title: Pathogen Class-specific Transcriptional Responses Derived from PBMCs Accurately Discriminate Between Fungal, Bacterial, and Viral Infections [ValidationCohort]

status: Public on Sep 28 2024

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

summary:
Host gene expression responses can be used to determine the etiology of acute infection. PBMCs were stimulated with bacterial, viral, and fungal stimuli and then analyzed for differential gene expression utilizing microarrays to derive pathogen class-specific gene expression classifiers of infection.
Validation Cohort: peripheral blood samples of human patients with acute viral, bacterial, or fungal infections

overall_design: In vitro human PBMC challenges were performed with bacteria (gram positive and gram negative), viruses (4 strains of influenza), and fungi (Cryptococcus and Candida). Exposed human cells were then analyzed for differential gene expression utilizing Affymetrix microarrays to derive pathogen class-specific gene expression classifiers. PBMC-derived signatures for each pathogen were applied to a dataset from peripheral blood samples of human patients with acute infection due to the same broad pathogen classes.

middle: M

first: Yiling

last: Liu

first: Ricardo

last: Henao

first: Ephraim

middle: L

last: Tsalik

first: Geoffrey

middle: S

last: Ginsburg

first: Elizabeth

last: Ramburg

first: Christopher

last: Woods

first: Micah

middle: T

last: McClain


title: Hepatic transcriptome profiles of ethanol-treated mice with HMGB1 knockout in hepatocytes and/or macrophages

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

summary: Background: We previously identified that high-mobility group box-1 (HMGB1) is increased and undergoes post-translational modifications (PTMs) in response to alcohol consumption. Here we hypothesized that specific PTMs, occurring mostly in hepatocytes and myeloid cells, could contribute to the pathogenesis of alcohol-associated liver disease (AALD). Methods: We used the Lieber-DeCarli (LDC) model of early alcohol-induced liver injury, combined with engineered viral vectors and genetic approaches to regulate the expression of HMGB1, its PTMs (reduced [H], oxidized [O], acetylated [Ac], both [O+Ac]), and its receptors (RAGE, TLR4) in a cell-specific manner (hepatocytes and/or myeloid cells). Results: Hmgb1 ablation in hepatocytes or myeloid cells partially protected, while ablation in both prevented steatosis, inflammation, IL1B production, and alcohol-induced liver injury. Hepatocytes were a major source of [H], [O], and [Ac] HMGB1, whereas myeloid cells produced only [H] and [Ac] HMGB1. Neutralization of HMGB1 prevented, whereas injection of [H] HMGB1 increased AALD, which was worsened by injection of [O] HMGB1. While [O] HMGB1 induced liver injury, [Ac] HMGB1 protected and counteracted the effects of [O] HMGB1 in AALD. [O] HMGB1 stimulated macrophage (MF) migration, activation, IL1B production and secretion. Ethanol-fed RageΔMye but not Tlr4ΔMye, RageΔHep, or Tlr4ΔHep mice were protected from AALD, indicating a crucial role of RAGE in myeloid cells for AALD. [O] HMGB1 recruited and activated myeloid cells through RAGE and contributed to steatosis, inflammation, and IL1B production in AALD. Conclusion: These results provide evidence for targeting [O] HMGB1 of hepatocyte origin as a ligand for RAGE signaling in myeloid cells and a driver of steatosis, inflammatory cell infiltration, and IL1B production in AALD. Importantly, we reveal that [Ac] HMGB1 offsets the noxious effects of [O] HMGB1 in AALD.

overall_design: The Lieber-DeCarli (LDC) model was used to provoke early alcohol-associated liver disease (AALD) in mice. An equal number of 10-week-old male and female mice were randomly assigned to either the control or the ethanol group, with 8 mice in each group. The control and ethanol LDC diets (Bio-Serv Inc., Frenchtown, NJ) are equicaloric and have the same composition of fat (42% of calories) and protein (16% of calories). The content of carbohydrates is 42% of total calories (dextrin-maltose) in the control diet and 12% of total calories in the ethanol diet, where up to 30% of carbohydrate calories are replaced by ethanol. To determine the contribution of the cellular source of HMGB1 and the involvement of RAGE and/or TLR4 signaling in AALD, equal number of 10-weeks-old male and female Hmgb1ΔHep, Hmgb1ΔMye, Hmgb1ΔHepΔMye, RageΔHep, RageΔMye, Tlr4ΔHep, Tlr4ΔMye, Hmgb1&RageΔHepΔMye and their corresponding control littermates were subjected to the LDC model of AALD. Upon acclimatization by feeding control LDC diet for three days, mice were fed the ethanol LDC diet with a progressive increase in the percentage of ethanol-derived calories from 10% (1 week) to 20% (1 week), 25% (2 weeks) and 30% (2 weeks). Mice pair-fed with similar calories derived from maltose-dextrin served as control. To further validate the role of HMGB1 in AALD, a separate cohort of WT mice and RageΔMye mice was injected i.p., a pan-HMGB1 neutralizing Ab (ST326052233, Shino-Test, Kanagawa, Japan) at a dose of 0.3 µg/g, [H] HMGB1 (230609, HMGBiotech) or [O] HMGB1 (230817, HMGiotech) at a dose of 0-0.1 µg/g throughout the ethanol feeding protocol.

first: Xiaodong

last: Ge

first: Natalia

last: Nieto


title: Pathogen Class-specific Transcriptional Responses Derived from PBMCs Accurately Discriminate Between Fungal, Bacterial, and Viral Infections [DiscoveryCohort]

summary:
Host gene expression responses can be used to determine the etiology of acute infection. PBMCs were stimulated with bacterial, viral, and fungal stimuli and then analyzed for differential gene expression utilizing microarrays to derive pathogen class-specific gene expression classifiers of infection.
Discovery Cohort: In vitro human PBMC challenges were performed with bacteria (gram postive and gram negative), viruses (4 strains of influenza), and fungi (Cryptococcus and Candida)

overall_design: In vitro human PBMC challenges were performed with bacteria (gram postive and gram negative), viruses (4 strains of influenza), and fungi (Cryptococcus and Candida). Exposed human cells were then analyzed for differential gene expression utilizing Affymetrix microarrays to derive pathogen class-specific gene expression classifiers.

middle: W


title: Cancer cells impair monocyte-mediated intratumoral T cell stimulation [R15287 YUMM1.7 T cells]

status: Public on Sep 27 2024

city: Vienna

first: Anais

last: Elewaut

address: Vienna Biocenter 1

country: Austria

institute: IMP

type: Expression profiling by high throughput sequencing

summary: The tumor microenvironment (TME) is programmed by cancer cells and critically influences antitumor immune responses. Within the TME, CD8+ T cells undergo full effector differentiation and acquire cytotoxic antitumor functions in specialized niches. While interactions with conventional type-1 dendritic cells (cDC1s) have been implicated in this proces, underlying cellular players and molecular mechanisms remain incompletely understood. Here, we show that inflammatory monocytes can adopt a critical role in intratumoral T cell stimulation. They express Cxcl9, Cxcl10 and Il15, but as opposed to cDC1s that cross-present antigens, inflammatory monocytes obtain and present peptide-major histocompatibility complex class I (pMHCI) complexes from tumor cells through “cross-dressing”. Hyperactivation of MAPK signaling in cancer cells hampers this process by coordinately blunting the production of type I interferon (IFN-I) and inducing the secretion of prostaglandin E2 (PGE2), impairing the inflammatory monocyte state and intratumoral T cell stimulation. Enhancing IFN-I production and blocking PGE2 secretion restores this process and thereby re-sensitizes tumors to T cell-mediated immunity. Together, our work uncovers a central role of inflammatory monocytes in intratumoral T cell stimulation, elucidates how oncogenic signaling disrupts T cell responses via counter-regulation of PGE2 and IFN-I, and proposes rational combination therapies to enhance immunotherapies.

overall_design: YUMM1.7OVA NTT and RTT cells were injected into Rag2-/- mice. 4 x 106 OT-1 T cells were injected intratumorally at day 7 post-injection. T cells were isolated 5 days after transfer. Alive T cells were isolated from tumors by FACS-sorting for CD45+CD3+CD8+ markers, n=14 NTT and  n=18 RTT tumors were pooled for each group.

first: Guillem

last: Estivill

first: Anna

middle: C

last: Obenauf


title: Cancer cells impair monocyte-mediated intratumoral T cell stimulation [R16355 YUMM1.7 NTT/RTT +- ACT]

overall_design: YUMM1.7OVA NTT and RTT cells were injected into Rag2-/- mice. Adoptive cell therapy (ACT) with OT-1 T cells was performed at day 7 post-injection and tumors were isolated at day 10 (72 hours post ACT), including also non-ACT treated tumors. The CD45+ alive immune cells were isolated by fluorescence-activated cell sorting (FACS) and subjected to single-cell RNA sequencing. For each condition, 3 tumors were pooled.


title: Human CFTR deficient iPSC-macrophages reveal impaired functional and transcriptomic response upon Pseudomonas aeruginosa infection

city: Hannover

first: Claudio

last: Rodriguez Gonzalez

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: Cystic fibrosis (CF) is a hereditary autosomal recessive disease driven by deleterious variants of the CFTR gene, leading, among other symptoms, to increased lung infection susceptibility. Mucus accumulation in the CF lung is, as of yet, considered as one important factor contributing to its colonization by opportunistic pathogens such as Pseudomonas aeruginosa. However, in recent years evidence was provided that alveolar macrophages, which form the first line of defense against airborne pathogens, seem to be intrinsically defective with regard to bactericidal functionality in the CF lung. To assess the impact of CFTR deficiency in human macrophages only insufficient systems are available. To address this problem and to evaluate the role of CFTR in human macrophages, we successfully differentiated human induced pluripotent stem cells (iPSC) from a CF p.Phe508del homozygous individual and a healthy donor into primitive macrophages (iMacΔF508 and iMacWT), respectively, and compared the bactericidal functionality in the relevant cell type. iMacΔF508 showed impaired P. aeruginosa clearance and intracellular killing capacity in comparison to iMacWT. Furthermore, iMacΔF508 exhibited a less acidic lysosomal pH, and upon P. aeruginosa infection, there were signs of mitochondrial fragmentation and autophagosome formation together with a hyperinflammatory phenotype and deficient type I interferon response. In summary, we present a defective phenotype in iMacΔF508 upon P. aeruginosa infection, which will constitute an ideal platform to further study the role of macrophages in the context of CF.

overall_design: In order to analyze RNA expression of iPSC derived macrophages (iMac) during P. aeruginosa infection, duplicate samples of RNA were isolated from cystic fibrosis (CF) and wild-type (WT) iMac  0, 60, 150 and 450 minutes post-infection.

