title: Cardiac transcriptome analysis of BBLN-transgenic mice by NGS

status: Public on Sep 18 2023

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: The study applied NGS to determine the cardiac transcriptomes of BBLN-transgenic mice with FVB/N background in comparison to those of non-transgenic FVB/N mice at an age of 8 months. The BBLN (Bublin coiled-coil protein) is the chromosome 9 open reading frame, C9orf16, with largely unknown function. To investigate the cardiac phenotype of increased cardiac BBLN transcript levels we generated BBLN-transgenic (Tg-BBLN) mice. Echocardiography documented that Tg-BBLN mice developed features of heart failure at an age of 8 months. To elucidate pathomechanisms of heart failure induced by BBLN, we performed NGS of the cardiac transcriptomes of eight-month-old, male, BBLN-transgenic mice with cardiac-specific expression of BBLN under control of the myocardium-specific, alpha-MHC promoter. The non-transgenic control group are age-matched, male, nontransgenic FVB/N mice. NGS data of this study document transcriptome changes underlying the heart failure phenotype induced by transgenic BBLN expression.

overall_design: Cardiac transcriptomes were determined by NGS of total hearts isolated from four male BBLN-transgenic (Tg-BBLN) mice at an age of 8 months. Tg-BBLN mice have an FVB/N background. Therefore,  four, age-matched, non-transgenic, male FVB/N mice were used as the non-transgenic control group. Hearts were isolated from male mice at the end of the observation period at an age of 8 months. The group size was n=4 male mice at an age of 8 months per group. Tg-BBLN mice showed symptoms of heart failure. NGS data of the cardiac transcriptome confirmed the heart heart failure phenotype induced by an increased cardiac BBLN transcript level. All the mice of the study were weaned at an age of 3 to 4 weeks. The mice were housed under SPF conditions in groups of 2-4 mice in individually ventilated cages  with a 12h dark cycle, and had free access to food and water until the end of the observation period at an age of 8 months.

first: Joshua

last: Abd Alla


title: Whole genome microarray gene expression profiling of right ventricular heart specimens from pediatric patients with Tetralogy of Fallot (TOF)

summary: Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect with a world-wide prevalence of 3 to 4 cases per 10,000 life births. TOF is a congenital heart disease with four major cardiac defects, i.e., ventricular septal defect, overriding aortic root, infundibular stenosis of the pulmonary artery, and  right ventricular hypertrophy. Treatment relies on correction surgery in early infancy. This study performed whole genome microarray gene expression profiling of cardiac specimens of the right ventricular outflow tract (RVOT), which were recovered during correction surgery of TOF from 11 pediatric patients diagnosed with TOF cardiac defects.

overall_design: Whole genome microarray gene expression profiling was performed of cardiac specimens of the right ventricular outflow tract (RVOT) of pediatric patients with Tetralogy of Fallot (TOF) and cyanosis. Cardiac specimens (muscle bundles that are routinely resected from the RV outflow tract as part of surgery) were recovered from 11 pediatric patients with sporadic TOF cardiac defects and cyanosis (repeated oxygen saturation measurements of ≤ 91.0 % on room air, and episodes of spells; 4 males, 7 females; age 23.2 ± 5.0 months).


title: Cohabitation of Piscirickettsia salmonis genogroups (LF-89 and EM-90): Synergistic effect on growth dynamics

status: Public on Oct 03 2023

city: Ås

first: Gabriela

last: Carril

address: Oluf Thesens vei 30

country: Norway

institute: Norwegian University of Life Sciences

type: Expression profiling by high throughput sequencing

summary: Piscirickettsia salmonis, the biological agent of SRS (Salmon Rickettsial Syndrome), is a facultative intracellular bacterium that can be divided into two genogroups (LF-89 and EM-90) with different virulence levels and patterns. There are studies that have found co-infection of these genogroups in salmonid farms in Chile, but it is essential to assess whether this competitive interaction within the host is related to virulence and changes in pathogen dynamics. In this work, we studied one isolate from each genogroup, EM-90 and LF-89 . The aim was to evaluate how co-cultures could affect their growth performance and virulence factors expression at in vivo cultures in Atlantic salmon. During in vivo co-cultures, transcriptomic analysis revealed an upregulation of transposases, flagellum-related genes (fliI and flgK), transporters and permeases that could unveil novel virulence effectors used in the early infection process of P. salmonis. Thus, our work has shown that the cohabitation of the genogroups of P. salmonis can modulate their behavior and virulence effectors expression. These data can contribute to new strategies and approaches to improve current health treatments against this salmonid bacterium.

overall_design: To investigate the transcriptomic changes of P. salmonis in single cultures compared to co-cultures of both genogroups, we inserted dialysis bags with the bacterial cultures inside Atlantic salmon for 6 days. Then extracted the total RNA to perform an RNA-seq analysis comparing the trasncriptomics profiles of EM-90 alone, LF-89 alone and EM-90 with LF-89 co-cultures.

first: Carril

last: Gabriela

first: Sørum

last: Henning


title: Whole genome microarray gene expression profiling of transgenic mouse hearts with four-fold increased BBLN contents

summary: The study performed whole genome microarray gene expression profiling of mouse hearts from BBLN-transgenic mice with four-fold increased cardiac BBLN (Bublin coiled coil protein) contents (Tg-BBLN-low) in comparison to non-transgenic FVB hearts. Tg-BBLN-low mice with four-fold increased cardiac BBLN expression under control of the myocardium-specific alpha-MHC promoter developed features of compensated heart failure with increasing age, which was characterized by a significantly reduced left ventricular ejection fraction as determined by echocardiography. To investigate the compensated heart failure phenotype of Tg-BBLN-low mice, whole genome micoarray gene expression profiling was performed. The microarray data show that moderately increased cardiac BBLN levels are sufficient to induce features of pathological cardiac remodeling.

overall_design: Whole genome microarray gene expression profiling was performed of mouse hearts from BBLN-transgenic mice with four-fold increased BBLN-contents. Hearts were isolated from eight-month-old, male Tg-BBLN-low mice and from male, age-matched non-transgenic FVB mice, which were used as controls.


title: The presence of Xanthine Dehydrogenase is crucial for the maturation of the rat kidneys

status: Public on Sep 20 2023

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

country: USA

institute: University of South Florida, College of medicine

summary: We hypothesized that XDH plays a role in nephrogenesis. Here we used SSXdh+/+, SSXdh+/-, and SSXdh-/- rat kidneys from the postnatal development period to test this hypothesis. In wildtype but not homozygote rat kidneys, XDH expression was significantly increased from postnatal day (PND) 5 to 15, indicating its importance in the maturation of the kidney. Even though both genotypes had similar glomerular density at birth, it was significantly lower in SSXdh-/- rats by PND21. Transcriptomic profiling of the kidneys revealed that many genes related to kidney formation were dysregulated by the lack of Xdh expression in this period. Functional and pathway analyses of the transcriptome data strongly suggested that Xdh affected these genes via epidermal growth factor (EGF) signaling disruption. This study showed that Xdh is essential for the kidney maturation process.

overall_design: All animals used for the current study were male. The pups were euthanized by decapitation under deep anesthesia (2%–3 % (vol/vol) isoflurane), and both kidneys were collected. One kidney was stored in Formalin for histological analyses, and the other was snap-frozen for molecular analyses. At all different postnatal day (PND) time points (days 0, 5, 15, and 21), the whole litter was collected from each pregnancy and genotyped. Transcriptomics was done using kidney cortex from each time point for all genotypes.

last: Staruchenko

first: Lashodya

middle: V

last: Dissanayake


title: Effect of ASPA C152W expression on the transcriptome in HEK293T cells

status: Public on Sep 27 2023

city: Copenhagen

first: Leonor

last: Rib

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

summary: Deep mutational scanning has revealed that some destabilized ASPA variants are toxic, including the C152W variant. To analyze this effect RNA seq was employed to identify genes that are differentially expressed upon ASPA C152W expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEK293T cells expressing wild-type ASPA and the ASPA variant C152W.

first: Martin

last: Grønbæk-Thygesen

first: Vasileios

last: Voutsinos

first: Line

last: Pedersen

first: Rasmus

last: Hartmann-Petersen


title: Cardiac transcriptome analysis of right and left ventricular heart specimens of BBLN-transgenic mice by NGS

summary: The study performed NGS to investigate the cardiac transcriptomes of right and left ventricular heart specimens of 3-4-month-old BBLN-transgenic mice with FVB/N background in comparison to those of non-transgenic FVB/N mice. BBLN-transgenic (Tg-BBLN) mice with myocardium-specific BBLN expression were generated to investigate the cardiac phenotype of increased cardiac BBLN transcript levels because the function of BBLN (Bublin coiled-coil protein), which is the chromosome 9 open reading frame(C9orf16), is largely unknown. Tg-BBLN mice with increased cardiac BBLN levels developed features of heart failure with increasing age. Pathomechanisms of heart failure induced by BBLN were investigated by NGS of right and left ventricular heart specimens of male, BBLN-transgenic mice (age: 3-4 months). NGS data reveal transcriptome changes in right and left ventricular heart specimens induced by increased expression of BBLN in the heart.

overall_design: Cardiac transcriptomes were determined by NGS of right and left ventricular heart specimens isolated from male BBLN-transgenic mice with FVB/N background. Age-matched, non-transgenic, male FVB/N mice were used as the control group. Right and left ventricular heart specimens were isolated from male mice at an age of 3-4 months  (n=4 mice per group). Tg-BBLN mice had features of heart failure, which was documented by echocardiographic assessment of the left ventricular cardiac ejection fraction. NGS data of right and left ventricular heart transcriptomes reveal transcriptome changes underlying the BBLN-induced heart failure phenotype. After weaning at an age of 3 to 4 weeks, all the mice of the study were housed in individually ventilated cages under SPF conditions with a 12h dark cycle. The mice had free access to food and water until the end of the observation period at an age of 3-4 months.


title: Oncogene EVI1 Drives Acute Myeloid Leukemia Via a Targetable Interaction with CTBP2

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of Usp28 knockout and re-consitution of wildtype or monomeric Usp28 on gene expression in hepatocellular carcinoma cells

status: Public on Sep 30 2023

city: Tübingen

first: Nikita

last: Popov

address: Otfried-Müller-Str 14

department: Clinical Tumor Biology

country: Germany

institute: University Hospital Tübingen

summary: Usp28-KO HLF cell lines were generated by CRISPR-Cas9. Usp28-KO cells expressing Usp28-WT, Usp28-Mono or a control vector were established by lentiviral transduction.

