title: Two-component intranasal vaccine against SARS-CoV-2 Omicron variant

city: Chengdu, Cihna

first: Xaingyu

last: Pan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Mucosal immunity plays a pivotal role in providing comprehensive protection against upper-airway infections and effectively limiting the shedding and transmission of SARS-CoV-2. Despite its critical importance, there remains a notable absence of nasal spray vaccines endorsed for global use by the World Health Organization. This could be due to the inability of current intranasal vaccines to induce strong mucosal and systemic responses in humans, thus urgently entailing a next-generation of intranasal COVID-19 vaccines with novel and safe technologies. In this study, we prepared a two-component intranasal vaccine that combines adenovirus vectors with a self-assembled subunit protein. Specifically, the adenovirus vector expresses the spike protein of XBB.1.5 variant (Ad5XBB.1.5), and were mixed with the recombinant protein that developed derived from the receptor binding domain (RBD) of XBB.1.5 (RBDXBB.1.5-HR). Combination of Ad5XBB.1.5 and RBDXBB.1.5-HR elicited superior humoral and cellular immunity against XBB.1.5-included variants compared with the individual components. Importantly, the STING signaling pathway was found to be crucial for the adjuvant effect of the adenovirus vector. In addition, to increase the broad-spectrum neutralizing capacities, a trimeric protein derived from the BA.5 variant (RBDBA.5-HR) was incorporated to formulate a three-component vaccine (Ad5XBB.1.5+RBDXBB.1.5-HR+RBDBA.5-HR), indicating the utilization of a combination of an adenovirus-vectored and subunit protein vaccines has the potential to serve as a next-generation intranasal vaccine platform. Of note, intranasally delivery of two-component vaccine provided protective immunity against live Omicron XBB.1.16 virus challenge in mice. Furthermore, the combination of adenovirus and subunit protein vaccine demonstrates excellent tolerability and safety in human subjects, and is able to induce enhanced mucosal immunity as well as high levels of sera neutralizing antibody in all participants. These findings underscore its suitability for clinical application in the prevention of SARS-CoV-2 variants encompassing XBB lineages.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on female C57BL/6 mice in PBS, as well as on Ad5XBB.1.5+RBDXBB.1.5-HR groups, including Sting-/- mice also receiving Ad5XBB.1.5+RBDXBB.1.5-HR immunization as previously described. Forty-eight hours after the final vaccination, the mice were euthanized for lung tissue collection. The lungs were minced with scissors and treated with tissue dissociation solution to generate a single-cell suspension.

first: Weiqi

last: Hong

first: Xiangyu

first: Xiawei

last: Wei


title: Single-Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA-Seq]

status: Public on Jun 02 2025

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

country: USA

institute: The University of Texas at Austin

type: Expression profiling by high throughput sequencing

summary: Retinal ganglion cells (RGCs) are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not regenerate after injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC survival after injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals, zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection (ONT) using isl2b:eGFP transgenic fish line, single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3, a cell population having progenitor and regenerative identity.

overall_design: Nine bulk RNA-seq libraries were prepared from FACS-purified retinal ganglion cells (RGC) from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue after optic nerve transection at each of 3 timepoints: 1, 5, and 7 days post-injury (dpi), and three from uninjured tissue on the same days.

first: Ashrifa

last: Ali

first: Hannah

last: Schriever

first: Dennis

last: Kostka

first: Taka

last: Kuwajima

first: Kristen

last: Koenig

first: Jeffrey

last: Gross


title: Exploring the effect  of aging, TNFα, and RBM25 on the gene expresssion of inner ear

city: Shanghai

first: Jiaoyao

last: Ma

state: Shanghai

address: No. 130, Dong'an Road, Xuhui District

country: China

institute: Fudan University

summary: Purpose:  The goals of this study are to explore the effect aging on gene expression of the inner ear. And the effect of RBM25 and TNFα on the gene expression on inner ear organod are explored.

overall_design: Methods: Inner ear tissues from the three ages, 3-month-old, 11-month-old, and 20-month-old, were collected. The bones of the inner ear were removed, and the tissues residing in the bone were all used for mRNA extraction. Inner ear organoids in four groups (Control, RBM25 knock down, TNF-α, and TNF-α+ RBM25 knock down) were collected for mRNA extraction.

first: Mingyu

last: Xia

first: Yunjie

last: Li

first: Wenyan


title: Single nucleus RNA sequencing  of mouse cochlea and utricle aging.

summary: The cochlea is the auditory sensory organ and the utricle detect linear acceleration and the pull of gravity. We performed single nucleus RNA sequencing to analyze changes of cell types and gene expression in cochlea and utricles during aging.

overall_design: Under a microscope, 3M, 9M and 12M mouse cochlea and utricles were harvested using microdissection forceps and digested for analysis using single-nucleus RNA sequencing.


title: Mucosal effects of tenofovir 1% gel wane over longer-term use but retain pro-proliferative and type I/III interferon pathway signatures

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

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

overall_design: Refer to individual Series


title: CNS-Targeted Base Editing of the Major Late-Onset Tay-Sachs Mutation Alleviates Disease in Mice

city: Bethesda

first: Richard

middle: L

last: Proia

state: MD

address: 10 Center Drive Room 9D11

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Late-onset Tay-Sachs (LOTS) disease is a lysosomal storage disorder most commonly caused by a point mutation (c.805G>A) in the HEXA gene encoding the α-subunit of the lysosomal enzyme β-hexosaminidase A. LOTS manifests as a range of gradually worsening neurological symptoms beginning in young adulthood. Here, we explored the efficacy of an adenine base editor (ABE) programmed with a small guide RNA (sgRNA) to correct the HEXA c.805G>A mutation. Base editing in LOTS patient fibroblasts successfully converted the pathogenic HEXA c.805A to G and partially restored β-hexosaminidase activity, with minimal genome-wide off-target editing. We generated a LOTS mouse model in which the mice exhibited decreased β-hexosaminidase activity, accumulation of GM2 ganglioside in the brain, progressive neurological manifestations, and reduced lifespan. Treatment of LOTS mice with the neurotropic virus AAV-PHP.eB carrying the ABE and an sgRNA targeting the LOTS point mutation partially corrected the c.805G>A mutation in the CNS, significantly increased brain β-hexosaminidase activity, and substantially reduced GM2 ganglioside accumulation in the brain. Moreover, the therapy delayed symptom onset and significantly extended median lifespan. These findings highlight the potential of base editing as an effective treatment for LOTS and its broader applicability to other lysosomal storage disorders.

overall_design: Compare gene expression profile between Control and AAV ABE base edited mice.