first: Débora

last: Basílio-Queirós

first: Anna-Lena

last: Neehus

first: Sylvia

last: Merkert

first: David

last: Tschritter

first: Sinem

last: Ünal

first: Jan

last: Hegermann

first: Matthias

last: Mörgelin

first: Jacinta

last: Bustamante

first: Manuel

last: Nietert

first: Ulrich

last: Martin

first: Burkhard

last: Tümmler

first: Antje

last: Munder

first: Nico

last: Lachmann


title: The pore-forming apolipoprotein APOL7C drives phagosomal rupture and antigen cross-presentation by dendritic cells

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: Splenic dendritic cells were isolated and processed using 10X genomics 3' gene expression kit v3.1, to assess APOL7C expression and response to poly(I:C)

overall_design: In the first experiment, a 1:1 ratio of panDC and CD45 positive cells, from the spleen were suspended in 50 ul of 1.0% BSA. In the second experiment, lineage  (TER-119, CD19, B220, TCRℬ, NK1.1, Siglec-f, F4/80) -negative, FLT3+ cells from the spleen were suspended in 50 ul of 1.0% BSA.  All samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines Next Gem Chemistry as per the manufacturer’s protocol. In brief, cultured cells were partitioned into Gel Bead-In-EMulsions (GEMs) using 10X Genomics 3' Gene Expression v3.1 technology. Quality control and cDNA quantification was performed using DTape station 1000. Sequencing was performed using Illumina NovaSeq with 100 cycle flow cells. We recovered around 8,500 cells / Sample, with a targeted sequencing depth of ~20,000 reads/cell.

first: Gerone

last: Gonzales

first: Jahanara

last: Rajwani

first: Nicole

last: Rosin

first: Johnathan

last: Canton

first: Jen

last: Nguyen

first: Song

last: Huang


title: A mutant Bcl11b protein interferes with Bcl11a function during T lymphocyte and neuronal development.

city: Kanagawa

first: Kazuki

last: Okuyama

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

department: IMS

country: Japan

institute: RIKEN Yokohama

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To understand the impact of Bcl11b N440K variant on the DNA recognition by TCF1, we performed ChIP-seq of Bcl11b with Bcl11b+/+ and Bcl11b+/N440K thymocytes.

overall_design: Investigation of differential binding peaks of TCF1 between Bcl11b+/+ and Bcl11b+/N440K thymocytes.

first: Ichiro

last: Taniuchi


title: Protein expression from paired biopsies from a patient with METex14 skiping non-small cell lung cancer before and after treatment with neoadjuvant tepotinib (42 days)

city: Darmstadt

first: Manon

middle: A

last: Simard

address: Frankfurterstraße 250

department: Research Unit Oncology

institute: Merck Healthcare KGaA

summary: Background: MET inhibitors have demonstrated efficacy in treating patients with non-small cell lung cancer (NSCLC) harboring METex14 skipping alterations. Advancements in spatial profiling technologies have unveiled the complex dynamics of the tumor microenvironment, a crucial factor in cancer progression and therapeutic response. Using spatial profiling, this study investigates the effects of the MET inhibitor tepotinib on the TME in a case of locally advanced NSCLC with a METex14 skipping alteration.  Methods: A patient with resectable stage IIIB NSCLC, unresponsive to neoadjuvant platinum-based doublet chemotherapy, received tepotinib following detection of a METex14 skipping alteration. Paired pre- and post-treatment biopsies were subjected to GeoMx Digital Spatial Profiling using the Cancer Transcriptome Atlas and immune-related protein panels to evaluate shifts in the tumor immune microenvironment (TIME).  Results: Tepotinib administration resulted in pathological downstaging to stage IA1, which allowed for a successful lobectomy and evidenced a significant pathological response. The TIME was transformed from an immunosuppressive to a more permissive state, with upregulation of antigen-presenting and pro-inflammatory immune cells. Moreover, a marked decrease in immune checkpoint molecules, including PD-L1, was noted. Spatial profiling identified discrete immune-enriched clusters, indicating the role of tepotinib in modulating immune cell trafficking and function.  Conclusions: Tepotinib appears to remodel the TIME in a patient with METex14 skipping NSCLC, possibly increasing responsiveness to immunotherapy. This case supports the integration of genetic profiling into the management of early and locally advanced NSCLC to guide personalized, targeted interventions. These findings highlight the need to further evaluate combinations of MET inhibitors and immunotherapies.

overall_design: On the GeoMx Digital Spatial Profiler, regions of interest of 250 micrometers in diameter were selected in the pre-treatment biopsy (15) and tepotinib-treated surgical resection (79) from the same patient, following barcoded antibody incubation (Immune Cell Profiling, Immune Cell Typing, Immune Activation Status, IO Drug Target & PI3K/AKT Signaling panels) and morphology marker staining using SYTO13, TTF1, CD3 and CD33.

first: Niki

last: Karachaliou

first: Felix

last: Geist

first: Carlos

last: Cabrera-Galvez

first: Santiago

last: Viteri

first: Nadine

last: Reischmann

first: Michael

last: Zuehlsdorf


title: Gene expression from paired biopsies from a patient with METex14 skiping non-small cell lung cancer before and after treatment with neoadjuvant tepotinib (42 days)

overall_design: On the GeoMx Digital Spatial Profiler, regions of interest of 250 micrometers in diameter were selected in the pre-treatment biopsy (15) and tepotinib-treated surgical resection (79) from the same patient, following hybridization of tissue with Cancer Transcriptome Atlas probes and custom probes for METex14, CLDN18.1, CLDN18.2, CEACAM5, spliced XBP1 and morphology marker staining using SYTO13, TTF1, CD3 and CD33.


title: Single Nucleus RNAseq dissection of choroid plexus tumor cell heterogeneity

city: Heidelberg

first: Anthony

last: Hill

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Schaller Research Group

institute: German Cancer Research Center (DKFZ)

summary: To examine the cellular and transcriptional heterogeneity of choroid plexus tumors we determined the single nucleus transcriptomes of 23,906 nuclei from normal choroid plexus and choroid plexus tumors. The resulting cellular atlas profiles cellular and transcriptional heterogeneity, copy number alterations, and cell-cell interaction networks in normal and cancerous choroid plexus. We observe changes in choroid plexus tumor epithelial cell gene transcription that correlate with genome wide methylation profiles. In addition, we characterize tumor-grade-specific tumor microenvironments that include altered macrophage and mesenchymal cell states, as well as changes in extracellular matrix components.

overall_design: Nuclei were isolated from fresh frozen samples of disease free human choroid plexus and human choroid plexus tumors and analyzed by snRNAseq.

middle: D

first: Annarita

last: Patrizi


title: Cancer cells impair monocyte-mediated intratumoral T cell stimulation [R12408 YUMM1.7 NTT/RTT/KO]

first: Anais

last: Elewaut

overall_design: YUMM1.7OVA cells were injected into Rag2-/- mice. Adoptive cell therapy (ACT) with OT-1 T cells was performed at day 7 post-injection and tumors were isolated at day 10 (72 hours post ACT). The CD45+ alive immune cells were isolated by fluorescence-activated cell sorting (FACS) and subjected to single-cell RNA sequencing.

first: Anna

last: Obenauf

first: Guillem

last: Estivill


title: Cancer cells impair monocyte-mediated intratumoral T cell stimulation [R15287 YUMM1.7 RTT IRF37/COX2i/AZA]

overall_design: YUMM1.7OVA cells were injected into Rag2-/- mice. Adoptive cell therapy (ACT) with OT-1 T cells was performed at day 7 post-injection and tumors were isolated at day 10 (72 hours post ACT). The CD45+ alive immune cells were isolated by fluorescence-activated cell sorting (FACS) and subjected to single-cell RNA sequencing. For each condition, 3 individual tumors were pooled.


title: Cancer cells impair monocyte-mediated intratumoral T cell stimulation [YUMM3.3]

overall_design: YUMM3.3 NTT and RTT cell lines were injected into C57BL6 mice and isolated at day 12 post injection. The CD45+ alive immune cells were isolated by fluorescence-activated cell sorting (FACS) and subjected to single-cell RNA sequencing. One tumor was used per condition.


title: A mutant Bcl11b protein interferes with Bcl11a function during T lymphocyte and neuronal development

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

overall_design: Refer to individual Series


title: A mutant Bcl11b protein interferes with Bcl11a function during T lymphocyte and neuronal development [ChIP-seq]

summary: To understand the impact of Bcl11b N440K variant on the DNA recognition by Bcl11b, we performed ChIP-seq of Bcl11b with Bcl11b+/+ and Bcl11b+/N440K thymocytes.

overall_design: Investigation of differential binding peaks of Bcl11b between Bcl11b+/+ and Bcl11b+/N440K thymocytes.

first: Motoi

last: Yamashita

first: Artemis

last: Koumoundourou

first: Christoph

last: Wiegreffe

first: Michiko

last: Ohno-Oishi

first: Samuel

last: Murphy

first: Xin

last: Zhao

first: Hideyuki

last: Yoshida

first: Takashi

last: Ebihara

first: Naoko

last: Satoh

first: Sawako

last: Muroi

first: Satoshi

last: Kojo

first: Hiroshi

last: Ohno

first: Tomohiro

last: Morio

first: Yibo

last: Wu

first: Jennifer

last: Puck

first: Hai-Hui

last: Xue

first: Stefan

last: Britsch


title: Anterior and Posterior regions of mouse embryos with combinatory mutations of Fuz and Gpr161

status: Public on Sep 26 2024

city: Austin

first: Sung Eun

last: Kim

address: 1400 Barbara Jordan Blvd

institute: The University of Texas at Austin

summary: Gpr161 and Fuz are Shh signaling molecules, and both null mutations are associated with neural tube defects in mice. As their genetic relationship in Shh signaling during neural tube development is unknown, we generated double homozygous null mutant mice for phenotyping and associated molecular changes. We observed the rescued NTD phenotypes in double homozygous null mutant embryos compared to those in single Gpr161 null mutant embryos. However, the range of rescued phenotypes is distinct between anterior and posterior NTDs. Therefore, we sought to identify the comparison in gene expression between the anterior and posterior regions of each genotype embryos and between each genotype.

overall_design:
We generated the samples for the anterior regions (above third branchial arches) and the posterior regions (below forelimbs) of WT, Gpr161 knock out (KO), Fuz KO, and double KO embryos at E10.5 to compare gene expression patterns of each genotyped embryo depending on the regions.

