title: Pseudomonas aeruginosa Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound Chronicity

status: Public on May 26 2024

city: Riverside

first: Manuela

last: Martins-Green

state: CA

address: 900 University Ave

institute: University of California, Riverside

summary: Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study   is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. We found that the planktonic bacteria under OS conditions overex-pressed quorum sensing genes that are important for the bacteria to communicate with each other, antioxidant stress genes important to reduce OS in the microenvironment for survival, biofilm formation genes and virulence genes. Additionally, we performed RNAseq in vivo and identified the activation of novel genes/pathways of the Type VI Secretion System (T6SS) involved in RPA pathogenicity. In conclusion, RPA appears to survive the high OS microenvironment in chronic wounds and colonizes these wounds by turning on virulence, biofilm-forming and survival genes. These findings reveal pathways that may be promising targets for new therapies aimed at dis-rupting PA-containing biofilms immediately after debridement to facilitate the treatment of chronic human wounds.

overall_design: RNAseq of Psuedomonas aeruginosa collected from nonchronic (control) and chronic wounds to understand the transcriptomic regulation of PA during infection in response to high levels of oxidative stress.

first: Jane

last: Kim


title: Spatial transcriptome analysis of muscle sections from Icos-/- NOD mice with established myositis

status: Public on May 29 2024

city: Rouen

first: Catalina

last: Abad

address: 22 Blvd Gambetta

country: France

institute: Inserm U1234

summary: Icos-/- NOD mice are a model of spontaneous myositis. By using Nanostring GeoMx technology (Mouse WTA), we aimed to investigate the differences in gene expression between myofibers of Icos+/+ NOD (WT) mice and myofibers from Icos-/- NOD mice either in direct contact or not with large infiltrate clusters.

overall_design: Using Nanostring technology, the transcriptomes of myofibers vs. immune cells were analysed separately by using desmin and CD45 markers. The present study includes the following AOIs: 4 AOIs from Icos+/+ NOD muscle (n=4 mice, 1 AOI/mouse, desmin+CD45-) , 6 AOIs from Icos-/- NOD muscle not directly adjacent to immune cell infiltrates  (PROX, n=6 mice, 1 AOI/mouse, desmin+CD45-),  8 AOIs from Icos-/- NOD muscle directly adjacent to immune cell infiltrates  (ADJ, n=6 mice, 1-2 AOI/mouse, desmin+CD45-), 8 AOIs from Icos-/- NOD muscle coresponsing to immune cell infiltrates (INF, n=6 mice, 1-2 AOI/mouse, desmin-CD45+).

first: Olivier

last: Boyer


title: Gene expression profile of the intestines at the different locations

status: Public on May 24 2024

city: Pittsburgh

first: Jing

last: Hu

state: PA

address: 5117 Centre Ave

country: USA

institute: Univeristy of Pittsburgh

type: Expression profiling by high throughput sequencing

summary: We performed RNA-seq analyses of intestinal epithelium using RNA extract from different intestinal locations: the cecum, the proximal colon, and the distal colon in different mice. Our results have revealed key pathway differences in these mice at different intestinal locations.

overall_design: Intestinal epithelium at different locations in different mice was collected for RNA extraction.

first: Chenxi

last: Gao

first: Huaibin

last: Ge


title: BTLA and PD-1 signals attenuate TCR-mediated gene expression

status: Public on May 27 2024

city: Dublin

first: Muhammad Zainul

last: Arifin

state: Co. Dublin

address: University College Dublin

department: School of Medicine

country: Ireland

institute: Systems Biology Ireland

summary: T cell coinhibitory immune checkpoints, such as PD-1 or BTLA, are bona fide targets in cancer therapy. Here we used a human T cell reporter line to measure transcriptome changes mediated by PD-1 and BTLA induced signalling. TCR/CD3 stimulation resulted in the upregulation of a large number of genes but also repressed a similar number of transcripts. PD-1 and BTLA signals attenuated transcriptomics changes mediated by TCR/CD3 signalling: upregulated genes tended to be suppressed and the expression of a significant number of downregulated genes was higher when PD-1 or BTLA signalling took place. BTLA was a significantly stronger attenuator of TCR/CD3 induced transcriptome changes than PD-1. A strong overlap between genes that were regulated indicated quantitative rather than qualitative differences between these receptors. In line with their function as attenuator of TCR/CD3 mediated changes we found strongly regulated genes to be prime targets of PD-1 and BTLA signalling.

overall_design: To assess how BTLA and PD-1 signalling impact gene transcription induced by TCR/CD3 stimulation, we used a Jurkat-NFkB::eGFP reporter cell line together with a T-cell stimulator cell system that stimulates Jurkat T-cells via the TCR-CD3 complex. We stably co-expressed PD-1 or BTLA in our reporter cells and generated T-cell stimulator cells expressing the cognate ligands PD-L1 or HVEM. PD-1 or BTLA-expressing reporter cells were left unstimulated or co-cultured with control stimulator cells or stimulator cells expressing PDL-1 or HVEM. Following 4, 20 and 48 hours of co-culture, deep RNA-seq was used to distinguish and quantify changes in gene expression in the reporter and stimulator cells. As we co-cultured Jurkat cells with stimulator cells, the count matrix contains both human (ENSG) and mouse (ENSMUSG) genes. Further gene filtering needs to be applied to the count matrix if the scope of analysis is only limited to the Jurkat cells.

first: Muhammad

middle: Z

first: Judith

last: Leitner

first: Donagh

last: Egan

first: Petra

last: Waidhofer-Söllner

first: Walter

last: Kolch

first: Vadim

last: Zhernovkov

first: Peter

last: Steinberger


title: Tumor suppressor Par-4 activates autophagy-dependent ferroptosis

city: Abu Dhabi

last: Arshad

state: Abu Dhabi

address: Saadiyat

country: United Arab Emirates

institute: New York University

summary: Ferroptosis is a unique iron-dependent form of non-apoptotic cell death characterized by devastating lipid peroxidation. Whilst growing evidence suggests that ferroptosis is a type of autophagy-dependent cell death, the underlying molecular mechanisms regulating ferroptosis are largely unknown. In this study, through an unbiased RNA-sequencing screening, we demonstrate the activation of a multi-faceted tumor-suppressor protein Par-4/PAWR during ferroptosis. Functional studies reveal that genetic depletion of Par-4 effectively blocks ferroptosis, whereas Par-4 overexpression sensitizes cells to undergo ferroptosis. More importantly, we have determined that Par-4-triggered ferroptosis is mechanistically driven by the autophagic machinery. Upregulation of Par-4 promotes activation of ferritinophagy (autophagic degradation of ferritin) via the nuclear receptor co-activator 4 (NCOA4), resulting in excessive release of free labile iron and, hence, enhanced lipid peroxidation and ferroptosis. Inhibition of Par-4 dramatically suppresses the NCOA4-mediated ferritinophagy signaling axis. Our results also establish that Par-4 activation positively correlates with reactive oxygen species (ROS) production, which is critical for ferritinophagy-mediated ferroptosis. Furthermore, Par-4 knockdown effectively blocked ferroptosis-mediated tumor suppression in the mouse xenograft models. Collectively, these findings reveal that Par-4 has a crucial role in ferroptosis, which could be further exploited for cancer therapy.

overall_design:
To identify unique factors modulating ferroptosis vulnerability.
We treated U87MG cells with type 2 ferroptosis activator RSL3 and conducted RNA sequencing (RNA-seq) analysis

first: Karthikeyan

last: Subburayan

first: Faisal

last: Thayyullathil

first: Siraj

last: Pallichankandy

first: Anees

middle: R

last: Cheratta

first: Ameer

last: Alakkal

first: Mehar

last: Sultana

first: Nizar

last: Drou

first: Palanikumar

last: Loganathan

first: Mazin

last: Magzoub

first: Vivek

middle: M

last: Rangnekar

first: Sehamuddin

last: Galadari


title: A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models [scRNA-seq: Rpe65-KO]

status: Public on Jun 06 2024

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: To determine the gene expression changes in the retina P57-P60 Rpe65-/- mice , we collected retina samples from Rpe65-/- and WT (C57BL/6J mice) mice, generated single-cell suspensions, and performed scRNA-Seq (10X Genomics). One group of Rpe65-/- mice was treated for 5 weeks via dietary administration of tamsulosin, metoprolol and bromocriptine drug (TMB) cocktail.

overall_design: Vehicle- and TMB-treated Rpe65-/- mice: One retina from seven male Rpe65-/- mice were pooled to prepare single-cell suspensions at a final concentration of 1,000 cells/µl. WT mice: One retina from three age-matched male C57BL/6J mice were pooled to prepare single-cell suspensions at a final concentration of 1,000 cells/µl. For each group, freshly dissociated cells (~10,000) were loaded into a 10x Genomics Chromium Single Cell system using v3 chemistry following the manufacturer's instructions.

first: Henri

last: Leinonen

first: Elliot

middle: H

last: Choi


title: Reversal of pulmonary veno-occlusive disease phenotypes by inhibition of the integrated stress response

status: Public on May 23 2024

city: san francisco

first: Akiko

last: Hata

state: CALIFORNIA

address: 555 Mission Bay Blvd. South, CVRI, ucsf, Room 252T

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary:
To investigate the effect of Mitomycin-C induced DNA damage on human pulmonary microvascular endothelial cells (hPMVECs), we treated the hPMVECs with 150µM MMC for 0h, 4h, and 14. Saline was used as vehicle.
We then performed RNA expression profile analysis using data obtained from RNA-seq of time dependendent MMC treated PMVECs.

overall_design: Comparative RNA expression profiling analysis of RNA-seq data for MMC treated hPMVECs.

