title: ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vitro]

city: Rehovot

first: Ido

last: Amit

overall_design: 8 weeks old C57BL/6 mice were sacrificed and bone marrow was isolated and cultured in the presence of human MCSF in C10 medium to generate BMDMs. At day 2, medium was replaced with fresh medium and MCSF . At day 6, cells were treated with murine IL4, TGFb, IL13, IL10, IFNg or left untreated. On day 7 for FACS sorting to SPID-seq scRNA-seq protocol.

first: Fadi

last: Sheban

first: Truong

last: San Phan

first: Ken

first: Florian

last: Ingelfinger

first: Chamutal

last: Gur

first: Yuval

last: Shapir Itai

first: Ronnie

last: Blecher-Gonen

first: Chunsong

last: Yu

first: Roberto

last: Avellino

first: Paulina

last: Chalan

last: Yofe

first: Vladimir

last: Yutkin

first: Pierre

last: Boyeau

first: Can

last: Ergen-Behr

first: Justin

last: Hong

first: Kfir

last: Mazuz

first: Rony

last: Dahan

first: Marcin

last: Kortylewski

first: Nir

last: Yosef

first: Assaf

last: Weiner


title: Dynamic regulation of murine RNA Polymerase III transcription during heat shock stress

status: Public on Mar 04 2025

city: Vancouver

first: Thomas

middle: F.

last: Nguyen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: UBC Life Sciences Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cells respond to many different types of stresses by overhauling gene expression patterns, both at the transcriptional and translational level. Under heat stress, global transcription and translation are inhibited, while the expression of chaperone proteins are preferentially favored. As the direct link between mRNA transcription and protein translation, tRNA expression is intricately regulated during the stress response. Despite extensive research into the heat shock response (HSR), the regulation of tRNA expression by RNA Polymerase III (Pol III) transcription has yet to be fully elucidated in mammalian cells. Here, we examine the regulation of Pol III transcription during different stages of heat shock stress in mouse embryonic stem cells (mESCs). We observe that global transcription of tRNAs is downregulated after 30 minutes of heat shock, followed by an overall increase in tRNA transcription after 60 minutes of heat shock. This effect is more evident in tRNAs, though other RNA Pol III gene targets are also similarly affected. Notably, we show that the down-regulation at 30 minutes of heat shock is independent of HSF1, the master transcription factor of the HSR, but that the subsequent increase in expression at 60 minutes requires HSF1. Taken together, these results demonstrate an adaptive RNA Pol III response to heat stress, and an intricate relationship between the canonical HSR and tRNA expression.

overall_design: CUT&Tag of RNA Polymerase III subunit RPC7 in wildtype and HSF1 knockout mouse embryonic stem cells (mESCs) subjected to varying lengths of heat shock treatment at 42C, either unconditioned (unCond) or preconditioned (preCond) with a prior heat shock.

middle: F

first: James

middle: Z

last: Kwan

first: Jennifer

middle: E

last: Mitchell

first: Jieying

middle: H

last: Cui

first: Sheila

middle: S

last: Teves


title: TP53 missense-specific transcriptional plasticity drives resistance against cell cycle inhibitors in pancreatic cancer [ChIP-Seq]

status: Public on Mar 05 2025

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

country: Germany

institute: University Medical Center Göttingen

summary: In ~70% of pancreatic ductal adenocarcinoma (PDAC) patients, the TP53 gene acquires gain-of-function (GOF) mutations leading to rapid disease progression. Specifically, missense p53 (misp53) GOF mutations associate with therapy resistance and worse clinical outcomes. However, the molecular functions of distinct misp53 mutants in plasticity and therapy response remain unclear. Integrating multi-center patients’ data and multi-omics, we report that the misp53R273H/C mutant is associated with cell-cycle progression and a basal-like state compared to the misp53R248W/Q mutant. Loss of misp53R273H/C decreased tumor growth and liver metastasis while prolonging survival in preclinical models. We found that misp53R273H/C specifically regulates the Rb/DREAM axis involved in cell cycle regulation. Notably, a clinical CDK4/6 inhibitor specifically reduced misp53R273H/C mutant expression. However, it triggered MAPK/ERK-mediated resistance mechanisms, enhancing cell survival and resistance to CDK4/6 inhibitors. Combining MAPK/ERK and CDK4/6 inhibitors reduced misp53R273H/C-associated oncogenic functions. Thus, distinct misp53 mutants show unique cell-intrinsic plasticity, therapeutic vulnerabilities, and resistance mechanisms.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for p53 in PANC1 and MiaPaCa2 cells.

first: Laura

last: Urbach

first: Lena

last: Wieland

first: Frederike

last: Penz

first: Stefan

last: Küffer

first: Rebecca

middle: D

last: Samuel

first: Lukas

last: Klein

first: Christof

last: Lenz

first: Ulrich

last: Sax

first: Michael

last: Ghadimi

first: Ramona

last: Schulz-Heddergott

first: Elisabeth

last: Hessmann

first: Volker

last: Ellenrieder

first: Nelson

last: Dusetti

middle: K


title: Rapid and Inducible Mislocalization of Endogenous TDP43 in a Novel Human Model of Amyotrophic Lateral Sclerosis [miRNA-seq]

status: Public on Mar 07 2025

city: Exeter

first: Akshay

last: Bhinge

address: Stocker Road

department: CBS

country: United Kingdom

institute: Living Systems Institute, University of Exeter

type: Expression profiling by high throughput sequencing

summary: In this study, we describe the development of a new model of TDP43 proteinopathy using human induced pluripotent stem cell (iPSC)-derived neurons. Utilizing a genome engineering approach, we induced the mislocalization of endogenous TDP43 from the nucleus to the cytoplasm without mutating the TDP43 gene or using chemical stressors

overall_design:
RNA was harvested from iPSC-derived motor neurons (MNs) displaying mislocalized or nuclear TDP43 at day 40 of the differentiation process.
RNA was harvested from iPSC-derived motor neurons (MNs) expressing an shRNA against TDP43. An shRNA targeting Renilla luciferase was used as a control.

first: Johanna

last: Ganssauge

first: Seema

last: Namboori


title: TP53 missense-specific transcriptional plasticity drives resistance against cell cycle inhibitors in pancreatic cancer [RNA-Seq]

first: Shiv

last: Singh

overall_design: RNA sequencing (ChIP-seq) in PANC1 and MiaPaCa2 cells following p53-specific siRNA or control siRNA.


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops [800U]

status: Public on Feb 28 2025

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

summary: In the metazoan genome, regulatory DNA elements called enhancers govern the precise spatiotemporal patterns of gene expression in specific cell types. However, how enhancers are spatially organized to regulate target genes remains poorly understood. Here, by improving the spatial resolution of single-cell 3D genome mapping to 5 kb with micrococcal nuclease in our new single-cell Micro-C method, we report a specialized 3D structure of enhancers termed “promoter stripes,” which start at the transcription start site (TSS) and extend in the direction of transcription on the contact map, linking the promoter to multiple downstream enhancers. Promoter stripes are formed by cohesin-mediated loop extrusion, which potentially brings multiple enhancers to the promoter. Furthermore, with high-resolution single-cell chromatin structures, we observed the prevalence of multi-enhancer hubs on genes with promoter stripes, wherein multiple enhancers form spatial cluster associating its promoter. Such observation was only made possible by single-cell 3D genome with the improved resolution.

overall_design: Single-cell Micro-C (MNase titration, 200U, 600U, 800U & 1000U)

first: Honggui

last: Wu

first: Jiankun

last: Zhang

first: Longzhi

last: Tan

first: Sunney


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops [200U]


title: A subcellular map of translational machinery composition and regulation at the single-molecule level [ALIBi_Lsg1_KD]

city: Palo Alto

first: Maria

last: Barna

state: CA

address: 240 Pasteur Dr, BMI 4500

department: Genetics

country: USA

institute: Stanford University

summary: Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. Here, we present ribosome expansion microscopy (RiboExM) to visualize individual ribosomes and an optogenetic proximity-labeling technique (ALIBi) to probe their composition. We generated a super-resolution ribosomal map, revealing unexpected subcellular translational hotspots and enrichment of 60S subunits near polysomes at the endoplasmic reticulum (ER). We found that Lsg1 tethers 60S to the ER and regulates translation of select proteins. Additionally, we discovered ribosome heterogeneity at mitochondria guiding translation of metabolism-related transcripts. Finally, we visualized ribosomes in neurons, revealing a dynamic switch between monosomes and polysomes in neuronal translation. Together, these approaches enable exploration of ribosomal localization and composition at unprecedented resolution.

overall_design: Rpl31-FLAG-TEV-AviTag-containing ribosomes were proximity biotinylated using ALIBi targeted to either the cytosol or endoplasmic reticulum. Biotinylated ribosomes were affinity purified and subjected to poly-A-enriched RNA-seq. Whole-cell RNA from the same cell lysates (input for affinity purification) was sequenced in parallel. In some cases, cells were treated with either a targeting or scrambled (control) siRNA prior to performing ALIBi-mediated enrichment of subcellular ribosome populations.

first: Adele

last: Xu


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops (SDS test)

overall_design: Single-cell Micro-C (with and without the addition of SDS)


title: Mutation of the white gene in Drosophila has widespread phenotypic and transcriptomic effects

status: Public on Mar 03 2025

city: Grand Rapids

first: April

last: Rickle

state: MI

address: 333 Bostwick Avenue

department: Metabolism and Nutritional Programming

institute: Van Andel Institute

summary: The white (w) gene is one of the most widely used genetic markers in Drosophila research, serving as a standard background mutation for transgene insertions and genetic manipulations. While its primary function is in eye pigmentation, w mutations have been associated with diverse phenotypic effects including in metabolism, behavior, and stress responses. However, many studies using w mutants do not account for differences in genetic background, raising concerns about the interpretation of experimental results. Given the potential confounding genetic effects and non-pigment related roles of w, we generated a well-controlled phenotyping dataset. To ensure that the observed phenotypic differences are attributable to white itself, rather than other genetic differences due to background, we established isogenic fly strains through backcrossing that differ only by the presence or absence of the white gene. Given the likely metabolic consequences of white gene dysfunction and its crucial role in neurotransmitter production, we focused our phenotyping assays on behavioral, metabolic and fitness related outcomes and performed transcriptomic analysis on adult fly heads. Our findings reveal widespread changes in adult brain gene expression and behavioral, metabolic and fitness traits, demonstrating that w mutations influence multiple biological processes beyond their established role in pigment transport. These results emphasize the necessity of genetic background control in Drosophila research and suggest that caution is warranted when using w mutants as a baseline for comparative studies.