overall_design: Gene expression profiling was perfromed using RNA-seq

first: Chao

last: Jin


title: Characterizing Pneumocystis carinii centromeres with ChIP-seq II

status: Public on Sep 11 2023

city: Bethesda

first: Ousmane

middle: Hamadoun

last: Cisse

state: MD

address: 10 Center Dr,

institute: National Institutes of Health

summary: Pneumocystis is a relevant genetic system to study centromere formation in relation with host adaptation. How centromeres are formed and maintained in strongly host adapted fungal pathogens is poorly investigated. Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. CENP-A, a variant of histone H3 is the epigenetic marker that define centromeres in most eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. Genome shuffling allows genome reconfiguration suitable for survival in new environment such as pathogen adaptation to new hosts. Here, we study the evolution of centromeres in closely related species of mammalian specific pathogens of the fungal phylum of Ascomycota. Long term culture of Pneumocystis species is currently untenable. Using heterologous complementation, we show that Pneumocystis CENP-A ortholog is functionally equivalent to fission yeast Cnp1. Using a short-term in vitro culture, infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 Mya ago. Each species has 17 unique short regional centromeres (< 10kb) in 17 monocentric chromosomes. The centromeres are flanked by heterochromatin. They span active genes, lack conserved DNA sequence motifs, and repeats.These features suggest an epigenetic specification of centromere function.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for centromeric histone CENP-A  in Pneumocystis carinii. P. carinii organisms were collected from infected lungs of corticoids-induced immunocompromised Sprague-Dawley male rats. Organisms were cocultured with a suspension of A549 and LET1 cells for 7 days

middle: H

first: Shelly

last: Curran

first: Joseph

last: Kovacs


title: Characterizing Pneumocystis carinii centromeres with ChIP-seq

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for centromeric histone CENP-A and CENP-C in Pneumocystis carinii. P. carinii organisms were collected from infected lungs of corticoids-induced immunocompromised Sprague-Dawley male rats


title: Developmental analysis of hiPSC-derived endothelial cells transplanted into mouse liver

status: Public on Sep 08 2023

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

summary: Human induced pluripotent stem cell (hiPSC)-derived endothelial cells were transplanted into mouse liver and isolated at several time-points to assess their developmental profile over time. They were compared to in vitro hiPSC-endothelial cells, and primary human liver sinusoidal endothelial cells (either freshly isolated or expanded in culture).

overall_design: In vitro hiPSC-endothelial cells (iECs), compared with iECs isolated 1, 2, 4, and 12 weeks post-transplantation into mouse, human primary liver sinusoidal endothelial cells (either freshly isolated or expanded in culture)

first: Kiryu

middle: K

last: Yap

first: Jose

middle: M

last: Polo

first: Geraldine

last: Mitchell


title: Rab30 regulates lipid homeostasis in the hepatocyte during fasting

status: Public on Sep 12 2023

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary: In order to facilitate inter-tissue communication and exchange of proteins, lipoproteins, and metabolites with the circulation, hepatocytes have an intricate and efficient intracellular trafficking system regulated by small Rab GTPases.  Rab30, a putative Golgi-localized Rab GTPase, is induced in the mouse liver by fasting and its expression is further amplified in liver-specific carnitine palmitoyltransferase 2 knockout mice (Cpt2L-/-) that lack the ability to oxidize fatty acids in a Pparα-dependent manner.  Live-cell super-resolution imaging and biochemical in vivo proximity labeling demonstrated that Rab30-marked vesicles are highly dynamic and interact with proteins throughout the secretory pathway.  Rab30 whole-body, liver-specific, and Rab30;Cpt2 liver-specific double knockout (DKO) mice are viable and display intact Golgi ultrastructure. However, the loss of Rab30 in Rab30;Cpt2 DKO mice suppresses serum dyslipidemia observed in Cpt2L-/- single knockout mice.  Corresponding with decreased serum triglyceride and cholesterol levels, Rab30;Cpt2 DKO mice exhibit decreased circulating but not hepatic ApoA4 protein, indicative of a trafficking defect.  Together, these data suggest a role for Rab30 in the selective sorting of lipoproteins to influence hepatocyte and circulating triglyceride levels particularly during times of excessive lipid burden

overall_design: RNA-seq on whole livers was performed to investigate differentially regulated genes in 24hr fasted livers of Rab30 whole-body knockouts (KO) and their littermates ("WT littermate to Rab30 whole-body KO"), Rab30 liver-specific KO, Cpt2 liver-specific KO, Rab30;Cpt2 liver-specific double knockouts (DKO), and Rab30;Cpt2 floxed control (littermates to DKO) male mice. Liver-specific knockouts were generated by crossing floxed lines to and albumin-Cre transgenic mouse line.

first: D

last: Smith

first: M

middle: J


title: Uncovering the role of FOXA2 in the development of human serotonin neurons

status: Public on Sep 07 2023

city: Shanghai

first: Ting

last: Xu

address: 1239 Siping Road

country: China

institute: Tongji University


title: Coordinated wound responses in a regenerative animal-algal photosymbiotic metaorganism

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: Animal regeneration requires coordinated responses of many cell types throughout the animal body. In animals carrying endosymbionts, cells from the other species may also participate in regeneration, but how cellular responses are integrated across species is yet to be unraveled. Here, we study the acoel Convolutriloba longifissura, which hosts symbiotic Tetraselmis green algae and can regenerate entire bodies from small tissue fragments. We show that animal injury leads to a decline in the photosynthetic efficiency of the symbiotic algae and concurrently induces upregulation of a cohort of photosynthesis-related genes. A deeply conserved animal transcription factor, runt, is induced after injury and required for the acoel regeneration. Knockdown of runt also dampens algal transcriptional responses to the host injury, particularly in photosynthesis related pathways, and results in further reduction of photosynthetic efficiency post-injury. Our results suggest that the runt-dependent animal regeneration program coordinates wound responses across the symbiotic partners and regulates photosynthetic carbon assimilation in this metaorganism.

overall_design: In the first condition, Acoels were amputated, and their RNA were extracted  at 0 or 3 hours post amputation. In the second condition, Acoels were treated with either control or Runt RNAi, amputated, and their RNA were extracted at different timepoints. In the third condition, we treated worms with low or high light exposure for varying duration before extracting their RNA. At least three replicates each containing five Acoel animals were used for RNA extraction for each condition.

first: Dania

last: Nanes Sarfati

first: James

last: Sikes

first: Bo

last: Wang


title: ScRNAseq of ex vivo human liver sinusoidal endothelial cells (hLSECs) and human iPSC-derived endothelial cells transplanted into mouse liver

summary: Human induced pluripotent stem cell (hiPSC)-derived endothelial cells were transplanted into mouse liver and isolated after 4 weeks post-transplantation, and compared to primary human liver sinusoidal endothelial cells. ScRNAseq was used to investigate the cell subpopulations present in each of the samples, including the pattern of zonation (regional difference in phenotype of subpopulations).

overall_design: 2 samples of hiPSC-endothelial cells isolated from mouse liver after 4 weeks, compared to primary human liver sinusoidal endothelial cells


title: Changes in Environmental Stress over COVID-19 Pandemic Likely Contributed to Failure to Replicate Adiposity Phenotype Associated with Krtcap3

status: Public on Sep 01 2023

city: Winston Salem

first: Alexandria

last: Szalanczy

state: NC

address: 575 Patterson Ave

department: Internal Medicine/Molecular Medicine

institute: Wake Forest University School of Medicine

summary: We previously identified Keratinocyte-associated protein 3, Krtcap3, as an obesity-related gene in female rats where a whole-body Krtcap3 knock-out (KO) led to increased adiposity compared to wild-type (WT) controls when fed a high-fat diet (HFD). We sought to replicate this work to better understand the function of Krtcap3 but were unable to reproduce the adiposity phenotype. In the current work, WT female rats ate more compared to WT in the prior study, with corresponding increases in body weight and fat mass, while there were no changes in these measures in KO females between the studies. The prior study was conducted before the COVID-19 pandemic, while the current study started after initial lock-down orders and was completed during the pandemic with a generally less stressful environment. We hypothesize that the environmental changes impacted stress levels and may explain the failure to replicate our results. Analysis of corticosterone (CORT) at euthanasia showed a significant study by genotype interaction where WT had significantly higher CORT relative to KO in Study 1, with no differences in Study 2. These data suggest that decreasing Krtcap3 expression may alter the environmental stress response to influence adiposity. We also found that KO rats in both studies, but not WT, experienced a dramatic increase in CORT after their cage mate was removed, suggesting a separate connection to social behavioral stress. Future work is necessary to confirm and elucidate the finer mechanisms of these relationships, but these data indicate the possibility of Krtcap3 as a novel stress gene.

overall_design:
To investigate the role of Krtcap3 in adiposity, we developed a whole-body Krtcap3 knock-out rat model and examined the obesity phenotype on a high-fat diet in two separate studies
We then performed gene expression analyses using the whole hypothalamus of 4 WT and 4 KO female rats from Study 1 and Study 2

first: Gina

last: Giorgio

first: Emily

last: Goff

first: Osborne

last: Seshie

last: Grzybowski

first: Jason

last: Klotz

first: Aron

last: Geurts

first: Eva

middle: E

last: Redei

first: Leah

middle: C

last: Solberg Woods


title: Sequencing of isolated glomeruli from low salt and high salt diet fed salt sensitve Dahl rats

city: Baton Rouge

first: Krisztian

last: Stadler

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: We report the comparison of low salt vs high salt diet fed Dahl rat kidney glomeruli by sequencing analysis

overall_design:
Dahl SS rats were fed a 0.4 % normal NaCl or a 4% high NaCl diet (Dyets, Inc) for 21 days starting at 8 weeks of age. Kidneys were isolated and glomeruli were isoalted by differentilal sieving and immediately snap frozen.
RNA was isolated by the TRIzol method, libraries and sequencing were done using a Lexogen/Illumina platform.

first: Daria

last: Ilatovskaya


title: Brain histone beta-hydroxy-butirylation couples metabolism with gene expression (RNA-seq)

status: Public on Aug 21 2023

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

address: Campus Dr

department: CS

institute: UC Irvine

summary: We report changes in the neural tissue transcriptome of mice subjected to fasting.

overall_design: RNA-seq in the occipital cortex of mice subjected to 48 hours of fasting or fed ad libitum

first: Pierre

last: Baldi

first: Paola

last: Tognini

first: Siwei

last: Chen

first: Tommaso

last: Pizzorusso

first: Sara

last: Cornuti


title: Uncovering the role of FOXA2 in the development of human serotonin neurons [scRNA-seq]

first: Ting

last: Xu

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of serotonin neurons derived from human pluripotent stem cells (hPSCs) and to compare the transcriptomic differences between FOXA2 knockout and wide type hPSCs-derived serotonin neurons.