first: Amit

last: Prabhakar

first: Rahul

last: Kumar

first: Meetu

last: Wadhwa

first: Prajakta

last: Ghatpande

first: Jingkun

last: Zhang

first: Carlos

middle: O

last: Lizama

first: Bhushan

middle: N

last: Kharbikar

first: Stefan

last: Graf

first: Carmen

last: Treacy

first: Nicholas

middle: W

last: Morrel

first: Brian

middle: B

last: Graham

first: Giorgio

last: Lagna


title: TWEAK/Fn14 signalling in Breast Cancer

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Reversible acetylation of HDAC8 regulates cell cycle

city: Shanghai

first: Chaowei

last: Sang

state: Shanghai Province

address: Songhu Road 2005

department: School of life science Fudan uniersity

country: China

institute: Fudan University


title: Multi-omics profiling of 5 Arabidopsis accessions in response to combined water and nitrogen deficiencies

city: Versailles

first: Olivier

last: Loudet

address: Rte de St Cyr

department: IJPB

institute: INRAE

summary: In this study, we build an in-depth multi-omics profile of 5 Arabidopsis accessions, in order to find the inner relations of N deficit, mild drought, and combined stress response at the physiological, metabolic and transcriptional level.

overall_design: Examination of 5 Arabidopsis accessions in response to 3 stress conditions

first: Zeyun

last: Xue


title: Effect of mutation at the K202 site of the HDAC8 on gene expression in HeLa cells

summary: HDAC8, a member of class I HDACs, plays a pivotal role in cell cycle regulation by deacetylating the cohesin subunit SMC3. While cyclins and CDKs are well-established cell cycle regulators, our knowledge of other regulators remains limited. Here we reveal acetylated K202 in HDAC8 as a key cell cycle regulator responsive to stress. K202 acetylation in HDAC8, primarily catalyzed by Tip60, negatively modulates HDAC8 activity, leading to increased SMC3 acetylation and cell cycle arrest. Furthermore, cells mimicking K202 acetylation display significant alterations in gene expression, potentially linked to changes in 3D genome structure, including enhanced chromatid loop interactions. K202 acetylation negatively impacts cell cycle progression by disrupting the expression of cell cycle-related genes and sister chromatid cohesion, resulting in G2/M phase arrest. These findings illuminate the reversible acetylation of HDAC8 as a novel cell cycle regulator, expanding our understanding of stress-responsive cell cycle dynamics.

overall_design: To directly examine the influence of K202 acetylation on cellular processes, we harnessed CRISPR/Cas9 technology to modify the HDAC8 gene in HeLa cells. We generated the K202Q missense mutation, which mimics the acetylated state, and concurrently, we also generated the K202R mutant. Monoclonal cells were screened and confirmed for successful mutation of the HDAC8 gene through DNA sequence analysis.

first: Xuedong

first: Jingxuan

last: Liu

first: Ziyin

last: Chen

first: Minhui

last: Xia

first: Miao

last: Yu

first: Wei


title: Integrating scRNA-seq and mRNA-seq to explore the differentiation mechanism of human nail stem cells mediated by onychofibroblasts

first: Xia

last: Fang

address: No. 639 Zhizaoju Road

institute: Shanghai 9th People’s Hospital

type: Expression profiling by genome tiling array

summary: The mechanisms governing nail stem cell (NSC) differentiation are coupled directly with their ability to orchestrate digit regeneration. Recently, onychofibroblasts (OFs), specialized mesenchymal cells residing beneath the nail matrix in the dermis, have emerged as potential regulators of nail differentiation. However, due to limited sample sources, the cellular properties and transcriptome information of OFs remain largely unexplored. In this study, we isolated human OFs and characterized their mesenchymal stem cell-like phenotypes. To delineate the molecular features of human OFs, we conducted mRNA-seq analysis on three samples of OFs and control fibroblasts from human nail units. Our analysis identified 294 genes that were upregulated in OFs compared to surrounding fibroblasts. Through integrated analysis with scRNA-seq data from human nail units, we confirmed that BMP4, secreted by OFs, is a pivotal signal involved in mesenchymal-epithelial interactions and nail development. Furthermore, we demonstrated that BMP4 derived from OFs mediates the in vitro differentiation of NSCs using a co-culture model. Gene set enrichment analysis highlighted the involvement of the TGF-beta pathway in the differentiation of nail epithelial cells. Consequently, we validated the effect of exogenous BMP4 on the activation of the SMAD-dependent pathway and NSC differentiation, along with the rescue effect of BMP receptor inhibition. Taken together, transcriptome analysis reveals the differentiation-inducing influence of OFs on human NSCs, with the BMP4/BMPR/SMADs signaling pathway playing a key role in this process. These findings establish a connection between the dermal microenvironment and NSC differentiation, suggesting that OFs, in conjunction with NSCs, may hold promise for the development of novel therapies targeting nail and digit defects, even severe limb amputation.

overall_design: To elucidate the molecular features of onychofibroblasts and  explore their role in coordinating nail development. We then performed mRNA-seq analysis on three human onychofibroblasts samples and three control human fibroblast samples derived from the proximal nail fold.


title: CUT & Tag analysis of primary human retinal microvascular endothelial cells

city: Chongqing

last: Fan

address: Youyi Road, No1

department: Urology

institute: The First affiliated hospital of Chongqing Medical University

summary: CUT & Tag analysis was conducted using primary human retinal microvascular endothelial cells treated with 0 or 100ng/ml VEGF.

overall_design: CUT& Tag was performed using the Hyperactive Universal CUT& Tag Assay Kit for Illumina (Vazyme). Briefly, Human retinal microvascular endothelial cells (HRMECs) were treated with 0 or 100 ng/ml VEGF for 24 h (Control and VEGF group respectively). Then the HRMECs were bound to concanavalin A-coated beads. After permeabilization and incubation with primary antibody (anti-H3K9la, PTM BIO, PTM-1419RM), the DNA was precisely tagmented with pA-Tn5 transposase and enriched by PCR to create sequencing-ready libraries. The library preparations were sequenced using the Illumina Novaseq platform and 150 bp paired-end reads were generated.

first: Shengping

last: Hou


title: Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: Ovsaho_COV362]

status: Public on May 22 2024

city: New York

first: Itai

last: Yanai

state: NY

address: 435 East. 30th St.

institute: NYU Langone Health

summary: Advancements in precision oncology over the past decades have led to new therapeutic interventions, but the efficacy of such treatments is generally limited by an adaptive process that fosters drug resistance. In addition to genetic mutations, recent research has identified a role for non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell-state transitions that occur in the adaptation to cancer therapies remain unknown and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell-state transitions accompanied by a progressive increase in cell fitness, which we denote as the 'resistance continuum'. This cellular adaptation involves a stepwise assembly of gene expression programmes and epigenetically reinforced cell states underpinned by phenotypic plasticity, adaptation to stress and metabolic reprogramming. Our results support the notion that epithelial-to-mesenchymal transition or stemness programmes-often considered a proxy for phenotypic plasticity-enable adaptation, rather than a full resistance mechanism. Through systematic genetic perturbations, we identify the acquisition of metabolic dependencies, exposing vulnerabilities that can potentially be exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell-state transitions.

overall_design: Drug-naïve ovsaho and cov362 cell populations were treated with olaparib in dose escalation from 1 to 40 uM of olaparib to generate resistant populations. Adapted (olaparib resistant) cell populations from the doses 5 uM (T5), 10 uM (T10), 20 uM (T20) and 40 uM (T40) of olaparib plus untreated controls (C) were collected for single-cell sequencing using the 10X genomics platform.

first: Gustavo

last: Starvaggi França


title: Cellular adaptation to cancer therapy along a resistance continuum [CRISPR-Screen: Kuramochi]

overall_design: Kuramochi cells from C (untreated) and adapted (olaparib resistant) T10 and T320 populations were sorted based on their CD24 and CD44 profiles and expanded before being transfected with CRISPR/Cas9 knockout metabolism library. After puromycin selection, cells were collected (initial time point) and expanded by 10 population doublings without drug treatment (C, T10 and T320) and on drug treatment (CD on 1 μM and T320D on 40 μM of olaparib), thus constituting the end time point of the screen. Guide RNAs were sequenced and depletion scores were determined for each sample based on the abundance of gRNAs at the end time point relative to the initial time point.


title: Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: A375_PC9]

overall_design: Drug-naïve A375 cells were treated in dose escalation from 30 nM to 4 uM of dabrafenib. Adapted cell populations (dabrafenib resistant) from the doses 30 nM, 60 nM, 125 nM, 250 nM, 500 nM, 1 uM, 2 uM and 4 uM (T003, T006, T0125, T0250, T0500, T1, T2 and T4) plus untreated control (C) were collected for single-cell sequencing using the 10X genomics platform. The same procedure was used to generate PC9 resistant cells to osimertinib. Drug-naïve PC9 cells were treated in dose escalation from 8 nM to 1.2 uM of osimertinib. Adapted cell populations (osimertinib resistant) from the doses 8 nM, 16 nM, 32 nM, 75 nM, 150 nM, 300 nM, 600 nM and 1.2 uM  (T0008, T0016, T0032, T0075, T0150, T0300, T0600, T1.2) plus untreated control (C). An additional population of persister cells was generated by acute treatment with 1.2 uM (P1.2) for 9 days. Cells were collected for single-cell sequencing using the 10X genomics platform.


title: Cellular adaptation to cancer therapy along a resistance continuum [ATAC-seq: Kuramochi]

overall_design: Adapted (olaparib resistant) Kuramochi cell populations to 5 uM (T5), 10 uM (T10), 20 uM (T20), 40 uM (T40), 80 uM (T80), 160 uM (T160) and 320 uM (T320) of olaparib plus untreated controls (C) were sorted based on their CD24/CD44 profiles and ATAC-Seq was performed. Drug-naïve Kuramochi cell populations were treated with olaparib for 9 days with 10 uM (P10) and 320 uM (P320) of olaparib and ATAC-Seq was performed. To evaluate the stability of the chromatin changes, the parental T320 cells were cultured without drug (T320W) for 120 days. Both T320 and T320W were either untreated or re-treated with 320 uM of olaparib for 2 days and ATAC-Seq was performed. Two replicates per condition were generated.