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Submitter states that missing raw files are due to file loss.
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first: Sung-Eun

first: Hyun-Yi


title: Intravenous chaperone treatment of late-stage Alzheimer's disease (AD) mouse model affects amyloid plaque load, reactive gliosis and AD related genes

status: Public on Sep 25 2024

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Treatment strategies that are efficient against established Alzheimer's disease (AD) are needed. BRICHOS is a molecular chaperone domain that prevents amyloid fibril formation and associated cellular toxicity. In this study, we treated an AD mouse model seven months after pathology onset, using intravenous administration of recombinant human (rh) Bri2 BRICHOS R221E. Two injections of rh Bri2 BRICHOS R221E per week for three months in AD mice reduced amyloid b (Ab) burden, and mitigated astro- and microgliosis, as determined by  glial fibrillary acidic protein (GFAP) and ionized calcium-binding adaptor molecule 1 (Iba1) immunohistochemistry. Sequencing of RNA from cortical microglia cells showed that BRICHOS treatment normalized expression of identified plaque-induced genes in mice and humans, including clusterin and GFAP. Rh Bri2 BRICHOS R221E passed the blood-brain barrier (BBB) in age-matched wildtype mice as efficiently as in the AD mice, but then had no effect on measures of AD-like pathology, and mainly affected the expression of genes involved in cellular shape and movement. These results indicate a potential of rh Bri2 BRICHOS against advanced AD and underscore the ability of BRICHOS to target amyloid-induced pathology.

overall_design: To investigat the effects of rh Bri2 BRICHOS treatment on microglial activation, we isolated cortical microglial cells from three mice from each of the four treatment groups, i.e. WT and AppNL-G-F mice treated with either PBS (veh) or rh Bri2 BRICHOS R221E, and performed bulk mRNA sequencing.

first: Ruixin

last: Zhang

first: Makiko

last: Ohshima

first: Yu

last: Wang

first: Antonin

last: Morance

first: Marianne

last: Schultzberg

first: Gefei

last: Chen

first: Jan

last: Johansson


title: Dynamics and single-cell transcriptomics of circulating immune cell populations in inflammatory bowel disease upon anti-integrin treatment

status: Public on Sep 24 2024

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: To explore cellular and transcriptional changes in circulation following vedolizumab treatment in ulcerative colitis patients: investigating inflammatory gene signatures and cell migration patterns predictive of therapeutic responses in IBD

overall_design:
We sequenced five age- and sex-matched controls and ten UC patients (n=5 responders and n=5 non-responders) before and six weeks after vedolizumab treatment. Samples sequenced: (1) UC, vedolizumab responders: n=5, 2 time points, week 0 and week 6 after treatment; (2) UC, vedolizumab non-responders: n=5, 2 time points, week 0 and week 6 after treatment; (3) healthy controls: n=5, sex- and age-matched controls. Peripheral blood samples were collected from the above-mentioned patients at specified time points before and during Vedolizumab therapy. Samples were obtained before the initial infusion of Vedolizumab (week 0) and prior to subsequent infusions (week 6, before the third infusion at week 6).

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Veronika

last: Horn

first: Camila

last: Cancino

first: Diana

last: Boesel

first: Konstantin

last: Fritz

first: Britta

last: Siegmund

first: Ahmed

middle: N

last: Hegazy


title: The HUSH-SETDB1-MORC2 epigenetic repressor complex restricts herpesvirus infection in association with PML nuclear bodies

city: LYON

first: Armelle

last: Corpet

state: Rhône-Alpes

address: Faculté de Médecine et de Pharmacie, 8 avenue Rockefeller

country: France

institute: Institut NeuroMyoGène (INMG)

summary: The establishment of latent herpes simplex virus 1 (HSV-1) infection is controlled by promyelocytic leukemia nuclear bodies (PML NBs). Viral genomes are recruited to PML NBs structures and chromatinized by repressive H3.3K9me3 modified H3.3 histone variant to form viral DNA-containing PML-NBs (vDCP NBs). Exactly how this occurs is unclear. Here we identify an essential role for the HUSH complex and its SETDB1 and MORC2 effectors in the establishment and maintenance of latent herpes simplex virus 1 (HSV-1) infection. ChIP-seq analyses conducted on latently/quiescently infected primary human fibroblasts highlight the association of the H3K9me3 mark with the entire viral genome. We demonstrate the necessity of HUSH, SETDB1, and MORC2 in the establishment of repressive heterochromatin in vDCP NBs. Depletion of these components prior to viral infection results in reduced H3K9me3 levels across the entirety of latent/quiescent HSV-1 genomes, with minimal impact on the cellular genome as a whole. Once latency is established, depletion of HUSH, SETDB1, or MORC2 by shRNAs or the HIV-2ROD Vpx protein, induces the reactivation of HSV-1 in infected primary human fibroblasts as well as in human induced pluripotent stem cell-derived sensory neurons (hiPSDN). We discovered that the viral protein ICP0 induces MORC2 degradation via the proteasome machinery. This process is concurrent with ICP0 capability to initiate full HSV-1 reactivation, as well as the significant reactivation of HSV-1 upon MORC2 depletion in hiPSDN. Our data demonstrate the potent antiviral restriction activity of the HUSH/SETDB1/MORC2 complex to a non-integrated human herpesvirus, its close association with PML NBs, and introduces a new target for anti-herpesvirus therapy.

overall_design: Chromatin Immunoprecipitation followed by DNA-Sequencing (ChIP-Seq) for H3K9me3 in human primary fibroblasts (BJ cells) infected or not with the HSV-1 in1374 strain.

first: Patrick

last: Lomonte


title: TF co-binding to nucleosome arrays

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: Cell type maintenance and conversion require the combined action of transcription factors (TFs), but the underlying principles remain elusive. Here, we investigated how four TF combinations lead to different reprogramming outputs by studying TF occupancy, nucleosome positioning, and genome 3D organization. We reveal that TF combinations target nucleosome with distinct 3D nucleosome conformations.  We also reveal that TFs employ different motif readout mechanisms to reach their cell type specific targets. Moreover, the ability of pioneer TFs to enable non-pioneer factors the access to closed chromatin is markedly different across combinations. Overall, our findings uncover distinct modes of action for TFs during reprogramming.

overall_design: ChIP-seq of four different TF combinations during early and final reprogramming. Mnase-seq and Micro-C in non-reprogrammed and fully-reprogrammed cells.


title: Pathogen Class-specific Transcriptional Responses Derived from PBMCs Accurately Discriminate Between Fungal, Bacterial, and Viral Infections.

first: Julie

last: Steinbrink


title: Large-scale Single-nuclei Profiling Identifies Role for ATRNL1 in Atrial Fibrillation

city: Cambridge

first: Matthew

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard


title: The GPR84 molecule is a mediator of a subpopulation of retinal microglia that promote TNF/IL-1α expression via the rho-ROCK pathway after optic nerve injury II

status: Public on Sep 30 2024

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

summary: We show that microglial gene expression patterns gradually change during RGC degeneration induced by optic nerve injury and ripasudil treatment.

overall_design: Examination of 2 different concentration of ripasudil treatment and vehicle treatment in Iba1-positive retinal cells.

first: Michiko

last: Ohno-Oishi

first: Masaaki

last: Yoshida

first: Taimu

first: Takaharu

last: Aizawa

first: Yuto

last: Sasaki

first: Shigeto

last: Maekawa

first: Makoto

last: Ishikawa

first: Kazuko

last: Omodaka

first: Chihiro

last: Kawano

first: Ryuji

last: Ohue-Kitano

first: Ikuo

last: Kimura

first: Toru

last: Nakazawa


title: Cancer cells impair monocyte-mediated intratumoral T cell stimulation

first: Anais

last: Elewaut


title: A mutant Bcl11b protein interferes with Bcl11a function during T lymphocyte and neuronal development [RNA-seq]

first: Kazuki

last: Okuyama

summary: CD24-TCRb- thymocytes emerged the thymus of mice carrying Bcl11b N440K variant and Tcf7 deficient mice. To investigate the feature of these cells, we performed RNA-seq.

overall_design: Investigation of feature genes expressed by target cell population (CD24-TCRb- thymocytes), and comparative gene expression profiling analysis of RNA-seq data for indicated genotype.

first: Motoi

last: Yamashita

first: Artemis

last: Koumoundourou

first: Christoph

last: Wiegreffe

first: Samuel

last: Murphy

first: Xin

last: Zhao

first: Hideyuki

first: Takashi

last: Ebihara

first: Naoko

last: Satoh

first: Sawako

last: Muroi

first: Satoshi

last: Kojo

first: Hiroshi

last: Ohno

first: Tomohiro

last: Morio

first: Yibo

last: Wu

first: Jennifer

last: Puck

first: Hai-Hui

last: Xue

first: Stefan

last: Britsch

first: Ichiro

last: Taniuchi


title: Large-scale Single-nuclei Profiling Identifies Role for ATRNL1 in Atrial Fibrillation [bulk RNA-seq]

first: Matthew

last: Hill

summary: Atrial fibrillation (AF) is the most common sustained arrhythmia in humans, yet the molecular basis of AF remains incompletely understood.  To determine the cell type-specific transcriptional changes underlying AF, we performed single-nucleus RNA-seq (snRNA-seq) on age- and sex-matched left atrial (LA) samples from 18 patients with AF and 16 controls without AF. From more than 175,000 nuclei we identified 15 cell types but found that only cardiomyocytes (CMs) and macrophages (MΦs) had a significant number of differentially expressed genes in patients with AF. Attractin Like 1 (ATRNL1) was strongly overexpressed in CMs among patients with AF and localized to the intercalated discs. Further, in both knockdown and overexpression experiments in atrial human embryonic stem cell-derived CMs (hESC-aCMs) we identified a potent role for ATRNL1 in cell stress response, cardiac conduction, cell junction organization and in modulation of the cardiac action potential. Finally, we prioritized genes at the known genetic loci for AF and identified an unexpected expression for a leading AF candidate gene, KCNN3. In sum, we have identified a role for ATRNL1 and other differentially regulated genes that may serve as potential therapeutic targets for this common arrhythmia.

overall_design: To characterize the cellular and molecular characteristics associated with the gene ATRNL1 in atrial cardiomyocytes (CMs), we performed bulk RNA-seq on human embryonic stem cell derived atrial cardiomyocytes (hESC-aCMs) treated with siRNAs against ATRNL1, scramble control siRNAs, and lentiviruses for overexpressing the short isoform of ATRNL1.


title: ROS-Responsive Nanoparticles for Bioimaging and Treating Acute Lung Injury by Improving the Homeostasis of Alveolar Macrophages

status: Public on Sep 23 2024

city: Chongqing

first: Haiyu

last: Li

address: No. 61 Puguobao Road, Bicheng Street, Bishan District

country: China

institute: Chongqing University of Chinese medicine

summary: To reveal the molecular biological mechanism of RCMNs in the treatment of acute lung injury, MH-S Cells were stimulated by LPS and treated with RCMNs followed by RNA-seq transcriptome analysis.Functional enrichment analysis of the genes that exhibited significant differential expression following RCMNs treatment revealed their primary involvement in several key biological processes, including mitochondrial respiratory chain complex IV assembly, oxidative phosphorylation, and mitochondrial respiratory chain complex I assembly. These findings suggest that RCMNs exert their therapeutic effects by modulating the expression of genes critical to mitochondrial function and energy metabolism. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis has revealed that RCMs primarily exert their biological functions by modulating several key signaling pathways, including the Calcium signaling pathway, TNF signaling pathway, and Toll-like receptor signaling pathway.