overall_design: FOXA2 knockout and widetype hPSCs-derived TPH2-positive serotonin neurons were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of EGFP signal and analyzed using scRNAseq.

first: Lining

last: Cao

first: Jianfeng

last: Lu


title: High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults (single-cell Gene Expression)

status: Public on Aug 20 2023

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: Seasonal influenza contributes to a substantial disease burden annually, resulting in approximately 10 million hospital visits and 50 thousand deaths in a typical year in the US. 90% of the annual mortality from influenza occurs in people over the age of 65. While influenza vaccination is the best protection against the virus, it is less effective for the elderly. This may be due to differences in the quantity or type of B cells induced by vaccination in older individuals. To investigate this possibility, we leveraged recent development in single-cell technology that allows for simultaneous measurement of both gene expression profile and the B cell receptor (BCR) at single-cell resolution. Pre- and post-vaccination peripheral blood B cells were sorted from three young and three older adults who responded to the inactivated influenza vaccine and were profiled using single-cell RNAseq with paired BCR sequencing. At pre-vaccination, we observed a higher somatic hypermutation frequency and a higher abundance of activated B cells in older adults than in young adults. Following vaccination, young adults mounted a more clonal response than older adults. The response involved a mix of plasmablasts, activated B cells, and resting memory B cells in both age groups. The response in young adults was dominated by expansion in plasmablasts, while the response in older adults also involved activated B cells. We observed a consistent change in gene expression in plasmablasts after vaccination between age groups but not in the activated B cells. These quantitative and qualitative differences in the B cell response may provide insights into the age-related change of influenza vaccination response.

overall_design: To understand the age-group difference in B cells underlying a successful vaccination response, we selected three young (20- to 30-years-old) and three older (60- to 100-years-old) subjects who responded to seasonal influenza vaccine with at least 4 fold increase of HAI titer for at least one vaccine strain from a cohort recruited at Yale University over the five vaccination seasons between 2010 and 2014.

first: Tony

last: Melillo

first: Mamie

last: Wang

first: Hailong

last: Meng

first: Albert

last: Shaw


title: Brain histone beta-hydroxy-butirylation couples metabolism with gene expression


title: High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults

relation:
SuperSeries of: GSE175522
SuperSeries of: GSE175523


title: Quantitative single-cell RNA-sequencing for alcohol- and formalin-fixed tissue sections with DRaqL; an efficient RNA recovery and cDNA amplification method for laser capture microdissection

city: Kashihara

first: Hiroki

last: Ikeda

address: 840 Shijo-Cho, Kashihara, Nara

country: Japan

institute: Nara Medical University

summary: Spatially resolved, single-cell transcriptome analysis of high quality remains challenging, despite the rise of high-resolution spatial transcriptomics.  Laser-capture microdissection (LCM) is widely used to isolate cells of interest from tissue sections.  Here, we developed DRaqL (Direct RNA recovery and quenching for LCM), a technique that allows efficient lysis of single, LCM-isolated cells from alcohol- and formalin-fixed tissue and stained frozen sections, and that is amenable to enzymatic reactions for cDNA amplification within the same sampling tubes.  Quantitative evaluations showed that single-cell RNA sequencing combined with DRaqL allowed transcriptomic profiling from frozen sections at an efficiency comparable with that from freshly dissociated cells, with small biases and errors in lowly expressed genes, in addition to allowing exon-exon junction profiling.  By applying this method to mouse ovarian frozen sections, we revealed a transcriptomic continuum of growing oocytes quantitatively associated with the size of oocytes and follicles, identified genes highly correlated with oocyte diameters, and detected oocyte-specific splice isoforms.  We further identified genes that were differentially expressed in granulosa cells depending on their distance from oocytes, suggesting distinct epigenetic regulatory mechanisms and cellular proliferation.  Thus, DRaqL provides an efficient cell lysis for single-cell cDNA amplification from frozen sections that is amenable to high-quality RNA sequencing analysis.

overall_design: Single-cell RNA-seq analysis of fresh and LCM mouse embryonic stem cells cultured in 2i conditioned medium by DRaqL technology, and RNA-seq analysis of LCM single oocyte and granulosa cell.

first: H

first: T

last: Takashima

first: K

last: Kurimoto


title: Brain histone beta-hydroxy-butirylation couples metabolism with gene expression (ChIP-seq)

first: Muntaha

last: Samad

summary: We report changes in beta-hydroxybutyrylation  of lysine (K) 9 on histone H3 in the occipital cortex of mice after 48 hour fasting.

overall_design: ChIP-seq of H3 K9 beta-hydroxybutyrylation in the occipital cortex of mice subjected to 48 hours fasting with respect to ad libitum (AL) fed mice

first: Pierre


title: High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults (single-cell BCR)


title: Upregulation of CYR61 by TGF-β and YAP signaling exerts a counter-suppression of hepatocellular carcinoma

status: Public on Aug 19 2023

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

institute: Nanchang University

summary: TGF-β and Hippo signaling are two critical pathways engaged in cancer progression by regulating both oncogenes and tumor suppressors, yet how the two pathways coordinately exert their functions in the development of hepatocellular carcinoma (HCC) remains elusive.  In this study, we firstly conducted an integrated analysis of public liver cancer databases and our experimental TGF-β target genes, identifying CYR61 as a pivotal gene relating to HCC development.  Evidence revealed that CYR61 is a direct target gene of TGF-β in liver cancer cells. In addition, TGF-β-stimulated Smad2/3 and the Hippo pathway downstream effectors YAP and TEAD4 can form a protein complex on the promoter of CYR61, thereby activating the promoter activity and stimulating CYR61 gene transcription in a collaborative manner.  Functionally, depletion of CYR61 enhanced TGF-β- or YAP activation-mediated growth and migration of liver cancer cells.  Consistently, ectopic expression of CYR61 was capable of impeding TGF-β- or YAP-induced malignant transformation of HCC cells in vitro, and attenuating HCC xenograft growth in nude mice.  Finally, Downregulation of CYR61 expression in HCC tissues than that in normal liver tissues is well associated with a bad clinical outcome in patients.  Together, these results add new evidence for the interplay between TGF-β and Hippo signaling and unveil an important tumor suppressor function of CYR61 in liver cancer.

overall_design: Two independent cell-culture replicates from the total population of HLE-Vector and HLE-CYR61 stable expression were used to generate total RNA.

first: Yan

last: Xiaohua


title: Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity

status: Public on Aug 07 2023

city: Santa Barbara

first: Alex

last: Chialastri

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

type: Methylation profiling by high throughput sequencing

summary: Transmission of 5-methylcytosine (5mC) from one cell generation to the next plays a key role in regulating cellular identity in mammalian development and diseases. While recent work has shown that the activity of DNMT1, the protein responsible for the stable inheritance of 5mC from mother to daughter cells, is imprecise; it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method that combines enzymatic detection of modified cytosines with nucleobase conversion techniques to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides. We find that the fidelity of DNMT1-mediated maintenance methylation is directly related to the local density of DNA methylation, and for genomic regions that are lowly methylated, histone modifications can dramatically alter the maintenance methylation activity. Further, to gain deeper insights into the methylation and demethylation turnover dynamics, we extended Dyad-seq to quantify all combinations of 5mC and 5-hydroxymethylcytosine (5hmC) at individual CpG dyads to show that TET proteins preferentially hydroxymethylate only one of the two 5mC sites in a symmetrically methylated CpG dyad rather than sequentially convert both 5mC to 5hmC. To understand how cell state transitions impact DNMT1-mediated maintenance methylation, we scaled the method down and combined it with the measurement of mRNA to simultaneously quantify genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from the same cell (scDyad&T-seq). Applying scDyad&T-seq to mouse embryonic stem cells transitioning from serum to 2i conditions, we observe dramatic and heterogenous demethylation and the emergence of transcriptionally distinct subpopulations that are closely linked to the cell-to-cell variability in loss of DNMT1-mediated maintenance methylation activity, with regions of the genome that escape 5mC reprogramming retaining high levels of maintenance methylation fidelity. Overall, our results demonstrate that while distinct cell states can substantially impact the DNA methylation maintenance machinery, there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Bulk M-M-Dyad-seq, M-H-Dyad-seq, H-M-Dyad-seq, and H-H-Dyad-seq profiles of E14 mESC grown under multiple conditions for 48 hours.
Bulk M-M-Dyad-seq, M-H-Dyad-seq, and H-H-Dyad-seq profiles of E14 mESC grown with 0.05 µM of Decitabine for 24 hours.
scDyad-seq profiles of K562 grown with 0.6 µM DAC for 24 hours or DMSO vehicle control.
scDyad&T-seq profiles of E14 mESC grown in serum or in 2i for 3, 6, or 10 days (2iD3, 2iD6, or 2iD10 respectively).

first: Siddharth

middle: S

last: Dey


title: CD20 is a mammalian odorant receptor expressed in a subset of olfactory sensory neurons that mediates innate avoidance of predators

status: Public on Aug 08 2023

city: Worcester

first: I-Hao

state: MA

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

summary: The mammalian olfactory system detects and discriminates between millions of odorants to elicit appropriate behavioral responses. While much has been learned about how olfactory sensory neurons detect odorants and signal their presence, how specific innate, unlearned behaviors are initiated in response to ethologically relevant odors remains poorly understood. Here, we show that the 4-transmembrane protein CD20, also known as MS4A1, is expressed in a previously uncharacterized subpopulation of olfactory sensory neurons in the main olfactory epithelium of the murine nasal cavity and functions as a mammalian odorant receptor that recognizes compounds produced by mouse predators. While wildtype mice avoid these predator odorants, mice genetically deleted of CD20 do not appropriately respond. Together, this work reveals a novel CD20-mediated odor-sensing mechanism in the mammalian olfactory system that triggers innate behaviors critical for organismal survival.

overall_design: To characterize role of the Ms4a genes in the mouse olfactory system, we generated the Ms4a6c knockout and whole Ms4a cluster knockout mice. To validate the gene expression of these knockout mice, we generate the cDNA library from the olfactory epithelium from wild-type, Ms4a6c KO, and whole Ms4a cluster knockout mice (3 biological replicates per geneotype.

first: Wang

last: I-Hao

first: Jiang

last: Hao-Ching

first: Greer

last: Paul


title: RNAseq of primary and recurrent ovarian cancer tumors with and without BRCA1/2 mutations

city: Los Angeles

first: Michelle

last: Jones

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: RNAseq was generated for a cohort of ovarian cancer patients to identify gene expression changes between primary and recurrent ovarian cancer tumors from patients with and without BRCA1/2 mutations

overall_design:
We performed RNAseq in 62 primary and  recurrent  tumors  from  28  patients  with  stage  III/IV  high  grade  serous  ovarian  cancer (HGSOC), of which 11 patients carried germline, pathogenic BRCA1 and/or BRCA2 mutations.