first: Maria

last: Allende

first: Mari

last: Kono

first: Y

middle: T

last: Lee

first: Samantha

middle: M

last: Olmsted

first: Vienna

last: Huso

first: Jenna

middle: Y

last: Bakir

first: Florencia

last: Pratto

first: Cuiling

first: Colleen

last: Byrnes

first: Galina

last: Tuymetova

first: Hongling

last: Zhu

first: Cynthia

middle: J

last: Tifft


first: Wei

last: Yusheng

state: New York

address: 227,South Road of Chongqian,Shanghai,China

institute: Shanghai Jiao Tong University of Medicine

summary: We observed that the deletion of Anp32b led to severe defects in ocular development, such as anophthalmia and microphthalmia. Moreover, Anp32b was highly expressed in the lens, and Anp32b−/− embryos with microphthalmia typically exhibited severely impaired lens development. Mechanistically, ANP32B directly interacted with paired box protein 6 (PAX6), a master transcriptional regulator of ocular development, and enhanced its transcriptional activity. In line with these findings, overexpression of PAX6 partially but significantly reversed the inhibition of proliferation observed in ANP32B knockdown cells. Collectively, our findings reveal that ANP32B-deficiency suppresses ocular development by repression of PAX6 and identify ANP32B as a viable therapeutic target for ocular developmental defects.

overall_design: RNA-seq data from the eye tissue of  Anp32b+/+/ Anp32b−/− embryos

first: Yusheng

last: Wei

first: Yun

last: Yu


title: Full-length transcriptome sequencing of longissimus dorsi muscle of yak and cattle-yak based on nanopore

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: Short-reading long RNA sequencing technology has been used to study the transcriptome of skeletal muscle of yak and cattle-yak, but it cannot accurately define full-length transcripts and alternative splicing isoforms. In this study, based on Oxford Nanopore Technologies ( ONT ) full-length sequencing technology, the longissimus dorsi transcription profiles of yak and cattle-yak were obtained. A total of 20323 new genes and 172870 new transcripts were identified, and 159700 new transcripts were successfully annotated. A total of 157812 AS events, 58073 SSRs, 57468 complete ORFs, 2296 transcription factors and 20404 lncRNAs were detected. The analysis found that different structural variations have specific functions, which contribute to the coordination of muscle development and the diversity of gene expression. In addition, the differentially expressed transcripts in longissimus dorsi muscle of yak and cattle-yak were involved in MAPK and JAK-STAT signaling pathway related to muscle development and growth. PPI analysis of differentially expressed transcripts suggested that TNNI2 may play a prominent role in the differences in muscle growth and meat quality traits between yak and cattle-yak. Our study enriched the transcriptome data of yak dorsal muscle and provided a reference for the production of yaks with higher meat yield and better meat quality.

sample_organism:
Bos grunniens
Bos grunniens x Bos taurus

overall_design: Based on ONT  full-length sequencing technology, the transcriptome data of longissimus dorsi muscle of yak and cattle-yak were obtained.

first: Mengli

last: Cao

first: Shaoke

last: Guo

first: Xian

first: Xingdong

last: Wang


title: Binding of KAP1 organizes HP1alpha for transcriptional silencing [ATAC-seq]

city: Dallas

first: Laura

last: Banaszynski

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Constitutive heterochromatin is enriched in repetitive elements, including endogenous retroviral element (ERV) sequences that must be repressed to sustain normal cell developmental programs and prevent chromosomal instability. ERVs are silenced through trimethylation of lysine 9 on histone H3 (H3K9me3) by ESET (also known as SETDB1, SET domain bifurcated 1, or KMT1E) and a co-repressor complex containing KAP1 (KRAB-associated protein 1, also known as tripartite motif-containing protein 28, Trim28) in mouse embryonic stem cells. H3K9me3 then serves as a scaffold for the recruitment of proteins that maintain ERVs in a transcriptionally silent state, including the HP1 proteins that themselves interact with the co-repressor KAP1. In this study, we provide structural insights into the KAP1-HP1 interaction. Further, we demonstrate that this interaction plays a role in maintaining inaccessible chromatin at specific ERV elements in embryonic stem cells (ESCs).

overall_design: ATAC-seq analysis in mouse embryonic stem cell lines. The piggybac transposase system was used to integrate transgenic KAP1-Flag or KAP1(V488E)-Flag into KAP1-fl/fl ESCs with an integrated ERT2-Cre cassette. Exogenous expression of WT or V488E mutant KAP1 was induced with 2 μg/mL doxycycline for 48hrs and maintained in doxycycline prior to endogenous KAP1 deletion. KAP1 deletion was induced with 2 μM 4-OHT (Sigma) treatment for 48hrs. Cbx1-/-;Cbx3-fl/fl;Cbx5-fl/fl;ERT2-Cre ESCs were obtained from PMID 29795351. HP1 deletion was induced with 2 μM 4-OHT (Sigma) treatment for 48hrs or 72 hrs.

first: Ryan

last: O'Hara

middle: A


title: Binding of KAP1 organizes HP1alpha for transcriptional silencing [CUT&Tag]

overall_design: CUT&Tag analysis in mouse embryonic stem cell lines. KAP1-fl/fl ESCs with an integrated ERT2-Cre cassette were treated with EtOH or with 2 μM 4-OHT (Sigma) for 48hrs.


title: Neuroimmune gene signature of prurigo nodularis compared to psoriasis and atopic dermatitis

city: Baltimore

first: Shawn

last: Kwatra MD

address: 1550 Orleans Street

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: Prurigo nodularis (PN) is a debilitating neuroimmune skin disease characterized by pruritic, raised, nodular lesions. Psoriasis and AD are classically characterized by Th1/Th17 and Th2 polarization, respectively, but the neuroinflammatory profile of PN remains poorly defined. We characterized the neuroimmune phenotype of PN compared to AD, psoriasis, and healthy controls (HC), through transcriptomic analysis of lesional and nonlesional skin biopsies from 25 PN patients, 27 AD patients, 15 psoriasis patients, and 12 HC using a custom neuroinflammation-focused NanoString panel of 770 genes. Analysis of affected versus unaffected skin revealed differentially expressed genes (DEGs, fold change>1.5, p<0.05) associated with Th1, Th2, and Th17 activation in all three diseases. Upregulated DEGs in PN compared to AD and psoriasis were primarily associated with extracellular matrix remodeling or neural function. Expression of IL-31 was upregulated in PN compared to psoriasis but not AD. Downregulated DEGs in PN compared to AD were associated with Th2 activation and glutamate receptors; those compared to psoriasis were related to Th1 and Th17 activation.  PN has a distinct neuroinflammatory signature characterized by intermediate Th1/Th17 and Th2 immune axis activation compared to AD and psoriasis, with increased levels of ECM dysregulation, neuronal abnormalities, and IL-31 activity.

overall_design: Transcriptome analysis was performed on a total of 26 lesional and 26 non-lesional skin biopsies from 26 PN patients (mean age 52.5 years, 76% female, and 64% African American), 26 lesional and 15 nonlesional biopsies from 26 AD patients (mean age 48.5 years, 37% female, and 44% African American), and 15 lesional biopsies from 15 psoriasis patients (mean age 54.1 years, 40% female, and 47% African American) patients, as well as 12 matched controls.

