title: CREB-Regulated Transcription During Glycogen Synthesis in Astrocytes

status: Public on Apr 30 2024

first: Jessica

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

summary: Glycogen storage, conversion and utilization in astrocytes play important roles in brain energy metabolism. The conversion of glycogen to lactate through glycolysis occurs through the coordinated activities of various enzymes, and inhibition of this process can impair different brain processes including formation of long-lasting memories. To replenish depleted glycogen stores, astrocytes undergo glycogen synthesis, a cellular process that has been shown to require transcription and translation during specific stimulation paradigms. However, the detailed nuclear signaling mechanisms and transcriptional regulation during glycogen synthesis in astrocytes remain to be explored. In this report, we study the molecular details of vasoactive intestinal peptide (VIP)-induced glycogen synthesis in astrocytes. VIP is a potent neuropeptide that triggers glycogenolysis followed by glycogen synthesis in astrocytes. We show evidence that VIP-induced glycogen synthesis requires CREB-mediated transcription that is Protein Kinase C and calcium-dependent but is independent of Protein Kinase A. In parallel to CREB activation, we demonstrate that VIP also triggers nuclear accumulation of the CREB coactivator CRTC2 only in astrocytic nuclei that also requires Protein Kinase C activity. Transcriptome profiles of VIP-induced astrocytes identified robust CREB-dependent transcription of glycogenic genes including the upregulation of Ppp1r3c along with robust repression of Phkg1, the catalytic subunit of phosphorylase kinase. Overall, our data demonstrates the importance of CREB-mediated transcription in astrocytes during stimulus-driven glycogenesis.

overall_design: To examine the extent of CREB-mediated transcription upon VIP induction, we transduced cortical astrocytes with either control or dominant negative ACREB expression vectors and treated cells with either PBS or VIP before harvesting RNA for RNAseq.

first: WeiLee

last: Lim

first: TohHean

last: Ch'ng


title: Drug efflux and lipid A modification by 4-L-aminoarabinose are key mechanisms of polymyxin B resistance in the sepsis pathogen Enterobacter bugandensis

status: Public on May 01 2024

city: Belfast

first: Inmaculada

last: Garcia-Romero

address: 97 Lisburn Rd

country: United Kingdom

institute: QUB

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanism of PmB resistance and heteroresistance in Enterobacter bugandensis by analysing the differential gene expression under PmB treatment.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for two Enterobacter bugandensis strains, E105227 and E104107, on presence and absence of the antibiotic PmB.
The RNA was extracted from cells growing in exponential phase and 3 replicates were done for each condition and strain.

first: Mugdha

last: Srivastava

first: Julia

middle: M

last: Feria

first: Miguel

middle: A

last: Valvano


title: Malignant ascites microenvironment induced macrophage reprogramming facilities epithelial ovarian cancer peritoneal metastasis

city: Hong Kong

first: Huogang

last: WANG

state: Not Applicable

address: 22 Sassoon Road

department: Obstetrics and Gynecology

country: China

institute: The University of Hong Kong

summary: Macrophages form a primary immune cells population in tumor tissues and malignant ascites microenvironment (MAM). They can be activated and polarized into tumor-associated macrophages (TAM) by the embedded environment and promote tumor progression and metastasis However, the molecular mechanisms of MAM in macrophage polarization and the effects on epithelial ovarian cancer (EOC) metastatic progression remain elusive. Here, we found that that MAM modulates RhoA-GTPase-F-actin-Hippo signaling cascade in facilitating M2-like macrophage polarization that, in turn, promotes tumor dissemination. PUFA  enriched magligant ascites microenvironment promote macrophage lipid oxidative phosphorylation and supression RhoA-GTPase-Yap1 axis. Genetic ablation Yap1 in macrophage exhibited M2-like polarization and enhanced ovrian tumor dissemination. Pharmacology inhibit Mst1/2 could rescue M2-like TAM polarization in MAM and alter the lipid oxidation of macrophages in MAM, more importantly, inhibit ovarian metastatic properties. Through comparasion primary TAM (P-TAM) and metastasis TAM (M-TAM), we proved that Hippo-Yap1 siganl results M-TAM with high M2/M1 ratio. These findings implicate critical functions of PUFA modulate RhoA-Hippo axis in facility TAM polarization and also suggest manipulation of PUFA metabolism or RhoA-Hippo siganl as a therapeutic strategy aganist EOC metastasis.

overall_design: Macrophages mRNA profiles of M1 macrophages and M1 macrophages treated with OCM , M2 macrophages and M2 macrophages treated with OCM

last: Wang

first: David

last: Chan


title: Integrative and Quantitative Analysis of Tumor Progression Reveals Fundamental Properties of Glioblastoma

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

country: Germany

institute: DKFZ

summary: Principle of tumor growth is one fundamental aspect of cancer biology and it remains to be superficially understood. Here we developed a set of genetic and mathematic tools allow integrative analysis of mouse glioblastoma (GBM) progression. Quantitative temporal imaging of mouse GBM and mathematic modeling suggest that mouse GBM grows exponentially, which led to the discovery that a sustainable exponential growth requires outward migrating brain tumor stem cells (BTSCs). Quantitative single cell tracing of BTSCs in vivo unravels symmetric expansion of BTSCs, asymmetric differentiation, and a non-reversible differentiation process during tumor progression. Mosaic tracing of BTSCs and non-BTSCs reveals a cellular temporal dynamic changes and cellular turnover. These experimentally collected parameters were integrated step by step to a quantitative mathematic model of GBM growth, which faithfully predicts tumor cellular architecture, tumor response to chemotherapy and BTSC therapy. Bulk and single cell RNA-Seq reveals distinct molecular hierarchy and molecular heterogeneity in BTSCs, which was confirmed by analyzing human GBM single cell RNA-Seq results. This study reveals basic developmental principles that govern tumor development, which provides novel understanding of cancer development, tumor heterogeneity and new approaches to treat GBM.

overall_design:
We performed single-cell RNAseq and bulk RNAseq from brain tumour cells and brain tumour stem cells from mice.
The sample titles represent:
B = bulk RNA-seq
S = single-cell RNA-seq
G = brain tumor stem cells
R = brain tumor cells

first: Chunxuan

last: Shao


title: Clonal evolution of the 3D chromatin landscape of relapsed ALL [ATAC-seq]

city: New York

first: Sonali

last: Narang

state: NY

address: 435 east 30th street

country: USA

institute: NYU Langone

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Relapsed pediatric B-cell acute lymphoblastic leukemia (B-ALL) remains one of the leading causes of cancer mortality in children. Up to 20% of children will suffer relapse and face a poor prognosis. Our recent work on the evolution of the epigenetic landscape from diagnosis to relapse demonstrates both substantial diversity in the chromatin landscape as well as shared relapse-specific superenhancer activation, highlighting the importance of chromatin changes in disease progression.  However, there is a gap in our understanding of B-ALL progression through the lens of three-dimensional (3D) chromosome topology. To uncover 3D chromatin architecture-related mechanisms underlying drug resistance in B-ALL, we performed Hi-C, ATAC-seq, and RNA-seq on 12 matched primary pediatric leukemia specimens at diagnosis and relapse. Mapping of structural variations (SVs) using Hi-C data revealed previously unidentified stable, diagnosis-specific, and relapse-specific SVs providing further evidence for clonal evolution as a mechanism for drug resistance. Moreover, Hi-C analysis revealed genome wide chromatin remodeling specifically in terms of A/B compartments, TAD interactivity, and chromatin loops. Integration with ATAC-seq and RNA-seq datasets revealed strong correlation with both gene expression and chromatin accessibility. Additionally, we identified recurrent A/B compartments and TAD interactivity changes across the patient cohort for which we were able to demonstrate a crucial role in the clonal evolution of B-ALL. Shared changes in 3D genome organization drive the expression of genes/pathways previously implicated in drug resistance as well. Lastly, enrichment analysis revealed key upstream regulators of 3D genome architecture in B-ALL disease progression. These results extend the landscape of genetic alterations in relapsed B-ALL through the addition of the 3D genomic landscape and identify a breadth of novel therapeutic targets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 12 matched primary pediatric leukemia specimens at diagnosis and relapse.

first: Yohana

last: Ghebrechristos

first: Nikki

last: Evensen

first: Sylwia

last: Jasinski

first: Talia

middle: H

last: Ostrow

first: Matthew

last: Witkowski

first: Iannis

last: Aifantis

first: Aristotelis

last: Tsirigos

first: William

middle: L

last: Carroll


title: Next Generation Sequencing Analysis of Gene expression of Min6 insulinoma cell line transfected with siNC, siSRSF1 or siSRSF2

status: Public on Apr 28 2024

city: 上海

first: WENJU

last: QIAN

state: 上海

address: 徐汇区岳阳路

institute: 上海中科院

summary: Assessment of the impact of SRSF1 or SRSF2 silencing in Min6 cell lines

overall_design: siASF-1 or siSC35-1 versus siNC Min6 cell transcriptome

first: Wenju

last: Qian

first: Ying

last: Feng


title: Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues

status: Public on Apr 26 2024

city: Ann Arbor

first: Elizabeth

last: Fogarty

state: MI

address: 1105 N. University Ave

institute: University of Michigan

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

overall_design: Refer to individual Series


title: Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues: ATAC-Seq Timecourse from Drosophila Eye and Brain

summary: Previous work in the developing Drosophila wing revealed that cell cycle genes are subject to two types of chromatin regulation. The majority of cell cycle genes exhibit a simple regulatory landscape, with promoters that remain accessible even after cell cycle exit. A few critical, rate-limiting cell cycle genes show a more complex and dynamic landscape, and enhancers near these genes show evidence of decomissioning after cell cycle exit has occurred. Here we address whether the findings made in the wing are applicable to other postmitotic tissues that persist for the lifetime of the animal: the eye and the brain. We find that these tissues show similar chromatin accessibility profiles at cell cycle genes, suggesting that these modes of regulation are shared across tissues and that multiple strategies support cell cycle gene repression in the postmitotic state. These include stable repression at the promoters of most cell cycle genes, combined with enhancer decommissioning at complex, rate-limiting genes.

overall_design: Chromatin accessibility was measured via ATAC-Seq in Drosophila eyes and brains at wandering third larval instar (L3), 24 hours and 44 hours after puparium formation (APF).

