title: Semaphorin 3E as a novel therapeutic target for neuropathic pain

status: Public on Feb 28 2025

city: Fukuoka

first: Takayuki

last: Fujii

state: Fukuoka

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

department: Department of Neurology

country: Japan

institute: Kyushu University

summary: We aimed to identify neuropathic pain (NP)-related immune semaphorins (SEMAs) and assess the efficacy of SEMA targeted therapy for NP. We quantified serum SEMA3A, 3E, 4A, 4D, and 7A in 45 patients with NP and 17 age- and sex-matched healthy controls (HCs) by enzyme-linked immunosorbent assay (ELISA). SEMA expression in DRG and peripheral nerve (PN) tissues of autopsied/biopsied patients with NP and controls as well as NP mouse model with partial sciatic nerve ligation (PSNL) was assessed by immunohistochemistry. Moreover, we intraperitoneally injected SEMA-blocking IgG or control IgG into PSNL-operated mice for 5 consecutive days immediately and 14 days after PSNL, and assessed mechanical hypersensitivity using von Frey filament on day 4 and 18 after PSNL. In vitro, we evaluated neurite outgrowth and the gene expression by RNA microarray analysis of mouse DRG neurons treated with or without SEMA3E. ELISA showed a significant increase of the SEMA3E in NP patients compared to HCs. Immunohistochemistry revealed enhanced SEMA3E expression in DRG and PN tissues of both NP patients and mouse model, especially in pro-inflammatory macrophages. SEMA3E-blocking IgG injection not only abolished the pro-inflammatory macrophage accumulation in PNs but also resolved hypersensitivity in PSNL-operated mice on both days 4 and 18. In vitro, SEMA3E treatment inhibited neurite outgrowth of DRG neurons accompanied with the upregulation of S100A9 which promotes neuroinflammation and downregulation of Dync1h1 that promote neurite outgrowth compared to non-treated DRG neurons. SEMA3E inhibition is a potential therapeutic strategy for NP via regulating neuroinflammation.

overall_design: To identify the genetic alternations within sensory neurons affected by SEMA3E, we performed an RNA array assay of primary adult mouse DRG neurons incubated with 3 different medium: control medium which contains DMEM and B27 supplement only, SEMA3E medium which contains recombinant SEMA3E 1 μg/ml, and high-level blocking-containg medium which contains recombinant SEMA3E 1 μg/ml and SEMA3E-blocking IgG 1 μg/ml.

first: Sato

last: Yoshidomi

first: Hiroyuki

last: Honda

first: Kaoru

last: Kashu-Yoshida

first: Yukino

last: Miyachi

first: Yuka

last: Inoue

first: Hidenori

last: Ogata

first: Ryo

last: Yamasaki

first: Toru

last: Iwaki

first: Noriko

last: Isobe


title: Comparative mRNA Profile Analysis from NAc of Adolescent Male Mice after Binge-Like Alcohol Exposure Eliciting Deficits in Context Fear Extinction Learning.

city: San Juan

first: Mario

middle: Ernesto

last: Lloret

state: Puerto Rico

address: Calle Norzagarai Instituto de Neurobiologia

department: Academic Affairs

country: USA

institute: Unversity of Puerto Rico Medical Sciences Campus

type: Expression profiling by high throughput sequencing

summary: Introduction: There is a high co-occurrence between trauma and stress-related diseases, such the formerly named post-traumatic stress disorder, and alcohol use disorder (AUD). This necessitates an understanding of the physiological and genetic factors contributing to this relationship. Binge drinking is the most common method of alcohol consumption among adolescent males and significantly increases the risk of developing comorbid stressor-related disorders and AUD. In experiments modeling the effects of a single binge-like alcohol exposure in male adolescent mice, we observed a clear deficit in context extinction learning. This exposure led to a significant initial increase in subsequent voluntary drinking on day one, as measured by the every-other-day (EOD) two-bottle choice drinking assay, which normalized thereafter. Methods: For this study we performed an mRNASeq analysis of mice nucleus accumbens (NAc), a region intricately involved in regulating both aversive contextual fear responses and reward, after EOD to profile the differential expression of mRNAs within this region. We also used immunohistochemistry of coronal brain slices to characterize expression of proteins associated with stress-related disorders and molecular alcohol tolerance, such as FKBP5, GSK3ß, and ß-catenin, within the striatum, nucleus accumbens (NAc), hippocampus, and basolateral amygdala (BLA). Results: Comparative mRNA profile analysis reveals significant long-term changes in gene expression induced by binge-like alcohol exposure, even 30 days after the initial exposure. Immunohistochemistry showed a full recovery of previously observed altered levels of target proteins prior to EOD. Conclusions: These findings suggest that the temporal activation of specific gene subsets plays a crucial role in the comorbidity of AUD and stressor-related diseases. Understanding these mechanisms can help develop more effective, integrated treatment approaches to improve outcomes for affected individuals. B13:AD13

overall_design:
This dataset comprises bulk mRNA-seq experiments conducted on tissue samples collected from the Nucleus Accumbens Core of adolescent male mice (postnatal days 35–55). The mice underwent a series of behavioral paradigms, including contextual fear conditioning, a single-day binge-like alcohol exposure, and context extinction trials. Twenty-four hours after completing extinction, they were introduced to an every-other-day (EOD) drinking assay, which lasted for 27 days. Tissue was collected and prepared for mRNA-seq analysis 24 hours after the completion of the EOD assay.

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first: Cristina

last: Velazquez-Marrero

last: Lloret-Torres

first: Abiel

last: Roche Lima


title: RNA-seq analysis of tetrahedral nucleic acid nanomaterials loaded with miR-124 for the treatment of mouse intracerebral hemorrhage

city: chongqing

first: Wanli

last: Yu

address: 118 Xingguang Avenue, Liangjiang New District, Chongqing

country: China

institute: chongqing medical university

summary: We used collagenase injection into the brain to model intracerebral hemorrhage in mice. Simply put, the mice were immobilized on a stereotaxic frame. 0.05U collagenase VII was injected sequentially into the caudate nucleus (bregma: 0.2 mm anterior, 2.3 mm right lateral, and 3.5 mm deep). Three days after the collagenase injection, we collected brain tissue from normal mice (control group), the hemorrhagic side of the brain from ICH mice (experimental group), and the hemorrhagic side of the brain from ICH mice after intravenous injection of 20 mmol miR124-TNA (intervention group).

overall_design: An intracerebral hemorrhage mouse model was established through collagenase injection, followed by the extraction of total RNA from the peri-hematoma brain tissue. Each group consisted of 3 replicates. A total of 3 groups were formed: the experimental group, the control group, and the intervention group. Finally, high-throughput transcriptome sequencing was performed on the Illumina NovaSeq.

first: Sihao

last: Chen

first: Haotian

last: Jiang

first: Dewei

last: Zhou

first: Yi

last: He

first: Xiangling

last: Pu

first: Yongqi

last: Dong

first: Ruixin

last: Wu


title: Innate Immune Pathway Activation To Modulate Mesenchymal Stromal Cell (MSC) Interaction With Synovium And Cartilage

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Osteoarthritis (OA) is a progressive degenerative condition prevalent in aged animals and humans. Regenerative cellular therapies have emerged as a treatment option for OA with mixed results in efficacy which have been attributed in part to heterogeneity within stromal cell populations and between donors. Activation of mesenchymal stromal cells (MSC) by priming their ligands prior to administration has been demonstrated as a means to generate more homogenous cell populations thereby potentially achieving more consistent outcomes with cell therapy administration. We have demonstrated improved functional and histological outcomes in a murine destabilization of the medial meniscus model of OA with primed MSC therapy. Therefore, the goal of this study was to evaluate and compare the immunomodulatory properties of two ligands on cytokine and gene expression of MSC themselves and the effect of primed MSC conditioned media on key joint cells to further understand that observed effect mechanistically in the context of OA.

overall_design: MSC were activated with either Toll-like receptor (TLR)-3 agonist polyinosinic:polycytidylic acid (pIC) or Stimulator of INterferon Genes (STING) agonist (2’3’cGAMP) at 10 ug/mL for 2 hours, washed and cultured an additional 24 hours to generate MSC conditioned media (MSC-CM). Key effector cells relevant to OA (peripheral blood derived macrophages, chondrocytes and synoviocytes) were stimulated with IL-1β and TNF-α and treated with activated MSC supernatants for 24 hours. The cells were washed and cultured an additional 24 hours and supernatants were collected. Secreted cytokines in conditioned media from MSC themselves and MSC-treated joint cells were measured by multiplex immunoassay and ELISA. Bulk RNA sequencing was performed on activated MSC and MSC-CM treated joint cells to determine transcriptomic responses to treatment via an Illumina based platform. Data analysis included comparison of differentially expressed genes and pathway analysis in treated vs. untreated MSC, macrophages, synoviocytes, and chondrocytes, and between treatment groups themselves.

first: Lyndah

last: Chow

first: Lynn

last: Pezzanite

first: Peter

last: Linde


title: The Fosl1-Kdm6b Axis Controls Skeletal Muscle Fibrosis by Regulating  Histone H3K27me3 [scRNA-seq]

city: Durham

first: Yarui

last: Diao

state: NC

address: 303 Research Drive

department: Cell Biology

institute: Duke University

summary: Skeletal muscle fibrosis, characterized by the replacement of functional muscle tissue with fibrotic scarring, leads to muscle function loss and potentially fatal respiratory failure, particularly in muscular dystrophy. The mechanisms driving muscle fibrosis is not yet fully understood. Our study utilized single-cell RNA-seq and single-nuclei ATAC-seq to analyze the transcriptome and chromatin accessibility of regenerating and dystrophic skeletal muscle, identifying a specific subset of fibro-adipogenic precursors (FAPs) enriched in dystrophic muscles, termed fibrotic FAPs. We further demonstrated that chronic inflammation upregulates Fosl1, an early response gene, which activates the expression of Kdm6b in fibrotic FAPs. Kdm6b, a histone demethylase, specifically removes the repressive histone H3K27me3 mark. Notably, targeting Kdm6b genetically and pharmacologically inhibits fibrotic di^erentiation in human and mouse FAPs in vitro and ameliorated muscle fibrosis in mouse models in vivo. Furthermore, constitutive activation of the Fosl1-Kdm6b pathway reduced H3K27me3 modification at critical fibrotic gene loci, leading to their transcriptional activation. Taken together, our findings reveal that chronic inflammation perpetuates the Fosl1-Kdm6b axis in FAPs, causing epigenomic reprogramming and altering the H3K27me3 landscape, which is essential for preventing fibrotic differentiation of FAPs and skeletal muscle fibrosis.

overall_design: Accessible chromatin-anchored interactions were captured from fibro-adipogenic progenitors in wildtype, Mdx, and Utrophin-dystrophin double knockout mice using the HiCAR assay.