first: Hannah

last: Cornman

first: Jaya

last: Manjunath

first: Shrey

last: Bhatt

first: Alexander

last: Kolhoff

first: Michael

last: Diaz

first: Weiying

last: Lu

first: Selina

last: Yossef

first: Emily

middle: Z

last: Ma

first: Brenda

last: Umenita Imo

first: Jingyi

last: Zhang

first: Kevin

middle: K

last: Lee

first: Thomas

middle: W

last: Pritchard

middle: G

last: Kwatra


title: Hair follicle stem cell fate supports distinct clinical endotypes in Hidradenitis Suppurativa

city: Créteil

first: Sophie

last: Hue

address: 1 rue du général Sarrail

country: France

institute: Henri Mondor APHP

summary: Hidradenitis suppurativa (HS) is a severe skin disorder affecting 1% of the global population. Its pathogenesis is multifactorial and poorly understood, involving aberrant keratinization and autoinflammation. Whether autoinflammatory events precede or follow hyperkeratotic changes in hair follicle (HF) epithelia is unknown. Using single-cell RNA sequencing (scRNA-Seq), we defined the cellular composition of HF cells, the primary cells involved in HS, and confirmed these findings in the Fol-HYDRA cohort. We identified three main cell families: i) HF matrix lineage enriched for MSX2, ii) non-matrix lineage enriched for KRT14, and iii) immune cells enriched for PTPRC. Unsupervised clustering of HF cells from controls and HS patients revealed significant differences in non-matrix cells, segregating patients into two groups. Group one is enriched in cluster 1 (IBL), while group two is enriched in cluster 0 (mORS), each displaying distinct transcriptomic changes. Gene set enrichment analysis showed IBLs enriched for keratinization genes and mORS for interferon response genes. Trajectory analysis revealed HF stem cells differentiating into either IBL or mORS pathways. Confirmed in 49 HS patients, these pathways correspond to different clinical phenotypes. Our findings provide a novel perspective on HS pathology, identifying two key pathways: one in keratinization and the other in inflammation. These pathways define different endotypes for HS patients, suggesting potential markers for personalized medicine.

overall_design: To investigate the cellular heterogeneity of hair follicles from HS patients compared to heathy donor, we performed single-cell RNA-Sequencing on hair follicles samples from 5 HS patients and 2 healthy donors.

first: Audrey

last: Onfroy

first: Francette

last: Jean-Louis

first: Philippe

last: Lecorvoisier

first: Fanny

last: Coulpier

first: Caroline

last: Boucle

first: Salwa

last: Abid

first: Emilie

last: Sbidian

first: Christina

last: Bergqvist

first: Pierre

last: Wolkenstein

first: Véronique

last: Godot

first: Yves

last: Lévy

first: Piotr

last: Topilko

first: Etienne

last: Audureau

last: Hüe


title: Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation [ChIP-Seq]

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

summary: The histone methyltransferase KMT2D (alias MLL4) is frequently mutated in medulloblastoma (MB). Heterozygous loss of KMT2D is prevalent in MB. However, the role of heterozygous KMT2D loss remains unknown. Here, we show that heterozygous Kmt2d loss highly promotes Ptch+/–-driven MB genesis in mice. Heterozygous Kmt2d loss upregulated tumor-promoting programs, including oxidative phosphorylation (OXPHOS), in Ptch+/–-driven MB genesis. Heterozygous Kmt2d loss extensively diminished enhancer signals and H3K4me3 signature, including those for transcription-repressive tumor suppressor genes (e.g., Ncor2). NCOR2 repressed the expression of tumor-promoting genes. Combinatory pharmacological inhibition of OXPHOS and the enhancer-decommissioning demethylase LSD1 drastically reduced the tumorigenicity of MB cells bearing heterozygous Kmt2d loss. These findings reveal the mechanistic basis underlying the MB-promoting effect of heterozygous KMT2D loss.

overall_design: ChIP assay was performed using a modified version of the previously described method (Dhar et al., 2016; Dhar et al., 2012). Cerebellar tissues were processed for ChIP using Ren lab's protocol from Roadmap Epigenome (https://www.encodeproject.org).  The ChIP-seq libraries were prepared using NEB adapters as described earlier (Alam et al., 2020). Libraries were multiplexed together, and sequencing was performed in Hiseq2000 or HiSeq4000 (Illumina). CUT&RUN assays were performed using CUTANA ChIC/ CUT&RUN Kit. Analysis was performed with Pluto (https://pluto.bio) software.

first: Shilpa

middle: S

last: Dhar

first: Min

last: Lee


title: Identification and mapping of human lymph node stromal cell subsets by combining single-cell RNA sequencing with spatial transcriptomics.

city: Utrecht

first: Cristoforo

last: Grasso

address: Heidelberglaan 25, 3584 CS Utrecht

country: Netherlands

institute: Prinses Maxima Centrum

summary: Lymph node stromal cells (LNSCs) have a crucial immunomodulatory function, but their heterogeneity in human is incompletely understood. Here, we report the single cell RNA sequencing (scRNA-seq) of 12’000 LNSCs isolated from a human lymph node (LN). This study comprehensively defines the gene signatures of 10 fibroblast subtypes: CCL21+SC, CCL19+SC, CD34+CXCL14+SC, pericytes, DES+SC, LAMP5+SC, NR4A1+BCAM+ SC, HLA-DR+SC, SEPT4+SC and GLDN+SC. To explore the heterogeneous stromal compartment within the complex LN tissue architecture, we integrated the scRNA-seq profiles of the identified LNSC subsets with a publicly available human spatial transcriptomic LN dataset and predicted their location within the complex LN tissue architecture. Each LNSC subtype was spatially restricted to specific LN regions, indicating different LNSC-lymphocyte interactions which was further investigated using NicheNet. The positioning of distinct LNSC subtypes in different LN regions sets the stage for future research on the relationship between LNSC-specific niches and immunomodulatory function during health and disease.

overall_design: LNs were collected from kidney transplantation recipients during living donor kidney transplantation. We have noticed that HLA-DR+ stromal cells represent only a small population within the stromal compartment of the lymph node. To ensure that sufficient HLA-DR+ stromal cells were included in the sorted cells used for sequencing, we included HLA-DR in the gating strategy of the sorting. We first gated on the HLA-DR+ (plus) and HLA-DR- (minus) stromal cells, subsequently we sorted DN, FRC, BEC and LEC based on PDPN and CD31 expression, resulting in two sorted cell suspensions. To assess the presence of a possible batch effect between these two samples, we added spike-in B cells in each sample.