first: Elli

last: Buchert

first: Yiqin

last: Ma

first: Ava

last: Nicely

first: Laura

last: Buttitta


title: Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues: RNA-Seq Timecourse from Developing Drosophila Eye

summary: Previous work in the developing Drosophila wing revealed that cell cycle genes are subject to two types of chromatin regulation. The majority of cell cycle genes exhibit a simple regulatory landscape, with promoters that remain accessible even after cell cycle exit. A few critical, rate-limiting cell cycle genes show a more complex and dynamic landscape, and enhancers near these genes show evidence of decomissioning after cell cycle exit has occurred. Here we address whether the findings made in the wing are applicable to other postmitotic tissues that persist for the lifetime of the animal: the eye and the brain. We find that these tissues show similar chromatin accessibility profiles at cell cycle genes, suggesting that these modes of regulation are shared across tissues and that multiple strategies support cell cycle gene repression in the postmitotic state. These include stable repression at the promoters of most cell cycle genes, combined with enhancer decommissioning at a few select, rate-limiting genes.

overall_design: Gene expression was measured via RNA-Seq in Drosophila eyes at wandering third larval instar (L3), 24 hours and 44 hours after puparium formation (APF).


title: Expression profiles of Eleocharis dulci during corm development

city: Wuhan

first: yan

last: huang

address: Wuhan East Lake New Technology Development Zone Jiufeng Road No.201

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

summary: A comparative time-course transcriptome analysis of corm development revealed different patterns of gene expression between cultivated and wild Eleocharis dulcis accessions with the highest number of differentially expressed genes (DEGs) at the middle swelling stage and some of the DEGs were significantly enriched for starch metabolic process.

overall_design: Our sampling strategy encompassed four distinct stages of corm development, i.e. Stage 1 (S1, initial swelling stage), Stage 2 (S2, middle swelling stage), Stage 3 (S3, late swelling stage), and Stage 4 (S4, maturity stage). The samples of each stage included three biological replicates. Raw reads were generated by the DNBSEQ-T7 platform.


title: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer (RNA-Seq)

status: Public on Apr 29 2024

city: Baltimore

first: Michael

last: Beer

state: MD

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

summary: We performed RNA-seq in a set of 13 gastric cancer cell lines to detect differential activation of regulatory programs.

first: Shamaine

middle: T

last: Ho

first: Patrick

last: Tan


title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition

status: Public on Apr 23 2024

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary:
Organoids can undergo pattern formation by spontaneously forming spatially-localised signaling centers called organisers.  Understanding how molecular pathways participate in this regulative process is a central challenge in biology. Here, we investigated self-organisation of a SHH-expressing floorplate in clonal neural tube organoids (NTOs). In NTOs, a pulse of retinoic acid (RA) applied at Day 2 triggers self-organisation of a FOXA2+ floorplate by Day 6. FOXA2 expression was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable “winning” floorplate.
We identified BMP signalling as a key governor of long-range cluster competition.

overall_design: RNA-expression for differential gene expression analysis in RA vs RA+BMP perturbations

first: Teresa

last: Krammer

first: Hannah

last: Stuart

first: Elly

last: Tanaka


summary: The neural tube (NT) has been a hallmark example of embryonic induction and patterning whereby the notochord induces an organiser, the floorplate, that secretes Sonic Hedgehog (SHH) to pattern the surrounding field of neural progenitors. On the other hand, NT organoids (NTOs) formed from embryonic stem cells (ESCs) undergo spontaneous floorplate formation and patterning in the absence of their normal embryonic inducers. Understanding how stem cells undergo regulative organiser formation is a central challenge in biology. Here, we investigated the self-organisation of a SHH-expressing floorplate organiser using clonal mouse NTOs. Expression of FOXA2, a floorplate transcription factor, was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable “winning” floorplate. We identified BMP signalling as a key governor of long-range cluster competition. FOXA2+ clusters expressed BMP4 ligand suppressing FOXA2 in receiving cells, while simultaneously expressing the BMP-inhibitor NOGGIN to secure FOXA2+ cluster survival. Genetic mutation of Noggin perturbed the floorplate not only in NTOs but also in vivo at the mid-hindbrain region of the mouse NT. These results demonstrate how the floorplate can form autonomously without its well-known inducer, the notochord, suggesting redundant mechanisms ensuring robustness. Defining molecular pathways that govern organiser self-organisation is critical in harnessing the developmental plasticity of stem cells toward directed tissue engineering.

overall_design: RNA-expression analysis of henerogenous genes according to FOXA2 expression (negative, low, medium and high) in neural tube organoids (Day 4)

first: Fernando

middle: B

last: Perez


title: Tumor-induced Natural Killer cell dysfunction is a rapid and reversible process uncoupled from the expression of immune checkpoints

status: Public on Apr 19 2024

city: Lyon

first: Kévin

last: Pouxvielh

state: France

address: 50 Avenue Tony Garnier

country: France

institute: U1111 - Centre International de Recherche en Infectiologie (CIRI)

summary: Natural Killer (NK) cells often become dysfunctional during tumor progression but the molecular mechanisms underlying this phenotype remain unclear. To explore this phenomenon, we set up new mouse lymphoma models activating or not NK cells. Both tumor types elicited IFN-I production, leading to the expression of a T cell exhaustion-like signature in NK cells, which included immune checkpoint proteins (ICPs). However, NK cell dysfunction occurred exclusively in the tumor model that triggered NK cell activation. Additionally, ICP positive NK cells demonstrated heightened reactivity compared to negative ones. Furthermore, the onset of NK cell dysfunction was swift and temporally dissociated from the induction of ICPs, which occurred as a later event during tumor growth. Finally, NK cell responsiveness was restored when stimulation was discontinued, and IL-15 had a positive impact on this reversion. Therefore, our data demonstrate that the reactivity of NK cells is dynamically controlled, and that NK cell dysfunction is a reversible process uncoupled from the expression of ICPs

overall_design: We used two models of tumor cells, one that do not stimulate NK cells (RMA) and the other one that strongly stimulate them (RMA-KR). Tumor cells were independently injected intraveneously in C57BL/6J mice and NK cells from RMA or RMA-KR bearing mice at different time of tumor growth (Early : Day+2 ; Intermediate : Day +4 or +7 respectively for RMA and RMA-KR ; Late : Day +9 or +14 respectively for RMA and RMA-KR), or from control mice, were sorted by flow cytometry and subjected to bulk RNAseq analysis. (n=4 for control ; n= 3 to 5 for each time point)

first: Marie

last: Marotel

first: Annabelle

last: Drouillard

first: Marine

last: Villard

first: Marion

last: Moreews

first: Anna

last: Bossan

first: Mathilde

last: Poiget

first: Liliane

last: Khoryati

first: Sarah

last: Benezech

first: Lucie

last: Fallone

last: Hamada

first: Noémi

last: Rousseaux

first: Louis

last: Picq

first: Yamila

last: Rocca

first: Aurore

last: Berton

last: Teixeira

first: Anna-Laure

last: Mathieu

first: Michelle

last: Ainouze

first: Uzma

last: Hasan

first: Alain

last: Fournier

first: Olivier

last: Thaunat

first: Antoine

last: Marçais

first: Thierry

last: Walzer


title: Blood Transcriptomics Implicate Epigenetics in the Acquisition of Disease Tolerance to Malaria

city: Stanford

first: Jason

last: Nideffer

state: CA

address: 240 Pasteur Drive

department: Medicine

institute: Stanford University

summary: To determine how blood transcriptomics are differentially regulated during symptomatic malaria versus asymptomatic parasitemia.

overall_design: Whole-blood samples from Ugandan children were analyzed by RNAseq. In most cases, samples are paired, and children were sampled when they were uninfected and also when they had either symptomatic malaria or asymptomatic parasitemia.

first: Maureen

last: Ty

first: Xuhuai

last: Ji

first: Prasanna

last: Jagannathan


title: Analysis of Spatial Transcriptomics for Unveiling the novel molecular characteristics of Recurrent and Non-Recurrent High-Grade Serous Ovarian Cancer

status: Public on Apr 18 2024

city: Incheon

first: Hye-Yeon

last: Ju

address: 119 Academy-ro Yeonsu-gu, Incheon Republic of Korea

country: South Korea

institute: Incheon National University

summary: Our study utilized spatial transcriptomics (ST) to interpret the tumor microenvironment to examine spatial characteristics across different sites in eight patients with HGSOC divided into recurrent (R, n = 5) and non-recurrent (NR, n = 3) groups based on a 60-month recurrence criterion. This study identified diagnostic and therapeutic targets for HGSOC, marking a step towards personalized medicine.

overall_design: We obtained ovarian cancer tissues from eight treatment-naïve patients who underwent cytoreductive surgery. Visium spatial transcriptomics analysis was performed on the eight patients with HGSOC: five in recurrent (R) and three in non-recurrent (NR) groups.

first: Seo

middle: Y

last: Youn

first: Jun

last: Kang

first: Min

last: Whang

first: Youn

middle: J

last: Choi

first: Mi-Ryung

last: Han


title: Efficacy of the oral nucleoside prodrug GS-5245 (Obeldesivir) against SARS-CoV-2 and coronaviruses with pandemic potential

status: Public on Apr 15 2024

city: Chapel Hill

first: Timothy

middle: P

last: Sheahan

state: North Carolina

address: 3113 MHRC 135 Dauer Drive, Campus Box 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: Despite the wide availability of several safe and effective vaccines that can prevent severe COVID-19 disease, the emergence of SARS-CoV-2 variants of concern (VOC) that can partially evade vaccine immunity remains a global health concern. In addition, the emergence of highly mutated and neutralization-resistant SARS-CoV-2 VOCs such as BA.1 and BA.5 that can partially or fully evade (1) many therapeutic monoclonal antibodies in clinical use underlines the need for additional effective treatment strategies. Here, we characterize the antiviral activity of GS-5245, Obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved RNA-dependent viral RNA polymerase (RdRp). Importantly, we show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-related Bat-CoV RsSHC014, Middle East Respiratory Syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant in vitro and highly effective as antiviral therapy in mouse models of SARS-CoV, SARS-CoV-2 (WA/1), MERS-CoV and Bat-CoV RsSHC014 pathogenesis. In all these models of divergent coronaviruses, we observed protection and/or significant reduction of disease metrics such as weight loss, lung viral replication, acute lung injury, and degradation in pulmonary function in GS-5245-treated mice compared to vehicle controls. Finally, we demonstrate that GS-5245 in combination with the main protease (Mpro) inhibitor nirmatrelvir had increased efficacy in vivo against SARS-CoV-2 compared to each single agent. We also evalulate the effect of antiviral therapy on host gene expression using RNAseq and show that therapeutic intervention reduces host inflammatory response as compared to vehicle controls during acute SARS-CoV-2 infection. Altogether, our data supports the continuing clinical evaluation of GS-5245 in humans infected with COVID-19, including as part of a combination antiviral therapy, especially in populations with the most urgent need for more efficacious and durable interventions.