overall_design: RNAseq profiling of heads from 1 week old male and female w+ and w- w1118 Drosophila. Each sample represents 10 pooled heads.

first: Krittika

last: Sudhakar

first: Alix

last: Booms

first: Ellen

last: Stirtz

first: Heidi

last: Lempradl


title: AMPK phosphosite profiling by label-free mass spectrometry reveals a multitude of mTORC1-regulated substrates

status: Public on Feb 27 2025

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

summary: The metabolic kinase AMPK regulates transcription in response to nutrient status. AMPK is highly phosphorylated at position Ser184 in the regulatory beta2-subunit, however it's function is unknown. Our preliminary data indicate AMPK dephosphorylated at beta2-Ser184 has elevated nuclear activity and down-regulates apoptotic pathways in response to environmental insult. Here we compare transcriptomes of HEK293T cells expressing either endogenous level beta2 WT or the non-phosphorylatable mutant beta2-Ser182Ala, to gain insight into functional effects of elevated nuclear AMPK activity

overall_design: To investigate alternation in gene expression and cell signalling network between WT and AMPK B2S184A KI of Hek 293T cell using data obtained from RNA-seq from 4 replicates each.

middle: M

first: Carl

middle: R

last: Walkley

first: Scott

last: Taylor

first: Jacki

last: Heraud-Farlow

first: Jonathan

last: Oakhill

first: Naomi

middle: X

last: Ling


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops [600U]

first: Xiaoliang

last: Xie

first: Honggui


title: Braingeneers mouse organoids

status: Public on Feb 24 2025

city: Santa Cruz

first: Lon

last: Blauvelt

address: 1156 High St

institute: University of California, Santa Cruz

summary: We characterized the cell composition of cortical organoids of dorsal forebrain identity derived from three independent cell lines using single-cell RNA sequencing to complement electrophysiological data from spontaneous neuronal activity.

overall_design: Single cell RNA sequencing was performed on 30 mouse cortical organoids from three separate cell lines (10 organoids per cell line).

first: Hunter

last: Schweiger

first: Sebastion

last: Hernandez

first: Gregory

last: Kaurala

first: Tal

last: Sharf

first: Mohammed

last: Mostajo-Radji


title: Whole genome transcriptomics reveal distinct atrial versus ventricular responses to neonatal hyperoxia

status: Public on Feb 25 2025

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

summary: Preterm infants exposed to supplemental oxygen (hyperoxia) are at risk for developing heart failure later in life. Rodent studies show that exposure to hyperoxia in early postnatal life causes heart failure later in life that resembles heart failure in humans who were born preterm. Neonatal hyperoxia exposure affected the left atrium and left ventricle differently, inhibiting the proliferation and survival of atrial cardiomyocytes while enhancing cardiomyocyte differentiation in the ventricle. In this study, whole genome transcriptomics revealed the left atria of neonatal mice are more responsive to hyperoxia than the left ventricle, with the expression of 4,285 genes affected in the atrium and 1,743 in the ventricle. While hyperoxia activated p53 target genes in both chambers, it caused greater DNA damage, phosphorylation of the DNA damage responsive ataxia telangiectasia mutated (ATM) kinase, mitochondrial stress, and apoptosis in the atrium. In contrast, hyperoxia induced the expression of DNA repair and growth arrest genes in the ventricle. Atrial cells also showed a greater loss of extracellular matrix and superoxide dismutase 3 (SOD3) expression, possibly contributing to the enlargement of the left atrium and reduced velocity of blood flow across the mitral valve seen in hyperoxia exposed mice. Diastolic dysfunction and heart failure in hyperoxia exposed mice may thus stem from its effects on the left atrium, suggesting chamber-specific therapies may be needed to address diastolic dysfunction and heart failure in people who were born preterm.

overall_design: C57BL/6J mice purchased from the Jackson Laboratories were used to generate newborn pups that were exposed to room air (21% oxygen) or hyperoxia (100% oxygen) between birth and postnatal day (PND) 4. The mice were then sacrificed by injecting with avertin and the thorax was exposed. The hearts were removed, and the left atria and ventricles were carefully separated with forceps and a tungsten needle. The separated atria and ventricle were used to isolate genomic DNA free RNA using the RNeasy plus kit (Qiagen, 74134). There were 4 experimental conditions with 5 individual mice in each group. The 4 experimental conditions are room air left atria (RA_LA), room air left ventricle (RA_LV), hyperoxia left atria (O2_LA), and hyperoxia left ventricle (O2_LV) where the number after LA or LV represents one of the five individual mice in that experimental group.

first: Ethan David

last: Cohen

first: Min

last: Yee

first: Michael A.

last: O'Reilly


title: TP53 missense-specific transcriptional plasticity drives resistance against cell cycle inhibitors in pancreatic cancer

first: Shiv

last: Singh

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

overall_design: Refer to individual Series


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops [scMicro-C, GM12878]

overall_design: Single-cell Micro-C

last: Wu

first: Jiankun

last: Zhang


title: Rapid modulation of gut microbiota composition by hypothalamic circuits in mice.

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: In recent years, the gut microbiota and derived metabolites have emerged as relevant players in modulating several brain functions, including energy balance control. This form of distant communication mirrors that of metabolic hormones (e.g., leptin, ghrelin), that convey information about the organism's energy status by exerting effects on diverse brain regions including the master homeostatic centre the hypothalamus. However, whether the hypothalamus is also able to influence gut microbiota composition remains enigmatic. Here, we present a proof-of-concept study designed to unravel this challenging question. To this aim, we employed chemogenetics (to selectively activate or inhibit the activity of hypothalamic POMC or AgRP neurons) or administered leptin or ghrelin centrally to mice. Subsequently, we conducted microbiota composition analysis throughout the gut using 16S rRNA gene sequencing. Our results showed that these brain interventions significantly changed the gut microbiota in an anatomical and short-term (2-4h) fashion. Transcriptomic analysis indicated that these changes were associated with the reconfiguration of neuronal and synaptic pathways in the duodenum concomitant with increased sympathetic tone. Interestingly, diet-induced obesity attenuated brain-mediated changes induced by leptin in gut microbiota communities and sympathetic activation. Our findings reveal a novel and unanticipated brain-to-gut axis that acutely attunes microbiota composition at fast timescales, with potential implications for meal-to-meal adjustments and systemic energy balance control.

overall_design: C57BL/6 male mice at 8 weeks of age were anesthetized and a stainless cannula was implanted in the right lateral ventricle. One day post-surgery, mice were divided into water or antibiotic treatment (ampicillin 1 g/L; neomycin 0.5 g/L in drinking water) groups. Following this treatment for 48h, either saline or leptin (3 µg) was delivered ICV and the mice were sacrificed 2 hours later. The duodenum was harvested and snap-frozen in liquid nitrogen. Frozen samples were processed for RNA isolation and subsequent RNA sequencing was performed. Duodenal mRNA was isolated using Trizol (Invitrogen) following standard protocols. Quantification and integrity analysis of total RNA were performed by analysing 1 μl of each sample in an Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit; Agilent). Total RNA strand-specific RNA libraries were generated using 150 ng of total RNA with the Illumina® Stranded RNA Prep Ligation kit with RiboZero Plus following the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq2000 (Illumina, Inc.) in paired-end mode with a read length of 2×50 bp.

first: Míriam

last: Toledo

first: Sara

last: Martínez

first: Matthias

last: Van Hul

first: Elena

last: Eyre

first: Rudy

last: Pelicaen

first: Anthony

last: Puel

first: Isabel

last: Moreno-Indias

first: Alicia

middle: G

last: Gómez-Valadés

first: Macarena

last: Pozo

first: Iñigo

last: Chivite

first: Maria

last: Milà-Guasch

first: Roberta

last: Haddad-Tóvolli

first: Arnaud

last: Obri

first: Júlia

last: Fos

first: Iasim

last: Tahiri

first: Sergio

last: Rodriguez

last: Ramírez

first: Erika

last: Monelli

first: Patrice

last: Cani

first: Rubén

last: Nogueiras

first: Marc

last: Claret

first: Berta

last: Laudo

first: Julica

last: Inderhees

first: Markus

last: Schwaninger


title: Single-cell transcriptomic profiling of immune landscape in triple-negative breast cancer during neoadjuvant chemotherapy

status: Public on Feb 20 2025

city: Moscow

first: Natalia

last: Moiseeva

state: Moscow

address: Kashirskoe Shosse 24

country: Russia

institute: N.N. Blokhin National Medical Research Center of Oncology

summary: Triple-negative breast cancer (TNBC) is the most aggressive subtype, typically requiring neoadjuvant chemotherapy (NAC) as an obligatory component of the treatment regimen. Achieving a pathological complete response to NAC is associated with improved long-term outcomes for patients with TNBC. The functional status of the immune system plays a critical role in NAC efficacy. Herein, we presented the first investigation of systemic and local immune landscape during the initial course of NAC treatment and identify factors that contribute to chemotherapy resistance of TNBC. Using single-cell RNA sequencing, we demonstrated that the transcriptional profile remained stable in a patient who responded to NAC, while a non-responder exhibited significant dysregulation in the expression of genes involved in stress response, apoptosis, immune cell proliferation, and differentiation within lymphocyte and monocyte populations. During the first course of NAC, circulating cytotoxic CD8 T cells in the non-responder patient overexpressed granzymes B and H, granulysin, and perforin. In contrast, expression of these factors decreased in CD8 T cells within the tumor. Finally, we identified for a first time a signature of myeloid-derived suppressor cells (MDSC) within the S100АhighMHClow monocyte population and calculated an MDSC score for both the responder and the non-responder TNBC patients. An elevated MDSC score in the non-responder was validated using data from an independent cohort of patients with poor NAC response. Our data underscores the importance of immune system functionality in determining chemotherapy efficacy in TNBC. Keywords: triple-negative breast cancer, immune cell, cytotoxic CD8 T cell, chemotherapy, myeloid-derived suppressor cell, single-cell RNA sequencing.