title: Cellular adaptation to cancer therapy along a resistance continuum [scRNA-Seq: Kuramochi_Persisters]

overall_design: Drug-naïve Kuramochi cell populations were treated with olaparib for 9 days with 10 uM (samples named as T10.P) and 320 uM (samples named as T320.P). Adapted (drug resistant) cell populations to the same doses, denoted as T10.A and T320.A were included, as well as drug naïve controls (C). Data contains two replicates per condition.


title: Cellular adaptation to cancer therapy along a resistance continuum [scRNA-Seq: Kuramochi]

overall_design: Drug-naïve Kuramochi cell line was treated with olaparib through a dose-escalation scheme that generated 10 populations (Untreated (C),and adapted lines T1 to T320

last: Starvaggi Franca


title: Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus [cortex]

status: Public on May 21 2024

city: Buenos Aires

first: Lucia

middle: Florencia

last: Franchini

state: Ciudad Autonoma de Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI-CONICET

summary: A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human Accelerated Regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The RBFOX1 locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here we examined the role of RBFOX1-HARs using transgenic zebrafish reporter assays and identified fifteen transcriptional enhancers that are active in the developing nervous system, ten of which displayed differential expression between the human and chimpanzee sequences. The engineered loss of two selected RBFOX1-HARs in knockout mouse models increased Rbfox1 expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of Rbfox1 target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by RBFOX1-HARs.

overall_design: Cerebral cortex were extracted from Rbfox1 ΔHAR.505/ΔHAR.505 and Rbfox1 +/+ mice at 8 postnatal (P8) days, with five independent biological samples per genotype

middle: F


title: Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. To address these limitations, we generated spatially resolved transcriptome maps of human IPF and bleomycin-induced mouse lung fibrosis.

overall_design: Female C57BL/6NCrl mice were challenged with 30 μl saline or bleomycin (Apollo Scientific, BI3543, Chemtronica Sweden; 40 µg/mouse) dissolved in saline via oropharyngeal route administration. Lungs were collected at day 7 (n=6 BLM, n=3 vehicle) or day 21 (n=6 BLM, n=3 vehicle) following administration. The mice were purchased from Charles River (Germany), and were 8 weeks + 5 days old at the time of study initiation. Animal handling conformed to standards established by the Council of Europe ETS123 AppA, the Helsinki Convention for the Use and Care of Animals, Swedish legislation, and AstraZeneca global internal standards. All mouse experiments were approved by the Gothenburg Ethics Committee for Experimental Animals in Sweden and conformed to Directive 2010/63/EU. The present study was approved by the local Ethical committee in Gothenburg (EA000680-2017) and the approved site number is 31-5373/11.

first: Lovisa

last: Franzén

first: Martina

last: Olsson Lindvall

first: Michael

last: Hühn

first: Victoria

last: Ptasinski

first: Laura

last: Setyo

middle: P

first: Astrid

last: Collin

first: Steven

last: Oag

first: Thomas

last: Volckaert

first: Annika

last: Borde

first: Joakim

last: Lundeberg

first: Julia

last: Lindgren

first: Graham

last: Belfield

first: Sonya

last: Jackson

first: Anna

last: Ollerstam

first: Marianna

last: Stamou

first: Patrik

middle: L

last: Ståhl

first: Jorrit

middle: J

last: Hornberg


title: DCAF15 control of cohesin dynamics sustains acute myeloid leukemia

city: Philadelphia

first: Luca

last: Busino

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

first: Grant

last: Grothusen

first: Renxu

last: Chang

last: Zhou

first: Phillip

last: Wulfridge

first: Kavitha

last: Sarma


title: Effect of mutation at the K202 site of the HDAC8 on 3D genomic structure in HeLa cells

first: Chaowei

last: Sang

summary: HDAC8, a member of class I HDACs, plays a pivotal role in cell cycle regulation by deacetylating the cohesin subunit SMC3. While cyclins and CDKs are well-established cell cycle regulators, our knowledge of other regulators remains limited. Here we reveal the acetylation of K202 in HDAC8 as a key cell cycle regulator responsive to stress. K202 acetylation in HDAC8, primarily catalyzed by Tip60, restricts HDAC8 activity, leading to increased SMC3 acetylation and cell cycle arrest. Furthermore, cells expressing the mutant form of HDAC8 mimicking K202 acetylation display significant alterations in gene expression, potentially linked to changes in 3D genome structure, including enhanced chromatid loop interactions. K202 acetylation impairs cell cycle progression by disrupting the expression of cell cycle-related genes and sister chromatid cohesion, resulting in G2/M phase arrest. These findings indicate the reversible acetylation of HDAC8 as a cell cycle regulator, expanding our understanding of stress-responsive cell cycle dynamics.

first: Xuedong

last: Li

first: Jingxuan

last: Liu

first: Ziyin

last: Chen

first: Minhui

last: Xia

first: Miao

last: Yu

first: Wei


title: Gene expression analysis of yeast strains with a nonsense mutation in the eRF3-coding gene highlights possible mechanisms of adaptation

city: St. Petersburg

first: Yury

middle: A

last: Barbitoff

address: Kantemirovskaya st. 2A

country: Russia

institute: Bioinformatics Institute

summary: In yeast Saccharomyces cerevisiae, there are two translation termination factors,  eRF1 (SUP45) and eRF3 (SUP35), which are essential for viability. Previous studies have revealed that presence of nonsense mutations in these genes leads to amplification of mutant alleles (sup35-n and sup45-n) which appears to be necessary for viability of such cells. However, the mechanism of this phenomenon remained unclear. In this study, we used RNA-Seq to reveal the complete set of gene expression changes that occur during cellular adaptation to the introduction of the sup35-218 nonsense allele. Our analysis demonstrated significant changes in the transcription of genes that control the cell cycle: decrease in the expression of genes of the anaphase promoting complex APC/C (APC9, CDC23), their activator CDC20 and an increase in the expression of FKH1 transcription factor, main cell cycle kinase CDC28 and cyclins that induce DNA biosynthesis. We propose a model according to which yeast adaptation to nonsense mutations in the translation termination factor genes occurs as a result of a delayed cell cycle progression beyond the G2-M stage, which leads to an extension of the S and G2 phases and an increase in the number of copies of the mutant sup35-n allele.

overall_design: Gene expression profiles (from RNA-seq) of cells of the U-14-D1690 and L-14-D1690 strains with a deletion of a normal chromosomal copy of SUP35 and bearing a wild-type allele of the corresponding gene on plasmids with either URA3 or LEU2 marker genes  (3 and 4 replicates, respectively) were compared to those of the 218-L-D1690 strain bearing a mutant sup35-218 allele of the same gene (3 replicates).

first: Evgeniia

last: Maksiutenko

first: Lavrentii

middle: G

last: Danilov

first: Anrew

last: Matveenko

first: Olga

last: Zemlyanko

first: Elena

last: Efremova

first: Svetlana

middle: E

last: Moskalenko

first: Galina

last: Zhouravleva


title: Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus

first: Lucia

last: Franchini


title: Cellular adaptation to cancer therapy along a resistance continuum [Whole Exome: Kuramochi]

first: Itai

last: Yanai

overall_design: Kuramochi cell populations adapted (olaparib resistant) to 10 uM (T10), 40 uM (T40) and 320 uM (T320) of olaparib and untreated cells (C) were collected for whole exome sequencing to evaluate copy number alterations and single nucleotide variants.

first: Gustavo

last: Starvaggi França


title: Human Cerebral Organoids: Cellular composition and subcellular morphological features

status: Public on May 16 2024

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

summary: In this study, we have analyzed the cell types that compose hCOs of 45 days of culture

overall_design: hCOs were generated directly from 2D cultures of pluripotent stem cells (AND2) 45 days of culture and analyzed using scRNAseq

first: Isabel

last: Liste

first: Rosa

last: González-Sastre


title: Netrin-1 engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair [scRNA-seq]

city: Zhengzhou

first: Jinsheng

last: Huang

address: 1th, East Jianshe Road

institute: Zhengzhou University

summary: The formation of vascular niche is pivotal during the early stage of peripheral nerve regeneration. This antecedent angiogenesis meets the nutrient requirements for subsequent rapid axon regeneration and remyelination. Nevertheless, the mechanisms of vascular niche in the regulation of peripheral nerve remain unclear. The axon guidance molecule Netrin-1 (NTN1) is widely expressed in peripheral nerves and particularly was found up-regulated in sciatic nerve stump after peripheral nerve injury (PNI). Herein, we demonstrated that NTN1-high endothelial cells (NTN1+ECs) were the critical component of vascular niche, fostering angiogenesis, axon regeneration and repair-related phenotypes. And we also found that NTN1+ECs derived exosomes (NTN1 EC-EXO) were involved in the formation of vascular niche as a critical role. Multi-omics analysis further verified that NTN1 EC-EXO carried a low-level expression of let7a-5p and activated key pathways associated with niche formation including focal adhesion, axon guidance, PI3K-AKT signaling pathway and mTOR signaling pathway. Taken together, our findings suggested the potential construction of a pre-regenerative niche induced by NTN1 EC-EXO, thereby establishing a conductive microenvironment for nerve repair and facilitating the functional recovery after PNI in the early injury phase.

overall_design: 9 samples from rat sciatic nerves. The A1, A2 and A3 are sciatic nerves in sham group (sciatic nerves without crush injury); the B1, B2 and B3 are sciatic nerves 3 days post crush injury; the C1, C2 and C3 are sciatic nerves 7 days post crush injury


title: Netrin-1 engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair

overall_design:
6 samples from PC12 cells
EC = EXO ctrl (exosomes derived from ctrl endothelial cells)
EN = EXO loaded with NTN1 (exosomes derived from NTN1 high-expressed endothelial cells)
PC12-EC = PC12 cells treated with EXO ctrl
PC12-EN = PC12 cells treated with EXO loaded with NTN1


title: Farnesyltransferase inhibition overcomes the adaptive resistance to targeted therapies in oncogene-addicted non-small cell lung cancer

status: Public on May 17 2024

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

summary: Drug-tolerance has emerged as one of the major non-genetic adaptive processes driving resistance to targeted therapy (TT) in non-small cell lung cancer (NSCLC). However, the kinetics and sequence of molecular events governing this adaptive response remain poorly understood. Here, we used the FUCCI (fluorescence ubiquitination cell cycle indicator) system to perform real-time monitoring of the cell cycle dynamics the EGFR-mutant NSCLC cell line HCC4006, which was previously subcloned to minimize the presence of potential pre-existing resistant cells. We performed scRNAseq on G1 (red) and S/G2 (green) cells sorted from untreated (DMSO), osimertinib-treated and osimertinib+tipifarnib-treated cells to identify molecular mechanisms implicated in the adaptive response to TT and the sensitivity of drug-tolerant cells to tipifarnib.