overall_design: 10-week old female BALB/c mice were infected at 1 x 10^4 PFU with SARS-CoV-2 MA10. Mice were treated BID starting at 12 hpi with vehicle, GS-5245 (4 mg/kg), PF-332 (40 mg/kg), or in combination of GS-5245 (4 mg/kg) + PF-332 (40 mg/kg). We then performed total RNAseq to examine host gene expression profiles on 3-5 mice per group. Differentially expressed genes between each group were identified, and pathway analysis was performed.

last: Shehan

first: Nicholas

last: Catanzaro

first: Cameron

last: Nguyen


title: microRNA profile in the serum of the cervical neoplasia

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Serum was collected from 63 patients of Group A with a normal cervix, cervical intraepithelial neoplasia (CIN), squamous cell carcinoma (SCC), or adenocarcinoma (AD) and 33 patients of Group B with a normal cervix or SCC. Three miRNAs (miR-16-5p, -223-3p and -451a) were commonly down-regulated in the Group A and the Group B.

overall_design: Two independent analyses using serum from 63 (Group A) and 33 (Group B) were used to select the candidate targetsby microarray analysis .

first: Takuma

last: Fujii


title: RNA sequencing  (RNA-seq) of ANKRD6 in MKN45 gastric cancer cells by shRNA

status: Public on Apr 10 2024

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

country: Spain

institute: Biodonostia

summary: Metastasis and recurrence are the major causes of poor outcome in gastric cancer (GC). We showed that ANKRD6 expression is associated with a poorer prognosis in 10 independent GC cohorts and with metastatic states and processes. Here, by transcriptomic profiling we have characterized the effect of ANKRD6 silencing in vitro and found that cells with ANKRD6 downregulation display an impairment in key metastatic processes such as the Epithelial-mesenchymal transition.

overall_design: The experiment was performed in MKN45 cells expressing shANKRD6 and the control plasmids after lentiviral infection on four independent replicates. After QC, one pair of samples (inf III) was dropped off from the analysis.

first: Ander

last: Matheu


title: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal mechanisms of chromatin-mediated transcriptional regulation

status: Public on Apr 12 2024

city: Durham

first: David

last: MacAlpine

state: NC

address: 308 Research Dr, Durham, NC 27710

department: Department of Pharmacology and Cancer Biology

institute: Duke University

summary: Epigenetic mechanisms contribute to gene regulation by altering the accessibility of the chromatin, resulting in transcription factor (TF) and nucleosome occupancy changes throughout the genome. A major challenge is defining and dissecting this complex chromatin-mediated code to model transcriptional regulation and predict gene expression. We address this by employing a factor-agnostic, reverse-genetics approach to capture TF and nucleosome occupancies genome-wide in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae using MNase-seq, totalling nearly 1,000,000 possible mutant-gene interactions. We developed a powerful, novel approach to quantify and identify chromatin changes genome-wide. Compared with existing gene expression data, well-established pathways were recapitulated solely by observing differences in TF and nucleosome occupancy, and we found distinct chromatin signatures associated with the upregulation/downregulation of genes. Finally, we demonstrated that these chromatin features are predictive of transcriptional activity, and leveraged these features to reconstruct transcriptional regulatory networks, resolving direct vs. indirect interactions and predicting the transcriptional activity of putative targets based on their chromatin dynamics. Overall, this demonstrates the powerful approach of combining a genetic perturbation with high-resolution epigenomic profiling that enables a closer examination of the interplay between TFs and nucleosomes genome-wide, providing a deeper, mechanistic understanding into the complex relationship between chromatin organization and transcription.

overall_design:
201 yeast knockout strains each with an individual gene deletion are profiled using MNase-seq.
RNA-seq data for GAL80 knockout yeast strains and wild-type yeast with galactose/dextrose induction

first: Kevin

last: Moyung

first: Yulong

last: Li

first: Alexander

last: Hartemink


title: miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue

status: Public on Apr 17 2024

city: Indianapolis

first: Michael

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

type: Non-coding RNA profiling by high throughput sequencing


title: Candida albicans PPG1, a serine/threonine phosphatase, plays a vital role in central carbon metabolisms under filament-inducing conditions: A multi-omics approach

city: Abu Dhabi

first: Andre

middle: Sanches

last: Barreiros

state: Abu Dhabi

address: Hamdan street

country: United Arab Emirates

institute: Khalifa University

summary: Candida albicansis the leading cause of life-threatening bloodstream candidiasis, especially among immunocompromised patients. The reversible morphological transition from yeast to hyphal filaments in response to host environmental cues facilitatesC.albicanstissue invasion, immune evasion, and dissemination. Hence, it is widely considered that filamentation represents one of the major virulence properties inC.albicans. We have previously characterized Ppg1, a PP2A-type protein phosphatase that controls filament extension and virulence inC.albicans. This study conducted RNA sequencing analysis of samples obtained fromC.albicanswild type andppg1Δ/Δ strains grown under filament-inducing conditions. Overall,ppg1Δ/Δ strain showed 1448 upregulated and 710 downregulated genes, representing approximately one-third of the entire annotatedC.albicansgenome. Transcriptomic analysis identified significant downregulation of well-characterized genes linked to filamentation and virulence, such asALS3,HWP1,ECE1,and RBT1.Expression analysis showed that essentialgenes involved inC.albicanscentral carbon metabolisms, includingGDH3,GPD1,GPD2,RHR2,INO1,AAH1, andMET14were among the top upregulated genes. Subsequent metabolomics analysis ofC.albicans ppg1Δ/Δ strain revealed a negative enrichment of metabolites with carboxylic acid substituents and a positive enrichment of metabolites with pyranose substituents. Altogether, Ppg1in vitroanalysis revealed a link between metabolites substituents and filament formation controlled by a phosphatase to regulate morphogenesis and virulence.

overall_design: Yeast extract-peptone-dextrose (YEPD) medium at 30°C was used as the standard non-filament-inducing growth condition for all strains. Liquid serum and temperature induction experiments were performed by growing strains overnight in YEPD medium at 30°C to an optical density at 600 nm (OD600) of ∼4.0 and diluting 1:10 into 50 ml of pre-warmed YEPD medium plus 10% serum at 37°C. Aliquots of cells harvested at specific post-induction time points 3 and 5 hours for RNA isolation. We selected 3 and 5 hours-time points as these times points show the most prominent phenotypic (filamentation) difference betweenC.albicanswild-type andppg1Δ/Δ strains. RNA extraction was performed using RNeasy Micro Kit (Qiagen GmbH, Germany), following the manufacturer’s instructions. Three biological replicates were obtained for each condition (W.T. and mutant). RNA sequencing was performed at BGI Group, Shenzhen, China. RNA was extracted from 8 samples belonging to two different strains, DK318 and MAY34. RNA obtained from 8 samples (Table 1) was sequenced using the BGISEQ-500 platform (Shenzhen, China), generating on average about 23.93 million reads per sample. The average mapping ratio with reference genomes was 96.92%, and the average gene mapping ratio was 82.77%; a total of 6,113 genes were detected. Sequence reads containing low-quality, adaptor-polluted and/or unknown high base (N) content were excluded from any further analysis. Retained sequence reads were further filtered using internal software SOAPnuke to produce a set of "clean reads" that was stored in FASTQ format as per each sample. Composition filtering statistics of raw data and quality metrics of clean reads. Clean filtered sequence reads were mapped to the reference genome using HISAT (hierarchical indexing for spliced alignment of transcripts) to perform the genome mapping step. Reads were mapped to the C. albicans strain SC5314 reference genome (assembly 21) (http://www.candidagenome.org).

first: Mohammad

last: Tahseen A L. Bataineh

first: Nelson

last: Cruz Soares

last: Harb Semreen

first: Stefano

last: Cacciatore

first: Nihar

last: Ranjan Dash

first: Mohamad

last: Hamad

first: Muath

last: Khairi Mousa

first: Jasmin

last: Shafarin Abdul Salam

first: Mutaz

middle: F

last: Al Gharaibeh

first: Luiz

last: Zerbini

first: Mawieh


title: Aberrant neurodevelopment in human iPS cell-derived models of Alexander disease.

status: Public on Apr 07 2024

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences


title: Aberrant neurodevelopment in human iPS cell-derived astrocyte-neuron co-culture model of Alexander disease

summary: Co-cultures of neurons and astrocytes derived from human iPS cells carrying a GFAP (R239C) mutation - an identified cause of Alexander disease (AxD) - were analyzed with single-cell RNA sequencing to assess cell population composition, differential gene expression, and cell-cell interaction differences in AxD co-cultures compared to controls. Oxygen-glucose deprivation (OGD) challenge was applied to identify differences in stress response. Our results suggested differentiation impairment especially in AxD astrocytes, represented by an enriched population of less differentiated cells and downregulation of mature astrocyte genes in AxD astrocytes-containing co-cultures. Furthermore, AxD co-cultures showed increased stress response represented by upregulation of metallothioneins and increased susceptibility to the OGD challenge.

overall_design: Neurons and astrocytes were derived from human iPS cells and cultivated in a 2D co-culture system. GFAP (R239C) cell line originated in Alexander disease patient fibroblasts and isogenic control cell line was prepared by mutation correction, as described previously (Battaglia et al. 2019). Co-cultures were challenged by OGD for four hours, followed by a 16 h recovery period, to assess the effect of mild stress on AxD and control co-cultures. Six samples in total (corrected neurons + corrected astrocytes, corrected neurons + AxD astrocytes, AxD neurons + AxD astrocytes, control and OGD set of samples) were analyzed with scRNA-seq, focusing on identification of cell populations, differences in their representation across samples, differential gene expression, and cell-cell interaction patterns.