overall_design:
The study enrolled two women who had been diagnosed with TNBC and underwent NAC. Both patients received 2-4 courses of adriamycin with cyclophosphamide followed by 4 NAC courses of taxanes before surgery. The first patient received a partial mastectomy and showed no evidence of tumors cells in the breast tissue or lymph nodes. The second patient demonstrated progression of TNBC during the fourth cycle of NAC. Therefore, the NAC was interrupted and a radical mastectomy was performed.  Two months after the surgery, metastases developed in her pelvic bones, leading to the patient’s death two months later. The patient with a poor response to therapy and unfavorable outcome was referred to 'Non-responder,' while the patient with a good response and favorable outcome was referred to 'Responder.' Peripheral blood samples were collected from both TNBC patients at three time points: before NAC and on days 3 and 21 after the administration of the 1st NAC course. For non-responder patient were available biopsy samples of tumor tissue before NAC and on days 3 and 21 after the first course of NAC. The cellular viability of all PBMCs and tissue samples exceeded 75%, as evaluated by Calcein (BD Bioscience, USA) vs DRAQ7 (Thermo Fisher Scientific, USA) via flow cytometry. According to the manufacturer’s protocol, 8 samples (6 PBMCs and 3 tumor cells suspensions) were labeled by Sample Tag and pooled for single-cell capture with the BD Rhapsody Single-Cell Analysis system (BD Bioscience, USA). Single-cell suspensions with PBS were loaded into microfluidic devices using the BD Rhapsody Single-Cell Analysis System (BD Bioscience, USA). Subsequently, the scRNA-seq libraries were constructed according to the protocol of the Immune Response Targeted Panel (Human) Single Cell RNA Library Kit (BD Bioscience, USA). Individual libraries were diluted and pooled according to the manufacturer’s recommendations. Finally, Illumina NextSeq 2000 sequencing was performed using NextSeq 2000 P2 reagents (100 cycles).
***NOTE: FASTQ files contain multiple samples multiplexed by Sample Tag of BD Rhapsody. All required information to demultiplex was provided in metadata.tsv and sample_info.txt.

last: Patysheva

last: Iamshchikov

last: Fedorenko

last: Bragina

last: Vostrikova

last: Garbukov

last: Cherdyntseva

last: Denisov

last: Gerashchenko


title: Transforming Growth Factor-β (TGFβ) Prevents Hypertension-Induced Aortic Dissection in Adult Mice via Extracellular Matrix Production

city: New Haven

first: George

last: Tellides

state: CT

address: 10 Amistad st, 337B

department: Surgery

institute: Yale University


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops [bulk Micro-C]

first: Xiaoliang

last: Xie

overall_design: bulk Micro-C

first: Honggui

last: Wu

first: Jiankun

last: Zhang

first: Longzhi

last: Tan

first: Sunney


title: Transcriptional Landscape for Endoplasmic Reticulum Stress in Alzheimer's Disease Patients-Derived Dermal Fibroblast

status: Public on Feb 21 2025

city: Suwon-si

first: yeojin

last: Kim

address: 164 World cup-ro

country: South Korea

institute: ajou Univ.

summary: Numerous studies have identified various risk factors associated with Alzheimer's disease (AD). However, the experimental limitations of disease modeling make it challenging to directly interpret these effects. These limitations include constraints of postmortem samples, animal experiments, and challenges associated with brain tissue studies. Ex-vivo experiments effectively address these issues by enabling patient-specific identification and highlighting potential biomarkers. In addition, patient-derived human dermal fibroblast effectively reflect the molecular anomalies that disrupt cellular homeostasis. This study aimed to use an ex-vivo platform to characterize the transcriptional profile of fibroblasts derived from patients with AD in response to endoplasmic reticulum (ER) stress and propose potential biomarkers. We utilized patient-derived fibroblasts to observe differentially responsive genes to ER stress in both healthy controls (N=22) and patients with AD (N=20) using RNA sequencing.

overall_design:
All participants were enrolled in the BICWALZS. It was launched in October 2016 by the Korea Disease Control and Prevention Agency and is part of the National Korea Biobank Project conducted at Ajou University Hospital. Participants were classified into healthy control and AD groups based on specific criteria.
we mimicked the ER stress environment in vitro by treating cells with thapsigargin at concentrations that allowed for cell survival.
Transcriptomic analysis of thapsigargin treated and non-treated fibroblast by Bulk RNA sequencing

first: Yeojin

first: You Jin

last: Nam

first: Sunwoo

last: Yoon

first: Donghyuk

last: Shin

first: Jin Young

last: Noh

first: Young Joon

last: Cho

first: Seongmin

first: Eun-Joo

first: Soo Hyun

first: Soo Youn

last: Lee

first: Byeong C.

first: Seong Hye

last: Choi

first: Sang Won

last: Seo

first: Jin Wook

first: Young-Sil

last: An

first: Bumhee

last: Park

first: Hee Young

last: Kang

first: Hyun Goo

last: Woo

first: Young Hyuk

first: Sunhwa

last: Hong

first: Sang Joon

last: Son

first: Sang-Rae

first: Chang Hyung

first: Hyun Woong

last: Roh


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops [1000U]

first: Xiaoliang

last: Xie

first: Honggui

last: Wu

first: Jiankun

last: Zhang

first: Longzhi

last: Tan

first: Sunney


title: Oxidative Stress Converts Benign Lesions to Cancer via a Self-Amplifying NRF2-EZH2 Loop [Quantseq_Nrf2Kras]

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Whether oxidative stress (OxS) acts mutationally or epigenetically to increase cancer risk is unknown. Pancreatic ductal carcinoma (PDAC) evolves from benign, low-grade PanIN (pancreatic intraepithelial neoplasia) lesions that frequently express oncogenic KRAS. Postulating that known risk factors convert benign PanIN to malignant progenitors via OxS and epigenetic mechanisms, we established a novel system to test this hypothesis.  Transient incubation of organoids, derived from pancreata with KrasG12D-induced low-grade PanIN, with H2O2 triggered irreversible malignant conversion mediated by an epigenetic network composed of NRF2, its direct transcriptional target EZH2, and EZH2-interacting transcription factors. Pharmacological or genetic activation of this network, maintained by a single NRF2 site in the EZH2 promoter, also triggered rapid malignant conversion and upregulation of malignancy-supportive metabolic genes that remained elevated in established PDAC.

overall_design: 8 wo pancreata of indicated genotypes: Nrf2Act-PEC,  WT, KrasG12D/PEC/Nrf2Act-PEC,  KrasG12D/PEC.

first: Laura

last: Antonucci

first: Angeles

last: Duran

first: Maria

middle: T

last: Diaz-Meco


title: Oxidative Stress Converts Benign Lesions to Cancer via a Self-Amplifying NRF2-EZH2 Loop [ATACseq_ChIPseq_RNAseq]

overall_design: EZH2-ablated and parental UN-KC-6141 cells. RNA-Seq, ATAC-Seq, H3K27ac ChIP-Seq, H3K4me3 ChIP-Seq in WT and EZH2KO. RNA-Seq in KRasG12D and WT 3 days and 7 days after cerulein-induced pancreatitis.

first: Isidoro

last: Cobo

first: Christopher

last: Glass


title: Oxidative Stress Converts Benign Lesions to Cancer via a Self-Amplifying NRF2-EZH2 Loop


title: Oxidative Stress Converts Benign Lesions to Cancer via a Self-Amplifying NRF2-EZH2 Loop [RNAseq_KC_EZH2KO_EEDKO]

overall_design: EZH2-ablated, EED-ablated, and parental UN-KC-6141 cells:  Understand  whether and how cell stress directly and broadly modifies the cancer epigenome, and how EZH2 affects the PDAC transcriptome

first: Chiara

last: Nicoletti


title: High-resolution 3D genome structures via single-cell Micro-C uncovers cohesin-mediated enhancer-promoter loops


title: Oxidative Stress Converts Benign Lesions to Cancer via a Self-Amplifying NRF2-EZH2 Loop [Quantseq_KC_KPC]

overall_design: EZH2-ablated and parental UN-KC-6141 and UN-KPC-961 cells:  Understand  whether and how cell stress directly and broadly modifies the cancer epigenome, and how EZH2 affects the PDAC transcriptome


title: Cocaine-context memories are transcriptionally encoded in nucleus accumbens Arc ensembles

status: Public on Feb 19 2025

first: Marine

last: Salery

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Learned associations between the rewarding effects of drugs and the context in which they are experienced are critical for context-induced relapse. While context re-exposure triggers the recall of such drug-related associative memories it is unclear whether this relies on the reactivation of and plasticity in neuronal populations previously engaged in their acquisition. Here, using the immediate early gene Arc, we captured a discrete population of nucleus accumbens (NAc) cells activated during the encoding of cocaine-context memory and showed that this neuronal ensemble is later reactivated upon context-induced recall. Furthermore, we show that ensembles recruited at early vs. late stages of memory encoding are largely distinct and contribute differentially to memory retrieval. Single nuclei RNA-sequencing of these ensembles identified plasticity-related transcriptional programs that segregate cocaine-recruited NAc engram-like cells beyond cell-type composition and revealed molecular features unique to distinct stages of memory processing. These findings suggest that activity-dependent transcription upon initial engram allocation further stamps cells for persistent plasticity programs and thereby supports memory traces at the single-cell level. This study also provides new insights into the mechanisms supporting pathological memory formation associated with cocaine exposure.

overall_design: Following cocaine conditionned place preference training and testing, Arc-positive nuclei from the nucleus accumbens of male and female ArcCreERT2 mice were sorted by flow cytometry (FANS) before snRNAseq analysis.

first: Arthur

last: Godino

first: Yu Qing

last: Xu

first: John

last: Fullard

first: Romain

last: Durand-de Cuttoli

first: Alexa

last: LaBance

first: Leanne

last: Holt

first: Scott

middle: J

last: Russo

first: Panos

last: Roussos

first: Eric

last: Nestler


title: Gene expression profiling of HIV and EBV-associated classic Hodgkin lymphomas from Malawi

city: Chapel Hill

first: Yuri

last: Fedoriw

address: 160 Medical Dr

institute: University of North Carolina - Chapel Hill

summary: To investigate the biological differences between EBV-/HIV-, EBV+/HIV- and EBV+/HIV+ classic Hodgkin lymphoma, we performed RNA sequencing of 19 pre-treatment formalin-fixed paraffin-embedded (FFPE) whole lymph node biopsies of cHL.