first: Xin

last: Lin

first: Arinze

middle: E

last: Okafor

first: Yuan

last: Wang

first: Yutong

last: Sha

first: Jianhong

last: Ou

first: Xiaolin

last: Wei

first: Yueyuan

last: Xu

first: Mande

last: Xue

first: Lizhi

last: Yi

first: Wenzhe

last: Luo

first: Changxin

last: Wan

first: Derek

last: Peters

first: Qing

last: Nie


title: 10x genomics single cell sequencing of yak testis at different developmental stages

city: Lanzhou

first: Xingdong

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

summary: Testis is the most important reproductive organ of men, and the integrity of its physiological function is crucial for the successful production of sperm. In this study, single-cell RNA sequencing technology was used to construct cell expression profiles of yak at different developmental stages and adult cattle-yak testicular tissues. The identification results of cell subsets and marker genes were analyzed, and the possible mechanisms were predicted.

sample_organism:
Bos grunniens
Bos grunniens x Bos taurus

overall_design: Single-cell RNA sequencing revealed a sequential change in the cell fate of yak testis development.

first: Xian

last: Guo

first: Ping

last: Yan

first: Jie

last: Pei


title: Temporal Evolution of Fibroblast Responses Following Salivary Gland Ductal Ligation Injury

city: Albany

first: Melinda

last: Larsen

state: NY

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

summary: Extracellular matrix remodeling is a natural response to injury but, excessive extracellular matrix accumulation or fibrosis, is a causative factor in hundreds of diseases that limit organ function and impede regenerative responses. Fibrosis is closely related to inflammation, both of which occur in the salivary glands of patients treated with radiation for head and neck cancers and in patients suffering from the autoimmune condition, Sjögren’s Disease. Despite the known involvement of fibrosis in disease and the inhibitory effects of fibrosis on tissue regeneration, the mechanisms through which fibrosis develops in the salivary gland are poorly understood. Stromal fibroblasts are the primary matrix-producing cells and are known to drive both fibrosis and inflammation. To define the signals produced by fibroblasts in response to injury, we induced a temporary obstructive injury though ligation of the primary submandibular and sublingual salivary gland ducts and then performed single-cell RNA sequencing and pathway analysis at timepoints immediately following the injury. Using bioinformatic approaches, we identified three unique fibroblast groups that dynamically respond to the injury. We characterized the changes in matrisomal and inflammatory gene expression over a 7-day time course and identified the group 2 fibroblasts to be the primary fibrogenic cells, although all groups produced ECM genes. Understanding how fibroblasts respond at early and late injury timepoints along with defining signaling pathways regulated by fibroblasts could lead to a better understanding of the contribution of fibroblast to acute injury responses to facilitate development of therapeutics that minimize fibrosis and promote regenerative gland responses in chronic disease states.

overall_design: Submandibular and sublingual mouse salivary glands were dissociated into single cells followed by two rounds of magnetic activated cell sorting (MACs) to deplete for epithelial cells expressing EpCAM and red blood cells expressing Ter119. The samples then went through one round of dead cell removal using Miltenyi dead cell removal kit.

first: Joey

last: Tavarez

first: James

last: Kenney

first: Sergo

last: Gabunia

first: Deirdre

last: Nelson


title: Deferoxamine as adjunct therapeutics for tuberculosis.

city: New Delhi

first: Ranjan

middle: Kumar

last: Nanda

address: International Centre for Genetic Engineering and Technology, New Delhi-110067, India

department: Translational Health Group

country: India

institute: International Centre for Genetic Engineering and Technology (ICGEB), New Delhi component

summary: Iron is critical for the survival of both the host and pathogens. Dysregulated iron metabolism is reported in tuberculosis patients, and therefore represents an opportunity for developing host-directed therapeutics. In this study, antimycobacterial properties of an iron chelator, i.e. Deferoxamine (DFO) and its impact on the transcriptomic changes in Mycobacterium tuberculosis (Mtb) and its impact on limiting host iron in C57BL/6 mice were explored. A group of mice received ferric carboxymaltose to create an iron overload condition and were aerosol infected with H37Rv Mtb. Mtb-infected mice received isoniazid (INH) and rifampicin (RIF) with or without DFO for tissue CFU assay, liver metabolite, iron quantification using GC-MS and ICP-MS, respectively. DFO showed comparable antimycobacterial properties like INH in in-vitro conditions. DFO-treatment deregulated 137 transcript levels in Mtb and majority were involved in stress response, encoding iron-containing proteins and downregulation of genes involved in essential vitamins and amino acid metabolism. Iron-overloaded mice exhibited significantly higher tissue mycobacterial burden at two weeks post-infection and the efficacy of INH and RIF were compromised. Iron chelation by DFO significantly reduced the tissue mycobacterial burden at 4 weeks post-treatment and, as an adjunct to INH and RIF, significantly lowered lung mycobacterial load within the first and second weeks of treatment compared to the group that received only INH and RIF. The intracellular pro-inflammatory cytokine levels in the lung CD4+ T-cells of INH and RIF-treated groups with or without DFO were found to be similar. DFO with RIF and INH treatment significantly altered liver arginine biosynthesis, which has a direct role in neutralizing ammonia and has an immune-supportive role. Currently, DFO is used for treating acute iron toxicity and in iron-overloaded thalassemic patients and holds promise as adjunct therapeutics for tuberculosis.

overall_design: Log-phase Mtb cultures actively growing in Middlebrook 7H9 medium supplemented with OADC were exposed to 0.1 mg/ml Deferoxamine to monitor their transcript level changes at day 5 post incubation compared to Mtb control.

first: Sandeep

middle: R

last: Kaushik

first: Nidhi

last: Nidhi

first: Sukanya

last: Sahu

first: Ashish

last: Gupta

first: Nikhil

last: Bhalla

first: Poonam

last: Dagar

first: Amit Kumar

last: Mohapatra

first: Adyasha

last: Sarangi

first: Bichitra

last: Biswal

first: Ranjan Kumar


title: RNA-Sequencing of Salmonella species inoculated in onion bulb tissue

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

summary: This study aimed to compare differentially expressed transcripts in Salmonella recovered from the inoculated onion bulbs using transcriptome profiling (RNA-seq). The Salmonella strains of Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation.  Transcriptomic analysis of  Salmonella was performed 1 day (24 hours) and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) . 925 and 736 genes were upregulated within 24 hours and seven days after inoculation, while the number of downregulated genes in the same timeframe was 690 and 826, respectively (FDR<0.05 and Abs (log 2(Y/X) >0).

sample_organism: Salmonella enterica subsp. enterica serovar Newport

overall_design: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs at 1 and 7 days after injection. The samples were used for total RNA extractions. For the Day 1 set of inoculated samples (ONtreatedlD1_1, ONtreatedlD1_2, ONtreatedlD1_3) and Day 7 inoculated samples (ONtreatedlD7_1, ONtreatedlD7_2, ONtreatedlD7_3) were compared to cultured Salmoenall strains (SalContrl_1,SalContrl_2, SalContrl_3).


title: Clonal Hematopoiesis Landscape in Frequent Blood Donors

city: Frankfurt

first: Darja

last: Karpova

address: Sandhofstrasse 1

department: Cell Therapeutics

country: Germany

institute: German Red Cross Blood Donor Service

summary: Donor blood saves lives, yet the potential impact of recurrent large-volume phlebotomy on donor health and hematopoietic stem cells (HSCs) remains largely unexplored. In our study, we conducted a comprehensive screening of 217 older male volunteer donors with a history of extensive blood donation (>100 life-time donations) to investigate the phenomenon of clonal hematopoiesis (CH). No significant difference in the overall incidence of CH was found in frequent donors (FD) compared to sporadic donors (<10 life-time donations, 212 donors). However, upon deeper analysis of mutations in DNMT3A, the most commonly affected gene in CH, we observed distinct mutational patterns between the FD and age/sex matched control donor (CD) cohorts. Functional analysis of FD enriched DNMT3A variants examined in CRISPR-edited human HSCs demonstrated their competitive outgrowth potential upon stimulation with erythropoietin (EPO), a hormone which increases in response to blood loss. In contrast, clones harboring leukemogenic DNMT3A R882 mutations increase upon stimulation with IFNy. Through concurrent mutational and immunophenotypic profiling of primary samples at single cell resolution, a myeloid bias of premalignant R882 mutant HSCs was found, while no significant lineage bias was observed in HSCs harboring EPO responsive DNMT3A variants. The latter exhibited preferential erythroid differentiation when persistent erythropoietic stress was applied to CRISPR-edited human HSC xenografts. Our data demonstrate a nuanced ongoing Darwinian evolution at the somatic stem cell level, with EPO identified as a novel environmental factor that favors HSCs carrying certain DNMT3A mutations.

overall_design: Whole Transcriptome RNASeq profiles of HUDEP-2 cells following CRISPR interference (CRISPRi) mediated downregulation of DNMT3A expression (n=9 each for DNMT3A gRNA compared to control gRNA)


title: Adverse outcome pathways of ionizing radiation investigated with multi-omics and benchmark dose modeling

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Background/Issue and Objectives: Health risks from chronic low dose radiation exposures encountered in environmental and occupational settings are uncertain. A key aspect to understanding health risks is precise and accurate modelling of the dose-response relationship. Benchmark dose (BMD) modeling is an approach used in chemical hazard assessments to identify the dose at which a pre-defined (e.g., 10%) change relative to background occurs. Herein, this method is being explored for radiation hazard assessments along with Adverse Outcome Pathways (AOPs), a knowledge framework of causally linked chains of key events (KEs) from a molecular initiating event to an adverse outcome (AO). Design/Method/Description: Blood was drawn from human participants (6 females and 8 males), and lymphocytes were isolated, cultured and X-irradiated at a lower dose-rate (LDR: 0.05 Gy/minute) and higher dose-rate (HDR: 1 Gy/minute) across nine different doses (0, 0.05, 0.10 0.25, 0.5, 1, 2, 4 and 6 Gy).  Transcriptomic and proteomic changes were then assessed 24 hours post-exposure. Concurrently, cell membrane integrity and cellular ATP level were also measured, which are markers of radiation injuries. BMD values were then derived for each endpoint and pathways enriched in omics data were compared with Kes in an existing AOP to leukemia (www.aopwiki.org/aop/432). Conclusions/Impacts/Outcomes/Implications/Next Steps: By using AOPs as an organizational framework and BMD modeling for dose-response analysis, it provides a pragmatic platform to analyse complex data for radiation hazard assessment. Future work will entail in-depth analysis of the responses specific to LDR and HDR and effects of confounding factors on BMD values.

overall_design: Blood was drawn from human participants (6 females and 8 males), and lymphocytes were isolated, cultured and X-irradiated at 1 Gy/minute across nine different doses (0, 0.05, 0.10 0.25, 0.5, 1, 2, 4 and 6 Gy).  Transcriptomic and proteomic changes were then assessed 24 hours post-exposure. Concurrently, cell membrane integrity and cellular ATP level were also measured, as phenotypic indicators. BMD values were then derived for each endpoint and pathways enriched in omics data including the associated BMDs were aligned with KEs in an AOP to leukemia (www.aopwiki.org/aop/432)

first: Ngoc

middle: Q

last: Vuong

first: Saadia

last: Khilji

first: Andrew

last: Williams

first: Nadine

last: Adam

first: Danicia

last: Flores

first: Kelly

last: Fulton

first: Isabel

last: Baltat

first: Susan

last: Twine

first: Kathleen

last: Cook

first: Premkumari

last: Kumarathasan

first: Ruth

last: Wilkins

first: Carole

middle: L

last: Yauk

first: Vinita

last: Chauhan


title: CITEseq of Mtb infected Collaborative Cross mice

city: Worcester

first: Christopher

last: Sassetti

address: 368 Plantation Street

institute: UMass Chan Medical School

summary: The purpose of this project was to profile the immune response to M. tuberculosis in the lungs of  4 genetically diverse mouse strains.