first: Werner

last: Dykstra

first: Yolanda

last: de Pablo

first: Oskar

last: Zetterdahl

first: Isaac

last: Canals

first: Charlotte

last: van Gelder

first: Harmjan

middle: R

last: Vos

first: Dolores

last: Perez-Sala

first: Mikael

last: Kubista

first: Pavel

last: Abaffy

first: Henrik

last: Ahlenius

first: Lukas

last: Valihrach

first: Elly

last: Hol

first: Milos

last: Pekny


title: Aberrant neurodevelopment in human iPS cell-derived neural organoid model of Alexander disease

summary: 3D-cultured unguided neural and cortical organoids derived from human iPS cells carrying a GFAP (R239C) mutation - an identified cause of Alexander disease (AxD) - and their isogenic controls were analyzed with scRNA-seq to investigate the effect of the GFAP mutation on brain development, cell type composition, and gene expression. Results of this analysis showed impaired astro- and neurogenesis in both types of organoids (unguided and cortical), including a lack of cells acquiring the astrocyte fate, and an increased abundance of cells differentiating into lineages other than neuroectodermal. The results also suggested dysregulation of extracellular matrix, membrane, and cytoskeleton components, which might have also affected their differentiation trajectories.

overall_design: The AxD cell line with a GFAP (R239C) mutation originated in Alexander disease patient fibroblasts, and an isogenic control cell line was prepared by mutation correction with CRISPR/Cas9, as described previously (Battaglia et al. 2019). 3D organoids were prepared using either unguided neural protocol (resulting in more diverse cell composition) and more targeted cortical protocol (DUAL SMAD inhibition directing cells towards cortical lineage). Organoids were harvested after 165 days in culture, with a variety of cell types including astrocytes present at this stage. Fixed single-cell suspensions from four samples (unguided control and AxD, cortical control and AxD) were prepared with 10X Genomics pipeline and scRNA-seq was performed to investigate changes in cell type composition, gene expression, and cell-cell interaction between the AxD cell line and controls.


title: Spatial transcriptomic analysis of Nf1+/- mouse brain

status: Public on Apr 05 2024

city: Houston

first: Yuan

last: Pan

state: TX

address: 6565 MD Anderson Blvd. Suite Z8.5000

institute: UT MD Anderson Cancer Center

summary: Regional differential gene expression analyses of brains from four 24w-old Nf1+/- mice

overall_design: 10 µm sections from fresh frozen, OCT embedded mouse brain tissue samples were collected on Visium Gene Expression Slides (10x Genomics, Pleasanton, CA). Sections were H&E stained and imaged (Keyence BZX 800). Sections were permeabilized for 10 minutes, followed by reverse transcription, cDNA synthesis, cDNA amplification and NGS library preparation as per manufacturer's protocol (10x Genomics, Pleasanton, CA). For sequencing, indexed libraries were pooled and sequenced over NovaSeq 6000 (Illumina inc. San Diego, CA) to obtain a minimum of 50,000 reads/spot (250 M reads/section). Raw sequencing reads were parsed through the Spaceranger analysis pipeline (10x Genomics, Pleasanton, CA) to generate the final readout.

first: Jared

last: Hysinger

first: Dhananjay

last: Wagh

first: John

last: Coller


title: Gene expression profile at single cell level of primary keloid fibroblasts treated with various radiotherapy modalities

city: Chengdu

first: Xiaoqian

last: Li

address: No.17 People's South Road

institute: Sichuan University

summary: Keloids are benign dermal tumors that arise from abnormal wound healing processes following skin lesions. Postoperative radiotherapy (PORT) is a clinically effective measure to reduce recurrence rates of keloid. We used single cell RNA sequencing (scRNA-seg) to analyze the different of  primary keloid fibroblasts treated with various radiation modalities.

overall_design: Primary keloid fibroblasts isolated from patients and analyzed using scRNA-seq.


title: Mitochondrial Stress-induced H4K12 Hyperacetylation Dysregulates Transcription in Parkinson's Disease

status: Public on Apr 03 2024

city: Ames

first: Minhong

middle: Neenah

last: Huang

state: Iowa

address: 1800 Christensen Dr

department: Deparment of Biomedical Sciences

institute: Iowa State University

summary:
Bulk RNA-Seq of littermate controls and Parkinson's disease (PD) transgenic mice models (n=3)

The goals of this study are to compare transcriptome profiling (RNA-Seq) in the specific brain region of littermate control and our PD transgenic mice model and look for differential expression genes of interest

overall_design: mRNA profiles of 16~17-week littermate controls and our PD transgenic mice


title: Digital Spatial Profiling identifies distinct molecular signatures of vascular lesions in Pulmonary Arterial Hypertension

status: Public on Apr 04 2024

city: Aurora

first: Rubin

last: Tuder

state: CO

address: 12700 East 19th Avenue

institute: University of Colorado

summary: Idiopathic Pulmonary Arterial Hypertension (IPAH) is a severe human disease, characterized by extensive pulmonary vascular remodeling due to plexiform and obliterative lesions, media hypertrophy, and alterations of adventitia. The objective of the study was to test the hypothesis that microscopic IPAH vascular lesions express unique molecular profiles, which collectively are different from control pulmonary arteries. We used digital spatial transcriptomics to profile the genome-wide differential transcriptomic signature of key pathological lesions (plexiform, obliterative, intima+media hypertrophy, and adventitia) in IPAH lungs (n= 11)  and compared these data to the intima+media and adventitia of control pulmonary artery (n=5). The IPAH lesions and pulmonary artery compartments were defined by the analyses of hematoxylin-eosin stained serial section, aided by labeling with CD31 (for endothelial cells), smooth muscle cell actin (SMA), and CD45 for inflammatory mononuclear cells, also in serial sections. Approximately 12 regions of interest (ROI) were sampled from a histological section of a paraffin-embedded block of each lung, which was selected based on the finding of enrichment for IPAH lesions or control pulmonary arteries.

overall_design:
A total of 211 ROIs were studied with 149 ROIs representing IPAH lesions with 39 plexiform lesions, 37 obliterative lesions, 36 intima+media hypertrophy, and 37 IPAH adventitia; of 62 ROIs of control lungs, including 34 intima+media and 28 control adventitia. The ROIs were selected largely based on the histopathological identification of each type of lesion (in IPAH lungs) or control pulmonary artery compartments. The selected ROIs were then processed by the GeoMx Nanostring platform, followed by whole genome sequencing.

*** FASTQ raw data files have been requested. ***

first: Sarah

last: Williams


title: Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration.

status: Public on Apr 01 2024

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Injury is a common occurrence in the life of most if not all organisms. Because injury and the extent of damage inflicted are not predictable events, pre-existing tissues must somehow determine how much tissue needs to be restored. It has been known for over a century that amputation position along a proximal-distal (P/D) axis determines the regeneration speed of amputated limbs in regeneration-competent animals1. Yet, it is not clear how an injured limb conveys positional information during regeneration to faithfully restore pre-existing morphologies and functions. Here, we profiled millimetric caudal fins regenerating proximal and distal amputations in the African killifish (Nothobranchius furzeri). We report position-specific, differential modulation of the spatial distribution, duration, and magnitude of proliferation, and the possibility to predict blastema sizes. Regenerating fins profiled by single cell RNA sequencing identified a Transient Regeneration-Activated Cell State (TRACS) enriched in extracellular matrix (ECM) components and modifiers that is proportionally amplified to match a given amputation position. We located this transient cell state to the basal epidermis by gene expression and confocal microscopy, and propose a role for these cells in transducing positional information to the regeneration blastema. Understanding the temporal deployment of regenerative cell states may hold the key to set up a successful regeneration event in organisms with limited regenerative abilities such as humans.

overall_design: Regenerating or homeostasis cells from caudal fins or dorsal fins were isolated by FACS according to live/nucleated signal and analyzed using scRNA-seq

first: Augusto

last: Ortega Granillo

first: Daniel

last: Zamora

first: Robert

last: Schnittker

first: Allison

last: Scott

first: Jonathon

last: Russell

first: Carolyn

middle: E

last: Brewster

first: Eric

last: Ross

last: Acheampong

first: Kevin

last: Ferro

first: Jason

last: Morrison

first: Boris

last: Rubinstein

first: Anoja

middle: G

last: Perera

first: Wei

last: Wang

last: Sánchez Alvarado


title: Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression [ENDPOINT]

status: Public on Mar 27 2024

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

summary: Human-specific changes in specific Siglecs is one of the reasons put forth as molecular mechanisms that could explain human proneness to developing cancers. The SIGLEC12 gene, which encodes the Siglec-XII protein mainly found on epithelial cells, has a fixed homozygous missense mutation in a critical arginine renders unable to recognize its natural ligand. Additionally, the gene harbors a polymorphic frameshift mutation that eliminates expression of the full-length protein in most humans. We hypothesized that dysfunctional Siglec-XII is involved in cancer progression in humans' epithelia. Here we report that the transgenic conditional expression of human Siglec-XII in mouse intestinal epithelia increased the number and size of cancers in a model of colitis-associated colorectal carcinoma (AOM/DSS). RNA sequencing of the colons at baseline and after AOM/DSS challenge derived a gene signature comprised of the differentially expressed genes (DEGs) between controls (Villin1-Cre-ER(T2)) and Siglec-XII-expressing mice, showing that upregulated DEGs in Siglec-XII mice were enriched for diverse bioenergetic processes.

overall_design: To investigate the impact of the expression of human SIGLEC12 in the development of mouse colon tumors, we developed a knock-in mouse model that allows the conditional expression of human SIGLEC12 only in the villi and crypts of the small and large intestine (SIGLEC12-Villin1-Cre-ERT). SIGLEC12 knock-in (SIGLEC12-Villin1-Cre-ERT) and control (Villin-Cre-RT) mice received 5 days treatment (10 mg/ml) with tamoxifen, to induce SIGLEC12 expression, followed by an intraperitoneal injection (10 mg/kg body weight) of azoxymethane (AOM) followed by 5 days of dextran sodium sulfate salt (DSS) treatment (2.0%) and 14 days of recovery. This cycle was repeated three times. After the fourth DSS cycle (87 days), mice were sacrificed, and colon tumors were harvested. We then performed gene expression profiling analysis using data obtained from RNA-seq of three mice for each condition.