overall_design:
We performed RNA sequencing of 19 pre-treatment formalin-fixed paraffin-embedded (FFPE) whole lymph node biopsies of cHL, inclusive of EBV-association and HIV status.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Samantha

last: Beck

first: Sophia

last: Roush

first: Tamiwe

last: Tomoka

first: Matthew

last: Painschab

first: Kate

last: Westmoreland


city: Pittsburgh

first: Kathryn

last: Torok

state: PA

address: 4401 Penn Ave

department: Pediatric Rheuamatology

institute: University of Pittsburgh

summary: Using transcriptomic profiling at single-cell resolution, we investigate cell-intrinsic and cell-extrinsic signatures associated with pathogenesis and inflammation-driven fibrosis in both adult and pediatric localized Scleroderma (LS) patients. We perform scRNA-seq on adult and pediatric LS patients and healthy controls. We then analyze the scRNA-seq data using an interpretable factor-analysis machine learning framework, SLIDE, that moves beyond predictive biomarkers to try and infer latent factors underlying LS pathophysiology. SLIDE is a novel latent factor regression-based framework that comes with rigorous statistical guarantees regarding identifiability of the latent factors, corresponding inference, and FDR control. We find distinct differences in the characteristics and complexity in the molecular signatures between adult and pediatric LS. SLIDE identified cell type-specific determinants of LS associated with age and severity and revealed insights into signaling mechanisms shared between LS and Systemic Sclerosis (SSc), as well as differences in onset of the disease in the pediatric compared with adult population. Our analyses recapitulate known drivers of LS pathology and find previously unidentified cellular signaling modules that stratify LS subtypes and define a shared signaling axis with SSc.In this study we compared 17 healthy and 27  LS samples evaluated by 10X Genomics single cell sequencing. Samples were processed and clustered for DEG analysis.

overall_design:
SLIDE analysis of the scRNA-seq data using an interpretable factor-analysis machine learning framework, that moves beyond predictive biomarkers to try and infer latent factors underlying LS pathophysiology.
NOTE: The current larger cohort of patients include 44 samples (16 new samples and 28 re-analyzed samples), 27 LS and 17 healthy. These were aggregated using CellRanger and processed via the Seurat pipeline with other R packages including Nichenet, Harmony, etc. The resulting dataset was then analyzed by computational biologists in the Das lab using their SLIDE model.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Aaron BI

last: Rosen

first: Anwesha

last: Sanyal

first: Theresa

last: Hutchins

first: Giffin

last: Werner

first: Jacob S

last: Berkowitz

first: Tracy

last: Tabib

first: Robert

last: Lafyatis

first: Heidi

last: Jacobe

first: Jishnu

last: Das


title: Regulation of tagatose catabolic gene cluster and development of a tagatose-inducible gene expression system in the probiotic Escherichia coli Nissle 1917

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

institute: Konkuk University

summary: Escherichia coli Nissle 1917 (EcN), a well-known Gram-negative probiotic bacterium, has been widely used to treat various intestinal disorders and has gained recognition as a promising platform for diverse biotechnological applications, validated by numerous institutions and researchers over the years However, despite its importance, developing suitable expression systems in EcN has been challenging due to the difficulty in meeting key criteria such as non-toxicity, biocompatibility, and tunable expression. Recently, we identified a gene cluster in EcN responsible for tagatose utilization, challenging the conventional belief that E. coli cannot metabolize tagatose. D-tagatose, a rare, low-calorie sugar naturally found in small amounts in dairy products and fruits, is recognized as safe by the FDA. Due to its poor digestibility in humans, only certain enteric microorganisms are capable of metabolizing it. In this study, we investigated the regulatory elements within this gene cluster using high-throughput differential RNA sequencing (dRNA-seq) and developed a tagatose-inducible expression plasmid, creating a tunable gene expression system for engineering EcN. We evaluated the performance of this novel system and successfully applied it to overproduce a pharmaceutical protein and an industrial enzyme under both aerobic and anaerobic conditions.

overall_design: Sample from the exponential phase of modified R (MR) medium containing D-tagatose were collected for total RNA extraction. The isolated RNA was then used for differential RNA sequencing (dRNA-seq) library preparation, following the established protocol.

first: Youngshin

last: Kim

first: Dohyeon


title: Dual RNA-seq analysis reveals the interaction between multidrug-resistant Klebsiella pneumoniae and host in a mouse model of pneumonia

status: Public on Feb 18 2025

first: Chenxi

last: Dai

address: Dongdajie

institute: Academy of Millitary Medical Sciences

summary: Multidrug-resistant Klebsiella pneumoniae (MDR-KP) poses a significant global health threat, associated with high morbidity and mortality rates among hospitalized patients. The interaction between MDR-KP and its host is highly complex. Here, we explored these interactions in a mouse model of pneumonia using dual RNA-seq analysis.Our results revealed that, compared to the low-dose group, the high-dose group significantly upregulated hypoxia and pro-inflammatory cytokine-related genes in the host, and siderophore-related genes in the bacteria. Correlation analysis demonstrated a significant association between siderophore-related genes and clusters of genes related to pro-inflammatory cytokines and hypoxia.

sample_organism:
Klebsiella pneumoniae
Mus musculus

platform_organism:
Klebsiella pneumoniae
Mus musculus

overall_design: Mice were infected with either high or low doses of Klebsiella pneumoniae strain NY13307. Dual RNA sequencing analysis of the lung tissues from infected mice was performed at 0 h, 6 h, 12 h, 18 h, and 24 h post-infection, with three mice per group.The lung tissues of healthy mice and the bacterial suspension in PBS were used as control groups for the host and bacteria, respectively.

first: Xiaolin

last: Song

first: Meng

last: Lv

first: Cuicui

last: Jiang

first: Lingfei

last: Hu

first: Yongqiang

first: Dongsheng

last: Zhou

first: Wenhui

last: Yang


title: LINC00622 transcriptionally promotes RRAGD to repress mTORC1-modulated autophagic cell death by associating with BTF3 in cutaneous melanoma

city: Guangzhou

first: can

last: li

address: Southern Medical University

institute: Southern Medical University

summary: We report a novel long noncoding RNA, LINC00622, which modulates the mTORC1-regulated autophagy in cutaneous melanoma. Functionally, LINC00622 acts as an oncogene to promote the proliferation, colony formation, migration and invasion in melanoma while suppressing cell death. Mechanically, LINC00622 associates and recruits BTF3 to transcriptionally enhance RRAGD expression for activating mTORC1 and inhibiting autophagic cell death, which contributes to the development of cutaneous melanoma. Our findings not only demonstrated the oncogenic role of LINC00622 via RRAGD/mTORC1 axis to repress autophagic cell death in cutaneous melanoma, but also offer novel treatment targets for melanoma therapy.

overall_design: To figure out the role of long non-coding RNA LINC00622 in melanoma and the underlying mechanism, RNA transcriptome sequencing was performed to globally characterize LINC00622-regulated transcriptome changes. LINC00622 knockdown by RNA interference in A375 and SK-MEL-28 cells. cells treated with siNC served as control.

first: Can

last: Li

first: Ke

last: Wang

first: Jieyu

last: Liu

first: Liang


title: Ambroxol Induced Myeloma Cell Death by Inhibiting Autophagy

status: Public on Feb 16 2025

city: Tokyo

first: Yutaka

last: Hattori

state: Japan

address: 1-5-30 Shiba-koen, Minato-ku

country: Japan

institute: Keio University, Faculty of Pharmacy

summary: Recently, newly developed drugs have significantly improved prognosis of patients with multiple myeloma (MM). However, most patients relapsed sooner or later, and thus, MM is still an incurable hematological malignancy. In addition, serious adverse events occasionally hamper to continue treatment. Exploitation of the new drugs that potentiate the anti-tumor activities and alleviate the adverse effects of the existing drugs is needed. Here, we found by drug repositioning that ambroxol hydrochloride (ambroxol) induces apoptosis of MM cells. Interestingly, turnover assay and reporter assay showed that ambroxol inhibits late stage of autophagy. Transmission Electron Microscope (TEM) observation also showed that MM cells treated with ambroxol revealed accumulation of autophagy vesicles in cytoplasm, supporting the result of inhibition of late stage autophagy. Existing anti-MM drugs demonstrate various effects on autophagy; panobinostat, a histone deacetylase inhibitor, induced autophagy while bortezomib and lenalidomide did not. Ambroxol revealed synergistic anti-myeloma effect with panobinostat because ambroxol was considered to inhibit activation of panobinostat-induced autophagy and also downregulated MCL1 expression. In KMS 11-xenograft model, ambroxol alone significantly delayed tumor growth, and synergistically enhanced panobinostat-induced inhibition of tumor growth. Interestingly, concomitant use of ambroxol with panobinostat alleviated panobinostat-induced diarrhea. Gene set enrichment analyses (GSEAs) and pathway analysis also showed that ambroxol increased expression of the genes related to autophagy inhibition and unfolded protein response. These results suggested that autophagy is a promising therapeutic target for multiple myeloma.

overall_design: To study molecular mechanisms for ambroxol-induced autophagy inhibition in myeloma cells, KMS21 and KMS34 were treated  with ambroxol 200 mM for 24 hours, and the comparative gene expressions were analysed between ambroxol-treated vs untreated cells.

first: Y

first: M

last: Matsushita


title: Sustained NF-kB activation allows mutant alveolar stem cells to co-opt a regeneration program for tumor initiation

city: Cambridge

first: Joo-Hyeon

last: Lee

email: jhl62@cam.ac.uk, leej49@mskcc.org

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

overall_design: Refer to individual Series

first: Frances

last: England

first: Benjamin

last: Simons


title: Sustained NF-kB activation allows mutant alveolar stem cells to co-opt a regeneration program for tumor initiation [Expt2]

summary: Tissue homeostasis relies on meticulously coordinated fate determination by resident stem cells through a tissue-wide feedback loop.  Dysregulation of this process is closely associated with tumorigenesis, yet the mechanisms distinguishing these phenomena remain in question. Here, we integrate comparative analyses of in vivo large-scale quantitative clonal dynamics and single-cell transcriptomics to unveil a key evolutionary trajectory within a single alveolar type II (AT2) stem cell, driving tissue-wide neoplastic transformation in the lung. Tracking thousands of AT2 clones throughout murine adulthood uncovers two independent homeostatic AT2 subpopulation scharacterised by unique cellular kinetics. Notably, a small AT2 subset undergoes substantial clonal expansion upon KrasG12D activation. The mutant AT2 cells follow a differentiation trajectory via emergent regenerative cell states, yet exhibit remarkable cell state equivalency with stochastic fate transitions, driving abnormal expansion with halted differentiation into mature AT1 cells. The genetic deletion of Il1r1 signalling impedes oncogenic expansion by disrupting this reprogramming trajectory, underscoring its significance in tumour initiation. Significantly, our analysis of oncogene-associated multi-colour reporter mouse models reveals a tissue- wide systemic injury response elicited by oncogenic clones in neighbouring wildtype AT2 cells, modulating their fitness programme. Moreover, we identify sustained NF-kB activation in reprogrammed cell states, setting neoplastic transformation apart from normal regeneration by preventing oncogenic exit into the differentiated AT1 state. Collectively, this work delineates the common mechanisms governing lineage infidelity across diverse tissues and proposes a compelling target amenable to therapeutic manipulation.