title: Development of a LRRC15-Targeted Radio-immunotheranostic Approach to Deplete Pro-tumorigenic Mechanisms and Immunotherapy Resistance

city: Los Angeles

first: Claire

last: Storey

state: CA

address: 10833 Le Conte Ave

institute: UCLA

summary: Leucine-rich repeat containing 15 (LRRC15) has emerged as an attractive biomarker and target for cancer therapy. We have developed a humanized monoclonal antibody (mAb), DUNP19, that specifically binds to a phylogenetically conserved LRRC15 epitope and is internalized by target-expressing cancer and stromal cells. In xenograft mouse models, Lutetium-177 labeled DUNP19 ([177Lu]-DUNP19) enables non-invasive imaging and precise radiotherapy to LRRC15-expressing cancer cells and murine cancer-associated fibroblasts (CAFs), halting tumor progression and prolonging survival with minimal toxicity. Transcriptomic analyses of [177Lu]-DUNP19-treated tumors reveal a loss of pro-tumorigenic mechanisms, including a transforming growth factor beta (TGFβ)-driven and LRRC15+ signature associated with immunotherapy resistance. Together, these results demonstrate that radio-theranostic targeting of LRRC15 with DUNP19 is a compelling precision medicine platform for image-guided diagnosis, eradication, and reprogramming of LRRC15+ tumor tissue that drives immuno-resistance and aggressive disease.

overall_design: Evaluation of transcriptomic changes induced by LRRC15-targeted radioimmunotherapy with 177Lu-DUNP19 in U118MG, HuO9, and HCC1954 xenograft models, compared to untreated (PBS-injected) controls

first: Mohamed

last: Altai

first: Katharina

last: Lückerath

first: Wahed

last: Zedan

first: Henan

last: Zhu

first: Marija

last: Trajkovic-Arsic

first: Julie

last: Park

first: Norbert

last: Peekhaus

first: Jens

last: Siveke

first: Diane

last: Abou

first: Haley

last: Marks

first: Enna

last: Ulmert

first: Hans

last: Lilja

first: Alexander

last: Ridley

first: Marcella

last: Safi

first: Constance

last: Yuen

first: Susanne

last: Geres

first: Liqun

last: Mao

first: Michael

last: Cheng

first: Johannes

last: Czernin

first: Ken

last: Herrmann

first: Laurent

last: Bentolila

first: Xia

last: Yang

first: Thomas

last: Graeber

first: Robert

last: Damoiseaux

first: Daniel

last: Thorek

first: David


title: Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation [CUT&RUN]

first: Pluto

last: Bio

first: Shilpa

last: Dhar

first: Min

last: Lee


title: RNA-seq differences between patients with ulcer pressures grade II vs patients with ulcer pressures grade III-IV

city: Boadilla del Monte

first: Andrea

middle: Escolar

last: Peña

state: Madrid

address: Urbanización Montepríncipe

country: Spain

institute: Universidad San Pablo CEU

summary: we want to find those markers and pathways that differ between patients with ulcer pressures grade II (less severe) than patients with ulcer pressures grade III-IV (severe)

overall_design: RNA isolated from serum. 10 patients per group

first: Carlos

last: Tarín Cerezo

first: Osvaldo

last: Graña Castro

last: Escolar-Peña

first: Paloma

last: Fernández Martínez

first: Juan Carlos

last: López-Rodríguez


title: Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation


title: Somatic mtDNA mutations at intermediate levels of heteroplasmy are a source of functional heterogeneity among primary leukemic cells

city: Memphis

first: Mondira

last: Kundu

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Hospital

summary: Purpose: Metabolic reprogramming is a key feature of cellular transformation. Although the mitochondrial genome encodes components of the electron transport chain that produce tumor-modifying metabolic signals, the contribution of somatic mtDNA mutations in cancer pathophysiology remains unclear. Here, we employed scRNA-seq to capture cell state changes associated with pathogenic, tumor-enriched mtDNA variants in primary leukemic blasts using single-cell RNA sequencing (scRNA-seq)

overall_design: Single-cell RNA sequencing (Chromium, 10X Genomics) of three B-ALL tumor samples that were positive for the t(1;19)(q23;p13) translocation (TCF3-PBX1+/E2A-PBX1+)

first: Kelly

last: McCastlain

first: Wenan

last: Chen

first: Ti-Cheng

last: Chang

first: Gang

last: Wu


title: Thyroid hormone receptor beta1 action in the resolution of liver fibrosis [bulk RNA-seq]

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Bulk RNAseq of liver from mice control and with hepatocyte specific ablation of the thyroid hormone receptor beta

overall_design: Mice were fed PTU/LID diet and treated with carbon tetrachloride 0.4 ul/g twice a week for four weeks 9 injections total. T3 was administer in drinking water on the last week of the carbon tetrachloride treatment at a concentration of 1 ug/ml.

first: Arturo

last: Mendoza

first: Anthony

last: Hollenberg


title: Thyroid hormone receptor beta1 action in the resolution of liver fibrosis


title: Chemical-based external stimulation reprograms BJs into FiNs (scATAC-seq)

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

summary: Here, we report that chemical-based external stimulation reprograms human BJs to generate human induced FiNs.  Using transcriptome,and chromatin accessibility, we identified the cells exhibited key features of FiNs in transcriptomic profiles, epigenetic status. In addition, we also analyzed the reprogramming process.

overall_design: Cells at the end of  0 day,3 day were analyzed by ATAC-seq.

first: Guodong

last: Wang

first: Dandan

last: Zhang

first: Liangshan

last: Qin

first: Ben

last: Huang


title: Machine-guided cell-fate engineering

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

summary: The creation of induced pluripotent stem cells (iPSCs) has enabled scientists to explore the derivation of many types of cells. While there are diverse general approaches for cell-fate engineering, one of the fastest and most efficient approaches is transcription factor (TF) over-expression. However, finding the right combination of TFs to over-express to differentiate iPSCs directly into other cell-types is a difficult task. Here were describe an automatable machine-learning (ML) pipeline, called \textit{CellCartographer}, that uses chromatin accessibility and transcriptomics data to design multiplex TF pooled-screening experiments for cell type conversions that then be iteratively refined. We validate this method by differentiating iPSCs into twelve diverse cell types at low efficiency in preliminary screens and then iteratively refine our TF combinations to achieve high efficiency differentiation for six of these cell types in < 6 days. Finally, we functionally characterized engineered iPSC-derived cytotoxic T-cells (iCytoT), regulatory T-cells (iTReg), type II astrocytes (iAstII), and hepatocytes (iHep) to validate functionally accurate differentiation.

overall_design: Gene expression profiling and relative barcoded gene expression with RNA-seq for various iPSC engineered cell lines. Gene expression profiling with RNA-seq includes 2-3 replicates per cell type and culturing condition compared to iPSCs grow in stem cell medium.

first: George

last: Church


title: Chemical-based external stimulation reprograms BJs into FiNs


title: Chemical-based external stimulation reprograms BJs into FiNs (bulk RNA-seq)

overall_design: Cells at the end of  0 day,2 day and 5 day were analyzed by RNA-seq.