first: Ajit

last: Varki


title: Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression [baseline]

summary: Human-specific changes in specific Siglecs is one of the reasons put forth as molecular mechanisms that could explain human proneness to developing cancers. The SIGLEC12 gene, which encodes the Siglec-XII protein mainly found on epithelial cells, has a fixed homozygous missense mutation in a critical arginine renders unable to recognize its natural ligand. Additionally, the gene harbors a polymorphic frameshift mutation that eliminates expression of the full-length protein in most humans. We hypothesized that dysfunctional Siglec-XII is involved in cancer progression in humans' epithelia. Here we report that the transgenic conditional expression of human Siglec-XII in mouse intestinal epithelia did not by itself cause carcinomas and RNA sequencing of the colons at baseline derived a gene signature without differentially expressed genes (DEGs) between controls (Villin1-Cre-ER(T2)) and Siglec-XII-expressing mice

overall_design: To investigate the impact of the expression of human SIGLEC12 in mouse epithelia, we developed a knock-in mouse model that allows its conditional expression only in the villi and crypts of the small and large intestine (SIGLEC12-Villin1-Cre-ERT). SIGLEC12 knock in mice (SIGLEC12-Villin1-Cre-ERT) and controls (Villin1-Cre-ERT) received 5 days treatment (10 mg/ml) with tamoxifen, to induce SIGLEC12 expression. After 7 days of the last tamoxifen administration mice were sacrificed, colons were harvested. We then performed gene expression profiling analysis using data obtained from RNA-seq of three mice for each condition.


title: Uterine injury during diestrus leads to embryo spacing defects and perturbations in the Cox-2 pathway in subsequent pregnancies

city: Palo Alto

first: Elisa

middle: Tiannuo

last: Zhang

address: 300 Pasteur Drive, Alway M311

institute: Stanford University School of Medicine

summary: Uterine injury from procedures such as Cesarean sections (C-sections) often have severe consequences on subsequent pregnancy outcomes, leading to disorders such as placenta previa, placenta accreta, and infertility. With rates of C-section at approximately 30% of deliveries in the US that are projected to continue to climb, an understanding of the mechanisms by which these pregnancy disorders arise and opportunities for intervention are sorely needed. However, there are currently no animal models to date that comprehensively assess the consequences of uterine injury. Here we describe the first rodent model of uterine injury on subsequent in utero outcomes. We observed four distinct phenotypes: reduced implantation events, increased rates of resorption, embryo misspacing, and placenta accreta-like features of reduced decidua and expansion of invasive trophoblasts. We also show that the appearance of embryo misspacing depends entirely on the phase of estrous cycle at the time of injury, leading us to identify differences in uterine wound healing as a function of estrous. Using RNA-seq, we identified perturbations in the expression of components of the COX-2 pathway after recovery from injury, a pathway that has previously been demonstrated to play an important role in embryo spacing. Therefore, we demonstrate that uterine damage in our novel mouse model engenders many uterine changes, most notably perturbed expression of COX-2 pathway-related genes, that ultimately lead to numerous placental and embryonic developmental defects with parallels to human pregnancy disorders.

overall_design: mRNA profiles of mouse uterine mRNA collected from untreated animals or after >1 mo. of recovery post-diestrus or estrus injury

first: Kristen

last: Wells

first: Julie

middle: C

last: Baker

first: Lars

last: Steinmetz


title: Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Macrophages adopt mural cell function and marker expression for vascular support following ischemia

status: Public on Apr 08 2024

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: We used scRNAseq to study if perivascular macrophages adopt a mural cell identity during tissue restoration in mouse models of ischemia

overall_design: A total of 755 tdTomato+PDGFRβ+/- cells and 372 tdTomato-PDGFRβ+ cells from ischemic muscles at day 21 post-ischemia onset, and a total 190 tdTomato+PDGFRβ+/- cells and 192 tdTomato-PDGFRβ+ cells from healthy muscle were FACS sorted into Smart-seq2 plates in two batches, and processed using the Smart-seq2 protocol (Picelli et al., 2013). The single-cell transcriptomic sequencing was performed at Eukaryotic Single Cell Genomics Facility at SciLifeLab, Stockholm.

first: Kristel

last: Parv

first: Catarina

last: Leite


title: Spatial transcriptomics of the Rhesus Macaque Hippocampus during homeostasis and chronic SIV CL757 infection

status: Public on Mar 26 2024

city: Woodland

first: Sonny

middle: Ramirez

last: Elizaldi

address: County Road 98 and, Hutchison Dr

department: Immunology

institute: University of California Davis

summary: We performed spatial transcriptomics using Nanostring's DSP platform on Rhesus Macaque Hippocampal Brain sections obtained from one uninfected control and one chronically infected with SIVCL757. Our goals were to (1) determine which differentially expressed genes (DGEs) could be attributed to SIV infection in the rhesus hippocampus, (2) determine if spatial transcriptomics could serve as a tool to identify leukocyte infiltrates in the SIV infected brain and (3) examine localization of leukocytes at homeostatasis and chronic SIV infection

overall_design: NanoString Digital Spatial Profiling (DSP) with Whole Transcriptome Atlas (WTA)/Human NGS profiling was performed on 1 SIVCL757 chronically infected hippocampal brain section compared to 1 healthy control.

first: Smita

last: Iyer

first: Liuliu

last: Pan


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-Seq3]

status: Public on Mar 25 2024

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.

overall_design: Tumor areas of 200-500 tumor cells invading perineurial structures (outside or inside of infiltrating nerves) were collected from FFPE pancreatic ductal adenocarcinoma (PDAC) tissues in a cohort of 14 patients. Single or multiples areas were processed per patient for a total of 42 samples.


title: Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression [CACO]

summary: Human-specific changes in specific Siglecs is one of the reasons put forth as molecular mechanisms that could explain human proneness to developing cancers. The SIGLEC12 gene, which encodes the Siglec-XII protein mainly found on epithelial cells, has a fixed homozygous missense mutation in a critical arginine renders unable to recognize its natural ligand. Additionally, the gene harbors a polymorphic frameshift mutation that eliminates expression of the full-length protein in most humans. We hypothesized that dysfunctional Siglec-XII is involved in cancer progression in humans' epithelia. Here we report that the forced expression of human Siglec-XII in caco-2 cells showed that differentially expressed genes in Siglec-XII cells were enriched for diverse bioenergetic processes.

overall_design: To explore the significance of human Siglec-XII in the progression of CRCs, we used Siglec-XII non-expressing Caco-2 cell line. Cells were transfected with either pCDNA-3.1-SIGLEC12 or with empty vector (control), forcing them to exogenously express full-length Siglec-XII and stable clones were selected. We then performed gene expression profiling analysis using data obtained from RNA-seq of three cultures for each condition.


title: Chromatin and gene expression profile at single nuclei level of CD45+ leukocytes from the rhesus brain parenchyma

summary: We used Chromium Single Cell Multiome ATAC + Gene Expression to analyze CD45+ leukocytes in the rhesus macaque brain during homeostasis and chronic SIV infection

overall_design: Leukocytes (CD45+ cells) of previously cryopreserved rhesus macaque brain single cell suspensions were isolated using MACS CD45 microbeads/column purification followed by Fluorescence-activated cell sorting (FACS) according to the presence of absence of CD45 signal. Nuclei were extracted according to 10x protocols and analyzed using single snATACseq

first: Jie

last: Li


title: Dynamic change of ac4C in mouse hippocampus during learning and memory

status: Public on Mar 24 2024

city: Shanghai

first: Domgmin

last: Yin

state: Shanghai

address: No.3663, Zhongshan North Road

institute: Shanghai Key Laboratory of Brain Functional Genomics

summary: N4-acetylcytidine (ac4C), the only known form of RNA acetylation, has recently been identified as an epitranscriptomic mechanism regulating mRNA stability and translation efficiency. However, the function and regulation of ac4C in the brain remain largely unknown. Here we performed transcriptome-wide mapping of ac4C in the hippocampus of adult mice that were trained in the Morris water maze, a protocol for learning and memory. We identified ~2100 ac4C-modified mRNAs that were upregulated after memories were formed but returned to normal levels after memories were forgotten.

overall_design: N4-acetylcytidine (ac4C) for acetylation modifiction of mRNA in hippocampus tissues (homogenates and synapse)

first: Hai-qian

last: Zhou

first: Jia-wei

first: Zhen

last: Zhu

first: Dong-sheng

last: Chen

first: Dong-min


title: Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer


title: Cardiac Transcriptomic Changes Induced by Early CKD in Mice Reveal Novel Pathways Involved in the Pathogenesis of Cardiorenal Syndrome Type 4

status: Public on Mar 22 2024

city: Guadalajara

first: Raquel

last: Echavarria

state: Jalisco

address: Sierra Mojada 800

department: Surgical research

country: Mexico

institute: CONACYT- Centro de Investigacion Biomedica de Occidente, IMSS

summary: Cardiorenal syndrome (CRS) type 4 is prevalent among the chronic kidney disease (CKD) population, with many patients dying from cardiovascular complications. However, limited data regarding cardiac transcriptional changes induced early by CKD is available. We used a murine unilateral ureteral obstruction (UUO) model to evaluate cardiac transcriptional regulation at 21 days post-surgery through RNA-seq and bioinformatics. UUO leads to significant kidney injury, low uremia, and pathological cardiac remodeling. RNA-seq analysis identified 76 differentially expressed genes (DEGs) in UUO hearts. Upregulated DEGs were significantly enriched in cell cycle and cell division pathways, immune responses, cardiac repair, inflammation, proliferation, oxidative stress, and apoptosis. Gene Set Enrichment Analysis further revealed mitochondrial oxidative bioenergetic pathways, autophagy, and peroxisomal pathways are downregulated in UUO hearts. Vimentin was also identified as an UUO-upregulated transcript. Our results emphasize the relevance of extensive transcriptional and epigenetic changes, mitochondrial dysfunction, homeostasis deregulation, fatty-acid metabolism alterations, and vimentin upregulation in CRS type 4 development.

overall_design: To investigate cardiac transcriptomic changes induced early by chronic kidney disease (CKD) in whole hearts from C57BL/6 male mice, we performed gene expression profiling analysis using data obtained from RNA-seq of mice subjected to unilateral urinary obstruction (UUO) for 21 days (n=3) vs. sham surgery (n=3).