overall_design: Lineage-labelled RFP+ or YFP+ cells were isolated from the distal lungs of either Sftpc-CreERT2; Confetti or Il1r1 loxP/loxP; Sftpc-CreERT2; R2Kras mice administered with  3 x 0.2mg/gbw tamoxifen and isolated at various timepoints post-induction as indicated. Individual libraries were prepared for each sample and sequenced via 10x Genomics


title: Succinate Dehydrogenase Regulates Homeostasis and Metabolic Integrity of Alveolar Macrophages

status: Public on Feb 07 2025

first: Seung Geun

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

institute: Seoul National University

summary: Lung tissue-resident macrophages (TRMs), including alveolar macrophages (AMs) and interstitial macrophages (IMs), are pivotal in maintaining both immune defense and tissue homeostasis. Although the distinct functional roles of these macrophage populations are well recognized, the specific metabolic pathways that support their functions are not fully understood. Comparative RNA sequencing analysis identified Sdha, a key enzyme in mitochondrial metabolism, as one of the most highly expressed and differentially regulated genes involved in metabolic pathways in AMs relative to IMs. This finding led us to investigate the role of succinate dehydrogenase complex subunit A (SDHA) in regulating AM metabolism and function. Here, we demonstrated that SDHA is crucial for maintaining AM homeostasis. Deletion of SDHA resulted in a significant reduction in AM populations without affecting IMs, highlighting an AM-specific requirement for SDHA. In the absence of SDHA, AMs underwent metabolic reprogramming towards glycolysis compared with IMs, along with significant transcriptional changes and cell death. Furthermore, SDHA-deficient AMs showed lipid accumulation and increased endoplasmic reticulum (ER) stress. These findings establish SDHA as a crucial regulator of AM metabolism and underscore the importance of maintaining metabolic integrity for AM function and survival within the lung microenvironment.

overall_design: RNA-seq profiling of FACS-sorted CD45+ CD11c+ F4/80+ SiglecF+ CD11b- alveolar macrophages from wildtype and Sdha-flox LysM-Cre knockout mice

first: Ein

first: Haaun

last: Moon

first: Doo Hyun

last: Chung


title: Chromatin regulator SMARCAL1 modulates cellular lipid metabolism

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Biallelic mutations of the chromatin regulator SMARCAL1 cause Schimke Immunoosseous Dysplasia (SIOD), characterized by severe growth defects and premature mortality. Atherosclerosis and hyperlipidemia are common among SIOD patients, yet their onset and progression are poorly understood. Using an integrative approach involving proteomics, mouse models, and population genetics, we investigated SMARCAL1's role. We found that SmarcAL1 interacts with angiopoietin-like 3 (Angptl3), a key regulator of lipoprotein metabolism. In vitro and in vivo analyses demonstrate SmarcAL1's vital role in maintaining cellular lipid homeostasis. The observed translocation of SmarcAL1 to cytoplasmic peroxisomes suggests a potential regulatory role in lipid metabolism through gene expression. SmarcAL1 gene inactivation reduces the expression of key genes in cellular lipid catabolism. Population genetics investigations highlight significant associations between SMARCAL1 genetic variations and body mass index, along with lipid-related traits. This study underscores SMARCAL1's pivotal role in cellular lipid metabolism, likely contributing to the observed lipid phenotypes in SIOD patients.

overall_design: Human hepatoma Huh7 cell lines with SMARCAL1 KO or WT SMARCAL1 were generated using CRISPR genome editing system. Total RNA from those cell lines were used for RNA-seq assays to detect the gene expression difference between the cells with SMARCAL1 KO and the control cells with WT SMARCAL1.


title: Identification and quantification of gene isoforms during the differentiation of human embryonic stem cells into pharyngeal endoderm and primordial germ cell-like cells

status: Public on Feb 17 2025

city: Ann Arbor

first: Kin Fai

last: Au

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Long-read RNA-seq is now widely applied for gene isoform identification and efforts to long-read RNA-seq for gene isoform quantification are emerging. We develop a software named miniQuant to quantify gene isoforms using long reads alone or in combination with short reads. We demonstrate the utility of miniQuant by its application in uncovering the expression dynamics of gene isoforms during the differentiation of human embryonic stem cells (ESC) into pharyngeal endoderm (PE) and primordial germ cell-like cells (PGC).

overall_design:
Using the in vitro differentiation systems we have recently developed, we generate definitive endoderm (DE) and pharyngeal endoderm (PE) (as described in our previous paper: DOI: https://doi.org/10.1101/2022.06.26.497457), and primordial germ cell-like cells (PGC) (as described in our previous paper: PMID: 37709760) from human embryonic stem cells (H1-hESC cell line), respectively.
We generate long-read RNA-seq data using Oxford Nanopore Technologies (ONT) PCR-cDNA sequencing (cDNA-ONT) and direct RNA sequencing (dRNA-ONT) protocols with one replicate, as well as short-read RNA-seq data using Illumina with three replicates.
We identify and quantify gene isoforms in ESC, PE and PGC samples.

first: Yunhao

first: Roberta

last: Sala

first: Andrea

last: Cipriano

first: Vittorio

last: Sebastiano

first: Chia-Lin

last: Wei

first: Kin-Fai


title: Endogenous aryl hydrocarbon receptor ligands-dysregulated transcriptomic profiles and endothelial function in human fetal endothelial cells

status: Public on Feb 10 2025

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

summary: Preeclampsia (PE) is a hypertensive disorder and a leading cause of maternal and fetal mortality and morbidity during human pregnancy. Aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, regulates vascular development and function during pregnancy. Here, we report the important role of endogenous AhR ligands in endothelial growth and function during pregnancy using human umbilical vein endothelial cells (HUVECs) as a model.  We found that ITE, ([2-(1’H-indole-3’-carbonyl)-thiazole-4-carboxylic acid methyl ester], an endogenous AhR ligand) decreased cell proliferation and monolayer integrity in HUVECs in vitro.  ITE also dysregulated transcriptomic profiles of HUVECs in a fetal sex-specific manner. The ITE-dysregulated genes were enriched in biological function and pathways highly relevant to cardiovascular diseases, vascular function, and inflammation responses. We conclude that dysregulation of endogenous AhR ligands may contribute to the PE-impaired endothelial function through fetal sex-specific regulation of endothelial transcriptomes. These AhR ligand-activated genes and pathways might represent promising therapeutic and sex-specific targets for PE-impaired endothelial function.

overall_design: To investigate the role of ITE on HUVECs function. Male and female HUVECs were treated with ITE.

first: Yingjie

last: Zhao

first: Chi

last: Zhou

first: Jing

last: Zheng


title: Multi-modal analysis of satellite cells reveals early impairments at pre-contractile stages of myogenesis in Duchenne muscular dystrophy

status: Public on Feb 06 2025

city: München

first: Sophie

last: Franzmeier

address: Veterinärstraße 13

institute: LMU Munich

summary: Recent studies on the role of myogenic satellite cells (SC) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SC in DMD patients and animal models. It remains unknown however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. Addressing this, we isolated SC from muscle biopsies of a porcine DMD model for characterization. Traction force microscopy (TFM) revealed that DMD SC produce a significantly higher strain energy than wild-type cells (WT; 0.136 ± 0.016 µJ vs. 0.057 ± 0.008 µJ). By RNA-seq, we identified 1,390 differentially expressed genes and proteomics measurements detected 1,261 proteins with altered abundance in DMD vs. WT. Dysregulated pathways uncovered by Gene Ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. We integrated the data using multi-omics factor analysis (MOFA) and identified five factors accounting for the variance with an overall higher contribution of the transcriptomic (61.95 %) than the proteomic data (54.02 %). Our findings suggest SC impairments to result from their own genetic abnormality rather than environmental influences and the observed biological changes are independent and not reactive to the pathological surrounding of DMD muscle.

overall_design: Gene expression analysis of RNA-seq data of myogenic SC derived from a translational porcine model for DMD compared to their healthy WT counterpart. Cells were harvested for sequencing during proliferation (PROL) and after differentiation into multinucleated myotubes (DIFF)

first: Shounak

last: Chakraborty

first: Armina

last: Mortazavi

first: Jan

middle: B

last: Stöckl

first: Jianfei

last: Jiang

first: Nicole

last: Pfarr

first: Benedikt

last: Sabass

first: Thomas

last: Fröhlich

first: Clara

last: Kaufhold

first: Michael

last: Stirm

first: Eckhard

last: Wolf

first: Jürgen

last: Schlegel

first: Kaspar

last: Matiasek


title: Targeting Ewing sarcoma cells via small molecule YK-4-279 treatment and downregulation of DHX9 helicase [1]

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: To investigate the function of DHX9 in Ewing sarcoma cell growth and proliferation, we targeted DHX9 gene by shRNA or EWS_FLI1/DHX9 interaction by YK-4-279 treatment.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of TC-71 cells treated with either DMSO or YK-4-279 2mM, or transfected with either control or DHX9 shRNAs.

first: M

middle: P

last: Paronetto

first: N

last: Mercatelli

first: R

last: Palombo


title: Single Cell Immune Profiling in Ankylosing Spondylitis Reveals Resistance of CD8+ T cells to Immune Exhaustion

city: Toronto

last: Tang

address: 60 Leonard Ave. 5KD-408

institute: University Health Network

summary: Persistent chronic inflammation is a hallmark of Ankylosing Spondylitis (AS), with cytotoxic T cells (CTLs) increasingly implicated in its pathogenesis. Ordinarily, T cell exhaustion follows sustained, persistent T cell activation to limit collateral tissue damage. Using mass cytometry and single-cell RNA sequencing (scRNA-seq), we identified a clonally expanded CTL subset in AS synovial fluid that expresses inhibitory receptors (PD-1, TIGIT, LAG-3) yet retains its effector capacity to express granzymes, perforin, TNF-a, and IFN-g. Gene expression profile of this CTL subset show downregulation of canonical exhaustion markers. At the protein level, TOX, a critical transcription factor regulating CTL exhaustion, is downregulated in PD-1+TIGIT+LAG-3+CTLs. In-silico trajectory analyses suggest these cells may differentiate into other effector CTL subsets. Our findings reveal a checkpoint-expressing CTL population in AS that resists exhaustion and retains an activated, effector phenotype. We propose that failure to undergo exhaustion may be a fundamental mechanism sustaining AS chronic inflammation.