title: Chemical-based external stimulation reprograms BJs into FiNs (scRNA-seq)

overall_design: Cells at the end of  0, 3, and 5 day were analyzed by scRNA-seq.


title: Herbal terpenoids activate autophagy and mitophagy through modulation of bioenergetics and protect from metabolic stress, sarcopenia and epigenetic aging [Quantseq_cell]

status: Public on Jun 01 2025

city: Lausanne

first: Philipp

last: Gut

address: route du Jorat 57

department: Nestlé Institute of Health Sciences

country: Switzerland

institute: Société des produits Nestlé SA

summary: Small molecular food components contribute to health benefits of diets rich in fruits, vegetables, herbs, and spices. The cellular mechanisms by which non-caloric bioactives promote healthspan are not well understood, limiting their use for disease prevention. Here, we deploy a whole organism, high-content screen in zebrafish to profile food-derived compounds for activation of autophagy, a cellular quality control mechanism promoting healthy aging. We identify thymol and carvacrol as activators of autophagy and mitophagy through short-acting dampening of mitochondrial membrane potential. Chemical stabilization of thymol-induced mitochondrial depolarization blocks mitophagy activation, suggesting a mitochondrial membrane-originating mechanism. Supplementation of thymol prevents excess liver fat accumulation in a diet-induced obesity mouse model, improves pink1-dependent heat stress-resilience in Caenorhabditis elegans and slows decline of skeletal muscle performance and epigenetic aging in SAMP8 mice. Thus, terpenoids from common herbs promote autophagy during aging and metabolic overload, making them attractive for nutrition-based healthspan promotion.

overall_design: 3' Quant-Seq profiling of primary mouse adult fibroblasts (MAFs) obtained from C57BL6/j mice. Cells were treated with DMSO or Thymol 100uM for 24h.

first: Gabriele

last: Civiletto

first: Dario

last: Brunetti

first: Giulia

last: Lizzo

first: Alix

last: Zollinger

first: Sylviane

last: Metairon

first: Jerome N

last: Feige


title: Transgene-free generation of long-term hematopoietic stem cells

city: Chestnut Hill

first: DHVANIT

last: SHAH

address: 72 Gerry Rd

institute: Dhvanit Shah Lab

summary: Analyze the role of cyclic stretch and Yoda1-mediated Piezo1 activaiton in the endothelial-to-hematopoietic transition

overall_design: Cyclic stretch and Yoda1-mediated Piezo1 activaiton

first: Giorgia

last: Scapin

first: Dhvnait

last: Shah


title: Herbal terpenoids activate autophagy and mitophagy through modulation of bioenergetics and protect from metabolic stress, sarcopenia and epigenetic aging [Quantseq_muscle]

overall_design: 3' Quant-Seq profiling of hindlimb muscle tissue collected from SAMP8 mice. Mice at the age of 8 months received thymol (20 mg/kg body weight per day) or vehicle for 3 months.


title: Single-Cell RNA-Seq Analysis of Rat Cavernous Tissue Reveals Cellular Heterogeneity and Molecular Alterations in Cavernous Nerve Injury-Induced Erectile Dysfunction

city: Zhuhai

first: Biao

last: Liu

address: meihuadong road

institute: The Fifth Affiliated Hospital, Sun Yat-sen University

summary: Erectile dysfunction (ED) secondary to cavernous nerve injury (CNI) is a common complication of pelvic surgeries, yet its cellular pathophysiology remains incompletely characterized. Here, we generated a high-resolution single-cell transcriptomic atlas of rat cavernous tissue following CNI. Our analysis identified dysregulated gene networks in key cell populations (e.g., fibroblast, endothelial cells, smooth muscle cells, Schwann cells, and macrophages) associated with fibrosis, vascular dysfunction, and axonal degeneration. This dataset provides a foundation for understanding CNI-mediated ED and discovering targets for nerve regeneration and tissue repair.

overall_design:
To induce CNIED, bilateral cavernous nerve injury was performed. Specifically, a hemostat was applied with full-tip closure to the cavernous nerve (CN) 5 mm distal to the major pelvic ganglion (MPG) for 1 minute. Rats in the control group underwent the same surgical procedure without nerve compression. Apomorphine (100 μg/kg) was used to screen CNIED rats. Penile tissues were harvested from the rats 4 weeks after nerve injury for further study.
see PRJNA1079907 for raw data


title: TMEM259 alleles modulate respiratory syncytial virus infection and ER-stress-triggered apoptosis

city: Hannover

first: Chris

last: Lauber

address: Feodor-Lynen Str. 7

country: Germany

institute: TWINCORE Centre for Experimental and Clinical Infection Research

summary: Respiratory syncytial virus (RSV) is a main cause of infant morbidity and mortality. Susceptibility factors for severe RSV bronchiolitis in previously healthy children are unclear. We analyze genetic variants in 5,141 genes involved in virus sensing, interferon (IFN) signaling and effector functions in a population of n=101 previously healthy infants with severe RSV bronchiolitis. Comparing allele frequencies of the patient cohort with the exome aggregation consortium dataset (ExAC) our analysis reveals 94 non-synonymous coding single nucleotide polymorphisms (SNPs) mapping to 79 potential risk genes. Follow up of genes expressed in human lung cells show that TMEM259 (also known as membralin), a protein involved in regulating endoplasmic reticulum (ER) stress and neuronal cell survival, restricts RSV infection. Analysis of engineered human airway cells endogenously expressing the TMEM259 major allele or the rs77868901 minor variant shows allele-dependent modulation of RSV infection and ER-stress induced apoptosis, but not IFN activity nor induction of IFN stimulated genes. TMEM259 abundance and polymorphisms modulate RSV infection likely by modulating the ER stress response and apoptosis. This data may aid future risk stratification and development of prevention and treatment strategies for RSV.

overall_design: RNA-seq profiling of 16HBE140, A427, A549, Calu-3, Hep-2 cell lines and human airway epithelial (HAE) cells.