first: Francisco

last: Munguia-Galaviz


title: C3G signal in native and allograft

status: Public on Mar 18 2024

city: New York

first: Ibrahim

last: Batal

state: NY

address: 630 W 168th street

department: Pathology & cell Biology

institute: Columbia University

summary:
C3 glomerulopathy (C3G), which encompasses C3 glomerulonephritis (C3GN) and dense deposit disease (DDD), results from dysregulation of the alternative complement pathway. Data on disease recurrence after kidney transplantation is limited, and details on histologic features of recurrent C3G are scarce. We aimed to evaluate C3G recurrence in the allograft, with a focus on histologic presentation and progression.  We retrospectively analyzed 18 patients with native kidney failure attributed to C3G (12 C3GN and 6 DDD) who received a kidney transplant from January 2016 to January 2023. Demographic, genetic, clinical, and histologic data were studied. The Nanostring 770 genes immune profiling panel was used for transcriptomic analysis. Disease recurrence was the primary outcome.   During a median follow-up period of 37 (18, 56) months, C3G recurrence occurred in 16 (89%) of patients (11 with C3GN and 5 with DDD), at a median of 33 (13, 141) days post-transplantation. Over a third (38%) of recurrent cases were detected in protocol biopsies, and only 31% of patients presented with >300 mg/g of proteinuria. Recurrence in index biopsies was mainly established through a combination of immunofluorescence and electron microscopy findings, while it showed only subtle histologic alterations and no characteristic transcriptomic signals. Over time, histologic chronicity indices increased, but all allografts were functioning at the end of follow-up. Patients with recurrence of C3GN and DDD showed overlapping immunofluorescence and electron microscopy findings and had similar recurrence rate and time to recurrence. The majority of patients with native kidney failure attributed to C3G developed disease recurrence very early after kidney transplantation, usually with minimal proteinuria, mild histologic alterations, and favorable short-term allograft survival. Immunofluorescence and electron microscopy played crucial role in detecting early, sub-clinical recurrence of C3GN and DDD, which showed significant overlapping features.
To identify transcriptomic signals that may distinguish recurrent C3G, we utilized the 770 genes PanCancer Immune Profiling Panel in a discovery cohort of native kidney biopsies followed by a testing cohort of allograft biopsies. For the discovery cohort, we residual tissue from formalin-fixed paraffin-embedded samples (FFPE) was used from 18 native kidney biopsies with C3G (11 C3GN and 7 DDD) and 36 native biopsies with other glomerular diseases (GD controls: 15 IgA nephropathy, 14 membranous nephropathy, 7 diffuse podocytopathy). For the testing cohort, we ass essedresidual FFPE tissue was used from 13 index allograft biopsies with recurrent C3G (combining 10 from our study with enough residual tissue and 3 additional cases that were added to increase sample size) and 41 allograft glomerular disease (GD) controls. Since recurrent GD is overall more commonly encountered than de novo GD although the frequency of latter might be underestimated20, the GD controls were selected to roughly reflect this notion [15 de novo GD (5 membranous nephropathy, 6 immune complex-mediated glomerulonephritis not otherwise specified, 3 IgA nephropathy, 1 HCV-associated glomerulonephritis) and 26 recurrent GD (10 membranous nephropathy, 8 IgA nephropathy, 7 diffuse podocytopathy, 1 HCV-associated glomerulonephritis)].

overall_design: Discovery cohort of native kidney biopsies followed by a testing cohort of allograft biopsies. For the discovery cohort, we residual tissue from formalin-fixed paraffin-embedded samples (FFPE) was used from 18 native kidney biopsies with C3G (11 C3GN and 7 DDD) and 36 native biopsies with other glomerular diseases (GD controll. For the testing cohort, we assessed residual FFPE tissue was used from 13 index allograft biopsies with recurrent C3G (combining 10 from our study with enough residual tissue and 3 additional cases that were added to increase sample size) and 41 allograft glomerular disease (GD) controls.


title: Antibiotics damage the colonic mucus barrier in a microbiota-independent manner I

status: Public on Mar 19 2024

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: Antibiotic use is a risk factor for development of inflammatory bowel diseases (IBDs). IBDs are characterized by a damaged mucus layer, which does not properly separate the host intestinal epithelium from the microbiota. Here, we hypothesized that antibiotics might affect the integrity of the mucus barrier. By systematically determining the effects of different antibiotics on mucus layer penetrability we found that oral antibiotic treatment led to breakdown of the mucus barrier and penetration of bacteria into the mucus layer. Using fecal microbiota transplant, RNA sequencing followed by machine learning and ex vivo mucus secretion measurements, we determined that antibiotic treatment induces ER stress and inhibits colonic mucus secretion in a microbiota-independent manner. This mucus secretion flaw led to penetration of bacteria into the colonic mucus layer, translocation of microbial antigens into circulation and exacerbation of ulcerations in a mouse model of IBD. Thus, antibiotic use might predispose to development of intestinal inflammation by impeding mucus production.

overall_design: We treated mice reared in the SPF facility with PBS or 2.5mg of vancomycin orally twice a day for three day, and transferred their gut microbiota to germ-free mice via fecal microbiota transfer (FMT). RNA was extracted and sequenced from both FMT donor and recipient mice.

first: Amir

last: Erez


title: PLPP1-deficiency-mediated ferroptosis induced by PD-1 signaling impairs antitumor activity of intratumoral CD8+ T cells I

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

summary: Metabolic programming plays a crucial role in T-cell activation. Herein, we describe how phospholipid metabolism regulates CD8+ T-cell function in patients with cancer. We found that phosphatidylcholine (PC) and phosphatidyl ethanolamine (PE) levels were lower in intratumoral CD8+ T cells than in circulating CD8+ T cells. The expression of phospholipid phosphatase 1 (PLPP1), an enzyme that catalyzes PE and PC synthesis, was also downregulated in CD8+ T cells upon infiltrating tumors. Moreover, unsaturated fatty acid-mediated ferroptosis was a major factor impairing the antitumor function of PLPP1-deficient CD8+ T cells infiltrated in tumors, accompanied by enhanced reactive oxygen species production and lipid peroxidation. The activation of programmed cell death 1 (PD-1) signaling in CD8+ T cells suppressed the PLPP1 expression by increasing GATA1 binding to the promoter region of PLPP1. PLPP1 expression was upregulated after anti-PD-1 therapy. Our findings revealed therapeutic potential of enhancing PLPP1 levels to restore CD8+ T-cell function.

overall_design: PLPP1fl/fl and Lckcre-PLPP1fl/fl CD8+ T cells were isolated from spleen and treated with arachidonic acid (AA) or octadecenoic acid (OA). RNA-seq and data analyses were conducted by SeqHealth Technology Co., Ltd. (Wuhan, China).

first: Yu

last: Ping


title: Rosiglitazone and Trametinib to treat basal bladder tumors

status: Public on Mar 15 2024

first: Cathy

last: Mendelsohn

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University Medical Center


title: Gut microbiota dysbiosis-mediated ceramides elevation contributes to corticosterone-induced depression by impairing mitochondrial function

first: Guanhao

last: Wang

address: Siping Road

institute: Tongji University

summary: Background: As a worldwide threat to mental health, depression affects about 322 million people globally. Recently, the role of gut microbiota dysbiosis on the pathogenesis of depression has received widespread attention, but the underlying mechanism remains elusive.Results: Corticosterone (CORT)-treated mice showed depressive-like behaviors, a reduction in hippocampal neurogenesis, and an altered composition of gut microbiota (GM). Fecal microbial transplantation (FMT) from CORT-treated mice transferred depressive-like phenotypes and their dominant GM, especially bifidobacterium and lactobacillus, to the recipients. Fecal metabolic profiling showed that the relative abundances of fecal ceramides were significantly increased in CORT-treated and the recipient mice. Metagenomic sequencing exposed that bifidobacterium and lactobacillus might be responsible for gut ceramides production in CORT-treated mice. We then found that treatment with ceramides via oral gavage was sufficient to recapitulate the depressive-like phenotypes in wild -type mice. Finally, RNA-sequencing data exposed that most of the differentially expressed genes (DEGs) between ceramides-treated mice and the control group were enriched in oxidative phosphorylation (OXPHOS) pathway. Conclusion: We conclude that chronic exposure to CORT leads to an altered GM composition and consequent ceramides production, thus leading to subtle mitochondrial OXPHOS dysfunction in hippocampus, which may contribute to the development of depressive disorders.

overall_design: Comparative gene expression profiling of RNA-seq data from hippocampus from CerM and Veh mice

first: Jianfeng

last: Lu


title: wt and sua7-1 nascent mRNA profiling in relation to termination of transcription

status: Public on Mar 02 2024

city: Bloomington

first: Jared

middle: Michael

last: Schrader

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: wt and sua7-1 nascent mRNA profiling was performed using the GRO-seq approach. Br-UTP labelling of nascent RNA followed by immunoprecipitation and cDNA library preparation with sequencing (peformed exactly as described in O'Brien et al., 2023). Three biological replicates were performed.

overall_design: wt and sua7-1 cells were cultured, nascent RNA was labelled, immunoprecipitated, cDNA library asssembled, and sequenced.

first: Michael

last: O'Brien

middle: M

first: Athar

last: Ansari


title: Rosiglitazone and Trametinib to treat basal bladder tumors [RNA-Seq]

summary: To investigate the anti-tumor effect of Rosiglitazone+Trametinib in basal bladder cancer, we tested the drug combination in BBN-induced basal tumor mouse model in vivo and BBN-derived tumor cell line BBN963 in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Rosiglitazone and Trametinib and vehicle treated basal tumor cells in vivo and in vitro. Comparative gene expression profiling analysis of RNA-seq data for all-trans retinoic acid and vehicle treated basal tumor BBN963 cells in vitro.

first: Tina

last: Xiang

first: Tiffany

last: Tate

first: Sakina

last: Plumber

last: Lee Mendelsohn


title: Modeling of Clinical Phenotypes in Systemic Lupus Erythematosus Based on the Platelet Transcriptome and FCGR2a Genotype