overall_design: Peripheral blood mononuclear cells (PBMCs) and synovial fluid mononuclear cells (SFMCs) isolated from AS patients annd healthy control subjuects were thawed, and then FACS (Fluorescence activated cell sorting)-sorted for CD45RO+ CD3+ CD8+ cells for single cell RNA sequencing. For three patients, CD45RO+ CD3+ CD8+ PD-1+ TIGIT+ CD127- cells were also FACS-sorted. We generated libraries for single cell immune profiling (10x Genomics; 5' Gene expression integrated with VDJ profiling).

first: Zoya

last: Qaiyum

first: Robert

last: Inman


title: Single cell transcriptomic profiling reveals a dynamic molecular landscape and the importance of ligand-receptor genes and transcription factors during the progression of colorectal cancer

status: Public on Feb 01 2025

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

institute: The Affiliated Hospital of Nanchang University

summary: By analyzing the scRNA-seq data from ten human colorectal specimens, which represent the four kinds of colorectal tissues (normal colorectal mucosa, inflammatory polyps, Adenomatous polyps and colorectal cancer), in combination with validation by immunofluorescence staining using expanded clinical samples, and together with verification using large scale TCGA and Kaplan–Meier data, we reveal a dynamic molecular landscape and the importance of ligand-receptor genes and transcription factors driving the colorectal carcinogenesis.

overall_design: Under informed consent and ethical review, a total of 10 colorectal specimens were collected from colon or rectum from patients who underwent endoscopy examination (non-CRC colorectal mucosa samples) or surgery (CRC samples) at Yichun People’s Hospital, Jiangxi, China

first: Huizhen

last: Fan

first: Jianwen

last: Sheng

first: Jianping

last: Liu

first: Yin

last: Zhu

first: Nianshuang

last: Li


title: Immune and tumor cell landscape in pediatric high grade gliomas

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: Single cell RNA-seq profiling of tumor, myeloid, and T cells from fresh pediatric high grade glioma samples

overall_design:
Gene expression profiling by high throughput single cell RNAseq of 28 patient tumor samples by both SmartSeq2 and 10X Genomics

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Jenna

last: LaBelle

first: Rebecca

last: Poetschke

first: Mariella

last: Filbin


title: Sustained NF-kB activation allows mutant alveolar stem cells to co-opt a regeneration program for tumor initiation [Expt1]

first: Joo-Hyeon

last: Lee

overall_design: Lineage-labelled RFP+ or YFP+ cells were isolated from the distal lungs of either Sftpc-CreERT2; Confetti or Sftpc-CreERT2; R2Kras mice administered with 3 x 0.2mg/gbw tamoxifen and isolated at various timepoints post-induction as indicated. Individual libraries were prepared for each sample and sequenced via 10x Genomics.

first: Frances

last: England

first: Benjamin

last: Simons


title: Treatment-Resistant Prostate Cancer Stem Cell Plasticity Governed by MUC1-C Uncovers a Common target for ADC Treatment

first: Keisuke

last: Shigeta

address: 450 Brookline Avenue

summary: Androgen receptor positive prostate cancer (PC), castration resistant prostate cancer (CRPC) and neuroendocrine prostate cancer (NEPC) represent a spectrum of malignancies that invariably become resistant to treatment with targeted and cytotoxic agents. There is no known common pathway responsible for these pleotropic mechanisms of resistance. The MUC1 gene is aberrantly expressed in CRPC and NEPC in association with poor clinical outcomes. The present results demonstrate that the oncogenic MUC1-C protein is necessary for resistance of (i) PC cells to enzalutamide (ENZ), and (ii) CRPC and NEPC cells to docetaxel (DTX). We show that MUC1-C-mediated ENZ and DTX resistance is conferred by upregulation of aerobic glycolysis and suppression of reactive oxygen species (ROS) necessary for self-renewal capacity. Common dependence of these drug-resistant phenotypes on MUC1-C for the cancer stem cell (CSC) state thus identified a potential new target for their treatment. cIn this context, we further demonstrate that targeting MUC1-C with an antibody-drug conjugate (ADC) is highly effective in suppressing (i) self-renewal of drug-resistant CRPC and NEPC CSCs and (ii) growth of t-NEPC tumor xenografts derived from drug-resistant cells and a patient with refractory disease. These findings reveal a shared MUC1-C-dependent pathway in drug-resistant CRPC and NEPC progression and identify MUC1-C as a target for their treatment with an ADC.

overall_design: RNA Seq in H660 Cell lines with MUC1-C shRNA silencing. We compared DMSO and DOX treatment cells for differential gene expression analysis. MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).


title: METTL3 Knockout Accelerates Hepatocarcinogenesis via Inhibiting Endoplasmic Reticulum Stress Response

status: Public on Feb 15 2025

first: Yan

last: Xu

state: Guangdong

address: No. 600 Tianhe Road

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: Hepatocellular carcinoma (HCC) is among the most common cause of cancer-related death worldwide. Previous studies showed that N6-methyladenosine (m⁶A), the most abundant chemical modification in eukaryotic RNAs, is implicated in HCC progression. Using liver-specific conditional knockout mice, here we found that loss of METTL3, the core catalytic subunit of m⁶A methyltransferase, significantly promoted hepatic tumor initiation under various oncogenic challenges, contrary to the previously reported oncogenic role of METTL3 in liver cancer cell lines or xenograft models. Mechanistically, METTL3 deficiency accelerates HCC initiation by inhibiting m6A/Manf/endoplasmic reticulum (ER) stress response. Our findings suggest a tumor-suppressive role for METTL3 in the early stages of HCC, emphasizing the importance of understanding the dynamic role of epigenetic regulation in tumorigenesis and targeted therapy.

overall_design: RNA-sequencing were conducted on liver tissues from Control and liver-specific METTL3 inducible knockout (Mettl3 cKO) mice 3 weeks post-hydrodynamic tail vein injection of c-MYC/sgP53 plasmids (4 individuals per group)

first: Qi

last: Zhang

first: Huaxin

last: Chen

first: Bo

last: Cui

first: Silin

last: Tu


title: Multi-omics deciphers details of chitin decomposition in soil by a model bacterial consortium.

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: Soil microorganisms carry out decomposition of complex organic carbon molecules, such as chitin. High diversity of the soil microbiome and complexity of the soil habitat has posed a challenge to elucidate specific interactions between soil microorganisms. Here, we overcame this challenge by studying a model soil consortium (MSC-2) that is composed of 8 species. The MSC-2 isolates were originally obtained from the same soil that was enriched with chitin as a substrate. Our aim was to elucidate specific roles of the 8 member species during chitin metabolism in soil. The 8 species were added to sterile soil with chitin and incubated for 3 months. Multi-omics was used to understand how the community composition, transcript and protein expression and chitin-related metabolites shifted during the incubation period. The data clearly and consistently revealed a temporal shift during chitin decomposition and defined contributions by individual species. A Streptomyces species was a key player in early steps of chitin decomposition, followed by other members of MSC-2. These results illustrate how multi-omics applied to a defined consortium untangles complex interactions between soil microorganisms.

sample_organism: Rhodococcus sp. (in: high G+C Gram-positive bacteria)

overall_design:
MSC-2 species were inoculated into sterile soil and incubated at KSC. A set of tubes was inoculated for each dilution and timepoint (five replicates). At each timepoint (0, 4, 8 and 12 weeks) that set of tubes (both dilutions) was stored at -80C. At the final 12 week timepoint all tubes were processed for RNA extraction and sequencing using Illumina technology.
RNA was aligned to reference genomes for each of the eight species using the Burrows Wheeler Aligner and counted using HTSeq. Raw counts were normalized using DESeq2 and comparisons were made between timepoints to identify differentially expressed genes

first: McClure

last: Ryan

first: Jansson

last: Janet

first: Rivas

last: Albert


title: Comprehensive resolution and classification of the Epstein Barr virus transcriptome

status: Public on Jan 31 2025

city: New Orleans

first: Truong

last: Nguyen

state: Louisiana

address: 1700 Tulane Avenue

department: Pathology

institute: Tulane University, School of Medicine

summary: Virus genomes harbor compacted repertoires of genes and regulatory elements. Through long-read sequencing, we provide a comprehensive Epstein Barr virus (EBV) transcriptome analysis, identifying 1453 transcript isoforms and resolving the major isoform of all but one lytic reading frame. Further, we categorize each transcript according to their dependence on viral DNA replication. We show that the late gene viral preinitiation complex, vPIC also activates early promoters/genes, we identify active alternate promoters with distinct dependencies on viral DNA replication, we discover biphasic promoters with embedded features of both early and late promoters. Genetic and chromatin interaction studies identify an enhancer function for the viral lytic origin of replication (OriLyt). We also observe substantial viral read-through transcription that likely causes transcriptional interference and fine tuning of viral promoter activity. In some loci with same direction overlapping gene configurations, polyA read-through is necessary to facilitate transcription through entire ORFs while also giving rise to highly abundant viral lncRNAs due to the partial nature of read-through. Altogether, this study identifies extensive viral transcriptome diversity, it resolves the major isoforms for nearly all lytic ORFs, and it identifies the alternative regulatory modes driving the temporal regulation of EBV lytic gene expression.

overall_design: This study systematically mapped the Epstein-Barr virus (EBV) transcriptome during lytic reactivation using two EBV-positive cell models (Akata and Mutu) and fluorescence-activated cell sorting to purify lytically reactivated cells. High-depth Oxford Nanopore Technologies (ONT) long-read cDNA sequencing was performed to capture full-length viral transcripts. Transcript features were validated and annotated using CAGE-seq (for TSS mapping), short-read RNA-seq (for splice junctions and expression), and ONT 3′ end analysis. Chromatin interactions were assessed with Micro-C/HiC, and polysomal profiling was used to evaluate translation of novel isoforms. Protein structures from new transcripts were predicted with AlphaFold3. All data were processed and integrated using a custom computational pipeline developed in Python, Perl, R, and Bash, enabling comprehensive classification of over 1,400 EBV transcript isoforms and revealing new regulatory mechanisms of viral gene expression.

first: Jia

last: Wang

first: Meggie

last: Lam

first: Harris

last: McFerrin

first: Tina

last: O’Grady

first: Claire

last: Roberts

first: Nicholas

middle: V

last: Otterloo

first: Trang

first: Melody

last: Baddoo

first: Dorota

last: Wyczechowska

first: Maria

last: Morales

last: Dong

first: Erik

last: Flemington


title: Formation of malignant, metastatic small cell lung cancers through overproduction of cMYC protein in TP53 and RB1 depleted pulmonary neuroendocrine cells derived from human embryonic stem cells

status: Public on Feb 14 2025

first: Yajas

last: Shah

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: We recently described our initial efforts to develop a model for small cell lung cancer (SCLC) derived from human embryonic stem cells (hESCs) that were differentiated to form pulmonary neuroendocrine cells (PNECs), a putative cell of origin for neuroendocrine-positive SCLC. Although reduced expression of the tumor suppressor genes TP53 and RB1 allowed the induced PNECs to form subcutaneous growths in immune-deficient mice, the tumors did not display the aggressive characteristics of SCLC seen in human patients. Here we report that the additional, doxycycline-regulated expression of a transgene encoding wild-type or mutant cMYC protein promotes rapid growth, invasion, and metastasis of these hESC-derived cells after injection into the renal capsule. Similar to others, we find that the addition of cMYC encourages the formation of the SCLC-N subtype, marked by high levels of NEUROD1 RNA. Using paired primary and metastatic samples for RNA sequencing, we observe that the subtype of SCLC does not change upon metastatic spread and that production of NEUROD1 is maintained. We also describe histological features of these malignant, SCLC-like tumors derived from hESCs and discuss potential uses of this model in efforts to control and better understand this recalcitrant neoplasm.

overall_design: Single-cell capture, reverse transcription, cell lysis, and library preparation were carried out by the WCM Epigenomics Core Facility using Chromium Single Cell 3’ v3 kits according to the manufacturer’s protocol (10x Genomics, USA). Single cell suspenions of RUES2-dervied RPM and RPM (T58A) day 50 cultures were prepared by incubating wells in 0.05% Trypsin/0.02% EDTA for 10-15 min. Digestions were then quenched with excess 0.1% BSA/PBS buffer and passed through 40μm mesh strainer. EGFP+ singlets were sorted at the WCM Flow Cytometry Core Facility on a BD Influx or Sony MA900 cell sorter. Each RUES2-dervied RPM and RPM(T58A) day 50 culture pools were isolated from 3 wells of a 12-well plate across two biological replicates, targeting ∼50,000 viable, EGFP+ viable cells per replicate. Cell counts were then adjusted to 6000-9000 cells/50uL in PBS by Trypan Blue exclusion to achieve an estimated capture of 4000-5000 cells. Sequencing was performed by the WCM Genomics Resources Core Facility on a HiSeq 2500 (Illumina, paired-end protocol with 26 base pairs for read 1 and 98 bases for read 2). Single cell RNA sequencing from RP cultures were obtained from previous experiments (5). Transcript abundance was quantified by mapping sequencing reads to a custom human transcriptome reference (GENCODE v42, hg38) that included EGFP and was performed using simpleaf/alevin-fry (12).

first: Eric

last: Gardner

first: Huanhuan

last: Chen

first: Harold

last: Varmus


title: LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by upregulating RHOB via HDAC1 suppression

city: Vienna

first: Quanah

last: Hudson

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

summary: Endometriosis is a common disease in women characterized by the growth of endometrial-like lesions at ectopic sites, associated with chronic pelvic pain and infertility. LINC01638 is a long non-coding RNA (lncRNA) that in several cancers has been implicated in the regulation of proliferation and epithelial-to-mesenchymal transition (EMT). Given that these processes are also important in endometriosis, we investigated the role of LINC01638 in this disease. We found that LINC01638 is upregulated in the epithelial layer of endometriosis lesions, and that knockdown of the gene in 12Z epithelial endometriosis cell line led to reduced proliferation, adhesion, migration and invasion. The reduction in proliferation was associated with increased p21 and p27 expression and G1 phase arrest of 12Z cells, showing that LINC01638 acts as an important epigenetic regulator of endometriosis epithelial cells cell cycle progression. Further, transcriptome analysis of LINC01638 control and knockdown cells revealed that a number of transcription factors associated with EMT are downregulated in the knockdown, including FOXC2, SNAI2, TWIST1 and ZEB1, along with the mesenchymal marker VIM. These genetic and phenotypic changes in 12Z knockdown cells were accompanied by a significant reduction in expression of cytoskeleton regulatory gene RHOB and an upregulation of HDAC1 expression. Chromatin immunoprecipitation analysis and HDAC1 inhibitory treatment in LINC01638 control and knockdown cells indicated that LINC01638 regulates RHOB expression via HDAC1 mediated regulation of its promoter acetylation. In vivo, RHOB is upregulated in the epithelial layer of endometriosis lesions compared to control and endometriosis patient eutopic endometrium, supporting a role in the disease. Together these results indicate that LINC01638 is an epigenetic regulator of pathogenesis of endometriosis promoting proliferation and EMT of endometriosis lesions.

overall_design: To investigate the role of LINC01638 in endometriosis we performed an siRNA knockdown experiment in the 12Z endometriosis epithelial cell line followed by transcriptomic analysis 72 hours post knockdown. We performed 50bp paired-end stranded total RNA-seq (Ribo-Zero depletion) with a NovaSeq SP Illumina machine on 3 control siRNA and 3 LINC01638 knockdown samples.

first: Iveta

last: Yotova

first: Florian

last: Pauler


status: Public on Feb 13 2025

state: LA

address: 1430 Tulane Avenue

institute: Tulane University

summary: Virus genomes harbor highly compacted repertoires of genes and regulatory elements. Here, we report the most comprehensive Epstein Barr virus (EBV) transcriptome analysis to date, significantly expanding the number of known transcript isoforms to 1453 and resolving the major isoform of all but one lytic open reading frame. We also categorize each transcript according to their dependence on viral DNA replication, classifying transcripts as “early”, “leaky late”, or “late”. We identify a role for the viral preinitiation complex, vPIC in not only facilitating late gene expression but also in contributing to the expression of early promoters/genes. These studies also increased our understanding of the complexity of viral regulatory programs by identifying significantly active alternate promoters with distinct dependencies on viral DNA replication as well as biphasic promoters with embedded properties of both early and late promoter features. Genetic analyses identified an enhancer function for the viral lytic origin of replication (OriLyt) throughout the virus genome. We found substantial viral read-through transcription that is predicted to cause transcriptional interference and fine tuning of the temporal regulation of viral promoters. Further, in some loci with same direction overlapping gene configurations, polyA read-through is necessary to facilitate transcription through the entire ORF, but also gives rise to highly abundant viral lncRNAs due to the partial nature of read-through. Altogether, this study identified extreme viral transcriptome diversity, it resolved the major isoforms for nearly all lytic ORFs, and it identified novel regulatory modes driving and fine-tuning the temporal regulation of EBV lytic gene expression.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: In this study, we aimed to significantly improve the resolution of the EBV transcriptome and to gain insights into regulatory processes controlling progression through the lytic gene expression cascade. To achieve this, we performed high-depth Oxford Nanopore Technologies (ONT) sequencing, used public CAGE-seq, and RNA-seq datasets through utilizing two distinct EBV reactivation models and we employed purification methods to selectively isolate reactivated cells from contaminating latent cells.

first: Truong

last: Nguyen


title: Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis

status: Public on Feb 12 2025

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly recognized for its medical and socioeconomic impacts, driven by diverse genetic and environmental factors. To address the urgent need for individually tailored therapies, we performed single-cell expression quantitative trait loci (sc-eQTL) analysis on liver biopsies from 25 MASLD patients and 23 controls. This approach identified over 3,500 sc-eQTLs across major liver cell types and cell state-interacting eQTLs (ieQTLs) with significant enrichment for disease heritability (for MASLD trait, ieQTL enrichment odds ratio = 10.27). We integrated transcription factors (TFs) as upstream regulators of ieQTLs, revealing 601 functional units (“quartets”) composed of TFs, cell states, ieSNPs, and ieGenes. From these results, we pinpoint the loss of an eQTL in EFHD1 during hepatocyte maladaptation associated with genotype-specific regulation by FOXO1, further contributing to the risk of MASLD. Our approach underscores the role of eQTL analysis in capturing crucial genetic variations that influence gene expression and clinical outcomes in complex diseases.

overall_design: Frozen liver tissues were processed to generate 10x Genomics-based snRNA-seq data in GENINUS (Seoul, Republic of Korea). Tissues were homogenized, and isolated nuclei was counted using flow cytometry (BD: FACSMelodyTM Cell sorter). 10x Genomics chromium instrument and cDNA synthesis kit v3 were used to generate barcoded cDNA libraries. cDNA library quality was determined using an Agilent Bioanalyzer. Two paired-end sequencing with a read length of 100 bp was performed with Illumina Novaseq6000.

first: Sung Eun

last: Hong

first: Kyung-Suk

last: Suh

first: Won

last: Kim


title: Agilent aCGH array data for meningioma samples

first: Scott

middle: Thomas

last: Ryall

state: Massachusetts

address: 75 Francis Street

institute: Brigham and Women's Hospital

type: Genome variation profiling by genome tiling array

summary: We analyzed 1042 meningiomas with whole-genome microarray including 12 meningiomas with multifocal sampling to characterize how CNV thresholds influence their molecular classification and outcome.

overall_design: Agilent aCGH arrays were performed according to the manufacturer's directions on DNA extracted from formalin-fixed paraffin embedded (FFPE) brain tumor specimes with a minimum of 60% tumor content as defined by a certified neuropathologist.

first: Wenya

middle: L

last: Bi

first: Ruchit

last: Patel


title: Affymetrix SNP array data for meningioma samples

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

overall_design:
Affymetrix OncoScanHD SNP arrays were performed according to the manufacturer's directions on DNA extracted from formalin-fixed paraffin embedded (FFPE) brain tumor specimes with a minimum of 60% tumor content as defined by a certified neuropathologist.
Note: Files labelled MN_545, MN_602, MN_610, MN_625 are lacking .cel files. These files were erroneously corrupted and were not able to be recovered.


title: Amprenavir Mitigates Pepsin-Induced Transcriptomic Changes in Normal and Precancerous Esophageal Cells

city: Milwaukee

first: Victor

last: Jin

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

summary: Background: Gastroesophageal reflux disease (GERD) is a chronic condition linked to inflammatory and cancerous alterations in esophageal epithelium. Despite the widespread use of acid suppressing proton pump inhibitors (PPIs), the incidence of esophageal adenocarcinoma (EAC) keeps increasing, underscoring the possible importance of nonacidic reflux components like pepsin in cancer development. Pepsin, a therapeutic target for GERD, has been associated with epithelial damage and metaplasia. Methods: The goal of this study was to investigate the effect of pepsin, at a transcriptional level, and to assess the potential therapeutic value of amprenavir, as a pepsin inhibitor, in vitro. Human esophageal cell lines, immortalized from normal (Het-1A) and Barrett’s esophagus (BAR-T), were exposed to pH 7.0 buffer containing pepsin and/or amprenavir for 1 hour (n=3). RNA-seq was conducted to detect differentially expressed genes (DEGs) with FDR ≤ 0.05 and |log2 fold change| ≥ 0.375, and Ingenuity Pathway Analysis (IPA) was performed to identify the top significantly biological pathways. Results: Pepsin exposure caused notable transcriptomic alterations in both Het-1A and BAR-T cells, specifically impacting mitochondrial function, oxidative phosphorylation, and pathways associated with epithelial integrity, cell signaling, and inflammatory responses. Amprenavir alleviated several of these effects, indicating a protective function in epithelial impairment resulting from peptic injury. Of interest, Het-1A and BAR-T cells demonstrated different reactions to pepsin treatment; BAR-T cells revealed more pronounced changes in pathways associated with wound healing, chronic epithelial formation, and repair, whereas Het-1A cells showed more substantial alterations in systemic damage and mitochondrial pathways. Conclusion: The results of this study underscore the detrimental impact of pepsin on esophageal epithelial cells despite PPI therapy and highlight amprenavir as a promising therapeutic option to mitigate pepsin-induced epithelial injury. Further research to validate these in vitro findings is warranted to assess the efficacy of amprenavir for GERD-related damage and carcinogenesis.

overall_design: RNA-seq was performed on two cell lines, Het-1A and BAR-T, under three conditions: "Control," "Pepsin," and "Pepsin+APR," with three replicates per condition, resulting in a total of 18 samples.

first: Pelin

last: Ergun

first: Tina

last: Samuels

first: Angela

last: Mathison

first: Tianxiang

last: Liu

first: Nikki

last: Johnston


title: Influence of Pleurotus sapidus fruiting bodies on performance, cecum microbiome and intermediary metabolism in liver and breast muscle of broilers

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: Despite the need to enhance feed production for monogastric farm animals, this challenge is complicated by the fact that natural resources are becoming increasingly limited and climate protection goals have to be considered. Thus, there is a need for alternative feed sources, which are produced in a resource-efficient and sustainable manner. Valorization of low-value agricultural sidestreams by edible fungi, such as Pleurotus sapidus (PSA), has been proposed as a strategy to utilize such sidestreams as a sustainable source of feed for monogastric farm animals, because P. spp. are capable of degrading a wide array of fiber-rich substrates. In a recent study, we have demonstrated that feeding a biotechnologically produced PSA mycelium to broilers does not affect growth performance and nutrient digestibility and causes only weak effects on the cecal microbiota community, the liver transcriptome and the plasma metabolome of broilers. In order to clarify if the effect of the mycelium differs from that of the fruiting bodies, the present study investigated the effect of PSA fruiting bodies on the performance, the gut microbiome and the transcriptome and the lipid metabolism in the liver of broilers.

overall_design: 72 male, 1-day-old Cobb 500 broilers were randomly assigned to three different groups and fed three different adequate diets containing either 0 (group PSA-F0), 25 (group PSA-F25) or 50 (group PSA-F50) g/kg diet of P. sapidus fruiting bodies in a three-phase feeding system (starter diet form day 1-10, grower diet from day 11-21, finisher diet from day 22-35).

first: Lea

last: Schäfer

first: Klaus

last: Eder


title: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

city: Chapel Hill

first: Karen

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Chromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory elements that may underlie genetic effects on gene expression and clinical quantitative traits. However, caQTL discovery has been limited by the sample sizes of previous studies. Here, we mapped caQTL in liver tissue from 138 human donors and identified caQTL for 35,361 regulatory elements. We identified 2,126 caQTL signals containing multiple regulatory elements, suggesting coordinated regulation of elements at these loci. CaQTL showed strong heritability enrichment and colocalization with genome-wide association study (GWAS) signals for traits relevant to liver function. We identified a colocalized caQTL at 667 GWAS signals for 17 traits, used multiple methods to predict target genes, and validated caQTL predictions at two loci using functional assays. These results demonstrate the power of caQTL to characterize gene regulation and predict regulatory mechanisms at GWAS loci.

overall_design: ATAC-seq on liver tissue from 138 human donors

first: Kevin

middle: W

last: Currin

first: Hannah

last: Perrin

first: Amy

middle: S

last: Etheridge

first: Swarooparani

last: Vadlamudi

first: Annie

middle: E

last: Musser

first: Gautam

last: Pandey

first: Abdalla

middle: A

last: Alkhawaja

first: K

last: Broadaway

first: Jonathan

last: Rosen

first: Arushi

last: Varshney

first: Amarjit

last: Chaudhry

first: Paul

last: Gallins

first: Yihui

last: Zhou

first: Stephen

middle: C

last: Parker

first: Laura

last: Raffield

first: Fred

last: Wright

first: Erin

last: Schuetz

first: Federico

last: Innocenti


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations [patient glioblastoma tumors]

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

summary: Glioblastoma (GBM) remains the most common and lethal adult malignant primary brain cancer with few treatment options. One of the most significant issues hindering GBM therapeutic development is intratumor heterogeneity. GBM tumors consist of multiple neoplastic cell types with distinct transcriptional profiles. Identifying compounds that target these different cell types requires a platform that predicts differential sensitivity and resistance of cells within GBM tumors. To address this, we developed a novel framework to generate tumor cell-type-specific disease signatures and their predicted drug sensitivity. We performed single-cell RNA sequencing of newly diagnosed and recurrent GBM tumors and identified compounds from the LINCS L1000 database with transcriptional response signatures selectively discordant with distinct single-cell transcriptional states within GBM tumors. We then validated in silico predictions with in vivo findings in mice as the aurora kinase inhibitor alisertib induced a shift from NPC-like to MES-like transcriptional states upon treatment. To allow other investigators to predict selective tumor cell type drug sensitivity in silico we developed a platform termed ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures).  Our studies suggest that ISOSCELES is a novel platform to identify cell populations that are sensitive and resistant to targeted therapies in GBM, which can inform treatment decisions in future clinical trials.

overall_design: Single-cell RNA sequencing analysis of 3 newly diagnosed and 3 recurrent (treated with RT & TMZ) patient glioblastoma tumors.

first: Robert

middle: K

last: Suter

first: Anna

middle: M

last: Jermakowicz


title: Extensive folding variability between homologous chromosomes in mammalian cells [ChIP-Seq]

status: Public on Jan 29 2025

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrueck Center for Molecular Medicine

summary: Genetic variation and  3D chromatin structure have major roles in gene regulation. Structural differences between genotypically different chromosomes and their effects on gene expression remain ill understood, due to challenges in mapping 3D genome structure with allele-specific resolution. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (ESC) line with high SNP density. Given its high efficiency of haplotype phasing, GAM resolves allele-specific 3D genome structures with high sensitivity. We discovered extensive genotype-specific folding of chromosomes in compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts and CTCF loops, often coinciding with allele-specific gene expression in association with Polycomb repression. We show that histone genes are expressed with allelic imbalance and involved in allele-specific chromatin contacts marked by H3K27me3. Functional analysis through conditional Ezh2- or Ring1b-knockdown shows a role for Polycomb repression in tuning histone protein levels. Our work reveals that the homologous chromosomes have highly distinct 3D folding structures, and their intricate relationships with gene-specific mechanisms of allelic expression imbalance.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA polymerase II phosphorylated on Serine 7 residues, RNA polymerase II phosphorylated on Serine 5 residues, and for histone modification H3K27me3, in F123 ESCs

first: Ibai

last: Irastorza-Azcarate

first: Rieke

last: Kempfer

first: Ren

last: Bing

first: Ana

last: Pombo


title: Activity-dependent gene regulations in PV+ interneurons

status: Public on Jan 28 2025

city: London

first: Martijn

last: Selten

address: 4th Floor, New Hunt's House, 18-20 Newcomen Street

department: CDN

institute: King's College London

summary: Neuronal activity is regulated in a narrow permissive band for the proper operation of biological neural networks. Changes in synaptic connectivities and network processes during key cognitive activity such as learning might disturb this balance, eliciting compensatory mechanisms to maintain network function1–3. In the neocortex, excitatory pyramidal cells and inhibitory interneurons exhibit robust forms of stabilising plasticity. However, while neuronal plasticity has been thoroughly studied in pyramidal cells4–8, comparatively little is known about how interneurons adapt to ongoing changes in their activity. Here we uncover critical cellular and molecular mechanisms underlying homeostatic regulation of parvalbumin-expressing (PV+) interneurons activity in mouse neocortex. We found that changes in the activity of PV+ interneurons drive cell-autonomous, bi-directional compensatory adjustments of the number and strength of inhibitory synapses received by these cells, specifically from other PV+ interneurons. High-throughput profiling of ribosome-associated mRNAs revealed that increasing the activity of PV+ interneurons leads to the cell-autonomous upregulation of Vgf, a gene encoding multiple neuropeptides. Functional experiments conclusively point towards the role VGF in mediating activity-dependent scaling of inhibitory synapses in PV+ interneurons. Our findings reveal an instructive role for VGF in regulating the connectivity among PV+ interneurons in the adult neocortex.

overall_design: RNAseq of ribosome-associated RNAs of PV+ interneurons from  PvalbFlp/+;Neurod6Cre/+ mice at P42-P70 stage. Mice were infected with AAV-flox-fdio-HA-RPL10a-T2A-myc-hM3Dq at P1 and later treated for 48h with CNO for (4 samples) to increase activity of PV+ interneurons or with vehicle control for (4 samples).

first: Clémence

last: Bernard

first: Fursham

last: Hamid

first: Alicia

last: Hanusz-Godo

first: Fazal

last: Oozeer

first: Christoph

last: Zimmer

first: Oscar

last: Marin


title: Gene expression profile at single cell level of bone marrow and brain cells from young adult and aged mouse after chewing diet (CD) and long-term high-fat diet (HFD) feeding

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Aging is one of the risk factors for various maladies such as cognitive deficit and frailty, which are exacerbated under obesity. We used single cell RNA sequencing (scRNA-seq) to analyze the alteration in bone marrow and brain after long-term HFD in both young adult and aged mouse.

overall_design: Bone marrow and brain cells of 9-month old after 7-month CD (n=3) or HFD (n=3) and 18-month old C57BL/6 mice after 12-month CD (n=3) or HFD (n=3) were isolated and analyzed using scRNAseq.

first: Yidan

last: Pang

first: Changqing

last: Zhang