overall_design: After acquiring RNA-Seq data derived from MH-S macrophages stimulated with RCMNs (1ug/mL) in the presence of LPS (100ng/mL), a comprehensive bioinformatics analysis was conducted to decipher the transcriptome profiles and pinpoint differentially expressed genes (DEGs). Initially, the raw sequencing reads underwent meticulous quality control assessments utilizing tools such as FastQC, aimed at evaluating sequence quality metrics. These reads might have been subjected to preprocessing procedures, including adapter trimming and filtering, to eliminate low-quality sequences.

first: Wenna

last: Fan

first: Yongyao

last: Tang

first: Fangzhou

last: Song


title: Effect of liver specific deletion of Zbtb7b on gene expression in liver of mice fasted for 24 hours

status: Public on Sep 20 2024

city: Shanghai

first: Yinglin

last: Han

address: 280 Chongqing South Road, Huangpu District

institute: Shanghai Jiao Tong University School of Medicine

summary: Here, we revealed that Zbtb7b is a suppressor of MASLD-related HCC. Zbtb7b deficiency in mouse hepatocytes increases de novo lipogenesis while hepatic fatty acid oxidation is inhibited. Consequently, lipid deposition in the liver is increased, which facilitating the progression of MASLD and eventually to HCC. Mechanistically, depletion of Zbtb7b drastically induced long noncoding RNA H19 expression, thereby driving hepatic de novo lipogenesis and suppressing fatty acid oxidation program to accelerate MASLD-related HCC progression.

overall_design: To investigate the role of Zbtb7b in function of liver, we established the Zbtb7b condition knock out mice in liver tissue by injecting Zbtb7bflox/flox mice 1x10^11 AAV2/8-TBG-Cre viral particles via the tail vein.

first: Xuyun

last: Zhao


title: Bile acid derivatives from gut microbiota promote GBPs-mediated activation of caspase-4/11 by LPS through lncRNA57RIK

status: Public on Sep 21 2024

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

summary: Gut microbiota contributes to the regulation of host immune response and homeostasis. Bile acid (BA) derivatives from gut microbiota can affect the differentiation and function of the immune cells. However, it is incompletely clear for the regulation of BA metabolites in the macrophages. We here find that BA metabolites can regulate sensitivity of macrophages to LPS and or Gram-negative bacteria. BA derivatives could induce lncRNA57RIK expression through sphingosine-1-phosphate receptor 2 (S1PR2) in the macrophages of mice and humans, which play a critical role in Gram-negative bacteria mediated IL-1β maturation and pyroptosis of macrophages. This lncRNA57RIK could bind intracellular proteases caspase-4/11 with guanylate-binding protein 1 (GBP1) in the human and mice together to cause LPS mediated activation of caspase-4/11. Murine or human lncRNA57RIK knockout (KO) macrophages did not produce response(s) to LPS or gram negative bacteria. LncRNA57RIK KO mice had also reduced inflammatory responses to LPS or Salmonella typhimurium (S.T) infection. Taken together, gut microbiota derived BA metabolites mediated lncRNA57RIK is necessary for LPS induced caspase-4/11 activation.

overall_design: Mouse BMDMs were treated with 100 µM deoxycholic acid or butyrate for 24h. One day later, all cells with or without deoxycholic acid/butyrate treatment were collected for RNA extraction.

first: Jianmei

last: Yue


title: Large-scale Single-nuclei Profiling Identifies Role for ATRNL1 in Atrial Fibrillation [snRNA-seq]

overall_design: To characterize the cellular and molecular characteristics associated with AF, we performed snRNA-seq on samples from the LA of human patients with AF who were not in heart failure (n=19) as well as non-AF controls (n=19).


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA interactome studies have revealed that hundreds of zinc finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), despite being annotated as DNA-interacting transcription factors. The RNA substrates of ZFPs and the functional significance of their potential roles as DNA- and RNA-binding proteins (DRBPs) remain largely uncharacterized. Here we present a systematic multi-omics analysis of the DNA and RNA binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc finger families. We show that multiple ZFPs are novel regulators of RNA splicing, polyadenylation, or stability. The examined ZFPs show widespread sequence-specific RNA binding ability and preferentially bind proximal to transcription start sites. Additionally, several ZFPs are DRBPs that bind their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DRBP that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation, shedding light on a large class of under-studied RBPs.

overall_design: Knocked down ZFPs in HEK293T cells using shRNA, followed by RNA-seq.

first: Maya

last: Gosztyla

first: Lijun

last: Zhan

first: Sara

last: Olson

first: Xintao

last: Wei

first: Jack

last: Naritomi

first: Grady

last: Nguyen

first: Lena

last: Street

first: Grant

last: Goda

first: Jonathan

last: Schmok

first: Manya

last: Jain

first: Easin

last: Uddin Syed

first: Eunjeong

last: Kwon

first: Wenhao

last: Jin

first: Eric

last: Kofman

first: Alexandra

last: Tankka

first: Allison

first: Valerie

last: Gonzalez

last: Lécuyer

first: Daniel

last: Dominguez

first: Marko

last: Jovanovic

first: Brenton

middle: R

last: Graveley

first: Gene

last: Yeo


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Ribo-STAMP cell lines]

first: Brian

last: Yee

overall_design: We used Ribo-STAMP cell lines (expressing RPS2-APOBEC1) and knocked down ZFPs using shRNA, followed by RNA-seq.

first: Maya

last: Gosztyla

first: Lijun

last: Zhan

first: Sara

last: Olson

first: Xintao

last: Wei

first: Jack

last: Naritomi

last: Li


title: Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

institute: Peking University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Endothelial Pim3 kinase protects the vascular barrier during lung metastasis (set2)

city: Helsinki

first: Niina

last: Santio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Endothelial cells (ECs) form a tissue-specific barrier for disseminating cancer cells in distant organs. However, the molecular regulation of the ECs in the metastatic niche is poorly understood. Here, we analyzed the transcriptional reprogramming of ECs in the lung metastatic niche six hours after the arrival of melanoma cells in the niche. We discovered a novel EC cluster derived from venous capillaries in response to infiltrating cancer cells, which was enriched for cell-cell communication pathways, including the Dll4, Vegf and Il6-Jak-Stat pathways. The Jak-Stat activated oncogenic Pim3 kinase was a marker of the cancer responding ECs, being upregulated in spontaneous metastasis models and in ECs of human cancer. Notably, PIM inhibition increased vascular leakage and metastatic colonization in vivo and impaired the EC barrier via decreased junctional Cadherin-5 and catenins a, b and d. Thus, PIM3 protects the EC barrier in the metastatic niche, which may impair the efficacy of PIM inhibitors in cancer therapies.

overall_design: To investigate transcriptome changes of endothelial cells during metastatic colonization, we isolated endothelial cells for scRNASeq from lungs of healthy mice and 6 hours after B16F10 cell injection into C57BL/6 mice via tail vein

first: Keerthana

last: Ganesh

first: Pihla

last: Kaipainen

first: Aleksi

last: Halme

first: Pipsa

last: Saharinen


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [SLAM-Seq]

overall_design: SLAM-seq of shRNA-mediated zinc finger knockdowns in HEK293T cells. Cells were incubated for 24hr with 4SU and uridine chase timepoints were taken at 0hr, 2hr, 4hr, and 8hr.

first: Grady

last: Nguyen

first: Lena

last: Street

first: Grant

last: Goda

first: Jonathan

last: Schmok

first: Manya

last: Jain

first: Easin

last: Uddin Syed

first: Eunjeong

last: Kwon

first: Wenhao

last: Jin

first: Eric

last: Kofman

first: Alexandra

last: Tankka

first: Allison

first: Valerie

last: Gonzalez

last: Lécuyer

last: Dominguez


title: CRISPR/Cas9 and cDNA overexpression screens to identify  transmembrane transporters involved in PROTAC sensitivity/resistance

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce selective protein degradation by linking an E3 ubiquitin ligase enzyme to a target protein. Here we used transporter-focused and genome-wide CRISPR/Cas9 as well as a barcoded solute carriere (SLC)-focused cDNA libraray to screen for transporters that are involved in the resistance or sensitivity to BET- and SLC9-targeting PROTACs.

overall_design: Drug resistance screens with CRISPR/Cas9 and cDNA overexpression libraries in HAP1 cells under PROTAC selection.

first: Gernot

last: Wolf

first: Conner

last: Craigon

first: Patrick

last: Essletzbichler

first: Svenja

last: Onstein

first: Esther

last: Uijttewaal

first: Vojtech

last: Dvorak

first: Ariel

last: Bensimon

first: Alessio

last: Ciulli


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Cut&Run]

first: Brian

last: Yee

summary: RNA interactome studies have revealed that hundreds of zinc finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), despite being annotated as DNA-interacting transcription factors. The RNA substrates of ZFPs and the functional significance of their potential roles as DNA- and RNA-binding proteins (DRBPs) remain largely uncharacterized. Here we present a systematic multi-omics analysis of the DNA and RNA binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc finger families. We show that multiple ZFPs are novel regulators of RNA splicing, polyadenylation, or stability. ZFPs show widespread sequence-specific RNA binding ability and preferentially bind proximal to transcription start and end sites. Additionally, several ZFPs are DRBPs that bind their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DRBP that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation, shedding light on a large class of under-studied RBPs.

overall_design: Cut&Run of V5-tagged zinc finger proteins expressed in HEK293T cells.

first: Maya

last: Gosztyla

first: Lijun

last: Zhan

first: Sara

last: Olson

first: Xintao

last: Wei

first: Jack

last: Naritomi

first: Jonathan

last: Schmok

first: Manya

last: Jain

first: Grady

last: Nguyen

last: Uddin Syed

last: Li

first: Brenton

last: Graveley

first: Gene

last: Yeo


title: RNA-seq analysis of differentially expressed genes between WT and siALDOA HT29 cells.