overall_design: Mice were infected with H37Rv and whole lungs were harvested at 4 weeks post infection and processed to a single cell suspension. We used 10x Genomics reagents to generate gene expression profiles and Biolegend TotalSeq Mouse Universal oligo-tagged antibody cocktail to capture protein expression.

first: Megan

middle: K

last: Proulx

middle: M


title: Characterization of Arabidopsis thaliana MYB47 and MYB95 transcription factors in response to jasmonic acid in leaves.

city: Krakow

first: Kenji

last: Yamada

state: Malopolska

address: Gronostajowa 7A

department: Malopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

summary: We have found that Arabidopsis thaliana paralogous two MYBs, namely MYB47 and MYB95, regulate TSA1 and BGLU18 expression and ER-body formation in response to jasmonic acid (JA). To comprehensively understand the transcriptional regulation of these MYBs in response to JA, we conducted RNA-seq analysis between JA-treated rosette leaves of wild-type and myb47myb95 knockout mutants, together with myc2myc3myc4 mutant that is defective in master transcriptional regulator of JA signaling pathway. The transcriptome data analysis revealed that MYB47 and MYB95 regulate a subset of JA-responsive genes, including ER-body and defense-related genes.

overall_design: RNA-seq of Arabidopsis leaves of wild type, myb47,95, and myc2,3,4 mutants that were treated with or without methyl jasmonate.

first: Jakub

last: Bizan

first: Arpan Kumar

last: Basak


title: Transcriptome sequencing unveils a novel mechanism underlying breed distinctions between thin- and fat-tailed sheep

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

type: Non-coding RNA profiling by high throughput sequencing

summary: Tail fat in sheep (Ovis aries), has evolved mainly in response to cold weather for better energy storage. As things stand, too much tail fat in sheep can lead to a reduction in feed utilisation and is also unpopular with consumers due to the excessive fat content in the tail of sheep. Therefore, the need to find the mechanism of tail fat formation is obvious. In this study, we elected to utilise Kazakh sheep, prolific Suffolk sheep, and their hybrid F2 generation as research objects. Sheep transcriptome sequencing technology was employed to screen and explore target candidate genes related to sheep tail fat deposition. Comparison with RNA-seq data from fat-tailed and thin-tailed tissue, the LncRNA-mRNA-miRNA axis was identified as main functional pathway in the formation of fat in tail. Our results offer valuable insights into the fat deposition of sheep and provide a significant genomic resource for future genetic studies and the enhancement of genome-assisted breeding in sheep and other domestic animals.

overall_design: Three healthy adult Kazakh sheep (HUS) which is fat-tailed, F2 generation (F2) of crossbreeding between Kazakh (HUS) and Suffolk sheep (SFK) and adult Suffolk sheep, lean-tailed, of nearly the same age were selected and uniformly reared and managed. Tail tissue samples are collected in December when tail fat deposition is at its highest. Tail fat samples were collected in the shortest possible time using specially treated surgical instruments for RNA experiments (all from the same side), frozen in liquid nitrogen and stored in a refrigerator at -80℃ for back-up. RNA was extracted from tail tissues, and the samples underwent stringent quality control based on the following criteria. First, agarose gel electrophoresis was used to assess RNA integrity and detect potential DNA contamination. Second, RNA concentration and purity were preliminarily quantified. Finally, the integrity of RNA was accurately measured.

first: Lei

last: Gao

first: Yiyuan

last: Zhang

first: Jingquan

last: Yang


title: Single-cell RNA sequencing of murine rotavirus infected mouse intestinal epithelial cells

city: St. Louis

first: Gaopeng

last: Hou

state: MO

address: McDonnell Pediatric Research Building, Rm 9220

department: molecular microbiology

institute: Washinton University inSt. Louis

summary: In a single-cell RNA sequencing experiment, we defined subsets of intestinal epithelial cells in 5-day-old mice and observed decreased transcript levels of sodium-hydrogen exchanger 3 (Nhe3) and Dra in several epithelial cell groups following rotavirus infection. In contrast, transcript levels of sodium-glucose cotransporter 1 (Sglt1), electrogenic sodium bicarbonate cotransporter (Nbce1), solute carrier family 12 member 2 (Nkcc1), and Cftr were unaffected. Furthermore, expression of Nhe3 and Dra was down-regulated in both rotavirus infected intestinal epithelial cells that contained rotavirus transcripts and uninfected bystander cells, suggesting induction of paracrine signaling.

overall_design: Five-day-old 129sv mice were infected with murine rotavirus D6/2 strain (5X10^6 PFU) for 12 hours, then the intestinal epithelial cells were isolated from mock infected and rotavirus infected mice seperately by EDTA-dithiothreitol extraction method.

first: Siyuan

last: Ding


title: Lipid metabolism reprograming by SREBP1-PCSK9 targeting sensitizes pancreatic cancer to immunochemotherapy

city: Hangzhou

first: Mengyi

last: Lao

state: Zhejiang

address: Qingchun 79 road

institute: Zhejiang university

summary: Pancreatic ductal adenocarcinoma (PDAC) treatment is challenging. Determining the metabolic pathways that regulate lipids will provide new insights into PDAC therapeutic strategies. Sterol regulatory element binding transcription factor 1 (SREBP-1) regulates multiple cancer pathways; however, its role in the tumor immune microenvironment and cancer immunotherapy is unknown. Herein, we integrated our large PDAC cohort data and identified that SREBP-1, as a master transcriptional regulator of lipogenesis, aggravated lipid metabolism reprogramming in PDAC. Furthermore, interrupting lipid metabolism by targeting SREBP-1 suppressed PDAC cell growth and enhanced antitumor immunity in vitro and in vivo. We demonstrated that SREBP-1 binds to the PD-L1 (programmed cell death 1 ligand 1) promoter to suppress its transcription. Importantly, SREBP-1 binds to the PCSK9 (proprotein convertase subtilisin/kexin type 9) promoter, which regulated PD-L1 levels via lysosome-mediated degradation and aggravated tumor microenvironment immunosuppression. Targeting the SREBP-1- PCSK9 axis using available drugs sustained the remission of aggressive PDAC by synergizing with anti-PD-1 and gemcitabine. In summary, targeting lipid metabolism suppressed tumor growth and relieved tumor immunosuppression in PDAC.

overall_design: RNA-seq profiling of wildtype KPC and PANC02 cells and their knockdown derivatives (shSrebf1)


title: RNA-Sequencing of onion bulbs inoculated with Salmonella

first: Vijay

last: Joshi

summary: The goal of this study was to compare differentially expressed transcripts in onion bulbs induced when inoculated with Salmonella using transcriptome profiling (RNA-seq) .Transcriptomic analysis of onion bulb tissue (Variety Don Victor) in response to Salmonella was performed 24 hours and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) in onion. Within 24 hours of inoculation, 4259 genes were upregulated while 3393 genes were downregulated. After 7 days, 8213 and 6417 genes were up and down-regulated, respectively, as shown below. (FDR<0.05 and Abs (log 2(Y/X) >0)

overall_design: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs at 1 and 7 days after injection. The samples were used for RNA extractions. For the Day 1 set of samples, uninoculated samples (ONControlD1_1, ONControlD1_2, ONControlD1_3) were compared to inoculated samples (ONtreatedlD1_1, ONtreatedlD1_2, ONtreatedlD1_3). For Day 7, samples (ONControlD7_1, ONControlD7_2, ONControlD7_3) were compared to inoculated samples (ONtreatedlD7_1, ONtreatedlD7_2, ONtreatedlD7_3).


title: The Fosl1-Kdm6b Axis Controls Skeletal Muscle Fibrosis by Regulating  Histone H3K27me3 [HiCAR]

first: Yarui

last: Diao

first: Xin

last: Lin

first: Arinze

last: Okafor

first: Yuan

last: Wang

first: Yutong

last: Sha

first: Jianhong

last: Ou

first: Xiaolin

last: Wei

first: Yueyuan

last: Xu

first: Mande

last: Xue

first: Lizhi

last: Yi

first: Wenzhe

last: Luo

first: Changxin

last: Wan

first: Derek

last: Peters

first: Qing

last: Nie


title: The Fosl1-Kdm6b Axis Controls Skeletal Muscle Fibrosis by Regulating  Histone H3K27me3 [bulk RNA-seq]

summary: Skeletal muscle fibrosis, characterized by the replacement of functional muscle tissue with fibrotic scarring, leads to muscle function loss and potentially fatal respiratory failure, particularly in muscular dystrophy. The mechanisms driving muscle fibrosis is not yet fully understood. Our study utilized single-cell RNA-seq and single-nuclei ATAC-seq to analyze the transcriptome and chromatin accessibility of regenerating and dystrophic skeletal muscle, identifying a specific subset of fibro-adipogenic precursors (FAPs) enriched in dystrophic muscles, termed fibrotic FAPs. We further demonstrated that chronic inflammation upregulates Fosl1, an early response gene, which activates the expression of Kdm6b in fibrotic FAPs. Kdm6b, a histone demethylase, specifically removes the repressive histone H3K27me3 mark. Notably, targeting Kdm6b genetically and pharmacologically inhibits fibrotic di^erentiation in human and mouse FAPs in vitro and ameliorated muscle fibrosis in mouse models in vivo. Furthermore, constitutive activation of the Fosl1-Kdm6b pathway reduced H3K27me3 modification at critical fibrotic gene loci, leading to their transcriptional activation. Taken together, our findings reveal that chronic inflammation perpetuates the Fosl1-Kdm6b axis in FAPs, causing epigenomic reprogramming and altering the H3K27me3 landscape, which is essential for preventing fibrotic di^erentiation of FAPs and skeletal muscle fibrosis.

overall_design: mRNA measurements from fibro-adipogenic progenitors in wildtype, Mdx, and Utrophin-dystrophin double knockout mice. Other comparisons include conditional knockout of Kdm6b in FAPs (using Pdgfra-Cre and Kdm6b-flox mice) versus genetically matched control (without Cre)).