overall_design: FUCCI-transduced HCC4006 subcloned cells were expanded in untreated (DMSO), osimertinib (1 µM) or osimertinib (1 µM)  + tipifarnib (1 µM)-containing medium for 4, 20 and 12 days respectively. Drug-containing medium was changed 24h before sorting. Cells were dissociated by trypsinisation, recovered in FACS buffer (0,04% BSA in PBS) and kept on ice. G1 (red) and S/G2 (green) cells were sorted at 4°C using FACS Melody (BD Biosciences).

first: Sarah

last: Figarol

first: Célia

last: Delahaye

first: Juan

last: Cerapio Arroyo

first: Gilles

last: Favre

first: Olivier

last: Calvayrac


title: Netrin-1 engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair [miRNA-seq EXO]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: 6 samples from HUVEC derived exosomes


title: Cellular adaptation to cancer therapy along a resistance continuum

summary:
This SuperSeries is composed of the SubSeries listed below.
Advancements in precision oncology over the past decades have led to new therapeutic interventions, but the efficacy of such treatments is generally limited by an adaptive process that fosters drug resistance. In addition to genetic mutations, recent research has identified a role for non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell-state transitions that occur in the adaptation to cancer therapies remain unknown and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell-state transitions accompanied by a progressive increase in cell fitness, which we denote as the 'resistance continuum'. This cellular adaptation involves a stepwise assembly of gene expression programmes and epigenetically reinforced cell states underpinned by phenotypic plasticity, adaptation to stress and metabolic reprogramming. Our results support the notion that epithelial-to-mesenchymal transition or stemness programmes-often considered a proxy for phenotypic plasticity-enable adaptation, rather than a full resistance mechanism. Through systematic genetic perturbations, we identify the acquisition of metabolic dependencies, exposing vulnerabilities that can potentially be exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell-state transitions.

overall_design: Refer to individual Series


title: Farnesyltransferase inhibition overcomes the adaptive resistance to targeted therapies in oncogene-addicted non-small cell lung cancer II

summary: Drug-tolerance has emerged as one of the major non-genetic adaptive processes driving resistance to targeted therapy (TT) in non-small cell lung cancer (NSCLC). However, the kinetics and sequence of molecular events governing this adaptive response remain poorly understood. Here, we performed transcriptomic profiling by RNAseq in a panel of EGFR-mutant NSCLC cell lines (PC9, HCC4006, H3255 and HCC827) that were previously subcloned to minimize the presence of potential pre-existing resistant cells. Cells were treated by either erlotinib (1 µM) or osimertinib (1 µM) for a short period (24h), until drug-tolerance (between 7 and 21 days), and until development of fully resistant proliferative cells (RPC).

overall_design: EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. PC9, HCC4006 and H3255 subclones were treated with DMSO (control) or with erlotinib at 1 µM for 24h, until drug-tolerance (7-to-21 days) or until development of fully resistant proliferative cells (RPC, only for PC9 and HCC4006 cells). RPC were isolated and amplified from individual early-emerging colonies, which were cultured and passaged for more than three months in the presence of the drug. HCC827 were treated with DMSO (control) or with osimertinib at 1 µM until drug-tolerance (11 days).


title: Polyadenylation of mRNAs encoding secreted proteins by TENT5 family of enzymes is essential for gametogenesis in mice

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: Cytoplasmic polyadenylation plays a vital role in gametogenesis, however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of 4 TENT5 poly(A) polymerases in mice fertility and gametogenesis.   TENT5B and TENT5C play crucial, but redundant roles in oogenesis, with double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP females display gain-of-function infertility effect with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, shown by sterility of males with either gene’s knockout mutation. Finally, Tent5a knockout significantly lowers fertility, although the underlying mechanism is not directly related to gametogenesis.   Through Direct RNA sequencing we discovered that TENT5 proteins polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motives analysis and reporter mRNA assay revealed that the presence of endoplasmic reticulum-leader represents the primary determinant of TENT5-mediated regulation.

overall_design: mRNA profiles from Tent5b-/- Tent5c -/- and WT female mice, generated by deep sequencing, in duplicate or triplicate, using Illumina NovaSeq 6000

first: Michał

last: Brouze

first: Agnieszka

last: Czarnocka-Cieciura

first: Olga

last: Gewartowska

first: Monika

last: Kusio-Kobiałka

first: Kamil

last: Jachacy

first: Marcin

last: Szpila

first: Bartosz

last: Tarkowski

first: Jakub

last: Gruchota

first: Paweł

last: Krawczyk

first: Seweryn

last: Mroczek

first: Ewa

last: Borsuk


title: Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: PDX]

first: Itai

last: Yanai

overall_design: The data refers to two sets of experiments using a patient derived xenograft model of high-grade serous ovarian cancer to study the cancer cell response to PARP inhibitor (talazoparib). In one set of experiments, we aimed to generate PARPi resistant tumors over three serial passages. Vehicles (2 replicates) and tumors from the first (2 replicates and third rounds (3 samples with 2 replicates) of treatment were collected for scRNA-Seq analysis. In a first round, mice were treated with a standard dose (0.33 mg/kg), which initially caused remission and treatment was interrupted. After an off-treatment period, tumors relapsed and treatment was re-introduced. Tumors did not respond to therapy upon relapse, thus indicating resistance (R1). One of the replicates (R1*) was reimplanted for a second round (R2) of treatment and this was followed by a third round (R3), both under continuous therapy. Again, tumors did not respond to therapy in both passages. In another set of experiments, PARPi (talazoparib) response was evaluated by treatment cohorts of mice (2 replicates each) with 4 doses (D1: 0.13 mg/kg , D2 0.23 mg/kg, D3: 0.33 mg/kg, D4: 0.66 mg/kg), plus untreated vehicles (2 replicates).

first: Gustavo

last: Starvaggi Franca

first: Timothee

last: Lionnet


title: The circular RNA circ_ATP8B regulates ROS production and antiviral immunity

status: Public on May 15 2024

city: St Petersburg

first: Rui

last: Zhou

state: FL

address: REB 4130, 501 6th Ave S

institute: Johns Hopkins University


title: Netrin-1 engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair [miRNA-seq]

first: Jinsheng

last: Huang

overall_design: 6 samples from PC12 cells


title: HIV-1 infection affects NAD capping of host cell snRNA and snoRNA

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

summary: NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. Interestingly, U1 snRNA was previously shown to be essential for HIV-1 replication. We provide evidence that the NAD cap reduces the stability of the U1 - HIV-1 pre-mRNA duplex. The importance of NAD RNA cap in HIV-1 infection was further supported by NAD decapping enzyme DXO overexpression, which led to increase in HIV-1 infectivity. This is the first example of NAD cap function in mammalian cells and suggests a general role of non-canonical RNA caps in antiviral innate immunity response.

overall_design: To identify RNAs with reduced NAD capping, we prepared four NAD captureSeq libraries from the sRNA fraction of MT4 noninfected and HIV-1 infected cells. NAD captureSeq relies on selective reaction of ADP-ribosyl cyclase (ADPRC) with 4-pentyn-1-ol and with NAD-RNA. After CuAAC reaction, the NAD capped RNA is tagged with biotin and captured on streptavidin beads. Captured RNA is then reversely transcribed and cDNA is used for preparation of NAD captureSeq library. To sort out non-specifically interacting RNA, ADPRC is omitted in negative control samples. To assess expression levels of sRNAs +/- HIV-1 infection, we generated sRNA-seq datasets from noninfected and HIV-1-infected MT-4 cells in triplicates.

first: Barbora

last: Benoni

first: Hana

last: Cahova


title: Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis

city: Tianjin

first: Ce

last: Song

address: Weijin road NO.94

institute: Nankai University

summary: Arabidopsis Lon1 serves dual roles as a mitochondrial protease and chaperone. Loss of Lon1 function reduced autophagy flux at transcriptional, protein and cellular levels. Meanwhile, changes occurred in the levels of cellular subunit proteins, especially a significant upregulation of mitochondrial proteins overall in lon1 mutants. Lon1 is a key enzyme in maintaining mitochondrial protein homeostasis. In lon1 mutants, other mitochondrial proteases including mitochondrial autophagy receptor proteins showed significant increases in abundance. Mitophagy is an important mechanism for cellular quality control. lon1-2atg5-1 double mutant were constructed to investigate how they cooperatively regulate mitochondrial protein homeostasis. Transcriptome sequencing results revealed that Lon1 inactivation led to widespread unfolded protein responses (UPRs) pathway activation in lon1-2atg5-1, consistent with lon1-2, while loss function of ATG5 inactivation did not affect mitochondrial homeostasis. The double mutant also exhibited independent plant phenotypes from single parents, yet more severe seed number and embryo development issues, suggesting an additive effect of lon1-2 and atg5-1. Protein Storage Vacuole (PSV) and oil body phenotypes also showed more severe developmental damage in the double mutants. Brassinosteroid (BR) acts as a key plant hormone controlling seed and embryo development. GO and KEGG analysis of genes simultaneously downregulated in lon1-2, atg5-1, and lon1-2atg5-1 revealed significant downregulation of genes involved in BR biosynthesis and its homeostasis, indicating that this may be one of the key factors leading to abnormal seed and embryo development in the mutants. In general, the loss function of Lon1 reduces autophagy flux and induces UPRs to regulate protein homeostasis. Meanwhile, the simultaneous absence of Lon1 and autophagy significantly down-regulates the expression of genes related to BR biosynthesis and homeostasis, thereby leading to pronounced blockage in the development of double mutant seeds and embryos.