[Update] 05-20-2024: The Sample titles were updated. The original titles are in the Sample description field.

first: Nicole

last: Gull

middle: R

first: Simon

middle: A

last: Gayther


title: Transcriptomic profiles of advanced colorectal adenomas from 40 Korean patients

city: Seoul

first: Jaeseung

last: Song

department: Life Science

country: South Korea

institute: Dongguk University

summary: We report the RNA-seq data of 40 advanced colorectal adenoma patients form Dongguk University Ilsan International Hospital. The polyps with a diameter of 1cm or greater were regarded as advenced colorectal adenoma and obtained through colonoscopy. The data consist of 22 tublar adenoma, 6 tublovillous adenoma, 5 sessile serrated adenoma/polyp, 1 traditional serrated adenoma, intramucosal adenocarcinoma, neuroendocrine tumor, hyperplastic polyp, inflammatory polyp, high grade dysplasia, and atypical glands with adjacent hyperplastic mucosa.

overall_design: Messenger RNA profiles of 40 advanced colorectal adenoma samples.

first: Wonhee

last: Jang

first: Daeun

last: Kim

first: Hyunwoo

last: Kang

first: Jong Wha

last: Joo


title: Role of RB1 in neurodegenerative diseases: Inhibition of post-mitotic neuronal apoptosis via Kmt5b

status: Public on Aug 02 2023

city: Guangzhou

first: Wei

last: Liu

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

summary: To better characterize the population of proliferating and apoptotic neuron in sibling and zrb1-ko, we performed 10× single-cell RNA sequencing (scRNA-seq) on whole-brain cells of sibling and zrbi-ko at 3 dpf.

overall_design: Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enriched analysis of differentially expressed genes (DEGs) in NSPCs, myelencephalon neurons or cerebellum neurons between sibling and zrb1-ko mutants was performed.

first: Shuang

last: Zhao

first: Haiping

last: Luo

first: Wenqing

last: Zhang

first: Zhibin

last: Huang


title: Induction of antiviral Interferon-Stimulated Genes (ISGs) by neuronal STING promotes the resolution of pain

status: Public on Aug 05 2023

city: Calgary

first: Christophe

last: Altier

address: 3300 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: Nociceptive neurons respond to inflammation, initiating protective reflexes and alerting the host. Here we found that TRPV1 nociceptors express and activate the cytosolic DNA-sensing protein Stimulator of Interferon Genes (STING) in response to inflammation. Neuronal activation of STING promotes signaling through TBK1 and triggers a Type I interferon (IFN-I) response. The absence of STING led to heightened pain responses to chemical irritants or heat. In contrast, mice expressing a nociceptor-specific gain-of-function mutation in STING exhibited an IFN gene signature that reduced nociceptor excitability and inflammatory hyperalgesia. Importantly, several IFN-regulated genes (IRGs) were specific to nociceptor ion channels responsible for controlling neuronal activity and pain threshold. Therefore, STING promotes a pain-resolving IFN-I signaling pathway in nociceptors, thereby preventing sensitization and persistent pain

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq between 4 TRPV1cre-GOF mice and 4 littermates controls (GOF).

first: Manon

last: Defaye


title: Genomic editing of pathogenic TNNI3 mutation in restrictive cardiomyopathy rescues diastolic dysfunction of human induced pluripotent stem cell-derived cardiomyocytes

city: Suita, Osaka

first: Wang

last: Renjie

address: 1-1 Yamadaoka

institute: Osaka University

summary: To investigate the physiological characteristics of cardiomyocytes (CM) in restrictive cardiomyopathy (RCM), we established RCM(heterozygous)-iPSC and produced RCM(homozygous)-iPSC and corrected Isogenic-iPSC using CRISPER-CAS9 technology. Then, we used the RNA-seq data obtained from these three iPSCs and three different healthy iPSC-derived CMs for gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RCM group(heterozygous and homozygous) and healthy group(Isogenic and three healthy controls)

first: Renjie

last: Wang

first: Hidekazu

last: Ishida


title: Therapeutic induction of mesenchymal-epithelial transition via epigenetic reprogramming curtails metastatic progression and sensitizes breast cancers to treatment

city: LEBANON

first: Diwakar

middle: Pattabiraman

last: Pattabiraman

state: NH

address: 1 Medical Center Drive

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq

city: Lebanon

first: Min Kyung

last: Lee

address: 1 Medical Center Dr

institute: Dartmouth College

summary: Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collected single nuclei RNA-seq data from 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues (84,700 nuclei) and characterized tumor heterogeneity and transcriptomic alterations. We distinguished cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observed pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identified transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment.

overall_design: Nuclei were isolated from pediatric central nervous system tumors and non-tumor pediatric brain tissue and analyzed using single nuclei RNA-seq (following 10X Genomics 3' VDJ protocol). Majority of the samples were multiplexed into a single 10x run. Please refer to the published paper for the details on the samples that were pooled into the same run.

first: Lee

last: Min Kyung

first: Christensen

last: Brock


title: Therapeutic induction of mesenchymal-epithelial transition via epigenetic reprogramming curtails metastatic progression and sensitizes breast cancers to treatment [RNA-seq]

summary: The epithelial-mesenchymal transition (EMT) is a developmental program that is co-opted by tumor cells to aid in their embarking on the metastatic cascade. Tumor cells that undergo EMT are known to be endowed by, amongst other traits, heightened resistance to chemotherapy. Despite a clear understanding of the role played by the EMT program in conferring cells with these aggressive traits, there are currently no therapeutic avenues specifically targeting the program. Here we show that treatment of mesenchymal-like breast cancer cells with eribulin, an FDA-approved drug for the treatment of advanced breast cancers, leads to a mesenchymal-epithelial transition (MET), accompanied by a loss of metastatic propensity and sensitization of tumor cells to subsequent rounds of chemotherapy. We uncover a novel alternate mechanism of action that provides evidence for eribulin pretreatment as a viable clinical mechanism of MET induction that curtails metastatic progression and the evolution of therapy resistance.

overall_design: RNA-seq.  PB3-Parental and PB3-resistant derivatives; erubilin, paclitaxel, or vinorelbine treatment.  Paired-end RNA-sequencing of three replicates per cell line.

first: Meisam

last: Bagheri

first: Owen

last: Wilkins


title: Therapeutic induction of mesenchymal-epithelial transition via epigenetic reprogramming curtails metastatic progression and sensitizes breast cancers to treatment [ATAC-seq]

overall_design: ATAC-seq; PB3-Parental and PB3-resistant derivatives; erubilin, paclitaxel, or vinorelbine treatment.  Paired-end RNA-sequencing of two replicates per cell line.


title: Therapeutic induction of mesenchymal-epithelial transition via epigenetic reprogramming curtails metastatic progression and sensitizes breast cancers to treatment [CUT&RUN-mouse]

overall_design: CUT&RUN. PB3 cells were treated with 300nM eribulin for 24, 48, and 72h. Paired-end RNA-sequencing of two replicates per cell line.


title: STING agonist alters the transcriptional profiles of HSPCs in melanoma-bearing mouse model

city: Beijing

first: Tianxiao

last: Xu

address: 52 Fucheng Road, Haidian District, Beijing

institute: Peking University Cancer Hospital

summary: In order to better understand the effects of STING agonist diABZI on HSPCs, the LSKs and GMPs were sorted from mice BM and subjected to RNA sequencing to explore the transcriptome alteration after diABZI treatment.

overall_design: Smart-Seq2 RNA sequencing in LSKs and GMPs from diABZI treated and control mice

first: Jie

last: Dai

first: Jun

last: Guo

first: Lu

last: Si


title: Eribulin induces mesenchymal-epithelial transition to curtail metastatic progression by altering the chromatin landscape of breast cancers cells

city: Bengaluru

first: Mohamed Ashick

last: Mohamed Saleem

state: Karnataka

address: #1519/10, 8Th A Main, 'Akshaya', Sahakaranagar

country: India

institute: LifeBytes India Pvt Ltd


title: SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans [sin-3(tm1276)]

status: Public on Oct 04 2023

city: Lyon

first: Cecile

last: Bedet

address: 46 allée d'Italie

department: Bilogie

country: France

institute: ENS de Lyon

summary: The SIN3 transcriptional coregulator influences gene expression through multiple interactions that include histone deacetylases (HDACs). Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability (ID)/autism syndromes, emphasizing its key role in development. However,  little is know on its complexity of interactions and functions in developmental processes. Here we show that loss of SIN-3, the single SIN3 homologue in Caenorhabditis elegans, results in maternal effect sterility associated with deregulation of the germline transcriptome, including derepression of X-linked genes. Using proteomics analysis we identify at least two SIN3 complexes containing distinct HDACs and differentially contributing to fertility. Single cell smFISH reveals that loss of sin-3 stochastically derepresses X linked genes in individual germ cells. We further identify acetylation marks whose abundance depends on SIN3. Together, this work provides a powerful paradigm for the in vivo study of SIN3 and associated proteins.

overall_design: Gene expression profiling of germlines from young adults sin-3(tm1276) mutant and wild-type (wt) worms (used as control)

first: Marion

last: Herbette

first: Francesca

last: Palladino

first: Valerie

last: Robert


title: Eribulin induces mesenchymal-epithelial transition to curtail metastatic progression by altering the chromatin landscape of breast cancers cells [scRNA-Seq]

overall_design: Mouse cells were sequenced from RNA and nucleus. Eight libraries for single cell/nuclei transcriptome data were obtained in 3 batches namely Run1, Run2 and Run3. Eribulin (ERI) and Paclitaxel (PAC) drugs were considered as treatment with various level of doses.     While Run1 and Run2 data were from single cell 3’ V3 sequencing (scRNA) protocol, Run3 was single nuclei RNA+ATAC V1 sequencing (snRNA multiome) protocol. FASTQ and count matrix were generated using 10x Genomics cellranger-3.1.0, 10x Genomics cellranger-4.0.0 and 10x Genomics cellranger-arc-1.0.0 for Run1, Run2 and Run3 respectively. Four libraries for single cell/nuclei ATAC data were obtained in 2 batches namely Run1 and Run3 using scATAC V1 and snATAC (multiome) V1 protocol respectively. FASTQ and peak count matrix were generated using 10x Genomics cellranger-atac-1.2.0 and 10x Genomics cellranger-arc-1.0.0 for Run1 and Run3 respectively. Cellranger reference mm10 was used as reference for all runs and technologies.    Count matrices were analysed using Seurat v3.1.4 pipeline (Stuart et al., 2019). Briefly, low quality cells (number of genes expressed < 200, percentage of UMIs in mitochondrial and ribosomal genes individually > 50) are filtered out. Using selected variably expressing genes and significant PCs from PCA, clustering and UMAP projection were generated. Pseudotime analysis was done against all samples merged dataset using Monocle3 v0.2.1 while considering “Untreated” cells as the root cells. Peak count matrices were analysed using Signac v1.1.1 pipeline. Briefly, low quality cells (fragments in peak regions < 1000 and >75000, percentage of UMIs in peaks > 20, ratio of UMIs in blacklist regions to that of peak regions > 0.05, nucleosome signal > 10 and TSS enrichment < 2) are filtered out. Using selected top features and 2 to 30 PCs from LSI, clustering and UMAP projection were generated.