title: Caloric restriction enhances the activity of anti-androgen therapy by inhibiting androgen receptor translation in prostate cancer

city: Indianapolis

first: Ricardo

last: Cordova

state: IN

address: 635 Barnhill Drive, MS4067

institute: Indiana University School of Medicine

summary: Epidemiological studies suggest that diet can impact the incidence, progression, and response to treatment of multiple cancers, including prostate cancer (PCa). In this study, we investigated the use of dietary interventions, specifically caloric or protein restriction, in combination with anti-androgen therapy as a treatment for PCa. We found that caloric restriction through alternate-day fasting (ADF) reduces androgen receptor (AR) expression and signaling. This reduction in AR enhances the antitumor activity of the AR antagonist enzalutamide in multiple mouse models of PCa. Mechanistic studies reveal that nutrient starvation via ADF predominantly decreases AR mRNA translation at the elongation stage due to amino acid limitation. Pharmacological agents that similarly impair translation elongation and promote ribosome collisions mimic the AR translation reduction observed with ADF. We propose that amino acid limitation through ADF impairs translation elongation in PCa, and AR mRNA translation is susceptible to this process, leading to a reduction in AR protein levels and enhancing AR-targeted therapy. This study suggests that fasting-induced caloric restriction may improve the efficacy of anti-androgen therapy in PCa.

overall_design: To investigate transcriptomic changes in B6MyC-CaP tumors in response to alternate-day fasting (ADF) and enzalutamide treatment.  B6MyC-CaP cells were implanted subcutaneously into male C57BL/6 mice. Once tumors were established, mice were randomized into four treatment groups: vehicle, enzalutamide (ENZ), alternate-day fasting (ADF), or a combination of ADF and ENZ treatment. Total RNA was isolated from tumors and submitted for RNAseq.

middle: A

first: May

last: Elbanna

first: Sabrina

last: Orsi

first: Christopher

last: Rupert

first: Noah

last: Sommers

first: Angela

middle: J

last: Klunk

first: Li

last: Shen

first: Jagannath

last: Misra

first: Jocelyne

middle: N

last: Hanquier

first: Yanqing

first: David

middle: W

last: Goodrich

first: Luigi

last: Fontana

first: Ronald

middle: C

last: Wek

first: Kirk

last: Staschke

first: Roberto

last: Pili


title: The Fosl1-Kdm6b Axis Controls Skeletal Muscle Fibrosis by Regulating  Histone H3K27me3 [Cut&Tag]

first: Yarui

last: Diao

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Measurements of transcription factor binding and histone mark genomic location from fibro-adipogenic progenitors in wildtype, Mdx, and Utrophin-dystrophin double knockout mice. Other comparisons include conditional knockout of Kdm6b in FAPs (using Pdgfra-Cre and Kdm6b-flox mice) versus genetically matched control (without Cre)).

first: Xin

last: Lin

first: Arinze

last: Okafor

first: Yuan

last: Wang

first: Yutong

last: Sha

first: Jianhong

last: Ou

first: Xiaolin

last: Wei

first: Yueyuan

last: Xu

first: Mande

last: Xue

first: Lizhi

last: Yi

first: Wenzhe

last: Luo

first: Changxin

last: Wan

first: Derek


title: Correlations of m6A Methylation-Related mRNAs with Thyroid Cancer

city: 福建省福州市

first: 瀛若

last: 林

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

summary: The specific role of m6A modification in the malignant progression of papillary thyroid carcinoma (PTC) without autoimmune thyroid disease (AITD)  remains unclear. We collected cancerous and para-cancerous tissues and associated clinical information form PTC patients without AITD to both identify differentially expressed genes and quantify m6A levels in the mRNA and ncRNA transcripts.

overall_design: We generated the following comparisons using Fold-change (FC) ≥ 1.5 or ≤ 0.5, and p < 0.05 were used to identify the differentially m6A methylated RNAs.The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. Two channel arrays were used for these samples but the data were analyzed as single-channel so that each sample represents either IP or supernatent and the sample table includes the normalized signal values.

first: Yingruo

first: Zhen

last: Jiang

first: Sheng

first: Huihao

last: Zhang

first: Ruhai


title: Influenza virus exposure shapes the B cell response to influenza vaccination fifty years later

city: Bethesda

first: Sarah

last: Andrews

state: Maryland

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Pre-existing immunity impacts vaccine responses to endemic respiratory viruses such as influenza, but directly connecting influenza infections early in life with immune responses decades later is difficult.  However, H2N2 stopped circulating in the human population in 1968, creating the opportunity to directly evaluate the impact of early H2N2 exposure on vaccine responses 50 years later.  Here, we vaccinate individuals born before (H2 Exposed) or after (H2 Naïve) 1968 with an H2 HA DNA plasmid and/or a ferritin nanoparticle vaccine.  H2 Exposed individuals generated a rapid B cell recall response that differed in potency, cross-reactivity, immunoglobulin repertoire, epitope targeting and phenotype from the de novo response in H2 Naïve individuals.  Furthermore, vaccinating with a DNA versus a protein nanoparticle vaccine altered the response in H2 Naïve but not H2 Exposed individuals.  This study clearly establishes and describes the life-long impact of influenza HA-specific memory B cells formed early in life on vaccine responses decades later.

overall_design: Memory b cells and plasmablasts were isolated at various timepoints from PBMCs of individuals undergoing vaccination against H2 influenza. Antibody derived tag, whole transcriptome, and VDJ libraries were generated for all samples.


title: The new cohort of EMT genes are activated by benzo(a)pyrene and/or SATB1 during the malignant transformation of breast epithelial cells

city: San Francisco

first: Terumi

last: Kohwi-Shigematsu

state: CA

address: 513 Parnassus Ave (HSW810)

department: Department of Orofacial Sciences

institute: UCSF

summary: Tumor metastasis, the migration of tumor cells from a primary site to distant organs, is the leading cause of death among cancer patients. Despite significant advancements in cancer research, much remains to be learned about how tumor cells acquire invasive properties at the molecular level. Here, we investigated the transcriptional program that enables breast epithelial cells to develop highly invasive malignant phenotypes. We focused on genes that promote epithelial-to mesenchymal transition (EMT), a process critical for both embryogenesis and cancer cell invasion, and we compiled a cohort of 339 genes associated with EMT functions with many identified in recent literature. Using an immortalized, non-malignant breast epithelial cell line, MCF10A, we analyzed changes in the transcriptional activity of these genes through Global Run-On Sequencing (GRO-seq) and RNA-seq following stable SATB1 transduction. SATB1 is a nuclear protein with genome-organizing functions that promotes metastatic cancer, including breast cancer. SATB1-expressing MCF10A cells acquire both tumorigenic and metastatic properties. We identified a total of 98 EMT promoting genes that were upregulated in SATB1-expressing MCF10A cells compared to control cells. Additionally, we investigated the effects of the chemical carcinogen benzo[a]pyrene (B[a]P), known to induce malignancy in MCF10A cells. Our findings revealed that B[a]P significantly upregulated 54 EMT genes after 3 hours. By day 3, this number increased to 72 genes, with 36 genes being common between those elevated by SATB1. Notably, the significant effects of B[a]P on EMT gene expression observed in MCF10A cells were largely diminished in SATB1 expressing MCF10A cells, suggesting that the pre-existing SATB1-regulated transcriptional program is dominant. Our results indicate that, despite the distinct causes of breast cancer, both the chemical carcinogen B[a]P and SATB1 activate many common EMT genes during the malignant transformation of breast epithelial cells. This suggests a key network of gene expression that drives the malignant phenotypes of these cells.

overall_design: We investigated the changes in the transcriptional program of breast epithelial cells using the MCF10A-1 cell line by stably expressing SATB1 compared to control cells, or by exposing MCF10A-1 cells to benzo[a]pyrene (B[a]P) compared to non-treated controls. We focused on studying a particular group of genes that function in promoting epithelial-to-mesenchymal transition (EMT), which is essential during embryogenesis as well as during cancer metastasis, as it promotes cell motility. We compiled a gene set consisting of 300 EMT genes from recent literature and from gene ontology (GO) lists, and we studied which of these genes are activated or upregulated when MCF10A-1 cells undergo malignant transformation and acquire metastatic phenotypes. We employed a method called GRO-seq, which detects nascent transcripts genome-wide to capture the early transcriptional response to environmental stimuli, as well as RNA-seq, which measures accumulated levels of mRNAs.

first: Yoshinori

last: Kohwi

first: Yelena

last: Vayn

first: Mari

last: Grange

first: Bao

last: Ho


title: Gene expression profile at single cell level of hepatocytes and non parenchymal cells (NPCs) isolated from a murine model of MASLD

city: MIlano

first: Paola

last: Dongiovanni

address: Via Pace 9

country: Italy

institute: Fondazione IRCCS Cà Granda ospedale Policlinico

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) embraces different conditions, including metabolic dysfunction-associated steatohepatitis (MASH), fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The landscape of cellular abnormalities occurring in the different stages of MASLD as well as the processes which drive MASLD evolution are not completely clarified. We used single cell RNAsequencing (scRNAseq) to unravel cellular heterogeneity affecting livers during the switching from simple steatosis towads MASH and and MASH-fibrosis.

overall_design: Heps and NPCs were isolated by in situ digestion and collagenase perfusion. Cells were separed by centrifugation, and live cells were FACS sorted. Heps fraction was CD45 depleted.

first: Marica

last: Meroni

first: Ettore

last: Mosca


title: Mitochondrial calcium uniporter links acetyl-CoA metabolism and H3K27 acetylation to maintain glioblastoma stem cells

city: Shanghai

first: Gguangqin

last: Liu

address: No. 130 Dong-An Road

institute: Fudan university

summary: Glioblastoma stem cells (GSCs) exhibit remarkable metabolic and epigenetic adaptability, contributing to therapeutic resistance and tumor recurrence. However, the mechanisms underlying this plasticity remain incompletely understood. Here, we identify a novel metabolic-epigenetic axis centered on the mitochondrial calcium uniporter (MCU) that governs GSC fate and tumor initiation. MCU is preferentially expressed in GSCs, and its knockdown significantly impairs GSC self-renewal and viability. Mechanistically, MCU enhances mitochondrial calcium uptake, promoting acetyl-CoA production via pyruvate dehydrogenase activation, which drives histone H3K27 acetylation at the TRIB3 locus to sustain stemness programs. In glioblastoma patients, higher MCU expression is correlated with increased acetyl-CoA levels, elevated H3K27 acetylation, enhanced TRIB3 expression, higher tumor grade, and poorer survival. Pharmacological inhibition of MCU with Berberine suppresses GSC growth and extends survival in mice. These findings establish MCU as a critical link between mitochondrial metabolism and epigenetic regulation, highlighting its potential as a therapeutic target for glioblastoma.

overall_design: RNA-seq profiling of glioblastoma stem cells (08-387 and T4121) and their MCU-knockdown derivatives.