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

summary: To investigate the biological function ALDOA in the colorectal cancer, we established HT29 cell lines in which the ALDOA gene has been knocked down by the small interfering RNA (siRNA) technique. We used a siRNA targeting ALDOA (KD) to knockdown ALDOA expression in HT29 cells. A scrambled siRNA (NC) was used as a control. Then RNA-Seq experiment was performed by Novogene Co., Ltd. (Beijing, China) to analyze gene expression changes in HT29 cells. For each sample, three independent biological replicates were performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT29 cells and its KD derivatives (siALDOA).

first: Liang

last: Sun


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RBNS]

overall_design: RNA bind-N-seq (RBNS) of recombinant ZNF277 or input control.

first: Lena

last: Street

first: Grant

last: Goda

first: Easin

first: Eunjeong

last: Kwon

first: Wenhao

last: Jin

first: Eric

last: Kofman

first: Alexandra

last: Tankka

first: Allison

first: Valerie

last: Gonzalez

last: Lécuyer

first: Daniel

last: Dominguez

first: Marko

last: Jovanovic


title: Endothelial Pim3 kinase protects the vascular barrier during lung metastasis (set3)

first: Niina

last: Santio

first: Keerthana

last: Ganesh

first: Pihla

last: Kaipainen

first: Aleksi

last: Halme

first: Pipsa

last: Saharinen


title: Endothelial Pim3 kinase protects the vascular barrier during lung metastasis

overall_design: To investigate transcriptome changes of endothelial cells during metastatic colonization, we isolated endothelial cells for scRNASeq from lungs of healthy mice and 6 hours after B16F10 cell injection into C57BL/6 mice via tail vein.


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [eCLIP]

first: Brian

last: Yee

overall_design: Enhanced immunoprecipitation and crosslinking followed by sequencing (eCLIP-seq) of V5-tagged zinc fingerp proteins expressed in HEK293T cells.

first: Maya

last: Gosztyla

first: Lijun

last: Zhan

first: Sara

last: Olson

first: Xintao

last: Wei

first: Jack

last: Naritomi

first: Grady

last: Nguyen

first: Jonathan

last: Schmok

first: Manya

last: Jain

last: Uddin Syed

last: Li

first: Brenton

last: Graveley

first: Gene

last: Yeo


title: Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation.

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Transcriptomic Analysis of Hofbauer Cells from Human Placental Tissue Infected with HIV, CMV, and ZIKV

city: Atlanta

first: Erica

last: Johnson

state: GA

address: 720 Westview Drive SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: This study involves the isolation of Hofbauer cells from human placental tissue at different gestation periods and their infection with HIV, CMV, and ZIKV. The transcriptomic profiles of these infected cells were analyzed using RNA-sequencing to identify differentially expressed genes and pathways.

overall_design: Hofbauer cells were isolated from human placental tissue and infected with HIV, CMV, and ZIKV. RNA was extracted, and RNA-sequencing was performed to analyze transcriptomic changes.

first: Viviane

last: Schuch

first: Daniel

middle: J

last: Hossack


title: Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor [RNA-seq]

status: Public on Sep 19 2024

city: Toronto

first: Michael

last: Taylor

state: ON

address: 686 Bay St.

institute: Hospital for Sick Children

summary: Investigate the DNA binding pattern as well as transcriptional consequences of ZIC1 and its medulloblastoma mutants in group 3 medulloblastoma cell lines and granule neuron progenitors

overall_design: Overexpression of ZIC1 (with or without N terminal FLAG tag) and its mutants in group 3 medulloblastoma cell lines or granule neuron progenitors, followed by RNA-Seq and ChIP-Seq for comparative analysis

first: John

last: Lee

first: Ran

last: Tao

first: Paul

last: Northcott


title: Disruption of Immune Responses By Type I Diabetes Exacerbates SARS-CoV-2 Mediated Lung Injury [scRNA-seq]

status: Public on Sep 16 2024

city: Philadelphia

last: Kass-Gergi

state: PA

address: 3900 Spruce St

department: Medicine

institute: University of Pennsylvania

summary: COVID-19 commonly presents as pneumonia, with those most severely affected progressing to respiratory failure. Patient responses to SARS-CoV-2 infection are varied, with comorbidities acting as major contributors to varied outcomes. Focusing on one such major comorbidity, we assessed whether pharmacological induction of Type I Diabetes Mellitus (T1DM) would increase the severity of lung injury in a murine model of COVID-19 pneumonia utilizing wild type mice infected with mouse-adapted SARS-CoV-2. Hyperglycemic mice exhibited increased weight loss and reduced blood oxygen saturation in comparison to their euglycemic counterparts, suggesting that these animals indeed experienced more severe lung injury. Transcriptomic analysis revealed a significant impairment of the adaptive immune response in the lungs of diabetic mice compared to those of control. In order to expand the limited options available for tissue analysis due to biosafety restrictions, we also employed a new technique to digest highly fixed tissue into a single cell suspension, originally designed for scRNA-Seq, which we then adapted for flow cytometric analysis.  Flow immunophenotyping and scRNA-Seq confirmed impaired recruitment of T cells into the lungs of T1DM animals. Additionally, scRNA-Seq revealed a distinct, highly inflammatory macrophage profile in the diabetic cohort that correlates with the more severe infection these mice experienced clinically, allowing insight into a possible mechanism for this phenomenon. Recognizing the near certainty that respiratory viruses will continue to present significant public health concerns for the foreseeable future, our study provides key insights into how T1DM results in a much more severe infection and identifies possible targets to ameliorate comorbidity-associated severe disease.

overall_design: We assessed whether pharmacological induction of T1DM would increase the severity of lung injury in a murine model of COVID-19 pneumonia by infecting STZ treated mice with MA30-SARS-CoV-2 and harvesting lungs from WT and T1DM mice at day 7 post infection for scRNA seq.

first: Andrew E

last: Vaughan


title: Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor [ChIP-seq]


title: GABPA regulates zygotic genome activation and pluripotency formation

status: Public on Sep 17 2024

city: Boston

first: Yi

last: Zhang

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

summary: Mammalian early embryo development incorporates a series of processes including maternal-to-zygotic transition (MZT), zygotic genome activation (ZGA) and lineage specification etc., coupled with totipotency decline and pluripotency formation. Identification of transcription factors (TFs) orchestrating these processes remains challenging. In this study, by taking advantages of targeted protein degron system in mice, which enabled us to study TF stage-specific functions in vivo, we identified and validated the Gabpa is not only a regulator of major ZGA, but also plays an essential role in epiblast lineage specification and pluripotency formation. GABPA together with other reported pluripotency regulators plays major roles in a stepwise manner during the pluripotency formation, highlighting a dynamic multi-factorial pluripotency regulation network throughout mammalian pre-implantation development.

overall_design: In this study, by generating dTAG mice and applying the low-input CUT&RUN technology, we identified and demonstrated that the transcription factor GA repeat binding protein alpha (Gabpa), which is a minor ZGA gene, is a key regulator in naïve pluripotency regulation. Our stage-specific degradation results revealed that GABPA is not only important for major ZGA, but also critical for ICM to naïve pluripotency transition by regulating numerous pluripotency genes.

first: Chengjie

last: Zhou

first: Meng

last: Wang

first: Chunxia


title: A pyrazole partially induces brassinosteroid-related gene expression, leading to salt stress sensitivity

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

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

department: CSRS

institute: RIKEN

summary: We report the gene expression profiles of Arabidopsis seedlings treated with or without DPAM-1 under salinity stress conditions.

overall_design: Arabidopsis thaliana (Col-0 ecotype) were grown on liquid MS medium (1mL/well in 24-well plates) at 22°C under 16-h-light/8-h-dark. DPAM-1 or coronatine treatment was performed at 4 days after germination. At 16h after DPAM-1 or coronatine had been applied and absorbed, 100 mM NaCl was added to the growth medium. Young seedlings were harvested at 2h after the onset of NaCl treatment.

first: Minoru

last: Ueda

first: Junko

last: Ishida

first: Satoshi

last: Takahashi

first: Atsushi

last: Nagano

first: Motoaki

last: Seki

first: Ayumi

last: Yamagami

first: Takeshi

last: Nakano

first: Florian

last: Pünner

first: Mai

last: Akakabe

first: Yoshinori

last: Sohtome

first: Mikiko

last: Sodeoka


title: Expression data from A. thaliana WT and gnat2 under control conditions and after 2 h treatment with high light or darkness

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary:
We used microarrays to detail the response of A. thaliana WT and gnat2 to high light and darkness treatments and identified distinct classes of regulated genes during this process.
In wildtype, the expression of 1,808 of 27,826 analysed transcripts was significantly (>2-fold, p<0.05) altered after high light treatment. Of those 1,808 transcripts, 943 were up- and 865 were downregulated. A similar response to high light was observed in gnat2, where 2,083 transcripts (1,126 up and 957 down) were significantly regulated upon high light stress. Similarly, lack of light resulted in an altered expression of 2,042 transcripts. Of those 2,042 transcripts, 979 were up- and 1,063 were downregulated. The gnat2 mutant responded similarly with 2,361 transcripts (1,195 up and 1,166 down) significantly regulated upon darkness. Under control conditions, only 38 transcripts except GNAT2 were differentially regulated between WT and gnat2. Overall the transcriptional responses of the WT and gnat2 to unexpected short-term darkness and high light were similar.

overall_design: Arabidopsis thaliana ecotype Co-0 and gnat2 mutants (SALK_033944) were grown on soil under short-day conditions (8 h light, 120 µmol m-2s-1 photon flux density, 23 °C and 50 % humidity). After 4.5 weeks, the plants were subjected to different light regimes interrupting the short-day light cycle. Two hours after the regular onset of light, the plants were treated with either high light illumination (HL, 1000 µmol m-2s-1) or darkness (D) for two hours. The control group (C) continued growth at 120 µmol m-2s-1. Immediately after treatment, the rosettes were harvested.

first: Markus

last: Wirtz

first: Laura

last: Armbruster


title: Prognostic and diagnostic value of metal metabolism in colorectal cancer

status: Public on Sep 15 2024

city: Moscow

first: Alexander

last: Modestov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

summary: Colorectal cancer (CRC) ranks as the second leading cause of cancer-related mortality globally and is the third most prevalent cancer. The effective treatment of CRC is challenged by tumor drug resistance, underscoring the urgent need for novel therapeutic strategies. It is well recognized that epigenetic modifications, particularly DNA methylation, significantly contribute to the initiation and advancement of CRC. Tumors frequently exhibit hypermethylation of specific gene promoters alongside a general hypomethylation of genomic DNA. In normal tissues, gene promoters, particularly those of tumor suppressor genes, are typically unmethylated, whereas they are often hypermethylated in cancerous tissues. Previous studies have identified the methylation status of the CpG island within the SLC30A10 gene as a reliable biomarker for CRC. Notably, a hypermethylated phenotype is inversely correlated with SLC30A10 expression. However, the precise functional implications of SLC30A10 suppression in the context of CRC progression remain to be elucidated.). The investigation of molecular pathways involved in metal metabolism in CRC has not been conducted previously at the transcriptomic level. Furthermore, the relationship between the mutational characteristics of tumors—such as individual mutations, mutational burden, and microsatellite instability—and the activity of genes related to metal metabolic pathways has not been explored. This project aims to be the first to examine the antitumor potential of modulating the transport systems for manganese and zinc ions in CRC. The molecular function of SLC30A10 is to export zinc (Zn) and manganese (Mn) ions from the cell. Additionally, SLC30A10 plays a crucial role in mitigating Mn-induced cytotoxicity and facilitates Zn transport to early endosomes while promoting endosomal recirculation to avert Zn toxicity. Our findings indicate that overexpression of SLC30A10 is correlated with the knockout of its functional antagonist, SLC39A14 in the HuTu80 and HCT-15 cell lines.