first: Gadisti

last: Mohamed

first: Mohammed

first: Subhadeep

last: Das

first: Nevena

middle: B

last: Ognjenovic

first: Hanxu

last: Lu

first: Ian

last: La Croix

first: Shivashankar

last: Nagaraj

first: Kristen

last: Muller

first: Scott

last: Gerber


title: Chromatin accessibility landscapes across B-ALL

status: Public on Oct 17 2023

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital


title: Therapeutic induction of mesenchymal-epithelial transition via epigenetic reprogramming curtails metastatic progression and sensitizes breast cancers to treatment [CUT&RUN-human]

first: Diwakar

last: Pattabiraman

overall_design: CUT&RUN. MDA cells were treated with 300nM eribulin for 24, 48, and 72h.  Paired-end RNA-sequencing of two replicates per cell line.

first: Meisam

last: Bagheri

first: Owen

last: Wilkins


title: Vedolizumab efficacy is associated with decreased intracolonic dendritic cells, not memory T cells [P444]

status: Public on Aug 01 2023

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Background: Vedolizumab, an antibody blocking integrin α4β7, is a safe and effective therapy for Crohn’s disease and ulcerative colitis. Blocking α4β7 from binding its cognate addressin MAdCAM-1 on intestinal blood vessel endothelial cells prevents T cells from migrating to the gut mucosa in animal models. However, data supporting this mechanism of action in humans is limited. Methods: We conducted a cross-sectional case-control study to evaluate the effect of vedolizumab on intestinal immune cell populations while avoiding the confounding effect resolving inflammation could have on the cellularity of the colonic mucosa in treatment-responsive patients. Colon biopsies from 71 case patients receiving vedolizumab were matched with biopsies from 71 control patients, similar in disease type, medications, anatomic location, and inflammation. Biopsies were analyzed by flow cytometry and full mRNA transcriptome sequencing of sorted T cells. Results: No difference was seen between vedolizumab recipients and controls in the quantity of any antigen-experienced lymphocyte subset, nor the quality of the transcriptome in any experienced T cell subset. Fewer naïve colonic B and T cells were seen in vedolizumab recipients than controls, regardless of response. The only immune population that was significantly reduced exclusively in the colonic mucosa of vedolizumab-responsive patients was CD1c+ (BDCA1+) dendritic cells. In blood, these dendritic cells ubiquitously express more α4β7 per cell than almost any other circulating leukocyte, but rapidly downregulate α4β7 expression upon vedolizumab exposure. Conclusions: The clinical efficacy of vedolizumab thus reveals integrin α4β7-dependent dendritic cell migration to the intestinal mucosa to be central to IBD pathogenesis.

overall_design: Cross-sectional case-control

first: Elisa

last: Boden

first: Ramya

last: Kongala

first: Duncan

last: Hindmarch

first: Donna

last: Shows

first: Julius

middle: G

last: Juarez

first: James

middle: D

last: Lord


title: Spatiotemporal hepatocyte heterogeneity impacts in vivo gene engineering [Visium Spatial Transcriptomics]

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: The liver is a central organ for physiology and metabolism, with hepatocytes being the main cell type responsible for most of its functions. Several previous studies investigated the cell types involved in tissue homeostasis and regeneration, however the mechanisms underlying post-natal liver growth and establishment of the mature hepatocyte phenotypes remain to be fully understood. Moreover, genetic modification of hepatocytes is emerging as a promising therapeutic approach, particularly for genetic diseases of the coagulation system and hepatic metabolism. Here, we investigate liver tissue dynamics in mice during post-natal growth and turnover in adulthood, by spatial transcriptomics, clonal analysis, and lineage tracing. We observe progressive establishment of metabolic zonation of hepatocytes and that only a fraction of hepatocytes proliferates in the newborn liver, generating most of the adult tissue. We assess the impact of these changes on both in vivo liver gene transfer and gene editing. We show that the age at treatment affects both the efficiency and lobule distribution of lentiviral vector-mediated gene transfer, and that preferential targeting of the more proliferating hepatocytes allows expansion of the genetically modified liver area. Overall, our findings provide new insights into the spatio-temporal dynamics of the liver during post-natal growth and hepatocyte heterogeneity, with broad implications for liver biology and therapeutic applications.

overall_design: Spatial transcriptomics of 17 mouse livers, from newborn, juvenile or adult mice, either LV-transduced, 3 days post LV, or age-matched untransduced mice.

first: Francesco

last: Starinieri

first: Michela

last: Milani

first: Ivan

last: Merelli

first: Alessio

last: Cantore


title: Aggregation of α-synuclein scaffolds RNA G-quadruplexes assembly leading to progressive neurodegeneration

status: Public on Jul 18 2023

city: Yokohama

first: Sefan

last: Asamitsu

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences

summary: Synucleinopathies are triggered by the aggregation of α-synuclein (αSyn), leading to progressive neurodegeneration. However, the intracellular mechanism of αSyn aggregation remains unclear. Here we show that assembly of RNA G-quadruplexes (rG4s) form scaffolds for αSyn aggregation, contributing to neurodegeneration. Purified αSyn binds rG4s directly through the N-terminus. rG4 itself undergoes phase separation and assembly by Ca2+, accelerating the sol-gel phase transition of αSyn. In αSyn preformed fibrils (PFF)-treated neurons, rG4s assembly composed of synaptic mRNAs co-aggregates with αSyn upon Ca2+ excess influx into cytoplasm, eliciting synaptic dysfunction. Artificial assembly of rG4s using an optogenetic approach evokes αSyn aggregation and neuronal dysfunction. Administration of 5-aminolevulinic acid (5-ALA), a prodrug of protoporphyrin IX (PpIX) that prevents phase separation of rG4s, attenuating αSyn aggregation, neurodegeneration, and progressive motor deficits in PFF-injected synucleinopathy mice. Together, assembly of rG4s due to dysregulation of intracellular Ca2+ homeostasis accelerates αSyn phase transition and aggregation may contribute to pathogenesis of synucleinopathies.

overall_design: Primary mouse cortical neurons (mCTXN) treated with vehicle or α-Syn PFF were crosslinked on ice cold RNase free PBS by irradiation with UV light (254 nm) at 150 mJ/cm2. Cells were harvested, lysed, and precleared on DynabeadsTM Protein G (Invitrogen) for 1 hour at 4 ℃. The precleared lysates were incubated at 4°C for three hours in a protein G magnetic beads immobilized with normal rabbit IgG (for control) or BG4 with anti-DYKDDDDK tag antibody. Purified protein-bound RNA fraction was subjected to library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). All libraries were sequenced on a NextSeq 500 sequencer (illumina).

first: Kazuo

last: Matsuo

first: Kohei

last: Maeda

first: Ginji

last: Komiya

first: Kenta

last: Kudo

first: Yusuke

last: Sakai

first: Susumu

last: Ikenoshita

first: Shingo

last: Usuki

first: Shiori

last: Funabashi

first: Yasushi

last: Kawata

first: Tomohiro

last: Mizobata

first: Norifumi

last: Shioda

last: Yabuki


title: Molecular and cellular responses in agroinfiltrated leaves of Nicotiana benthamiana expressing suppressor of silencing P19 and influenza H5 virus-like particles

city: Quebec

first: Louis-Philippe

last: Hamel

state: Quebec

address: 2552 boul. du Parc-Technologique

institute: Medicago

summary: Transient expression of P19 and influenza hemagglutinin induces a unique molecular signature in Nicotiana benthamiana leaf cells that are used as protein bio-factories for production of plant-made vaccines.

overall_design: Differential gene expression profiling of RNAseq data for N.Benthamiana leaves.

first: Rachel

last: Tardif

first: Francis

last: Poirier-Gravel

first: Asieh

last: Rasoolizadeh

first: Chantal

last: Brosseau

first: Geneviève

last: Giroux

first: Jean-François

last: Lucier

first: Marie-Claire

last: Goulet

first: Adam

last: Barrada

first: Élise

last: Roussel

first: Marc-André

last: Comeau

first: Pierre-Olivier

last: Lavoie

first: Peter

last: Moffett

first: Dominique

last: Michaud

last: D'aoust


title: Vedolizumab efficacy is associated with decreased intracolonic dendritic cells, not memory T cells

first: Stephanie

last: Osmond


title: An adaptive biomolecular condensation response is conserved across environmentally divergent species

status: Public on Jul 31 2023

city: Chicago

first: D Allan

last: Drummond

state: IL

address: 929 E 57th Street

institute: University of Chicago

summary: Cellular responses to maladaptive environmental changes—stresses—allow for organismal adaptation to diverse and dynamic conditions. Across the tree of life, cells upregulate a highly conserved transcriptional program in response to so-called proteotoxic stresses such as heat shock. Correspondingly, in eukaryotes, these stresses induce the formation of biomolecular condensates, clusters of mRNA and protein which are referred to as stress granules under severe stress. However, major questions remain about this stress-induced response. How conserved is the condensation response relative to the transcriptional response? How does it vary across environmental niches, and to what extent does it correspond with the conserved transcriptional response? To answer these fundamental questions, we studied the growth, transcriptional, and condensation heat-induced stress responses in three fungal species adapted to thrive in different thermal environments: cryophilic S. kudriavzevii, mesophilic S. cerevisiae, and thermotolerant K. marxianus. Here we show that transcriptional heat shock responses track each species’ evolved temperature range of growth. Further, orthologous proteins—including poly(A)-binding protein, Pab1, a core marker of stress granules—form condensates in vivo at temperatures systematically tuned to the temperature at which the organisms activate the transcriptional heat shock response and slow their growth. In vitro, purified Pab1 from each species condenses autonomously at niche-specific temperatures. Homologous mutations in Pab1 cause similar shifts in relative condensation temperature across species, and crucially, mutations which suppress condensation in vitro also reduce fitness during heat stress. Our findings indicate that stress-induced protein condensation is adaptive, conserved, integrated with the growth and transcriptional responses, and tuned to features of the cellular and organismal environment to initiate at niche-specific levels.