first: Guangqin

first: Haoqian

first: Siqi

last: Chen

first: Jiayi

first: Xin

last: Pan


title: Medicago SPX1 and SPX3 recruit nitrogen-fixing microbes to promote growth through controlling flavonoid biosynthesis

city: WAGENINGEN

first: Peng

last: Wang

address: Hoevestein 239 12B007

institute: Wageningen university

summary: Forming symbiotic associations with beneficial microbes are important strategies for sessile plants to acquire nitrogen and phosphorus nutrients from the soil. Root exudates play key roles on set-up of the rhizosphere microbiome. According to the needs for nitrogen or phosphorus, plants can adjust the root exudates composition to attract proper microbes. Flavonoids are a group of secondary metabolites that are well studied in shaping the root microbiome, especially the root nodule symbiosis in legumes. Here, we show the medicago truncatula phosphate sensors SPX1 and SPX3 regulate flavonoids biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes were less recruited in spx1spx3 double mutant root rhizosphere. This was caused by lower flavonoids biosynthesis related genes expression, which resulted in lower flavonoids levels in the root exudates compared to wild type plant R108. Further analysis indicates the regulation of flavonoids biosynthesis is through the SPX1 and SPX3 interaction transcription factor PHR2. We propose the SPX-PHR phosphate homeostasis regulation network also control microbe-dependent nitrogen acquisition according to phosphate levels. Thus, SPX1 and SPX3 play important roles to keep a microbe-dependent nitrogen and phosphorus absorption balance for optimal growth.

overall_design: R108 wild type and spx1spx3 mutant roots grew in low Pi conditions


title: Integrative epigenomic profiling of hepatocellular carcinoma uncovers aberrant cis-regulatory changes and potential prognostic indicators [ChIP-seq]

city: Hong Kong China

first: Cheuk Yin

last: CHENG

address: The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong

department: Life Science

country: Hong Kong

summary: Hepatocellular carcinoma (HCC) exhibits widespread epigenetic aberrations; however, the underlying transcriptional regulatory landscape remains underexplored. Here, we performed integrated analyses with genome-wide profiles of the transcriptomes, histone modifications and DNA methylation from patient-derived HCC tumors and controls. We identified both global and focal epigenetic alterations including large-scale DNA methylation loss, and dysregulation of cis-regulatory elements (CREs) associated with genes involved in cell cycle control, immune responses, and extracellular matrix organization. Notably, we discovered that transcriptional upregulation of Glypican-3 (GPC3), a diagnostic biomarker and immunotherapeutic target for HCC, was linked to the reactivation of a fetal liver super-enhancer (SE). This SE, in concert with DNA hypomethylation of two CpG islands, modulated GPC3 expression. Global DNA hypomethylation also contributed to transcriptional dysregulation of retrotransposon-derived CREs. Specifically, we observed that patients with high expression of a HERVE-int-driven long non-coding RNA transcript showed poorer disease outcomes and specific molecular signatures associated with better response to immunotherapy. Our results highlight this and other retrotransposons as potential prognostic indicators and a predictive signature for immunotherapy response. Taken together, our findings provide insights into the role of epigenetic dysregulation of CREs and retrotransposons in hepatocarcinogenesis, which could benefit the clinical management of HCC.

overall_design: H3K27ac and H3K4me3 ChIP-seq were conducted for wildtype HepG2 and PLC cells

first: Clooney

last: Cheng

first: MingFung

last: Cheung

first: AhYoung

last: Lee

first: Julie

middle: Y

last: Ang

first: Ignacio

last: Riquelme Medina

first: Grace

last: Lo

first: Qiong

last: Wu

first: Savio

last: Ho-Chit Chow

first: Kevin

last: Yip

first: Alfred

middle: S

first: Danny

last: Leung


title: Integrative epigenomic profiling of hepatocellular carcinoma uncovers aberrant cis-regulatory changes and potential prognostic indicators [RNA-seq]

institute: The Hong Kong University of Science and Technology

overall_design: RNA-seq was conducted for wildtype HepG2 and PLC cells, and HepG2-THE1D and PLC-HERVE-int knockdown cells


title: Partial beta cell loss induces transient compensatory proliferation II

city: BErgen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

summary: Loss of functional β-cells is a pivotal event in the dysregulation of glucose homeostasis observed in diabetes. While the plasticity of β-cells in response to increased metabolic demand has been extensively studied, the common drivers of β-cell proliferation and the molecular mechanisms governing regeneration in humans remain elusive. Here, we investigated the proliferative response following targeted chemical ablation of β-cells using diphtheria toxin (DT) and streptozotocin (STZ) in mice.   Hemizygous expression of the RIP-DTR transgene enabled efficient partial ablation of β-cells, leading to close to 50% β-cell loss five days post ablation, stabilizing at this level up to 10 weeks post ablation. Transcriptomic analysis revealed a dynamic molecular landscape following ablation, with early activation of tissue remodeling and clearance of dead cells, followed by transient activation of regenerative signaling pathways.   Furthermore, we observed a distinct proliferative boost in the immediate aftermath of ablation, characterized by upregulation of cell cycle progression markers. Interestingly, long-term follow-up revealed compound stress from partial β-cell loss and high-fat diet feeding induced a robust proliferative response, albeit with a negative impact on β-cell signature.   Additionally, single low-dose STZ injections induced partial β-cell loss and compensatory proliferation, with the regulatory landscape deregulated by STZ injection in the long term. The compound stress of high-fat diet and STZ ablation further altered the islet transcriptional landscape, particularly affecting metabolic pathways.   Overall, our study provides insights into the dynamic response of β-cells to partial ablation and highlights the impact of compound stressors on islet function and metabolism, shedding light on potential strategies for promoting β-cell regeneration in diabetes.    Loss of functional β-cells is a pivotal event in the dysregulation of glucose homeostasis observed in diabetes. While the plasticity of β-cells in response to increased metabolic demand has been extensively studied, the common drivers of β-cell proliferation and the molecular mechanisms governing regeneration in humans remain elusive. Here, we investigated the proliferative response following targeted chemical ablation of β-cells using diphtheria toxin (DT) and streptozotocin (STZ) in mice.   Hemizygous expression of the RIP-DTR transgene enabled efficient partial ablation of β-cells, leading to close to 50% β-cell loss five days post ablation, stabilizing at this level up to 10 weeks post ablation. Transcriptomic analysis revealed a dynamic molecular landscape following ablation, with early activation of tissue remodeling and clearance of dead cells, followed by transient activation of regenerative signaling pathways.   Furthermore, we observed a distinct proliferative boost in the immediate aftermath of ablation, characterized by upregulation of cell cycle progression markers. Interestingly, long-term follow-up revealed compound stress from partial β-cell loss and high-fat diet feeding induced a robust proliferative response, albeit with a negative impact on β-cell signature.   Additionally, single low-dose STZ injections induced partial β-cell loss and compensatory proliferation, with the regulatory landscape deregulated by STZ injection in the long term. The compound stress of high-fat diet and STZ ablation further altered the islet transcriptional landscape, particularly affecting metabolic pathways.   Overall, our study provides insights into the dynamic response of β-cells to partial ablation and highlights the impact of compound stressors on islet function and metabolism, shedding light on potential strategies for promoting β-cell regeneration in diabetes.    Loss of functional β-cells is a pivotal event in the dysregulation of glucose homeostasis observed in diabetes. While the plasticity of β-cells in response to increased metabolic demand has been extensively studied, the common drivers of β-cell proliferation and the molecular mechanisms governing regeneration in humans remain elusive. Here, we investigated the proliferative response following targeted chemical ablation of β-cells using diphtheria toxin (DT) and streptozotocin (STZ) in mice.   Hemizygous expression of the RIP-DTR transgene enabled efficient partial ablation of β-cells, leading to close to 50% β-cell loss five days post ablation, stabilizing at this level up to 10 weeks post ablation. Transcriptomic analysis revealed a dynamic molecular landscape following ablation, with early activation of tissue remodeling and clearance of dead cells, followed by transient activation of regenerative signaling pathways.   Furthermore, we observed a distinct proliferative boost in the immediate aftermath of ablation, characterized by upregulation of cell cycle progression markers. Interestingly, long-term follow-up revealed compound stress from partial β-cell loss and high-fat diet feeding induced a robust proliferative response, albeit with a negative impact on β-cell signature.   Additionally, single low-dose STZ injections induced partial β-cell loss and compensatory proliferation, with the regulatory landscape deregulated by STZ injection in the long term. The compound stress of high-fat diet and STZ ablation further altered the islet transcriptional landscape, particularly affecting metabolic pathways.   Overall, our study provides insights into the dynamic response of β-cells to partial ablation and highlights the impact of compound stressors on islet function and metabolism, shedding light on potential strategies for promoting β-cell regeneration in diabetes.

overall_design: Mice were followed up at different timepoints following partial ablation using either a RIP-DTR system or STZ mediated ablation. Islets were isolated and analyzed with bulk transcriptomics to identify the molecular response to partial beta-cell loss.

first: Andreas

middle: F

last: Mathisen

first: Ulrik

last: Larsen

first: Natalie

last: Kavli

first: Andrei

last: Vacaru

first: Ana-Maria

first: Luiza

last: Ghila

first: Pedro

last: Herrera


title: Diverse Fgfr1 signaling pathways and endocytic trafficking regulate early mesoderm development I

city: New York

first: James

last: Clark

state: New York

address: 1468 Madison Ave, Annenberg 25-70, Box 1020

department: Cell Developmental Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary: The Fibroblast growth factor (FGF) pathway is a conserved signaling pathway required for embryonic development. Activated FGF receptor 1 (FGFR1) drives multiple intracellular signaling cascade pathways, including ERK/MAPK and PI3K/AKT, collectively termed canonical signaling. However, unlike Fgfr1 null embryos, embryos containing hypomorphic mutations in Fgfr1 lacking the ability to activate canonical downstream signals are still able to develop to birth, but exhibit severe defects in all mesodermal-derived tissues. The introduction of an additional signaling mutation further reduces the activity of Fgfr1, leading to earlier lethality, reduced somitogenesis, and more severe changes in transcriptional outputs. Genes involved in migration, ECM-interaction, and phosphoinositol signaling were significantly downregulated, proteomic analysis identified changes in interactions with endocytic pathway components, and cells expressing mutant receptors show changes in endocytic trafficking. Together, we identify processes regulating early mesoderm development by mechanisms involving both canonical and non-canonical Fgfr1 pathways, including direct interaction with cell adhesion components and endocytic regulation.

overall_design:
To investigate changes in transcription during mesoderm development with or without canonical FGF signaling, we created mouse lines containing point mutations in key effector binding residues.
We then collected tailbud tissue from E8.5 mouse embryos to use for gene expression profiling.
Comparative gene expression profiling between wild-type and mutant FGFR1 tissue was used to determine changes in GO and KEGG term gene sets. We compared wild type to Fgfr1 FCPG, wild type to Fgfr1 FCSPG, and Fgfr1 FCPG to Fgfr1 FCSPG.

