title: An abundance of binary promoter switches in lineage-determining transcription factors indicates a digital component of cell fate determination

status: Public on Oct 27 2023

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: An examination of transcription factor genes revealed an abundance of convergent and divergent sense/antisense promoter pairs, suggesting that competing promoters may control cell fate determination. We used 5' single cell RNAseq (5' scRNAseq) to examine divergent and convergent transcription in CD34+ hematopoietic progenitors, freshly purified innate lymphocytes from tonisl, and peripheral blood NK cells

overall_design: Peripheral blood NK cells were purified using the RosetteSep Human NK Cell Enrichment Cocktail (STEMCELL Technologies). CD34+ hematopoietic progenitor cells were enriched using the Indirect Human CD34 MicroBead Kit (Miltenyi Biotec). Following cell sorting, cells were stained for flow cytometry and CD34+ cells were further purified via sorting to >99.9% purity on an FACSAria II cell sorter (BD Biosciences).Purified CD34+ progenitors were cultured for 2 weeks with OP9 stroma, FLT3-ligand, KIT-ligand, and IL3. Human innate lymphoid cells were enriched from fresh tonsil tissue and blood samples  using a custom human NK cell enrichment RosetteSep reagent containing a mixture of bivalent antibodies against glycophorin A and CD3, CD4, CD19, CD20, CD36, CD66b, and CD123.

first: Stephen

last: Anderson

first: Hongchuan

last: Li

first: Michael

last: Ruesch

first: Caprice

last: Eisele

first: Aharon

last: Freud


title: The GLI-code controls HNF1A levels during in-vitro foregut differentiation

city: BErgen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

type: Expression profiling by high throughput sequencing

summary: Differentiation of human induced pluripotent stem cells towards pancreatic islet endocrine cells is a complex process, involving the stepwise modulation of key developmental pathways, such as the Hedgehog signaling inhibition during early differentiation stages. In tandem with this active inhibition, key transcription factors for the islet endocrine cell fate, such as HNF1A, show specific changes in their expression patterns. Here we designed a forthright pilot study aimed at investigating the potential interconnection between HH-signaling inhibition and the increase in the HNF1A expression during early regeneration, by inducing changes in the GLI code. This unveiled a link between the two, where GLI3-R mediated Hedgehog target genes inhibition is apparently required for HNF1A efficient expression.

overall_design: PGP1 iPSc were differentiated toward pancreatic endocine cell fate following the differentiation protocol by Rezania 2014. At different stage 3, 4, 5, 6, and 7 samples were collected for mRNA sequencing. The experiment was run in triplicates.

first: Lucas

last: Unger

first: Andreas

middle: F

last: Mathisen

first: Thomas

middle: A

last: Legøy

first: Luiza

last: Ghila


title: Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus [RNA-Seq 1]

status: Public on Oct 17 2023

city: Los Angeles

first: Kelsey

last: Martin

state: CA

address: 615 Charles E Young Drive South

department: Biological Chemistry

country: USA

institute: UCLA

summary: Long-term memory formation is dependent on gene expression changes in the hippocampal region of the brain. Aging-related memory impairments and incidence of pathological memory disorders such as Alzheimer’s disease differ between males and females, and yet little is known about how aging-related changes to the transcriptome and chromatin environment differs between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus of both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response, cell adhesion, and synaptic function, and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic activity. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Overall, sex differences in both gene expression and chromatin accessibility were amplified with aging, revealing that although some aspects of hippocampal aging are sex-independent, underlying sex differences in gene expression and chromatin dynamics in aging may shed light on sex differences in aging-related and pathological memory loss.

overall_design: RNA-Seq with polyA selection from hippocampus of young adult (10 week) or aged (80 week) male and female mice. Four biological replicates/group were sequenced, for a total of 16 samples.

first: Jennifer

middle: M

last: Achiro

first: Yang

last: Tao

first: Fuying

last: Gao

first: Chia-Ho

last: Lin

first: Marika

last: Watanabe

first: Sylvia

last: Neumann

first: Giovanni

last: Coppola

first: Douglas

middle: L

last: Black

middle: C


title: Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus [RNA-Seq 2]

overall_design: RNA-Seq from hippocampus of young adult (10 week) or aged (80 week) male and female mice. Four biological replicates/group were sequenced, for a total of 16 samples.


title: Hypoblast from human pluripotent stem cells regulates epiblast development [RNA-seq]

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Recently, several studies using cultures of human embryos together with single-cell RNA-seq (scRNA-seq) analyses have revealed differences between humans and mice, necessitating the study of human embryos 1-8. Despite the importance of human embryology, ethical and legal restrictions have limited post-implantation stage studies. Thus, recent efforts have focused on developing in vitro self-organising models using human stem cells 9-18. Here, we established a genetic approach to generate authentic hypoblast cells (nHyC) - known to give rise to one of the two extraembryonic tissues essential for embryonic development - from naïve human pluripotent stem cells (hPSCs). Our nHyCs spontaneously assemble with naïve hPSCs to form a three-dimensional bilaminar structure (bilaminoids) with a pro-amniotic-like cavity. In the presence of additional naïve hPSC-derived analogues of the second extraembryonic tissue, the trophectoderm, the efficiency of bilaminoid formation increases from 20% to 40%, and the epiblast within the bilaminoids continues to grow due to IL6 secreted by the trophectoderm. Furthermore, we show that bilaminoids robustly recapitulate the patterning of the anterior-posterior axis and the formation of cells reflecting the pre-gastrula stage, whose emergence can be shaped by genetically manipulating the DKK1/OTX2 hypoblast-like domain. We therefore model and reveal mechanisms by which the two extraembryonic tissues efficiently guide the stage-specific growth and progression of the epiblast as it establishes the post-implantation landmarks of human embryogenesis.

overall_design: Analyzing transcriptional profiles in naïve PSCs, primed PSCs, PDGFRA positive cells induced by GATA6 o/e from naive and primed PSCs; induced by 7F, 4F, and 2F from naïve PSCs and bilaminoids at day 6, day9.

first: Takumi

last: Okubo

first: Takuya

last: Yamamoto


title: Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories

status: Public on Nov 01 2023

city: Beijing

first: jingyu

last: wang

address: xueyuan street

country: China

institute: THU

summary: The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge through the implementation of different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons, as they represent a relatively small proportion of all cortical cells, migrate tangentially from their embryonic origin to the cerebral cortex, and have a protracted development. Here we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells, the most diverse subclass of inhibitory neurons in the mouse cerebral cortex. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is further refined during early postanal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons. Thus, the diversification of SST+ inhibitory neurons involves a temporal cascade of unique molecular programs driving their divergent developmental trajectories.

overall_design: We dissected the neocortex of SstCre/+;RCE mice at embryonic stage (E) 16.5, postnatal stage (P) 1, and P5 and performed fluorescent activated cell sorting (FACS) to obtain cell populations enriched in SST+ neurons. We then examined gene expression in individual cells using 10x Genomics Chromium sequencing. We performed RNA sequencing on a total of 12,324 cells from the three developmental stages.

first: Josephine

last: Fisher

first: Zhen

last: Long

first: Marieke

last: Verhagen


title: Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation

status: Public on Oct 28 2023

city: Würzburg

first: Chase

middle: Lawrence

last: Beisel

address: Josef-Schneider Straße 2

department: Helmholtz-Institute for RNA-based Infection Research (HIRI)

country: Germany

institute: Helmholtz Centre for Infection Research (HZI)

type: Non-coding RNA profiling by high throughput sequencing

summary: CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host’s genomic DNA, leading to lethal self-targeting. While self-targeting can be circumvented through different mechanisms, natural examples remain poorly explored. Here, we investigate extensive self-targeting by two CRISPR-Cas systems encoding an astonishing 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans. We show, based on transcriptomics analyses, that the native I-C and I-F1 systems are actively expressed and that CRISPR RNAs are properly processed. When expressed in Escherichia coli, each Cascade complex binds its PAM-flanked DNA target to block transcription, while the addition of Cas3 paired with genome targeting induces cell killing. While exploring how X. albilineans survives self-targeting, we predicted putative anti-CRISPR proteins (Acrs) encoded within the bacterium’s genome. Screening of identified candidates with cell-free transcription-translation systems and in E. coli revealed two Acrs, which we named AcrIC11 and AcrIF12Xal, that inhibit Cas3 but not Cascade of the respective system. These findings reveal how a bacterium tolerates extensive self-targeting through two CRISPR-Cas systems and expand the suite of Cas3-inhibiting Acrs.

overall_design: To assess CRISPR array processing and cas gene expression in X. albilineans, we performed RNA-Seq and small RNA-Seq in duplicates.

first: Franziska

last: Wimmer

first: Frank

last: Englert

first: Katharina

middle: G

last: Wandera

first: Omer

middle: S

last: Alkhnbashi

first: Scott

middle: P

last: Collins

first: Rolf

last: Backofen


title: Gene expression profile at single cell level of thyroid cells from thyroid cancer tissues

city: DAEJEON

first: SEONG EUN

last: LEE

address: 282 MUNHWA-RO

country: South Korea

institute: CHUNGNAM NATIONAL UNIVERSITY

summary: We performed single-cell RNA sequencing (scRNA-seq) on 3 normal thyroid, 7 papillary thyroid cancer (PTC), and 5 anaplstic thyroid cancer (ATC) cases. We used scRNA-seq to analyze serirne/glycine metabolism in thyroid tumors.

overall_design: The thyroid cells were obatained from tissues of papillary thyroid cancer and anaplastic thyroid cancer for single-cell RNA sequencing.

first: Seong

middle: E

last: Lee

first: Seongyeol

last: Park

first: Bon

last: Koo

first: Yea

last: Kang


title: Identification of a Therapeutically Targetable JAK-STAT Enriched Androgen Receptor (AR) and AR Splice Variant Positive Triple Negative Breast Cancer Subtype [MDA-MB-453]

status: Public on Oct 31 2023

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with no targeted therapeutics. The luminal androgen receptor (LAR), one of the six TNBC subtypes, constitutes 15% of TNBC and is enriched for AR and AR-target genes. Here, we show that a cohort of TNBC not only expresses full-length AR (AR-FL) at a much higher rate (~80%) than previously reported, but also expresses AR splice variants (AR-SVs) (~20%), subclassifying the LAR-TNBC subtype into LAR-FL, LAR-AR-SV, or dual positive. Higher AR and AR-SV expression and corresponding aggressive phenotypes were observed predominantly in specimens obtained from African American women. RNA sequencing of LAR TNBC specimens indicates an enrichment of hallmark interferon, JAK-STAT, and androgen signaling pathways, which were exclusive to AR-expressing epithelial cancer cells as demonstrated by spatial genomics. LAR and LAR-AR-SV TNBC cell proliferation, orthotopic cell line and patient-derived xenograft, and patient-derived tumor explants growth were inhibited by AR N-terminal domain (NTD)-binding selective AR degrader (SARD) that irreversibly inhibits AR or by the JAK inhibitor ruxolitinib. Subsequent biochemical analysis suggests that STAT1 is an AR coactivator, and SARD or ruxolitinib blocks this coactivation. Collectively, our work identifies and characterizes a pharmacologically targetable and previously unreported TNBC subtype predominantly in African American women and identifies a growth-promoting interaction between AR and JAK-STAT signaling.