overall_design: Arabidopsis thaliana is Columbia-0 (Col-0) background. T-DNA insertion mutant lon1-2 (AT5G26860, SALK_012797), atg5-1 (AT5G17290, SAIL_129_B07) and lon1-2atg5-1 double mutant are owned by our laboratory. Arabidopsis grown best under 16/8 hours light / dark cycle at room temperature (18-22 ° C), with light intensity of 120-150 µ mol / m2 (normal conditions). Seven-day-old seedlings were harvested in biological triplicate under normal conditions. Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (DNBSEQ-T7) and 125bp/150bp paired-end reads were generated.

first: Lei

last: Li


title: RNAseq and WGBS of Vaccinium corymbosum

status: Public on May 20 2024

city: Beijing

first: Zejia

last: Wang

address: Yanyuan Street

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: We did whole-genome methylation sequencing for 21 Vaccinium samples. This project attempts to analyze the improvement breeding process of cultivated blueberry from two aspects of heredity and epigenetic inheritance.

sample_organism:
Vaccinium corymbosum
Vaccinium darrowii

platform_organism:
Vaccinium corymbosum
Vaccinium darrowii

overall_design: This dataset contains RNA-seq and WGBS data of cultivated blueberries.

first: Qikun

last: Liu


title: Transcriptomic profiling of thymic dysregulation and viral tropism after neonatal roseolovirus infection

city: Saint Louis

first: Andrei

last: Belean

state: Missouri

address: 4939 Children’s Place

department: IM-Rheumatology

institute: Washington University in Saint Louis

summary: Herpesviruses, including the roseoloviruses, have been linked to autoimmune disease. The ubiquitous and chronic nature of these infections as well as the temporal dissociation between acute infection and autoimmune disease onset have made establishing a causal association challenging. We have shown that murine roseolovirus (MRV), which is highly related to human roseoloviruses, induces thymic atrophy and disruption of central tolerance after neonatal infection. Moreover, neonatal MRV infection results in development of autoimmunity in adult mice, long after resolution of acute infection. This suggests that MRV induces durable immune dysregulation. In these studies, we utilized single-cell RNA sequencing (scRNAseq) to study the tropism of MRV in the thymus and determine cellular processes in the thymus that were disrupted by neonatal MRV infection. We then utilized tropism data to establish a cell culture system. Herein, we describe how MRV alters the thymic transcriptome during acute neonatal infection.We found that MRV infection results in major shifts in inflammatory, differentiation and cell cycle pathways in the infected thymus. We also observed shifts in the relative number of specific cell populations. Moreover, utilizing expression of late viral transcripts as a proxy of viral replication we identified the cellular tropism of MRV in the thymus. This approach demonstrated that double negative, double positive, and CD4 single positive thymocytes, as well as medullary thymic epithelial cells were infected by MRV in vivo. Finally, by applying pseudotime analysis to viral transcripts, which we refer to as "pseudokinetics," we identified viral gene transcription patterns associated with specific cell types and infection status. We applied this information to establish the first cell culture systems susceptible to MRV infection in vitro. Our research provides the first complete picture of MRV tropism in the thymus after neonatal infection. Additionally, we identified major transcriptomic alterations in cell populations in the thymus during acute neonatal MRV infection. These studies offer important insight into the early events that occur after neonatal MRV infection that disrupt central tolerance and promote autoimmune disease

overall_design: Mice were injected on Day of Life (DoL)  with either an MRV infection or a saline solution (Mock). Thymi were harvested on DoL6 for scRNA sequencing.

first: Bigley

last: Tarin

first: Michael

last: Paley

first: Elisha

last: Roberson


title: Interfering with aggregated α-synuclein in advanced melanoma leads to a major upregulation of MHC class II proteins

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Melanoma is the most serious and deadly form of skin cancer and with progression to advanced melanoma, the intrinsically disordered protein α-synuclein is upregulated to high levels; and while toxic to dopaminergic neurons in Parkinson’s disease, it is highly beneficial for primary and metastatic melanoma cells. To gain detailed insights, both at the level of the proteome and the transcriptome, into this exact opposite role of α-synuclein in advanced melanoma, we performed proteomic studies of high-level α-synuclein-expressing primary and metastatic human melanoma cell lines and proteomic and transcriptomic studies of metastatic human melanoma xenografts treated systemically with the diphenyl-pyrazole small-molecule compound anle138b, which binds to and interferes with the oligomeric structure of α-synuclein. The results of these studies reveal that interfering with oligomerized α-synuclein in these tumor xenografts led to a substantial upregulation of expression of major histocompatibility complex proteins in the melanoma cells, the latter of which is pertinent to enhancing anti-melanoma immune responses.

overall_design: RNA-seq analysis of WM983-B human melanoma tumor xenografts treated systemically with the diphenyl-pyrazole small-molecule compound anle138b, which binds to and interferes with the oligomeric structure of α-synuclein

first: Claudia

last: Fokken

first: Ivan

last: Silbern

first: Orr

last: Shomroni

first: Kuan-Ting

last: Pan

first: Sergey

last: Ryazanov

last: Leonov

first: Nadine

last: Winkler

first: Henning

last: Urlaub

first: Christian

last: Griesinger

first: Dorothea

last: Becker


title: Generation and characterization of mature hepatocyte organoids for liver metabolic studies

city: Boston

first: Yuchen

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

summary: The liver plays a central role in whole body metabolic regulation. Studies of liver metabolism are mostly done in vivo in animal models due to the lack of reliable in vitro systems that can recapitulate liver metabolic functions and their regulation. Hepatocyte organoids (HOs) generated in vitro recently are powerful tools for liver regeneration. Here we developed a novel culture condition that enabled successful generation of mature hepatocyte organoids (MHOs) with metabolic functions characteristic of adult livers. We showed that the MHOs can be used to study gene expression that exhibit zonal patterns in vivo, hepatic proliferation during tumorigenesis and metabolic alterations in disorders of both alcoholic and non-alcoholic fatty liver diseases.

overall_design: To induce hepatic maturation of HOs, several culture conditions were tested in the experiments. The HOs were switched to the maturation medium for HO maturation. Samples were collected on day 3, day 6, and day 12 after the medium switch. Each sample group has three replicate samples.

first: Yingzi

last: Yang


title: MHV68 ORF50stop Vaccine Gene Expression

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: RNA-sequencing from MHV68 ORF50 stop and WT virus infected 3T12 cells (timepoint) post infection.

sample_organism:
Mus musculus
Murid gammaherpesvirus 4

platform_organism:
Mus musculus
Murid gammaherpesvirus 4

overall_design: Triplicate samples of ORF50 stop and WT virus infected cells, total of 6 samples.

first: Chad

last: Hogan

first: Varvara

last: Kirillov

first: Laurie

middle: T

last: Krug


title: Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus [midbrain]

first: Lucia

last: Franchini

summary: A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human Accelerated Regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The RBFOX1 locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here we examined the role of RBFOX1-HARs using transgenic zebrafish reporter assays and identified fifteen transcriptional enhancers that are active in the developing nervous system, ten of which displayed differential expression between the human and chimpanzee sequences. The engineered loss of two selected RBFOX1-HARs in knockout mouse models increased Rbfox1 expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of Rbfox1 target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by RBFOX1-HARs.

overall_design: Midbrains were extracted from Rbfox1 ΔHAR.321/ΔHAR.321 and Rbfox1 +/+ mice at 14.5 embryonic (E14.5) days, with five independent biological samples per genotype.


title: Neoadjuvant sintilimab plus chemotherapy in early-stage EGFR-mutant NSCLC: phase 2 trial interim results (NEOTIDE/CTONG2104)

first: Yuxuan

last: Sun

address: Yiheyuan Road

summary: We launched an investigator-initiated, Simon’s two-stage design trial of neoadjuvant sintilimab combined with carboplatin and nab-paclitaxel (nab-PC) in early-stage EGFR-mutant NSCLC (Clinicaltrial.gov number NCT05244213). Here we report the first interim results of stage 1 cohort which met the overall primary endpoint in advance, and multi-omics profiling of neoadjuvant immunotherapy combination in early-stage EGFR-mutant patients. We performed in-depth single-cell RNA/TCR sequencing (scRNA/TCR-seq) of cells derived from 11 resected tumors as well as 34 tumors from real-world cohort which were all confirmed wild-type lung adenocarcinoma (LUAD) or adeno-squamous carcinoma (ASC) and received neoadjuvant immunochemotherapy as control. By associating the tumor microenvironment (TME) and with responses, we uncovered heterogeneous mechanisms of primary resistance, providing insights into further strategic developments of combination regimens to improve the clinical outcome of EGFR-mutant NSCLC patients.

overall_design:
Non-erythrocytic living cells of 11 EGFR-mutant non-small cell lung cancer (NSCLC) and 34 wild-type lung adenocarcinoma (LUAD) or adeno-squamous carcinoma (ASC) that received neoadjuvant immunochemotherapy were isolated by gating 7AAD−CD235a− cells using Fluorescence-activated cell sorting (FACS), and analyzed using  scRNA/TCR-seq.