first: Philippe

last: Soriano


title: Partial beta cell loss induces transient compensatory proliferation I


title: Comparative omics reveals unanticipated metabolic rearrangements in a high-oil mutant of plastid acetyl-CoA carboxylase

city: Columbia

first: Jose Roberto

last: Da Silva Nascimento

address: 1201 Rollins Street

department: Life Sciences Center

institute: University of MIssouri

summary: Heteromeric acetyl-CoA carboxylase (ACCase) catalyzes the ATP-dependent carboxylation of acetyl-CoA to produce malonyl-CoA, the committed step for de novo fatty acid synthesis.  In plants, ACCase activity is controlled at multiple levels, including negative regulation by biotin attachment domain-containing (BADC) proteins, of which the badc1/3 double mutant leads to increased seed triacylglycerol accumulation. Unexpectedly, the Arabidopsis badc1/3 mutant also accumulates more protein. The metabolic consequences from both higher oil and protein were investigated in developing badc1/3 seed using global transcriptomics, translatomics, proteomics, metabolomics and other biomass measurements. Changes included increased storage proteins and lipid-droplet packaging proteins, increased SDP1 lipase, altered organic acid metabolism, and reduced extracellular lipid synthesis perhaps offsetting the increase in TAG. We present a model of how Arabidopsis adapted to deregulated ACCase, resulting in more oil, and altered flux through pathways that partition carbon and propose targets for future bioengineering of seed storage reserves.

overall_design:
To investigate the matabolic consequences of increased oil content due to knocking out genes BADC1 and BADC3 in Arabidopsis. We perfomed gene expression analysis using data from Arabidopsis deveoping seeds colected at 9-10 days after flowering from a badc1/badc3 double knockout line compared to wild-type (Col0) line.Total RNA was purified using the NucleoSpin® RNA Plant kit (MACHEREY-NAGEL), as recommended by the manufacturer. Raw Illumina sequencing data was processed using the Cufflinks suite. Reads were mapped to the Arabidopsis reference genome, and gene expression was analyzed.
We also performed translatomics analysis using plants expressing a transgene, HF-RPL18, tagged with a 6X histidine-FLAG epitope, driven by the glycinin promoter from soybean. The HF-RPL18 gene was cloned into the pBinGlyRed3 vector and transformed into Agrobacterium tumefaciens, which was then used to transform wild-type (Col-0) and badc1/3 plants via the floral dip method. T1 seeds were screened for DsRed fluorescence and RPL18 protein expression using an Anti-FLAG antibody. For ribosome-associated RNA enrichment, samples were incubated with EZ view Red Anti-FLAG M2 Affinity Gel to isolate the FLAG-tagged ribosomes. RNA was extracted from the beads using a miniprep kit. For RNA-Seq and TRAP-Seq data analysis, raw Illumina sequencing data was processed using the Cufflinks suite. Reads were mapped to the reference genome, and gene expression was analyzed. Translation efficiency (TE) was calculated by comparing TRAP-Seq reads to total RNA-Seq reads, with significant changes identified through Z-score normalization.

last: Nascimento

first: Amr

last: Kataya

first: Chunhui

last: Xu

first: Matthew

middle: G

last: Garneau

first: Athen

last: Kimberlin

first: Thiya

last: Mukherjee

first: Somnath

last: Koley

first: Brian

middle: P

last: Mooney

first: Dong

first: Philip

middle: D

last: Bates

first: Doug

last: Allen

first: Abraham

last: Koo

first: Jay

last: Thelen


title: Diverse Fgfr1 signaling pathways and endocytic trafficking regulate early mesoderm development II

overall_design:
To investigate changes in transcription during mesoderm development with or without canonical FGF signaling, we created mouse lines containing point mutations in key effector binding residues.
We then collected tailbud tissue from E9.5 mouse embryos to use for gene expression profiling.
Comparative gene expression profiling between wild-type and mutant FGFR1 tissue was used to determine changes in GO and KEGG term gene sets.


title: PD-1 regulates ILC3-driven intestinal immunity and homeostasis

city: Melbourne

first: Cyril

last: Seillet

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: Interleukin-(IL) 22 production by intestinal group 3 innate lymphoid cells (ILC3) is critical to maintain gut homeostasis. However, IL-22 needs to be tightly controlled; reduced IL-22 expression is associated with intestinal epithelial barrier defect while its overexpression promotes tumor development. Here, using a single cell RNAseq approach, we identified a core set of genes associated with increased IL-22 production by ILC3.

overall_design: ILCs from the small intestine of wild-type mice were sorted for scRNA-seq. ILCs were identified as Live/Dead-CD45+ Lin- (CD3, CD11b, B220, TER119, TCRb, CD19, NK1.1, F4/80) CD127+ immune cells were sorted from small intestines of C57BL/6 mice (n=3).

first: Le

last: Xiong

first: Peter

last: Hickey

first: Casey

last: Anttila

first: Tracey

last: Baldwin


title: Calcineurin is a central regulator of process S and governs sleep homeostasis in locus coeruleus

city: Beijing

first: Rui

last: Zhou

address: NIBS

institute: NIBS

summary: Sleep need accumulates during waking and dissipates during sleep to maintain sleep homeostasis (process S). Besides regulation of daily sleep amount, a hallmark of process S is the homeostatic sleep regulation: sleep loss causes increased amount and intensity of subsequent recovery sleep. The central regulators of process S and specific brain regions that govern sleep homeostasis in mammals remain unclear. Here, we report that enhanced calcineurin activity in the mouse brain neurons sharply increases non-rapid eye movement sleep (NREMS) to average ~17-h/day. Knockout of calcineurin in adult mouse brain diminishes baseline NREMS to average ~4-h/day, but also abolishes recovery NREMS owing to inability to accumulate sleep need during wakefulness. Calcineurin promotes baseline NREMS in both excitatory and inhibitory neurons and by antagonizing PKA and activating SIK3 via S551 dephosphorylation. Moreover, calcineurin is specifically required in the locus coeruleus-noradrenergic (LCNA) neurons for the transcriptomic and homeostatic responses to sleep loss. While chemo-/optogenetic activation of LCNA neurons increases the amount and intensity of NREMS, ablation and inhibition of LCNA neurons diminish recovery NREMS following sleep deprivation. These results establish calcineurin as a central regulator of process S and identify LC as a potential sleep need center that governs NREMS homeostasis in mice.

overall_design: Differential expression analysis of locus coeruleus (LC) from normal slept (S6) or 6-h sleep-deprived (SD6) ABC-Ctrl (WT) and ABC-CnB1KO (KO) mice

first: Huixiang

last: Zhang

first: Xin

last: Yin

first: Can

last: Liu

first: Bin

last: Li

first: Tao

last: Cai

first: Qinghua


title: Lenalidomide-induced pure red cell aplasia: clinical characteristics and mechanistic analysis

first: Hu

last: Qi

state: Beijing

address: No.5 Yiheyuan Road,Haidian District

institute: Peking University

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

overall_design: Refer to individual Series


title: Lenalidomide-induced pure red cell aplasia: clinical characteristics and mechanistic analysis [bulkRNA-seq]

summary: The RVd therapy, combining lenalidomide, bortezomib, and dexamethasone, is a mainstay treatment for multiple myeloma, typically eliciting immune activation and myeloma cell clearance, alleviating anemia and associated symptoms. In a unique multiple myeloma case, the patient developed pure red cell aplasia (PRCA) following RVd treatment, despite the absence of common PRCA triggers. In vitro analyses revealed severe erythropoiesis impairment in this patient, with lenalidomide emerging as a pivotal disruptor of erythroid development, potentially driving PRCA. Single-cell transcriptome analysis unveiled a notable increase in hyperactive cluster of differentiation (CD)8+ T cells in the patient's bone marrow. The few remaining erythroid progenitors in the patient's bone marrow exhibited developmental dysfunction and immune-related pathway activation. Unexpectedly, these erythroid cells displayed abnormally high expression of major histocompatibility class I (MHCI). Functional assays demonstrated that the addition of lenalidomide further augmented MHCI expression in the patient's erythroid progenitors. Drug-induced increases in antigen presentation by immune erythrocytes emerged as the potential driving force behind hyperactive T cell attacks and subsequent development of PRCA. This study not only elucidates the mechanism underlying lenalidomide-induced PRCA in this rare case, but also underscore the importance of considering the MHCI gene in erythroid cells during clinical trials and drug administration.

overall_design: Bulk RNA-seq: After treatment with indicated drugs in erythroid differentiation medium for 6 days. The CD71+ erythroid progenitor cells were sorted by fluorescence-activated cell sorting (FACS). Sequencing libraries were prepared by Novogene, and 150 bp paired-end sequencing of each condition with two biological replicates was obtained in a HiSeq X-Ten (PE150, Illumina) by Novogene (Beijing).

first: Qi

last: Hu

first: Yang

first: Qiuyu

last: Yue

first: Shuo

first: Fan

last: Lin

first: Xiao-Jun

last: Huang

first: Jin

last: Lu

first: Hsiang-Ying

last: Lee


title: Peripheral mRNA expression of first-episode drug-naïve patients with schizophrenia

city: Yangzhou

first: Bo

last: Pan

state: Jiangsu

address: No.136, JiangYangZhongLu

department: Department of Pharmacy

institute: Yangzhou University Medical College

summary: Schizophrenia is a complex mental disorder. Accurate diagnosis and classification of schizophrenia has always been a major challenge in clinic due to the lack of biomarkers. Therefore, identifying molecular biomarkers, particularly in the peripheral blood, is of great significance. This study aimed to identify immune-related molecular biomarkers of schizophrenia in peripheral blood. Eighty-four Peripheral blood leukocytes of first-episode drug-naïve (FEDN) patients with schizophrenia and 97 healthy controls were collected and examined using high-throughput RNA-sequencing. Differentially-expressed genes (DEGs) were analysed. Weighted correlation network analysis (WGCNA) was employed to identify schizophrenia-associated module genes. The CIBERSORT algorithm was adopted to analyse immune cell proportions. Then, machine-learning algorithms including random forest, LASSO, and SVM-RFE were employed to screen immune-related predictive genes of schizophrenia. The RNA-seq analyses revealed 734 DEGs. Further machine-learning-based bioinformatic analyses screened out three immune-related predictive genes of schizophrenia (FOSB, NUP43, and H3C1), all of which were correlated with neutrophils and natural killer cells resting.

overall_design: This study was to screen peripheral biomarkers of schizophrenia using high-throughput RNA-seq. A total of 181 participants were recruited in the present study, including 84 first-episode drug-naïve (FEDN) schizophrenia patients and 97 healthy controls.

first: Xiaowei

last: Tang

first: Xiaoli

last: Zhu

first: Jianjun

last: Weng

first: Ping

last: Yu

first: Xueying


title: Effect of platelet on mouse osteosarcoma cell line K7M2 gene expression

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: To investigate the cooperative function of platelet in the regulation of osteosarcoma metastases, we coculture OS K7M2 cell lines with mouse platelet.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K7M2 cells and platelet treated K7M2 cells.

first: Junjie

last: Gao

first: Changqing

last: Zhang

first: Wenkan

last: Zahang


title: Glycation-lowering compounds inhibit ghrelin signaling to reduce food intake, lower insulin resistance, and extend lifespan.