overall_design: MDA--MB-453 cells were maintained in charcoal-stripped FBS containing medium for 48 hours. Medium was changed again and treated with vehicle or 3 uM UT-105 in the presence of 0.1 nM R1881. Cells were harvested 20 hours after treatment, RNA was extracted, and sequenced (n=3/group).

first: Ramesh

last: Narayanan


title: Profiling of IL-33 target genes incytotoxic T cells, T helper 1 and T helper 2 cells

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To decipher the T cell subset-specific consequences of IL-33 sensing, we profiled early changes in transcriptional activity of in vitro differentiated CTLs, Th1 cells and Th2 cells upon short-term stimulation with IL-33.

overall_design: Comparative gene expression profiling analysis of the effects of IL-33 on CTLs, Th1 and Th2 cells using RNA-Seq and single-cell RNA-Seq of WT- and Il1rl1-ExAB-KO CTLs after an acute LCMV infection.

first: Tobias

last: Brunner

first: Sebastian

last: Serve

first: Anna-Friederike

last: Marx

first: Maria

last: Dzamukova

first: Nayar

last: Duran

first: Phillipe

last: Saikali

first: Christoph

last: Kommer

first: Frederik

last: Heinrich

first: Gitta

last: Heinz

first: Thomas

last: Höfer

first: Mir-Farzin

last: Mashreghi

middle: D

last: Pinschewer

first: Ralf

last: Kühn

first: Max

last: Löhning


title: Mitochondrial SHMT2 is a crucial therapeutic target in dedifferentiated thyroid cancer

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

institute: KRIBB

summary: The roles of the serine/glycine metabolic pathway (SGP) have recently been evident in certain types of tumor physiology; however, the pathological  relevance of SGP in undifferentiated thyroid cancer remains unexplored. Herein, we employed a comparative transcriptome analysis of bulk RNA sequencing coupled with single-cell RNA sequencing, showing that the high expression of SHMT2 and MTHFD2 is tightly associated with a low thyroid differentiation score (TDS) and poor clinical features in thyroid cancer. In addition, unique metabolic reprogramming of SGP-relevant pathways in dedifferentiated cancer cells, and a distinct trajectory of a subpopulation of tumor cells with a high mitochondrial one-carbon pathway was observed. More importantly, such dramatic changes are functionally relevant, as inhibition of SHMT2 significantly compromises mitochondrial respiration and decreases tumor  size by upregulating TDS markers. Taken together, our results highlight the importance of the mitochondrial one-carbon pathway, including SGP, in undifferentiated thyroid cancer and suggest that SHMT2 is a novel therapeutic target.

overall_design: RNA-seq data of 632 fresh frozen tissues were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using NextSeq 500 platform (Illumina).

first: Seong

last: Lee

first: Seongyeol

first: Shinae

last: Yi

first: Seon-Kyu

last: Kim

first: Bon

last: Koo

first: Yea

last: Kang


title: Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus

first: Kelsey

last: Martin

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Induction of innate immune responses reverses HIV cognitive disease in mice: profile by RNAseq in the brain

status: Public on Oct 24 2023

city: New York

first: Alejandra

last: Borjabad

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine

summary: The extent of HIV immunodeficiency and related diseases has been greatly reduced by suppressive antiretroviral therapy but roughly 50% of infected people continue to develop mild neurocognitive disorder.   We established an experimental approach to investigate HIV brain disease by infection of wildtype mice with the chimeric HIV, EcoHIV.  The toll-like receptor 3 ligand, polyinosinic-polycytodylic acid (poly I:C), was used to induce innate immune responses prior to or during EcoHIV infection resulting in prevention of infection or reduced virus burden and reversed behavioral disease, respectively.  Here we employed RNAseq to profile brain gene expression in EcoHIV infected mice at the time of cognitive impairment and its reversal in infected, poly I:C treated mice.  We confirmed RNAseq findings by QPCR of a small set of transcripts.  The major pathways down-regulated by infection involved neuronal function and this dysregulation was largely reversed by poly I:C treatment.  Innate immune responses were the major functional pathways induced in infected, poly I:C treated mice that were absent in infected, untreated mice.  Our findings provide a framework to identify essential brain cell genes dysregulated by HIV infection and identify a complementary set of immune response genes that block infection and its associated brain disease.

overall_design:
To investigate the effect of Poly I:C in mice infection with the chimeric EcoHIV virus. Four groups: uninfected and infected, treated or not with Poly I:C, 3 mice each group. Brain tissue from the striatum was subjected to RNA sequencing.
---------------------------
The authors have not provided information to group each sample in the respective group.

first: Baojun

last: Dong

first: David

middle: J

last: Voslky

first: Mary

last: Potash


title: DNA damage repair in barley following double-strand breaks and its dependence on ATR

status: Public on Oct 19 2023

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

summary: Maintaining genome integrity presents a particular challenge for plants due to their sedentary lifestyle, which disables direct avoidance of unfavorable external conditions. Additionally, plants’ metabolic processes generate reactive molecules as by-products of e.g. photosynthesis, creating internal DNA-damaging conditions. Due to this, plants have developed a unique and strictly regulated web of DNA damage responses (DDR). We initiated analysis of the DDR system in cultivated barley (Hordeum vulgare), a temperate cereal model with a large and repeat rich genome. A series of DNA damaging assays was established to describe barley plants’ phenotypic response to chemically induced DNA double-strand breaks. The efficacy of assays as a tool to be used for assessing potential new DDR barley mutants was demonstrated. DNA damage response network activation in barley was assessed by transcriptome analysis using RNA sequencing for wild type and mutant in the DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (ATR). Considering the barley genome had only recently been sequenced, and it lacks the in-depth gene analysis, a list of potential DNA damage response genes in barley was compiled based on their homology with Arabidopsis genes. The comparison of transcripts in wild-type plants and atr mutants following genotoxic stress

overall_design: 7 days old  WT (Sebastian) and mutant (hvatr.g) barley seedlings grown on solid medium in vitro were transformed for six hours into liquid medium with or without 500 μg/ml zeocin.

first: Jovanka

last: Vladejic

first: Martin

last: Kovačik

first: Miriam

last: Szurman-Zubrzycka


title: RNA-Seq of ST2+ cytotoxic T cells, T helper 1 and T helper 2 cells

first: Pawel

last: Durek

summary: The pleiotropic alarmin interleukin-33 (IL-33) promotes the activity of many innate and adaptive immune cell subsets. Its receptor ST2 is constitutively expressed at high levels by type 2-biased immune cells including CD4+ T helper 2 (Th2) cells, innate lymphoid cells type 2 and highly potent regulatory T cells, allowing rapid sensing of IL-33 alarmin signals (Peine et al., 2015). In contrast, during viral infections, antiviral CD8+ cytotoxic T cells (CTLs) and CD4+ Th1 cells express ST2 at a low level in a transient and activation dependent way, suggesting that the ST2-coding gene Il1rl1 is regulated in a cell-type specific manner (Bonilla et al., 2012). To better understand the transcriptional regulation of the Il1rl1 gene in distinctly polarized T cells, we here performed RNA-Sequencing of in vitro activated, ST2 expressing CTLs, Th1 and Th2 cells.

first: Tobias

last: Brunner

first: Sebastian

last: Serve

first: Anna-Friederike

last: Marx

first: Maria

last: Dzamukova

first: Nayar

last: Duran

first: Phillipe

last: Saikali

first: Christoph

last: Kommer

first: Frederik

last: Heinrich

first: Gitta

last: Heinz

first: Thomas

last: Höfer

first: Mir-Farzin

last: Mashreghi

first: Daniel

last: Pinschewer

first: Ralf

last: Kühn

first: Max


title: MZ1, a BRD4 inhibitor, exerted its anti-cancer effects by targeting the super-enhancer-regulated gene SDC1 in Glioblastoma [ChIP-Seq]

status: Public on Oct 16 2023

city: Suzhou

first: Gen

last: Li

state: Jiangsu

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

summary: Glioblastoma (GBM) is a relatively more common primary central nervous system tumor with a high degree of malignancy, high mortality, and complex surgical complete resection. MZ1 is a von Hippel-Lindau tumor suppressor (VHL)-based pan-BET-targeting PROTAC, which can bind to the target proteins (BET proteins, including BRD2, BRD3, and BRD4) and recruit them to the ubiquitin/ proteasome system for degradation. However, the function of MZ1 has not been assessed in GBM cells so far. In the present study, ChIP-Seq analysis was performed to explore the effect of MZ1 on GBM cells.

overall_design: U87 cells were treated with control (DMSO) or MZ1 for 48h, and then harvested for ChIP with H3K27Ac antibody.


title: MZ1, a BRD4 inhibitor, exerted its anti-cancer effects by targeting the super-enhancer-regulated gene SDC1 in Glioblastoma


title: Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus [ATAC-Seq]

first: Kelsey

last: Martin

overall_design: ATAC-Seq from hippocampus of young adult (10 week) or aged (80 week) male and female mice. Six biological replicates for young adult male, 7 biological replicates for aged adult male, 8 biological replicates each for young and aged female, for a total of 29 samples.

first: Jennifer

last: Achiro

first: Yang

last: Tao

first: Fuying

last: Gao

first: Chia-Ho

last: Lin

first: Marika

last: Watanabe

first: Sylvia

last: Neumann

first: Giovanni

last: Coppola

first: Douglas

last: Black


title: MZ1, a BRD4 inhibitor, exerted its anti-cancer effects by targeting the super-enhancer-regulated gene SDC1 in Glioblastoma [RNA-Seq]

summary: To investigate the function of MZ1 in the regulation of gene expression, we treated U87 cells with control (DMSO) or MZ1, respectively. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and MZ1 treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87 cells treated with  control (DMSO) or MZ1 for 48h.


title: Transcriptome and DNA methylation analyses highlight the role of menstrual cycle phase in tumorigenesis of endometriosis-related ovarian carcinoma histotypes [methylation]

status: Public on Oct 13 2023

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

type: Methylation profiling by genome tiling array

summary: Epithelial ovarian cancer, or ovarian carcinoma (OC), is a diverse disease. Two of the rarer subtypes, clear cell OC (CCOC) and endometrioid OC (ENOC), both arise from ovarian endometriotic cysts, particularly atypical endometriosis. CCOC and ENOC have similar mutation profiles and share a common cell of origin, but their cellular phenotypes and clinical outcomes are distinct; in particular, CCOC has poor clinical survival. The most well-known difference between the histotypes is the universal overexpression of HNF1B (Hepatocyte nuclear factor-1β) in clear cell tumors and overexpression of ESR1 in ENOC. It is not well understood how these discrete histotypes arise from the same cell of origin. Via transcriptional (n=57) and DNA methylation analysis (N=127) of these rare tumors, we show that CCOC closely resembles secretory endometrium in transcriptional profile; whereas ENOC transcriptomes resemble proliferative endometrium.

overall_design: This dataset represnts 127 samples profiled by 450K methylation array. The samples are from ovarian tumor subtypes: clear cell (N=19), endometrioid (N=48), and high-grade serous (N=60).

first: Hui

last: Shen


title: Transcriptome and DNA methylation analyses highlight the role of menstrual cycle phase in tumorigenesis of endometriosis-related ovarian carcinoma histotypes [RNA-Seq]

overall_design: 57 tumor samples from clear cell ovarian cancer (N=28) or endometrioid ovarian cancer (N=29) were profiled with RNAseq


title: Quantification of Bir1-dependent differential gene expression in swollen Aspergillus fumigatus conidia

status: Public on Oct 10 2023

city: Hanover

first: Elisa

middle: Marie

last: Vesely

state: NH

address: 74 College St

department: Microbiology and Immunology

institute: Dartmouth College

summary: This study aimed to understand the differences in gene expression when comparing Aspergillus fumigatus swollen conidia that overexpress an artifical Bir1 construct (strain published in Shlezinger et. al 2017) versus a parental control strain in RPMI + 0.5ug/mL voriconazole. The purpose of this experiment was to understand what basal expression differences may drive a decreased susceptibility to hydrogen peroxide upon subsequent treatment (not tested in this submission). The main results show that there is a significant upregulation of mitochondrial-related genes, included aconitate hydratase. These differences may account for increased susrvival upon cellular stressors in this strain background.

overall_design: RNA-seq profiling of swollen Conidia representing various genotypes: A. fumigatus wt strain, ATCC46645 +Histone H2A:: mRFP fusion, ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX, ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX-N 1-446aa.

first: Matthew

middle: R

last: James

first: Robert

last: Cramer

first: Tobias

last: Hohl


title: A type 1 immunity-restricted promoter of the IL-33 receptor gene drives antiviral T cell responses

first: Pawel

last: Durek

summary:
The pleiotropic alarmin interleukin-33 (IL-33) promotes the activity of many innate and adaptive immune cell subsets. Its receptor ST2 is constitutively expressed at high levels by type 2-biased immune cells including CD4+ T helper 2 (Th2) cells, innate lymphoid cells type 2 and highly potent regulatory T cells, allowing rapid sensing of IL-33 alarmin signals (Peine et al., 2015). In contrast, during viral infections, antiviral CD8+ cytotoxic T cells (CTLs) and CD4+ Th1 cells express ST2 at a low level in a transient and activation dependent way, suggesting that the ST2-coding gene Il1rl1 is regulated in a cell-type specific manner (Bonilla et al., 2012). To better understand the transcriptional regulation of the Il1rl1 gene in distinctly polarized T cells, we here performed RNA-Sequencing of in vitro activated, ST2 expressing CTLs, Th1 and Th2 cells. Further, to decipher the T cell subset-specific consequences of IL-33 sensing, we profiled early changes in transcriptional activity of CTLs, Th1 cells and Th2 cells upon stimulation with IL-33. Lastly, to better understand the role of IL-33 during an acute infection with lymphocytic choriomeningitis virus (LCMV), activated CD44+ CTLs were flowcytometrically sorted from infected C57BL/6 wildtype and Il1rl1 gene-targeted mice (Il1rl1-ExAB-/-) and subjected to combined single-cell gene expression and single cell TCR-Seq analysis.

This SuperSeries is composed of the SubSeries listed below.

last: Brunner

first: Sebastian

last: Serve

first: Anna-Friederike

last: Marx

first: Maria

last: Dzamukova

first: Nayar

last: Duran

first: Phillipe

last: Saikali

first: Christoph

last: Kommer

first: Frederik

last: Heinrich

first: Gitta

last: Heinz

first: Thomas

last: Höfer

first: Mir-Farzin

last: Mashreghi

first: Daniel

last: Pinschewer

first: Ralf

last: Kühn

first: Max

last: Löhning


title: Transcriptome and DNA methylation analyses highlight the role of menstrual cycle phase in tumorigenesis of endometriosis-related ovarian carcinoma histotypes.

first: Ian

last: Beddows


status: Public on Oct 04 2023

city: La Jolla

first: Yang

last: Li

address: 9500 Gilman Dr

institute: University of California San Diego

summary: A comparative atlas of single-cell chromatin accessibility in the human brainRecent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (ATAC-seq), we explored open chromatin landscapes across 1.1 million cells in 42 brain regions from three adults. Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly a third of the cCREs demonstrated conservation and chromatin accessibility in the mouse brain cells. We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer’s disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders.

overall_design: single-nucleus ATAC-seq in 42 human brain regions from three neurotypical male donors

last: Preissl

first: Bing

last: Ren


title: Hypoblast from human pluripotent stem cells regulates epiblast development

first: Yasuhiro

last: Takashima

first: Takumi

last: Okubo

first: Takuya

last: Yamamoto


title: Extracellular Matrix Viscoelasticity Promotes Liver Cancer Progression in Pre-Cirrhotic NASH

status: Public on Oct 14 2023

city: Stanford

first: Weiguo

last: Fan

address: 300 Pasteur Dr., M207 Alway Bldg.

institute: Stanford University School of Medicine

summary: Type 2 diabetes mellitus (T2DM) is a major risk factor for hepatocellular carcinoma (HCC). Changes in extracellular matrix (ECM) mechanics contribute to cancer development, and increased stiffness is known to promote HCC progression in cirrhotic conditions. T2DM is characterized by an accumulation of advanced glycation end products (AGEs) in the ECM; however, how this affects HCC in non-cirrhotic conditions is unclear. Here, we find that in patients and animal models AGEs promote changes in collagen architecture and enhance ECM viscoelasticity, with greater viscous dissipation and faster stress relaxation, but not changes in stiffness. High AGEs and viscoelasticity combined with oncogenic b-catenin signaling promote HCC induction, while inhibiting AGEs production, reconstituting the clearance receptor AGER1, or breaking AGE-mediated collagen crosslinks reduce viscoelasticity and HCC growth. Matrix analysis and computational modeling demonstrate that lower interconnectivity of AGEs-bundled collagen matrix, marked by shorter fiber length and greater heterogeneity, enhance viscoelasticity. Mechanistically, animal studies and 3D cell cultures show that enhanced viscoelasticity promotes HCC cell proliferation and invasion through an integrin β1–Tensin 1–YAP mechanotransduction pathway. These results reveal for the first time that AGEs-mediated structural changes enhance ECM viscoelasticity, and that viscoelasticity can drive cancer progression in vivo, independent of stiffness.

overall_design: Ragefl/fl (WT) mice were subjected to chow, FFD, or HiAD for 14 weeks. A group of HiAD-fed mice was injected i.p. daily with PM. A cohort of RageHepKO mice was placed on HiAD for 14 weeks as published10. RNA was prepared from three mice per each group, and RNA sequencing was performed at Novogene (USA). Gencode gene annotations version M18 and the mouse reference genome major release GRCm38 was derived from https://www.gencodegenes.org/. Dropseq tools v1.1249 were used for mapping the raw sequencing data to the reference genome.

first: Yisi

first: Natalie

last: Török


title: Identification of a Therapeutically Targetable JAK-STAT Enriched Androgen Receptor (AR) and AR Splice Variant Positive Triple Negative Breast Cancer Subtype [project4]

last: Johnson

overall_design: To investigate the transcriptome differences between cells that express only full-length AR and cells that express full-length AR and AR-V7. MDA-MB-453 (AR+ve) LAR TNBC cells were stably transfected with AR-V7. RNA from parental and AR-V7 -positive cells was extracted and sequenced.

first: Ramesh

last: Narayanan

first: Sarah

last: Asemota


title: Identification of a Therapeutically Targetable JAK-STAT Enriched Androgen Receptor (AR) and AR Splice Variant Positive Triple Negative Breast Cancer Subtype [project3]

overall_design: MDA-MB-453 cells were implanted in female NSG mice. Once the tumors reach 100-200 mm3, the animals were randomized and treated with vehicle or 60 mg/kg/day UT-105 or enzalutamide orally. Tumor volume was measured twice weekly. At the end of the study (28 days of treatment) the animals were sacrificed, tumors isolated, and weighed. RNA was extracted from the tumors and sequenced.

first: Jeremiah

last: Holt

first: Narayanan

last: Ramesh


title: Defining STAT5 target genes in thymic precursor cells at pre- and post-commitment stages

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

summary: STAT5 is critical for inducing lineage specifying transcription factors, establishing effector gene programs, upregulating IL-2Rα (also known as CD25), and supporting cell survival in response to environmental cues in mature T cells.  Although it has been shown that IL-7-induced STAT5 signaling is also essential for survival of thymic precursor cells, the exact roles of STAT5A and STAT5B and their target genes that contribute to the developmental program in early thymic development have been unknown.    To define STAT5 target genes in these early T-cell progenitors, we have performed CRISPR-Cas9 mediated acute deletion of Stat5a and Stat5b in combination.  We first carried out preliminary experiments to determine the stages in which IL-7 could induce maximal STAT5 phosphorylation in thymic double negative (DN) cells (B. Shin, unpublished data).  We then focused on genes responding to loss of STAT5 in two different stages: CD25+ Bcl11b- pre-commitment stage, and CD25+ Bcl11b+ post-commitment stage.  Of note, to generate these early pro-T cells in OP9-DLL1 coculture, we exploited bone-marrow precursor cells expressing a Bcl2 transgene to minimize survival defects due to loss of STAT5A and STAT5B.    Our data show that STAT5 is necessary, in both pre- and post-commitment stages, for optimal expression of the IL-2Rα gene (Il2ra), which is constitutively expressed in normal DN2 and DN3 pro-T cells. This dataset further defines a distinct set of additional genes responding more strongly to loss of STAT5 in pro-T cells. The linked manuscript by R. Spolski et al. and other datasets referenced therein include data documenting the genomic occupancy of STAT5B in corresponding stages.    In summary, our data define STAT5-responsive target genes during early T development.

overall_design: Bone-marrow progenitor cells from B6.CRISPR-Cas9;Bcl2;Bcl11b-mCherry/mCherry  transgene expressing mice were incubated with IL-7, Flt3-ligand (Flt3l), and SCF for overnight. Three sgRNAs against Stat5a and three sgRNAs against Stat5b were retrovirally introduced, and infected cells were cultured on OP9-DLL1 stromal cells with IL-7 and Flt3l.  After 6 days post infection, Lineage marker (Lin)- infection marker+ CD25+ mCherry- (Bcl11b reporter negative, pre-commitment stage) and CD25+mCherry+ (Bcl11b reporter negative, post-commitment stage) cells were FACS sorted and subjected to bulk RNA-seq.

first: Peng

first: Rosanne

last: Spolski

first: Jangsuk

last: Oh

first: Warren

last: Leonard

first: Ellen

middle: V

last: Rothenberg


title: Identification of a Therapeutically Targetable JAK-STAT Enriched Androgen Receptor (AR) and AR Splice Variant Positive Triple Negative Breast Cancer Subtype

first: Daniel


title: Gene expression profile analysis of the molecular mechanism of HOXD10 regulating epithelial ovarian cancer cells

status: Public on Oct 03 2023

city: Kaohsiung

first: ChiaYi

last: Hsu

state: State...

address: No. 100, Shih-Chung 1

department: Graduate Institute of Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

summary: Epithelial ovarian cancer (EOC) is the most common type of ovarian cancer. Although studies have reported that downregulation of HOXD10 expression may contribute to the migration and invasion abilities in EOC, much remains to be fully elucidated. The present study aimed to identify different gene expression profiles of HOXD10 overexpression from the Human OneArray microarray and bioinformatics for the regulation of the progression of EOC cells. Bioinformatics analysis revealed that the pathways of the genes with different expressions were related to oxidative phosphorylation and mitochondrial function. Although the detailed regulatory mechanism between HOXD10 and the targeted oxidative phosphorylation genes is not yet fully understood, the findings of the present  provide novel insight on HOXD10-mediated pathways for cancer metabolism, carcinogenesis, and the progression of EOC.

overall_design: Examination of HOXD10 in TOV112D

first: C

middle: Y

last: Tsai

first: H

middle: W

last: Lo

first: Y

last: Ou

last: Lin

last: Chen

first: E


title: Transcriptomic profiling change of MDA-MB-231 cells overexpressing DNAJC12

status: Public on Oct 07 2023

city: Chengdu

first: MENGJIA

last: SHEN

address: 37 Guoxue Alley

institute: West China School of Medicine/West China Hospital of Sichuan University

summary:
Purpose: DnaJ heat shock protein family (Hsp40) member C12 (DNAJC12) belongs to Hsp40/DnaJ protein family containing a J domain.The goal of this study is to compare the transcriptomic profiling change of MDA-MB-231 cells overexpressing DNAJC12 compared with MDA-MB-231 cells transfected with empty vector.
Methods: 5×10^6 cells of each sample were collected, and total RNA was extracted using TRIZOL. After extraction, the RNA integrality was validated by Agilent 2100 bioanalyzer, and the qualified RNA was used to establish an RNA library, which was checked by quality control with Agilent 2100 bioanalyzer before sequencing. Transcriptome sequencing was achieved by Illumina Novaseq platform.

overall_design: MDA-MB-231 were divided into two groups transfected with DNAJC12v or empty vector separately, and each group contains 3 replicates.

first: Mengjia

last: Shen


title: Gene profiling changes in mouse bone marrow derived macrophages upon SUMOylation inhibition

status: Public on Oct 05 2023

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: SUMOylation, a posttranslational modification, regulates protein function by covalent attachment of small ubiquitin-like modifier (SUMO) proteins to a lysine (Lys) residue on target proteins. Here we use ML-792, a selective SUMO-activating enzyme (SAE) inhibitor, to inhibit global SUMOylation in macrophages derived from bone marrow of C57BL/6 mice. Mouse bone marrow cells isolated from 6–10 weeks C57BL/6 mice were cultured in IMDM medium supplemented with 10% (vol/vol) FBS and 10 ng/mL of macrophage colony-stimulating factor (M-CSF). After 6–8 days of differentiation, the cells were treated with vehicle or ML-792 at 0.5 μM for 24 h. Total RNA was purified using miRNeasy RNA isolation kit (Qiagen) then Ribo-Zero RNA-seq was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine macrophages treated with or without SUMO E1 inhibitor ML-792

first: Li

last: Du

first: Yuan

first: Min-Hsuan


title: Glycolysis induced by METTL14-related m6A methylation is essential for macrophage phagocytosis and phenotype in cervical cancer

city: Jinan

first: baoxia

last: cui

address: Wenhua

institute: Qilu Hospital of Shandong Univerity

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most abundant mRNA modification in mammals and it plays a vital role in various biological processes. However, the roles of m6A on cervical cancer tumorigenesis, especially macrophages infiltrated in the tumor microenvironment (TME) of cervical cancer, are still unclear. We analyzed the abnormal m6A methylation in cervical cancer, using CaSki and THP-1 cell lines, that might influence macrophages' polarization and/or function. In addition, C57bl-6j and Balb/c-nude mice were used for validation in vivo In this study, MeRIP-Seq analysis revealed the m6A profiles in cervical cancer. Then, we discovered the high expression of METTL14 (methyltransferase 14, N6-adenosine-methyltransferase subunit) in cervical cancer tissues can promote the proportion of PD-1 positive tumor-associated macrophages (TAMs), which have an obstacle to devour tumor cells. Functional, changes of METTL14 in cervical cancer inhibits the recognition and phagocytosis of macrophages to tumor cells. Mechanistically, the abnormality of METTL14 could target the glycolysis of tumor in vivo and vitro. Moreover, lactate acid produced by tumor glycolysis has an important role in the PD-1 expression of TAMs as a proinflammatory and immunosuppressive mediator. The study revealed the effect of glycolysis regulated by METTL14-related methylation on the expression of PD-1 and phagocytosis of macrophages, which showed that METTL14 was a potential therapeutic target for treating advanced human cancers.

overall_design: To study the m6A methylation levels in cervical cancer and normal tissues.

first: Baoxia

last: Cui

first: Bingyu

last: Wang


title: scGEX/scTCR-Seq of CD44+ cytotoxic T cells in LCMV-infected Wildtype and Il1rl1-ExAB-/- mice

first: Pawel

last: Durek

summary: To study the effect of IL-33 sensing on CD8 T cell differentiation during acute infection with lymphocytic choriomeningitis virus (LCMV), activated CD44+ CTLs were flowcytometrically sorted from infected C57BL/6 wildtype and Il1rl1 gene-targeted mice (Il1rl1-ExAB-/-) and subjected to combined single-cell gene expression and single cell TCR-Seq analysis.

overall_design: Comparative gene expression profiling analysis of the effects of IL-33 on CTLs, Th1 and Th2 cells using RNA-Seq and single-cell RNA-Seq of WT- and Il1rl1-ExAB-KO CTLs after an acute LCMV infection.

first: Tobias

middle: M

last: Brunner

first: Sebastian

last: Serve

first: Anna-Friederike

last: Marx

first: Maria

last: Dzamukova

first: Nayar

last: Duran

first: Phillipe

last: Saikali

first: Christoph

last: Kommer

first: Frederik

last: Heinrich

first: Gitta

middle: A

last: Heinz

first: Thomas

last: Höfer

first: Mir-Farzin

last: Mashreghi

last: Pinschewer

first: Ralf

last: Kühn

first: Max

last: Löhning


title: Steatosis Drives monocyte-derived Macrophage Accumulation in Human Metabolic Dysfunction-Associated Fatty Liver Disease

status: Public on Oct 01 2023

city: St. Louis

first: Joel

last: Schilling

state: MO

address: 660 S. Euclid Ave

department: Internal Medicine

institute: Washington University School of Medicine

summary:
Background & Aims: Metabolic dysfunction-associated fatty liver disease (MAFLD) is a common complication of obesity with a hallmark feature of hepatic steatosis. Recent data from animal models of MALFD have demonstrated substantial changes in macrophage composition in the fatty liver. In humans, the relationship between liver macrophage heterogeneity and liver steatosis is less clear.
Methods: Liver tissue from 21 participants was collected at time of bariatric surgery and analyzed using flow cytometry, immunofluorescence, and H&E microscopy. Single-cell RNA sequencing was also conducted on a subset of samples (n=3). Intrahepatic triglyceride content was assessed via MRI and tissue histology. Mouse models of hepatic steatosis were used to investigate observations made from human liver tissue.
Results: We observed variable degrees of liver steatosis with minimal fibrosis in our participants. Single-cell RNA sequencing revealed four macrophage clusters that exist in the human fatty liver encompassing Kupffer cells (KC) and monocyte-derived macrophages (MdM). The genes expressed in these macrophage subsets were similar to those observed in mouse models of MAFLD.  Hepatic CD14+ monocytes/macrophage number correlated with the degree of steatosis. Using mouse models of early liver steatosis we demonstrate recruitment of MdMs precedes KC loss and liver damage and that MdMs may serve a role in lipid uptake during MAFLD.
Conclusions: The human liver in MAFLD contains macrophage subsets that align well with those that appear in mouse models of fatty liver disease. Recruited myeloid cells correlate well with the degree of liver steatosis in humans and this occurs prior to changes in KC number.  MdMs appear to have a role in lipid uptake during early stages of MALFD.

overall_design: CD45 cells were freshly isolated from human liver tissue collected at the time of laproscopic gastric bypass surgery.


title: A TetR-family regulator of an RND efflux system that directs artemisinin resistance in Vibrio cholerae

city: Seongnam

first: Shin-Yae

last: Choi

institute: CHA University

summary: Artemisinin (ARS) displayed bactericidal activity against Vibrio cholerae. To assess the mechanistic details of its antibacterial action, we have isolated V. cholerae mutants with enhanced ARS resistance and identified a gene (VCA0767), whose loss-of-function resulted in the ARS resistance phenotypes. This gene (atrR) encodes a TetR family transcriptional regulator, and its deletion mutant displayed the reduction in ARS-induced ROS formation and DNA damage. Transcriptomic analysis revealed that the genes encoding an RND efflux pump operon (vexRAB) and the outer membrane component (tolC) were highly upregulated in the artR mutant, suggesting that AtrR might act as a negative regulator of this operon and tolC. Gene deletion of vexR, vexB or tolC abrogated the ARS resistance of the atrR mutant and, more importantly, the ectopic expression of VexAB-TolC was sufficient for the ARS resistance, indicating that the increased expression of the VexAB-TolC efflux system is necessary and sufficient for the ARS resistance of the atrR mutant. The cytoplasmic accumulation of ARS was compromised in the vexBtolC mutant, suggesting that the VexAB-TolC might be the primary efflux system exporting ARS to reduce its toxicity inside of the bacterial cells. The atrR mutant displayed resistance to erythromycin as well in a VexR-dependent manner. This result suggests that AtrR may act as a global regulator responsible for preventing intracellular accumulation of toxic chemicals by enhancing the RND efflux system.