first: Sibylle

last: Haid

first: Martin

last: Wetzke

first: Isra

last: Nurhassen

first: Vanessa

last: Milke

first: Daniel

last: Todt

first: Melle

last: Holwerda

first: Ronald

last: Dijkman

first: Thomas

last: Zillinger

first: Danny

last: Jonigk

first: Matthias

last: Lange

first: Christina

last: Grethe

first: Jessica

last: Wenzl

first: Bianca

last: Klee

first: Cornelia

last: Gottschick

first: Rafael

last: Mikolajczyk

first: Lars

last: Kaderali

first: Robert

last: Geffers

first: Yeremia

last: Adhisantoso

first: Jan

last: Voges

first: Jörn

last: Ostermann

first: Gesine

last: Hansen

last: Pietschmann


title: Transcriptome analysis to study expression under desiccation stress of Salmonella enterica subsp. enterica serovar Agona str. 460004 2-1 on low moisture food (cereal)

city: College Park

first: Sultana

last: Solaiman

address: 5001 Campus Drive

institute: US Food and Drug Administration

summary: Salmonella enterica serovar Agona (S. Agona) is a foodborne pathogen that caused recurrent multistate outbreaks associated with cereal between 1998 and 2008, underscoring the endurance of Salmonella over time in low-moisture food (LMF) processing facilities. In this study, we aimed to determine the molecular mechanism of survival of S. Agona in LMF and confirm their impact on phenotype by the knockout study. S. Agona strain (CFSAN 000477), isolated from cereal, was selected for this study. A 100µl suspension with a concentration of ~10^11 cfu/ml was inoculated into 3g of rice cereals. Three replications of inoculated cereals were subjected to desiccation stress (aw ≤ 0.25) for 24h at room temperature (25⁰C). Inoculated cereal samples were collected at 6 timepoints post-inoculation. Cells were separated from the food matrix for RNA extraction. RNA sequencing was performed using the NextSeq 2000 platform. Read counts were generated with Salmon v1.9.0. Downstream analysis was conducted with R and KEGG mapper. There were 1120 differentially expressed genes (DEGs) in S. Agona in response to desiccation stress (Padj < 0.01, |log2FoldChange| >1), with 647 downregulated and 473 upregulated. Functional analysis of downregulated DEGs revealed that most of the genes were associated with metabolic pathways, followed by translation, suggesting slower growth in the surviving population. The top 3 upregulated genes/operons: kdp and ccm operon, and tisB were knocked out and checked for survival study. Approximately 1-2 log reduction (p>0.05) was noticed in the survival of the mutants compared with the wild type. This transcriptome data suggests that Salmonella Agona survives in low-moisture food by conserving energy, lowering metabolism, and reducing replication.

overall_design: RNA sequencing of Salmonella Agona inoculated on cereal at 0-, 0.5-, 1-, 2-, 4- and 24- hour post-drying time points.

first: Ellie

last: Meeks

first: Ian

last: Hines

first: Jie

last: Zheng

first: Maria

last: Hoffmann


title: Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer

city: Nanjing

first: Nignjun

last: Duan

address: 300 Guangzhou Road

institute: JSPH

summary: Primary trastuzumab resistance poses a significant challenge in the treatment of HER2-positive breast cancer. Despite various proposed mechanisms and responses to address this resistance, current treatments remain less effective, highlighting the need for new targets and insights. Our research, which integrates epigenomic and 3D genomic architectural data, suggests that changes in promoter modifications, specifically H3K4me3 and H3K27me3, along with differential active enhancers and promoter-enhancer interactions, may contribute to differential gene expression in trastuzumab-resistant versus sensitive cells. Notably, we identified SGK1, which lies downstream of both the PI3K-AKT and mTOR signaling pathways, exhibits overexpression associated with increased H3K4me3 signals at its promoter and enhanced promoter-enhancer interactions in trastuzumab-resistance cells. The overexpression of SGK1 supports cell survival and stimulates proliferation, making it a potential critical factor driving primary trastuzumab resistance. These discoveries provide new insights into the mechanisms underlying primary trastuzumab resistance in HER2-positive breast cancer, which may pave the way for developing more effective diagnostic and treatment strategies in the future.

overall_design: To investigate the gene expression changes of HER2 positive breast cancer cells during primary trastuzumab resistance formation, we checked the genomic distributions of histone modifications, RNA polymerase II and transcriptional factor from both primary resistant JIMT1 cells and sensitive SKBR3 cells.

first: Duan

last: Ningjun

first: Hua

last: Yijia

first: Zhou

last: Zhengxing

first: Li

last: Wei

first: Yin

last: Yongmei


title: The Medusa Mutant Disrupts Ovule Integument Identity Specification and Female Gametophyte Development in Mimulus nudatus

city: Raleigh

first: Albert

last: Tucci

email: atucci@alumni.unc.edu, atucci@ncsu.edu

state: North Carolina

address: 100 Pillsbury Circle

department: Plant and Microbial Biology

institute: North Carolina State University

summary: Here we identify and characterize a spontaneous mutant allele that disrupts the initiation and specification of the ovule integument in Mimulus nudatus. The mutant phenotype is characterized by the early arrest of the ovule integument or alternatively, the delayed development of a carpel-like structure in place of the integument. Additionally, medusa mutant ovule primordia fail to develop female gametophytic structures.  Morphological analyses indicate that a nucellar domain is specified within the ovule and a megaspore-like cell is often specified, but that cell aborts before generating the female gametophyte. We mapped the position of the mutation to a location on Chromosome1. Mapping revealed a primary candidate gene that was a member of a family of MADS-domain containing transcription factors with sequence similarity to the Arabidopsis BEL1 gene (At5G41410) and is an orthologue of the Mimulus guttatus gene MgTOL.A0789.1. Analysis of the sequence of the Mimulus nudatus homolog (referred hereafter as MnBEL1) locus, revealed the insertion of a mitochondrial DNA genomic fragment within the MnBEL1 locus that segregated with the medusa mutant phenotype. The mitochondrial insertion sequence is predicted to disrupt the coding sequence of MnBEL1.  RNA expression analysis revealed dramatically reduced levels of the expression of the MnBEL1 in gynoecia from medusa mutant plants relative to wild type sisters. RNA seq analysis revealed that the medusa mutant seedpods failed to express MnBEL1 at wildtype levels.  RNA sequence data comparisons between wildtype and medusa mutant seedpods also identified a set of genes, that are expressed in wildtype seedpods, but that are expressed at very low levels or that are not detected in the medusa seed pods. Homologues of many of these genes have been previously shown to be strongly expressed in female gametophyte in Arabidopsis. This RNA seq analysis further indicates a strong developmental disruption and identifies sets of genes with expected roles in female gametophyte development in Mimulus species for further investigation. Our evidence strongly suggests that MnBEL1 is a true functional orthologue of AtBEL1. To the best of our knowledge, these studies provide the first mutational analysis of a BEL1 orthologue outside of Arabidopsis and indicate the functional conservation of this gene between Mimulus and Arabidopsis. This work also presents the first identification of a mutational event in Mimulus that is linked to an insertion of a mitochondrial sequence in the nuclear genome.