overall_design: This study aimed to examine the involvement of the SLC39A8, SLC39A14, SLC30A3, and SLC30A10 genes in the progression of colorectal cancer (CRC). To achieve this, gene editing was performed in two cell lines: HCT-15, which harbors a KRAS mutation, and HuTu80. Biallelic mutations of the SLC39A8, SLC39A14, SLC30A3, and SLC30A10 genes were introduced using CRISPR/Cas9 technology in both cell lines. The genetic constructs were cloned into the pSpCas9(BB)-2A-GFP (PX458) plasmid (Addgene). Overexpression experiments in both cell lines were conducted using the pCDH-EF1-MCS-IRES-copGFP plasmid (SBI, USA), where GFP was replaced with a puromycin resistance selection marker. ORF clones for SLC39A8 (NM_022154.5), SLC30A3 (NM_003459.5), SLC30A10 (NM_018713.3), and SLC39A14 (NM_015359.6) were obtained from Origene for the construction of lentiviral vectors.

first: Margarita

last: Kamynina

first: Julian

last: Rozenberg

first: Anton

last: Buzdin


title: All-defined NGN2 neuron protocol reveals multifaceted signatures of neuronal maturation [scRNA-seq]

city: South San Francisco

first: Mitchell

last: Rezzonico

address: 1 DNA Way

institute: Genentech

summary: Direct conversion of iPSCs into neurons by NGN2 over-expression is a popular method for disease modeling. Here we report a standardized method to generate functional excitatory cortical neurons using clonal, targeted engineered iPSC lines and defined reagents. We demonstrate that our protocol generates consistent excitatory cortical neurons at scale. These cultures can be maintained healthily for at least 150 days and expresses the majority of the GWAS genes found in autism, Parkinson’s disease, and Alzheimer’s disease. Comprehensive temporal omics, functional, and morphological profiling demonstrated continued progression of neuronal maturation. Deep functional characterization through transcriptomic, imaging, and functional assays revealed the coordinated action of multiple pathways in neuronal maturation. Our method and profiling data can serve as reference for developing human in vitro neuronal models for disease modeling.

overall_design: Single-cell RNA-seq of iPSC-derived NGN2-induced neurons. Neurons were collected at differentiation days 28, 42, and 56. For additional details, please refer to Shan et al.

first: Xiwei

last: Shan

first: Ai

last: Zhang

middle: G

first: Claire

last: Jeong


title: All-defined NGN2 neuron protocol reveals multifaceted signatures of neuronal maturation [bulk timecourse]

overall_design: Bulk RNA-seq of iPSC-derived NGN2-induced neurons. Neurons were collected at differentiation days 14, 21, 28, 42, and 56. For additional details, please refer to Shan et al.


title: Subset-specific mitochondrial and DNA damage shapes T cell responses to fever and inflammation

city: Nashville

first: Jeffrey

last: Rathmell

state: Tennessee

address: 110 21st Avenue South

institute: Vanderbilt University

summary: Heat is a cardinal feature of inflammation that affects enzymes and molecular complexes, yet the effects on immune cells remain uncertain. We show heat broadly increased inflammatory activity of CD4+ T cell subsets and decreased Treg suppressive function. Heat-exposed Th1 cells, however, selectively developed mitochondrial stress with elevated reactive oxygen species and DNA damage driven by dependence on electron transport chain complex 1 (ETC1), which rapidly decreased activity. While Tp53 and Sting eliminated damaged Th1 cells, those that adapted showed improved long-term activity. Th1 cells with DNA damage and ETC1 signatures were also detected in Crohn’s disease and rheumatoid arthritis. Fever-relevant heat thus selectively induces mitochondrial stress in Th1 cells that drives apoptosis or adaptation to maintain genomic integrity and improve T cell function.

overall_design: To investigate the effects of heat on T cells, we cultured Naïve, Th0, Th17, and iTreg cells in differentiating cytokine media for 4 days at 37˚C or 39˚C. 6 replicates of each T cell subset are available. Naïve cells serve as the control cell group.

first: Darren

last: Heintzman

first: Rachael

last: Smith

first: Emilie

last: Fisher

first: Xiang

last: Ye

first: Andrew

last: Patterson

first: Joel

middle: H

last: Elasy

first: Kelsey

last: Voss

first: Channing

last: Chi

first: Ayaka

last: Sugiura

first: Gabriel

last: Rodriguez

first: Nowrin

middle: U

last: Chowdhury

first: Emily

last: Arner

first: Evan

last: Krystoviak

first: Frank

last: Mason

first: KayLee

middle: K

last: Steiner

first: Wasay

last: Khan

first: Lana

last: Olson

first: Angela

last: Jones

first: Hanna

last: Hong

first: Lindsay

last: Bass

first: Katherine

last: Beier

first: Wentao

last: Deng

first: Costas

last: Lyssiotis

first: Dawn

last: Newcomb

last: Bick

first: W

first: John

last: Wilson


title: Macrophage depletion alleviates pain-related behaviors in osteoarthritic mice

status: Public on Sep 13 2024

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

summary: The objectives of this study were to determine the effect of macrophage depletion on pain-like behaviors, joint damage, and DRG molecular changes in both male and female mice with osteoarthritis.

overall_design: Systemic macrophage depletion was achieved using the macrophage Fas-Induced apoptosis (MaFIA) strain of mice and giving i.p. injections of AP20187 or vehicle control once per day for five consecutive days to male mice in which osteoarthritis was induced by destabilization of the medial meniscus (DMM) surgery, 8 weeks after the surgery, or to male naïve mice that were age-matched. L3-L5 dorsal root ganglia were collected from the same side as the knee surgery, pooled, and RNA was extracted for bulk RNAseq.

first: Anne-Marie

last: Malfait

first: Terese

last: Geraghty


title: Ectopic expression of transcriptional regulatory proteins reveals two classes of late genes during chlamydial development, corresponding to the IB and EB cell type.

status: Public on Sep 11 2024

first: Scott

middle: Stephen

last: Grieshaber

state: ID

address: 875 Perimeter Drive MS 3051

department: Biological Sciences

institute: University of Idaho

summary: The bacteria in the chlamydiales order are obligate intracellular parasites of eukaryotic cells. They are reliant on an infectious cycle consisting of at least three phenotypically distinct cell forms termed the reticulate body (RB), the intermediate body (IB) and the elementary body (EB). The EB is infectious but does not replicate. The RB replicates in the host cell but is non-infectious, while the IB is an intermediate form that transitions to the EB form. Within this order, the genus Chlamydia contains the causative agents of a number of important pathogens of humans. C. psittaci causes zoonotic infections resulting in pneumonia, while C. pneumoniae is a human pathogen that causes respiratory disease and is linked to atherosclerosis. Biovars of C. trachomatis are the causative agents of trachoma, the leading cause of preventable blindness worldwide, as well as sexually transmitted infections with the potential to cause pelvic inflammatory disease and infertility. Irrespective of the resulting disease, all chlamydial species share the same obligate intracellular life cycle and developmental cell forms. In this study we investigated the role of four transcriptional regulators on chlamydial gene expression and completion of the developmental cycle. We ectopically expressed the transcriptional repressor Euo, each of the two nucleoid associated proteins HctA and HctB and the two component sensor kinase CtcB in the RB. All four blocked development of infectious EBs. Transcriptional analysis using RNA-seq and differential expression clustering revealed three classes of gene expression. FISH analysis demonstrated that these classes corresponded to distinct cell forms revealing the gene expression profile of the RB, IB and EB developmental forms. Additionally, these data revealed that the genes for the T3SS were cell type restricted. The structural genes for the T3SS were expressed primarily in the IB while the two translocons were expressed in distinct cell types one in the RB and the other in the EB. Overall these data show that the chlamydial developmental cycle produces three distinct regulons corresponding to the RB, IB and EB cell forms and that the T3SS is expressed in a cell form specific manner suggesting defined functional roles for the T3SS in specific cell forms.

overall_design: RNA-seq analuysis of Chlamydia trachomatis ectopicaly expressing the regulatory proteins, Euo, HctA, CtcB and HctB

first: Nicole

first: Cody

last: Appa

first: Anders

last: Omsland


title: Single cell transcriptomics of the cerebral cortex in mice lacking the PRC2 gene Eed

city: Brisbane

first: Michael

last: Piper

state: QLD

address: The University of Queensland, St Lucia

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

summary: The Polycomb Repressive Complex 2 (PRC2) regulates corticogenesis, yet how PRC2 influences cell identity in the mature brain is poorly defined. Using a mouse model in which the PRC2 gene Eed is conditionally deleted from the developing mouse dorsal telencephalon, we performed single nuclei RNA sequencing on the cortical plate of adult heterozygote and homozygote Eed knockout mice compared to controls.

overall_design: Using a mouse model in which Eed is conditionally knocked out from all cells derived from the dorsal telencephalon (Emx1-iCre), we performed single nuclei RNA sequencing (snRNA-seq) on the cortical plate of a control (CTRL), a heterozygous (Eed-cHet) knockout, and a homozygous (Eed-cKO) mouse.

first: Laura

last: Currey

first: Lachlan

last: Harris


title: RNA-sequencing of non-small cell lung cancer tissue samples

status: Public on Sep 12 2024

city: Korolev

first: Daniil

middle: Vitalievich

last: Luppov

state: please choose

address: 1/9 Karla Libknehta Street, Upt 12

institute: Sechenov University

summary: Lung cancer is the deadliest cancer worldwide. In this study, we obtained RNA-sequencing data from 61 lung cancer samples. We hope that this data can improve the understanding of this disease.

overall_design: Lung cancer tissues were taken from 61 patients and subjected to RNA sequencing. For all biosamples, informed written consent for participation in this study (including publication of anonymised clinical, transcriptomic and genetic data) was obtained from patients or their legal representatives. All experimental biosamples were blocks of formalin fixed, paraffin embedded (FFPE) tumour tissue. Before further analysis, all biosamples were evaluated by a pathologist to confirm the origin of the tumour tissue, and only samples with tumour cell content greater than 50% were subjected to further analysis.  RNA sequencing was performed at the Department of Pathology and Laboratory Medicine of the University of California, Los Angeles, and at the Clinical Genomic Bioinformatics Laboratory of the I.M. Sechenov First Moscow State Medical University. RNA sequencing was performed on an Illumina HiSeq 3000 system for single-end sequencing with a read length of 50 bp, generating at least 30 million raw reads per sample.

first: Elena

last: Poddubskaya

first: Marina

last: Lyadova

first: Maxim

last: Sorokin

first: Maria

last: Suntsova

first: Anton

last: Buzdin


title: Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome

city: Irvine

first: Negin

last: Rahimzadeh

address: 3224 Biological Sciences III

institute: UCI

summary: The highly dynamic regulatory networks involved in brain processes can result in specific gene expression patterns across distinct cell types. The single-nucleus and spatial transcriptomics data allow us to better understand these patterns. This study involved the analyses of the brains of mice and  humans with Alzheimer’s Disease (AD) and Down Syndrome.

overall_design: Spatial and single nuclei transcriptomics analysis of Alzheimer's Disease and Down Syndrome in human and mouse brain tissue using single-nucleus RNA-seq and visium platform.

first: Morabito

last: Samuel

first: Miyoshi

last: Emily

first: Swarup

last: Vivek


title: Single-cell RNA-sequence reveals the transcriptional dynamics of tumor immune microenvironment by autophagy inhibition in cancer cells

city: Fukuoka

first: Chikanori

last: Tsutsumi

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

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

summary: In this study, we investigated the impact of autophagy inhibition in cancer cell on the tumor immune microenvironment (TIME) of orthotopic syngeneic pancreatic ductal adenocarcinoma (PDAC) tumors. Dendritic cells (DCs) in the cancer cell autophagy inhibited tumors showed significantly higher expression of genes related to DC functions such as antigen-presentation, migration, IFN response, compared to control tumors. Our results indicate that autophagy inhibition in cancer cells induce the enhancement of adoptive tumor immunity via DC activation in PDAC.

overall_design:
Mouse PDAC cell lines were established from the primary PDAC tumors of KrasG12D/+, Trp53R172H/+, Pdx-1-Cre (KPC) mice. Autophagy-deficient KPC cells were generated by transfection with shRNAs targeting the autophagy-related gene, Atg7. KPC shNC / KPC shATG7 were transplanted into the pancreas of C57BL/6 mice, and we compared the transcriptional difference between the orthotopic syngeneic PDAC tumors transplanted KPC shNC or KPC shATG7.
1 sample integrated from 3 orthotopic syngeneic PDAC tumors transplanted KPC shNC. 1 sample integrated from 3 orthotopic syngeneic PDAC tumors transplanted KPC shATG7.

first: Koki

last: Oyama

first: Kohei

last: Nakata


title: YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, 3' single cell RNA sequencing

status: Public on Sep 09 2024

city: La Jolla

first: Farhoud

last: Faraji

address: 3855 Health Sciences Drive, Floor 2, Room 2345, Bay KK

department: Moores Cancer Center

institute: UC San Diego Health

summary: Single cell RNA sequencing of whole tongue epithelia from control mice or transgenic mice expressing HPV16E6-E7 and/or YAP1S127A

overall_design: Fifteen days after transgene induction, cells were isolated from whole tongue epithelia, and subjected to oligo-dT-based mRNA selection, cDNA library preparation, and sequencing on Illumina NovaSeq6000.

first: Sydney

middle: I

last: Ramirez

first: J Silvio

last: Gutkind


title: Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor

first: Michael

last: Taylor

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

overall_design: Refer to individual Series


title: YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, bulk RNA sequencing

summary: Bulk RNA sequencing of tongue epithelia-derived, transgene-selected primarily cultured cells from control mice or transgenic mice expressing HPV16E6-E7 and YAP1S127A

overall_design: Fifteen days after transgene induction, cells were isolated from whole tongue epithelia, sorted for GFP expression, cultured, then subjected to oligo-dT-based mRNA selection, cDNA library preparation, and sequencing on Illumina NovaSeq6000.


title: YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, CUT&TAG sequencing for YAP, H3K27ac, and H3K27me3

summary: Cleavave Under Targets and Tagmentation (CUT&TAG) sequencing for YAP, H3K27ac, and H3K27me3 of tongue epithelia-derived, transgene-selected primarily cultured cells from control mice or transgenic mice expressing HPV16E6-E7 and YAP1S127A

overall_design: Fifteen days after transgene induction, cells were isolated from whole tongue epithelia, sorted for GFP expression, cultured, then subjected to CUT&TAGseq, library preparation, and sequencing on Illumina NovaSeq6000.


title: YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, ATAC sequencing

summary: Assay for Transposase Accessible Chromatin (ATAC) sequencing of tongue epithelia-derived, transgene-selected primarily cultured cells from control mice or transgenic mice expressing HPV16E6-E7 and YAP1S127A

overall_design: Fifteen days after transgene induction, cells were isolated from whole tongue epithelia, sorted for GFP expression, cultured, then subjected to ATACseq, library preparation, and sequencing on Illumina NovaSeq6000.


title: Endothelial Pim3 kinase protects the vascular barrier during lung metastasis

city: Helsinki

first: Niina

last: Santio

address: Haartmaninkatu 8

department: Research Program Unit, CAN-PRO

institute: University of Helsinki

summary: To investigate transcriptome changes of endothelial cells during cancer cell response, we studied HUVEC RNA expression in conditioned medium derived from empty plates versus B16-F10 melanoma cultures.

overall_design: Endothelial cells (ECs) form a tissue-specific barrier for disseminating cancer cells in distant organs. However, the molecular regulation of the ECs in the metastatic niche is poorly understood. Here, we analyzed the transcriptional reprogramming of cultured human ECs (HUVECs) in response to potential signal mediators sectered to the cultured medium by B16-F10 melanoma cells. Melanoma cells were cultured for 48h, after which conditioned medium was collected, spun and added to replace HUVEC culture medium.  As a control, HUVEC cultures were treated with conditioned medium stored in similar conditions on empty plates. HUVEC cells were cultured in conditioned medium for 16 h after which total RNA was isolated  and processed for mRNA-Seq.

first: Pihla

last: Kaipainen

first: Aleksi

last: Halme

first: Pipsa

last: Saharinen


title: TF ChIP-seq Drosophila melanogaster

status: Public on Oct 06 2024

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

summary: A catalog of transcription factor (TF) binding sites in the genome is critical for  deciphering regulatory relationships.  Here we present the culmination of the efforts of the  modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model  organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding  events in vivo in two major model organisms, Drosophila melanogaster (fly)  and Caenorhabditis elegans (worm).  These datasets comprise 605 TFs identifying 3.6M sites in  the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the  regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters  termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT)  regions, and that the importance of consensus sequence motifs bound by TFs depends on  metapeak size and complexity.  Combining ChIP-seq data with single cell RNA-seq data in a  machine learning model identifies particular TFs with a prominent role in promoting target gene  expression in specific cell types, even differentiating between parent-daughter cells during  embryogenesis.  These data are a rich resource for the community that should fuel and guide  future investigations into TF function.  To facilitate data accessibility and utility, all strains  expressing GFP-tagged TFs are available at the stock centers for each organism.  The chromatin  immunoprecipitation sequencing data are available through the ENCODE Data Coordinating  Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that  provides rapid access to processed data sets and summary analyses, as well as widgets to probe  the cell type-specific TF-target relationships.

overall_design: Reanalysis of raw data files in BioProject PRJNA63463  using ENCODE TF/Histone ChIP-Seq pipeline version 1.3.6  https://github.com/ENCODE-DCC/chip-seq-pipeline2

first: Michelle

last: Kudron

first: Alec

last: Victorsen

first: Bridget

last: Lear

first: Jiahao

last: Gao

first: Jinrui

last: Xu

first: Swapna

last: Samanta

first: Emily

last: Frink

first: Adri

last: Tran-Pearson

first: Chau

last: Huynh

first: Dionne

last: Vafeados

first: Ann

last: Hammonds

first: William

last: Fisher

first: Martha

last: Wall

first: Greg

last: Wesseling

first: Vanessa

last: Hernandez

first: Zhichun

last: Lin

first: Mary

last: Kasparian

first: Kevin

last: White

first: Ravi

last: Allada

first: Mark

last: Gerstein

first: LaDeana

last: Hillier

first: Susan

last: Celniker

first: Valerie

last: Reinke

first: Robert

last: Waterston


title: Time-dependent enhancement of mRNA vaccines by 4-1BB costimulatory antibodies

status: Public on Sep 04 2024

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: mRNA vaccines have demonstrated efficacy against COVID-19. However, concerns regarding waning immunity and breakthrough infections have motivated the development of next-generation vaccines with enhanced efficacy. In this study, we investigated the impact of 4-1BB costimulation on immune responses elicited by mRNA vaccines in mice. We first vaccinated mice with an mRNA vaccine encoding the SARS-CoV-2 spike antigen like the Moderna and Pfizer-BioNTech vaccines, followed by administration of 4-1BB costimulatory antibodies at various times post-vaccination. Administering 4-1BB costimulatory antibodies during the priming phase did not enhance immune responses. However, administering 4-1BB costimulatory antibodies after 96 hours elicited a significant improvement in CD8 T cell responses, leading to enhanced protection against breakthrough infections. A similar improvement in immune responses was observed with multiple mRNA vaccines, including vaccines against common cold coronavirus, human immunodeficiency virus (HIV), and arenavirus. These findings demonstrate a time-dependent effect by 4-1BB costimulation and provide insights for developing improved mRNA vaccines.

overall_design: Bulk RNA-Sequencing of SARS-CoV-2 specific CD8 T cells taken 7 days after vaccination of mice with an mRNA vaccine followed with treatment with a control antibody (n=4) or 4-1BB agonistic antibody (n=4).

first: Pablo

last: Penaloza-MacMaster

first: Sarah

last: Sanchez


title: All-defined NGN2 neuron protocol reveals multifaceted signatures of neuronal maturation [bulk_media]

first: Mitchell

last: Rezzonico

overall_design: Bulk RNA-seq of iPSC-derived NGN2-induced neurons. Neurons were cultured in either home brew media or mouse astrocyte-conditioned media and collected at differentiation day 42. For additional details, please refer to Shan et al.

first: Xiwei

last: Shan

first: Ai

last: Zhang

first: Claire

last: Jeong


title: tRNA sequencing Drosophila wildtype and ectopic neuroblast brains

status: Public on Sep 05 2024

city: Merced

first: Michael

last: Cleary

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

summary: tRNA quantification of neuron-biased and neuroblast-biased Drosophila larval brains

overall_design: RNA from dissected wildtype and ectopic neuroblast brains (insc-Gal4>UAS-aPKC_caax) was used for total tRNA quantification using the hydro-tRNAseq method

first: Mike


title: Spatiotemporal Single-Cell Roadmap of Human Skin Wound Healing (Single-cell-Wound)

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

institute: Karolinska Institutet

summary: The process of wound healing in humans is poorly understood. To identify spatiotemporal gene expression patterns during human wound healing, we performed single cell and spatial transcriptomics profiling of human in vivo wound samples.

overall_design:
We obtained the human skin wound tissues by recruiting healthy volunteers and we collected wound tissues at different time points to reflect different healing stages (intact skin, wound day1, day 7, and day 30). Samples from different wound healing stage were analyzed by single cell and spatial transcriptomics sequencing.

*** The raw sequencing data are available for controlled access in European Genome–phenome Archive (EGA) under the accession code EGAS50000000571 ***

first: Zhuang

last: Liu


title: β-caryophyllene sensitizes hepatocellular carcinoma cells to chemotherapeutics and inhibits cell malignancy through targeting MAPK signaling pathway

status: Public on Sep 03 2024

city: Hangzhou,

first: Guangyue

last: Li

state: Zhejiang

address: No.600 Dunyu Rd., Xihu District

institute: westlake university

summary: In hepatocellular carcinoma (HCC) development, cancer cells generally exhibit increased cell proliferation due to mutations and aberrant expressions of key regulatory genes. The current study determines the cytotoxic effects of β-caryophyllene (BCP) alone or in combination with doxorubicin (DOX) and cisplatin (DDP) on HCC cells and also elucidates the underlying mechanism of BCP to exert its anticancer activities. HepG2, SMMC-7721 HCC cells, and HL-7702 normal liver cells were treated with BCP, DOX, and DDP individually or in their combinations. Cell proliferation assay, flow cytometric assay, and Western blot analysis were used to evaluate the cytotoxic effects of these treatments. Transwell assays were used to examine the effects of BCP on migration and invasion of HCC cells. RNA-seq studies were used to determine the primary target genes of BCP-treated HepG2 cells. Integrative analysis of differentially expressed genes (DEGs) of RNA-seq data with a TCGA dataset of HCC patients identified BCP-targeted genes that were verified by RT-qPCR. Ectopic gene expression, cell viability, and colony formation assay were performed to validate the primary targets of BCP. The results found that, BCP selectively inhibited HCC cell proliferation while exhibited relatively low toxicity to normal liver cells; however, DOX and DDP showed higher toxicity in normal cells than that in HCC cells. Importantly, in combinatorial treatments, BCP synergistically enhanced cytotoxicity of DOX and DDP in HCC cells but this effect is markedly reduced in HL-7702 cells. BCP-treated HCC cells exhibited decreased migration and invasion ability versus the control. Furthermore, RNA-seq analyses of BCP-treated HepG2 cells identified 433 protein-coding DEGs with over 1.5-fold change. Integrative analyses revealed five BCP-targeted DEGs regulating the MAPK signaling pathway. Among these five genes, three displayed a significantly positive correlation of their expression with the overall survival of HCC patients. As a primary target, PGF was significantly downregulated by BCP treatment, and its exogenous expression desensitized HCC cells to the inhibition of BCP treatment. In summary, BCP inhibits malignant properties of HCC and synergistically sensitizes the anticancer activity of DOX and DDP. In HCC cells, BCP primarily targets PGF and MAPK signaling pathway.

overall_design: To investigate the effect of BCP treatment alone or in combination with DOX and DDP on liver cancer cells and normal liver cells. Subsequently, by high-throughput transcriptome analysis (RNA-seq) of HepG2 cells, examine the specific genes and signaling pathways altered by BCP treatment.

first: Irum

last: Basheer

first: Li

last: Guangyue

first: Sui

last: Guangchao


city: New York

first: Xuanrong

last: Chen

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: The androgen receptor (AR) is the central determinant of prostate tissue identity and differentiation, controlling normal, growth-suppressive prostate-specific gene expression. It is also a key driver of prostate tumorigenesis, becoming “hijacked” to drive oncogenic transcription. However, the regulatory elements determining the execution of the growth suppressive AR transcriptional program, and whether this can be reactivated in prostate cancer (PCa) cells remains unclear. Canonical androgen response element (ARE) motifs are the classic DNA binding element for AR. Here, we used a genome-wide strategy to modulate regulatory elements containing AREs to define distinct AR transcriptional programs. We find that activation of these AREs is specifically associated with differentiation and growth suppressive transcription, and this can be reactivated to cause death in AR+ PCa cells. In contrast, repression of AREs is well tolerated by PCa cells, but deleterious to normal prostate cells. Finally, gene expression signatures driven by ARE activity are associated with improved prognosis and luminal phenotypes in human PCa patients. This study demonstrates that canonical AREs are responsible for a normal, growth-suppressive, lineage-specific transcriptional program, that this can be reengaged in PCa cells for potential therapeutic benefit, and genes controlled by this mechanism are clinically relevant in human PCa patients.

overall_design: Gene expression profiling with RNA-seq in LNCaP with inducible expression of MACC constructs.

last: Augello

first: Christopher

last: Barbieri


title: ChIP-seq in LNCaP with inducible expression of MACC constructs.

overall_design: Genome binding/occupancy profiling by high throughput sequencing in LNCaP with inducible expression of MACC constructs.


title: RNA-sequencing across different passages of mesenchymal stem cells from three donors.

city: Shanghai

first: Rao

last: hanyu

address: Huashan Road NO.1954

institute: Shanghai Jiao Tong University

summary: To explore the biological diiference following MSC proliferation, we isolated MSCs from three umbilical cord tissues obtained from three donors, hereinafter referred to C56, C59 and C60. MSCs from each donor were then cultured and harvested at passage 2, 6 and 10 respectively (hereinafter referred to P2, P6 and P10).  We next conducted global transcriptomics studies.

overall_design: MSCs from each donor were cultured and harvested at passage 2, 6 and 10 to represent different stages of cell proliferation.

first: Hanyu

last: Rao


city: liverpool

first: Iain

middle: M

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

institute: Liverpool John Moores University

summary: Circulating maternal miRNA is a promising source of biomarkers for antenatal diagnostics. The hybridisation-based NanoString nCounter is a popular global screening tool due to its simplicity and ease-of-use but there is a lack of standardisation in analysis methods. In this study we used a rodent model to examine the effect of user-defined variables within the data processing software nSolver upon reported changes in maternal blood miRNA during pregnancy. These included the choice of normalisation and background correction methods as well as the background threshold applied. Our results suggest that these variables greatly influence the output of the nSolver software. Changes in a total of 31 miRNAs were detected, but many of these were only picked up by a single combination of analysis variables and no reported change was common to all. RT-qPCR validated changes in 4 miRNAs with known roles in pregnancy (miR-183, miR-196c, miR-431, miR-450a) from a panel of 14 candidates in which changes were supported by multiple analysis workflows. No single nSolver analysis workflow had successfully identified all four validated changes. We then reverse-engineered the nSolver analysis to further investigate the effect of each step in the analysis upon the count data.  Our results highlight the need for standardised nCounter data analysis methods and detailed reporting of these methods in papers. We suggest that robust data can only be obtained by examining multiple analysis workflows.

overall_design:
Experimental design was 6x6. A control non-pregnant group of 6 rats was compared to a pregnant group of 6 (gestational age E14.5). Maternal blood was obtained by post-mortem cardiac puncture. Total RNA prepared from 1.5ml platelet-free plasma. Osa-miR-414 exogenous spike-in added to samples.

Assessment of NanoString technology as a tool for profiling circulating miRNA in maternal blood during pregnancy.
Adamova P, Powell AK, Dykes IM.
Extracell Vesicles Circ Nucleic Acids. 2024;5:571-96.

first: Petra

last: Adamova

first: Andrew

last: Powell


title: Spatiotemporal Patterns of Gene Expression During Development of a Complex Colony Morphology

first: Gareth

last: Cromie

address: 720 Broadway Avenue

institute: PNRI

summary: Clonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. Here, we examine colony development in a yeast strain (F13) that produces colonies with a highly structured “ruffled” phenotype in the colony periphery and an unstructured “smooth” phenotype in the colony center. We demonstrate that in the F13 genetic background deletions of transcription factors can either increase (dig1 deletion, sfl1 deletion) or decrease (tec1deletion) the degree of colony structure. We identify genes responding additively and non-additively to the genotype and spatiotemporal factors and cluster these genes into a number of different expression patterns, including patterns that correlate closely with the degree of colony structure in each sample and include genes with known roles in the development of colony structure. Individual deletion of 26 genes sampled from different clusters identified 5 with strong effects on colony morphology (BUD8, CIS3, FLO11, MSB2 and SFG1), all of which eliminated or greatly reduced the structure of the F13 outer region.

overall_design: To investigate the development of colony structure, we carried out gene expression analysis on F13 and the three deletion strains using RNA-seq. Samples were taken early in colony growth (day2), which precedes ruffled phenotype development in F13, and from the peripheral and central regions of colonies later in development (day5), at which time these regions are structured and unstructured (respectively) in F13.

first: Zhihao

last: Tan

first: Michelle

last: Hays

first: Amy

last: Sirr

first: Eric

last: Jeffery

first: Aimée

last: Dudley


title: YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, bulk RNA sequencing II

first: Farhoud

last: Faraji

summary: Bulk RNA sequencing of tongue epithelia from control mice or transgenic mice expressing HPV16E6-E7 and/or YAP1S127A

overall_design: Fifteen days after transgene induction, RNA was isolated from whole tongue epithelia, and subjected to oligo-dT-based mRNA selection, cDNA library preparation, and sequencing on Illumina NovaSeq6000.

first: Sydney

last: Ramirez

first: J Silvio

last: Gutkind


title: Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing

status: Public on Sep 01 2024

city: Norwich

first: Thomas

middle: Cameron

last: McLean

state: Norfolk

address: Norwich Research Park

department: Molecular Microbiology

institute: John Innes Centre

summary: Long-range gene regulation is rare in bacteria and is confined to the classical DNA looping model. Here, we use a combination of biophysical approaches, including X-ray crystallography and single-molecule analysis, to show that long-range gene silencing on the plasmid RK2, a source of multidrug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. We find that KorB is a CTPase clamp that can entrap and slide along DNA to reach distal target promoters. We resolved the tripartite crystal structure of a KorB-KorA-DNA co-complex, revealing that KorA latches KorB into a closed-clamp state. KorA thus stimulates repression by stalling KorB sliding at target promoters to occlude RNA polymerase holoenzymes. Altogether, our findings explain the mechanistic basis for KorB role-switching from a DNA-sliding clamp to a co-repressor, and provide a new paradigm for the long-range regulation of gene expression.

overall_design: Illumina paired-end deep-sequencing to determine plasmid copy number in relation to genome copy number

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