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

department: School of Medicine

institute: New York University

summary:
Background: The clinical heterogeneity of SLE with its complex pathogenesis remains challenging as we strive to provide optimal management. The contribution of platelets to endovascular homeostasis, inflammation and immune regulation highlights their potential importance in SLE. Prior work from our group showed that the Fcγ receptor type IIa (FcγRIIa)–R/H131 biallelic polymorphism is associated with increased platelet activity and cardiovascular risk in SLE.  The study was initiated to investigate the platelet transcriptome in patients with SLE and evaluate its association across FcγRIIa genotypes and distinct clinical features.
Methods:  Fifty-one patients fulfilling established criteria for SLE (mean age = 41.1±12.3, 100% female, 45% Hispanic, 24% black, 22% Asian, 51% white, mean SLEDAI = 4.4±4.2 at baseline) were enrolled and compared with 18 demographically matched control samples. The FCGR2a receptor was genotyped for each sample, and RNA-seq was performed on isolated, leukocyte-depleted platelets. Transcriptomic data were used to create a modular landscape to explore the differences between SLE patients and controls and various clinical parameters in the context of FCGR2a genotypes.
Results: There were 2,290 differentially expressed genes enriched for pathways involved in interferon signaling, immune activation, and coagulation when comparing SLE samples vs controls. When analyzing patients with proteinuria, modules associated with oxidative phosphorylation and platelet activity were unexpectedly decreased. Furthermore, genes that were increased in SLE and in patients with proteinuria were enriched for immune effector processes, while genes increased in SLE but decreased in proteinuria were enriched for coagulation and cell adhesion. A low-binding FCG2Ra allele (R131) was associated with decreases in FCR activation, which further correlated with increases in platelet and immune activation pathways. Finally, we were able to create a transcriptomic signature of clinically active disease that performed significantly well in discerning SLE patients with active clinical disease form those with inactive clinical disease.
Conclusions: In aggregate, these data demonstrate the platelet transcriptome provides insight into lupus pathogenesis and disease activity, and shows potential use as means of assessing this complex disease using a liquid biopsy.

overall_design: RNA-seq of purified platelets from SLE patients and controls

first: Jeffrey

middle: S

last: Berger

first: Jill

last: PBuyon

first: Kelly

middle: V

last: Ruggles

first: Hanane

last: Bannoudi

first: Elliot

last: Luttrell-Williams

first: Tessa

last: JBarrett


title: RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal Wound Healing

status: Public on Mar 11 2024

city: Columbia

first: Rajiv

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

summary: Transparent avascular cornea providing two third refraction to the eye. Restoration of corneal transparency and clear vision in a traumatic eye involves the action of many cytokines and signaling pathways. Out of several factors, stromal keratocytes/fibroblasts (CSFs) play a central role in corneal repair and wound healing. Post trauma, keratocytes/fibroblasts produce myofibroblasts to facilitate wound repair by synthesizing and secreting large extracellular matrix components, collagens, and alpha-smooth muscle actin stress fibers. This study aimed to perform RNASeq data analysis and pathway enrichments to gain a better understanding of gene regulation in corneal fibroblasts and myofibroblasts in corneal wound repair.

overall_design: To investigate differential gene expression, pathway enrichment, and gene regulation in corneal fibroblasts and myofibroblasts in corneal wound repair

first: Rajnish

last: Kumar

first: Ratnakar

last: Tripathi

first: Nishant

last: Sinha


title: Prediction and validation of a human immunodeficiency with CRISPR

city: Los Angeles

first: Joey

middle: Han Tang

last: Li

address: 615 Charles E. Young Dr S

institute: UCLA

summary: Inborn errors of immunity (IEI) result in increased morbidity and mortality from infections. However, discovering new IEIs is limited by the clinical identification of rare patient cohorts. To predict immunodeficiency-associated genes in a patient-independent approach, we performed a targeted CRISPR-Cas9 knockout screen in healthy human donor-derived PBMCs and identified myocyte enhancer factor 2C (MEF2C) as essential for primary human natural killer (NK) cell functionality ex vivo. MEF2C haploinsufficient (MCHS) patients and mice displayed impaired NK cell development, ex vivo function, and increased susceptibility to viral infection. MEF2C was required for cytokine-induced changes in NK cell metabolism and SREBP-mediated lipid homeostasis, and oleic acid supplementation restored MCHS patient NK cell cytotoxic function. Thus, we demonstrate a CRISPR-based methodology in primary human immune cells to accelerate the identification of new IEIs, and apply this approach to predict and validate a new NK cell immunodeficiency associated with metabolic and functional defects.

overall_design: Mouse and human NK cells were CRISPR RNP edited with control sgRNAs (Rosa26 or TRAC) or targeting MEF2C. Cells were expanded in IL-2/15 and total RNA was extracted for library preparation.

middle: H

first: Adalia

last: Zhou

first: Cassidy

middle: D

last: Lee

first: Siya

middle: N

last: Shah

first: Jeong

last: Ji

first: Vignesh

last: Senthilkumar

first: Eddie

last: Padilla

first: Andréa

last: Ball

first: Qinyan

last: Feng

first: Luke

last: Riggan

first: Alain

last: Greige

first: Ajit

last: Divakaruni

first: Fran

last: Annese

first: Jessica

last: Cooley-Coleman

first: Steven

middle: A

last: Skinner

first: Christopher

middle: W

last: Cowan

first: Timothy

last: O'Sullivan


title: The role of quiescent thymic progenitors in TAL/LMO2-induced T-ALL chemotolerance

city: Worcester

first: Michelle

last: Kelliher

state: Massachusetts

address: 364 Plantation Street, Lazare Research Building, 470H

institute: UMass Chan Medical School

summary: Relapse in T-cell acute lymphoblastic leukemia (T-ALL) may signify the persistence of leukemia-initiating cells (L-ICs). Ectopic TAL1/LMO expression defines the largest subset of T-ALL, but its role in leukemic transformation and its impact on relapse-driving L-ICs remain poorly understood. In TAL1/LMO mouse models, double negative-3 (DN3; CD4−CD8−CD25+CD44−) thymic progenitors harbored L-ICs. However, only a subset of DN3 leukemic cells exhibited L-IC activity, and studies linking L-ICs and chemotolerance are needed. To investigate L-IC heterogeneity, we used mouse models and applied single-cell RNA-sequencing and nucleosome labeling techniques in vivo. We identified a DN3 subpopulation with a cell cycle–restricted profile and heightened TAL1/LMO2 activity, that expressed genes associated with stemness and quiescence. This dormant DN3 subset progressively expanded throughout leukemogenesis, displaying intrinsic chemotolerance and enrichment in genes linked to minimal residual disease. Examination of TAL/LMO patient samples revealed a similar pattern in CD7+CD1a− thymic progenitors, previously recognized for their L-IC activity, demonstrating cell cycle restriction and chemotolerance. Our findings substantiate the emergence of dormant, chemotolerant L-ICs during leukemogenesis, and demonstrate that Tal1 and Lmo2 cooperate to promote DN3 quiescence during the transformation process. This study provides a deeper understanding of TAL1/LMO-induced T-ALL and its clinical implications in therapy failure.

overall_design: Relapsed T-cell acute lymphoblastic leukemia patient derived xenografts were engrafted into NOD scid gamma mice at low passage. Human CD45+: CD7+ CD1a- (hL-IC) or CD7+ CD1a+ (DP) leukemic subpopulations were then sorted using fluorescence-activated cell sorting (FACS) and analyzed by RNA-seq

first: Kevin

last: O'Connor

first: Haibo

last: Liu

first: Lihua

middle: J

last: Zhu


title: Spatial transcriptomic profiling of precursor lesions of gallbladder adenocarcinoma

status: Public on Mar 01 2024

city: Brussels

first: Frederic

last: Lemaigre

address: Avenue Hippocrate, 75

department: de Duve Institute

country: Belgium

institute: UCLouvain

summary: Genomic and epigenomic studies support that adenocarcinomas of the gallbladder develop according to a metaplasia-biliary intraepithelial neoplasia (BilIN)-adenocarcinoma histogenic sequence, in which metaplasia and BilIN are non-cancerous lesions of the epithelium. Moreover, recent genomic data suggest that adenocarcinoma can develop in a BilIN-dependent or -independent way, pointing toward patient-specific tumourigenic processes. Spatial transcriptomic data addressing these processes are still missing. Here, using GeoMx digital spatial profiling (NanoString), we characterized the spatial transcriptome of normal gallbladder epithelium, BilINs and adenocarcinoma coexisting within the same samples. To address intra-patient variability we profiled the whole transcriptome of a high number of regions of interest (ROIs) per sample in two patients (Patient #1, 81 year old woman: 24 ROIs; Patient #2, 53-year old man:32 ROIs), with each ROI covering approximately 200 cells of normal epithelium, low-grade BilIN, high-grade BilIN or adenocarcinoma. Our results showed that each type of lesion displayed little transcriptomic variability within the same patient, but differed significantly between patients. They also suggested that adenocarcinoma can derive from high-grade BilIN or from low-grade BilIN, with co-existing high-grade BilIN evolving via a distinct process in the latter case. We also provide strong evidence for patient-specific tumourigenic mechanisms, characterized by distinct sequences of signalling pathway activation. Among those pathways, we functionally investigated SEMAPHORIN 4A (SEMA4A) and provided evidence that repression of SEMA4A expression, as is observed in the gallbladder samples of the two patients, can enhance cell migration and survival, and perturb polarisation of the epithelial cells. In conclusion, our results support that gallbladder adenocarcinoma develops according to patient-specific processes that can be promoted by repression of SEMA4A. They underscore the need to gain gene expression data in addition to histological information to evaluate the risk of low-grade preneoplastic lesions.

overall_design:
We investigated formalin-fixed paraffin-embedded sections from two patients. Patient #1, gallbladder section: normal epithelium, 4 regions of interest (ROIs); Low-grade BilIN, 8 ROIs; High-grade BilIN, 6 ROIs; Adenocarcinoma, 6 ROIs. Patient #2, gallbladder section 1: normal epithelium, 8 ROIs. Patient #2, gallbladder section 2: Low-grade BilIN, 6 ROIs; High-grade BilIN, 12 ROIs; Adenocarcinoma, 6 ROIs.

