title: Compartmentalization of human B cell responses in early life through induction of bronchus-associated lymphoid tissue

city: New York

first: Peter

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Infants and young children are more susceptible to common respiratory pathogens compared to adults, but can fare better against novel pathogens like SARS-CoV-2. The mechanisms by which infants and young children mount effective responses to respiratory pathogens are unknown. Here, we demonstrate through study of lungs and lung-associated lymph nodes (LLN) from infant and pediatric organ donors, aged 0-13 years, that bronchus-associated lymphoid tissue (BALT), develops in lungs during the first year of life. BALT structures, consisting of B cell follicles and T cell zones, increase in numbers in the early years, and subsequently decrease over childhood coincident with accumulation of memory T cells in the lung. Early life BALT contains germinal centers and supports B cell differentiation, clonal expansion, somatic hypermutation, and immunoglobulin class switching. High dimensional flow cytometry reveals seeding of lungs by newly formed B cells (transitional cells) during infancy coincident with the timing of maximal BALT formation. We further demonstrate increased lung-localized B cell responses during respiratory virus infection in infants. Together, our findings provide novel evidence for BALT as an early life adaptation for mobilizing in situ immune protection to the diverse respiratory challenges during this formative life stage.

overall_design: CITE-seq/scBCR-seq

first: Rei

first: Joshua

last: Gray

first: Donna

last: Farber


title: NF-kB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells [ATAC-seq]

status: Public on May 25 2023

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The NF-kB family of transcription factors orchestrates signal-induced gene expression in a diversity of cell types. Cellular responses to NF-kB activation are regulated at the level of cell- and signal-specificity, as well as differential use of family members (subunit specificity). Here we used time-dependent multi-omics to investigate selective functions of Rel and RelA, two closely related NF-kB proteins, in primary B lymphocytes activated via the B cell receptor. Despite large numbers of shared binding sites genome wide, Rel and RelA directed kinetically distinct cascades of gene expression in activated B cells. Single-cell RNA-Seq revealed marked heterogeneity of Rel- and RelA-specific responses and sequential binding of these factors was not a major mechanism of protracted transcription. Moreover, nuclear co-expression of Rel and RelA led to functional antagonism between the two factors. By rigorously identifying target genes of each NF-kB subunit, these studies provide insights into exclusive functions of Rel and RelA in immunity and cancer.

overall_design: Pooled splenic B cell from 5 C57BL/6 mice (#000664, The Jackson Laboratory) (WT) were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 0, 1, 4, or 18 hour (ATAC_0h, ATAC_1h, ATAC_4h, and ATAC_18h, respectively, N = 2 mice per condition). Nuclei were isolated and processed for ATAC-Seq.

first: Mingming

last: Zhao

first: Cheryl

middle: A

last: Sherman-Baust

first: Amit

last: Singh

first: Mary

last: Kaileh

first: Krystyna

last: Mazan-Mamczarz

first: Jamie

last: Joy

first: Yongqing

last: Zhang

first: Kevin

middle: G

last: Becker

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

first: Ranjan

last: Sen


title: NF-kB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: NF-kB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells [ChIP-seq]

overall_design: A total of 22 B cell samples from WT C57BL/6 mice (#000664, The Jackson Laboratory) were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 1, 4, or 18 hours respectively, or left untreated. ChIP-Seq was performed using anti-RelA antibody (sc-372, Santa Cruz; N=2 for each of the 0, 1, and 4 hour time points), anti-Rel antibody (sc-71, Santa Cruz; N=2 for each of the 0, 1, and 18 hour time points), anti-H3K27ac antibody (ab4729, Abcam; N=2 for the 0 hour time point), anti-H3K4me1 antibody (ab8895, Abcam; N=2 for the 0 hour time-point) and anti-H3K4me3 antibody (ab8580, Abcam; N=2 for each of the 0, 1, and 18 hour time points).


title: NF-kB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells [scRNA-seq]

overall_design: Twelve 10,000 targeted B cell samples from floxed RelA mice (RelA-flfl (gift from Harmel-Laws Steinbrecher), N=1 for 0, 1, and 4 hour time points), RelA conditional knock-out (RelA-cKO (RelA-flfl x Cd19-cre) (006785, The Jackson Laboratory) mice, N=1 for 0, 1, and 4 hour time points), Rel knock-out mice (Rel-KO (gift from Hsia Cheng), N=1 for 0, 1, and 18 hour time points), and wildtype C57BL/6 mice (WT (006785 - The Jackson Laboratory), N=1 for each 0, 1, and 18 hour time points) were processed though the 10X Genomics 3' Gene Expression V.3.0 pipeline.


title: NF-kB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells [RNA-seq]

overall_design: A total of 44 splenic B cell sample pools were isolated from 5 wildtype C57BL/6 mice (#000664, The Jackson Laboratory) (WT), 5 RelA fl/fl mice (gift from Harmel-Laws Steinbrecher) (RelA-flfl), 5 RelA cKO mice (cross between RelA fl/fl and Cd19-cre (006785, The Jackson Laboratory) (RelA cKO), or 5 Rel KO mice (gift from Hsia Cheng) (Rel KO). Each sample was treated with 10μg/ml goat anti-mouse IgM Fab`2 for 0, 1,  4, or 18 hour (N = 2 per condition). In addition, WT mice were pre-treated for 1 hour with 1uM BAY 11-7082 (BAY) and treated with 10μg/ml goat anti-mouse IgM Fab`2 for 1,  4, or 18 hours (N = 2 per condition). RNA was extracted from all samples and processed through RNA-Seq.


title: Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct [RNA-seq]

status: Public on May 24 2023

city: Dallas

first: Michael

middle: K

last: Rosen

state: TX

address: 6001 Forest Park Rd., ND8.124

department: Biophysics

institute: UT Southwestern Medical Center

summary: Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma (NC). Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.

overall_design: Comparative gene expression analysis of RNA-seq data for HEK293 T-Rex Flp-In - based stable cell lines, expressing BRD4-NUT or its mutants or BRD4-p300 or its mutants, in a doxycycline-inducible manner.

first: Martyna

last: Kosno

first: Simon

middle: L

last: Currie

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct


title: Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HEK293 T-Rex Flp-In - based stable cell lines, expressing BRD4-NUT, BRD4-NUT(MIN) or BRD4-p300, in a doxycycline-inducible manner. ChIP-seq performed using anti-NUT antibody for BRD4-NUT and BRD4-NUT(MIN) - expressing cell lines. ChIP-seq performed using anti-histone H3K27 acetyl antibody for BRD4-NUT(MIN) and BRD4-p300 - expressing cell lines.


title: Single-Cell Transcriptomics of Epstein-Barr Virus and Human Herpesvirus 6 Coinfection

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

summary: Epstein-Barr virus (EBV) and human herpesvirus 6 (HHV-6) infection is widespread among people. Here I describe single-cell RNA sequencing of two lymphoblastoid cell lines harboring both episomal EBV and inherited chromosomally integrated HHV-6. Rare instances of HHV-6 expression appear enriched with EBV reactivation.

sample_organism:
Homo sapiens
human gammaherpesvirus 4
Human betaherpesvirus 6A
Human betaherpesvirus 6B

overall_design: Single-cell RNA-seq transcriptomes of lymphoblastoid cell lines coinfected with Epstein-Barr virus and human herpesvirus 6


title: Comprehensive profiing of clinical JAK inhibitors in myeloproliferative neoplasms

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

overall_design: HEL cells were treated in duplicate for 4 hour or 48 hours with DMSO control or 500nM of JAK inhibitors

first: Stephen

middle: T

last: Oh


title: Neoantigen-specific stem cell memory-like CD4+ T cells mediate immunotherapy of solid tumors

city: La Jolla

first: Spencer

last: Brightman

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: The expansion of neoantigen (NeoAg)-specific T cells often accompanies clinical responses to immunotherapies, highlighting the importance of these cells for antitumor immunity. While NeoAg-specific CD8+ T cells have been broadly studied, the role of NeoAg-specific CD4+ T cells is less well understood. To study the antitumor mechanisms of NeoAg-specific CD4+ T cells, we sorted single CD4+ T cells specific for an epitope derived from a mutated clathrin heavy chain gene (CLTCH129>Q) expressed by the murine squamous cell carcinoma VII (SCC VII) tumor. T cell receptor (TCR) sequencing analysis revealed the presence of four distinct TCR clonotypes and expression of these TCRs in primary cells was sufficient to confer preferential recognition of CLTCH129>Q as compared to the corresponding wildtype CLTC epitope. Despite differences in TCR avidity, both moderate and high avidity CD4+ T cells were capable of proliferating to similar levels in response to tumor antigen in vivo and enhancing primary tumor immunity in a CD8+ T cell- and CD40L-dependent manner. Finally, we demonstrate that adoptive cellular therapy (ACT) with T stem cell memory (TSCM)-like CLTCH129>Q-specific CD4+ T cells differentiated ex vivo in culture with IL-7 and IL-15 promotes therapeutic tumor immunity associated with enhanced T cell persistence, maintenance of adoptively transferred TSCM-like cells in the tumor-draining lymph node (tdLN), and activation of CD8+ T cells in the tdLN. Overall, these findings illuminate the mechanistic role of NeoAg-specific CD4+ T cells in tumor immunity, provide insights into the impact of TCR avidity on the helper functions of CD4+ T cells, and highlight the therapeutic potential of ACT with TCR-engineered CD4+ T cells.

overall_design: Neoantigen-specific TCR engineered CD4+ T cells cultured in either IL-7 and IL-15 or IL-2 were adoptively transferred into SCC VII tumor-bearing mice one day following cyclophosphamide preconditioning. 9 days following adoptive transfer, tumors and lymph nodes from 2 replicate animals per condition were collected, single cell suspensions were made, and adoptively transferred CD90.1+ CD4+ T cells were sorted from each for RNA-sequencing

middle: E

first: Leila

last: Chihab


title: Thermoneutrality and severe malaria: investigating the effect of warmer environmental temperatures on the inflammatory response and disease progression