city: Novato

first: Pankaj

last: Kapahi

address: 8001 Redwood Blvd

institute: Buck Institute

summary: Non-enzymatic reactions in glycolysis lead to the accumulation of methylglyoxal (MGO), a reactive precursor to advanced glycation end-products (AGEs), which has been hypothesized to drive obesity and aging-associated pathologies. A combination of nicotinamide, lipoic acid, thiamine, pyridoxamine, and piperine (Gly-Low), was identified to lower glycation by reducing MGO and MGO-derived AGE, MG-H1, in mice. Administration of Gly-Low reduced food consumption, lowered body weight, improved insulin sensitivity, and increased survival in both leptin receptor-deficient (Leprdb) and wild-type C57B6/J mice. Unlike caloric restriction, Gly-Low modulated hypothalamic signaling by upregulating mTOR pathway signaling to inhibit ghrelin-mediated hunger response. Gly-Low also slowed hypothalamic aging and increased survival when administered as a late-life intervention, suggesting its potential benefits in ameliorating age-associated decline by inducing voluntary caloric restriction and reducing glycation.

overall_design: We profiled hypothalamic transcripts from male C57BL/6J mice at three ages under different treatment paradigms: 1) young (4-month-old) male C57BL/6J mice fed a control or glycation-lowering (Gly-Low) diet for 1 week, 2) aged (25-month-old) male C57BL/6J mice fed a control or glycation-lowering (Gly-Low) diet for 5 months and 3) young (3-month-old) male C57BL/6J mice fed a control diet for 1 week. We used differential expression anaysis to assess genes and pathways that change under acute treatment (1 week) in young mice and to assess how genes that change with age (old control vs young control) are influenced by prolonged (5 month) Gly-Low treatment of old mice (old Gly-Low vs old control).

first: Lauren

last: Wimer

first: Kiyomi

last: Kaneshiro

first: Jessica

last: Ramirez

first: Neelanjan

last: Bose

first: Martin

last: Valdearcos

first: Muniesh

last: Shanmugam

first: Dominique

middle: O

last: Farrera

first: Parminder

last: Singh

first: Jennifer

last: Beck

first: Durai

last: Sellegounder

first: Lizbeth

middle: E

last: Najera

first: Lisa

last: Ellerby

first: Soo-Jin

last: Cho

first: John

last: Newman

first: James

last: Galligan

first: Suneil

last: Koliwad


title: Lenalidomide-induced pure red cell aplasia: clinical characteristics and mechanistic analysis [scRNA-seq]

first: Hu

last: Qi

overall_design: scRNA-Seq experiment: Single-cell capture was achieved by the BD Rhapsody system. The Seurat package (with default settings) was used for normalization and scaling of the expression matrix.

first: Qi

last: Hu

first: Yang

last: Liu

first: Qiuyu

last: Yue

first: Shuo

last: Zhou

first: Fan

last: Lin

first: Xiao-Jun

last: Huang

first: Jin

last: Lu

first: Hsiang-Ying

last: Lee


title: Differential lncRNA and mRNA expression in Hirschsprung's disease (HSCR)

city: xuzhou

first: jianjun

last: zhang

state: jiangsu

address: 18 Su Di North Road, Quanshan District

department: Department of Neonatal Surgery

institute: Xuzhou Children’s Hospital

summary: To investigate and compare the lncRNA and mRNA expression in HSCR from the  aganglionic and normal aganglionic

overall_design: 6 total samples ,3 was the aganglionic of HSCR,3 was the normal aganglionic of HSCR

first: Fengli

first: Jianjun

last: Zhang

first: Tongsheng

last: Ma


title: Soil bacterial diversity around a hospital and university precinct in South India over a 12-month period.

city: Bundoora

first: Anya

last: Shindler

state: VIC

address: 1 Kingsbury Drive

institute: La Trobe University

summary: This study identified and compared the bacterial diversity  and clinically relavent bacterial strains around a newly developed hospital and university precinct in southern India for a period of twelve months.

overall_design: Soil samples were taken from fourty plots next to a Hospital and University in sourthern India over the period of twelve months.  The samples underwent 16S sequencing to determine how the soil microbiota was affected by seasons and being in close proximaty to healthcare facilities.

first: Shalini

last: Kunhikannan

first: Cassandra

middle: R

last: Stanton

first: Jayson

last: Rose

first: Ashley

last: Franks

first: Sumana

last: Mns

last: Kumar

first: Steve

last: Petrovski

first: Colleen

last: Thomas


title: Human iPSC-derived nephron progenitor cells treat AKI and CKD in mouse models

status: Public on Feb 27 2025

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: The number of patients requiring dialysis therapy continues to increase worldwide due to the lack of effective treatments for chronic kidney disease (CKD). Furthermore, no curative treatments for acute kidney injury (AKI) have been established. The therapeutic effects of human induced pluripotent stem cell-derived nephron progenitor cells (hiPSC-NPCs) on AKI have been reported in mice but not clinically confirmed. There are also no reports examining the therapeutic potential of hiPSC-NPCs on CKD. Although large numbers of uniform hiPSC-NPCs are required for cell therapies for AKI and CKD, effective expansion cultures remain to be developed. Here, we established a CFY (CHIR99021, FGF9, Y-27632) medium for cell culture that enables more than 100-fold proliferation of hiPSC-NPCs from multiple hiPSC lines in two passages. We demonstrated that hiPSC-NPCs expanded by CFY or their conditioned medium alone attenuate kidney injury and improve survival in cisplatin-induced AKI mice. We also observed that hiPSC-NPCs prevented kidney functional decline, interstitial fibrosis, and senescence in aristolochic acid-induced CKD mice. In addition, we discovered c-MET as a specific cell surface marker for hiPSC-NPCs and confirmed that purified c-MET+ hiPSC-NPCs have therapeutic effects on AKI and CKD. Furthermore, we found that hiPSC-NPCs exerted their therapeutic effects in AKI and CKD mice by secreting vascular endothelial growth factor A (VEGF-A). Together, expanded hiPSC-NPCs are useful cell therapies for AKI and CKD, and may open new avenues for treating kidney diseases.

overall_design: RNA-seq profiling of bulk cells and cells purified with OSR1 and SIX2 (OSR1+SIX2, OSR1+SIX2-, OSR1-SIX2-) at day11 of nephron progenitor cell differentiation.

first: Kenji

last: Osafune

first: Toshikazu

last: Araoka

first: Kosuke

last: Toyohara

first: Hiraku

last: Tsujimoto

first: Tomoko

last: Kasahara

first: Shin-ichi

last: Sueta


title: Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP) Promotes Regeneration of Corneal Epithelial Cells via NR4A1 Signaling Pathway

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: PACAP is a neuropeptide that promotes lacrimal fluid secretion, but its direct action on corneal injury remains to be clarified. Therefore, the effect of PACAP on corneal epithelial repair was clarified using mouse corneal wound-injury model and human corneal epithelial culture cells. PAC1-R mRNA and its immunoreactivity was detected in mouse and corneal epithelium. In corneal wound-injury model mice, PACAP eye drop significantly reduced the injured area at 12 hours, and the effect was cancelled by co-treatment with the PACAP receptor antagonist. PACAP heterozygous and PAC1-R knockout mouse delayed the corneal healing. Although surgical removal of the lacrimal gland attenuates corneal healing, PACAP eye drop on the eyes significantly recuperated corneal damage. In an in-vitro study, PACAP treatment in human corneal epithelial cells significantly decreased the injury area induced by scratching. PACAP treatment in the in-vitro human corneal epithelial cell experiments significantly reduced the area of injury and abolished the corneal repair effect due to the inhibitory effect of Ara-C on proliferation. DNA whole-genome microarray analysis suggested that the nuclear receptor NR4A1 is an important factor in corneal epithelial proliferation, and THPN, which induces nuclear export of NR4A1, suppressed PACAP-induced proliferation of human corneal epithelial cells and the repair effect of mouse corneal epithelium. These data suggest that PACAP stimulates corneal repair by corneal epithelial proliferation via PAC1-R and NR4A1 transcriptional activity. PACAP could be a good candidate as an eye-drop medication for corneal injury disease including dry eye syndrome.

overall_design: Whole genomic DNA microarray was performed in HCEC2 cells (total RNA was extracted using RNeasy Micro Kit), suggests wound healing by PACAP.

first: Michio

last: Yamashita

first: Tomoya

last: Nakamachi

first: Junko

last: Shibato

first: Fumiko

last: Takenoya

first: Hitoshi

last: Hashimoto

first: Randeep

last: Rakwal

first: Seiji

last: Shioda


title: Unraveling the mechanism of JPI-547 in human pancreatic cancer cells through transcriptome analysis.

city: Seoul

first: Kyoung-Seok

last: Oh

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Cancer Research Institute

summary: This study aimed to elucidate the mechanism underlying the action of the dual PARP/Tankyrase inhibitor JPI-547 through RNA-sequencing. Focusing on human pancreatic cancer cell lines with either homologous recombination repair deficiency or Wnt-addiction, the investigation sought to uncover critical insights into the compound's mode of action.

overall_design: Capan-1 and HPAF-II cells treated with 1µM of olaparib or JPI-547 for 72 h were subjected to bulk RNA-seq.


title: Organ growth control in the absence of Hippo signaling

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

summary: Organs of all animals reliably grow to a specific size and it is widely thought that such developmental growth control is instructed by the Hippo signaling pathway. This is based on studies in flies and mice showing that deregulation of Hippo signaling causes dramatic tissue overgrowth of various organs. Here we use two major developmental paradigms and provide evidence that removing the key transcriptional downstream effectors of the Hippo pathway does not abolish organ growth control. Specifically, eliminating the function of the Hippo downstream co-activators Yki as well as Yap/Taz that complex with TEAD family transcription factors did not interfere with organ growth control in the developing mouse liver or Drosophila eye. Rather, mutant cells were able to proliferate appropriately during development, properly exit the cell cycle, and form organs of normal size. Remarkably, a complementing whole transcriptome analysis of mutant Drosophila eye imaginal discs corroborated these genetic findings. It showed that loss of the single TEAD transcription factor Scalloped (Sd) fully reverted the effect of overexpression of hyperactivated Yki back to a wildtype gene expression profile. In contrast, Sd/Yap/Taz proved to be crucial for cell survival in injury response models, namely X-ray irradiation of flies and toxic liver injury in mice. Therefore, we propose that Hippo signaling is dispensable for instructing normal organ growth and instead suggest that the classical Hippo mutant overgrowth phenotypes represent a de facto Yap/Taz/Yki gain-of-function situation that does not reflect an endogenous role in growth control. Instead, we hypothesize that the potency of Yap/Taz/Yki to drive tissue overgrowth draws from their broad and primary function in injury responses.

overall_design: RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type eye discs and genetic perturbations of Yki and sd.

first: Jelle

last: Jacobs

first: Maxime

last: De Waegeneer

first: Lucia

last: Romanelli

first: Mardelle

last: Atkins

first: Georg

last: Halder


title: Decreased expression of EZH2 in granulosa cells contributes to endometriosis-associated infertility by targeting IL-1R2 [RNA-Seq]

city: Hangzhou

first: Xiang

last: Lin

state: Zhejiang province

address: No. 3 Qingchun East Road, Shangcheng District, Hangzhou, 310000, China

department: Assisted Reproduction Unit, Department of Obstetrics and Gynecology;