>>>Submitter states that the raw data will be submitted to GSA.<<<

first: Wenzhao

last: Zhong

first: Chao

last: Zhang

first: Dingcheng

last: Yi

first: Benyuan

last: Jiang


title: RNA-seq analysis of B cells cultured with LPS and IL-12 and/or IFN gamma

city: Pittsburgh

first: Mark

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose: We aimed to find genes differentially regulated by IL-12 and IFNg alone, and in combination, over 4 and 24 hours of stimulation.
Methods : Spleens were processed and B cell cultures prepared, in triplicate, according to the manuscript. After the indicated times, cells were washed in PBS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C.
Results: At 4 hours, the main effect of IL-12 is to induce IFNg production from B cells, whereas IFNg induces many gene changes. Comparing 24 hours to the 4 hour stimulation, IFNg alone was insufficient to maintain the majority of IFNg-induced 4 hour changes, while adding IL-12 sustained a portion of the 4 hour gene changes. Additionally, in combination IL-12 and IFNg cooperate to induce unique gene changes that are not shared with either the individual cytokines at either timepoint.

overall_design: We used recombinant IL-12 and IFNg or anti-IL-12 and anti-IFNg blocking antibodies to assess the contribution of each cytokine alone and in combination.

first: Rebecca

last: Elsner

first: Shuchi

last: Smita


title: Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer [Spatial transcriptomics on de-identified human ONB samples]

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

summary: The olfactory epithelium relies on active neuron regeneration from basal stem cells and is susceptible to olfactory neuroblastoma (ONB), a rare, aggressive tumor of unclear origins. Here, we establish a new, highly-penetrant, genetically-engineered mouse model of ONB with alterations in Rb1/Trp53/Myc that exhibit a NEUROD1+ immature neuronal state. ASCL1 loss leads to emergence of non-neuronal histopathologies, including a POU2F3+ microvillar-like state. We find ONB tumor heterogeneity to recapitulate developmental states of multipotent globose basal cells (GBCs), which our data demonstrate is a cell of origin for ONB. Similar to small cell lung cancer (SCLC), mouse and human ONB exhibit: mutually exclusive ASCL1, NEUROD1, and POU2F3- like states, an immune-cold tumor microenvironment, intratumoral subtype heterogeneity comprising neuronal and non-neuronal lineages, and subtype plasticity—as evidenced by barcode-based lineage tracing and single-cell transcriptomics. Collectively, our findings highlight conserved developmental trajectories between ONB and SCLC subtypes with significant implications for ONB classification and treatment.

overall_design:
We performed multiplexed and spatially resolved transcriptomic profiling using the NanoString GeoMx digital spatial profiling (DSP) platform, with mostly default parameters. 5 µm sections from high quality archival ONB tissue blocks was mounted on glass slides for profiling. In total, we included 12 seperate ONB specimens, and 1 normal control OE. Two adjacent sections were cut and positioned on separate slides to allow for side-by-side H&E comparison. Following deparaffinization, antigen retrieval was performed with Tris-EDTA buffer (pH 9.0) in a steamer for 20 min. Slides were then incubated for 15 min at 37°C in PBS buffer with 0.1 µg/mL proteinase K for RNA target exposure. In situ hybridization was conducted by incubating slides with GeoMx Human Whole Transcriptome Atlas Probe Mix (NanoString) overnight at 37°C. Slides were then stained with fluorescence-conjugated morphology markers for two hr at RT with the following labels: Syto 83 nuclear dye (NanoString) 250nM, CD45-532 (NovusBio cat# NBP2-34528AF532) 7.50µg/mL, TUBB3-594 (Biolegend, cat# 657408) 1:50, KI67-647 (CST cat# 12075) 1:100. Slides were then loaded on the NanoString GeoMx DSP instrument, and 2-3 representative ROIs in spatially distinct locations were selected based on tumor morphology and antibody staining markers. In general, ROIs were 200-600µm in diameter, and contained 100-300 nuclei. Note, some tumor specimens also contained normal overlying OE, which was captured for controls. ROIs were then segmented based on morphology markers, and RNA probe oligos were photocleaved and collected in the following order: CD45, KI-67, TUBB3, negative. Oligos were then processed for library preparation according to the standard Nanostring protocol, with the exception that beads were dried for 1 min instead of 5. DNA libraries were sequenced on an Illumina NovaSeq 6000 S-Prime flow cell with a read length of 2x27bp and a 5% PhiX spike-in by volume. Output .fastq files from sequencing runs were converted to .dcc using the GeoMx NGS Pipeline with default parameters.

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

first: John

last: Finlay

first: Bradley

last: Goldstein


title: Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer [Single cell RNA seq on RPM and RPMA GBC-derived allograft tumors, CellTagged]

overall_design: We harvested normal globose basal cells (GBCs) via immunomagnetic selection for KIT from the pooled olfactory epithelium of n=3-4 Rb1 fl/fl; Trp53 fl/fl; Myc T58A (RPM) or Rb1 fl/fl; Trp53 fl/fl; Myc T58A; Ascl1 fl/fl (RPMA) mice, not exposed to Cre, 10 days following methimazole lesioning. RPM and RPMA GBCs were transformed by treatment with Cre and transduced with a lentiviral barcode-based lineage-tracing technology termed CellTag V1 (established by Samantha Morris's lab, Kong et al., Nature Protocols, 2020). Transformed, CellTagged  GBC's were  implanted with Matrigel into the flanks of Scid/Beige mice.  Upon outgrowth of the GBC-organoid-derived allografts, tumor cells were collected and  processed for single-cell RNA sequencing. Allograft tumors were processed into single cell suspensions, and subject to  10X Genomics single-cell gene expression library construction (Dual-Index 3' GEX) followed by downstream Illumina-based sequencing.

first: Abbie

last: Ireland


title: Myelin-reactive B cells exacerbate the severity of CD4+ T cell-driven CNS autoimmunity in an IL-23-dependent manner

status: Public on May 14 2024

city: Quebec

first: Reda

last: Fazazi

state: Qc

address: 2705 blvd Laurier

country: Canada

institute: Laval University

summary: B cells and T cells collaborate in multiple sclerosis (MS) pathogenesis. IgH[MOG]mice possess a B cell repertoire skewed to recognize myelin oligodendrocyte glycoprotein (MOG). Here, we show that upon immunization with the T cell-obligate autoantigen, MOG[35-55], IgH[MOG] mice develop rapid and exacerbated experimental autoimmune encephalomyelitis (EAE) relative to wildtype (WT) counterparts, characterized by aggregation of T and B cells in the IgH[MOG] meninges and by CD4+T helper 17 (Th17) cells in theCNS. Unusually, production of the Th17 maintenance factor IL-23 is observed from IgH[MOG]CNS-infiltrating and meningeal B cells, andin vivoblockade of IL-23p19 attenuates disease severity in IgH[MOG] mice. In the CNS parenchyma and dura mater of IgH[MOG] mice, we observe an increased frequency of CD4+PD-1+CXCR5-T cells that share numerous characteristics with the recently described T peripheral helper (Tph) cell subset. Further, CNS-infiltrating B and Tph cells from IgH[MOG] mice show increased reactive oxygen species (ROS) production. Meningeal inflammation, Tph-like cell accumulation in the CNS and B/Tph cell production of ROS were all reduced upon p19 blockade. Altogether, MOG-specific B cells promote autoimmune inflammation of the CNS parenchyma and meninges inan IL-23 dependent manner.

overall_design: B220+ B cells and CD4+PD1+CXCR5- (Tph cells) were sorted from the CNS of IgH[MOG] mice and WT control at peak EAE to perform mRNA sequencing.

first: Mohamed Reda

first: Manu

last: Rangachari


title: Integration of ATAC and RNA-Sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [ATAC]

city: Muenster

first: Kleio

last: Petratou-Busswinkel

address: Röntgenstraße 16

institute: Institute for Cardiovascular Organogenesis and Regeneration

summary: Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation, and notochord sheath cells, which serve as non-classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research, the genetic regulation of bone formation, as well as mechanisms of transcriptional control of entpd5a, remain largely unknown. Here, using a newly generated transgenic line, we isolate classical and non-classical osteoblasts from zebrafish embryos and performed both ATAC-Seq and RNA-Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation, Hox family factors are involved in governing spinal ossification via non-classical osteoblasts. We further present a resource-driven analysis of the entpd5a promoter, experimentally validating the ATAC-Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio-temporally regulated promoter/enhancer interactions taking place in the entpd5a locus.

overall_design:
We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head (classical) and trunk (non-classical) osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC-Seq and RNA-Seq and analysed data at first individually, to establish open chromatin regions and gene expression profiles, respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.

***3 Samples lack raw data --GSM8264132, GSM8264135, and GSM8264141***

first: Petratou

last: Kleio

first: Schulte-Merker

last: Stefan


title: Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer

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: Dorsomorphin (DM) inhibits AMPK, upregulates Wnt and Foxo genes and promotes activation of dormant follicles

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: We record the application of RNA sequencing of murine ovarian follicles +/- DM

overall_design: Differential gene expression comparison

first: Julie

last: Madsen

first: Karin

last: Lykke-Hartmann


title: The circular RNA circ_ATP8B regulates ROS production and antiviral immunity [RNA-Seq]

first: Rui

last: Zhou

summary: Circular RNAs (circRNAs) are widely expressed in eukaryotes. However, only a subset has been functionally characterized. We have identified and validated a collection of circular RNAs in Drosophila melanogaster. We show that the circular RNA circ_ATP8B is induced by viral infection and that depletion of circ_ATP8B, but not its linear sibling, compromises viral infection both in cultured cells and in vivo. In addition, our analyses reveal that circ_ATP8B is enriched in the fly gut and that gut-specific depletion of circ_ATP8B attenuates viral replication in an oral infection model. Furthermore, we find circ_ATP8B-depletion resulted in increased levels of reactive oxygen species (ROS) and enhanced expression of Duox (Dual oxidase), which produces ROS. Genetic and pharmacological manipulation of circ_ATP8B-depleted flies that reduce ROS levels rescue the viral replication defects elicited by circ_ATP8B depletion. Notably, circ_ATP8B and Duox associate with each other, and that expression of various versions of circ_ATP8B that are competent in binding Duox, but not a mutant circ_ATP8B that is incapable of binding Duox, restores physiological levels of ROS in circ_ATP8B-depleted cells. Lastly, our data show that Gaq, a subunit of G protein required for optimal Duox activity, acts downstream of circ_ATP8B to regulate Duox activity. We conclude that circ_ATP8B regulates anti-viral immunity by modulating Duox-dependent ROS production.

overall_design: This study aims to identify RNAs that are differentially expressed upon depletion of the circular RNA circ_ATP8B in vivo. Flies carrying a shRNA transgene against circ_ATP8B or a control shRNA transgene against GFP were crossed to flies carrying the ubiquitously expressed Actin (Act)-Gal4 driver. Total RNAs were extracted from 4-7 day old male and female Act>shGFP and Act>sh-circ_ATP8B flies and subjected to RNA-seq to identify genes that are impacted by circ_ATP8B depletion.

first: Weihong

last: Liang

first: Wei

last: Liu

first: Xiao

last: Xiong

first: Jennifer

last: Li

first: Jian

first: Ranjan

last: Perera


title: ATAC-seq of bone marrow ILC2 lineages and Lung ILC2 steady state

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

address: 1-8-1 Inohana, Chuou-ku

department: Department of Allergy and Clinical Immunology

country: Japan

institute: Chiba University

summary: ATAC-seq were performed for bone marrow ILC2 lineages and lung ILC2 of C57BL/6 mice and G3SEKO mice.

first: Hiroki

last: Furuya

first: Yosuke

last: Toda


title: Single cell RNA sequencing for α lymphoid progenitor

summary: The single-cell transcriptional analysis of bone marrow progenitors and subsequent analysis revealed that GATA3 induction in late ILC2-committed precursor depends on the G3SE lesion and that the upregulation of GATA3 in the late ILC2-precursor is required for the transition to mature ILC2.

overall_design: Single cell RNA-sequencing was performed in α lymphoid progenitor of WT mice and G3SEKO (GATA3-related tandem Super-Enhancers Knock-Out) mice


title: UPF1 is required for gene expression in mitochondria and for the elimination of paternal mtDNA

status: Public on May 10 2024

city: Birmingham

first: Matthew

last: Wright

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary: UPF1 is a well-conserved RNA helicase in eukaryotes, involved in nuclear and cytoplasmic processes of gene expression. This study presents ChIP-seq evidence for its RNA-dependent association with mtDNA transcription sites in Drosophila S2 cells, and RNA-seq data indicating its requirement for the correct expression of mtDNA genes. UPF1 localisation in mitochondria was observed by immunostaining and GFP-tagging in different fly tissues and cell types. During spermatogenesis, depletion of UPF1 but not of other NMD factors, resulted in major defects in meiosis and cytokinesis, leading to complete sterility. Notably, the few spermatids produced show abnormalities in the formation of the nebenkern and, unlike the wild type, retain the mtDNA.

overall_design: To investigate transcriptomic changes in salivary gland cells, when depleted of UPF1, UPF2 and UPF3 by UAS induction of shRNA targeting the respective mRNA, and to investigate transcriptomic changes in Drosophila S2 cells, when depleted of UPF1

first: Anand

middle: K

last: Singh

first: Hannah

last: Dixon

first: Emily

last: Price

first: Elizabeth

middle: C

last: Connolly

first: Alessandro

last: di Maio

first: Jonathon

last: Barlow

first: Marco

last: Catoni

first: Yun

last: Fan

first: Saverio

last: Brogna


title: SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (RNA-Seq)

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

summary: Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. Epigenetic changes were more apparent in animals with longer periods of untreated SIV infection and correlated well with changes in corresponding gene expression. Known SIV integration sites did not vary due to SIV status but did contain more open chromatin in rhesus macaque memory T cells, and the expression of proteasome-related genes at the pre-SIV timepoint correlated with subsequent viremia.

sample_organism:
Macaca mulatta
Macaca nemestrina

platform_organism:
Macaca mulatta
Macaca nemestrina

overall_design: RNAseq and ATACseq of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in rhesus macaques and pig-tail macaques prior to SIV infection, during chronic SIV infection, and after administration of ARVs.

first: Andrew

middle: R

last: Rahmberg

first: Tovah

last: Markowitz

first: Joseph

last: Mudd

first: Alexandra

middle: M

last: Ortiz


title: The circular RNA circ_ATP8B regulates ROS production and antiviral immunity [circRNA-Seq]

first: Rui

last: Zhou

address: REB 4130, 501 6th Ave S

overall_design: This study aims to identify circular RNAs that are differentially expressed upon viral infection. Total RNAs were extracted from cultured Drosophila SL2 cells that were either uninfected or infected with Flock House virus. Ribosomal RNAs and linear RNAs were removed and the enriched circular RNA fraction was subjected to RNA-seq to identify circular RNAs.

first: Weihong

last: Liang

first: Wei

last: Liu

first: Xiao

last: Xiong

first: Jennifer

last: Li

first: Jian

first: Ranjan

last: Perera


title: Spatial transcriptomic profiling of Patient and Patient-corrected bioengineered vascular grafts.

status: Public on May 08 2024

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

summary: Spatial transcriptomic profiling of two replicates of Patient and two replicates of Patient-corrected bioengineered vascular grafts harvested at week 8 post-implantation.

overall_design: A Loeys-Dietz syndrome-associated pathogenic variant in Patient induced pluripotent stem cells (PatientA230T/+) was corrected using CRISPR/Cas9 gene editing resulting in Patient-corrected (Patient+/+) cells. Patient-corrected (Patient+/+) samples are denoted as iWT in the sample identifiers. The resulting human induced pluripotent stem cells were differentiated into smooth muscle cells through cardiovascular progenitor cells. The smooth muscle cells were seeded on meshes to generate bioengineered vascular grafts. The bioengineered vascular grafts  were implanted into nude rats and were harvested at week 8 post-implantation. Formalin-Fixed Paraffin-Embedded (FFPE) sections of the harvested vascular grafts were processed using 10X Visium Spatial Gene expression for FFPE. Human transcriptome probe kit was used for the gene expression measurements.


title: Single-cell transcriptome profiling of zebrafish pancreatic beta-cells segregated by CaMPARI-based calcium labeling.

status: Public on May 07 2024

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: Coordination of cell activity trough Ca2+ waves enables pancreatic β-cells to secrete precise quantities of insulin in response to blood sugar. However, how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single-molecule RNA detection, we reveal a gene-signature depicting a molecularly and metabolically distinct state of first responder β-cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder β-cells .

overall_design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence-activated cell sorting (FACS) The primary islets from 4 months post-fertilization Tg(ins:CaMPARI) animals were dissected from the fish after euthanasia.  Each islet was placed in a well of 24-well plate with 5 ml of DPBS medium supplemented with calcium, magnesium (ThermoFisher, 14040141), along with the appropriate concentration of D-Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently, the entire 24-well plate was photoconverted using a 405 nm LED array (Loctite, 1167593) for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller (Loctite, 1359255) was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE (ThermoFisher, 12563029) at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation, TrypLE was inactivated with 10% FBS, and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded, and the pellet re-suspended in 500 µl of HBSS (without Ca2+, Mg2+).  To remove debris, the solution was passed over a 30 µm cell filter (Miltenyi Biotec, 130-041-407).  To remove dead cells, calcein violet (ThermoFisher, C34858) was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC (Fluorescein isothiocyanate) for green fluorescence; and PE (Phycoerythrin) for red fluorescence.  Single-cell RNA-Sequencing For single-cell RNA-Seq, β-cells isolated from Tg(ins:CaMPARI) islets were subjected to profiling using Smart-Seq2 protocol from Takara.  For this, islets were isolated, photoconverted ex vivo, dissociated and FAC-sorted as described above.  β-cells were collected from two conditions: responsive β-cells displaying photoconversion at 2.5 mM; and non-responsive β-cells without photoconversion at 16.5 mM.  Photoconversion was defined as a high red-to-green ratio.  For FACS of each condition, index sorting was utilized, and the cells were collected in 96-well plate containing lysis buffer (2 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB)).  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication (Singh et al., Scientific Reports, 2018; doi: 10.1038/s41598-018-35218-5).

first: Nikolay

last: Ninov


title: IRF2BP2 counteracts the ATF7/JDP2 heterodimer to prevent inflammatory overactivation in AML cells.

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg


title: A Single Cell RNA Sequence Atlas of the Early Drosophila Larval Eye

city: Houston

first: Komal Kumar

last: Bollepogu Raja

state: TX

address: One Baylor plaza

department: Pathology and Immunology

country: USA

institute: baylor college of medicine

summary: TheDrosophilaeye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis. However, a single cell RNA sequence resource that captures gene expression dynamics from the initiation of differentiation to the specification of different cell types in the larval eye disc is lacking. Here, we report transcriptomic data from 13,000 cells that cover six developmental stages of the larval eye. Our data show cell clusters that correspond to all major cell types present in the eye disc ranging from the initiation of the morphogenetic furrow to the differentiation of each photoreceptor cell type as well as early cone cells. We identify dozens of cell type-specific genes whose function in different aspects of eye development have not been reported. These single cell data will greatly aid research groups studying different aspects of early eye development and will facilitate a deeper understanding of the larval eye as a model system.

overall_design: The Drosophila larval eye disc was dissected and dissociated into single cells using collagensae and dispase.

first: Komal

first: Kelvin

last: Yeung

first: Yumei

last: Chen

first: Graeme

last: Mardon


title: Rapid systemic responses of Arabidopsis to waterlogging stress are mediated by the ROS wave

status: Public on May 06 2024

city: Columbia

first: Pallav

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

summary: We show that an abrupt waterlogging treatment of Arabidopsis thaliana plants triggers a systemic ROS and calcium wave response, and that the waterlogging-triggered ROS wave response is dependent on RBOHD, calcium-permeable channels GLR3.3 and GLR3.6, and aquaporin PIP2;1 proteins. We further show that waterlogging stress is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation and is partially dependent on RBOHD. Interestingly, the abrupt waterlogging stress resulted in the triggering of a rapid hydraulic wave response and the transient opening of stomata on leaves. Taken together, our findings reveal that the initiation of waterlogging stress in plants is accompanied by rapid systemic transcriptomic and physiological responses that involve the ROS, calcium, and hydraulic waves. These findings reveal that systemic plant responses to waterlogging stress are rapid and at least partially dependent on cell-to-cell signaling mechanisms.

overall_design: 30 samples were analyzed; included two genotypes (Col-0 and rbohD); 4 time points for Col-0 (0,10,30,60 min) and 2 time points for rbohD (0 and 60 min); systemic leaves; 3 repeats composed from 15 plants for each genotype in each time point; Col-0 and 0min were control/reference samples

first: M

last: Peláez-Vico

first: A

last: Tukuli

first: P

first: D

last: Mendoza-Cózatl

first: T

last: Joshi

first: R

last: Mittler


title: Fetal brain response to maternal inflammation requires microglia [Maternal_Inflammation]

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: In utero infection and maternal inflammation can adversely impact fetal brain development. Maternal systemic illness, even in the absence of direct fetal central nervous system infection, is associated with an increased risk of autism and schizophrenia in affected offspring. The cell types mediating the response of the fetal brain to maternal inflammation are largely unknown, hindering the development of therapies to prevent and treat adverse neuropsychiatric outcomes. Here, we show that microglia are enriched for expression of receptors for relevant pathogens and cytokines throughout embryonic development.

overall_design: We injected pregnant mice with either poly(I:C) to induce maternal immune activation, or saline controls. We isolated microglia from the somatosensory (S1) cortex of the pups at E13, E15, and P14, and performed single-cell RNA sequencing to asses microglial subtypes and response to maternal immune activation. We also performed single-nucleus RNA sequencing of the developing S1 cortex at E15.5 in Csf1r null mice and wild-type littermate controls after maternal poly(I:C) or saline injection at E12.5.

first: Bridget

last: LaMonica Ostrem

first: Jeffrey

last: Stogsdill

first: Tyler

last: Faits

first: Nuria

last: Dominguez Iturza

first: Kwanho

last: Kim

first: Aviv

last: Regev

first: Joshua

middle: Z

last: Levin


title: Fetal brain response to maternal inflammation requires microglia [Developing_Microglia]


title: The tissue-resident regulatory T cell pool is shaped by transient multi-tissue migration and a conserved residency program. scRNA-Seq profiling of mouse tissue Tregs with TCR sequencing and CITE-Seq

status: Public on May 03 2024

first: Adrian

last: Liston

address: Tennis Court Road

institute: University of Cambridge

summary: The tissues are the site of many important immunological reactions, yet how the immune system is controlled at these sites remains opaque. Recent studies have identified Foxp3+ regulatory T cells (Tregs) in non-lymphoid tissues, with unique characteristics compared to lymphoid Tregs. However, tissue Tregs have not been considered holistically across tissues. Here we performed a systematic analysis of the Treg population residing in non-lymphoid organs throughout the body, revealing shared phenotypes, transient residency and common molecular dependencies. Tissue Tregs from different non-lymphoid organs shared T cell receptor (TCR) sequences, with functional capacity to drive multi-tissue Treg entry, and were tissue-agnostic on tissue homing. Together these results demonstrate that the tissue-resident Treg pool in most non-lymphoid organs, other than the gut, is largely constituted by broadly self-reactive Tregs, characterised by transient multi-tissue migration. This work suggests common regulatory mechanisms may allow pan-tissue Tregs to safeguard homeostasis across the body.

overall_design: scRNA-Seq was performed using 10x Genomics 5’ VDJ Single Cell Immune Profiling. Tregs were flow sorted on a BD Influx, Aria, Jazz or Fusion on the basis of CD4+Foxp3Thy1.1+ i.v.CD45- CD19-CD11b-CD8-F4/80-. Cells were labeled with Hashtag TotalSeq regents and loaded onto the 10x Chromium Controller. Sequencing was performed on an Illumina HiSeq. Data was processed in R using scripts as detailed below.

first: Oliver

last: Burton

first: Vaclav

last: Gergelits

first: Orian

last: Bricard


title: Inactivation of mitochondrial complex IV in Physcomitrium patens reveals the essential role of respiration in coordinating plants metabolism.

city: Padova

first: Tomas

last: Morosinotto

address: Via Ugo Bassi 58b

department: Department of Biology

country: Italy

institute: University of Padova

summary: Photosynthetic organisms use sunlight as energy source but rely on respiration during the night and in non-photosynthetic tissues. Respiration is also active in photosynthetically active cells, where its role is still unclear due to a lack of viable mutants. We previously isolated plants lacking a functional complex I (ndufa5). Plants lacking cytochrome c oxidase (complex IV) activity are generally lethal but were here isolated exploiting the possibility of generating knockout lines through vegetative propagation in the moss Physcomitrium patens.  ndufa5 plants showed alterations in carbon and nitrogen metabolism that are consistent with those reported in other Complex I mutants in vascular plants. One of the general features of Complex I-deficient plants, that was observed also in ndufa5, is the induction of the alternative oxidase (AOX). We found the metabolic alterations and the AOX induction in ndufa5 to be more severe by the end of the night than during day. The transcriptome of ndufa5 plants suggests that mitochondria-to-nucleus retrograde signalling pathways are strongly induced by the end of the night, which are probably mediated by a homolog of the transcription factor ANAC017, described in vascular plants.  cox11 mutants showed severely impaired growth, with an altered composition of the respiratory apparatus and increased electron transfer through the alternative oxidase. The light phase of photosynthesis remained largely unaffected while the efficiency of carbon fixation was moderately reduced. Transcriptomic and metabolomic analyses showed that the disruption of the cytochrome pathway had broad consequences for carbon and nitrogen metabolism. A major alteration in nitrogen assimilation was observed with a general reduction in amino acid abundance. A partial rescue of the growth could be obtained by growing the plants with an external supply of amino acids but not with sugars, demonstrating that respiration in plant photosynthetic cells plays an essential role at the interface between carbon and nitrogen metabolism and a key role in providing carbon skeletons for amino acid biosynthesis.

overall_design: To investigate the role of respiration, we generated NDUFA5 KO and COX11 KO  lines by exploiting homologous recombination in P. patens. A segment of the NDUFA5 or COX11 gene was disrupted by an antibiotic resistance cassette. Two independent NDUFA5 KO and two independent COX11 KO lines were used in this experiment. The transcriptome of WT, NDUFA5 KO and COX11 KO plants was studied at three different zeitgeber times (ZT0, ZT2, ZT6).

first: Antoni

last: Vera-Vives

first: Marco

last: Mellon

first: Anna

last: Segalla

first: Edoardo

last: Bizzotto

first: Stefano

last: Campanaro

first: Alessandro

last: Alboresi


title: IRF2BP2 counteracts the ATF7/JDP2 heterodimer to prevent inflammatory overactivation in AML cells [ChIP-seq]

first: Robert

last: Liefke

summary: Acute myeloid leukemia (AML) is a hematological malignancy characterized by abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of cell-intrinsic inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that IRF2BP2 interacts with the AP-1 heterodimer ATF7/JDP2, which is involved in activating inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene-activating function. Loss of IRF2BP2 leads to overactivation of inflammatory pathways, resulting in strongly reduced proliferation. Our research indicates that a precise equilibrium between activating and repressive transcriptional mechanisms creates a pro-oncogenic inflammatory environment in AML cells. The ATF7/JDP2-IRF2BP2 regulatory axis is likely a key regulator of this process and may, therefore, represent a promising therapeutic vulnerability for AML. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.

overall_design: ChIP-Seq of IRF2BP2 and ATF7 in THP1 cells. Experiments were performed in widltype cells, and cells that were ATF7 and JDP2 were knockout.

first: Sabrina

last: Fischer

first: Bastian

last: Stielow

first: Andrea

last: Nist


title: Nuclear receptor expression in lung tissue after vaping exposure

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: The emerging concern about chemicals in electronic cigarettes, even those without nicotine, de-mands the development of advanced criteria for their exposure and risk assessment. This study aims to highlight the sensitivity of lung nuclear receptors (NRs) to electronic cigarette e-liquids, independent of nicotine presence, and the influence of the sex variable on these effects.

overall_design: Adult male and female C57BL/6J mice were exposed to electronic cigarettes with 0%, 3% and 6% nicotine daily (70 ml, 3.3s, 1 puff per min/30 min) for 14 days, using the inExpose full body chamber (SCIREQ). Following exposure, lung tissue was harvested and RNA extracted. The expression of 84 NRs was determined using the RT2 profiler mRNA array (QIAGEN).

first: Shikha

last: Sharma


title: SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq)

first: Jason

last: Brenchley

first: Andrew

last: Rahmberg

first: Tovah

last: Markowitz

first: Joseph

last: Mudd

first: Alexandra

last: Ortiz


title: Xenografted human iPSC-derived neurons with the familial Alzheimer’s disease APPV717I mutation reveal dysregulated transcriptome signatures linked to synaptic function and implicate LINGO2 as a disease signaling mediator

city: New York

first: Gunnar

last: Hargus

state: NY

address: 650W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

summary: Alzheimer’s disease (AD) is the most common cause of dementia, and disease mechanisms are still not fully understood. Here, we explored pathological changes in human induced pluripotent stem cell (iPSC)-derived neurons carrying the familial AD APPV717I mutation after cell injection into the mouse forebrain. APPV717I mutant iPSCs and isogenic controls were differentiated into neurons revealing enhanced Aβ42 production, elevated phospho-tau, and impaired neurite outgrowth in APPV717I neurons. Two months after transplantation, APPV717I and control neural cells showed robust engraftment but at 12 months post injection, APPV717I grafts were smaller and demonstrated impaired neurite outgrowth compared to controls, while plaque and tangle pathology were not seen. Single-nucleus RNA-sequencing of microdissected grafts, performed two months after cell injection, identified significantly altered transcriptome signatures in APPV717I iPSC-derived neurons pointing towards dysregulated synaptic function and axon guidance. Interestingly, APPV717I neurons showed an increased expression of genes, many of which are also upregulated in postmortem neurons of AD patients including the transmembrane protein LINGO2. Downregulation of LINGO2 in cultured APPV717I neurons rescued neurite outgrowth deficits and reversed key AD-associated transcriptional changes related but not limited to synaptic function, apoptosis and cellular senescence. These results provide important insights into transcriptional dysregulation in xenografted APPV717I neurons linked to synaptic function, and they indicate that LINGO2 may represent a potential therapeutic target in AD.

overall_design: We performed gene expression analysis on differentiated neurons in vitro and single-nucleus RNA-seq (snRNA-seq) on micro-dissected grafts.

first: Wenhui

last: Qu