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

summary: Most studies using murine disease models are conducted at a housing temperature of 20ºC that is sub-optimal (ST) for mice, eliciting changes in metabolism and response to disease. Experiments performed at a thermoneutral temperature (TT) of 37ºC have revealed an altered immune response to pathogens and experimental treatments in disease models (e.g. cancer, obesity, Alzheimer’s disease). These alterations in metabolic activity have implications for the use of murine models to understand human diseases and their translation to clinical research. How such conditions affect the inflammatory response to infection with Plasmodium berghei ANKA (PbA) and subsequent disease progression is unknown.  We hypothesized that changes in environmental temperature modulate immune cells and modify host response to malaria disease. To test this hypothesis, we conducted two sets of experiments to determine: (1) the inflammatory response of bone-marrow derived macrophages (BMDM) to infectious agents at different environmental temperatures and (2a) the inflammatory response to malarial agents injection in a peritonitis model and (2b) disease progression in PbA-infected mice at TT compared to ST.  Firstly, BMDMs were incubated and stimulated with LPS at a fever-like temperature (FT; 39ºC), TT (37ºC) or low-temperatures (LT; 30ºC) mimicking ST for 6, 12 and 24 hours. We observed an that BMDMs released increased inflammation markers (i.e. nitric oxide and pro-inflammatory cytokine at FT and TT compared to LT, with an increase overtime.  Secondly, C57BL6 mice were acclimatized for 3 weeks at TT (28 – 31ºC) or ST (20 – 22ºC). In one study, mice were injected intraperitoneally with nHZ or Leishmania at both temperatures, and immune cells were counted and subtyped from the peritoneal cavity (PEC) fluid. Cytokine concentrations and extracellular vesicle (EV) profiles were also determined from the PEC. Apart from Leishmania injection resulting in decreased cell recruitment and a higher phagocytosis of nHZ in mice housed at TT, we did not observe many temperature-based differences. We found 398 upregulated and 293 downregulated pro-inflammatory genes in mice injected with nHZ, that were similar to those previously elicite with Leishmania injections, at both temperatures. EV profile did not differ significantly at TT compared to ST but we report the presence of proteosome-derived and platelet-derived EVs in a murine parasitic murine model at both temperatures.  In another study, mice were injected with luciferase-tagged PbA-infected RBCs and monitored until death. We observed metabolic changes (i.e. lower body weight and temperature loss) in mice housed at TT but these did not result to noticeable changes in survivability, parasite organ sequestration or serum cytokine levels compared to ST.   To our knowledge, these experiments are the first to investigate the effect of thermoneutrality on a malaria murine model. Despite results suggesting that thermoneutrality does not significantly alter severe malarial disease progression or host inflammatory response to parasitic agents, we found important metabolic difference in mice housed at TT. Our results offer insights on how thermoneutrality might impact a severe malaria murine model and directions for more targeted investigations. This constitutes a first step in elucidating factors that may explain the lack of translatability to clinical trial.

overall_design: Total RNA extracted from peritoneal cavity lavages recovered 6h following IP injection of either PBS (control), native hemozoin (nHZ), or 108 Leishmania major promastigotes.  Three mice were injected per group, for mice housed at thermoneutral (TT) or suboptimal temperature (ST). One PBS-TT sample had to be excluded due to low diversity in the library and sequencing coverage.

first: Martin

last: Olivier

first: Fiorella

last: Vialard


title: Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARS-CoV-2 Nucleocapsid protein

city: Chicago

first: Lavanya

last: Visvabharathy

state: IL

address: 5812 S. Ellis Ave.

department: Surgery

institute: University of Chicago

summary: Many people experiencing long COVID symptoms, or post-acute sequelae of SARS-CoV-2 infection (PASC), suffer from debilitating neurologic symptoms (Neuro-PASC). Although symptoms of Neuro-PASC are widely documented, it is still unclear whether virus-specific adaptive immunity is affected in these individuals. We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated CD4+ T cell responses toward the C-terminal region of SARS-CoV-2 Nucleocapsid protein when examined both functionally and using TCR sequencing. In contrast, Neuro-PASC patients also have diminished activation of CD8+ memory T cells and increased IL-6 production to Nucleocapsid. Elevated plasma immunoregulatory and reduced pro-inflammatory and antiviral response signatures were evident in Neuro-PASC patients compared with COVID convalescent controls without lasting symptoms, correlating with worse neurocognitive dysfunction. These data provide new insight into the impact of virus-specific cellular immunity on the pathogenesis of long COVID and pave the way for the rational design of predictive biomarkers and therapeutic interventions.

overall_design:
Genomic DNA samples from Neuro-PASC (NP; experimental) and COVID convalescent controls (CC; control) underwent TCR-sequencing through the Adaptive Biotechnologies ImmunoSEQ platform.
***Adaptive Biotechnologies does not release raw data.***

first: Igor

last: Koralnik


title: Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells

city: Rehovot

first: Yonatan

last: Stelzer

state: Israel

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

summary: Eviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central mechanism shaping the epigenome. Here, we implemented a recently established sensor system that enables measuring genome-wide incorporation and exchange of canonical and non-canonical histone variants in mouse embryonic stem cells. While exchange of all measured variants scales with transcription, variant-specific patterns are associated with transcription elongation and Polycomb binding. We found considerable exchange rates of canonical H3.1 and H2B in heterochromatin and repeat elements where non-canonical H3.3 is stably incorporated but not exchanged. This unexpected association between H3.3 incorporation and the exchange of H3.1 and H2B is also evident in active promoters and enhancers, which we validated using HIRA knockout cells harboring the sensor system. The sensor system provides a powerful experimental framework with quantitative readout, facilitating functional studies of histone dynamics and epigenetic gene regulation in vivo.

overall_design: ChIP-seq in WT or HIRA KO mESC cell lines carrying histone exchange sensor with two biological replicates per condition. Also, ChIP-seq of hepatocytes derived from transgenic mice carrying either H3.3- or H3.1-modified sensor and mouse embryonic fibroblasts derived from E12.5 embryos with H3.1-modified sensor.

first: Marko

last: Dunjic

first: Felix

last: Jonas

first: Gilad

last: Yaakov


title: PHF8 enables immune evasion by silencing endogenous retroelements

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

country: China

institute: East China Normal University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: PHF8 enables immune evasion by silencing endogenous retroelements [ChIP-seq]

summary:
Immunotherapy is currently a prime approach to cancer treatment. Despite the promise of immunotherapies such as immune checkpoint blockade on multiple cancers, most patients do not have a response or become resistant to treatment. Recent work indicate that epigenetic therapies converge with cancer immunotherapy through ‘viral mimicry’, the antiviral response triggered by endogenous nuclei acids that derived from aberrantly transcribed endogenous retrotransposons. However, epigenetic factors that regulate endogenous retrotransposons and further modulate the immune sensitivity of tumor cells is largely unknown.
Here we identified the histone demethylase PHD finger protein 8 (PHF8, KDM7B), a Jumonji C domain-containing protein that erases repressive histone marks as an essential mediator of immune escape. We found that depletion of PHF8 abrogates tumor growth, induces immune memory and augments sensitivity to immune checkpoint blockade in multiple tumor models without directly affecting tumor cell proliferation.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PHF8 in CT26 control and Phf8 KO cells.

first: Jiangping

last: He

first: Guangliang

last: Hong

first: Xiufeng

last: Pang


title: PHF8 enables immune evasion by silencing endogenous retroelements.


title: Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: The network of thymic stromal cells provides essential niches with unique molecular cues controlling T-cell development and selection. Recent single-cell RNA-sequencing studies uncovered a large transcriptional heterogeneity among thymic epithelial cells (TEC) demonstrating a previously unappreciated complexity. However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here we deconvoluted by massively parallel flow cytometry and machine learning known and novel TEC phenotypes into novel subpopulations and related these by CITEseq to the corresponding TEC subtypes defined by the cells’ individual RNA profiles. This approach phenotypically identified perinatal cTEC, physically located these cells within the cortical stromal scaffold, displayed their dynamic change during the life course and revealed their exceptional efficiency in positively selecting immature thymocytes. Collectively, we have identified novel markers that allow for an unprecedented dissection of the thymus stromal complexity, the cells physical isolation and assignment of specific functions to individual TEC subpopulations.

overall_design: Cells were isolated from 1- and 16-week-old mice and depleted of CD45+ cells by autoMACS. Subsequently cells were stained for CD45, EpCAM1, Ly51, Ter119 and with PI. In addition cells were stained with antibodies coupled to oligonucleotides directed against CD9, CD40, CD49a, CD54, CD63, CD73, CD83, CD117, CD146 (human with cross reactivity to mouse), CD200, CD274, HVEM, Ly6D, Ly6C/Ly6G (Gr1), MadCAM1, Podoplanin, CD80, CD86, MHCII, Sca1, CD31, EpCAM1, CD36, CD133, CD157, CD300LG and the Ulex europaeus agglutinin I (UEA1) lectin labeled with biotin, followed by secondary staining with streptavidin-PE coupled to an oligonucleotid. CD45-Ter119-EpCAM1+ and CD45-Ter119-EpCAM1- cells were sorted in a 70% to 30% ratio into a 1.5 mL tube containing FACS buffer for the 1-week-old and 16-week-old samples, respectively. For both timepoints an estimate of 28000 total cells were loaded on two wells of a 10x Genomics Chromium Single Cell Controller.

first: Fabian

last: Klein

first: Anastasiya

last: Börsch

first: Stefano

last: Maio

first: Georg

last: Holländer


title: PHF8 enables immune evasion by silencing endogenous retroelements [ATAC-seq]

overall_design: ATAC-seq data for CT26 control (n=2), Phf8 KO (n=2), or IFNγ-treated CT26 control (n=2), Phf8 KO (n=2) cells.


title: PHF8 enables immune evasion by silencing endogenous retroelements [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CT26 control (n=8), Phf8 sh1 (n=8), and Phf8 sh2 (n=8) tumor tissues; PANC28 control (n=3) and sgPHF8 (n=3) cells; CT26 control (n=3), sgPhf8 (n=3) and sgPhf8+Phf8 (n=3) cells.


title: Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA-seq]

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George st

department: Genetics/Internal Medicine

institute: Yale University

summary: Investigate the role of miR128 in the EHT process and the formation of nHSPCs

overall_design: Comparative gene expression  analysis of RNA-seq data for WT and MT samples for miRNA128 in Human and Fish

first: Joey

middle: J

last: Ghersi

first: Gabriel

last: Baldissera

first: Jared

last: Hintzen

first: Stephanie

last: Luff

first: Siyuan

last: Cheng

first: Ivan

middle: F

last: Xia

first: Christopher

middle: M

last: Sturgeon


title: Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: Spatial single-cell sequencing of meiosis I arrested oocytes indicates acquisition of maternal transcripts from the soma

city: Houston

first: Swathi

last: Arur

state: Texas

address: 6767 Bertner Ave,

department: Genetics

institute: MD Anderson Cancer Center

summary: Maternal RNAs are stored from minutes to decades in oocytes throughout meiotic arrest. The nature and dynamics of maternal RNAs during this arrest remain uncharted. We address this by performing single-oocyte RNA sequencing on arrested and maturing C. elegans oocytes.  We discovered a population of transcripts that increases as the arrested meiosis I oocyte ages, but ruled out ERK signaling and nascent transcription as a mechanism for this increase. Instead, we report extracellular communication from neighboring somatic cells as a mechanism for the increase in transcripts during meiosis I arrest. These analyses provide a single-cell resolution of the RNA landscape during the developmental history of a meiosis I arrested oocyte and as it prepares for oocyte maturation and embryonic progression.

overall_design: Comparative gene profiling analysis of RNA seq data from different ages of oocytes in the Caenorhabditis germline

first: Kenneth

last: Trimmer

first: Peisen

last: Zhao

first: Jacob

last: Seemann

first: Shin-Yu

last: Chen

first: Sudip

last: Mondal

first: Adela

last: Ben-Yakar


title: PHF8 enables immune evasion by silencing endogenous retroelements [CHIP-seq]

first: Yanan

last: Liu

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me1, H3K9me2, H3K9me3, H3K27me2 and H4K20me1 in CT26 control and Phf8 KO cells.

first: Jiangping

last: He

first: Guangliang

last: Hong

first: Xiufeng

last: Pang


title: Effect of depletion of RALY on gene expression  of A549 cells.

city: Hefei

first: Kailiang

address: Huangshan Road, Shushan district

institute: University of Science and Technology of China

summary:
To investigate the effect of depletion of RALY on gene expression of A549 cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sh-ctrl and sh-RALY.

first: Hao

last: Hu

first: KaiLiang


title: Impaired angiogenesis in diabetic critical limb ischemia is mediated by a miR-130b-INHBA signaling axis [Human umbilical cells endothelial cells]

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

summary: We report transcriptomic changes in human umbilical vein endothelial cells after transfection of negative control mimic and hsa-miR-130b-3p mimic.

overall_design: Human umbilical cells endothelial cells (HUVECs;Lonza) were cultured in endothelial cell growth medium (EGM2;Lonza) and transfected using Lipofectamine 2000 (Invitrogen) with negative control mimic and hsa-miR-130b-3p mimic. Cells were harvested and RNA-Seq analysis was performed using Illumina HiSeq2500 V4 2x150 bp  (Genewiz, South Plainfield, NJ).

first: Henry

middle: S

last: Pérez-Cremades

first: Rulin

last: Zhuang

first: Anurag

last: Jamaiyar

first: Jingshu

first: Aspasia

last: Tzani

first: Jorge

last: Plutzky

first: Philip

middle: P

last: Goodney

first: Mark

last: Creager

first: Marc

last: Sabatine

last: Bonaca

middle: W

last: Feinberg


title: NanoSTRING dendritic cell subpopulation

status: Public on May 23 2023

city: Stanford

first: David

last: Seong

state: California

address: 299 Campus Drive

institute: Stanford

summary:
High-dimensional approaches have revealed emerging heterogeneity within dendritic cells (DC), including a population of transitional DC (tDC) present in mouse and human. However, tDC origin and relationship to other DC subsets are not fully understood because their phenotype partially overlaps with previous definitions of conventional DC precursors (pre-cDC). Here, we show that tDC are distinct from other well-characterized DC and pre-cDC. By combining single-cell transcriptomics, high-dimensional immunophenotyping, lineage tracing and adoptive transfer experiments, we demonstrate that murine tDC originate from bone marrow progenitors shared with plasmacytoid DC (pDC) that are distinct from CD115-expressing conventional DC progenitors. In the periphery, tDC contribute to the pool of Esam+ type 2 DC (DC2), and these tDC-derived DC2 harbor pDC-related developmental features. tDC have lower turnover than pre-cDC2, capture antigen, respond to stimuli, and potently antigen-specific naïve T cells, all characteristics of differentiated DC. Different from pDC, viral sensing by tDC results in IL-1β secretion and fatal immune pathology in a model of murine coronavirus. Our findings suggest that tDC are a distinct pDC-related lineage with a DC2 differentiation potential and unique pro-inflammatory function during viral infections.
The objective of this experiment was to evaulate the transcriptional changes in various dendritic cell subpopulations

overall_design: Nanostring on sorted subsets of dendritic cells

first: Marcela

last: Alcántara-Hernández

first: Sanjana

last: Saravanan

first: Juliana

last: Idoyaga


title: RNA Sequencing Analysis of Wild-type and Adgrg2-KO Caput Epididymal Transcriptomes

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

summary: Purpose: The goal of this study is to detect differentially expressed genes, between wild-type (WT) and Adgrg2-/Y (Adgrg2-KO) caput epididymis by RNA sequencing  Methods: Caput epididymal mRNA profiles of 8-week-old WT and Adgrg2-KO mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000.  Results: RNA-seq data identified differentially expressed transcripts.  Conclusions: Our results show that the expression of many genes was slightly downregulated in Adgrg2-KO caput epididymis compared with WT one.

overall_design: Caput epididymal mRNA profiles of 8-week-old WT and Adgrg2 KO mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000.

first: Masahito

last: Ikawa


title: Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA-seq]

first: Stefania

last: Nicoli

first: Joey

last: Ghersi

first: Gabriel

last: Baldissera

first: Jared

last: Hintzen

first: Stephanie

last: Luff

first: Siyuan

last: Cheng

first: Ivan

last: Xia

first: Christopher

last: Sturgeon


title: Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring

city: Kansas City

first: Robert

middle: H.

last: Lane

address: 2401 Gillham Rd

institute: Children's Mercy

type: Methylation profiling by high throughput sequencing


title: Transcriptomic profiling of retinal cells reveals a subpopulation of microglia/macrophages expressing Rbpms marker of retinal ganglion cells (RGCs) that confound identification of RGCs

city: Farmington

first: Ephraim

last: Trakhtenberg

state: Connecticut

address: 263 Farmington Ave

department: Neuroscience

institute: UConn Health

summary: Analysis of retinal ganglion cells (RGCs) by scRNA-seq is emerging as a state-of-the-art method for studying RGC biology and subtypes, as well as for studying the mechanisms of neuroprotection and axon regeneration in the central nervous system (CNS). Rbpms has been established as a pan-RGC marker, and Spp1 has been established as an αRGC type and macrophage marker. Here, we analyzed by scRNA-seq retinal microglia and macrophages, and found Rbpms+ subpopulations of retinal microglia/macrophages, which pose a potential pitfall in scRNA-seq studies involving RGCs. We performed comparative analysis of cellular identity of the presumed RGC cells isolated in recent scRNA-seq studies, and found that Rbpms+ microglia/macrophages confounded identification of RGCs. We also showed using immunohistological analysis that, Rbpms protein localizes to stress granules in a subpopulation of retinal microglia after optic nerve injury, which was further supported by bioinformatics analysis identifying stress granule-associated genes enriched in the Rbpms+ microglia/macrophages. Our findings suggest that the identification of Rbpms+ RGCs by immunostaining after optic nerve injury should exclude cells in which Rbpms signal is restricted to a subcellular granule, and include only those cells in which the Rbpms signal is labeling cell soma diffusely. Finally, we provide solutions for circumventing this potential pitfall of Rbpm-expressing microglia/macrophages in scRNA-seq studies, by including in RGC and αRGC selection criteria other pan-RGC and αRGC markers.

overall_design: We generated 10x Genomics 3’-droplet based scRNA-seq dataset of macrophage/microglia from adult (10 weeks old) uninjured and injured (2 weeks after ONC) retinas/optic nerves from mice  of both sexes using methods we previously described (Rheaume et al 2018; Xing et al, 2023). ONC injury was performed at 8 weeks. Cells from were loaded for capture onto the Chromium System using the v2 single cell reagent kit (10X Genomics). Following capture and lysis, cDNA was synthesized and amplified (12 cycles) as per manufacturer's protocol (10X Genomics). After demultiplexing and aligning to the mouse genome and transcriptome (mm10) using the CellRanger pipeline and merging/integration in Rstuduio, 1168 macrophage/microglia passed quality control (including filters of a minimum of 200 genes and a maximum of 6500 genes). Batches were merged, normalized and scaled using Seurat. Batch correction/integration of datasets was performed using the R package harmony.

first: William

middle: C

last: Theune


title: CARD9 attenuates Ab pathology and modifies microglial responses in an Alzheimer’s disease mouse model

city: Charlottesville

first: Daniel

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

institute: University of Virginia School of Medicine

summary: Although significant progress in recent years has been made in defining key innate immune receptors involved in Alzheimer’s disease (AD), our knowledge of the specific intracellular signaling molecules that coordinate immune responses in AD remains poorly defined. In these studies, we have identified a previously undescribed role for the innate immune signaling molecule CARD9 in an amyloid beta (Ab)-mediated mouse model of AD. We specifically demonstrate that CARD9 deletion in the 5xFAD mouse model of AD leads to impaired control of Ab, worsened cognitive decline, and aberrant microglial activation. We further show that pharmacological activation of CARD9 provides a strategy to boost Ab clearance from the hippocampus. Collectively, these findings uncover a previously uncharacterized molecular signaling molecule used by the innate immune system in Ab-mediated neurological disease, and help to establish CARD9 as a novel molecular player that can be targeted in AD.

overall_design: Comparison of 5xFAD microglial response with or without Card9 function. 4 replicates per group of non disease (WT), Card9-deficient, 5xFAD, and 5xFAD Card9 deficient

first: Hannah

last: Ennerfelt

first: Coco

last: Holliday

first: Kristine

last: Zengeler

first: Ashley

last: Bolte

first: Tyler

last: Ulland

first: John

middle: R

last: Lukens


title: Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring [RNA-seq]

summary: Exposure to adverse early-life environment (AME) increases the incidence of developing adult-onset non-alcoholic fatty liver disease (NAFLD). DNA methylation has been postulated to link AME and late-onset diseases. The objective was to investigate whether and to what extent hepatic DNA methylome was perturbed prior to the development of NAFLD in offspring exposed to AME in mice. AME constituted maternal western diet and late-gestational stress. Male offspring livers at birth (d0) and weaning (d21) were used for evaluating DNA methylome and transcriptome using reduced representation of bisulfite sequencing and RNA-seq, respectively. We found AME caused 5,879 differentially methylated regions (DMRs) and zero differentially expressed gene (DEG) at d0, and 2,970 and 123, respectively at d21. Majority of the DMRs were distal from gene transcription start sites and did not correlate with DEGs. The DEGs at d21 were significantly en-riched in GO biological processes characteristic of liver metabolic functions. In conclusion, AME drove changes in hepatic DNA methylome which preceded perturbations in the hepatic metabolic transcriptome, which preceded the onset of NAFLD. We speculate that subtle impacts in dynamic enhancers lead to long-range regulatory changes that manifest over time as gene network alter-nations to increase the incidence of NAFLD later in life.

overall_design: Comparative analysis of RRBS and RNA-seq data from the livers of C57bl/6 male mouse offspring (at birth and weaning) of dams experienced adverse maternal

middle: H

first: Tomi

last: Pastinen

first: Qi

last: Fu

first: Warren

last: Cheung

first: Amber

middle: V

last: Majnik

first: Xingrao

last: Ke


title: AHR protects against lung vascular leakage in viral infection

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: We have identified the apelin-APJ axis as a mechanism of protection mediated by AHR signalling in lund=g endothelial cells. This RNAseq experiment will compare the effects of apelin receptor blockade on endothelial and epithelial responses in the lung during influenza infection.

overall_design: Endothelial cells and epithelial cells isolated from influenza infected (d6) mice treated with the apelin receptor antagonist (MM54) or PBS controls will be compared by RNAseq analysis.

first: Jack

last: Major

first: Stefania

last: Crotta


title: Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring [RRBS]

first: Robert

last: Lane

middle: A


title: Association of Antifolate Response Signature Status and Clinical Activity of Pemetrexed-Platinum Chemotherapy in Non-Small Cell Lung Cancer - The Piedmont Study

city: Durham

first: Joel

last: Eisner

state: NC

address: 100 Capitola Dr. Suite 275

institute: GeneCentric Therapeutics, Inc

summary: The Piedmont study is a prospectively designed retrospective evaluation of a new 48-gene antifolate response signature (AF-PRS) in patients with locally advanced/metastatic NS-NSCLC treated with pemetrexed-containing platinum doublet chemotherapy (PMX-PDC). The study tested the hypothesis that the AF-PRS selects for patients with NS-NSCLC that preferentially respond to PMX-PDC, with a goal of providing clinical support for AF-PRS as potential diagnostic test. Overall, 53% of patients were AF-PRS(+), which was associated with extended PFS, but not OS, vs. AF-PRS(-) (16.6 vs. 6.6 mo; p = 0.025).  In patients who were Stage I-III patients at time of treatment, PFS, but not OS, was further extended in AF-PRS(+) vs. AF-PRS(-) (36.2 vs. 9.3 mo; p = 0.03).  A complete response (CR) to therapy was noted in 14 of 95 patients.  AF-PRS(+) preferentially selected a majority (79%) of CRs, which were evenly split between patients Stage I-III (6 of 7) and Stage IV (5 of 7) at time of treatment. AF-PRS identified a significant population of patients with extended survival and/or clinical response following PMX-PDC treatment.  AF-PRS may be a useful diagnostic test for patients indicated for systemic chemotherapy, especially when determining the optimal PDC regimen for locally advanced disease.

overall_design:
Residual pre-treatment FFPE tumor samples and clinical data were analyzed from 105 patients treated with 1st-line (1L) PMX-PDC.  95 patients had sufficient RNA sequencing (RNAseq) data quality and clinical annotation for inclusion in the analysis. Associations between AF-PRS status and associate genes, and outcome measures including progression-free survival (PFS) and clinical response were evaluated.
------------------------------------
Authors state "Fastq files not not providied due to patient privacy concerns".

first: Greg

last: Mayhew

first: James

last: Davison

first: Kirk

last: Beebe

first: Yoichiro

last: Shibata

first: Yuelong

last: Guo

first: Carol

last: Farhangfar

first: Farhang

first: Josh

last: Uronis

first: Jeffrey

last: Conroy

first: Michael

last: Milburn

first: Neil

last: Hayes

first: Kathryn

last: Mileham


title: Inter- and trans-generational impact of H3K4 methylation in neuronal homeostasis

city: København

first: Steffen

last: Abay-Nørgaard

state: København

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

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


title: Inter- and trans-generational impact of H3K4 methylation in neuronal homeostasis (RNA-Seq)

summary: to investigate the function of set-2 and set-2-related environmental changes on the transcriptome we performed RNAseq during different environmental changes and in set-2 mutant and wild type descendants at different generations

overall_design: All RNAseq was performed at L4 stage

first: Marta

last: Tapia

first: Mandoh

last: Zeijdner

first: Jeonghwan

last: Kim

first: Kyoung

last: Won

first: Bo

last: Porse

first: Anna

last: Salcini


title: Inter- and trans-generational impact of H3K4 methylation in neuronal homeostasis (ChiP-Seq)

summary: To investigate the function of set-2 on the H3K4me3 landscape we performed ChIPseq in set-2 mutants and wild type descendants at different generations

overall_design: All ChIPseq was performed at L4 stage


title: Leukemic hematopoiesis

city: Cambridge

first: Brian

last: Huntly

address: Hills Road

department: Department of Haematology

institute: University of Cambridge


title: Integration of cancer-related genetic landscape of Eph receptors and ephrins with proteomics identifies a crosstalk between EPHB6 and EGFR

city: Saskatoon

first: Franco

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan

summary: Eph receptors and their ephrin ligands are viewed as promising targets for cancer treatment, however targeting them is hindered by their context-dependent functionalities. To circumvent this, we explored molecular landscapes underlying their pro- and anti-malignant activities. Using unbiased bioinformatics approaches, we constructed a cancer-related network of genetic interactions (GIs) of all Ephs and ephrins to assist their therapeutic manipulation. We also applied genome-wide genetic screening and BioID proteomics, and integrated them with machine learning approaches to select the most relevant GIs of one of Eph receptors, EPHB6. This revealed a crosstalk between EPHB6 and EGFR, and further experiments confirmed EPHB6 ability to modulate EGFR signaling, enhancing both proliferation of cancer cells and tumor development. Taken together, our observations identify a new mechanism of action of EPHB6, suggesting its targeting might be beneficial in EGFR-dependent tumors, and confirm that Eph family genetic interactome presented here can be effectively exploited in developing new treatment approaches.

overall_design: Samples were collected at two different time points after infection with the 90k shRNA libraries and probes were prepared to hybridize to microarray chips to identify SL partners of EphB6 gene.

first: Glinton

last: Hanover

first: Frederick

first: Andrew

last: Freywald


title: RNA-seq analysis of differentially expressed genes between WT and shTRIM21 HCT116 cells.

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: No. 199, Ren'ai Road

institute: Suzhou Medical College of Soochow University

summary:
To investigate the biological function TRIM21 in the colorectal cancer, we established HCT116 cell lines in which the TRIM21 gene has been knocked down by shRNA.
We used a lentiviral shRNA technique to knockdown TRIM21 expression in HCT116 cells. A scrambled shRNA (shRNA/Control) was used as a control. We then performed RNA-Seq with Cloud-seq Biotech Inc. (Shanghai, China) to analyze gene expression changes in HCT116 cells. For each sample, three independent biological replicates were performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells and its KD derivatives (shTRIM21).

first: Hua

last: Wu


title: Differential gene expression in the colons of mice lacking neuregulin-4

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: Growth factors are essential for maintenance of intestinal health at homeostasis and during inflammation. We have previously shown that exogenous treatment with the growth factor neuregulin-4 (NRG4) promotes colonocyte survival during cytokine challenge and is protective in acute models of intestinal inflammation. However, the role of endogenously expressed NRG4 in colitis is not well understood. Using NRG4-/- mice, we tested the effect of endogenous NRG4 on colitis. NRG4-/- and wild type cage-mate mice were subjected to an IL-10R neutralization model of chronic colitis. NRG4-/- mice displayed reduced inflammatory cytokine expression in the colon and a reduction in tissue CD8+ T cells at 5 weeks post induction of colitis. In unchallenged NRG4-/- mice, baseline numbers of colonic CD8+ T cell numbers were unchanged. However, there was a significant decrease in splenic CD8+ T cells. RNA sequencing from colonic homogenates showed a loss of St3gal4, a sialyltransferase involved in immune cell trafficking, in the NRG4-null animals. This loss was verified in both tissue and epithelium. The regulation of St3gal4 by NRG4 was confirmed with ex vivo epithelial colon organoid cultures from NRG4-/- mice and by induction of St3gal4 in vivo following NRG4 treatment. Together our data suggest that NRG4 regulates colonic epithelial ST3GAL4 and thus the recruitment of CD8+ T cells, but also has systemic effects on T cell maturation. These effects may combine to stimulate immune mediated inflammation during IL-10R neutralization colitis.

overall_design: RNA-sequencing of full thickness colonic biopsies from 6 wildtype and 5 Nrg4-/- adult (11-12 wks-old) co-housed mice

first: Jessica

last: Bernard

middle: Y

first: Mark

last: Frey


title: Transitional dendritic cells are distinct from conventional DC2 precursors and mediate proinflammatory antiviral responses

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

summary: By combining single cell transcriptomics and proteomics approaches, with lineage tracing and adoptive transfer experiments, we next demonstrate that tDC originate from a bone marrow precursor shared with plasmacytoid DCs (pDCs). Using new lineage tracing mouse models, we evaluated tDC plasticity and reveal their acquisition of Esamhi conventional DC type 2 (cDC2) features. Finally, we present tDC capacity to quickly response to stimulation and potently activate antigen-specific naïve T cells, demonstrating that these cells harbor functions of differentiated DCs. Our findings clarify tDC nature and reveal these cells as a unique lineage of DCs related developmentally to pDCs.

overall_design: Splenic DCs from 2 mice were CD135-enriched and counted. The sample was split in two: 30% was stained and DC subsets were sorted fresh; 70% was resuspended at 10x106/mL and stimulated with the LPRC adjuvant cocktail [LPS 100ng/mL, Poly(I:C) 25ug/mL, Resiquimod 2.5ug/mL and CpG-A (ODN 2216) 6ug/mL] for 3h before staining and sorting. RNA was extracted from immediately after sorting using the NucleoSpin RNA XS kit (Takara Bio) according to manufacturer’s instructions.

first: Marcela

last: Alcántara-Hernández

first: Juliana

last: Idoyaga

first: David

last: Seong

first: Eduardo

last: Esteva


title: Antagonizing the irreversible thrombomodulin-initiated proteolytic signaling alleviates age-related liver fibrosis via senescent cell killing

status: Public on May 22 2023

first: Liuyang

last: Wang

address: 213 Research Drive

institute: Duke University

summary: Cellular senescence is a stress-induced, stable cell cycle arrest phenotype which generates a pro-inflammatory microenvironment, leading to chronic inflammation and age-associated diseases. Determining the fundamental molecular pathways driving senescence instead of apoptosis could enable the identification of senolytic agents to restore tissue homeostasis. Here, we identify thrombomodulin signaling as a key molecular determinant of the senescent cell fate. Although normally restricted to endothelial cells, thrombomodulin is rapidly upregulated and maintained throughout all phases of the senescent program in aged mammalian tissues and in senescent cell models. Mechanistically, thrombomodulin activates a proteolytic feed-forward signaling pathway by stabilizing a multi-protein complex in early endosomes, thus forming a molecular basis for the irreversibility of the senescent program and ensuring senescent cell viability. Therapeutically, thrombomodulin signaling depletion or inhibition using vorapaxar, an FDA-approved drug, effectively ablates senescent cells and restores tissue homeostasis in liver fibrosis models. Collectively, these results uncover proteolytic thrombomodulin signaling as a conserved pro-survival pathway essential for senescent cell viability, thus providing a pharmacologically exploitable senolytic target for senescence-associated diseases.

overall_design: To determine THBD’s necessity in establishing senescence, THBD was depleted in IMR90 cells undergoing HRas-induced senescence or palbociclib-induced senescent Huh7 cells. Bulk RNA-seq are performed .

first: Christopher

last: Pan

first: Xiao-Fan


title: Single cell RNA-seq profiling of patient-derived Merkel cell carcinoma tumor samples

city: Long Beach

first: Ling

last: Gao

email: ling.gao@va.gov, lingg3@hs.uci.edu

address: 5901 E.7th Street

institute: Department of Veterans Affairs

summary: Merkel cell carcinoma (MCC), a rare but aggressive neuroendocrine cancer of the skin, remains a challenge in the era of precision medicine. MCC tumor heterogeneity has been attributed to the variant disease etiologies, mediated by either UV exposure or Merkel cell polyomavirus (MCPyV). However, over the years it has become clear that these two groups are largely similar in clinical presentation, prognosis, and treatment response to immune-checkpoint inhibitors. We therefore dissected the transcriptomic heterogeneity of a panel of patient tumors samples, at the single-cell resolution, to gather further insights.

overall_design: Resected patient tumors were dissociated and cleared of any red blood cells to obtain a single-cell suspension. Live cells were thereafter sorted by flow cytometry and used for preparing libraries. Each library was then sequenced and the resulting single cell transcriptomic data was analyzed.

first: Aarthi

last: Kannan

first: Bhaba

middle: K

last: Das


title: Aryl hydrocarbon receptor (AHR)-dependent protection against lung vascular leakage in viral infection

first: Andreas

last: Wack

summary: Disruption of the lung endothelial-epithelial cell barrier during respiratory virus infection causes cell and fluid accumulation in the air spaces and compromises vital gas exchange function. Endothelial cell dysfunction is known to exacerbate tissue damage; however, it is unclear whether the lung endothelium engages in tissue-protective activity during viral infection. Here we show that the environmental sensor aryl hydrocarbon receptor (AHR) is predominantly active in endothelial cells and protects against influenza-induced lung damage. Endothelial-specific AHR deletion caused increased vascular leakage in air spaces and enhanced influenza-induced lung tissue pathology. Global expression profiling revealed limited AHR-dependent regulation of vessels in the steady-state lung. However, following influenza-induced tissue damage and inflammation, AHR engages tissue-protective programmes in endothelia and prevents a dysplastic keratinised and apoptotic signature in the airways of infected lungs.

overall_design: Wild-type (wt) mice or mice with taregetd disruption of the AHR locus in endothelial cells were infected with influenza virus or treated with vehicle (PBS), and lung epithelial or endothelial cells were prepared on day 6 of infection for transcriptomic analysis.

first: Jack

last: Major

first: Stefania

last: Crotta


title: Novel TCR sequencing and cloning methods for sensitive and quantitative interrogation of repertoires and rapid isolation of tumor-reactive TCRs

city: Epalinges

first: Raphael

last: Genolet

address: Biopole 3, Chemin des Boveresses 155

department: Departement d'oncologie UNIL-CHUV

institute: Centre Hospitalier Universitaire Vaudois (CHUV)

summary: We report on SEQTR, a novel high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible and accurate as compared to commonly-used multiplex PCR and 5'RACE assays.

overall_design:
Analysis of blood and TILs repertoire
**RAW data not provided for the ImmunoSEQ samples since Adaptive Biotechnologies does not release raw data.**

first: George

last: Coukos

first: Alexandre

last: Harari


title: Identification of miRNAs regulating MAPT expression and their analysis in plasma of patients with dementia

city: Trento

first: Michela

middle: A.

last: Denti

address: Via Sommarive 9

department: Department of Cellular, Computational and Integrative Biology

country: Italy

institute: University of Trento

summary:
Background: Dementia is one of the most common diseases in elderly people and hundreds of thousand new cases per year of Alzheimer’s disease (AD) are estimated. While the recent decade has seen significant advances in the development of novel biomarkers to identify dementias at their early stage, a great effort has been recently made to identify biomarkers able to improve differential diagnosis. However, only few potential candidates, mainly detectable in cerebrospinal fluid (CSF), have been described so far.
Methods: We searched for miRNAs regulating MAPT translation. We employed a capture technology able to find the miRNAs directly bound to the MAPT transcript in cell lines. Afterwards, we evaluated the levels of these miRNAs in plasma samples from FTD (n = 42) and AD patients (n = 33) and relative healthy controls (HCs) (n = 42) by using qRT-PCR.
Results: Firstly, we found all miRNAs that interact with the MAPT transcript. Ten miRNAs have been selected to verify their effect on Tau levels increasing or reducing miRNA levels by using cell transfections with plasmids expressing the miRNAs genes or LNA antagomiRs. Following the results obtained, miR-92a-3p, miR-320a and miR-320b were selected to analyse their levels in plasma samples of patients with FTD and AD respect to HCs. The analysis showed that the miR-92a-1-3p was under-expressed in both AD and FTD compared to HCs. Moreover, miR-320a was upregulated in FTD vs. AD patients, particularly in men when we stratified by sex. Respect to HC, the only difference is showed in men with AD who have reduced levels of this miRNA. Instead, miR-320b is up-regulated in both dementias, but only patients with FTD maintain this trend in both genders.
Conclusions: Our results seem to identify miR-92a-3p and miR-320a as possible good biomarkers to discriminate AD from HC, while miR-320b to discriminate FTD from HC, particularly in males. Combining three miRNAs improves the accuracy only in females, particularly for differential diagnosis (FTD vs. AD) and to distinguish FTD from HC.

overall_design: Three samples treated with the MAPT capture biotinylated oligonucleotide and three samples treated with the SCRAMBLE capture biotinylated oligonucleotide were analysed


title: Comparative binding patterns of Chromatin Regulators in normal versus leukemic hematopoiesis [ChIP-Seq]

first: Brian

last: Huntly

summary: Cellular differentiation-trajectories require extensive alterations in chromatin structure and function, elicited by a diverse array of chromatin-factors (CFs). Using haematopoiesis as a model-system, we combined bulk ex vivo and single-cell in vivo CRISPR screens to comprehensively characterise the role of CF families in cell-fate decisions. We uncover marked lineage specificities for many CFs, dissecting specific CF-dependencies in vivo at single-cell resolution. This highlights functional diversity among related CFs (i.e. BAF-subcomplexes, MLL-methyltransferases), but also reveals functional redundancy among unrelated Repressive-complexes that restrain excessive myeloid differentiation. Epigenetic-profiling, molecularly explains CF lineage-dependencies, identifying differentiation stage-specific interactions between individual CFs and lineage-determining Transcription Factors (TFs). Intriguingly, non-canonical BAF remodeler disruption abrogates myeloid-TF function generating a pre-leukaemia phenotype. Screening CF functions in leukemia, we show that leukaemia cells abrogate normal CF function, restraining differentiation trajectories by engaging in novel CF-TF interactions that suggest potential therapeutic avenues. Together, our work greatly elucidates the role of CFs and their TF-partners across normal and malignant haematopoiesis.

overall_design: Here we have analysed the binding patterns of the canoncal-BAF subunit Smarcb1 and the H3K4-methyl writers Kmt2d (MLL4) and Kmt2a (MLL1) in normal myelopoiesis and in a murine leukemic model driven by the Npm1c/Flt3-ITD mutations. For the normal hematopoiesis we have profiled early myeloid progenitors (GMPs) FACs-sorted from bone-marrow as Lin-, ckit+, sca1-, FcgR-III+, cD34-), in vivo FACs-sorted bone marrow monocytes (Lin-, CD11b) and exvivo derived monocytes (expanded from LSK prgenitors with Flt3-ITD, G-CSF, IL3 and GM-CSF). Leukemic cells were purified from primary tumours and expanded exvivo for few passages with SCF, IL3 and IL6. Freshly isolated cells were dual-crosslinked with 3 mM EGS+DSG+DMA for 20 minutes followed by 1% Formaldehyde for 5 minutes. Chromatin extracts were prepared by nuclei isolation with an hypotoniic buffer (25 mM Hepes 7.5 M, 10 mM NaCl, 0.2% Igepal + Protease Inhibtors), followed by sonication in 0.5% SDS, 5 mM EDTA. Chromatin extracts were quantified and diluted 5x to reach a concentration of 150 mM NaCl, 0.1% SDS, 1% Tx-100, 1 mM EDTA, 1X Prot Inh. Immunoprecpitation was carried out overnight (10-12 h) with the appropiate amount of the relevant antibody and the immuno-complexes were captured on the following day by incubation with ProtA + ProtG Magna-ChIP beads (Sigma). After that, DNA was purified with SPRI beads and libraries were prepared using the NEB Next Ultra II kit (NEB).

last: Lara-Astiaso

first: Ainhoa

last: Goñi-Salaverri

first: Julen

last: Mendieta-Esteban

first: Nisha

last: Narayan

first: Cyntia

last: Del Valle

first: Torsten

last: Gross

last: Giotopoulos

first: Mar

last: Navarro-Alonso

first: Jon

last: Zazpe

first: Francesco

last: Marchese

first: Natalia

last: Torrea

first: Isabel

last: A Calvo

first: Cecile

last: K Lopez

first: Diego

last: Alignani

first: Aitziber

last: Lopez

first: Borja

last: Saez

first: Jake

last: Taylor-King

first: Felipe

last: Prosper

first: Nikolaus

last: Fortelny


title: Comparison of methods to generate a pooled Enterococcus faecalis Tn library from arrayed library plates

city: Minneapolis

first: Julia

last: Willett

state: Minnesota

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

institute: University of Minnesota

summary: The goal of this study was to determine how the method of pooling (combining mutants) for bacteral Tn libraries affected mutant distribution.  Previously we generated a pooled version of a~6,800 Tn mutant library in Enterococcus faecalis OG1RF by plating and scraping individual mutants.  Here, we combined liquid cultures grown in deep well plates.  DNA from the new pooled library was extracted, and TnSeq was used to compare mutant distribution between the old (plate scraping) and new (liquid pooling) Tn library formats.  This is important because it will guide best practices for handling large collections of bacterial mutants.

overall_design: TnSeq using purified genomic DNA from bacterial samples


title: The first transcriptomic atlas of the adult lacrimal gland reveals epithelial complexity and identifies novel progenitor cells in mice

city: La Jolla

first: Helen

last: Makarenkova

state: CA

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

summary: The lacrimal gland (LG) secretes aqueous tears. Previous studies have provided insights into the cell lineage relationships during tissue morphogenesis. However, little is known about the cell types composing the adult LG and their progenitors. Using scRNA-seq, we established the first comprehensive cell atlas of the adult mouse LG to investigate cell hierarchy, their secretory repertoire and sex differences.

overall_design: For each sample (1 Female and 2 Males), six dissected LGs of three animals aged of 2 months were combined and processed for scRNAseq analysis

first: Vanessa

last: Delcroix

first: Olivier

last: Mauduit

first: Hyun

last: Lee

first: Anastasiia

last: Ivanova

first: Takeshi

last: Umazume

first: Sarah

last: Knox

first: Cintia

last: de Paiva

first: Darlene

last: Dartt


title: Gene expression profiles of OT-1 T cells co-cultured with MHC-I Negative Tumors and Antigen Loaded Macrophages

first: Emily

middle: Claire

last: Lerner

email: emily.sherber@duke.edu, ecs74@duke.edu

state: North Carolina

address: 303 Research Drive

institute: Duke University School of Medicine

summary:
OT-1 T-cells were co-cultured either alone in T-cell media supplemented with IL-2 (50IU/mL IL-2), with OVA loaded macrophages, or with both OVA loaded macrophages and CT2A-TRP2-β2mKO tumor cells. Cells were cultured at a 5:1 T-cell to tumor ratio, and 2:1 T-cell to macrophage ratio. After 24 h of co-culture, CD8 T-cells were FACS sorted, and RNA extracted (RNeasy Mini Kit, Qiagen). RNA was analyzed on an nCounter MAX Analysis System (Nanostring) with the PanCancer Immune profiling panel (Nanostring) according to manufacturer instructions. Expression dat
OT-1 T-cells were isolated from OT-1 mice by culturing OT-1 splenocytes in T-cell media supplemented with 50IU/mL IL-2 and 1 μM OVA SIINFEKL peptide (Anaspec) for 48 h. Cells were purified for CD8 T-cells as described above and subsequently cultured in TCM with 50IU/mL IL-2, splitting every 24h for a total of 4 days.

overall_design: Gene sets from OVA-activated OT-1 T cells co-cultured with OVA antigen-negative CT2A-TRP2-B2mKO tumor cells or from OVA-activated OT-1 T cells alone were both compared against naïve OT-1 T cells. OVA negative B2mKO tumor lines were used to ensure the absence of tumor-TCR interactions. OT-1 TCR activation for these experiments was accomplished by concomitant culture with OVA MΦ.

first: Peter

middle: E

last: Fecci


title: Gene expression profile at single cell level of P26 WT, Tspan12 KO, F4L5.13 treated Tspan12 KO mice retina

first: Harald

last: Junge

state: MN

address: 2001 6th St SE

department: Department of Opthalmology

summary: We used single cell RNA sequencing (scRNA-seq) to discover the gene expression changes in Tspan12 KO retina, and evaluated the effect of F4L5.13 (Frizzled4:LRP5 agonist) treatment on transcriptional normalization in Tspan12 KO retina.

overall_design: Retinas from P26 WT, Tspan12 KO, F4L5.13 treated Tspan12 KO mice were dissociated into single cells using papain solution and analyzed using scRNAseq.

first: Lingling

last: Zhang

first: Zhe

last: Chen


title: Bilineal differentiated liver carcinoma cells generates highly aggressive escape variants

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

summary:
Background & Aims: Combined HCC/iCCA is a rare liver tumor type. We generated a transgenic mouse model (AlfpCre+-Trp53fl/fl/Alb-HBs+ tg mouse) which developed next to HCC combined HCC/iCCA (cHCC/iCCA). We compared bilineal differentiated liver carcinoma cell lines generated from primary liver tumors of AlfpCre+-Trp53fl/fl/Alb-HBs+ tg mice and transplanted them into C57BL/6J mice to monitor there agressiveness. We compared the geneexpression profile from those primary liver carcinoma cell lines with IFNγ treatment (pCCL-IFNγ) and without treatment (pCCL) with explanted primary carcinoma cell line (pCCL-ex).
Results: Here we describe that elimination of HBs+ in pCCL by HBs/(Kb/S190-197)-specific CD8 T cells describes a potential immune escape mechanism for highly aggressive cHCC/iCCA-type liver carcinomas.

overall_design: Total RNA was isolated from murine whole carcinoma cell lines, and the quality was analyzed by a bioanalyzer. Agilent Mouse Gene Expression Microarrays 8x60K were used.

last: Qiu

first: André

last: Lechel

first: Reinhold

last: Schirmbeck


title: Comparative binding patterns of Chromatin Regulators in normal versus leukemic hematopoiesis [ATAC-Seq]

first: Brian

last: Huntly

overall_design: Here we have used ATAC-seq to analyse the chromatin accessibility patterns of multipotent blood progenitors (LSK cells) knocked-out for specific Chromatin Factors exvivo differentiated under conditions permiting multilineage (Lin. priming) or myeloid (Mye) differentiation.

first: David

last: Lara-Astiaso

first: Ainhoa

last: Goñi-Salaverri

first: Julen

last: Mendieta-Esteban

first: Nisha

last: Narayan

first: Cyntia

last: Del Valle

first: Torsten

last: Gross

first: George

last: Giotopoulos

first: Mar

last: Navarro-Alonso

first: Jon

last: Zazpe

first: Francesco

last: Marchese

first: Natalia

last: Torrea

first: Isabel

last: A Calvo

first: Cecile

last: K Lopez

first: Diego

last: Alignani

first: Aitziber

last: Lopez

first: Borja

last: Saez

first: Jake

last: Taylor-King

first: Felipe

last: Prosper

first: Nikolaus

last: Fortelny

middle: J


title: Identification of Predictive Factors in Advanced Pancreatic Cancer Through Extracellular Vesicle Analysis

city: Meldola

first: Tania

last: Rossi

state: FC

address: Via Piero Maroncelli 40

department: Biosciences Laboratory

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

type: Non-coding RNA profiling by high throughput sequencing

summary: The goal of this study is to find a molecular signature that can predict response or resistance to Gemcitabine + Nab-paclitaxel therapy in pancreatic cancer (PC), to aid treatment selection for each patient. To this end, we analyzed blood-derived extracellular vesicles (EV).

overall_design: EV analysis was performed on a cohort of 21 patients with PC (metastatic, locally advanced) (PCp). Samples were collected prior to first-line treatment (Gemcitabine + Nab-paclitaxel). EVs were isolated from plasma by SEC. Then we analyzed the EV RNA cargo through RNA Seq technology.

first: Ivan

last: Vannini

last: Fabbri


title: Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

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

overall_design: Refer to individual Series


title: Bulk RNAseq analysis of dorsal root ganglia from global Nav1.7 knockout mice

city: South San Francisco

first: James

last: Maksymetz

address: 1 DNA Way

institute: Genentech, Inc

summary: We investigated changes in gene expression of dorsal root ganglia (DRG) isolated from global (pCAGG-CreER x Nav1.7 floxed) Nav1.7 knockout mice using bulk RNA sequencing. We found an upregulation of Penk and downregulation of Ceacam10 in Nav1.7 knockouts compared to controls, as well as other gene expression changes similar to those previously reported for Nav1.7 knockout mice (https://doi.org/10.1038/ncomms9967). We identified that genes selectively expressed in the C low-threshold mechanoreceptor (cLTMR) class of DRG neurons showed a general reduction in expression in Nav1.7 knockouts compared to littermate controls.

overall_design: Comparative gene expression profiling by RNAseq was performed on lumbar DRGs from Nav1.7 cKO (CreER+, N = 3) and littermate control (CreER-, N = 3) mice.

first: Lunbin

last: Deng

first: Michelle

last: Dourado

first: Min

last: Jung

first: Kevin

last: Huang

first: Josh

last: Kaminker

first: David

last: Hackos


title: Systematic screening of chromatin factors identifies divergent roles across haematopoiesis and leukaemia [scRNA-Seq]

first: Brian

last: Huntly

address: Hills Road

overall_design: Perturb-seq profiling of  CF-KOs in in vivo, ex vivo, and leukemia model systems

last: Lara-Astiaso

first: Ainhoa

last: Goñi-Salaverri

first: Julen

last: Mendieta-Esteban

first: Nisha

last: Narayan

first: Cyntia

last: Del Valle

first: Torsten

last: Gross

first: George

last: Giotopoulos

first: Mar

last: Navarro-Alonso

first: Jon

last: Zazpe

first: Francesco

last: Marchese

first: Natalia

last: Torrea

first: Isabel

last: A Calvo

first: Cecile

last: K Lopez

last: Alignani


title: Heat promotes melanogenesis by increasing the paracrine effects in keratinocytes via the TRPV3/Ca2+/Hh signaling pathway

status: Public on May 20 2023

city: Changsha

first: Lan

last: Zhang

state: --- Select One ---

address: 172 Tongzipo road, Yuelu District, Changsha city, Hunan Province

institute: 中南大学

summary: Global warming and rising temperature significantly increase the incidence of heat stress, which is known to affect the process of inflammation and aging. However, the effect of heat stress on skin melanogenesis is not fully known. We found that healthy foreskin tissues underwent significant pigmentation when exposed to 41℃. Furthermore, heat stress promoted melanogenesis in pigment cells by increasing the paracrine effects of keratinocytes. High-throughput RNA sequencing showed that heat stress activates the Hedgehog (Hh) signaling pathway in keratinocytes. The agonists of Hh signaling promote the paracrine effect of keratinocytes on melanogenesis. In addition, TRPV3 agonists activate the Hh signaling in keratinocytes and augment its paracrine effect on melanogenesis. The heat-induced activation of Hh signaling is dependent on TRPV3-mediated Ca2+ influx. Heat exposure promotes melanogenesis by increasing the paracrine effects in keratinocytes via the TRPV3/Ca2+/Hh signaling pathway. Our findings provide insights into the mechanisms of heat-induced skin pigmentation.

overall_design: The experiment was divided into two groups, with a control group of three samples and an experimental group of three samples. The control group treated HaCaT cells at 37℃ for 3 days, 1 hour per day, while the experimental group treated HaCaT cells at 41℃ for 3 days, 1 hour per day.

first: Hongliang

last: Zeng

first: Ling

last: Jiang

first: Chuhan

last: Fu


title: Heat shock factor 1 specifically potentiates c-MYC-mediated transcription independently of the canonical heat-shock response

city: Frederick

first: Chengkai

last: Dai

state: Maryland

address: Building 560, Room 32-31B, Center for Cancer Research, Mouse Cancer Genetics Program

department: CCR

institute: National Cancer Institute

summary: Despite its pivotal roles in biology, how the transcriptional activity of c-MYC is attuned quantitatively remain poorly defined. Here, we show that heat shock factor 1 (HSF1), the master transcriptional regulator of the heat-shock response, acts as a key modifier of the c-MYC-mediated transcription. HSF1 deficiency diminishes c-MYC DNA binding and dampens its transcriptional activity genome-widely. Mechanistically, c-MYC, MAX, and HSF1 assemble into a transcription factor complex on DNAs and, surprisingly, the DNA binding of HSF1 is dispensable. Instead, HSF1 physically recruits the histone acetyltransferase GCN5, thereby promoting histone acetylation and augmenting c-MYC transcriptional activity. Thus, our studies reveal that HSF1 specifically potentiates the c-MYC-mediated transcription, distinct from its role in the canonical heat-shock response. Importantly, this mechanism of action engenders two distinct c-MYC activation states, primary and advanced, which may be important to accommodate diverse physiological and pathological conditions.

overall_design: To elucidate the impact of HSF1 on the c-MYC-mediated transcriptional program, we compared the genome occpancy of c-MYC between Hsf1 WT and Hsf1 CKO mouse embryonic fibroasts (MEFs) by CUT&RUN-seq with E Coli spike-in normalization control. Furthermore, we compared the gene expression between MEFs transfected with control siRNAs and MEFs transfected with Hsf1-targeting siRNAs by RNA-seq with ERCC ExFold spike-in normalization control.

first: Meng

last: Xu

last: Lin

first: Babul

middle: M

last: Ram

first: Omprakash

last: Shriwas

first: Kun-Han

last: Chuang

first: Siyuan

first: Kuo-Hui

last: Su

first: Zijian

last: Tang


title: Osteoarthritic chondrocytes undergo a glycolysis-related metabolic switch upon exposure to IL-1β or TNF-α

city: Nantes

first: Anais

last: Defois

address: 1 place Alexis Ricordeau

country: France

institute: Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR 1229

summary: Inflammation, which is mainly sustained  by pro-inflammatory cytokines such as IL-1β, TNF-α, and IL-6, plays an important role in osteoarthritis progression. However, the therapeutic failures of recent clinical trials evaluating anti-IL-1, anti-TNF, and anti-IL-6 drugs highlight the lack of overall understanding of the effects of these cytokines on chondrocytes. Here, we generated a comprehensive transcriptomic and proteomic dataset of osteoarthritic chondrocytes treated with these cytokines to describe their pro-inflammatory signature and compare it to the transcriptome of non-osteoarthritic chondrocytes. We first identified specific dysregulation of metabolic-related genes in OA chondrocytes. A metabolic shift, toward increased glycolysis at the expense of mitochondrial respiration, was specifically identified and confirmed by Seahorse® assay of osteoarthritic chondrocytes treated with IL-1β or TNF-α. These data show a strong association between inflammation and metabolism, indicating that understanding metabolic dysregulations should be a focus of future investigations for the design of therapies for osteoarthritis.

overall_design: This experiment compare the gene expression of untreated primary human chondrocytes (control) and treated during 24h with IL-1beta (1ng/mL) or TNF-alpha (25 ng/mL) or IL-6 (50 ng/mL). We used two types of chondrocytes : primary human chondrocytes from  OA patients undergoing total knee surgery (OAC) or primary human chondrocytes from non-osteoarthritic joint of patients undergoing scoliotic surgery (NC).

first: Anaïs

first: Nina

last: Bon

first: Alexandre

last: Charpentier

first: Mélina

last: Georget

first: Frédéric

last: Blanchard

first: Marie-Astrid

last: Boutet

first: Jérôme

last: Guicheux

first: Claire

last: Vinatier


title: Gene expression in control or MAD2L1BP (R285*) human MI oocyte

city: Hefei

first: Caoling

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

summary: SMARTseq2  identified different gene expression in control or MAD2L1BP (R285*) human MI oocyte

overall_design: MI oocytes retrieved from unidentified control or the MAD2L1BP (R285*)  patient were used for Mini-bulk SMART-seq2

first: Wenqing

last: Li

first: Caolin


title: An ethanol extract of Coptidis rhizoma induces apoptotic cell death in induced pluripotent stem cells and suppress teratoma formation

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: We explored whether an ethanol extract of coptidis rhizoma (ECR) exhibited anti-teratoma activity and identified the main active components involved in the selective elimination of undifferentiated iPSCs.

overall_design: We profiled gene expresion in vehicle-treated iPSCs (control) and iPSCs treated with 5 μg/mL of an ECR (ECR-Low) or 10 μg/mL of an ECR (ECR_High).

first: Aeyung

last: Kim

first: Sun-Ku

last: Chung


title: Vascularization of cardiac organoids controls the extracellular matrix environment and regulates organoid functionality

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Crosstalk between cardiac cells is critical during heart development but its role in organ maturation is still largely uncharacterised. Here, we show that endothelial cells increase the force of contraction and enhance the expression of mature sarcomeric proteins and extracellular matrix (ECM) components in human pluripotent stem cell derived cardiac organoids (hCO). Endothelial cells regulate cardiac maturation and function both directly through secretion of ECM molecules and indirectly via paracrine signaling. Laminin α5, an endothelial enriched ECM protein, was identified as a key regulator of cardiac maturation and contractility in vitro. In vivo loss-of-function studies in mice confirmed that Lama5 was required for myocardial expansion during heart development in vivo. In addition, paracrine PDGF signaling was identified as a mediator of increased ECM deposition and cardiac contractility in hCO. This study uncovers matrix regulatory functions of endothelial cells governing cardiac maturation and highlights the importance of multicellularity for organoid models.

overall_design: Lymphatic endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56)  hearts were isolated by enzymatic dissociation and FACS. RNA sequencing (RNA-seq) was performed on these cell populations to generate a transcriptomic atlas of the major cardiac cell populations during cardiac development, repair and regeneration.

first: Gregory

last: Quaife-Ryan

first: Enzo

last: Porrello


title: Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow through Oxford Nanopore sequencing

status: Public on May 19 2023

city: Hong Kong

first: Xudong

last: Liu

address: Tat Chee Avenue Kowloon Tong

institute: City University of Hong Kong

summary: Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking.   We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites.  This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.

overall_design: Wild-type Tubingen (TU) zebrafish lines were obtained from the Zebrafish International Resource Center (ZIRC, USA). The study received approval from the Committee on the Use of Laboratory and Research Animals (CULATR) at the University of Hong Kong (HKU). Kidney marrow from 8-month-old WT zebrafish was collected, dissociated in 0.9X PBS via pipetting, and filtered through a 40 µm nylon cell strainer (Corning, NY, USA). Some samples underwent treatment with eBioscience™ 1x RBC Lysis Buffer (Invitrogen, MA, USA) to lyse red blood cells, and these samples were designated as the KM group. Samples without red blood cell lysis were categorized as the KMB group. The resulting cells were centrifuged at 500g for 5 minutes, resuspended, filtered, and washed twice with 0.9X PBS for DNA extraction. Genomic DNA was extracted using QIAamp DNA Kits (Qiagen, Germany).

first: Ying

last: Ni

first: Dandan

last: Wang

first: Silin

last: Ye

first: Mengsu

last: Yang

first: Xuan

last: Sun

first: Anskar

last: Leung

first: Runsheng


title: HIV-1 activates oxidative phosphorylation in infected CD4 T cells in a human tonsil explant model

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Human immunodeficiency virus type 1 (HIV-1) leads to a chronic, incurable infection that causes immune activation, resulting in chronic inflammation in people with HIV-1 (PWH) despite virologic suppression on antiretroviral therapy (ART). The mechanisms underlying this chronic inflammation are multifactorial; literature supports the role of lymphoid structures as reservoirs for viral latency and immune activation. The cell type-specific transcriptomic changes induced by HIV-1 infection in lymphoid tissue have not been analyzed. Human tonsil explants from four donors were infected with HIV-1 ex vivo. Single-cell RNA sequencing (scRNA-seq) was performed to evaluate the represented cell types and the impact of infection, differential gene expression, and inflammatory signaling pathways. Infected CD4+ T cells exhibited increased respiratory electron transport pathway genes, activating oxidative phosphorylation. Additionally, macrophages exposed to the virus but uninfected demonstrated increased NLRP3 inflammasome pathway genes, activating the NLRP3 inflammasome and stimulating proinflammatory signaling pathways and pyroptotic cell death. These observations support important mechanistic understanding to drive the development of therapeutic strategies to eradicate disease in PWH.

overall_design: Single cell RNA-seq experiment:  Human tonsil explants infected with HIV-1NL-CI, a CXCR4-tropic fluorescent reporter virus with mCherry in place of nef where nef is expressed on an IRES

first: Talia

last: Swartz

first: Kristin

last: Beaumont


title: Bulk RNA sequencing of MCPyV positive and negative patient derived Merkel cell carcinoma cell lines

city: Long Beach

first: Ling

last: Gao

state: California

address: 5901 E.7th Street

institute: Department of Veterans Affairs

summary:
To investigate cell line intrinsic factors dictating cell fate and therapeutic vulnerabilities
Gene expression profiling of cell lines based on their proximity and viral status