*** FASTQ raw data files have been requested. ***

first: Frédéric

middle: P

first: Sophie

last: Pirenne

first: Axelle

last: Loriot


title: Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties

status: Public on Mar 07 2024

first: Kärt

last: Mätlik

address: 1230 York Ave

institute: Rockefeller University

summary: Astrotactin 2 (ASTN2) is a transmembrane, neuronal protein that functions in receptor trafficking and modulates cerebellar Purkinje cell (PC) synaptic activity. We recently reported a family with a paternally inherited intragenic ASTN2 duplication, with a range of neurodevelopmental disorders, including autism spectrum disorder (ASD), learning difficulties and speech and language delay. To provide a genetic model for the role of the cerebellum in ASD-related behaviors and study ASTN2 role in cerebellar circuit function, we generated global and Purkinje cell-specific conditional Astn2 knockout (KO and cKO, respectively) mouse lines. Astn2 KO mice exhibit strong ASD-related behavioral phenotypes, including a marked decrease in separation-induced pup ultrasonic vocalization (USV) calls, increased hyperactivity and repetitive behaviors, altered social behaviors, and impaired cerebellar-dependent eyeblink conditioning. Increased hyperactivity and repetitive behaviors were also prominent in Astn2 cKO animals. By Golgi staining,  Astn2 KO PCs have region-specific changes in dendritic spine density and filopodia numbers. Proteomic analysis of Astn2 KO cerebellum reveals a marked upregulation of ASTN2 family member, ASTN1, a neuron-glial adhesion protein. Immunohistochemistry and electron microscopy demonstrates a large increase in Bergmann glia volume in the molecular layer of Astn2 KO animals. Electrophysiological experiments indicate a reduced frequency of spontaneous EPSCs, as well as increased amplitudes of both spontaneous EPSCs and IPSCs in the Astn2 KO animals, suggesting that pre- and post-synaptic components of synaptic transmission are altered. Thus, ASTN2 regulates ASD-like behaviors and cerebellar circuit properties.

overall_design: We crossed Astn2 WT and KO mice with Tg(Pcp2-L10a-EGFP) bacTRAP line to analyze Purkinje cell-specific gene expression changes in mice lacking ASTN2. Cerebella from WT and KO littermates were isolated at P21 and translating mRNA was isolated using the TRAP methodology.

first: Michalina

last: Hanzel

first: Kayla

last: Fernando

first: Susan

middle: E

last: Maloney

first: Shiaoching

last: Gong

first: Jiajia

last: Zhao

first: H

last: Pasolli

first: Henrik

last: Molina

first: Joseph

last: Dougherty

first: Court

last: Hull

first: Mary

last: Hatten


title: The lncRNA Firre functions as a rapid regulator of transcription from a distance [ChIP-Seq]

city: Boulder

first: John

last: Rinn

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

summary: There are currently over 16,000 long-noncoding RNAs (lncRNAs) annotated in mammalian genomes, a number on par with protein-coding genes. Numerous studies have demonstrated that lncRNAs can influence gene expression programs but lack the temporal resolution to identify the immediate regulatory events. Thus, even for the most well-studied lncRNAs, the early and primary targets remain elusive, even though they are a prerequisite to elucidating lncRNA mechanisms. Here we describe a multifaceted effort to determine the primary targets of a lncRNA and the underlying temporal dynamics. We combine several genetically defined loss- and gain-of-function, rescue, and inducible lncRNA models to resolve gene regulatory events temporally from 30 minutes to four days. Applying this approach, we find that in mouse ES cells, the lncRNA Firre regulates the expression of 29 high-confidence target genes. Firre-regulated gene expression is not mediated by epigenetic events nor the proximal binding of the Firre lncRNA to its target genes. Instead, Firre induces nascent transcription and increases chromatin accessibility within minutes, resulting in mature transcripts of the primary target genes about an hour later. Overall, this study suggests Firre functions as a rapid RNA-based transcriptional regulator from a distance.

overall_design: ChIP-seq for H3K27me3 in mESCs after inducing the lncRNA Firre using doxycyline in a Firre KO and WT background.

first: Christian

last: Much

first: Michael

last: Smallegan

middle: L


title: The Firre lncRNA acts as a transcriptional activator [PRO-Seq]

summary: There are currently over 16,000 long-noncoding RNAs (lncRNAs) annotated in mammalian genomes, a number on par with protein-coding genes. Numerous studies have demonstrated that lncRNAs can influence gene expression programs but lack the temporal resolution to identify the immediate regulatory events. Thus, even for the most well studied the early and primary targets of lncRNAs remains elusive. Here we describe a multifaceted effort to determine the primary targets of a lncRNA and the underlying temporal dynamics. Our approach combines several genetically defined loss-of and gain-of-function, rescue, and inducible lncRNA models. We further resolved gene regulatory events temporally (30 min to four days). Applying this approach, we find that the lncRNA Firre is an RNA-based transcriptional activator.  These transcriptional activation events are not mediated by the epigenetic regulators PRC2, WDR5, or G9A, nor are they due to the proximal binding of the Firre lncRNA. Instead, Firre activates transcription by increasing chromatin accessibility (approximately 30 min after induction) and activating primary target genes (about an hour later). Overall, this study suggests Firre functions as an RNA-based transcriptional activator.

overall_design: PRO-seq time courses in mESCs after inducing the lncRNA Firre transgene using doxycycline in a Firre KO background. Dataset includes a short time course with 0min, 15min, and 30 min time points and three replicates.

first: Isabela

middle: T

last: Pereira

first: Tenaya

middle: K

last: Vallery

first: Daniel

middle: R

last: Hernandez

first: Robin

last: Dowell


title: Role of Renal Tubule Cpt1a in Murine Kidneys

city: St. Louis

first: Steven

last: Funk

address: 660 S. Euclud Ave

institute: Washington University

summary: To compare the transcriptional profile in renal tubules conditional deletion of Cpt1a, to floxed littermate controls.

overall_design:
All mice were males and on a mixed background.
Kidneys were either from mice that had Cpt1a deleted specifically in renal tubules (crossing Cpt1a floxed mice with Pax8-rTTA;tetO-Cre, which will be called Cpt1aCKO) or floxed controls. They had been treated for 3 weeks with doxycycline to activate Cre at age5-8 weeks.

first: Leslie

last: Gewin


title: Rosiglitazone and Trametinib to treat basal bladder tumors [ATAC-Seq]

first: Cathy

last: Mendelsohn

overall_design: Comparative gene expression profiling analysis of ATAC-seq data for RosiTram and vehicle treated basal tumor cells in vivo.

first: Tina

last: Xiang

first: Tiffany

last: Tate

first: Sakina

last: Plumber

last: Lee Mendelsohn


title: The lncRNA Firre functions as a rapid regulator of transcription [RNA-seq]

overall_design: RNA-seq time courses in mESCs after inducing the lncRNA Firre using doxycyline in a Firre KO and WT background. Dataset includes a long (96-hour) time course with 5 time points and three replicates and a short timecourse (5.5-hour) with 12 time points and two replicates. Cell lines with an inducible Firre transgene were compared to genetically matched controls to control for the effect of doxycycline on gene expression.

first: Erika

last: Lasda

first: Jordan

last: Lewandowski


title: The lncRNA Firre functions as a rapid regulator of transcription

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

overall_design: Refer to individual Series


title: The lncRNA Firre functions as a rapid regulator of transcription [ATAC-seq]

overall_design: ATAC-seq time course in mESCs after inducing the lncRNA Firre using doxycyline. A 2.5-hour timecourse was performed with 6 time points and one replicate at each timepoint. Cell lines with an inducible Firre transgene were compared to genetically matched controls to control for the effect of doxycycline on chromatin accessibility.


title: Modulation of apple leaf transcriptome by QTLs and infection by Venturia inaequalis

status: Public on Feb 28 2024

city: Beaucouzé

first: Laure

last: Perchepied

address: 42 rue Georges Morel

institute: INRAE

summary: Induction of whole genome gene expression level changes in leaves of grafted apple genotypes exhibiting contrasted QTL architecture (from one to a combination of three QTL) after the inoculation of the pathogenic fungus Venturia inaequalis

overall_design: A total of 16 samples, corresponding to two biological replicates (A and B) for both untreated and treated samples (i.e Water and Venturia inaequalis strain EU-B04) and for four  categories of QTLs, were used for differential gene expression analysis. The first class is composed of four genotypes with no favourable alleles (NoscabQTL) for neither qT1, qF11 or qF17 QTLs. The second class is composed of four genotypes with favourable alleles solely for the qT1 QTL (qT1). The third class is composed of four genotypes with favourable alleles from both qF11 and qF17 QTLs (qF11qF17). Finally, the fourth class is composed of  four genotypes with favourable alleles of all three QTLs  qT1, qF11 and qF17 (qT1qF11qF17).

first: Juliette

last: Bénéjam

first: Elisa

last: Ravon

first: Christelle

last: Heintz

first: Charles-Eric

last: Durel

first: Matthieu

last: Gaucher

first: Marie-Noëlle

last: Brisset


title: Control ChIP-seq from whole organism (ENCSR535RLJ)

status: Public on Feb 27 2024

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Input control for ChIP-seq on transgenic flies expressing CG11696-eGFP fusion proteins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TI caused by SARS-CoV-2

status: Public on Feb 29 2024

city: Bergen

first: Harleen

last: Grewal

address: The Laboratory Building, 5th floor, 5021

department: Department of Clinical Science

country: Norway

institute: University of Bergen

summary: The host transcriptional profile was compared between patients with RTI caused by SARS-CoV-2, other viral aetiology, and bacterial aetiology in order to identify differentially expressed genes and activation of host immune pathways

overall_design: Bacterial etiology (n=8), Viral etiology (n=8), SARS-CoV-2 (n=8)

first: Dhanasekaran

last: Sivakumaran


title: TF ChIP-seq from whole organism (ENCSR535LKO)

summary:
ChIP-seq against eGFP-pqm-1 in L3 larva worms.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR534YJS)

summary:
Input ChIP-seq in L4 larva worms.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from whole organism (ENCSR533AOQ)

summary:
ChIP-seq on transgenic worms expressing cebp-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from whole organism (ENCSR534TFA)

summary:
ChIP-seq of transgenic worms expressing CEH-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR530KZU)

summary:
This is the ChIP-seq control of transgenic worms expressing vab-7-eGFP fusion proteins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR530FXD)

summary:
ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR534JVP)

summary:
Input ChIP-seq in late embryonic worms.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from whole organism (ENCSR532EVV)

summary:
ChIP-seq on transgenic flies expressing Dbx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR529PRD)

summary:
ChIP-seq on transgenic flies expressing CG9437-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from whole organism (ENCSR530MRJ)

summary:
ChIP-seq on transgenic flies expressing CG8319-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from whole organism (ENCSR532BHA)

summary:
Input control for ChIP-seq on transgenic flies expressing CrebB-eGFP fusion proteins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from whole organism (ENCSR529XPL)

summary:
ChIP-seq on transgenic worms expressing saeg-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR528YHA)

summary:
Input ChIP-seq in young adult worms.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from whole organism (ENCSR843KFW)

summary:
Input control for ChIP-seq on transgenic flies expressing maf-S-eGFP fusion proteins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf