title: Diminished Immune Cell Adhesion in Hypoimmune ICAM-1 Knockout Human Pluripotent Stem Cells

city: Madison

first: Matthew

last: Brown

state: WI

address: 600 Highland Avenue, H4/733 CSC

institute: University of Wisconsin-Madison

summary: Gene edited human pluripotent stem cells (hPSCs) are a promising platform for developing reparative cellular therapies that evade immune rejection. Existing first-generation hypoimmune strategies have used CRISPR/Cas9 editing to modulate genes associated with adaptive immune responses, but have largely not addressed the innate immune cells, such as neutrophils, that mediate inflammation and rejection processes occurring early after graft transplantation. We identified the adhesion molecule ICAM-1 as a hypoimmune target that plays multiple critical roles in both adaptive and innate immune responses post-transplantation. In our experiments, we found that ICAM-1 blocking or knock-out (KO) in hPSC-derived cardiovascular therapies imparted significantly diminished binding of multiple immune cell types. ICAM-1 KO resulted in diminished T cell proliferation responses in vitro and in longer in vivo retention/protection of KO grafts following immune cell encounter in NeoThy humanized mice. The ICAM-1 KO edit was also introduced into existing first-generation hypoimmune hPSCs and prevented immune cell binding. This promising hypoimmune editing strategy has the potential to improve transplantation outcomes for regenerative therapies in the setting of cardiovascular pathologies and several other diseases.

overall_design: The iPSCs were originally from a thymus donor, and reprogrammed using episomal methods. Wild-type and ICAM-1 KO iPSCs, as well as WT-derived cardiomyocytes (CMs), in biological replicate cell culture wells were harvested for mRNA isolation. Librarys were made and the samples were sequenced on an Illumina sequencer

first: Sayandeep

last: Saha

first: William

last: Haynes

first: Jiwon

last: Seo

first: Natalia

last: Del Rio

first: Elizabeth

last: Young

first: Jue

first: Alexis

last: Holm

first: Mireya

last: Pimentel

first: Lauryn

last: Flannagan

first: Liupei

last: Huang

first: Wesley

last: Blashka

first: Lydia

last: Murphy

first: Merrick

last: Scholz

first: Abigale

last: Henrichs

first: Jayalaxmi

last: Suresh Babu

first: John

last: Steill

first: Jeremy

last: Kratz

first: Ron

last: Stewart

first: Timothy

last: Kamp


title: Enhancing Non-Small Cell Lung Cancer Treatment Utilizing Natural Killer Cell-Derived Extracellular Vesicles (NKEVS) As A Novel Adoptive Cellular Therapeutic [PBMC]

status: Public on Jul 09 2025

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

country: USA

institute: TGen

type: Expression profiling by high throughput sequencing

summary: An established mechanism contributing to Immune Checkpoint Inhibitor (ICI) therapy failure is tumor evasion of T-cell responses via downregulation of human leukocyte antigen (HLA). Conversely, the effector function of Natural Killer (NK) cells is enhanced in the absence of HLA expression, making NK-based cellular therapies an attractive option for tumors that are resistant to ICIs. We investigated the preclinical efficacy of using selective isolation of NK cells and harvesting of NKEVs in NSCLC. Single-cell RNAseq (scRNAseq) was used to examine the cellular landscape in PBMCs and tumor tissue. NK cells were isolated from PBMCs, expanded in vitro, and NK-derived EVs (NKEV) were collected and the EV RNA and protein cargo was characterized using proteomics and transcriptomics. The functional capabilities of patient derived NKEVs were assayed with 3-dimensional organoid-like structures derived from patient tumor cells.  This work described the cellular landscape in NSCLC circulating and tumor infiltrating immune cells. Additionally, it demonstrated that NKEVs can be successfully harvested from patient derived, expanded NK cells, and highlighted their anti-tumor properties in combination with standard-of-care therapies.

overall_design: Samples from NSCLC patients (n=10) enrolled in the study were collected at Baylor Scott and White, by trained medical personnel. Specifically, a blood sample was collected pre- and post- tumor resection surgery, and PBMCs were isolated via density gradient separation. From the tumor resection, whatever tissue was left behind after pathology and diagnostic tests, was snap frozen in preparation for scRNAseq. Everything was collected, and kept frozen at Baylor Scott and White, and shipped to the Translational Genomics Research Institute for analysis.

first: Ronan

last: Kelly

first: Kendall

last: Van Keuren Jensen

first: Joanna

last: Palade


title: The spatial landscape of glial pathology and T-cell response in Parkinson’s disease substantia nigra [pdtcrseq]

status: Public on Jul 10 2025

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

summary: Recent evidence, including identification of specific peripheral T-cell receptor sequences, indicates the adaptive immune response is associated with disease pathogenesis. However, the properties of T-cells in the brain regions where neurons degenerate are uncharacterized. We have analyzed the identities and interactions of T-cells in PD in post-mortem brain tissue using single nucleus RNA sequencing, spatial transcriptomics and T-cell receptor sequencing. We found that T-cells in the substantia nigra of PD brain donors exhibit a CD8+ resident memory phenotype, increased clonal expansion, and altered spatial relationships with astrocytes, myeloid cells, and endothelial cells. We also describe regional differences in astrocytic responses to neurodegeneration. Our findings nominate potential molecular and cellular candidates that allow a deeper understanding of the pathophysiology of neurodegeneration in PD. Together, our work represents a major single nucleus and spatial transcriptional resource for the fields of neurodegeneration and PD

overall_design:
Analysis of human brain samples using snRNAseq, spatial transcriptomics, and TCR sequencing merged with computational techniques to analyze glial pathology and T-call response in PD
TCR-seq data of alpha and beta chains in the substantia nigra of human patients between control and Parkinson patient

first: Maxwell

last: Ma

first: Fahad

last: Paryani

first: Kelly

last: Jakubiak

first: Shengnan

last: Xia

first: Susumu

last: Antoku

first: Adithya

last: Kannan

first: Jaeseung

last: Lee

first: Nacoya

last: Madden

first: Juncheng

last: Li

first: David

last: Chen

first: Gunnar

last: Hargus

first: Aayushi

last: Mahajan

first: Xena

last: Flowers

first: Ashley

last: Harms

last: Sulzer

first: James

last: Goldman

first: Peter

middle: A

last: Sims

last: Al-Dalahmah


title: mTORC1 inhibition activates the integrated stress response (ISR) in  TALL-1 cell line

city: Padova

first: Loredana

last: Urso

address: Via Gattamelata

department: IDMO

country: Italy

institute: Istituto Oncologico Veneto

summary: mTOR sensitized T-ALL cell lines and patient-derived xenografts (PDX) from patients with R/R T-ALL to the BCL-2 inhibitor Venetoclax.

overall_design: TALL-1 cells  were treated with vehicle or 10 µM Everolimus for  4 and 12 hours in presence or absence of ISRIB. RNAseq was performed on each samples.

first: Micol

last: Silic-Benussi

first: Alberto

last: Corradin

first: Vincenzo

last: Ciminale


title: Enhancing Non-Small Cell Lung Cancer Treatment Utilizing Natural Killer Cell-Derived Extracellular Vesicles (NKEVS) As A Novel Adoptive Cellular Therapeutic [EV RNA]

first: Eric

last: Alsop

overall_design: Samples from NSCLC patients (n=10) enrolled in the study were collected at Baylor Scott and White, by trained medical personnel. Specifically, a blood sample was collected pre- and post- tumor resection surgery, and PBMCs were isolated via density gradient separation. From the tumor resection, whatever tissue was left behind after pathology and diagnostic tests, was snap frozen in preparation for scRNAseq. Everything was collected, and kept frozen at Baylor Scott and White, and shipped to the Translational Genomics Research Institute(TGen) for analysis. At TGen, PBMCs were thawed, the NK cells were isolated via negative selection and magnetic beads, and cultured in suspension for 2-4 weeks. Cell culture medium was retrieved every 48 hours, and size exclusion chromatography was used to isolate the extracellular vesicles.

first: Ronan

last: Kelly

first: Kendall

last: Van Keuren Jensen

first: Joanna

last: Palade


title: Replisomes restrict SMC translocation in vivo

status: Public on Jul 07 2025

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Structural maintenance of chromosomes (SMC) complexes organize genomes by extruding DNA loops. How collisions between SMC complexes and DNA polymerases are resolved in vivo remains poorly understood. Taking advantage of the ability to load SMC complexes at defined sites in the Bacillus subtilis genome, we investigated this problem. We engineered head-on and head-to-tail collisions between SMC complexes and the replisome, and monitored SMC translocation by time-resolved ChIP-seq and Hi-C and replisome progression by marker frequency analysis.  We report that SMC complexes do not affect replication progression. By contrast, the replisome blocks SMC translocation regardless of collision orientation. Combining experimental data with simulations, we determined that SMC is first blocked by the replisome and then released from the chromosome. However, occasionally SMC can bypass the replisome and continue translocating. Our findings establish that the replisome is a barrier to SMC-mediated DNA-loop extrusion, with implications for chromosome organization in all organisms.

overall_design: Hi-C, ChIP-seq and whole genome sequencing expriments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich medium.


title: prdm1a is at the Core of Lateral Line Sensory Hair Cell Developmental and Evolutionary Gene Regulatory Networks

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: In vertebrates, mechanosensory hair cells (HCs) in the ear transduce vibrations into sound. Aquatic vertebrates possess exterior lateral line HCs to detect water vibrations to orient themselves and for predator avoidance. HCs in many species regenerate following death, but mammalian HCs lack this ability, causing hearing/vestibular defects. Experimentally-induced regeneration in mice results in incomplete differentiation of immature HCs. Here, we show that the transcription factor prdm1a controls the lateral line HC network in zebrafish. Loss of prdm1a results in a significant loss of hair cells and causes proliferation and regeneration defects. scRNA-seq and ATAC-seq demonstrate a HC fate switch, and ectopically expressing prdm1a and cloning and mutating enhancers demonstrates direct interaction between prdm1a and putative target genes behind the altered cell fate. Therefore, prdm1a is an ideal gene for investigating the network needed to correctly differentiate a functioning HC, a major unmet milestone in restoring hearing.

overall_design: Two conditions: prdm1a mutant and homeostasis control. Three independent biological replicates per condition.

first: Jeremy

last: Sandler

first: Abhinav

last: Sur

first: Nhung

middle: T

last: Tran

first: Logan

last: Sabin

first: Malcolm

last: Cook

first: Elizabeth

last: Ellis

first: Ya-Yin

last: Tsai

first: Jeffrey

last: Farrell

first: Tatjana

last: Piotrowski


title: Adipocyte RNA-binding protein CELF1 promotes beiging of white fat through stabilizing Dio2 mRNA

status: Public on Jul 05 2025

city: Chongqing

first: Ting

last: Zeng

address: No. 1 Medical College Road

country: China

institute: Chongqing medical university

summary: RNA-binding proteins (RBPs) regulate diverse cellular processes at post-transcriptional level and play roles in adipocyte development. However, their involvement in the beiging of white fat remains unclear. Here we screened RBPs in inguinal adipose tissues in response to cold stimulation and identified CUG-BP Elav-like family member 1 (CELF1) as a novel regulator that promotes white fat beiging. Adipocyte-specific Celf1 deficiency impairs cold-induced beiging and reduces energy expenditure. Mechanistically, RNA immunoprecipitation RNA-seq (RIP-seq) and functional experiments revealed that CELF1 stabilizes the mRNA of the key thermogenic regulator Dio2 by binding to its 3'UTR, thereby promoting local triiodothyronine (T3) production. CELF1 augments isoproterenol-induced activation of beige adipocytes and increases mitochondria respiration capacity in vitro, and CELF1 overexpression ameliorates diet-induced obesity and metabolic dysfunction. Hence, our study identifies CELF1 as a physiological regulator of metabolic stress in activating thermogenesis and promoting energy expenditure at the post-transcriptional level, suggesting that targeting CELF1 to locally increase the T3 production may serve as a promising therapeutic strategy for combating obesity and related metabolic disorders.

overall_design: To find the target of CELF1 regulating white fat beiging, we performed RNA immunoprecipitation followed by RNA sequencing (RIP-seq) using IgG or CELF1 antibody in differentiated primary adipocytes treated with isoproterenol.


title: Bulk mRNAseq in control and Cnp-Cre_RelA cKO mouse spinal cords

status: Public on Jul 04 2025

city: Niigata City

first: Norihisa

last: Bizen

address: 757 Ichibancho, Asahimachi-dori, Chuo Ward

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Niigata University

summary: We sequenced mRNA extracted from the cerebral cortices including hippocampi of mice at postnatal day 14 (P14) and compared the gene expression levels between the control group and the RelA conditional knockout (Cnp-Cre; RelA cKO) group.

overall_design: At P14, mRNA was extracted from the cerebral cortices including hippocampi of three control mice and three RelA cKO mice. The extracted mRNA was sequenced using the Illumina NovaSeq 6000 platform to generate mRNA expression profiles.

first: Kamonrapat

last: Sompub

first: Hirohide

last: Takebayashi


title: Enhancing CAR T Cell Therapy in Patients with Pancreatic Cancer

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Patients with advanced pancreatic ductal adenocarcinoma (PDAC) have a median survival time of less than a year, highlighting the urgent need for treatment advancements. We conducted a phase 1 clinical trial assessing the safety and feasibility of intravenous and local administration of anti-mesothelin CAR T cells in patients with unresectable or metastatic PDAC. Though therapy was well tolerated, limited clinical efficacy was observed. Analyses of patient samples provide insights into mechanisms of treatment resistance. Using single-cell genomic approaches, we found that CAR T cells post-infusion express exhaustion signatures, including previously identified transcription factors ID3 and SOX4, and display enrichment for Treg and GZMK+ phenotypes. Single knockout of ID3 or SOX4 appeared to enhance efficacy in xenograft models, but eventually failed, whereas double-knockout ID3 and SOX4 CAR T cells exhibit prolonged relapse-free survival, demonstrating sustained therapeutic effect and a potential avenue for engineering a more potent CAR T cell in pancreatic cancer.

overall_design: Examines gene expression by single-cell RNA-seq in T cells isolated from two patients undergoing a CAR T cell clinical trial, with isolation at 7 or 26 days post-CAR T infusion (isolation time not replicated); or tumor-infiltrating lymphocytes (TILs) extracted from three mice with recurrent tumors that had been treated with human CAR T cells, with two replicates subject to SOX4 knockout and one WT control.

first: M

last: Aznar

first: Charly

middle: R

last: Good

first: Julie

middle: S

last: Barber-Rotenberg

first: Sangya

last: Agarwal

first: Wesley

last: Wilson

first: Alex

last: Watts

first: Zhen

last: Zhang

first: Donna

last: Gonzales

first: Greg

first: Wei-Ting

last: Hwang

first: Austin

middle: K

last: Rennels

first: Andrew

middle: J

last: Rech

first: Shunichiro

last: Kuramitsu

first: Karl

middle: M

last: Glastad

first: Katherine

last: Alexander

first: Gabriela

last: Plesa

first: Emily

last: Dowd

first: Andrea

last: Brennan

first: Donald

middle: L

last: Siegel

first: Janos

last: Tanyi

last: Haas

first: Drew

last: Torigian

last: Nadolski

first: Vanessa

middle: E

last: Gonzalez

middle: O

last: Hexner

first: Joseph

last: Fraietta

last: Jadlowsky

first: Regina

last: Young

first: Shelley

last: Berger

first: Carl

middle: H

last: June

first: Mark

last: O’Hara


title: The gene expression profile of milk somatic cells of small  ruminant lentivirus-seropositive and -seronegative dairy goats (Capra hircus) during their first lactation.

status: Public on Jul 03 2025

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary: Caprine arthritis and encephalitis (CAE), caused by small ruminant lentivirus (SRLV), is a key disease of goats, with chronic inflammation of joints and brain symptoms, leading to losses in milk production and animal trade. In this study we analyzed gene expressions in milk somatic cells (MSCs) of seropositive (SRLV-SP) and seronegative (SRLV-SN) goats to identify transcriptomic changes using a non-invasive sampling method. Materials and Methods: The study was conducted on goats of two Polish breeds (Polish Improved White and Polish Improved Fawn) in their first lactation, kept at the Institute of Genetics and Animal Biotechnology Polish Academy of Sciences. MSCs were isolated from milk and gene expression was analyzed using Goat Gene Expression microarray. The results were verified by RT-qPCR for five genes (DUSP26, PRLR, SCARA3, APBB2, OR4F4). Statistical analysis was performed in Gene Spring 12 software. Results: Microarrays showed reduced expression of DUSP26, PRLR, SCARA3, APBB2 and OR4F4 genes in SRLV-SP goats. RT-qPCR confirmed changes for DUSP26, SCARA3 and APBB2. Functional analysis indicated associations with immune processes and HIV-like pathways. Discussion: The results suggest that SRLV induces transcriptomic perturbations, especially in immunity-related genes. MSCs are an effective model for non-invasive studies, and further studies may support strategies for combating CAE.

overall_design: The experiment was performed on 8 transcriptomic microarrays using a common reference design. The common reference (Cy3) comprised a pool of equal amounts of RNA from 7 healthy goats in 4th lactation from both Polish breeds (PWI n=4 and PFI n=3). Samples were taken after finishing of lactation period. Experimental samples (Cy5) were collected from two groups of goats at the climax of their first lactation were selected for the study; SRLV-seronegative goats (SRLV-SN; N=4) and SRLV-seropositive goats (SRLV-SP; N=4). in 1st lactation  and RNA was isolated from   MSC.

first: Joanna

last: Pławińska-Czarnak

first: Jarosław

last: Kaba

first: Emilia

last: Bagnicka


title: Comparative miRNA transcriptome profiling across six adipose depots in buffaloes

status: Public on Jul 02 2025

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

type: Non-coding RNA profiling by high throughput sequencing

summary: To profile miRNA expression variations across six adipose depots, a total of 36 adipose samples underwent high-throughput small RNA sequencing.

overall_design: Small RNA-seq was performed on 36 adipose samples (6 buffaloes, 6 depots) to compare miRNA expression between subcutaneous (BSAT, SSAT, IAT) and visceral (OAT, PCAT, PRAT) adipose depots.

first: Jieping

last: Huang


title: Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

summary: Growth-limiting droughts (GLD) impair tissue expansion and delay developmental transitions but are often not considered as stressors, as many physiological traits are only slightly altered relative to well-watered counterparts. Concurrently, cell size, biochemical make up, and transcriptome profiles vary along the leaf blade in accordance with the partitioning of distinct functions to spatially defined regions of the leaf. This suggests that because different parts of the leaf have underlying differences in their transcriptome profiles, they might respond to GLD in distinctive ways. Moreover, how antagonistic stressors influence physiology and gene expression in different zones of leaves is an open question. In this study, we profiled growth, anatomy, and gas exchange in Asian rice (Oryza sativa) leaves developed in well-watered and GLD conditions, with or without a secondary heat shock. We dissected leaves into seven equal-length segments for transcriptome analysis in these conditions. We hypothesized that GLD would make the leaves more sensitive to heat shock and would disrupt the underlying heterogeneity of the leaf transcriptome. GLD plants were more strongly affected by heat shock with respect to gas exchange and the number and types of genes that were differentially expressed and that these differences varied along the leaf blade. We developed an eFP browser tool with these data to facilitate exploration and hypothesis testing. These findings show that even mild drought treatments are sufficient to impact responses to antagonistic stressors and that substantial within-organ variance exists with respect to stress responses.

overall_design: RNA-seq of fully expanded rice leaves developed in well-watered or growth-limiting drought conditions, with or without a 30-minute heat shock. Leaves were dissected into seven equal-length segments, and the middle five were sequenced, with four replicates each.

first: Sean

last: Robertson

first: Solihu

last: Sakariyahu

first: Elisa

last: Gan

first: Obaid

last: Maqsood

first: Asher

last: Pasha

first: Nicholas

last: Provart


title: RACK7 Senses and Fine-Tunes Enhancer Activity [ChIP-Seq]

city: ShangHai

first: HongJie

last: Shen

address: Dongan road 131

institute: Fudan University

summary: Enhancers regulate dynamic gene expression in a spatiotemporal specific manner. A number of positive as well as negative regulators of enhancers have been reported so far. However, whether and how these regulators sense enhancer activity dynamics remains unclear. In this study, we show that a specific enhancer regulator, RACK7, swiftly re-distributes from repressed enhancers to activated enhancers in response to a plethora of acute stimulations. We further show that this process depends on transcription and RACK7 positively regulates enhancer activation by promoting the recruitment of RNA polymerase II. Taken together, our findings suggest that RACK7 senses enhancer activity changes and facilitates their activation during acute stimulations.

overall_design: HeLa and MCF-7 cells are maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, 1% Non-Essential Amino Acids, 1% Penicillin-Streptomycin Solution. When preparing for E2 stimulation in MCF-7 cells, the cells are transferred to a Phenol Red-free RPMI-1640 Medium supplemented with 10% Charcoal Stripped Fetal Bovine Serum, 1% Non-Essential Amino Acids, 1% Penicillin-Streptomycin Solution, 1% Glutamine for three days prior to 17β-estradiol (E2) treatment. The culture medium is replaced on the second day, and a 1-hour treatment with 100 nM E2 or equal volume of EtOH was administered prior to cell harvest. For PBS or epidermal growth factor (EGF) treatment in HeLa cells, the cells are transferred to a medium containing 0.5% fetal bovine serum, refresh the culture medium on the second day. Following a 48h of serum starvation, the starved cells are then subjected to a 20-minute treatment with 50 ng/mL of EGF.

first: Li

last: Dong

first: Wenqi

last: Xu

first: Hongjie


title: Acute Aerobic Exercise Alters PBMC microRNA Expression: Insights into Sport- and Sex-Specific Variations

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: Studying microRNAs in the immune cells of athletes offers a novel perspective on the molecular regulation of immune function and recovery, potentially uncovering strategies to enhance performance and resilience to physical stress. However, PBMC microRNA expression in endurance athletes, such as runners and cyclists, remains underexplored, especially with regard to sex differences. This study aimed to (i) assess sport- and sex-specific differences in PBMC microRNA expression induced by acute aerobic exercise in runners and cyclists, (ii) evaluate the impact of maximal (trial A) and sub-maximal (trial B) exercises, and (iii) examine correlations between PBMC microRNAs and exercise performance. Methods: A total of 58 participants were included: 22 runners (9 females), 18 cyclists (9 females), and 18 active controls (9 females). Participants underwent VO2max and time-to-exhaustion tests, with blood samples collected pre- and post-exercise to analyze PBMC microRNA levels. Results: Runners exhibited a stronger microRNA response than cyclists or controls, with significant sex-based differences. After maximal intensity exercise, 279 microRNAs (255 upregulated) were altered in runners, compared to only 7 microRNAs (none upregulated) in cyclists. Exercise intensity and duration had sport-specific effects on microRNA expression. Time-to-exhaustion in runners and weekly training volume in both groups were significantly associated with changes in PBMC microRNA profiles. Conclusion: This study reveals that PBMC microRNA expression in response to acute aerobic exercise is sport- and sex-specific, providing new insights into the molecular adaptations of endurance athletes and their relationship to athletic performance.

overall_design: Small RNA-Seq profiling of Human peripheral blood mononuclear cells (PBMCs) before and immediately after exercise.

last: Shalmon

first: Rawan

last: Ibrahim

first: Ifat

last: Israel-Elgali

first: Meitar

last: Grad

first: Rani

last: Shlayem

first: Ilan

last: Youngster

first: Mickey

last: Scheinowitz

first: Noam

last: Shomron


title: Mechanical signaling in aging

city: Bryan

first: Andreea

last: Trache

state: TX

address: 402 John Sharp Pkwy

department: Medical Physiology

institute: Texas A&M University

summary: Aging is an independent risk factor for cardiovascular disease. Preventing age-induced arterial dysfunction and the associated risk of cardiovascular disease remains a signiﬁcant clinical challenge. Aerobic exercise, which induces a temporary increase in both blood flow and pressure in active tissue, has been shown to reduce macroscale arterial stiffening in humans. The purpose of this study was to investigate the effects of mechanical stimuli on improving aging pathophysiology of VSM cells isolated from soleus feed arteries (SFA). We hypothesized that exposure to external mechanical stimulation enhances formation of smooth muscle alpha-actin (SMα-actin) fibers and cell-matrix adhesions in aged VSM cells. Ex-vivo functional studies were used to assess myogenic contractility of VSM in isolated SFA from young (4 months) and old (24 months) Fischer 344 rats. These data indicated that pre-treatment of isolated aged SFA with a short-duration increase in intraluminal pressure rescued contractility. The mechanical stretch-induced remodeling of the cellular architecture was assessed in VSM cells isolated from young and old SFA. To dissect the mechanisms involved, the structural and functional properties of VSM cells were assessed by using mechanical stimulation combined with fluorescence confocal microscopy. Results showed that aged VSM cells respond faster than young cells to 2D biaxial cyclic stretch by increasing actin stress fiber formation and vinculin recruitment at cell-matrix adhesions. In addition, hydrostatic pressure treatment applied to aged VSM cells plated on stiffer substrates restores actin fibers and integrin β1 recruitment. Taken together, these findings suggest that discrete VSM cell mechanical properties and their ability to adapt to external mechanical signals are key in restoring VSM contractility in aging. These results are significant because they provide a novel understanding of the mechanisms by which mechanical stimulation improves VSM contractility in aged resistance arteries. Our results provide new insights into the role of VSM in vascular aging and highlight a new direction for mitigating age-related effects via mechanical stimulation-induced VSM remodeling.

overall_design: RNA-seq profiling of Fisher 344 rat smooth vascular muscle cells (VSMC) of  soleus feed arteries (SFA) in old (24 months) and young (4 months) age groups.

first: Amin

last: Mohajeri

first: Song

middle: Y

last: Shin

first: Samuel

last: Padgham

first: Devon

last: Boland

first: Dana

middle: P

last: Ratterree

first: Jacob

last: Blizman

first: Gang

last: Han

first: Christopher

last: Woodman


title: Regulation of Epstein–Barr Virus latency by histone variant H2A.Z [RNA-seq]

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Chromatin structure plays a central role in the regulation of Epstein-Barr Virus (EBV) latency. The histone variant H2A.Z.1 has been implicated in chromatin structures associated with initiation of transcription and DNA replication. Here, we examined the role of H2AZ.1 in the regulation of EBV chromatin and gene expression during EBV latent infection in two different EBV cancer cell models. We found that H2A.Z.1 is highly enriched with EBNA1 binding sites at oriP and Qp, and to a lesser extent with transcriptionally active CTCF binding sites on the EBV genomes in both Mutu I Burkitt lymphoma (BL) and SNU7-19 EBV-associated gastric carcinoma (EBVaGC) cell lines. RNA-interference depletion of H2A.Z.1 resulted in the reactivation of viral lytic genes (ZTA and EAD) and increases viral DNA copy numbers in both MutuI and SNU719 cells.  H2A.Z depletion also led to a decrease in EBNA1 binding to oriP and Qp, on the viral episome as well as on plasmids independently of other viral genes and genomes. H2A.Z.1 depletion also reduced peaks of H3K27ac and H4K20me3 at regulatory elements in the EBV genome.  In the cellular genome, H2A.Z.1 colocalized with only a subset of EBNA1 binding sites and H2A.Z.1 depletion altered transcription of genes associated with myc targets and mTORC1 signaling.  Taken together, these findings indicate that H2A.Z.1 plays an important regulatory role in the regulation of EBNA1 chromatin binding and function in the EBV episome and host chromosome, as well as the epigenetic programming of the latent episome.

overall_design: SNU-719 cells were treament with siControl and siH2A.Z, after 9 days the celles were recollected and processed to western blot, RNA-seq and ChIP-seq.

first: Leonardo

last: Castro-Muñoz

first: Davide

last: Maestri

first: Leena

last: Yoon

first: Bhanu

middle: C

last: Karisetty

first: Italo

last: Tempera

first: Paul

last: Lieberman


title: The changes of OsTSN1 binding-genes in wildtype, P6-overexpression transgenic plants, SRBSDV-infected rice plants and SRBSDV-uninfected rice plants [RNA-seq]

city: Hangzhou

first: Ming

last: Zeng

address: 866 Yuhangtang Road

institute: Zhejiang university

summary: Membraneless biomolecular condensates formed through liquid-liquid phase separation (LLPS) are known to play key roles in plant growth and stress responses. How plant viruses utilize LLPS to escape host immunity remains largely unexplored. Here, we present evidence demonstrating that the P6 protein encoded by southern rice black-streaked dwarf virus (SRBSDV) undergoes LLPS. P6 interacts with OsTSN1 and triggers the assembly of P6-OsTSN1-containing droplets that co-localize with stress granules (SGs). Within these P6-OsTSN1-containing droplets, P6 enhances the nuclease activity of OsTSN1 via promoting its multimerization to degrade transcripts with G-A-rich motifs of two transcription factors (TFs), OsNAC15 and OsLHY. These TFs regulate the transcription of OsJAZ6, OsJAZ12, and OsATG8C, involved in jasmonic acid (JA)- and autophagy-associated defense pathways in plants. Additionally, the degradation of OsNAC15 and OsLHY transcripts in the P6-OsTSN1-containing droplets in SGs weakens JA- and autophagy-mediated defenses in rice, facilitating SRBSDV infection. Interestingly, similar to SRBSDV P6, intrinsically disordered region (IDR)-containing RNA silencing suppressors encoded by other rice viruses such as rice black-streaked dwarf virus and rice stripe virus, also interact with OsTSN1, promoting the degradation of OsNAC15 and OsLHY transcripts to enhance viral infection. Our findings indicate that OsTSN1 acts as a central positive regulator of virus infection in rice, convergently co-opted by viruses. These insights help us to better understand the roles of LLPS and OsTSN1 in virus infection in rice.

overall_design: RNA-seq profiling of wildtype, P6-overexpression transgenic plants, SRBSDV-infected rice plants and SRBSDV-uninfected rice plants.

first: Shuai

last: Fu

first: Jianxiang

last: Wu


title: Effect of Hypergravity on Transcriptomic and Electrophysiological Properties of Rat Ventricular Cardiomyocytes

city: Moscow

first: Stanislav

last: Shilejko

address: Ostrovityanova str., 1

country: Russia

institute: RSMU

summary: This study investigates the impact of hypergravity (4g for 14 days) on the transcriptomic and electrophysiological profiles of rat ventricular cardiomyocytes. Using RNA sequencing, we identified significant changes in the expression of mechanically gated and mechanosensitive ion channel genes. Electrophysiological analyses revealed increased sensitivity of stretch-activated currents (ISAC) to mechanical stimuli in hypergravity-exposed cardiomyocytes. These findings highlight how altered gravitational conditions modulate cardiac cellular responses, with implications for understanding mechanoelectric feedback in both physiological and extreme environments.

overall_design: Male Wistar rats (8 weeks old) were divided into two groups: hypergravity-exposed and control. The hypergravity group was subjected to 4g centrifugal force for 14 days (8 hours/day). Ventricular cardiomyocytes were isolated from both groups for RNA sequencing and electrophysiological analysis. RNA-Seq was performed to profile transcript levels of ion channels, while patch-clamp techniques assessed the sensitivity of stretch-activated currents (ISAC) to mechanical deformation. Data include raw RNA-Seq files and processed expression values for mechanically sensitive ion channels.


title: Pseudorabies virus induces Natural killer cell depletion by GSDMD-mediated inflammation and pyroptosis to promote infection and lung injury

city: Yangling

first: Jing

last: Chen

address: Xinong road #22

institute: Northwest Agriculture & Forestry University

summary: To further explain why GSDMD deletion can significantly weaken the pathogenic ability of PRV and explore what role do GSDMD play and how do GSDMD act in the process of PRV infection and induction of tissue injury, we firstly sequenced the transcriptome of over 13,275 unselected cells of inflammatory cells isolated from the lung of PRV-infected WT mice and PRV-infected Gsdmd-/- mice using scRNA-seq .

overall_design: WT mice and Gsdmd-/- mice (n = 5, per group) were inoculated intraperitoneally with PRV-RJ strain (2 ×103 TCID50) for 48 h, respectively. For the lung single-cell suspension, the lungs were resuspended with PBS containing 0.1 % Collagenase type I (SCR103, Sigma-Aldrich), 0.05 % DNase I (D5025, Sigma-Aldrich), and 5 % FBS (13011-8611, Tianhang Biotechnology). After incubation at 37 °C for 60 min, the samples were pestled and filtrated with a 200-mesh sieve, pelleted (300 g, 5 minutes), and resuspended in ACK red blood cell lysis buffer (Gibco A1049201) for 3 minutes, after which the buffer was inactivated by adding excess processing buffer. Cells were then filtered through a 70 μm strainer, pelleted again (300 g, 5 minutes), and resuspended in PBS buffer, counted, and immediately processed for single-cell RNA sequencing.

first: Guangming

last: Zhao

first: Dewen

last: Tong

first: Yong

last: Huang


title: KAT7 coupled with ACSS2 boosts transcription through regulation of histone β-hydroxybutyrylation [ChIP-seq]

city: Tianjin

first: wang

middle: si

last: yu

address: No. 22, Meteorological Tai Road, Heping District

institute: Tianjin Medical University

summary: Histone lysine β-hydroxybutyrylation (Kbhb) links ketone metabolism to gene transcription. However, the regulatory mechanism that kenogenesis-derived β-hydroxybutyrate, present throughout cells at low concentration, orchestrates this histone mark remains largely unknown. Here, we unveil a KAT7-ACSS2 module in which ACSS2 locally generates β-hydroxybutyryl-CoA (BHB-CoA), thereby bolsters histone Kbhb through fueling KAT7. Specifically, we show that KAT7 serves as a histone β-hydroxybutyryltransferase that prefers to modulate β-hydroxybutyrylation on histone H3 lysine 9 (H3K9bhb) by utilizing ACSS2-directed BHB-CoA. Moreover, ACSS2 senses β-hydroxybutyrate and translocates into the nucleus wherein it binds to and colocalizes with KAT7 at gene promoter regions. We further show that KAT7 coupled with ACSS2 regulates specific activation of genes associated with tumor cell survival through histone Kbhb. Collectively, our findings reveal that KAT7-ACSS2 module promotes histone β-hydroxybutyrylation by providing BHB-CoA locally, highlighting the importance of linking metabolic enzyme ACSS2 and KAT7 for histone Kbhb as well as offering insight into the regulatory mechanism of cellular metabolite on epigenetic modification and gene transcription.

overall_design:
Chromatin immunoprecipiation DNA sequencing (ChIP-seq) for transcriptionnal activator KAT7/HBO1, ACSS2 as well as histone modifications H3K9bhb in KAT7/HBO1-WT or KAT7/HBO1-KO HeLa cells.
KAT7/HBO1 vendor: CST, catalog number: 58418, lot/batch number: 1
ACSS2 vendor:Abclonal, catalog number: A12334, lot/batch number: 4000000690
H3K9bhb vendor:PTM Biolabs, catalog number: PTM-1250RM, lot/batch number: RL072623

first: Siyu

last: Wang

first: Ziping

last: Niu


title: Genome-wide chromatin state in myoblasts lacking Daxx [ChIP-Seq]

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

summary: DAXX, a H3.3 histone chaperone known for its role in heterochromatin maintenance, has been understudied in the context of gene expression regulation. In this study, we generated Daxx knockout myogenic cells and observed a significant loss of myogenic markers expression and impaired differentiation. Transcriptome analysis revealed broad dysregulations in Daxx KO cells, including loss of myogenic identity and a concurrent upregulation of genes involved in DNA replication and telomere maintenance. Chromatin immunoprecipitation followed by sequencing demonstrated a marked reduction in H3.3 deposition, particularly in intronic and intergenic regions. Further analysis indicated that loss of DAXX leads to decreased H3K27ac at myogenic loci and a shift in repressive histone marks, which led to impaired gene expression. Intriguingly, double knockout of Daxx and Hira resulted in distinct transcriptomic alterations, demonstrating that DAXX and HIRA have both overlapping and unique roles in H3.3 incorporation. Our work also suggests the presence of additional histone chaperone complexes in maintaining chromatin integrity in myoblasts. Our findings establish DAXX as a critical regulator of myogenic gene expression and muscle cell identity through a distinct mechanism from that of HIRA and highlighted an unanticipated plasticity in the deposition loci for DAXX and HIRA in myoblasts.

overall_design: Examining the changes in H3.3 incorporation and associated changes in histone modifications in the absence of Daxx in myoblasts

first: Virginia

last: Zoglio

first: Sarah

last: Chebouti

first: Fayez

last: Issa

first: Frederic

last: Relaix


title: N,N-dimethyltryptamine protects against experimental stroke via blood-brain barrier stabilization and reduction of neuroinflammation

status: Public on Jul 01 2025

city: Szeged

first: Maria

last: Deli

address: Temesvari krt. 62.

department: Institute of Biophysics

country: Hungary

institute: HUN-REN Biological Research Centre

summary: N,N-Dimethyltryptamine (DMT) is a psychoactive molecule naturally present in the brains of mammals, including humans. Due to its neuroprotective effect in experimental stroke, DMT is under clinical evaluation, yet its mechanism of action remains poorly understood. Here we show that DMT protects against stroke by stabilizing the blood-brain barrier (BBB) and by mitigating neuroinflammation. In a transient middle cerebral artery occlusion (tMCAO) model of stroke in rats, treatment with DMT reduced infarct volume, and restored tight junction integrity and BBB function in vitro and in vivo. DMT also reduced cerebral edema, attenuated astrocyte dysfunction and shifted serum protein composition towards an anti-inflammatory, neuroprotective state. Finally, DMT suppressed the release of proinflammatory cytokines and chemokines in brain endothelial cells and peripheral immune cells, and reduced microglial activation, all in a sigma-1 receptor-dependent manner. Together, our findings demonstrate that the protective effect of DMT relies on its interaction with the vascular and immune systems, which can be harnessed to complement current stroke therapy.

overall_design: Gene expression profiling analysis of primary rat brain endothelial cells from endothelial cell-pericyte-astrocyte co-cultures in vitro. Treatments include normoxia, OGD/R, OGD/R + DMT, and OGD/R + DMT + BD1063, n=5-6 samples (corresponding to endothelial lysates from 5-6 individual culture inserts) per group.

first: Marcell

last: László

first: Judit

last: Vigh

first: Anna

last: Kocsis

first: Gergő

last: Porkoláb

first: Zsófia

last: Hoyk

first: Tamás

last: Polgár

first: Fruzsina

last: Walter

first: Attila

last: Szabó

first: Srdjan

last: Djurovic

first: Béla

last: Merkely

first: Alán

last: Alpár

first: Ede

last: Frecska

first: Zoltán

last: Nagy

first: Mária

first: Sándor

last: Nardai


title: Identification of RRP1 binding sites using seCLIP-seq in IL-1β stimulated RAW 264.7 cells.

city: Suzhou

first: Zhou

last: Yumei

address: No.100,Chongwen Road

institute: Suzhou Institute of Systems Medicine,Chinese Academy of Medical Sciences

summary: How RRP1 control RNA processing and regulation in macrophage inflammation is important. Here is the identification for RRP1 binding sites by using  the single-end enhanced CLIP(seCLIP) in RAW 264.7 cells.

overall_design: To identify the interaction sites between RRP1 and its RNA targets  in IL-1β stimulated RAW264.7, seCLIP-seq analysis can be performed.

first: Yumei

last: Zhou

first: Mengxuan

last: Li

first: Ke

last: Jin


title: Obox1 deficiency induceds subfertility in female mice

city: Shanghai

first: Li

last: Wu

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

institute: Tongji University

summary: Obox1 was considered to be a maternal factor participates in oogenesis and follicle development, but its function remains largely undefined. In this study, we demonstrated that Obox1-null female mice displayed subfertility as evidenced by decreased litter size. Obox1 deficiency resulted in less oocytes production. The levels of female sex hormones and gonadotropins, especially luteinizing hormone (LH), were significantly decreased both in ovaries and serum at diestrus. Further studies showed that Obox1-null ovaries were hypo-reactive to LH. There are still more unruptured follicles in the ovaries after superovulation in Obox1-null ovaries. The number of corpus luteum (CL) and serum concentration of progesterone (P4) reduced, and the steroidogenesis-related genes were aberrant in Obox1-null mice. In conclusion, Obox1 deficiency impaired ovulation and luteinization and led to female subfertility.

overall_design: Wild type (WT) or Obox1 knockout (KO) female mice (6-8 weeks old) were treated with 5 IU PMSG which was followed 46-48 hours later by treatment with 5 IU hCG. Mice were euthanized by cervical dislocation 16 hours after hCG injection and MII oocytes from oviducts were collected for RNA-sequencing.

first: Jiacheng

last: Shen

first: Zhenzhen

last: Hou

first: Shaorong

last: Gao


title: Early synergy between IFNγ-inducible Gbp4 and Irgb6 in the olfactory bulb contributes to experimental cerebral malaria pathology

city: Tokyo

first: Julia

last: Matsuo-Dapaah

address: 4-6-1 Shirokanedai, Minato-ku

department: Institute of Medical Science

institute: University of Tokyo

summary: Cerebral malaria (CM) is a severe and often fatal complication of Plasmodium falciparum infection. Although much progress has been made in understanding CM, the precise pathogenesis remains elusive. The olfactory bulb (OB) has emerged as a critical site of immunopathology in experimental cerebral malaria (ECM) models, but its contribution to disease progression is not fully understood. To investigate the molecular mechanisms driving early ECM pathogenesis, we conducted transcriptomic profiling of the OB to identify key gene signatures associated with disease onset. Our analysis revealed significant early upregulation of IFN-inducible GTPases, particularly Irgb6 and Gbp4, effectors downstream of IFN-γ, but not IFN-α/β signalling, suggesting their involvement in ECM pathology. Using Gbp4-/-, Irgb6-/-, and double knockout (Irgb6-/- Gbp4-/-) mice, we identified a synergistic pathological role for these GTPases. Mechanistically, we found that double-knockout mice exhibited increased infiltration of CD4+ and CD8+ T cells into the brain but with reduced T cell functionality and impaired antigen presentation by endothelial cells, leading to enhanced parasite accumulation in the OB. This disruption in immune regulation ultimately conferred improved survival in the Irgb6-/- Gbp4-/- mice and indicated the pathological impact of Gbp4 and Irgb6 in ECM.  These findings reveal that Gbp4 and Irgb6 synergistically play crucial roles in the early immunopathogenesis of ECM by modulating antigen processing and presentation in the OB, thereby shaping immune cell dynamics. Our work shows the dual role of Irgb6 and Gbp4 GTPases in host defence and immunopathology and offers new insights into ECM mechanisms and potential therapeutic targets for CM intervention.

overall_design: RNA-sequencing of olfactory bulb tissues from wildtype C57BL/6 mice at day 0 (naïve), day 3, and day 6 after Plasmodium berghei ANKA(PbA) infection.

first: Cevayir

last: Coban


title: RACK7 Senses and Fine-Tunes Enhancer Activity [Chromatin associated RNA-seq]

first: HongJie

overall_design: MCF-7 cells are maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, 1% Non-Essential Amino Acids, 1% Penicillin-Streptomycin Solution. When preparing for E2 stimulation in MCF-7 cells, the cells are transferred to a Phenol Red-free RPMI-1640 Medium supplemented with 10% Charcoal Stripped Fetal Bovine Serum, 1% Non-Essential Amino Acids, 1% Penicillin-Streptomycin Solution, 1% Glutamine for three days prior to 17β-estradiol (E2) treatment. The culture medium is replaced on the second day, and a 1-hour treatment with 100 nM E2 or equal volume of EtOH was administered prior to cell harvest.

last: Dong

first: Wenqi

last: Xu

first: Hongjie


title: Extracellular vesicles as prospective biological indicators for midgestational placental complications in the mouse

city: Montreal

first: Bioinformatics

last: Platform

state: Quebec

address: 1001 Decarie Blvd

institute: RI-MUHC

summary: This study investigates the miRNA content of extracellular vesicles (EVs) isolated from placental tissue at embryonic day 10.5 (D10.5) in a conditional Nodal knockout mouse model that exhibits abnormal placentation. EVs were isolated from enzymatically digested placentae of both Nodal^loxP/loxP (control) and Nodal^Δ/Δ (KO) mice. Small RNA sequencing was performed on isolated EVs to identify differentially expressed miRNAs associated with disrupted placental development.

overall_design: Placentae were collected from Nodal^loxP/loxP (n=3) and Nodal^Δ/Δ (n=3) embryos at D10.5. EVs were isolated using enzymatic digestion followed by size-exclusion chromatography. Small RNA libraries were prepared from EV RNA and sequenced. Expression profiles were compared between the two groups to identify miRNAs linked to placental dysfunction.

first: Daniel

last: Dufort

first: Elaine

last: Lee

first: Parinaz

last: Kazemi


title: KAT7 coupled with ACSS2 boosts transcription through regulation of histone β-hydroxybutyrylation [RNA-seq]

first: wang

last: yu

overall_design:
To investigate functions of KAT7/HBO1 in epigenetic regulation,  KAT7/HBO1-deletion HeLa cell lines were established by overexpressing sgRNA targeted at KAT7.
We therefore performed high-throughout sequencing for HBO1-WT and HBO1-KO upon BHB stimulation.
We therefore performed high-throughout sequencing for HBO1-WT with or without ACSS2 inhibitors upon BHB stimulation.
We therefore performed high-throughout sequencing for HBO1-WT in presence or absence of BHB stimulation.

first: Siyu

last: Wang

first: Ziping

last: Niu


title: Single-cell RNA-seq of peripheral blood mononuclear cells from kidney-transplant recipients with stable renal function versus graft dysfunction

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

summary: Kidney transplantation restores renal function in patients with end-stage renal disease, yet long-term graft failure remains common and is often driven by immune dysregulation. We performed droplet-based single-cell RNA sequencing (10x Genomics 3′ v3 chemistry) on peripheral-blood mononuclear cells (PBMCs) collected from adult kidney-transplant recipients who either maintained stable renal function (Ctrl, n = 10) or displayed biopsy-proven graft dysfunction (PTRI, n = 10).

overall_design: After excluding those with active infection or recent hospitalization, ten patients with stable estimated glomerular filtration rate (eGFR ≥ 60 mL min⁻¹ 1.73 m⁻²) formed the control group, whereas ten patients with at least a 25 % eGFR decline and biopsy-confirmed chronic antibody-mediated rejection constituted the dysfunction group. Approximately 10 mL of peripheral blood was drawn into EDTA tubes 6–12 months post-transplant and processed within two hours; PBMCs were isolated by Ficoll density centrifugation, washed in PBS + 0.04 % BSA, and confirmed to have >90 % viability. Equal cell numbers from donors belonging to the same clinical group were pooled to create two composite suspensions that were loaded onto a Chromium Controller for single-cell capture, cDNA amplification and library construction. Paired-end 150-bp sequencing was performed on an Illumina NovaSeq 6000 targeting ~50 000 read pairs per cell. Raw BCL files were demultiplexed and aligned to GRCh38 using Cell Ranger 3.1; barcodes with <200 or >6000 detected genes, mitochondrial reads >15 %, or predicted doublets were removed.

first: Hao

last: Jiang

first: Zhijun

last: Cao


title: HERVHLin modulates pluripotency and protects the genome from active retroelements by rewiring the conserved LIN28A/let-7 pathway

city: Berlin

first: Amit

last: Pande

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbruck Center for Medicine

summary: Sequential waves of coding transcript expression mark genome reactivation during embryonic development and reprogramming to pluripotency. We additionally observed two distinct waves of non-coding retrotransposable element (RE) expression: an initial wave of younger, partially active REs (LINE-1, SVA, and Alu), followed by older HERVH elements. These waves are not merely correlative, as HERVH depletion leads to an increase in transposition of L1, Alu, and SVA elements. We identified a great apes-specific subgroup of HERVH (N=101), termed HERVHLin, characterized by a motif with duplicated LIN28 binding sites, which alone inhibits L1 transposition. HERVHLin transcripts bind to LIN28 and allow let-7 microRNA to mature, rewiring the conserved LIN28-let-7 regulatory axis. Full locus HERVHLin knockout (KO) results in increased LINE-1 transposition, rescued by the let-7 mimic. HERVHLin KO presents an EMT-like phenotype, downregulation of RE-defense and pluripotency-specific genes, underscoring the role of HERVHLin in genome protection of pluripotent stem cells.

overall_design: HERVHlin chrX knock-out clone (chrX-KO_H1) and control clone (chrX-ctrl_H1) were cultured for 5 or 4 sequential passages (respectively), which were treated like technical replicates, collected for RNA isolation and total RNA sequencing with rRNA depletion was performed. Differentially expressed genes between chrX-ctrl_H1 and chrX-KO_H1 were analysed

first: Aleksandra

last: Kondrashkina

first: Egor

last: Semenchenko


title: Genome-wide CRISPR knockout screen identifies Activating Transcription Factor (ATF1) as an activator of HIV gene expression that restricts entry into latency

city: Beer Sheva

first: Ran

middle: Taube Pathology Rm

last: Taube

state: ISRAEL

address: Biotechnology Building 3, room 324

department: Microbiology

institute: Ben Gurion University

summary: Introduction of antiretroviral therapy has limited the spread of HIV and improved clinical outcomes. Yet, a complete cure for infection remains out of reach, as in the face of therapy, a transcriptionally silent but replication-competent provirus persists in a long-lived cell reservoir. Towards identifying new host proteins that regulate HIV gene transcription and latency, we performed a genome-wide CRISPR knockout screen in human CD4+ T cells. We identified the Activating Transcription Factor as a regulator of HIV gene transcription. ATF1 is recruited to the HIV promoter and activates viral gene expression. Gain and loss of function experiments demonstrate that depletion of ATF1 expression decreases HIV gene expression and promotes latency in primary CD4+ infected T cells. Interestingly, ATF1 regulates CCR5 expression and indirectly affects R5-tropic HIV infection. Mechanistically, ATF1 depletion impairs occupancy of RNA Polymerase II on the HIV promoter, and this is accompanied with elevated levels of H3K9me3 repression histone mark around the viral promoter. Genome wide analysis of ATF1 shows that it occupies cellular gene promoters including HIV, thereby controls gene targets that indirectly affect HIV infection. We conclude that ATF1 is an activator of gene transcription that dictates HIV gene expression via both direct and indirect mechanisms.

overall_design: Jurkat T cells that stabley express HA-ATF1 were subjected to CUT and RUN analysis according to the Epocipher protocol. Samples were subjected to NGS sequencing (pair end). Experiment was performed with several antibodies including: HA (abcam) and H3K4me3 (Ephchipher) and IgG as control. Replicates were performed for each antibody experiment. Libraries were generated according to   the Epicipher kit

first: Alona

last: Kuzmina

first: Seraj

last: Wattad

first: Praveenkumar

last: Murugavelu

first: Noa

last: Amir

first: Nili

last: Tickotsky

first: Liron

last: Levin


title: RACK7 Senses and Fine-Tunes Enhancer Activity [TT-Seq]

first: HongJie

last: Shen

address: Dongan road 131

institute: Fudan University

summary: Enhancers regulate dynamic gene expression in a spatiotemporal specific manner. A number of positive as well as negative regulators of enhancers have been reported so far. However, whether and how these regulators sense enhancer activity dynamics remains unclear. In this study, we show that a specific enhancer regulator, RACK7, swiftly re-distributes from repressed enhancers to activated enhancers in response to a plethora of acute stimulations. We further show that this process depends on transcription and RACK7 positively regulates enhancer activation by promoting the recruitment of RNA polymerase II. Taken together, our findings suggest that RACK7 senses enhancer activity changes and facilitates their activation during acute stimulations.

first: Li

last: Dong

first: Wenqi

last: Xu

first: Hongjie


title: Single cell RNA sequencing of Human Fetal Liver and Thymus samples

city: Singapore

first: Pavanish

last: Kumar

state: Not Applicable

address: 20 collage road, The Academia, Discovery Tower, Level-8 Translation Immunology Institute (TII)

country: Singapore

institute: Translational Immunology Institute (TII), SingHealth-DukeNUS

summary: Single cell RNA TCR sequencing data reveal antigenic selection in T effector cells in peripheral liver tissue samples

overall_design:
FACS sorting of CD45+CD3+CD14- T cells were performed with the BD FACS ARIA II system and FCS sorting data was collected via the BD FACSDiva software. Sort-enriched T cells were prepared for single-cell RNA-sequencing (scRNA-seq) using the Chromium Next GEM Single Cell 5ʹ v2 (Dual Index) protocol (10X Genomics) according to manufacturer’s recommendations. Single cells were encapsulated into droplets with a 8 gel bead in emulsion (GEMs) method using the 10X Chromium controller, where each mRNA transcript is tagged with a unique oligonucleotide barcode. Downstream library constructions were done using Library Construction kit (10X Genomics) with Chromium Single Cell Human TCR Amplification Kit (10X Genomics) and barcoded with i7 Illumina adapter indexes from Dual Index Kit TT Set A (10X Genomics). Pooled libraries are then sequenced on the Illumina HiSeq 4000 platform.

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

first: Jing Yao

last: Leong

first: Sharifah Nur

last: Hazirah


title: Analysis of the transcriptomic changes of myoblasts lacking Daxx or both Daxx and Hira histone chaperones

first: Joana

last: Esteves de Lima

first: Virginia

last: Zoglio

first: Sarah

last: Chebouti

first: Fayez

last: Issa

first: Frederic

last: Relaix


title: The somites are a source of nephron progenitors in zebrafish

status: Public on Jun 30 2025

city: Auckland

first: Alan

last: Davidson

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: The University of Auckland

summary: For over a century it has been believed that the vertebrate kidney arises exclusively from the intermediate mesoderm[1]. Here, we overturn this paradigm by demonstrating that some nephrons, the functional units of the kidney originate from the somites blocks of paraxial mesoderm best known for their contribution to muscle and connective tissues.  Using a combination of the GESTALT technique to assign developmental ancestry, somite transplantation experiments and Cre-lox fate-mapping, we show that somites can contribute to the nephrons in the adult zebrafish kidney.  Our findings uncover an unexpected developmental connection between the somites and kidneys, potentially offering new pathways for developing regenerative treatments for kidney diseases.

overall_design: Single nuclei RNA sequencing profiling on 1.5-month old zebrafish Brain, Muscle and Kidney tissues, GESTALT technique to track developmental ancestry

first: Zhenzhen

last: Peng

first: Thitinee

last: Vanichapol

first: Phong

middle: D

last: Nguyen

first: Hao-Han George

last: Change

first: Katrinka M

last: Kocha

first: Lori L

last: O'Brien

first: Peter D

last: Currie

first: Peng

last: Huang

first: Alan J


title: CRISPR screening reveals that RNA helicase DDX41 triggers ribosome biogenesis and cancer progression through R-loop-mediated RPL/RPS transcription

first: Xianghuo

last: He

address: No 270, Dong An Road

summary: Our findings showed that high-expressed DDX41 translocates to the R-loop structure of RPL/RPS genes, accelerating their transcription and promoting ribosome biogenesis. Additionally, acetyltransferase KAT8 is required for H3K9ac modification of the DDX41 promoter, while NR2C1/NR2C2 are responsible for regulating DDX41 transcription.

overall_design: Whole-transcriptome sequencing (RNA-Seq) was performed to identify the downstream target genes regulated by DDX41 in HUH7 cells.   Chromatin immunoprecipitation followed by sequencing (ChIP-seq) of DDX41 and R-ChIP-seq to identify the distribution of DDX41 or R-loops in genome of HUH7 cells. ChIP-seq of H3K9ac, KAT8, NR2C1 and NR2C2 to identify the enrichment of KAT8, NR2C1 and NR2C2 on DDX41 promoter region of HUH7 cells.

first: Hongquan

last: Li

first: Shenglin

first: Zhiao

last: Chen


title: sham: Control vs. different time point post spinal cord injury

first: Liming

last: Cheng

address: Siping Road No.1239

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Analysis of the transcriptional expression and m6A modification data of mice with different time point post spinal cord injury versus the sham controls.

overall_design: eight-condition experiment, sham vs. different time point post spinal cord injury. Biological replicates: 3 replicates.

first: Xu

last: Xu

first: Gao

last: Feng

first: Qixin

first: Bairu

first: Wenyu

last: Liang

first: Runzhi

first: Yuchen

last: Liu

first: Zhibo

first: Yanjing

last: Zhu

first: Guafa

last: Lin

first: Bei

last: Ma

first: Letao

last: Yang

first: Shaorong

last: Gao

first: Rongrong


title: Genome-wide changes in chromatin accessibility in myoblasts lacking Daxx [ATAC-Seq]

first: Joana

last: Esteves de Lima

first: Virginia

last: Zoglio

first: Sarah

last: Chebouti

first: Fayez

last: Issa

first: Frederic

last: Relaix


title: Identifying RRP1-bound RNA sequences in IL-1β stimulated BMDMs

first: Zhou

last: Yumei

summary: How RRP1 control RNA processing and regulation in macrophage inflammation is important. Here is the screening for potential RRP1-bound RNA sequences using RIP-seq in bone marrow derived macrophages (BMDMs).

overall_design: To identify dynamically changed RNA sequences in IL-1β stimulated BMDMs that potentially bind to RRP1, RIP-seq analysis can be performed.

first: Yumei

last: Zhou

first: Mengxuan

last: Li

first: Ke

last: Jin


title: Dynamically Urethra-Adapted and Obligations-Oriented Trilayer Hydrogels Integrate Scarless Urethral Repair

city: shanghai

first: Yang

last: Ming

address: No.600 yishan road

institute: Shanghai jiao tong universiay affiliated sixth people's hospital

summary: In urethral damage/stricture prevention, open and harsh urethral microenvironments as well as the isotropic compression and swelling properties of exogenous implants render urethral repair intractable. Here, a dynamically urethra-adapted and obligation-oriented trilayer hydrogel was constructed for integrated scarless urethral repair. The bottom diethylacrylamide -hydroxyethylacrylamide (D-H) hydrogel featuring high anti-fouling performance, the upper swellable verteporfin (VP)-loaded N,N'-methylenebisacrylamide-poly (N-isopropylacrylamide) (BP) with a hydrophilic Janus surface promote urethral regeneration through expediting cell migration and proliferation and the rigid and water-resistant Zein middle layer opposes urine voiding-arised BP shedding and resists inward BP swelling-driven urethral occlusion and urine permeation. Importantly, systematic proteomic and genomic analyses revealed that such hydrogel scaffolds expedite regeneration, alleviate inflammation and regulate extracellular matrix secretion, where BP swelling-induced outgrowth for fibrosis and scar formation is significantly inhibited by VP through the blockade of the scar-associated YAP signaling pathway. These microenvironment-adaptable design concepts provide a rationale for engineering urethral regeneration scaffolds.

overall_design: We used a newly designed urethral repair stent for in vivo repair and reconstruction, and analyzed the mechanism by which the new urethral stent promotes urethral repair through sequencing

first: Ming

first: Maocheng

last: Zuo

first: Ranxing

first: Kaile

last: Zhang

first: Wenzhuo

last: Fang

first: Kun

first: Qiang

last: Fu


title: Global effects on gene and retroelement expression upon HUSH function abrogation in ERVK3-1 knockout cells

city: West Haven

middle: A

last: Slavoff

state: CT

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University - West Campus

summary: ERVK3-1 is a ubiquitously expressed 109-amino acid endogenous retroviral Rec microprotein. We hereby report its physical and functional interaction with the HUSH complex via PPHLN1. Deletion of the ERVK3-1 coding sequence in HEK293T cells resulted in significant upregulation of ZNF genes and pseudogenes - established classes of HUSH targets. Increased expression of genes involved in immune recognition and signaling - especially the MAGE family - was also noted, consistent with the current knowledge on HUSH depletion increasing L1 expression and consequently, interferon signaling. Analysis of ERV expression from the same RNA-Seq dataset shows widespread dysregulation as well.

overall_design: RNA-Seq analysis (rRNA depletion) of wild-type HEK293T cells (WT), ERVK3-1 knockout HEK293T cells (ERVK3-1 KO2), and HEK293T cells transiently expressing Cas9 with a non-target guide RNA to look at differential gene expression with spike-in controls.

first: Ayodya

last: Jayatissa

first: Nadiya

last: Jaunbocus

first: Betel

last: Erkalo

first: Kevin

last: Jiang

first: Shu-Jian

last: Zheng

first: Haomiao

last: Su

first: Lichong

last: Yan

first: Jin-Young

last: Choi

first: Joan

last: Vaughan

first: Antonella

last: Bacchiocchi

first: Zhenkun

first: Xiongwen

last: Cao

first: Ruth

last: Halaban

first: Alan

last: Saghatelian

first: Joseph

last: Craft

first: Grace

last: Chen


title: Effects of NorUDCA on the Transcriptomic Landscape of Differentiating Murine Pathogenic Th17 Cells In Vitro

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary: 24-Nor-ursodeoxycholic acid (NorUDCA) is a novel therapeutic bile acid for treating immune-mediated cholestatic liver disease, such as primary sclerosing cholangitis (PSC). Since PSC strongly associates with TH17-mediated tissue inflammation, we explored NorUDCA’s immunomodulatory potential on TH17 cells. Using an unbiased bulk RNA sequencing approach, we discovered that brief exposure (4 hour) to NorUDCA reshapes transcriptomic landscape of murine pathogenic (p)TH17 cells with top enriched pathways of mTORC1 signaling, hypoxia, Myc and associated metabolic processes, such as glycolysis and OXPHOS. NorUDCA treatment also modulates expression of several genes involved in KEGG glutamine pathway, indicating NorUDCA might affect pTH17 cell glutamine metabolism. Taken together, our bulk RNA sequencing data demonstrate NorUDCA’s therapeutic efficacy in modulating pTH17 immunometabolism, potentiating future clinical applications for treating TH17-mediated disease and beyond.

overall_design: Transcriptomic profiling of murine pathogenic TH17 cells in the presence with or without 4-hour NorUDCA treatment

first: Ci

last: Zhu

first: Michael

last: Trauner

first: Christoph

last: Bock

last: Schuster


title: Regulation of Cortical Neurogenesis by MED13L via Transcriptional Priming and its Implications for MED13L Syndrome

city: SHanghai

first: Yulan

last: Zhao

address: North Zhongshan Rd 3663#

institute: East China Normal University

summary: MED13L is highly susceptible to neurodevelopmental disorders, yet the underlying developmental mechanisms remain poorly understood. We developed a gene knockout mouse model of MED13L syndrome to elucidate these mechanisms. Homozygous Med13l-null mice exhibit neonatal lethality and severe cortical neurogenesis deficits due to impaired differentiation of neural progenitors. In contrast, heterozygous Med13l-null mice are viable but display characteristic behavioral deficits of MED13L syndrome, including impaired learning and memory, reduced motor coordination, and heightened anxiety. Heterozygous mice also present with microcephaly and simplified neuronal morphology in the motor cortex. Conditional knockout of Med13l in the forebrain pyramidal lineage corroborated the motor and histological deficits observed. Proteomic, transcriptomic, and single-cell RNA sequencing analyses suggest that MED13L regulates cortical neurogenesis by priming developmental genes for transcriptional activation as a component of the mediator complex. These findings provide insights into the molecular and neurodevelopmental underpinnings of MED13L syndrome, paving the way for potential therapeutic strategies.

overall_design: To compare the gene expression profile of homozygous Med13l-null (KO), heterozygous (Het) and wild-type (WT) mice, we isoltaed total RNA from E13.5 embryonic cortex of 3 groups, with each group including 3 brain tissues.  To compare the cell distribution of KO, Het and WT mice, we isolated the E13.5 embryonic cortical tissues and obtain 3 samples by pooling tissues from 5 individual embryos with the same genotype for each sample.

first: Jia

last: Li

first: Yuzhu

last: Hao

last: Cui

first: Xiaoxiao

last: Wu

first: Ji

last: Ma

first: Shuangyi

last: Xie

first: Yi-Hsuan

last: Pan

first: Xuelian

last: He

first: Xiao-Bing

last: Yuan


title: PAM-flexible adenine base editing rescues hearing loss in a humanized MPZL2 mouse model harboring an East Asian founder mutation

city: Seoul

first: Sohyang

last: Jeong

address: 71, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

summary: Hearing loss is one of the most prevalent sensory disorders, but no commercial biological treatments are currently available. Here, we identify an East Asia-specific founder mutation, the homozygous c.220C>T mutation in MPZL2, that contributes to a significant proportion of hereditary deafness cases in our cohort study. We find that the disease-causing mutation can be targetable by adenine base editors (ABEs) that enable A·T-to-G·C base corrections without DNA double-strand breaks. To demonstrate this, we develop a humanized mouse model (hMPZL2Q74X/Q74X) that recapitulates human MPZL2 deafness and leads to progressive hearing loss. A PAM-flexible ABE variant with reduced bystander and off-target effects (ABE8eWQ-SpRY:sgRNA3) is packaged in dual adeno-associated viruses (AAVs) and injected into the inner ear of hMPZL2Q74X/Q74X mice and effectively corrects the mutation. This treatment significantly restores hearing function, improves inner ear structural integrity, and reverses altered gene expression. Base editing may hold therapeutic potential for hereditary deafness, including most cases of MPZL2 deafness.

overall_design: RNA-seq profiling of mouse cochlear membranous labyrinth tissue from hMPZL2Q74X/Q74X, Mpzl2 WT, and hMPZL2Q74X/Q74X treated with AAV-ie-ABE8eWQ-SpRY:sgRNA3 at P28 to explore the molecular pathways involved in the cochlear histopathology caused by the MPZL2 c.220C>T mutation.

first: Shao Wei

last: Hu

first: Luoying

last: Jiang

first: Hansol

last: Koo

first: Zijing

last: Wang

first: Won Hoon

last: Choi

first: Biyun

first: Heeyoung

last: Seok

first: Yi

last: Zhou

first: Min Gu

last: Kim

first: Dan

last: Mu

first: Huixia

last: Guo

first: Ziyi

first: Sung Ho

last: Jung

first: Yingting

last: Zhang

first: Ho Byung

last: Chae

first: Liheng

first: Sung-Yeon

last: Lee

first: Luo

first: Myung-Whan

last: Suh

first: Yang

last: Xiao

first: Moo Kyun

last: Park

first: Honghai

last: Tang

first: Jae-Jin

last: Song

first: Xi

first: Ai

first: Jun Ho

first: Sangsu

last: Bae

first: Sang-Yeon

first: Yilai

last: Shu


title: DNA methylation alterations of driver genes in blood of high-altitude pulmonary edema ( RRBS)

city: Nanjing

first: Qiong

last: Li

address: Dingjiaqiao Road 87#

institute: Southeast University

type: Methylation profiling by high throughput sequencing

summary: Epigenetics may play an important role in the occurrence and development of high-altitude pulmonary edema. To investigate the DNA methylation driving genes associated with high-altitude pulmonary edema, we also performed reduced representation bisulfite sequencing (RRBS) for blood identify differences of DNA methylation status of 10 HAPE patients and 10 healthy volunteers.

overall_design: We performed reduced representation bisulfite sequencing (RRBS) for blood of 10 HAPE patients and 10 healthy volunteers. All of the participants and health care volunteers were Han Chinese people between the ages of 18 and 65 who had travelled to Tibet.

first: Yan

last: Shen

first: Fujin

last: Fang

first: Chuanli

last: Yang

first: Yu

last: Dong


title: Transcriptional heterogeneity and molecular regulation of totipotency-to-pluripotency transitions in Porcine EPSCs

city: Wuhan

first: Wu

last: Linhui

state: Hubei

address: No.1 Shizishan Street

department: College of Animal Science and Veterinary Medicine

institute: Huazhong Agricultural University

summary: The molecular characteristics of EPSCs have long been debated. While human EPSCs (hEPSCs) resemble eight-cell and morula-stage embryos, mouse EPSCs (mEPSCs) more closely resemble post-implantation epiblasts. This study explores the developmental potential and molecular characteristics of porcine expanded pluripotent stem cells (pEPSCs), uncovering their unique transcriptional heterogeneity and similarities to both morula and post-implantation epiblast stages. By performing single-cell transcriptomic analysis, three distinct subpopulations (C1, C2, and C3) were identified, corresponding to totipotency, naïve pluripotency, and primed pluripotency. The use of dual fluorescence reporter systems highlighted transitions between these states, resembling embryonic development. Key findings reveal a dynamic balance model of LEUTX and OTX2 in regulating pluripotency transition that OTX2 promotes the shift from totipotency to primed pluripotency by promoting pluripotency and lineage-priming genes, while LEUTX enhances totipotency by activating totipotency genes. LEUTX-overexpressing cells demonstrated enhanced developmental potential and stability in vitro. The study established a conserved framework for understanding state transitions mediated by OTX2 and LEUTX, with implications for regenerative medicine, developmental biology, and highlight the potential of pEPSCs in agricultural and biomedical applications.

overall_design: This study aims to comprehensively profile the chromatin accessibility, transcription factor binding, and gene expression in pig pEPSCs using multiple high-throughput sequencing technologies, including ATAC-seq, ChIP-seq and RNA-seq. The dataset includes pEPSCs samples under various conditions, including wild-type, gene overexpression (e.g., OTX2, LEUTX), and knockout (e.g., OTX2), as well as wild-type and OE_OTX2 4-cell embryo stages.

first: Linhui

last: Wu

first: Peng

last: Su


title: Pomacea canaliculata eye: a new system to study full camera-type eye regeneration [embryonic development time-course]

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Eyes are complex, delicate sensory organs that can be irreversibly damaged by disease or aging. Finding solutions to repair eyes has been difficult because no animal model has been available to study the complete regeneration of a camera-type eye. To study camera-type eye regeneration we can study partial or limited regeneration in vertebrates or complete regeneration of different types of eyes with simpler structure in animals with higher regenerative potential. I discovered an invertebrate organism, the freshwater apple snail Pomacea canaliculata, with camera-type eyes, yet capable of full regeneration after complete amputation. After cellular and molecular study of P. canaliculata eye and their regeneration dynamic, we developed tools to edit genes and test their functions. We found that, like in humans, eye development in these animals is controlled by the expression of the gene pax6. It is now possible to unravel the genetic basis of camera-type eye regeneration, which may provide new opportunities for therapeutic interventions. This work represents the foundation to use P. canaliculata as a valuable research system in the field of regeneration, not only to bring more knowledge about complex organs regeneration, but also to shed light, for the first time, on the process of complete camera-type eye regeneration.

overall_design: Pomacea canaliculata embryonic development time-course containing Stage 2, Stage 3, Stage 4, Stage 5, Stage 6, Stage 7, Stage 8, Stage 9, Stage 10 and hatchling animals.

first: Alice

last: Accorsi

first: Eric

last: Ross

first: Brenda

last: Loredo

first: Melainia

last: McClain

first: Tim

last: Corbin

first: Shane

last: Merryman

first: Alejandrom

last: Sánchez Alvarado


title: Gene expression profile at single cell level of whole lungs of mice collected from bleomycin or PBS-treated young and old mice at day 14, day 28 and day 60 post injection

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: We use scRNA-seq to monitor the resolution of bleomycin-induced fibrosis in capillary endothelial cells and the impact of aging on these mechanisms

overall_design: Young (7 weeks) or old (18 months) mice were injected with PBS or bleomycin to induce transient alveolar damages. Their whole lungs were harvested at the bleomycin-induced fibrotic response peak at day 14, and during the resolution phase at day 28 and 60 post injection. At each time point for both young or old mice, single cell libraries of bleomycin and PBS treated lung samples (3 replicates each) were pooled using cell hashing and jointly sequenced.

first: Marin

last: Truchi

first: Grégoire

last: Savary

first: Alberto

last: Baeri

first: Cédric

last: Girard-Riboulleau

first: Virginie

last: Magnone

first: Pascal

last: Barbry

first: Nicolas

last: Pottier

first: Bernard

last: Mari


title: Spatial RNA sequencing of bleomycin-treated young and old mice lungs at day 14 and day 28 post injection

summary: We monitored lung fibrosis formation and resolution in young and old mice by generating a series of spatial transcriptomics datasets using the 10x Genomics Visium platform

overall_design: Young (7 weeks) or old (18 months) mice were injected with PBS or bleomycin to induce transient alveolar damages. At the bleomycin-induced fibrotic response peak at day 14 and during the resolution phase at day 28 post injection, their lungs were embedded in OCT and stored at -80°C. OCT blocks were cryosectioned at 10µm thickness on capture areas of Visium 10 Genomics slide.

first: Marie-Jeanne

last: Arguel

first: Clémentine

last: de Schutter


title: Lung injury shifts pulmonary capillary endothelial cells towards regeneration-associated Lrg1+ subpopulations with delayed dynamics in aged mice

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

overall_design: Refer to individual Series


title: High-throughput transcriptomics screening of mixtures of BPA alternatives reveal additive effects in vitro

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Humans are regularly exposed to mixtures of BPA alternative chemicals through their diets, consumer products and other sources. Like BPA, many alternatives perturb nuclear hormone receptors and are considered endocrine disrupting chemicals. We used high-throughput transcriptomics (HTTr) to evaluate the potency and potential modes of action of seven mixtures of BPA alternatives, along with their 12 individual components, in MCF-7 breast cancer cells. Our primary aim was to explore whether alternatives present in mixtures act additively. MCF-7 cells were exposed to chemicals (0.001 – 50 µM) for 48 h in serum-free conditions and TempO-Seq (BioSypder Inc.) was used to determine global and estrogen receptor alpha (ERα)-specific transcriptomic changes. Transcriptomic points of departure were derived using benchmark concentration (BMC) modelling. We first identified the concentration at which global transcriptional activity was robustly altered. Then, a novel ERα transcriptomic biomarker was used to identify ERα agonists and model a predicted ERα activation point of departure. Mixtures modelling was employed to predict potency of BPA alternatives and test for additive effects in vitro. Ingenuity Pathway Analysis (IPA; Qiagen) was used to identify upstream regulators and canonical pathways from genes fitting BMCs. All seven mixtures had additive effects across all transcriptomic points of departure modelled. BPAF was the most potent individual chemical tested overall, followed by BPA and BPC. The ERα transcriptomic biomarker classified all mixtures as ERα activators along with several individual BPA alternatives. Pathway analysis revealed that all mixtures and most individual components perturbed similar upstream regulators and pathways, suggesting common modes of action. These data support the use of HTTr as part of new approach methodologies to assess the toxicological potency of mixtures in vitro.

overall_design: MCF-7 cells were exposed (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 uM; 48hrs) to 7 different mixtures of BPA alternative chemicals and 12 individual chemicals (BPA, BPAF, 4,4’-BPF, BPC, BPS, P201, BPAP, 2,4’-BPS, 2,4’-BPF, BPB, BPZ, TMBPF), along with controls (solvent: 0.1% DMSO; E2: 0.1 nM, 1 nM). Mixtures 1 – 6 were equimolar: mix 1 (BPA + BPAF), mix 2 (mix 1 + BPC), mix 3 (mix 2 + 4,4’-BPF), mix 4 (mix 3 + BPAP), mix 5 (mix 4 + BPS), mix 6 (mix 5 + 2,4’-BPF + P201 + 2,4’-BPS). Mixture 7 (BPAF + 4,4'-BPF + BPA + BPB + BPZ + BPS + BPAP) was non equimolar and had a different exposure concentration range (0.66, 1.3, 2.6, 5.2, 10.5, 21 uM). All exposures were for 48 hours in serum-free conditions (DMEM + 2% BSA + 1% P/S).


title: eIF2A regulates cell migration without overtly affecting translation [RIP-Seq]

status: Public on Jun 27 2025

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

country: Spain

institute: CRG

summary: The RNA-binding protein eIF2A has been implicated in a variety of cellular processes including tumorigenesis. This role has been attributed to its function as alternative translation initiation factor. However, the mechanisms by which eIF2A regulates translation and its contribution to oncogenic transformation are unclear. Here, we shed light on these aspects using a melanoma cell model consisting of the non-tumoral melanocytic cell line MelST and its metastatic counterpart obtained by RasV12 overexpression (MelSTR). Depletion of eIF2A from MelST and MelSTR cells revealed acquired dependencies upon Ras transformation for migration. Surprisingly, analysis of the transcriptome (RNA-Seq) and translatome (ribosome profiling) upon eIF2A depletion showed minor to no changes in translation. RIP-Seq and RT-qPCR furthermore indicate that eIF2A binds mRNA targets in a translation-independent manner. Interestingly, protein interactome analyses point towards a function of eIF2A in cytoskeletal remodeling and indeed we can show that eIF2A localizes to the centrosome and affects its composition and orientation, linking eIF2A with migration. In addition, eIF2A promotes migration in a manner that depends on its RNA-binding activity. Together, these results indicate that eIF2A does not function as a translation factor in melanoma cells, but through a novel function which is based on its RNA-binding activity and its connections to the centrosome.

overall_design: To identify eIF2A mRNA targets in MelST and MelSTR,  RNA-immunoprecipitation (RIP-) sequencing of was performed in both cell lines in triplicates. Anti-eIF2A antibody (abcam #ab169528) was used to immunoprecipitate eIF2A. As a negative control, RNA-seq of input samples and RNA-seq of IgG immunoprecipitation were included.

first: Jennifer

last: Jungfleisch

first: Fátima

last: Gebauer


title: Identifying Multiple Genomic Abnormalities and Predicting Neoantigens from Single Tumor Cells [PRJNA1110294]

city: ShangHai

first: Da

last: Lin

address: No. 650 Songjiang Road

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

summary: Tumors exhibit high heterogeneity due to distinct genomic aberrations in individual cells. Despite this, no methods currently exist to detect these genomic abnormalities at the single-cell level. To address this, we developed Uniform Chromosome Conformation Capture (Uni-C), an efficient method that precisely detects a variety of genomic anomalies in single cells, including single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), copy number variations (CNVs), structural variations (SVs), and focal amplifications such as extrachromosomal DNA (ecDNA) and homogeneously staining regions (HSRs). Utilizing Uni-C, we characterized varied structural variations and detailed the structure of ecDNA in circulating tumor cells (CTCs), highlighting their extensive heterogeneity. We also observed differences in chromatin conformation across CTCs in mitosis and interphase, potentially serving as markers for cell vitality. Additionally, by using genomic data from Uni-C, we detected driver gene mutations in CTCs and predicted neoantigens, significantly advancing early cancer detection and treatment strategies.

overall_design: To maintain the stability of chromatin spatial conformation throughout the experiment, we first employed EGS (ethylene glycol bis (succinimidyl succinate)) and formaldehyde for dual crosslinking of the cells, followed by lysis to release the nuclei. To prevent the aggregation of nuclei due to centrifugation, we excluded all centrifugation steps in later experimental stages. We used a 4-base cutter restriction endonuclease to enzymatically fragment the chromatin, conducting end-repair and proximity ligation within the same reaction setup. After proximity ligation, we transferred individual nuclei into an alkaline lysis buffer using a glass capillary, setting the stage for further single-nucleus amplification. For amplification of single nuclei, we utilized a heat-resistant phi29 DNA polymerase along with a mixture of dNTPs and Alpha Thiol-modified ddNTPs, and exonuclease-resistant random primers. During the extension process, the encounter with Alpha Thiol-modified ddNTPs terminates the extension reaction, thus controlling the size of the amplification products to be below 2 kb. The resulting shorter amplified products make it difficult for random primers to rebind, allowing only the original single-cell genome to serve as a template for further amplification. This prevents over-amplification of certain genomic regions and achieves uniform whole-genome amplification, significantly enhancing genome coverage. Moreover, the addition of the fast, heat-resistant phi29 polymerase has reduced the amplification time to approximately 2 hours. The amplified products from single nuclei were then subjected to size selection, followed by the preparation of libraries for high-throughput sequencing.

first: Xinyu

last: Li

first: Xiaochen

last: Gao


title: eIF2A regulates cell migration without overtly affecting translation

overall_design: To identify direct eIF2A mRNA targets and the binding regions in melanoma SKMEL-147 cell lines,  iCLIP  was performed in triplicates. Anti-eIF2A antibody (abcam #ab169528) was used to immunoprecipitate eIF2A. As a negative control, non UV crosslinked samples were included.


title: Plasma miRNA as Potential Biomarkers for Hand-arm vibration disease

city: Guangzhou

first: Hanjun

last: Zheng

address: Xinzao street, Panyu district, Guangzhou, Guangdong, China.

institute: Guangzhou Medical University

summary:
MicroRNAs (miRNAs) have an essential function as post-transcriptional regulators in a variety of processes. miRNAs involvement and variation have mainly been studied in various disorders. Our study is the first to evaluate miRNA expression in hand-arm vibration disease (HAVD), an increasing occupational disease in China and the rest of the world. HAVD can cause injuries in microcirculation in the fingertip and induce the vibration-induced white finger (VWF), which can negatively affect patients’ quality of life. In this current study, we aimed to explore the mechanisms of development and progression of HAVD.
We extracted total RNAs from the plasma of 24 metal workers and divided them into 3 groups: workers who reported VWF, workers exposed with occupational hand-transmitted vibration (HTV) without VWF, and control group. Genome-wide microarray gene chip was used to acknowledge the different miRNAs expression profiles. Functional analyses were operated to predict how those miRNAs work in VWF.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 24 samples. The aim of this study was to examine whether olasma microRNAs is useful as a biomarker for Hand-arm vibration disease (HAVD).

first: Maosheng

last: Yan


title: Systems genetics of partner quality: Quantitative variation in gene expression and qualitative variation in plasmid-borne gene clusters underlies symbiosis variation

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

summary: We leverage a model nitrogen-fixing plant symbiont and integrate genomics, phenotypes, and gene expression data to associate sets of gene clusters, which are frequently gained and lost in natural populations, with plant growth. We reveal novel structural and modular genetic processes with implications for the function and inheritance of symbiosis function in plant-microbe interactions.

overall_design: In single-inoculation experiments, two plant genotypes of Medicago truncatula, A17 and DZA, were inoculated with 20 naturally occurring strains of Sinorhizobium meliloti.

first: Muhammad Rizwan

last: Riaz

first: Ivan

last: Sosa-Marquez

first: Hanna

last: Lindgreen

first: Rebecca

last: Doyle

first: Mario

last: Romero

first: Katy

last: Heath


title: Lung structural cell dynamics are altered by influenza virus infection experience leading to rapid immune protection following viral re-challenge

city: Glasgow

first: Graham

middle: Michael

last: Hamilton

state: Lanarkshire

address: University Avenue

department: MVLS Shared Research Facility - Molecular Analysis

country: United Kingdom

institute: University of Glasgow

summary: Lung structural cells, including epithelial cells and fibroblasts, form barriers against pathogens and trigger immune responses following infections such as influenza A virus. This response leads to the recruitment of innate and adaptive immune cells required for viral clearance. Some of these recruited cells remain within the lung following infection and contribute to enhanced viral control following subsequent infections. There is growing evidence that structural cells can also display long-term changes following infection or insults. Here we investigate long-term changes to mouse lung epithelial cells, fibroblasts, and endothelial cells following influenza virus infection and find that all three cell types maintain an imprint of the infection, particularly in genes associated with communication with T cells.  Lung epithelial cells from IAV-infected mice display functional changes by more rapidly controlling influenza virus than cells from naïve animals. This rapid anti-viral response and increased expression of molecules required to communicate with T cells demonstrates sustained and enhanced functions following infection. These data suggest lung structural cells could be effective targets for vaccines to boost durable protective immunity.

overall_design: Lungs were taken from C57BL/6 mice that were either naïve (control) or had been infected with influenza A virus 10 or 40 days previously. Lungs were digested with Collagenase P, Dispase and DNase and CD45+ cells removed using magnetic beads. Cells were stained with antibodies to Epithelial cells (EpCAM1), Fibroblasts (CD140a) or blood endothelial cells (CD31) and live cells of each types sorted ex vivo by FACS. For each sample, cells were combined from 6-8 mice. Cells were pelleted, resuspended in a small volume and centrifuged through a QiaShredder. RNA was prepared using a mini or micro RNAeasy kit from Qiagen. RNA was purified from total RNA (100ng) using poly-T oligo‑attached magnetic beads (Life Technologies, CA, USA). Sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB) in accordance with the manufacturer's recommendations. Products were purified and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system. After the clustering of the index-coded samples, each library preparation was sequenced on an Illumina NextSeq™ 500 platform with 2x75bp paired end sequencing. An average sequencing depth of 20M reads per sample was achieved.

first: Megan

last: MacLeod


title: Macropinocytosis maintains CAF subtype identity under metabolic stress in pancreatic cancer [nanoString nCounter]

city: La Jolla

first: Cosimo

last: Commisso

state: CA

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Pancreatic ductal adenocarcinoma (PDAC) tumors are glutamine-deficient, and both tumor cells and cancer-associated fibroblasts (CAFs) rely on this amino acid to maintain fitness and induce macropinocytosis as an adaptive response. CAFs play a critical role in sculpting the tumor microenvironment, yet how adaptations to metabolic stress impact the stromal architecture remains elusive. In this study, we find that macropinocytosis sustains the myCAF phenotype under glutamine limitation by preventing inflammatory reprogramming. Our data demonstrate that metabolic stress induces an intrinsic inflammatory CAF (iCAF) program through MEK-ERK signaling. We find that blocking macropinocytosis in vivo promotes myCAF-to-iCAF transitions, remodeling the tumor stroma. Importantly, stromal remodeling driven by macropinocytosis inhibition—including iCAF enrichment, collagen reduction, immune cell infiltration, and vascular expansion—sensitizes PDAC tumors to immunotherapy and chemotherapy. Our findings reveal that inhibiting macropinocytosis promotes an inflammatory, less fibrotic tumor microenvironment that can be leveraged to improve therapeutic responses in PDAC.

overall_design: Gene expression profiling of KPC subcutaneous tumors treated with DMSO or EIPA, using nanoString nCounter Mouse PanCancer immune profiling panel

first: Yijuan

last: Zhang


title: Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens

city: Seattle

first: Betty Chentzu

last: Yu

state: WA

address: 1100 Fairview Ave N

department: Computational Biology

institute: Fred Hutchinson Cancer Center

summary: Aging is one of the greatest risk factors for chronic diseases. Research on aging at the cellular level, especially in adult stem cells, is conducive to a comprehensive understanding of the molecular processes of aging. We performed multiple systematic genome-wide CRISPR interference (CRISPRi) screenings in human primary mesenchymal stem cells (MSC) derived from adipose tissues. Notably, we identified potential novel regulators in the progress of MSC senescence in terms of both replicative senescence and inflammatory induced senescence. Combining the functional genomic data with 405 GWAS datasets, including 50 aging-related studies, we observed that the inflammatory aging signatures identified from the CRISPRi screenings were significantly associated with diverse aging processes, suggesting novel signatures to analyze and predict aging status and aging-related disease. These novel signatures verified from the comprehensive functional genomics and genetic datasets may provide targets to interfere with the aging process as well as to improve cell therapy products.

overall_design: The goals of this study were (i) to identify novel senescence-promoting genes in adult stem cells, (ii) to characterize novel senescence-promoting genes in a specific inflammatory milieu(iii) and to decipher the inflammatory aging process by comparing two solid screening platforms (IL-6 minus and IL6 plus), thus highlight the biomarker for  pathological aging and therapeutic potential of MSC by manipulating the senescence-promoting genes.


title: eIF2A regulates cell migration without overtly affecting translation [Ribo-Seq]

first: Neus

last: Mestre-Farràs

overall_design: To characterize the translation role of eIF2A in MelST and MelSTR cells, independent triplicates of RNA-Seq and Ribo-Seq libraries were generated for both cell lines in shCTL and sheIF2A conditions. For each cell line, changes between sheIF2A and shControl were correlated between RNA-seq and Ribo-seq to determine how mRNAs are regulated.

first: Jennifer

last: Jungfleisch

first: Fátima

last: Gebauer


title: Identifying Multiple Genomic Abnormalities and Predicting Neoantigens from Single Tumor Cells [PRJNA1110293]

first: Da

last: Lin

first: Xinyu

last: Li

first: Xiaochen

last: Gao