first: In-Young

last: Chung

first: Hee-Won

last: Bae

first: You-Hee

last: Cho


title: Inflammatory response of 3D brain microvessels to TNF and Plasmodium falciparum

status: Public on Sep 30 2023

city: Seattle

first: Ying

last: Zheng

state: WA

address: 1400 NE Campus Parkway

department: Bioengineering

institute: University of Washington

summary: Sequestration of Plasmodium falciparum-infected erythrocytes (IEs) in the brain microcirculation is a hallmark of cerebral malaria (CM), leading to endothelial activation, microvascular occlusion, brain swelling, and death. The inflammatory pathogenesis is however poorly understood, partly due to the lack of suitable in vitro platforms to study CM biology. Here, we used 3D perfusable brain microvessels to investigate combinatorial pathogen and host inflammatory stimuli over the in situ parasite maturation and IE rupture. Whereas tumor necros factor (TNF) potently upregulated adhesion molecules and inflammatory pathways, and uniformly recruited leukocytes throughout the microvessels, P. falciparum-IEs upregulated unique stress response pathways, induced minor junctional disturbances and low levels of endothelial apoptosis, and preferentially recruited leukocytes at IE binding regions. Furthermore, parasites delayed recovery from TNF stimulation and enhanced inflammatory responses. Our findings offer insights into CM biology, and suggest that multiple events intersect to promote brain barrier inflammation in CM.

overall_design: Comparative gene expression analysis from RNA seq data for 3D brain microvessels fabricated using primary human brain microvascular endothelial cells (HBMECs) treated with either TNF or control and perfused with either normal or Plasmodium falciparum-infected human red blood cells

first: Howard

last: Caitlin

first: Joof

last: Fatou

first: Smith

last: Joseph

first: Zheng

last: Ying


title: Coculturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells

status: Public on Sep 26 2023

city: Tromsø

first: Anne

middle: Merethe

last: Hanssen

address: Hansine Hansens veg 18

department: Medical Biology

institute: University of Tromsø

summary: Better understanding of S. aureus throat colonization in the presence of other competing/coexisting microbes may provide insight into S. aureus adaptation to the human throat and recurrence of infection. In this work, we explore the responses triggered by the encounter between two common throat bacteria, S. aureus and S. anginosus, in the presence of human tonsillar epithelial cells. We performed an in vitro coculture experiment followed by RNA sequencing. A total of 332 and 279 significant DEGs with p-value < 0.05 and Log2 fold change > |2| were identified after 1 h and 3 h of post-infection, respectively. Our study identified several transcripts in S. aureus that might be important when facing a potential competitor during throat colonization. These transcripts may be useful in the development of treatments against S. aureus throat colonization and could be further investigated to better understand their roles in the immune response.

overall_design: The study involved co-culturing of S. aureus with S. anginosus, and both being exposed with/without HTEpiC at 1 h and 3 h of interaction with the host. We performed RNA sequencing to identify interaction-induced transcriptional alterations, visualization of differentially expressed genes (DEGs), and gene enrichment analysis to identify important gene ontology (GO) terms involved by those DEGs.

first: Srijana

last: Bastakoti

first: Maiju

last: Pesonen

first: Clement

last: Ajayi

first: Kjersti

last: Julin

first: Jukka

last: Corander

first: Mona

last: Johannessen


title: The Transcriptional and Phenotypic Characteristics that Define Alveolar Macrophage Subsets in Acute Hypoxemic Respiratory Failure

first: Carmen

last: Mikacenic

state: Washington

address: 1201 Ninth Avenue

institute: Benaroyra Research Institute

summary: The transcriptional and phenotypic characteristics that define alveolar monocyte and macrophage subsets in acute hypoxemic respiratory failure (AHRF) are poorly understood.  We applied CITE-seq (single-cell RNA-sequencing + cell-surface protein quantification) to bronchoalveolar lavage fluid and peripheral blood cells longitudinally collected from subjects with AHRF to identify novel alveolar monocyte/macrophage subsets, and then validated their identity in an external cohort using flow cytometry.  We identified 2 monocyte and 6 macrophage subsets in alveolar samples using CITE-seq data.  Some of the subsets had similar transcriptional profiles as those reported in healthy subjects (metallothionein genes) or patients with COVID-19 (LGMN-expressing).  We also identified novel subsets with transcriptional signatures that straddled previously reported monocyte and macrophage subsets.  We used information from CITE-seq to determine cell-surface proteins that distinguish transcriptional subsets (CD14, CD163, CD123, CD71, CD48, CD86, and CD44).  In the external cohort, we found a higher proportion of CD163/LGMN alveolar macrophages was associated with mortality.  We report a parsimonious set of cell-surface proteins that can distinguish alveolar monocyte/macrophage subsets using scalable approaches that can be applied to clinical cohorts.

overall_design: These data contain 10x Gene Expression and Feature Barcode (CITE-seq) data from Bronchial Alveolar Lavage samples from twelve samples taken from eight intubated patients at two timepoints. Each bam file corresponds to a single sample from a single patient at a timepoints (denoted v1 or v2 for time). Four patients were suffering from Acute Respiratory Distress Syndrom (ARDS) at time of first sample (SLK3, SLK7, SLK22, SLK23).

first: Eric

last: Morrell

first: Sarah

last: Holton

first: Matthew

last: Lawrance

first: Marika

last: Orlov

first: Zoie

last: Franklin

first: Mallorie

last: Mitchem

first: Hannah

last: DeBerg

first: Vivian

middle: H

last: Gersuk

first: Ashley

last: Garay

first: Elizabeth

last: Barnes

first: Ted

last: Liu

first: Ithan

last: Peltan

first: Angela

last: Rogers

first: Steven

last: Ziegler

first: Mark

last: Wurfel


title: Single‐cell RNA sequencing reveals characteristics of myeloid cells in pulmonary post-acute sequelae of SARS-CoV-2

status: Public on Sep 25 2023

city: Honolulu

first: Juwon

last: Park

state: HI

address: 651 Ilalo St.

department: Tropical Medicine, Medical Microbiology and Pharmacology

institute: University of Hawaii at Manoa

summary: To understand the immune response and cellular characteristics of individuals with persistent pulmonary symptoms after COVID-19 infection, single-cell RNA sequencing was performed on peripheral blood mononuclear cells from both control and pulmonary post-acute sequelae of SARS-CoV-2 (PPASC) participants. Increased myeloid-lineage cells and up-regulated genes associated with pulmonary symptoms and fibrosis were observed in PPASC. Fibrosis-related pathways were up-regulated, while immune pathways were down-regulated. Metabolic alterations in PPASC were also identified. These findings suggest a potential role of myeloid-lineage cells in driving PPASC.

overall_design: Live CD45+ cells were sorted by fluorescence-assisted cell sorting and subjected to scRNA-seq utilizing the 10X Genomic Chromium system. scRNA-seq done on three samples two for PASC and and one for Control

first: Alexandra

last: Gurary

first: Karolina

last: Peplowska

first: Dean

last: Logan

first: Hyundong

last: Yoon

first: Vedbar

last: Khadka


title: Yeast beta-glucan diets alter bone-marrow derived macrophage function

status: Public on Sep 21 2023

city: Dublin

first: Aaron

last: Walsh

address: Trinity Translational Medicine Institute

department: Department of Clinical Medicine

country: Ireland

institute: Trinity College Dublin

summary: Fungal beta-glucans are major drivers of trained immunity which increases long-term protection against secondary infections. Heterogeneity in beta-glucan source, structure and solubility alters interaction with the phagocytic receptor Dectin-1 and could impact strategies to improve trained immunity in humans. Using a panel of diverse beta-glucans we describe the ability of a specific yeast-derived whole-glucan particle (WGP) to reprogramme metabolism and thereby drive trained immunity in human monocyte-derived macrophages in-vitro and mice bone-marrow in-vivo. Presentation of pure, non-soluble, non-aggregated WGPs led to the formation of the Dectin-1 phagocytic synapse with subsequent lysosomal mTOR activation, metabolic reprogramming and epigenetic rewiring. Intraperitoneal or oral administration of WGP drove bone-marrow myelopoiesis and improved mature macrophage responses, pointing to therapeutic and food-based strategies to drive immune training. Thus, the investment of a cell in a trained response relies on specific recognition of beta-glucans presented on intact microbial particles through stimulation of the Dectin-1 phagocytic response.

overall_design:
We used RNA-seq to assess the effect of the yeast-derived beta-glucan Wellmune on bone marrow-derived macrophages (BMDM) in mice.
The experiment included four groups: (1) LPS-stimulated BMDM from Wellmune-fed mice, (2) LPS-unstimulated BMDM from Wellmune-fed mice, (3) LPS-stimulated BMDM from inulin-fed mice, and (4) LPS-unstimulated BMDM from inulin-fed mice.
We compared gene expression by BMDM between Wellmune- and inulin-fed mice with and without LPS treatment.

first: Frederick

last: Sheedy


title: Identification of a Therapeutically Targetable JAK-STAT Enriched Androgen Receptor (AR) and AR Splice Variant Positive Triple Negative Breast Cancer Subtype [project2]

city: Memphis

first: Daniel

last: Johnson

address: 71 S Manassas

institute: UTHSC

summary: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with no targeted therapeutics. The luminal androgen receptor (LAR), one of the six TNBC subtypes, constitutes 15% of TNBC and is enriched for AR and AR-target genes. Here, we show that a cohort of TNBC not only expresses full-length AR (AR-FL) at a much higher rate (~80%) than previously reported, but also expresses AR splice variants (AR-SVs) (~20%), subclassifying the LAR-TNBC subtype into LAR-FL, LAR-AR-SV, or dual positive. Higher AR and AR-SV expression and corresponding aggressive phenotypes were observed predominantly in specimens obtained from African American women. RNA sequencing of LAR TNBC specimens indicates an enrichment of hallmark interferon, JAK-STAT, and androgen signaling pathways, which were exclusive to AR-expressing epithelial cancer cells as demonstrated by spatial genomics. LAR and LAR-AR-SV TNBC cell proliferation, orthotopic cell line and patient-derived xenograft, and patient-derived tumor explants growth were inhibited by AR N-terminal domain (NTD)-binding selective AR degrader (SARD) that irreversibly inhibits AR or by the JAK inhibitor ruxolitinib. Subsequent biochemical analysis suggests that STAT1 is an AR coactivator, and SARD or ruxolitinib blocks this coactivation. Collectively, our work identifies and characterizes a pharmacologically targetable and previously unreported TNBC subtype predominantly in African American women and identifies a growth-promoting interaction between AR and JAK-STAT signaling.

overall_design: To investigate the transcriptome of patient specimens that express androgen receptor (AR), AR splice variants, and specimens that do not express either AR or AR splice variants, RNA was extracted from prospectively collected patient specimens and sequenced.

first: Sarah

last: Asemota

first: Jeremiah

last: Holt

first: Narayanan

last: Ramesh


title: Single-cell transcriptomic analysis (scRNA-seq) of healthy adult human parietal pleura

city: Cambridge

first: Stefan

last: Marciniak

address: Hills Road

department: CIMR

country: United Kingdom

institute: University of Cambridge

summary: The pleural lining of the thorax regulates local immunity, inflammation and repair. A variety of conditions, both benign and malignant including pleural mesothelioma, can affect this tissue. A lack of knowledge concerning the mesothelial and stromal cells comprising the pleura has hampered the development of targeted therapies. Here we present a comprehensive single cell transcriptomic atlas of the human parietal pleura.

overall_design: Healthy adult human parietal pleura were obtained from patients undergoing video-assisted thoracoscopic surgery (VATS) for pneumothorax. Tissue was minced, digested, filtered, and red blood cells were lysed. Dead cells and cellular debris were removed by Fluorescence-activated cell sorting (FACS) and live cells were submitted for scRNA-seq.

first: Joanna

last: Obacz

first: Jose

last: Valer

first: Reshma

last: Nibhani

first: Taylor

last: Adams

first: Jonas

middle: C

last: Schupp

first: Niki

last: Veale

first: Amanah

last: Lewis-Wade

first: Jasper

last: Flint

first: John

last: Hogan

first: Giuseppe

last: Aresu

first: Aman

last: Coonar

first: Adam

last: Peryt

first: Giulia

last: Biffi

first: Naftali

last: Kaminski

first: Hayley

last: Francies

first: Doris

last: Rassl

first: Matthew

last: Garnett

first: Robert

last: Rintoul


title: Role of Caveolin 1 in metabolic programming of fetal brain

status: Public on Sep 20 2023

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: Caveolae are plasma membrane invaginations found in most cells of mammals. Caveolin-1 (Cav1) encodes a major protein of the lipid rafts of these membrane structures. Cav1-null mice, though viable, show various phenotypic defects. At an early adult age, these mice show brain aging that resemble brain of one and half year old wildtype mice, and exhibit symptoms that are hallmarks of Alzheimer’s disease. It is not known if the ablation of Cav1 in these mice impacts the brain at the fetal stage that then influences brain function later in life. Single nuclei RNA sequencing was performed with fetal brain of wildtype and Cav1 knockout mice. Results showed that specific metabolism genes were differentially expressed bewteen different glial cells.

overall_design: Single nuclei RNA sequencing was performed with fetal brain of wildtype and Cav1 knockout mice by 10X Genomics.

first: Maliha

last: Islam

middle: K


title: RNA-seq of prostate cancer cell lines co-culture with osteoblasts or osteoclasts

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center

summary: Clinically, osteolytic phenotype is rare in prostate cancer. The molecular mechanism of bone metastasis in PCa is not fully understood. We performed RNA-seq to identify osteogenic and tumor associated roles in prostate cancer by a co-culture of osteoblasts (MG63) and prostate cancer cells (C4-2, C4-2B, 22Rv1 and DU145). We compared osteoblastic prostate cancer with osteolytic prostate cancer to evaluate the difference in phenotype of bone metastasis.

overall_design: Osteolytic prostate cancer (DU145 and 22RV1) and osteoblastic prostate cancer (C4-2 and C4-2B) were either mono-cultured or co-cultured with MG63 in horizontal co-culture system (NICO-1). Total RNA was extracted after 5days culture.

first: Kagenori

last: Ito

first: Yusuke

last: Yamamoto


title: An improved protocol for targeted differentiation of human iPSCs into HLA-G expressing trophoblasts cells enabling modelling of placenta-related disorders.

status: Public on Sep 14 2023

city: Hannover

first: Sylvia

last: Merkert

address: Carl-Neuberg-Str. 1

department: LEBAO

institute: Hannover Medical School

summary: Abnormalities at any stage of trophoblast development may result in pregnancy-related com-plications. Many of these adverse outcomes are discovered later in pregnancy, but the underly-ing pathomechanisms constitute during the first trimester. Acquiring developmentally relevant material to elucidate the disease mechanisms is difficult. Human pluripotent stem cell (hPSC) technology can provide a renewable source of relevant cells. BMP4, A83-01, and PD173074 (BAP) treatment drives trophoblast commitment of hPSCs towards syncytiotrophoblast (STB) but lacks extravillous trophoblast (EVT) cells. EVTs mediate key functions during placentation, remodel-ing of uterine spiral arteries, and maintenance of immunological tolerance. We optimized the protocol for more efficient generation of HLA-Gpos EVT-like trophoblasts from primed hiPSCs. Increasing the concentrations of A83-01 and PD173074, while decreasing bulk cell density re-sulted in the increase of HLA-G of up to 71%. Gene expression profiling support the advance-ments of our treatment regarding the generation of trophoblast cells. The reported differentia-tion protocol will allow the on-demand access to human trophoblast cells enriched for HLA-Gpos EVT-like cells, allowing the elucidation of placenta-related disorders and to investigate the im-munological tolerance towards the fetus, overcoming the difficulties in obtaining primary EVTs without the need for a complex differentiation pathway via naïve pluripotent or trophoblast stem cells.

overall_design: Samples included are: Isis human induced pluripotent stem cells (hiPSC), D9 BAP differentiated Isis hiPSC, D9 BhAhP differentiated Isis hiPSC, and D21 BhAhP differentiated Isis hiPSC. All with a biological replicate.

first: Ulrich

last: Martin

first: On-Chung

middle: I

last: Shum


title: Expression profiling in exosomal miRNAs of diabetes, diabetes with coronary microcirculation disorder, and diabetes with coronary artery disease

status: Public on Sep 15 2023

city: Nanjing

first: Yihai

last: Liu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

summary: Due to the insidious onset and the difficulty to diagnose and intervene, it is particularly important to find the diagnostic markers of diabetic coronary microcirculation disorder (CMD) and therapeutic targets. Circulating exosomes, as endogenous exosomes derived from multiple tissue cells, mediate communication between cells and tissues, may serve as a key point for future diagnosis, prognosis and personalized treatment of CMD in diabetes. Therefore, we isolated serum exosomes from patients with diabetes, as well as patients with CMD or coronary artery disease (CAD) respectively. We explored the differences in characteristics between three circulating exosomes.

overall_design: Serum samples were obtained from 3 diabetes patients, 3 diabetes with CMD, and 3 diabetes with CAD. The serum-derived exosomes were isolated by ultracentrifugation. Exosomal miRNA profiling was sequencing on Illumina HiSeq X Ten.

first: Y

first: L

middle: N

last: Kang


title: DNA-directed termination of RNA Polymerase II transcription I

status: Public on Sep 11 2023

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: RNA polymerase II (RNAPII) transcription involves initiation from promoters, transcript elongation through the gene body, and cessation of transcription in the downstream terminator regions. In contrast to bacteria, where terminators often contain specific DNA elements to direct RNAP dissociation1, termination by RNAPII is thought to be driven entirely by protein co-factors1-3. Here we use biochemical reconstitution to shed new light on RNAPII termination. Unexpectedly, transcription through a terminator region by pure RNAPII results in a significant amount of intrinsic polymerase dissociation at specific sequences containing T-tracts. A combination of biochemistry and single molecule analysis indicates that such intrinsic termination involves pausing without backtracking prior to spontaneous RNAPII dissociation from the DNA template. Importantly, while the ‘torpedo’ Rat1-Rai1 RNA exonuclease (XRN2 in humans) works inefficiently on paused or stopped polymerases, it greatly stimulates intrinsic termination. By contrast, elongation factor Spt4-Spt5 (DSIF in humans) suppresses such termination.  Genome-wide analysis in yeast using 3’-end sequencing further supports the idea that transcriptional termination occurs by transcript cleavage at the polyA site exposing a new RNA-end  that allows loading of the Rat1-Rai1 torpedo, which then catches up with a destabilised RNAPII at intrinsic termination sites containing T-tracts to terminate transcription.

overall_design: In this study, we explored whether S.cerevisiae RNAPII intrinsic termination sites (T-tracts on the non-template strand) identified in vitro plays a function in RNAPII termination in vivo. To do so, we applied 3'end sequencing method to determine the 3'end of RNA transcripts. We carried out 3'end sequencing experiment in both wild type yeasts and rrp6 depletion yeasts, with or without in vitro polyadenylation by E.coli polyA polymerase (EPAP). After determining that transcripts are indeeded preferentially released at T-tracts, we performed the same 3'end sequencing experiments in Rat1(Xrn2 in humans) anchor away (Rat1AA) and Ysh1 (CPSF73 in humans) anchor away (Ysh1-AA) yeast strains, further confirming that transcripts released at T-tracts are indeed due to transcription termination rather than transcript cleavage by cleavage and polyadenylation factors (CPF in yeast, CPSF in humans). De novo motif discovery confirmed the presence of T-tracts at 3'end of transcripts from 3'end sequencing datasets.

first: Zhong

last: Han

first: George

last: Moore

first: David

last: Lopez-Martinez

first: Li

last: Wan

first: A

middle: B

last: Svejstrup

last: Rueda

first: Jesper

middle: Q


title: A common graft formation pathway in Norway spruce and Arabidopsis thaliana identifies the PAT gene family as conserved regulators of tissue attachment and wound healing

city: Uppsala

first: Ai

last: Zhang

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

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

overall_design: Refer to individual Series


title: Tissue Specific Age Acceleration in the Sperm of Oligozoospermic Men

status: Public on Sep 08 2023

city: Provo

first: Timothy

middle: G

last: Jenkins

state: UT

address: 4005 Life Sciences Building

department: Cell Biology and Physiology

institute: Brigham Young University

summary: To determine if disease can modify aging patterns in an affected tissue without altering the aging patterns of other tissues, blood and semen of individuals with oligozoospermia (n=10) were compared to the blood and semen of individuals with normozoospermia (n=24). The Horvath and Jenkins age calculators were utilized to predict the epigenetic age of blood and sperm through the use of DNA methylation. Using these calculators, it was found that sperm of oligozoospermic men were predicted to be significantly older than the sperm of normozoospermic men; however, there was not a significant epigenetic age difference in blood. These results lead to the conclusion that tissue specific aging is occurring in sperm of oligozoospermic individuals but not in unaffected somatic tissues (in our case, blood).

overall_design: Whole blood samples as well as semen samples were taken from 34 men diagnosed with either oligozoospermia or normozoospermia. Epigenetic ages were then assesed in each tissue type to identify unique aging signatures between tissue types.

first: Kenneth

last: Aston

first: Kelaney

last: Stalker

first: Chad

last: Pollard


title: DNA-directed termination of RNA Polymerase II transcription


title: Reprogramming of Lipids Metabolism Determines Maternal-to-Zygotic Transition in Early Development

status: Public on Sep 07 2023

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

summary: Metabolic reprogramming of glucose and amino acids has been documented to affect early development. Here, we show that peroxisome-mediated β-oxidation is involved in lipids reprogramming to achieve H3K4me3 erasure and then zygotic genome activation (ZGA) in early embryo development. The metabolic patterns of fatty acids (FAs), triglyceride (TG) and phospholipid (PL) are reprogrammed during the oocyte-to-embryo transition. Very long-chain fatty acids (VLCFAs), arachidonic acid (ARA), phosphatidylethanolamine (PE), lysophosphatidylethanolamine (Lyso-PE), lysophosphatidylcholine (Lyso-PC), and methyl donors are stored in oocytes, and after fertilization, they are converted into phosphatidylcholine (PC) at the 2-cell stage. Mitochondrial β-oxidation prevails in oocytes, while peroxisomal β-oxidation plays a critical role in shortening the VLCFA to form TG and synthesize PC and balancing the ratio of saturated and unsaturated FAs, which consumes the methyl donors as conducive to H3K4me3 erasure at the 2-cell stage. Inhibiting the peroxisome-mediated β-oxidation disrupts lipids metabolism remodellingH3K4me3 erasure and subsequent ZGA, leading to embryo arrest at the 2-cell stage. Oocytes from obese mice show I a relatively low level of VLCFAs, defective peroxisomal β-oxidation, and incomplete H3K4me3 erasure and ZGA. Microinjection of two saturated fatty acids, palmitic and myristic acids, rescues 2-cell arrest caused by peroxisome-mediated β-oxidation inhibition and obesity, and overexpressing Pemt to consume the methyl donors has the same rescue effect. These results elucidate a novel link among the peroxisomal-β-oxidation-mediated lipid metabolism reprogramming, H3K4me3 modification and ZGA during oocyte-embryo transition, and may provide a unique approach to improve reproduction in obese women.

overall_design: Control embryos at 2-cell stages and siAcox1 embryos at 2-cell embryos for three replicates are performed RNA sequencing.

first: Linli

first: Guohui

last: Zhangxiao

first: Xie

last: Feng

first: Shiming

last: Luo

first: Qingyuan

last: Sun

first: Xianghong

last: Ou


title: snRNA 3' end sequencing

status: Public on Sep 06 2023

city: La Jolla

first: Tiantai

last: Ma

state: CA

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD


title: The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5’ cap trimethylation [global seq]

summary: Competing exonucleases that promote 3’ end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3’ exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity towards canonical snRNAs by recognizing Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.

overall_design: Nascent small RNA (100nt-500nt) 3' end RNA sequencing in control or TOE1depleted HEK 293T-REx TOE1-degron cells.

first: Erica

middle: S

last: Xiong

first: Rea

last: Lardelli

first: Jens

last: Lykke-Andersen


title: The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5’ cap trimethylation [gene specific seq]

overall_design: Gene-specific snRNA 3' end sequencing using gene-specific primers


title: Reprogramming of Cis-regulatory networks during skeletal muscle atrophy [snATAC-seq]

city: Houston

first: Zhaoyong

last: Hu

state: Texas

address: One Baylor Plaza

department: Nephrology

institute: Baylor college of medicine

summary: Current atlas of regulatory sequences controlling skeletal muscle atrophy are still incomplete and lack cell type resolution. We applied single-cell chromatin accessibility assays (snATAC) to normal and denervated skeletal muscle from mice. We integrated these snATAC datasets with our single-nucleus RNA-sequence dataset to reveal the status of open chromatin. Using these datasets, we delineated chromatin accessibility maps in both normal and atrophic muscles and identified cis-regulatory elements (CREs) in all type of cell in skeletal muscle that may regulating muscle protein metabolism, energy metabolism and transcription activities, thus, provided a rich resource for understanding gene regulatory programs in skeletal muscle and related disorders.

overall_design: Single-nucleus ATAC-seq in normal and denervated mice.

first: Hongchun

last: Lin

first: Hui

last: Peng

first: Yuxiang

first: Yanlin

last: Wang

first: Sandhya

last: Thomas

first: William

middle: E

last: Mitch

first: Zheng


title: Epigenetic changes during skeletal muscle atroph [ChIP-seq]

summary: The epigenomic regulation is a part of Gene Regulatory Network (GRN). During we study the reprogramming of GRN adaptive to atrophic stimulation in skeletal muscle, we performed Histone 3 lysine 27 (H3K27) acetylation (H3K27ac) ChIP-seq assay using mouse skeletal muscle with or without denervation. This dataset combining with our snATAC datasets enable us to infer the candidate enhancer that could regulate muscle protein metabolism and energy metabolism during atrophy.

overall_design: H3K27ac ChIP-seq in normal and denervated mice.


title: RBM33 Acts as an m6A Reader Essential for ALKBH5-mediated m6A Demethylation and Head and Neck Squamous Carcinoma Tumorigenesis [RIP-seq]

status: Public on Sep 05 2023

city: Chicago

first: Allen

last: Zhu

state: Illinois

address: 929 E 57th St, Room E331

institute: University of Chicago

summary: Head and neck squamous cell carcinoma (HNSC) is one of the most common malignant cancers worldwide. However, it is always detected at an advanced stage because of a lack of biomarkers for early diagnosis. Here, we identify the RNA binding motif protein 33 (RBM33) is commonly up-regulated in HNSC and it is essential for tumorigenesis. Mechanistically, RBM33 is an m6A reader protein and forms a complex with ALKBH5. RBM33 plays crucial roles in ALKBH5-mediated mRNA m6A demethylation not only by recruitment ALKBH5 to substrate but also activation its demethylase activity through inhibition it’s SUMOylation. Moreover, global transcriptomic and epitranscriptomic analyses identify that DDIT4 is a functional downstream target gene for RBM33 in HNSC and RBM33-mediated HNSC tumorigenesis by inhibition the mTOR pathway through the inhibition of m6A-dependent DDIT4 mRNA decay. Taken together, our study uncovers a novel molecular mechanism that RBM33/ALKBH5/m6A/DDIT4/mTOR axis regulates HNSC progression through the inhibition of mTOR pathway and targeting RBM33 may be a promising strategy for HNSC treatment.

overall_design: To determine whether ALKBH5 and RBM33 shares the majority of the binding sites, and also to determine whether ALKBH5 substrate accessibility depends on RBM33 transcriptomic wide, UM-SCC-1 cells stably expressing strep-Vec, strep-ALKBH5, strep-RBM33, strep-ALKBH5+RBM33 siRNA#1, strep-ALKBH5+RBM33 siRNA#2 were used for RIP-Seq analyses.

first: Fang

last: Yu

first: Shun

last: Liu

first: Chuan

last: He

first: Zhijian

last: Qian


title: Gene Expression of Single Extrahepatic Biliary Cells

status: Public on Sep 22 2023

city: New Haven

first: Vikas

last: Gupta

address: 1 Gilbert Street

institute: Yale School of Medicine

summary: These datasets look at the murine profile of extrahepatic biliary cells, primarily epithelial, in normal conditions and under mosaic Ctnnb1 gain of function.

overall_design: Extrahepatic biliary cells were isolated from 3 replicates under normal conditions and under mosaic Ctnnb1 gain of function.


title: Adrenal Abcg1 controls cholesterol flux and steroidogenesis

city: Bern

first: Emanuele

last: Pignatti

address: Freiburgstrasse 15

country: Switzerland

institute: University of bern

summary: Cholesterol is the precursor of all steroids, but how cholesterol flux is controlled in steroidogenic tissues is poorly understood. The cholesterol exporter ABCG1 is an essential component of the reverse cholesterol pathway and its systemic inactivation results in neutral lipid redistribution to macrophages. However, the function of ABCG1 in steroidogenic organs is not explored. To model this question, we inactivated the ortholog Abcg1 gene in the mouse adrenal cortex. Abcg1 disruption led to an adrenal-specific increase in transcripts involved in cholesterol uptake and de novo synthesis, and to an 80% increase in corticosterone production. Importantly, this phenotype was not recapitulated by inactivation of the cholesterol exporter Abca1. The absence of any change in lipid profile suggested that adrenal Abcg1 is not involved in cholesterol export to a clinically relevant extent.

overall_design: mRNA from adrenal glands from 4 control mice (carrying only the cre recombinase), and 4 mice in which Abca1 was conditionally inactivated, were sequenced and compared to the mRNA from 4 mice in which Abcg1 was conditionally inactivated.


title: RBM33 Acts as an m6A Reader Essential for ALKBH5-mediated m6A Demethylation and Head and Neck Squamous Carcinoma Tumorigenesis [m6A-seq]

overall_design: To identify the functional downstream target genes responsible for the observed phenotype, UM-SCC-1 cells stably expressing scramble, ALKBH5 siRNA#1, ALKBH5 siRNA#2, RBM33 siRNA#1, RBM33 siRNA#2 were used for m6A-Seq analyses.


title: Temporal scRNAseq of metastasizing tumor cells and lung endothelial cells

status: Public on Oct 02 2023

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

institute: German Cancer Research Center

summary: During metastasis, cancer cells travel the circulation to colonise distant sites. Due to the rarity of these events, the immediate cell fate decisions of metastasising tumour cells (mTC)  are poorly understood and the role of the endothelium, as dissemination interface, remains elusive. Using a novel combinatorial mTC enrichment approach, we provide a first transcriptional blueprint of the early colonisation process

overall_design: Mice were intravenously injected with tumor cells. Lung endothelial cells and distinct tumor cell subpopulations were isolated 1.5 days and 3.5 days post-injection, respectively. Uninjected leftover tumor cells and lung endothelial cells from uninjected mice served as baseline controls.

first: Hellmut

last: Augustin


title: Differential gene expression analysis of cycle gene knockout Aedes aegypti mosquito

status: Public on Sep 04 2023

city: College Statioon

first: Vinaya

last: Shetty

state: TX

address: Heep Center, 2475 TAMU, 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

summary: This study explores the impact of disrupting the circadian clock through a Cycle gene knockout (KO) on the transcriptome of Aedes aegypti mosquitoes. The investigation aims to uncover the resulting alterations in gene expression patterns and physiological processes. Transcriptome analysis was conducted on Cyc knockout (AeCyc-/-) and wild-type mosquitoes at four time points in a light-dark cycle. The study identified system-driven genes that exhibit rhythmic expression independently of the core clock machinery. Cyc disruption led to altered expression of essential clock genes, affecting metabolic processes, signaling pathways, stimulus responses and immune responses. Notably, gene ontology enrichment of odorant binding proteins, indicating the clock's role in sensory perception. The absence of Cyc also impacted various regulation of metabolic and cell cycle processes was observed in all time points.

overall_design: we performed RNA-seq on a Cyc-/- Ae. aegypti line (AeCyc-/-), lacking a functional circadian clock due to a mutation in the core clock gene. By comparing the transcriptomic profiles of Cyc-/- mosquitoes with wild-type (WT) individuals under a light-dark (LD) cycle, we elucidated the intricate network of genes and pathways influenced by the absence of a functional circadian clock. Understanding the molecular mechanisms governing their circadian rhythm and related physiological processes may offer valuable insights into regulating mosquito biology, vector competence, and contribute to innovative strategies for controlling mosquito populations and curtailing mosquito-borne diseases.

first: Zach

last: Adelman

first: Michel

last: Slotman


title: Effects of paternal pathogenic viral infection

status: Public on Sep 17 2023

city: Worcester

first: Noah

middle: Jacob

last: Silverstein

state: Massachusetts

address: 373 Plantation, Biotech 2, suite 319

department: Molecular Medicine

institute: UMass Chan Medical School

summary: We performed single cell RNAseq characterization of whole mouse lung during influenza A virus infection.

overall_design: We performed single cell RNA-seq on total lung single cell suspension from C57BL/6J animals infected with the Influenza A virus (IAV) A/Puerto Rico/8/34 (PR8) as well as uninfected controls.

middle: J

first: Jeremy

last: Luban


title: DNA-directed termination of RNA Polymerase II transcription II

first: Richard

last: Mitter

first: Zhong

last: Han

first: George

last: Moore

first: David

last: Lopez-Martinez

first: Li

last: Wan

first: A

last: Svejstrup

last: Rueda

first: Jesper


title: TRPM8 inhibits substance P release from primary sensory neurons via PKA/GSK-3beta to protect colonic epithelium in colitis

status: Public on Sep 12 2023

city: Shanghai

first: Zehua

last: Zhang

state: --- Select One ---

address: No. 150 Jimo Road

institute: Tongji University School of Medicine

summary: Transient receptor potential melastatin 8 (TRPM8) is a cold sensory receptor in primary sensory neurons that regulates various neuronal functions. Substance P (SP) is a pro-inflammatory neuropeptide secreted by the neurons, and it aggravates colitis. However, the regulatory role of TRPM8 in SP release is still unclear. Our study aimed to investigate TRPM8’s role in SP release from primary sensory neurons during colitis and clarify the effect of SP on colonic epithelium. We analyzed inflammatory bowel disease patients’ data from the Gene Expression Omnibus dataset. Dextran sulfate sodium (DSS, 2.5%)-induced colitis in mice, mouse dorsal root ganglion (DRG) neurons, ND7/23 cell line, and mouse or human colonic organoids were used for this experiment. TRPM8, TAC1 and WNT3A expressions were significantly correlated with the severity of ulcerative colitis in patients and DSS-induced colitis in mice. The TRPM8 agonist (menthol) and the SP receptor antagonist (Aprepitant) can attenuate colitis in mice, but the effects were not additive. Menthol promoted calcium ion influx in mouse DRG neurons. TRPM8 inhibited the combination of PKAca from the cAMP signaling pathway and GSK-3β from the Wnt/β-catenin signaling pathway, thereby inhibiting the role of β-catenin in promoting the release of SP from ND7/23 cell line. Long-term stimulation with SP inhibited proliferation and enhanced apoptosis in both mouse and human colonic organoids. Conclusively, TRPM8 inhibits SP release from primary sensory neurons by inhibiting the interaction between PKAca and GSK-3β, thereby inhibiting the role of SP in promoting colonic epithelial apoptosis and relieving colitis.

overall_design: We stimulated ND7/23 cells with 100 μM menthol or/and 100 ng/ml Wnt3a for 6 h and performed RNA sequencing.

first: Z


title: The BHLHE40‒PPM1F‒AMPK pathway regulates energy metabolism and is associated with the aggressiveness of endometrial cancer

city: Fukuoka City

first: Kazuo

last: Asanoma

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: BHLHE40 is a basic helix-loop-helix transcription factor that is involved in multiple cell activities including differentiation, cell cycle, and epithelial-to-mesenchymal transition. While there is growing evidence to support the functions of BHLHE40 in energy metabolism, little is known about the mechanism. In this study, we found that BHLHE40 expression was downregulated in cases of endometrial cancer of higher grade and advanced disease. Knockdown of BHLHE40 in endometrial cancer cells resulted in suppressed oxygen consumption and enhanced extracellular acidification. Suppressed pyruvate dehydrogenase (PDH) activity and enhanced lactated dehydrogenase (LDH) activity was observed in the knockdown cells. Knockdown of BHLHE40 also led to dephosphorylation of AMPKα Thr172 and enhanced phosphorylation of PDHA1 Ser293 and LDHA Tyr10. These results suggested that BHLHE40 modulates PDH and LDH activity by regulating the phosphorylation status of PDHA1 and LDHA. We found that BHLHE40 enhanced AMPKα phosphorylation by directly suppressing the transcription of an AMPKα-specific phosphatase, PPM1F. Our immunohistochemical study showed that the expression of BHLHE40, PPM1F, and phosphorylated AMPKα correlated with the prognosis of endometrial cancer patients. Because AMPK is a central regulator of energy metabolism in cancer cells, targeting the BHLHE40‒PPM1F‒AMPK axis may represent a strategy to control cancer development.

overall_design: The gene expression profiles of control HHUA endometrial cacer cells and BHLHE40-knockdown HHUA cells were examined using microarrays. Three replicates per group were analyzed.

first: Atsushi

last: Doi


title: The length and strength of compartmental interactions are modulated by condensin II activity [Hi-C]

status: Public on Sep 03 2023

city: Philadelphia

first: Eric

last: Joyce

state: PA

address: 415 Curie Blvd, CRB 570

institute: Perelman School of Medicine, University of Pennsylvania

summary: Condensin II plays a crucial role in shaping chromosome structure throughout the cell cycle, but its specific functions during interphase have remained unclear. In this study, we utilized Oligopaints and Hi-C techniques to investigate how changes in condensin II levels affect chromosome organization across various length scales. Our findings reveal that condensin II has a significant impact on long-range interactions within chromosomes, which are essential for the organization of intrachromosomal compartments. Importantly, these effects occur independently of the chromatin state. Furthermore, overexpression of condensin II during interphase leads to the formation of "peri-centric super stripes" observed through Hi-C analysis, indicating a disruption of the boundary between heterochromatin and euchromatin on Drosophila chromosomes. Collectively, our results challenge the existing belief that compartments form without the involvement of a loop extruder and suggest that condensin II activity is a prerequisite for driving proximity between distal compartmental domains within chromosomes.

overall_design:
To investigate the consequences of condensin II depletion on gene expression, we depleted the condensin II subunit Cap-H2 in the Drosophila BG3 cell line. We performed RNA-sequencing in Cap-H2 knockdown and control (Brown knockdown) cells.

***Please note that all sample records (including their raw and processed data files) have been updated on Feb 12, 2024.

first: Randi

last: Isenhart

first: Son

last: Nguyen

first: Chris

last: Ellison


title: The length and strength of compartmental interactions are modulated by condensin II activity [RNA-Seq]


title: The length and strength of compartmental interactions are modulated by condensin II activity

overall_design: Refer to individual Series


title: Knockdown of Hyaluronan synthase 2 suppresses liver fibrosis in mice via induction of transcriptomic changes similar to 4MU treatment

status: Public on Aug 30 2023

city: Moscow

first: Noreen

last: Halimani

address: Bol'shoy Bul'var, 30, стр 1

department: Faculty of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Hepatic fibrosis remains a significant clinical challenge due to ineffective treatments. 4-methylumbelliferone (4MU), a hyaluronic acid (HA) synthesis inhibitor, has proven safe in phase one clinical trials. In this study, we aimed to ameliorate liver fibrosis by inhibiting HA synthesis. We compared two groups of mice with CCl4-induced fibrosis, treated with 4-methylumbelliferone (4MU) and hyaluronan synthase 2 (HAS2) targeting siRNA (siHAS2). The administration of 4MU and siHAS2 significantly reduced collagen and HA deposition, as well as biochemical markers of hepatic damage induced by repeated CCl4 injections. The transcriptomic analysis revealed converging pathways associated with downstream HA signalling. 4MU- and siHAS2-treated fibrotic livers shared 405 upregulated and 628 downregulated genes. These genes were associated with xenobiotic and cholesterol metabolism, mitosis, endoplasmic reticulum stress, RNA processing, and myeloid cell migration. The functional annotation of differentially expressed genes (DEGs) in siHAS2-treated mice revealed attenuation of extracellular matrix-associated pathways. In comparison, in the 4MU-treated group, DEGs were related to lipid and bile metabolism pathways and cell cycle. These findings confirm that HAS2 is an important pharmacological target for suppressing hepatic fibrosis using siRNA.

overall_design:
The aim of this study was to validate HAS2 as an important pharmacological target in hepatic fibrosis. Furthermore we also wanted to elucidate key biological processes responsible for 4MU's antifibrotic capacity
In this study, we utilized a CCL4-induced murine model of fibrosis to execute a parallel investigation wherein HAS2 was pharmacologically inhibited by 4MU or its mRNA expression was repressed by siRNA. Using Next generation RNAseq we compared the transcriptomic signatures of 4MU or siRNA mediated inhibition of HAS2.This experimental design allowed us to delineate common and unique pathways downstream of HA signalling transduction.
Mice were divided into 2 main groups based whether they received CCL4 IP injection. Mice which received CCL4 were assigned fibrotic whilst mice wich did not receive CCL4 were assigned healthy (fibrotic or healthy). Each group comprised 4 subgroups based on the treatment received. In the fibrotic mice group we had the model (CCl4 only), 4MU adminstered (4MU.CCL4), siHAS adminstered (siHAS2.CCL4) siLuc adminstered (siLuc.CCL4/ non-targeting control). For the healthy group we also had 4 groups. Instead of CCL4, all mice in this group were injected with olive oil into the IP namely: control(oil+ tail vein injection of PBS), 4MU administered, siHAS2 adminstered and siLuc adminstered.all siRNA and PBS (for control mice ) was injected intravenously via the tail vein

first: Mikhail

last: Nesterchuk

first: Alexandra

last: Tsitrina

first: Marat

last: Sabirov

first: Irina

last: Andreichenko

first: Nataliya

middle: O

last: Dashenkova

first: Alexey

middle: M

last: Kulikov

first: Timofei

last: Zatsepin

first: Roman

last: Romanov

first: Arsen

last: Mikaelyan

first: Yuri

middle: V

last: Kotelevtsev


title: Reprogramming of Cis-regulatory networks during skeletal muscle atrophy

first: Zhaoyong

last: Hu