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine;

summary: The mechanism by which endometriosis, a common gynecological disease characterized by chronic pelvic pain and infertility, causes infertility remains elusive. Luteinized unruptured follicle syndrome, the most common type of ovulatory dysfunction, is a cause of endometriosis-associated infertility involving reduced numbers of retrieved and mature oocytes. Ovulation is controlled by luteinizing hormone and paracrine signals produced within the follicle microenvironment. Generally, interleukin (IL)-1β is elevated in endometriosis follicular fluid, whereby it amplifies ovulation signals by activating extracellular-regulated kinase 1/2 and CCAAT/enhancer binding protein β pathways. However, this amplification of ovulation by IL-1β does not occur in patients with endometriosis. To illuminate the mechanism of ovulatory dysfunction in endometriosis, we analyzed the impact of oxidative stress and IL-1β expression in endometriosis follicles. We found that oxidative stress decreased EZH2 expression and reduced H3K27Me3 levels in endometriosis ovarian granulosa cells (GCs). Selective Ezh2 depletion in mice ovarian GCs reduced fertility by disturbing cumulus-oocyte complex expansion and reducing epidermal growth factor-like factor expression. Gene expression and H3K27Me3 ChIP-sequencing of GCs revealed IL-1 receptor 2 (IL-1R2), a high-affinity IL-1β-receptor that suppresses IL-1β-mediated inflammatory cascades during ovulation, as a crucial target gene of the EZH2-H3K27Me3 axis. Moreover, IL-1β addition did not restore ovulation upon Ezh2 knockdown, indicating a vital function of IL-1R2 in endometriosis. Thus, our findings show that reducing EZH2 and H3K27Me3 in GCs suppressed ovulatory signals by increasing IL-1R2 expression, which may ultimately contribute to endometriosis-associated infertility.

overall_design: To compare global gene expression profiled between WT-GCs (n = 4) and KO-GCs (n = 3), WT and KO mice were injected with 5 IU PMSG, and 48h later 5 IU HCG was injected to induce ovulation. No less than 2 × 10^6 mGCs were collected from WT and KO mice ovaries, and these cells were further used to perform RNA-seq. According to the results of quality control measurements by Biomarker Technologies (BMKCloud, Beijing, China), 2.5 ug RNA from WT-GCs and 2.5 ug RNA from KO-GCs were ultimately used for transcriptome analysis. The process of RNA-seq mainly includes sample detection, library construction, quality control, and sequencing on an high-throughput sequencing platform (Illumina, San Diego, CA, USA). Approximately 24008 genes were successfully annotated.

first: Xiaomei

last: Tong

first: Yinli

last: Zhang

first: Weijia

last: Gu

first: Qianmeng

last: Huang

first: Yi

first: Feng

last: Zhuo

first: Fanxuan

last: Zhao

first: Xiaoying

last: Jin

first: Chao

last: Li

first: Dong

first: Songying

first: Yongdong

last: Dai


title: The transcription factor ZNF469 regulates collagen production in liver fibrosis [RNA-Seq]

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

summary: Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world’s population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.

overall_design: The medium was changed the following day and cells were incubated in the same low FBS medium with addition of TGF-β (Gibco, PHG9214), for 24h (qPCR), 4 and 7 days (RNA-seq).

first: Quanhu

last: Sheng

first: Jonathan

last: Brown

first: Sebastian

last: Steinhauser

last: Ramirez-Solano


title: Decreased expression of EZH2 in granulosa cells contributes to endometriosis-associated infertility by targeting IL-1R2 [ChIP-Seq]

first: Xiang

overall_design: A ChIP assay was performed using a Simple ChIP® Enzymatic Chromatin IP Kit (9003, Cell Signaling Technology) in accordance with the manufacturer’s instructions. ChIP-grade anti-H3K27Me3 (9733, Cell Signaling Technology) and negative control Normal Rabbit IgG (2729, 1 µg per IP sample; Cell Signaling Technology) were used for IP. ChIP-enriched DNA and input DNA were subjected to deep sequencing (ChIP-Seq). ChIP fold enrichment was calculated using the comparative Ct method. ChIP-PCR was performed to verify the results of ChIP-Seq.


title: Preoperative exercise induces anti-tumor Kupffer cells to prevent surgical stress-promoted colorectal cancer liver metastasis

city: CHARLOTTESVILLE

first: Chengli

last: Shen

state: Virginia

address: 345 Crispell Dr.

institute: University of Virginia

summary: We have employed single-cell RNA sequencing using the 10x Genomics platform to investigate the immune cell distribution in the liver of Sedentary (Sed) and preoperative exercise (PEx) mice following surgical stress-promoted colorectal cancer liver metastasis model. The liver immune microenvironment plays a critical role in tumor progression and response to PEx. This study provides a comprehensive immune landscape at single-cell resolution, offering novel insights into how PEx modulates hepatic immune cell populations to mitigate surgical stress-induced tumor progression.

overall_design: Following surgical stress-promoted colorectal cancer liver metastasis, hepatic immune cells from the livers of Sed and PEx mice were isolated using CD45+ MACS beads and analyzed through single-cell RNA sequencing to characterize immune cell distribution and functional heterogeneity.

first: Zhang

last: Yunwei

first: Shen

last: Chengli

last: Hongji


title: Genome binding/occupancy profiling of ALKBH5 by high throughput sequencing  [CUT&RUN]

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary: Alkylation repair homolog protein 5 (ALKBH5) binds to RNA and mediates RNA m6A demethylation. However, whether ALKBH5 binds to DNA is largely unknown. In this study, our CUT&RUN data show that ALKBH5 can bind to DNA in Hepa1-6 cells.

overall_design: To investigate whether ALKBH5 regulates gene expression by binding to DNA, primary hepatocytes were infected with Ad-FLAG-ALKBH5 adenovirus, and CUT&RUN assay was performed.

first: Kaixin

last: Ding


title: Sox9 and Nfi transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors.

city: Stockholm

first: Behzad

last: Yaghmaeian Salmani

state: Solna, Stockholm

address: Department of Cell and Molecular Biology (CMB) Karolinska Institute,, Biomedicum, Solnavägen 9, Solna, Stockholm, P.O. Box 285 SE-171 77 Stockholm, Sweden

department: CMB

country: Sweden

institute: Karolinska Institute

overall_design: Refer to individual Series


title: Sox9 and Nfi transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors [bulkRNA]

summary: Correct timing of neurogenesis is critical for both generating the correct number and subtypes of glia and neurons in the embryo, as well as preventing tumours and the depletion of stem cell pools in the adults. Here we analyse how the midbrain dopamine neuron (mDA) progenitors transition into cell cycle arrest (G0) and begin to mature into ependymal cells. The comparison of mDA progenitors from different embryonic stages revealed the upregulation of Nfi and Sox9 transcription factors during development. Their conditional inactivation in the early embryonic midbrain leads to delayed G0 entry and ependymal maturation, reduced gliogenesis, and increased generation of neurons, including mDA neurons. In contrast, their inactivation in late embryogenesis does not result in mitotic re-entry, suggesting that these factors are necessary for the G0 induction, but not for its maintenance. Our characterisation of mDA-progenitor-derived adult ependymal cells by single-cell RNA sequencing and histology show that they both retain several progenitor features but also secrete neuropeptides and contact neighbouring cells and blood vessels, indicating that these cells may form a novel part of the circumventricular organ system.

overall_design: RNA-seq profiling of Lmx1aCreERT2-labelled mouse floor plate cells collected from E11, E13, E18 and P70 by laser capture microdissection (LCM) as well as neurosphere and ependymal sphere cultures derived from adult lateral ventricle and midbrain aquaduct respectively.

first: Laura

last: Lahti

first: Nikolaos

last: Volakakis

first: Linda

last: Gillberg

last: Yaghmaeian-Salmani

first: Katarína

last: Tiklová

first: Nigel

last: Kee

first: Hilda

last: Lundén-Miguel

first: Maarten

last: Werkman

first: Michael

last: Piper

first: Richard

last: Gronostajski

first: Thomas

last: Perlmann


title: Decreased expression of EZH2 in granulosa cells contributes to endometriosis-associated infertility by targeting IL-1R2

first: Xiang

last: Lin


title: CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development

city: Buffalo

first: Dahong

state: Other

address: 955 Main Street

department: Biochemistry

institute: SUNY Buffalo

summary: We performed RNA-seq, ATAC-seq and CUT&Tag to determine CTCF-regulated transcriptome, accessibility and CTCF association with chromatin during retinal rod development

overall_design: We FACS-isolated rods for all multi-omics analyses and compare control and CTCF-KO rods

first: Saumya

last: Keremane

first: Silu

last: Wang

first: Elissa

last: Lei


title: Comprehensive Analysis of Relapsed-Refractory Mature B-cell Non-Hodgkin Lymphoma in Children and Adolescents

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

summary: Outcome of paediatric B-cell Non-Hodgkin Lymphoma (B-NHL) has significantly improved in the last decades due to risk adapted strategies and the addition of immunotherapy, (survival >90%). However, limited progress has been achieved in relapsed patients, mostly Burkitt lymphoma (<30%). Validation of prognostic biomarkers to identify candidates to novel therapies is imperative. This retrospective study reports on clinical and therapeutic data of 46 children and adolescents with relapsed B-NHL, including integrative molecular data of 16 (35%) cases. TP53 alterations were identified in 10 (60%) patients which were associated with worse outcome. Our data support the focus on TP53 as a potential biomarker.

overall_design:
Outcome of pediatric B-cell Non-Hodgkin Lymphoma (B-NHL) has significantly improved in the last decades due to risk adapted strategies and the addition of immunotherapy, (survival >90%). However, limited progress has been achieved in relapsed patients, mostly Burkitt lymphoma (<30%). Validation of prognostic biomarkers to identify candidates to novel therapies is imperative. This retrospective study reports on clinical and therapeutic data of 45 children and adolescents with relapsed B-NHL, including integrative molecular data of 17 (37%) cases.
CNAs were examined in 23 samples from 17 patients (from 8 patients available at diagnosis, 5 patients with paired samples, and 5 patients with only relapse samples). using Oncoscan (22 samples) or Cytoscan (1 sample) platforms (ThermoFisher Scientific, Waltham, MA, USA) according to standard protocols. Gains and losses and regions of CN neutral loss of heterozygosity (CNN-LOH) were evaluated using Nexus Biodiscovery v9.0 software (Biodiscovery, Hawthorne, CA, USA).
CNAs were identified in all investigated samples. Median CNAs was 5.5 at diagnosis (range 0–19) and 7 at relapse (range 1–88). No differences were observed in terms of genomic complexity between diagnosis and relapse (mean 6.9 vs 16 CNA/case, p-value 0.47), nor between our R/R series and B-NHL series not enriched in relapse cases. We investigated the CN profile of the 17 patients with available material. Recurrent CNAs (>20%) included 1q21.1-q25.3, and 13q31.3 gains, and 4p16.3, 4q34.3-q35.3, 9q21.3-q22.32, 17p13.1-p11.2/TP53, and Yp11.31-q11.23 losses. CNN-LOH of 17p13.3-p11.2 including TP53 were also recurrent, affecting 29% of the patients.

first: Sara

last: Mato