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the cell lines

first: Aarthi

last: Kannan

first: Bhaba

last: Das


title: Transcriptome-based chemical screens identify CDK8 as a common barrier in multiple cell reprogramming systems

city: 海淀区

first: Jun

last: Li

state: 北京市

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

institute: Peking University


title: Transcriptome-based chemical screens identify CDK8 as a common barrier in multiple cell reprogramming systems [Drug-seq2]

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

summary: Fibroblasts can be chemically induced to pluripotent stem cells (CiPSCs) through an extraembryonic endoderm (XEN)-like state or directly converted into other differentiated cell lineages. However, the mechanisms underlying chemically-induced cell fate reprogramming remain unclear. Here, a transcriptome-based screen of biologically active compounds uncovered that CDK8 inhibition was essential to enable chemically-induced reprogramming from fibroblasts into XEN-like cells, then CiPSCs. RNA-seq analysis showed that a CDK8 inhibitor, MSC2530818, inhibited pro-inflammatory pathways that suppress chemical reprogramming, and facilitated the induction of a multi-lineage priming state, indicating the establishment of plasticity in fibroblasts. CDK8 inhibition also resulted in chromatin accessibility profile and Pol II occupation profile similar to that under initial chemical reprogramming. Moreover, CDK8 inhibition greatly promoted transgene-mediated reprogramming of mouse fibroblasts into hepatocyte-like cells, and chemical reprogramming of human fibroblasts into adipocytes. These collective findings thus define CDK8 as a general molecular barrier in multiple cell reprogramming processes, and as a common target for inducing plasticity and cell fate conversion.

overall_design: MEF cells were cultured in CFAE+8 plus compounds (MCE Cat.No. HY-L009,RackCode: SA00153143) medium for 4 days and analyzed using Drug-seq2

first: Yunfei

last: Bai

first: Yang

first: Zhongya

last: Song

last: Yong

last: Zhao


title: Molecular determinants of Hsp90 recognition of Src kinase revealed by deep mutational scanning

city: Seattle

first: Douglas

last: Fowler

state: Washington

department: Genome Sciences

institute: University of Washington

summary: Protein tyrosine kinases are involved in regulating growth and proliferation in cells and are often hyperactive in cancerous tissue. Tyrosine kinase inhibitors have been used to limit hyperactivity but become ineffective due to the appearance of resistance mutations. A common trait of hyperactive protein kinases is its strict client relationship with molecular chaperone Hsp90. However, the mechanism behind Hsp90 client kinase recognition is poorly understood. Here we measure the functional effect of thousands of single amino acid variants in the Src kinase domain to identify positions invovled in Hsp90 client recognition.

overall_design: A barcoded plasmid library of Src variants was expressed in S. cerevisiae and four samples were collected during duplicate outgrowth experiments. Plasmid DNA was extracted from each sample from which barcodes were amplified and counted via Illumina sequencing. Barcodes were linked to a corresponding variant sequence using a barcode sequence map.

first: Dustin

last: Maly


title: Single cell RNAseq analysis of dorsal root ganglia from global and cLTMR-specific Nav1.7 knockout mice

first: James

last: Maksymetz

summary: We investigated changes in gene expression and cell type abundance using single cell RNA sequencing of dorsal root ganglia (DRG) isolated from global (pCAGG-CreER x Nav1.7 floxed) and C-low threshold mechanoreceptor (cLTMR)-specific (Slc17a8-Cre x Nav1.7 floxed) Nav1.7 knockout mice. We identified a reduction in the fraction of cLTMRs and a concomitant emergence of a distinct cell cluster located closely to cLTMRs in the UMAP projection in global Nav1.7 knockout DRGs. This novel cell cluster expressed previously described cLTMR markers with distinct gene expression changes such as a downregulation of Ceacam10 and an upregulation of Penk expression. We further found that cLTMR-specifc knockout of Nav1.7 induced the same shift in cLTMR cells to a knockout-specific cluster with upregulated Penk expression.

overall_design: Single cell RNAseq libraries were prepared from lumbar DRGs (L4,5,6) isolated bilaterally from adult, global Nav1.7 knockout (CreER+, N = 7) and littermate controls (CreER-, N = 5) 4 week post-tamoxifen dosing. scRNAseq libraries were also prepared from lumbar DRGs isolated from adult cLTMR-specific Nav1.7 knockout (N = 2) and littermate controls (N = 2).

first: Michelle

last: Dourado

first: Kevin

last: Huang

first: Josh

last: Kaminker

first: David

last: Hackos


title: PHDs-seq: A Large-scale Phenotypic Screening Method for Drug Discovery through Parallel Multi-readout Quantification [Targeted RNA-seq: KF-b1_1204]

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

summary: High-throughput phenotypic screening is a cornerstone of drug development and the main technical approach for stem cell research. However, simultaneous detection of activated core factors responsible for cell fate determination and accurate assessment of directional cell transition are difficult using conventional screening methods that focus on changes in only a few biomarkers. The PHDs-seq (Probe Hybridization based Drug screening by sequencing) platform was developed to evaluate compound function based on their transcriptional effects in a wide range of signature biomarkers. In this proof-of-concept demonstration, several sets of markers related to cell fate determination were profiled in adipocyte reprogramming from dermal fibroblasts. After validating the accuracy, sensitivity and reproducibility of PHDs-seq data in molecular and cellular assays, a panel of 128 signalling-related compounds was screened for the ability to induce reprogramming of keloid fibroblasts (KF) into adipocytes. Notably, the potent ATP-competitive VEGFR/PDGFR inhibitor compound, ABT869, was found to promote the transition from fibroblasts to adipocytes. This study highlights the power and accuracy of the PHDs-seq platform for high-throughput drug screening in stem cell research, and supports its use in basic explorations of the molecular mechanisms underlying disease development.

overall_design: Targeted Gene expression profiling analysis of PHDs-seq data for human skin cells (KF) treated with AD medium (DMEM/high glucose, 1% ITS, 0.5mM isobutylmethylxanthine, 1 μM dexamethasone) or KF medium.

last: Chi

last: Yang

first: Xin

last: Zhou

last: Liu


title: PHDs-seq: A Large-scale Phenotypic Screening Method for Drug Discovery through Parallel Multi-readout Quantification

address: 北京市海淀区颐和园路5号北京大学王克桢楼207


title: Transcriptome-based chemical screens identify CDK8 as a common barrier in multiple cell reprogramming systems [RNA-seq]

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

overall_design: Comparative gene expression profiling analysis of RNA-seq data in MEFs with MEF medium, CFAE+8, CFAE+8+MSC, CFAE+6 (C, CHIR99021; F, Forskolin; A, AM580; E, EPZ04777; 6, E-616452; 8, A-83-01; MSC, MSC2530818) induction for 4 days, respectively.


title: Lymph node medulla is a quorum sensing niche for developing dendritic cells [preDC]

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Conventional dendritic cells (cDC) and macrophages form complex networks that are essential for tissue homeostasis and immune defence. While the differentiation and residency of macrophages is regulated within distinct tissue niches, it is unclear whether DC development in tissues follows similar principles given their short life-span. By studying cDC development using fate mapping and depletion/reconstitution approaches, we found that preDC undergo distinct developmental stages. This development that preceded DC maturation was guided within the medullary cords of LNs. Intravital imaging and in situ photoconversion showed that preDC homed via medullary vessels and used them as guiding structures for their migration to the LN parenchyma. Infection-induced relocation of cDCs changed the availability of lymphocyte-derived Flt3l in the medulla which accelerated preDC development to ensure their local replenishment and responsiveness. Uncovering these principles of the spatiotemporal development of cDC and their complex cellular networks may guide novel angles for immunotherapy against cancer.

overall_design:
B6 wt mice were left untreated. Prtn3-Ert2Cre.lsl.tdTomato mice were treated either at day 3, 5 or 7 before organ harvest with tamoxifen. sdLN from all mice were isolated and digested with Collagenase D and DNase I. preDC were sorted based on CD11c, MHCII and CD135 expression using FACS AriaIII. The 4 different treatment conditions were stained with different antibody Hashtags before sorting and pooled for sequencing after the sort.

Hashtag definitions:
Hashtag1_TotalA0301: day 3
Hashtag2_TotalA0302: day 5
Hashtag3_TotalA0303: day 7
Hashtag4_TotalA0304: ctrl

first: Konrad

last: Knöpper

first: Panagiota

last: Arampatzi

first: Wolfgang

last: Kastenmüller


title: Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence [RNA-Seq]

first: Lorant

last: Szekvolgyi

summary: Arabidopsis NODULIN HOMEOBOX (NDX) is a plant-specific transcriptional regulator whose role in small RNA biogenesis and heterochromatin homeostasis has recently been described. Here we extend our previous transcriptomic analysis to the flowering stage of development. We performed mRNA-seq and small RNA-seq measurements on inflorescence samples of wild-type and ndx1-4 mutant (WiscDsLox344A04) Arabidopsis plants. We identified specific groups of differentially expressed genes and noncoding heterochromatic siRNAs (hetsiRNAs) whose transcriptional activity were significantly changed in the absence of NDX. Overall, we provide a comprehensive data source on the coding and noncoding transcriptomes of NDX-deficient Arabidopsis flowers to serve as a basis for further studies and analyses on NDX function.

overall_design: Gene expression analysis of RNA-seq data for A. thaliana Col-0 wild type and ndx1-4 mutant (5-week-old plant, flower, 2 replicas).

first: Orsolya

last: Feró

first: Zsolt

last: Karányi

first: Éva

last: Nagy

first: Ágnes

last: Mosolygó-L

first: Henrik

last: Szaker

first: Tibor

last: Csorba

first: Lóránt

last: Székvölgyi


title: Bisphenol C inhibits liver and intestinal cell proliferation in larval zebrafis

city: hangzhou

first: jiafeng

last: chen

state: zhejiang

address: yuhangtang road 866

institute: zhejiang university

summary: Considering Bisphenol C can be widely detected, this study reveals developmental defects in the liver and intestine of zebrafish exposed to BPC and delves into the specific and comprehensive mechanisms involved.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 72hpf zebrafish with or without BPC exposure

first: Jinfeng

first: Jiebo

last: Lin

first: Jiafeng

last: Chen


title: PHDs-seq: A Large-scale Phenotypic Screening Method for Drug Discovery through Parallel Multi-readout Quantification [Targeted RNA-seq: KF-b2_0118]

first: Jun

last: Li

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

last: Chi

first: Yang

last: Yang

first: Zhongya

last: Song

last: Yong

first: Xin

last: Zhou

last: Zhao