sample_organism:
Kluyveromyces marxianus
Saccharomyces cerevisiae
Saccharomyces kudriavzevii

overall_design: Total RNA was extracted from three yeast species - S. cerevisiae, S. kudriavzevii, and K. marxianus - with and without an 8 minute, species specific heat shock. There are two biological replicates for each species and temperature.

first: Samantha

last: Keyport Kik

first: Jared

last: Bard

first: David


title: Eribulin induces mesenchymal-epithelial transition to curtail metastatic progression by altering the chromatin landscape of breast cancers cells [scATAC-Seq]

first: Mohamed Ashick

last: Mohamed Saleem

first: Meisam

last: Bagheri

first: Gadisti

last: Mohamed

first: Mohammed

first: Subhadeep

last: Das

first: Nevena

last: Ognjenovic

first: Hanxu

last: Lu

first: Ian

last: La Croix

first: Shivashankar

last: Nagaraj

first: Kristen

last: Muller

first: Scott

last: Gerber

first: Diwakar

last: Pattabiraman


title: Single-cell RNA sequencing of CD11b+ Ly6C+ Ly6G- sorted bone marrow cells from radiation control and severe aplastic anemia mice

status: Public on Jul 19 2023

city: Albany

first: Katherine

last: MacNamara

state: New York

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

summary: During immune-mediated severe aplastic anemia (SAA) monocytes (CD11b+ Ly6C+ Ly6G-) signficantly increase by both frequency and number within the bone marrow. We isolated BM monocytes from F1 hybrid mice (C57BL/6;Balb/c) induced with SAA via the splenocyte-transfer model. We utilized single-cell RNA sequencing (scRNA-seq) to analyze the heterogenity of BM monocytes during SAA.

overall_design: CD11b+ Ly6C+ LyG- bone marrow (BM) cell were isolated from 3 radiation control and 3 SAA-induced mice by Flouresence-activated cell sorting (FACS). Mice in each group were pooled and then analyzed by scRNA-seq.

first: Grazda

last: Rachel

first: MacNamara

last: Katherine


title: RNA Bind-N-Seq for purified α-Synuclein and BG4 (scFV for G-quadruplex)

status: Public on Jul 17 2023

city: Kumamoto

first: Yasushi

last: Yabuki

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Genomic neurology

institute: Kumamoto University

summary: Aggregation of α-synuclein may trigger the development of synucleinopathies, a progressive neurodegenerative disease such as Parkinson's disease and Dementia with Lewy bodies. We demonstrate RNA initiates α-synuclein phase transition in vitro, however, RNA binding ability and its motif remain unclear. Here, we indicate purified human α-synuclein protein preferentially binds to guanine-rich RNA sequences by RNA Bind-N-Seq using a pool of random 24-mer RNA oligonucleotides in vitro. Importantly, these hit motifs were required consecutive guanines not random, suggesting that RNA G-quadruplexes binds to α-synuclein. We also confirmed that GC content and skew of α-synuclein-enriched RNA sequences were similar to that of BG4 (G-quadruplex antibody)-enriched RNA sequences. Taken together, these data suggest that α-synuclein binds to RNA-formed G-quadruplex.

overall_design: To investigate α-synuclein-bound RNA motifs, human α-synuclein was incubated with 24-mers randomized RNA pools. BG4 known as G-quadruplex antibody is utilized for positive control.

first: Sefan

last: Asamitsu

first: Shingo

last: Usuki

first: Norifumi

last: Shioda


title: N4-acetylcytidine of Nop2 mRNA is Required to the Transition of Morula-to-Blastocyst

city: harbin

first: rui

last: cheng

address: 92 Xidazhi Street

institute: Harbin Institute of Technology

summary: N-acetyltransferase 10 (NAT10)-mediated N4-acetylcytidine (ac4C) modification is crucial for mRNA stability and translation efficiency, yet the underlying function in mammalian preimplantation embryos remains unclear.

overall_design: RNA-sequencing of fifty dsGFP- or dsNat10-injected morulae were performed by Beijing Genomics Institute (Shenzhen, China). The library preparation was performed following the SMARTseq2 protocol. After library construction, all samples were sequenced on DNBSEQ platform with paired-end. The raw reads were trimed using trim_galore. The clean reads were mapped to mouse genome (GRCm38) using HISAT with default parameter. The reads of each gene were counted by Htseq-count.

first: Mengyun

last: Wang

first: Qiong

last: Wu


title: Spatiotemporal hepatocyte heterogeneity impacts in vivo gene engineering

first: Stefano

last: Beretta

overall_design: Refer to individual Series


title: Multi-omic profiling of cutaneous leishmaniasis infections reveals microbiota-driven mechanisms underlying disease severity

status: Public on Jul 27 2023

city: Philadelphia

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

summary:
Leishmania braziliensis infection results in inflammation and skin injury, with highly variable and unpredictable clinical outcomes. Here, we investigated the potential impact of microbiota on infection-induced inflammatory responses and disease resolution by conducting an integrated analysis of the skin microbiome and host transcriptome on a cohort of 62 L. braziliensis-infected patients. We found that overall bacterial burden and microbiome configurations dominated with Staphylococcus spp. were associated with delayed healing and enhanced inflammatory responses, especially by IL-1 family members. Dual RNA-seq of human lesions revealed that high lesional S. aureus transcript abundance was associated with delayed healing and increased
expression of IL-1β. This cytokine was critical for modulating disease outcome in L.
braziliensis-infected mice colonized with S. aureus, as its neutralization reduced pathology and inflammation. These results implicate the microbiome in cutaneous leishmaniasis disease outcomes in humans and suggest host-directed therapies to mitigate the inflammatory consequences.

overall_design: Whole transcriptome bulk RNA-seq biopsies collect from the lesions of patients with cutaneous leishmaniasis

first: Daniel

middle: P

last: Beiting

first: Phillip

last: Scott

first: Elizabeth

last: Grice


title: Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [miRNA-seq]

status: Public on Jul 15 2023

city: Wuhan

first: Yiqi

state: State...

address: Shizishan Street

institute: Huazhong Agricultural University, China

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we performed whole-transcriptome sequencing of bladder tumors and their peritumoral tissues to identify differentially expressed circ-, lnc-, mi-, and mRNAs.

overall_design: Whole trascriptome analysis of total RNA data on circRNA, lncRNA and mRNA for bladder cancer tissues and normal tissues.

first: Sanhe

last: Liu

first: Shaozhong

last: Wei

first: Zhiqiang

last: Dong


title: Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer


title: Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice

status: Public on Jul 14 2023

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary:
We investigated the effects of per- and polyfluroralkyl substance exposure on FRG liver-chimeric humanized mice on a C57Bl/6 background. These PFAS included PFOA, PFOS, and GenX. These mice were exposed to water ad libitum for 28 days to reach human relevant serum concentrations.
We then performed RNA-Sequencing on isolated whole liver lysate to determine differentially expressed genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PFOA, PFOS, and GenX (n of 3 per group) exposed humanized mice and compared to the control group. cDNA was sequenced using 2 lanes targeting 25 million reads/sample.

first: Sumedha

last: Gunewardena

first: Udayan

last: Apte


title: Whole Transcriptome Sequencing Identifies a Competitive Endogenous RNA Network that Regulates the Immunity of Bladder Cancer [RNA-seq]


title: Oncogene EVI1 Drives Acute Myeloid Leukemia Via a Targetable Interaction with CTBP2 [ChIP-Seq]

status: Public on Jul 12 2023

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

institute: Erasmus MC

summary: Acute myeloid leukemia (AML) driven by the activation of EVI1 due to chromosome 3q26/MECOM rearrangements is incurable with current chemotherapy regimens. Insight into the mechanism by which EVI1 drives myeloid transformation is needed to target EVI1 in those leukemias. Here we demonstrate recurrent interaction of CTBP1/2 with a unique PLDLS motif in EVI1, which is indispensable for leukemic transformation of 3q26/MECOM rearranged AML. A PLDLS competitor construct outcompetes EVI1 to CTBP1/2 binding and inhibits AML proliferation in xenotransplant models. This proof-of-concept study opens the possibility to target one of the most incurable forms of AML using specific inhibitors directed to EVI1/CTBP1/2 interaction. Our findings have important implications for other tumour types with aberrant expression of EVI1 or other oncogenic transcription factors that also depend on CTBP1/2 interaction.

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) for EVI1, CTBP2, various transcription factors (MYCB, p300, RUNX1, ERG) and histone modifications (H3K27ac, H3K27me3, H3k9me3) in the 3q26-rearranged leukemia cell lines MUTZ3 and MOLM1. This was done in three different sets of experiments: a) in untreated and unmodified MUTZ3; b) in MUTZ3 that expresses either PLDLS or PLASS, peptides that interfere with EVI1/CTBP interaction; c) in a modified MUTZ3 cell line (1675) transduced with a lentiviral vector with Doxycycline (Dox)-inducible PLDLS.

first: Dorien

last: Pastoors

first: Roger

last: Mulet

first: Eric

last: Bindels


title: AGO10-dependent gene expression under cytokinin treatment and control conditions

status: Public on Jul 01 2023

city: Tübingen

first: Sebastian

last: Wolf

state: Baden-Württemberg

address: Auf der Morgenstelle 32, ZMBP, ZMBP

institute: ZMBP, Universität Tübingen

summary: To investigate the role of AGO10 in the buffering of cytokinin responses we grew the ago10-1 mutant and the Col-0 wildtype on plates for six daysbefore treting with mock solution or cytokinin for 2 hours. Then root tips excised and RNA was extracted using a commercial kit.

overall_design: Comparative gene expression analysis of Col-0 and ago10-1 root tips grown on half-strength MS medium mock treated or treated with the synthetic cytokinin 6-Benzyladenine

first: Liese

last: Schnurbusch


title: Extracellular Vesicle miRNA response to resistance exercise training in men and women

status: Public on Jun 30 2023

city: Pittsburgh

first: Brad

last: Nindl

address: 3860 South Water

institute: University of Pittsburgh

summary: Profile of small RNA contents of plasma Evs in men and women at rest and after a bout of acute resistance exercise both before and after 12 weeks of chronic resistance exercise training. We profile how acute and chronic weight training imapcts EV small RNA contents and how this differs in men and women.

overall_design: Longitudinal 12 week exercise training study, with four different time points

first: Chris

last: Kargl


title: LKRSDH-dependent histone modifications of insulin-like peptide sites contribute to age-related circadian rhythm changes

status: Public on Jun 26 2023

city: Beijing

first: Pengfei

last: Lv

address: No. 2, Old Summer Palace West Road

institute: China agricultural university

summary: To investigate the role of epigenetic modifications H3K27me3 and h3r17me2 in aging.

overall_design: To clarify the relationship between H3R17me2 and H3K27me3, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments targeting H3R17me2 and H3K27me3 in 3-day-old w1118 control, 3-day-old LKRSDHMB01942 mutant, 40-day-old w1118 control and 40-day-old LKRSDHMB01942 mutant flies to obtain maps of H3R17me2 and H3K27me3 distribution along chromosomes.


title: The quorum-sensing agr system protects Staphylococcus aureus from oxidative stress

status: Public on Jun 20 2023

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

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


title: Transcriptomic profiling of D37712 Salmonella enterica strain under infection-relevant conditions

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

summary: RNA-sequencing of sublineage 2.2 Salmonella Enterica strain D37712 under in vitro growth conditions (EEP, MEP, LEP, ESP, LSP, 25ºC, NaCl, low Fe2+ shock, low Mg2+ shock, anaerobic shock, anaerobic growth, oxygen shock, NonSPI2, InSPI2, peroxide shock, and nitric oxide shock) and murine RAW265.7 macrophages.

overall_design: Three biological replicates in ESP, anaerobic growth, NonSPI2, and InSPI2, and a single experiment in EEP, MEP, LEP, ESP, LSP, 25ºC, NaCl, low Fe2+ shock, low Mg2+ shock, anaerobic growth, oxygen shock, NonSPI2, peroxide shock, and nitric oxide shock; and two biological replicates of  anaerobic shock.

first: Rocío

last: Canals

first: Benjamin

last: Kumwenda

first: Carsten

last: Kröger

first: Xiaojun

last: Zhu

first: Nicolas

last: Wenner

first: Blanca

last: Perez-Sepulveda

middle: V

first: Karsten

last: Hokamp

first: Melita

last: Gordon

first: Jay

last: Hinton


title: A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Motor neurons (MNs) are the cellular targets of multiple adult-onset diseases. Because distinct MN populations differ in disease susceptibility, it is important to define in animal models the degree of diversity within adult MNs. Here, we generated a comprehensive molecular resource of adult MNs in C. elegans. Single-cell RNA-sequencing of 12,603 cells revealed that all eight morphologically defined MN classes of the ventral nerve cord and its flanking ganglia subdivide into 29 distinct subclasses, almost quadrupling the degree of their previously described diversity. We find that four of the six C. elegans Hox genes delineate most, but not all MN subclasses. Strikingly, all 29 subclasses are delineated by unique expression codes of neuropeptide genes and receptors, critical for extra-synaptic (wireless) signaling. Leveraging the C. elegans connectome, we found a strong correlation between molecularly and connectivity defined MN subclasses. Beyond providing a valuable resource and searchable database (spinalcordatlas.com), our study identifies Hox and neuropeptide codes as key molecular descriptors of adult MN diversity, codes likely conserved in MNs across species.

overall_design: Ventral nerve cord MNs were isolated from two strains of worms. Two samples were collected from both CZ631 juIs14 [acr-2::GFP] and KRA257 kasIs2 [lin-39p::RFP] worms. MNs were isolated by FACS and analyzed by 10X Genomics 3' single-cell RNA sequencing.

first: Seth

last: Taylor

first: Jayson

last: Smith

first: Paschalis

last: Kratsios


title: Single-cell RNA-sequencing of human innate lymphoid cells (ILCs) and natural killer (NK) cells in the vascular and tissue compartment of the lung in MISTRG humanized mice

status: Public on Jun 27 2023

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

summary: ILCs and NK cells are innate immune cells that act as sentinels of healthy tissue function. However, it is largely unknown how ILCs and NK cells are recruited into distinct tissue niches and how they adapt to specific anatomical niches within tissues. Using an in-vivo model for human immune cells (MISTRG humanized mice), we determined the gene signatures of human ILCs and NK cells in the vascular and tissue niche of the lung by single-cell RNA-sequencing.

overall_design:
We combined intravascular cell labeling with single-cell RNA-sequencing to define the gene signatures of human lung ILCs and NK cells in the vascular and tissue compartment of MISTRG mice engrafted with human CD34+ hematopoietic stem and progenitor cells (HSPCs).

***RAW data not provided due to Swedish legislation and European GDPR***

first: Arlisa

last: Alisjahbana

first: Imran

last: Mohammad

first: Yu

last: Gao

first: Elza

last: Evren


title: The quorum-sensing agr system protects Staphylococcus aureus from oxidative stress  (overnight growth)

first: Gregory

last: Putzel

summary: The agr quorum-sensing system clearly links Staphylococcus aureus metabolism to virulence, but little is known about how agr alters metabolism to affect cell survival during severe stress. Recently, we reported that agr activity increases survival of bacteria during treatment with lethal concentrations of H2O2, a crucial host defense against S. aureus.  Here we report that protection by agr extends to growth resumption during the exit from stationary phase. The data indicate that the agr functionality of a cell’s ancestor affects stress-resiliency after resuming growth.  Protection against killing by H2O2 depended on the agr effector molecule RNAIII and Rot, a transcription factor targeted by RNAIII. Expression data revealed that Δagr strains shift to fermentation, suggesting that agr promotes aerobic respiration. Epistasis between mutation of agr and sortase, which anchors surface proteins to the cell wall, suggested that reduced killing by H2O2 of wild-type agr strains acts through down-regulation of surface proteins that perturb respiration. Respiration generates reactive oxygen species (ROS), moderate amounts of which can protect from subsequent challenge by lethal concentrations, explaining agr-mediated protection against subsequent lethal H2O2 doses. Increased survival of wild-type agr cells in response to H2O2 required sodA, which dismutates O2-  to H2O2, suggesting that sodA helps induce the low, protective levels of ROS triggered by agr.  Additionally, detrimental effects of the Δagr mutation require ahpC, which functions to decrease the intracellular level of H2O2.  Deletion of ahpC or sortase attenuated neutrophil-mediated killing of Δagr strains, demonstrating the importance of priming in anticipation of impending immune attack.

overall_design: For each combination of genotype (YF13 vs BS1302) and treatment (H202 vs untreated), three biological replicates were used.

first: Magdalena

last: Podkowik

first: Bo

last: Shopsin


title: The quorum-sensing agr system protects Staphylococcus aureus from oxidative stress  (5 hour growth)

overall_design: Six samples both LAC wild type and LAC agr KO


title: Itaconate enhances oncolytic virotherapy via multitarget inhibition of antiviral and inflammatory pathways

status: Public on Jun 15 2023

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

institute: Aarhus University

summary: 4 octyl itaconate (4-OI) is a known anti-inflammatory chemical that activates Nrf2 signaling. Here, we are exploring the capacities of 4-OI to promote the spread of oncolytic Vesicular Stomatitis Virus (VSVd51M) in pLenti control kidney adenocarcinoma 786-O cell line and in Nrf2 knock out 786-O.

overall_design: 786-O empty vector (pLenti) control and CRISPR-edited NRF2-KO cells were seeded in 12 well plate and treated with 4-OI for 24 hours (75 uM). Next day, cell were infected with VSVd51M at an MOI of 0.01. At 17 hours post-infection, RNA was extracted using the high pure RNA isolation kit (Roche, 11828665001) and frozen at -70 °C. RNA sequencing was performed in collaboration with BGI Europe Genome Center.

first: Naziia

last: Kurmasheva

first: Maureen

last: Higgins

first: Laureano

last: de la Vega

last: Olagnier


title: Phototherapy restores deficient type I interferon production and enhances antitumor responses in mycosis fungoides

status: Public on Jun 14 2023

city: Boston

first: Rachael

last: Clark

state: MA

address: 221 Longwood Ave EBRC 501

department: Dermatology

institute: Brigham and Women's Hospital


title: The Factor Inhibiting HIF regulates T cell differentiation and anti-tumor efficacy

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

institute: University of Cambridge

summary: T cells must adapt to variations in tissue microenvironments; these adaptations include the degree of oxygen availability. The hypoxia-inducible factor (HIF) transcription factors control much of this adaptation, and thus regulate many aspects of T cell activation and function. The HIFs are in turn regulated by oxygen-dependent hydroxylases: both the prolyl hydroxylases (PHDs) which interact with the VHL tumor suppressor and control HIF turnover, and the asparaginyl hydroxylase known as the Factor inhibiting HIF (FIH), which modulates HIF transcriptional activity. To determine the role of this latter factor in T cell function, we generated T cell-specific FIH knockout mice. We found that FIH regulates T cell fate and function in a HIF-dependent manner and show that the effects of FIH activity occur predominantly at physiological oxygen concentrations. T cell-specific loss of FIH boosts T cell cytotoxicity, augments T cell expansion in vivo, and improves anti-tumor activity in mice. Specifically inhibiting FIH in T cells may therefore represent a promising strategy for cancer immunotherapy.

overall_design: RNA expression was measured by RNA-Seq at day 3 following activation of MACS-sorted mouse CD8+ T cells from Hif1an-floxed dLck Cre- or Vhl-floxed dLck Cre- (‘WT’) , Hif1an-floxed dLck Cre+ (‘FIH KO’), Vhl-floxed dLck Cre+ (‘VHL KO’) and Hif1an--floxed/Vhl--floxed dLck Cre+ (‘FIH/VHL KO’) mice using anti-CD3/anti-CD28 Dynabeads in the presence of recombinant human IL-2 for 3 days.

first: Pedro

last: Cunha

last: Velica

first: Lena

last: Krause

first: Madara

last: Brice

first: Laura

last: Barbieri

first: Milos

last: Gojkovic

first: Iosifina

last: Foskolou

first: Helene

last: Rundqvist

first: Randall

last: Johnson


title: Phototherapy restores deficient type I interferon production and enhances antitumor responses in mycosis fungoides [I]

summary: NanoString based gene expression data from skin biopsies from nine mycosis fungoides patients before and after phototherapy as well as four healthy donor skin as a comparator

overall_design: RNA was extracted from skin biopsies taken from nine mycosis fungoides patients before and after treatment with phototherapy (PUVA) as well as from four skin biopsies from healthy donors as a comparator.

first: Zizi

last: Yu

first: Pablo

last: Vieyra-Garcia

first: Theresa

last: Benezeder

first: Jack

last: Crouch

first: John

middle: T

last: O'Malley

first: Phillip

last: Devlin

first: Ahmed

last: Gehad

first: Qian

last: Zhan

first: Johann

last: Gudjonsson

first: Mrinal

last: Sarkar

first: Michelle

last: Kahlenberg

first: Nega

last: Gerard

first: Jessica

last: Teague

first: Thoma

last: Kupper

first: Nicole

last: LeBoeuf

first: Cecilia

last: Larocca

first: Marianne

last: Tawa

first: Bohdan

last: Pomahac

first: Simon

last: Talbot

first: Dennis

last: Orgill

first: Peter

last: Wolf


title: Phototherapy restores deficient type I interferon production and enhances antitumor responses in mycosis fungoides [II]

first: Rachael

last: Clark

first: Zizi

last: Yu

first: Pablo

last: Vieyra-Garcia

first: Theresa

last: Benezeder

first: Jack

last: Crouch

first: John

last: O'Malley

middle: K


title: Analysis of  gene expression of LPS-stimulated monocyte from CAD patients

status: Public on Jun 11 2023

city: Heidelberg

first: Chang

last: Lu

address: Im Neuenheimer Feld 130

institute: Heidelberg University

summary:
Data for the publication 'Identification of a Gene Network Driving the Attenuated Monocyte Response to Lipopolysaccharide of Hypertensive Coronary Artery Disease Patients'.
Dissection of the impact of CVD risk factors on monocyte phenotype at the gene expression level, and in particular on their response to trauma and infection response.
For any questions about the dataset, please contact Erik Biessen‘s Lab, Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands

overall_design: Total RNA obtained from LPS stimulated monocytes of CAD patients.

first: Anton

last: Jan van Zonneveld

first: J

middle: W

last: Jukema

first: Adriaan

last: Kraaijeveld

first: Johan

last: Kuiper

first: Gerard

last: Pasterkamp

first: Erik

last: Biessen

first: Marjo

last: Donners


title: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape [CUT&RUN]

status: Public on Jun 08 2023

city: Chicago

first: Alexandra

last: Bradu

address: 924 East 57th Street

institute: University Of Chicago

summary: T cells trigger non-specific signaling pathways to elicit specialized effector functions to eliminate pathogens and cancers. Chromatin accessibility at T effector loci prior to antigen encounter poises cells to couple antigen recognition to the activation of lineage-specific responses. Here, by tracing the chromatin accessibility profiles unique to T effector functions during development, we find that the majority of T effector loci become accessible prior to antigen receptor expression. Epigenomic feature analysis, biochemical studies, and inducible perturbations identified two mechanistic linchpins: the physical association of the mSWI/SNF remodeling complex to the pleiotropic transcription factor (TF) RUNX1, and the cooperativity between RUNX1 and lineage-defining TFs PU.1 and BCL11B that respectively facilitate the establishment and maintenance of chromatin accessibility at T effector loci in early thymocyte progenitors. These findings reflect a design principle that allows distinct cell types to use the same signaling pathways to execute disparate roles which collectively orchestrate the immune response.

overall_design: CUT&RUN for BAF155 in wild type and Bcl11b cKO murine thymocytes.

first: Noah

last: Gamble

first: Jason

last: Caldwell

first: Joshua

last: McKeever

first: Olubusayo

last: Bolonduro

first: YeEun

last: Kim

first: Benjamin

last: Parks

first: Sandy

last: Klemm

first: William

last: Greenleaf

first: Gerald

last: Crabtree

first: Andrew

last: Koh


title: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape [ATAC-seq]

overall_design: ATAC-seq profiling was performed at various stages of development in wild-type untreated, wild-type FK506-treated, Smarca4 cKO, Bcl11b cKO, and Runx1 cKO murine thymocytes.


title: RAVER1 interconnects TGFB signaling, EMT and miR/RISC activity by modulating alternative splicing [A549_RAVER1_KD]

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: The depletion and deletion of RAVER1 substantially impairs the 2D-proliferation of tumor cells, vitality in 3D cell models and the growth of subcutaneous xenografts in nude mice. Disturbance of RAVER1 affects various cancer hallmark pathways manifesting in deregulated E2F/DREAM-controlled transcription and broadly hampered microRNA-dependent gene silencing. In carcinoma-derived cell models, impaired control by microRNAs (miR) leads to the upregulation of various tumor suppressors like BTG2, which is suppressed by the most abundant oncomiR 21-5p.

overall_design: Poly-A RNA-seq of lung cancer-derived A-549 cells, transfected with either control siRNAs (siC) or siRNAs directed against RAVER1 or PTBP1. Three biological replicates per condition

first: Alice

last: Wedler

first: Stefan

last: Hüttelmaier


title: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape

status: Public on Jun 07 2023

relation:
SuperSeries of: GSE234329
SuperSeries of: GSE234330
SuperSeries of: GSE248159

overall_design: Refer to individual Series


title: A ligation-independent sequencing method reveals tRNA fragments with blocked 3' termini

status: Public on Jun 06 2023

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Despite the numerous sequencing methods available, the vast diversity in size and chemical modifications of RNA molecules makes the capture of the full spectrum of cellular RNAs a difficult task. By combining quasirandom hexamer priming with a custom template switching strategy, we developed a method to construct sequencing libraries from RNA molecules of any length and with any type of 3’ terminal modification, allowing the sequencing and analysis of virtually all RNA species. Ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to comprehensively characterize changes in small non-coding RNAs and mRNAs simultaneously, with performance comparable to separate dedicated methods. With LIDAR, we comprehensively characterized the coding and non- coding transcriptome of mouse embryonic stem cells, neural progenitor cells, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared to traditional ligation-dependent sequencing methods, and uncovered the presence of tDRs with blocked 3’ ends that had previously escaped detection. Our findings highlight the potential of LIDAR to systematically detect all RNAs in a sample and uncover new RNA species with potential regulatory functions.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Gene expression in mES cells +/- serum, NPC, and sperm using traditional pA sequencing, LIDAR, TAKARA, or NEB ligation-based sequencing.

first: Alessandro

last: Scacchetti

first: Roberto

last: Bonasio


title: Identification of Ligand-Receptor Pairs that Drive Human Astrocyte Development

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

summary: We tested a group of five neuronally-secreted ligands and validated their synergistic contributions to astrocyte development within both human cortical organoids and primary fetal tissue.

overall_design: We performed differential gene expression and fold change analysis using data obtained from targeted and bulk RNA-seq of purified fetal astrocyte cell cultures and 3 different organoid lines at three time points.

first: Anna

last: Voss

first: Samantha

last: Lanjewar

first: Maureen

last: Sampson

first: Alexia

last: King

last: Hill

first: Anson

last: Sing

first: Caitlin

last: Sojka


title: Comparative transcriptomic analysis revealing the potential mechanisms of erythritol-caused mortality and oviposition inhibition in Drosophila melanogaster

status: Public on Jun 01 2023

city: chongqiong

first: Lei

last: Li

address: central road daxuecheng

institute: CHONGQIONG NORMAL UNIVERSITY

summary: To study the causes of Drosophila melanogaster death and disorder of reproduction caused by erythritol feeding

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of Drosophila melanogaster fed by ordinary culture medium with(T) or without erythritol(CK) at two time points(3 days and 4 days).

Please note that raw data has been lost and thus is not provided.

first: lei


title: STAT3 protects hematopoietic stem cells from intrinsic interferon signaling and loss of long-term blood-forming activity

status: Public on Jun 02 2023

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: The transcriptional regulator signal transducer and activator of transcription 3 (STAT3) has a well-established anti-inflammatory function in mature myeloid cells. This role, however, has precluded an understanding of STAT3 function in hematopoietic stem and progenitor cells (HSPCs), as Stat3 deletion in the hematopoietic system induces systemic inflammation, which can impact HSPC activity. Thus, novel approaches to uncouple STAT3 function in HSPCs from the effects of systemic inflammation are needed. To address this, we established competitive mixed bone marrow (BM) chimeric mice with CreER-mediated conditional Stat3 deletion in 20% of the hematopoietic compartment. After confirming a lack of detectable inflammation in mice with Stat3-deficient BM, we found that, in contrast to Stat3-sufficient controls, Stat3-deficient HSPCs had impaired hematopoietic activity and failed to undergo expansion in BM. Single-cell RNA sequencing of Lin-ckit+Sca1+ (LSKs) BM cells revealed an altered transcriptional landscape in Stat3-deficient hematopoietic stem cells (HSCs) and multipotent progenitors, as evidenced by the intrinsic activation of cell cycle, stress response, and interferon signaling pathways. Consistent with their deregulation, Stat3-deficient LSKs accumulated γH2AX over time. Following secondary BM transplantation, Stat3-deficient HSPCs failed to reconstitute peripheral blood effectively, indicating a severe functional defect in the HSC compartment. Our results reveal essential roles for STAT3 in HSCs and suggest the potential for using targeted synthetic lethal approaches with STAT3 inhibition to remove defective or diseased HSPCs.

overall_design: Lin-ckit+Sca1+ cells (LSKs) were purified by fluorescence-activated cell sorting (FACS) from mixed bone marrow chimeric mice and processed for single cell RNA sequencing. The mixed bone marrow chimeric mice contained Stat3-sufficient CreER+ cells and wild-type competitor cells (control group), or Stat3-deficient CreER+ Stat3f/f cells and wild-type competitor cells (test group) in a 1:1 ratio. Stat3 gene deletion was enforced by tamoxifen treatment of the bone marrow chimeric mice 8 weeks prior to LSK purification.

first: Bhakti

last: Patel

first: Simona

last: Colla

first: Stephanie

last: Watowich


title: Differential binding of PARP-1 domains  (ZNII-YFP ChIP-seq)

status: Public on May 25 2023

city: Grand Forks

first: Gbolahan

last: Bamgbose

state: ND

address: 501 N Columbia Rd

department: Biomedical Sciences

institute: University of North Dakota

summary: We interrogated the differential binding of PARP-1 domains (ZnI, ZnII, AD-WGR) and a ZnI mutant in Drosophila via ChIP-seq of third-instar larvae.

overall_design: We performed ChIP-seq using third-instar larvae expressing ZNII-YFP and Control animals (3 biological replicates per group).

first: Sarah

last: Johnson

first: Tulin

last: Alexei


title: Differential binding of PARP-1 domains  (AW-YFP ChIP-seq)

overall_design: We performed ChIP-seq using third-instar larvae expressing AW-YFP (Automodification and WGR domains) and Control animals (3 biological replicates per group).