were transferred into pot mix and allowed to grow in the glass greenhouse at 20-25 °C and with 50%-60% air humidity under a cycle of light/16 h and dark/8 h. The transformed plants were subjected to identification by PCR, Southern blotting, and real-time quantitative PCR.
Drought treatment started at 5-leaf stage of maize through natural mix drought without watering until to moderate drought (50% moisture for pot mix). The pot mix moisture in the parallel control was controlled at 70% by watering.
When the pot mix was in moderate drought and severe drought respectively, sampling started and exogenous ABA was applied. The exogenous ABA application was conducted by spraying 15 mg/L ABA (Sigma, USA) on whole plants once while the leaves in control treatment were sprayed with an equal volume of tap water.
The transcriptome sequencing was conducted on the second fully-expanded leaves down from the top of T4 transgenic line plants 9 d after spraying ABA on whole plants and parallel control plants, which were sampled at 10:00 a.m.

first: You-Zhi

last: Li


title: Telomere-to-mitochondria signaling by ZBP1 mediates replicative crisis (RIP-Seq)

summary: Interaction between ZBP1 and TERRA-derived RNA fragments

overall_design: Formaldehyde RNA immunoprecipitation (fRIP-Seq) performed on growing IMR90E6E7 expressing WT ZBP1(S)-Flag and transduced with shRNA against TRF2. ZBP1 Immunoprecipitation was performed at day 12 post-shRNA transduction. Input (total RNA) serves as a control.

first: Joe

last: Nassour

first: Jan

last: Karlseder


title: Alterations in PTPN11 and other RAS-/MAP-Kinase pathway genes define ganglioglioma with adverse clinical outcome and atypic histopathological features

status: Public on Nov 30 2022

city: Erlangen

first: Samir

last: Jabari

state: Bavaria

address: Schwabachanlage 6

department: Department of Neuropathology

institute: Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU)

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of human low grade epilepsy associated brain tumor tissue. The Illumina Infinium 450K and 850K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450.000 and 850.000 CpGs in formalin-fixed paraffin-embedded surgical brain samples. Samples included 280 cases with various brain tumor diagnosis including low grade epilepsy associated tumors and non-epilepsy autopsy controls.

overall_design:
Bisulphite converted DNA from the 280 (86 NEW) human surgical brain samples were hybridized to the Illumina Infinium 450k and 850k Human Methylation Beadchip Arrays
Diagnosis descriptions:  DNT: dysembryoplastic neuroepithelial tumor; GG: Ganglioglioma; isomorpic astro.: diffuse astrocytome MYB- MYBL1 -altered; PXA: pleomorphic xanthoastrocytoma.

first: Lucas

last: Hoffmann

first: Roland

last: Coras

first: Katja

last: Kobow

first: Javier

last: López-Rivera

first: Dennis

last: Lal

first: Costin

last: Leu

first: Imad

last: Najm

first: Peter

last: Nürnberg

first: Jochen

last: Herms

first: Patrick

middle: N

last: Harter

first: Christian

middle: G

last: Bien

first: Thilo

last: Kalbhenn

first: Markus

last: Müller

first: Hajo

last: Hamer

first: Sebastian

last: Brandner

first: Karl

last: Rössler

first: Ingmar

last: Blümcke


title: Pathway-specific tuning mechanisms in the metabolism of lignin and plastic aromatic carbons in Comamonas testosteroni

status: Public on Nov 17 2022

city: Evanston

first: Ludmilla

last: Aristilde

state: IL

address: 2145 Sheridan Rd

department: Civil and Environmental Engineering

institute: Northwestern University

summary: Widely reported discrepancies between metabolic flux and transcripts or enzyme levels in bacterial metabolism imply complex regulation mechanisms need to be considered, especially in new bacterial platforms for bioremediation and bioproduction. Comamonas testosteroni strains, which metabolize various natural and xenobiotic aromatic compounds, represent such platforms whose metabolic regulations are still unknown. Here, we identify analogous multi-level regulation mechanisms in the metabolism of two lignin-related (4-hydroxybenzoate and vanillate) and one plastic-related (terephthalate) aromatic compounds in C. testosteroni KF-1, a wastewater isolate. Transcription-level regulation controlled initial catabolism and cleavage of the compounds, but subsequent carbon fluxes in central carbon metabolism are governed by metabolite-level thermodynamic regulation. Quantitative 13C-fingerprinting of tricarboxylic acid cycle and cataplerotic reactions elucidate key carbon routing that is not evident from enzyme abundance changes. Therefore, as-needed transcriptional activation of aromatic catabolism is coupled with metabolic fine-tuning of central metabolism, thus delineating pathway candidates for different metabolic manipulations.

overall_design: RNA-seq was performed on exponentially growing Comamonas testosteroni strains grown in a minimal media with either 4-hydroxybenzoate, Vanillate, Terepthalate, or Succinate as carbon sources. Three biological replicates per experiment were performed.

first: Rebecca

last: Wilkes

first: Darren

last: Parker

first: Adam

last: Guss


title: Reconstructing human Brown Fat developmental trajectory in vitro

status: Public on Dec 01 2022

city: Boston

first: Jyoti

last: Rao

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

summary: Brown adipocytes represent a specialized type of mammalian adipocytes able to uncouple nutrients catabolism and ATP generation to dissipate energy as heat. They play an important role in mammals, allowing non-shivering thermogenesis to regulate body temperature in response to cold exposure. In humans, the brown fat tissue is dispersed in small depots found throughout the neck and trunk region. Increasing brown fat activity either with drug treatment or with cell therapy approaches are considered as potential approaches for the treatment of metabolic syndrome and obesity. The recent development of in vitro differentiation strategies relying on human pluripotent stem cells (hPSCs) offers in theory the possibility to produce unlimited amounts of BAT. A strategy efficiently applied to several tissues is to recapitulate step by step the development of the tissue of interest by exposing hPSCs to the signaling cues used during normal embryonic development. However, this strategy has proven difficult to implement for brown fat as the development of this tissue is poorly characterized. Here, we first used single cell RNA sequencing to characterize the development of interscapular brown fat in mouse. Our analysis identified a previously unrecognized population of brown adipocytes precursors characterized by expression of the transcription factor GATA6. We showed that this precursor population can be efficiently generated from hPSCs by modulating the signaling pathways identified our transcriptomic analysis in paraxial mesoderm precursors differentiated in vitro. These precursors can in turn be efficiently converted into functional brown adipocytes which can respond to adrenergic stimuli by increasing their metabolism resulting in heat production.

overall_design: Single-cell mRNA sequencing of embryonic mouse brown adipocytes and human induced pluripotent stem cell derived brown adipocytes.

first: Olivier

last: Pourquié


title: RNA-seq of yeast with human chr7 YACs

status: Public on Nov 15 2022

city: Cambridge

first: Carl

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary: RNA-seq was performed of S. cerevisiae harboring human chr7 YACs in order to gauge the frequency and form of transcription in naïve DNA (i.e. DNA that did not evolve in the host cell)

overall_design:
The YACs HSC7E1068 and HSC7E481 — originally constructed by the Scherer lab as part of the human chromosome 7 specific YAC library — was obtained from the Centre for Applied Genomics (TCAG) (Toronto, Ontario) as a yeast extract peptone dextrose (YPD) stab. Based on the RNA-seq data, the YACs comprised from 80,372,600 to 81,132,754 (HSC7E1068) and 87,346,480 to 88,157,340 (HSC7E481) of human chromosome 7 (hg38), which was consistent with the previously mapped locations. To select for yeast containing the YACs, yeast were streaked onto synthetic defined (SD) -URA plates containing adenine sulfate (Sunrise Science, USA) and were grown at 30 °C for two days. Colony PCR was performed on red colonies to confirm the presence of the YAC1068 and YAC481 with primer sets E1068F (5’-CGCTGAGGACAACACAGTCT-3’), E1068R (5’-ACACTGTCTGGAAAGCTCGG-3’) and E481F (5’-GCTCATAGCATGGCTTGTGC-3’), E481R (5’-CCCACTCCTACTGTAGCCCT-3’) respectively, using a protocol described previously (73). Primers were designed to amplify a portion of CD36 and ABCB1 - genes reported to be found in YAC1068 and YAC481 respectively (74), which was later confirmed by our RNA-seq results.
Yeast colonies containing either YAC1068 or YAC481 were grown in liquid SD-URA to an OD600 of ~0.3 - 0.6. Total RNA was extracted from liquid yeast cultures using the hot acid phenol method, described previously (75). Genomic DNA was removed from RNA using Turbo DNase following the manufacturer's instructions (Invitrogen). Extracted RNA was prepared for strand specific sequencing by the Biomedical Research Centre Sequencing Core (UBC, Vancouver) using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and polyA selection (NEB). Libraries were sequenced on an Illumina Miseq machine using 300 cycles, generating 20 million paired end reads.

first: Cassandra

last: Jensen