overall_design: An inbreed line (form from ≥ 6 generations of self-fertilization) of Mimulus nudatus (GMR2) was grown in a chamber at 18-hour days, 21°C, 30% relative humidity. Mutant plants showing carpeloid ovules were serendipitously discovered among the population and were selected as pollen donors for further genetic crosses with wild-type (Wt) plants for the generation of F1, and F2 plants. Since the carpeloid ovule phenotype is recessive, and it is only manifested in the F2 generation, 150 F2 plants were screened phenotypic- and genotypically to identify heterozygous/homozygous Wt and mutant lines. Because the carpeloid ovules are difficult to detached from the septum, we isolated total RNA as follows: three biological replicates of homozygous Wt and mutant plants were selected for harvesting 6 gynoeciums/plant from opened flowers, and then the valves were removed to collect the ovules attached to the septum. Ovules/septum were immediately collected in cold TRIzol LS (Ambion) for further total RNA isolation. We used the RNeasy Micro Kit (Qiagen) with the following modifications: ovules/septum in cold TRIzol were ground gently with a pellet pestle in a 1.7 mL microcentrifuge tube for 2 min then mixed with 220 uL of chloroform. The solution was then shaken vigorously by hand for 15 s, then incubated for 2 min at room temperature followed by a centrifugation at 12,000g for 15 min at 4 °C to separate phases. Total RNA was isolated according to the manufacturer’s instructions, which includes in column Dnase-I treatment for removal of contaminated DNA. We generated and sequenced a total of 6 RNA sequencing libraries. The RNA integrity number for all samples >7.3, as determined by an Agilent 2100 Bioanalyzer. Six strand-specific complementary DNA (cDNA) libraries were prepared from approximately 100 ng of total RNA by the North Carolina State University Genomic Science Laboratory (GSL) using a NEB Ultra Directional Library Prep Kit for Illumina then sequenced on an Illumina NovaSeq 6000. Average size of the cDNA fragment was approximately 350 bp.

first: Miguel

last: Flores-Vergara

first: Elen

last: Oneal

first: Gabrielle

last: Flanders

middle: C

last: Williams

first: Alessandro

last: Ruiu

last: Franks


title: T cell phenotypes are determinants of outcome in pulmonary arterial hypertension and their alteration by parenteral prostacyclins improves outcomes

city: Nashville

first: Jonathan

last: Kropski

department: Medicine

institute: Vanderbilt University Medical Center

summary: Single-cell RNA-sequencing was performed of 5 pulmonary hypertension lungs removed at the time of lung transplant surgery.

overall_design: 10X Genomics 5' scRNA-seq of fresh single-cell suspensions from PH lungs (n=5) removed at the time of lung transplant. Expression profiles were compared to declined donor controls (from GSE135893 and GSE227136)

first: Anna

last: Hemnes

first: Alexander

last: Linsalata

first: James

last: West


title: Model systems and unique biological features of high and low-grade colorectal cancer (CRC) revealed by xenografting 84 human CRC cell lines

city: Heidelberg

first: John

last: Mariadason

state: VIC

address: 145 Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: Colorectal cancers (CRCs) present across a range of differentiation grades which impacts patient outcome and management, however the molecular features and drivers of differentiation status are not fully understood. To address this, 84 commonly used human CRC cell lines were grown as xenografts in mice, revealing models of low-grade (LG) and high-grade (HG) CRC. Transcriptional profiling revealed coordinate downregulation of multiple transcription factors involved in intestinal development and differentiation, markers of colonic lineage-specific differentiation, and effectors of normal functions of the colonic epithelium. Mechanistically, multiple genes suppressed in HG tumours harbored promoter methylation, indicative of stable epigenetic silencing. Strikingly, markers of LGR5+ colon stem cells were suppressed in HG tumours, while markers of cell proliferation, fetal-like intestinal stem cells, and non-canonical cell types including mesenchymal cells were increased. These changes manifested in HG cell line displaying increased proliferation, migration and metastatic capacity. Importantly, CRC cell line-derived transcriptional profiles of differentiation grade were reflected in LG and HG patient-derived tumour organoids and primary CRCs, revealing cell lines accurately model differentiation grade. The models and tumour differentiation-related properties identified herein may inform new approaches for tailored CRC treatments based on tumour grade.

overall_design: 2 million cells from 8 colorectal cancer cell lines were injected subcutaneously into the flank of eight-week old male Balb/c nu/nu mice  in a 150 μL suspension consisting of a 1:1 mixture of cells resuspended in DMEM-F12 (Invitrogen) and BD Matrigel Basement Matrix (BD Biosciences). When tumours reached 1 cm3  xenografts were harvested and snap frozen. RNA was isolated from each xenograft and quantified using a Qubit 4.0 Fluorometer. Library preparation for RNAseq and next generation sequencing was outsourced to the Australian Genome Research Facility (AGRF).

first: Mariadason

last: John

first: Sieber

last: Oliver

first: Mouradov

last: Dmitri

first: Luk

last: Ian


title: The repairing role of phycocyanin from Spirulina in chronic refractory wound healing and mechanism analysis

city: Wenzhou

first: Jun

last: Ying

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

institute: Wenzhou Medical University

summary: This study aimed to explore the therapeutic potential of cyano-phycocyanin (C-PC) to improve the efficiency of chronic refractory wound healing processes. The hormone induced chronic refractory skin ulcer model were established on the backs of mice. Assessment of wound-healing efficiency of C-PC was evaluated by analyzing total wound closure, recovery percentage and epidermal thickness of wounds. Hematoxylin-eosin, Masson trichrome and immunohistochemical analysis were performed to evaluate the re-epithelialization, inflammatory response, granulation tissue formation and fibrotic tissue formation. Differentially expressed genes were identified through RNA-seq, polymerase chain reaction (PCR) array and confirmed by quantitative PCR (qPCR). Cell viability was determined using a cell counting kit-8 (CCK-8) assay, migration and angiogenesis were detected by wound healing and tube formation assays. The related protein expression was analyzed by Western blot. The results demonstrated a significantly higher wound-healing rate in C-PC group compared to the control group at 3, 7, 14, and 21 days (p< 0.05). The mechanism may involve increased collagen accumulation, promotion of angiogenesis and reduction in the infiltration of inflammatory cells. Additionally, VEGFR-2 was highly likely to be the target for C-PC. Thus, C-PC may hold potential for the treatment of wound healing and ischemic/ reperfusion injuries.

overall_design: RNA-seq analysis of mouse skin tissue treated with C-PC in the early, middle, and late stages of wound healing


first: Nignjun

last: Duan

overall_design:
To investigate the gene expression changes of HER2 positive breast cancer cells during primary trastuzumab resistance formation, we checked the transcriptional data from both primary resistant JIMT1 cells and sensitive SKBR3 cells. The SKBR3 samples were reanalyzed from Series GSE244533.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Duan

last: Ningjun

first: Hua

last: Yijia

first: Zhou

last: Zhengxing

first: Li

last: Wei

last: Yongmei


title: SIRT7 regulates NUCKS1 chromatin binding to elicit metabolic and inflammatory gene expression in senescence and liver aging.

city: Philadelphia

first: Khoa

last: Tran

address: 3400 Civic Blvd

institute: University of Pennsylvania

summary: Sirtuins, a class of highly conserved histone/protein deacetylases, are heavily implicated in senescence and aging. The regulation of sirtuin proteins is tightly controlled both transcriptionally, translationally and via localization within the cell. While Sirtuin proteins are associated with aging, how their levels are regulated during aging across cell types and how they elicit tissue-specific age-related cellular changes are unclear. Here, we demonstrate that SIRT7 is targeted for degradation during senescence and liver aging. To uncover the significance and regulation of SIRT7 loss, we performed proteomics analysis and found that the E3 Ligase TRIP12 reduces SIRT7 levels during senescence. We identified the HMG box transcription factor NUCKS1 as a new SIRT7 interactor. We found that NUCKS1 is recruited onto chromatin during senescence, mediated by SIRT7 loss and accompanied by increased NUCKS1 acetylation. Depletion of NUCKS1 delayed senescence upon DNA damage leading to reduced inflammatory gene expression. Examination of transcriptional regulation by NUCKS1 during senescence revealed target genes of transcription factors NFKB1, RELA, and CEBP—all previously associated with senescence. Consistently, in Sirt7 KO mouse liver and in naturally aged livers, NUCKS1 was recruited to chromatin, bound at promoters and enhancers of age-related genes, including transcription factor Rela, and these bound sites had increased accessibility during aging. Overall, our results uncover NUCKS1 as a novel interactor of SIRT7, showing that proteosomal loss of SIRT7 during senescence and liver aging promotes chromatin binding of acetylated NUCKS1 to induce metabolic and inflammatory genes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Investigate the function of SIRT7 mediated regulation of NUCKS1 in senescence and liver aging. To assess SIRT7 function during liver aging, RNA-sequencing of WT or SIRT7 KO livers was performed on young and aged livers. To determine NUCKS1 role in eliciting senescence associatd gene expression, RNA-sequencing of shRNA targeting control or NUCKS1 was done in proliferating and senescent IMR90 lung fibroblasts.

first: Khoa A

first: Shelley

last: Berger


title: Mycophenolic acid treatment drives the emergence of novel SARS-CoV-2 variants

city: Bochum

first: Richard

middle: JP

last: Brown

state: NRW

address: Universitätsstr. 150

institute: Ruhr University

summary: Mycophenolic acid (MPA) is commonly used in immunosuppressive regimens following solid organ transplantation. We demonstrate that MPA treatment reproducibly inhibits the replication of a range of viruses, including severe respiratory syndrome coronavirus 2 (SARS-CoV-2).xlxs. Mechanistically, we identified cellular guanosine triphosphate pool depletion as a key mediator of this antiviral effect. Strikingly, this inhibition can be overcome which was correlated with the emergence of three breakthrough mutations in the SARS-CoV-2 genome (S P812R, ORF3 Q185H, and E S6L). Subsequent analyses confirmed that the combination of these mutations conferred accelerated replication kinetics, higher viral titres and more rapid onset of cytopathic effects, but not MPA resistance. Comparison of global transcriptional responses to infection highlighted dysregulation of specific cellular gene programs under MPA treatment prior to breakthrough mutation emergence. Together, these findings identify viral and host drivers of variant emergence under immunosuppression. They also advocate for close monitoring of immunosuppressed patients, where emergence of novel viral variants with a fitness advantage may arise.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: SARS-CoV-2 was passaged in untreated or mycophenolic acid treated A549-ACE2-TMPRSS2 (A549-A/T) cells. For selected viral passages (p3, p5, p9, and p15) total RNA of infected A549-A/T cells was isolated. We compared host transcriptional responses in A549-A/T cells infected with SARS-CoV-2.

first: Toni Luise

last: Meister

first: Maximilian K

last: Nocke

first: Richard J

middle: P

first: Daniel

last: Todt

first: Eike

last: Steinmann

first: Stephanie

last: Pfaender


title: The impact of the halogenated phenazine HP-29 on the transcriptome of Streptococcus mutans with or without zinc supplementation

city: Gainesville

first: Jessica

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: We sought to identify transcriptomic changes that arise when S. mutans is cultivated in the presence of HP-29 with or without zinc supplementation. Mid-logarithmic broth cultures of Streptococcus mutans UA159 were exposed to 0.025uM HP-29 or to 0.025uM HP-29 and 0.5mM ZnSO4 for 30 minutes.  We compared this transcriptomic data to that of control cultures that were grown in medium (BHI) without exposure to HP-29 or ZnSO4

overall_design: Cultures of S. mutans UA159 were inoculated in BHI and grown to mid-logarithmic phase (OD600 = 0.4), then split into three tubes: 1) BHI control, 2) 0.025uM HP-29, 3) 0.5mM ZnSO4 + 0.025uM HP-29.  These samples were incubated for an additional 30 minutes, then harvested by centrifugation, and then bacterial pellets resuspended in 1 mL RNA Protect Bacterial Reagent (Qiagen).  Total RNA was isolated and prepared for RNA-Seq analysis.

first: Hannah

last: Hosay

first: Robert

last: Huigens III

first: Jose

last: Lemos


title: Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [smallRNA-Seq]

city: Beijing

first: Han

last: Wang

address: No.5 Yiheyuan Road

institute: Peking University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs, including ta-siRNAs, play crucial roles in various processes in plants. Efforts have been made for decades to elucidate the biogenesis and function of ta-siRNAs. Though the key proteins involved in ta-siRNA biogenesis have been identified, the subcellular localization where ta-siRNAs are processed remains largely unexplored. Remarkably, non-coding TAS transcripts were reported to be bound by ribosomes, the machinery responsible for protein translation. Utilizing edited TAS genes in Arabidopsis, a combination of sRNA-seq, mRNA-seq, RIP-seq, and degradome-seq was employed to investigate the role of ribosomes in ta-siRNA biogenesis in this study. In the two-hit model, deletion of ribosome-binding regions resulted in a decrease in the abundance of intact TAS3 transcripts but did not significantly affect ta-siRNAs production or the efficiency of miRNA-guided cleavage. Conversely, the deletion of ribosome-binding regions led to a significant reduction in ta-siRNA abundance without affecting mRNA levels in the one-hit model. These findings indicate that in the two-hit model, ribosomes primarily stabilize TAS transcripts, while in the one-hit model, they suppress miRNA cleavage but facilitate subsequent processing. Collectively, this study proposes a model that ribosomes play distinct roles in the one-hit and two-hit models of ta-siRNA biogenesis, and provides a new angle to investigate the tangled connection between small RNAs, including miRNA and ta-siRNA, and translation.

overall_design: To explore the role of ribosomes in the ta-siRNA synthesis process of Arabidopsis thaliana and the differences between the one-hit model and the two-hit model, we studied Arabidopsis thaliana WT, tas3a/b/c and tas2-1, tas2-2 ,tas2-3, sRNA-seq and mRNA-seq were performed for tas2-3, and AGO1 RIP-seq was performed for tas3a/b/c and WT, and degradome-seq was performed for WT and tas2-3.

first: Qiming

last: Wen

first: Minglei

last: Zhao

first: Hualong

last: He

first: Jie

last: Cui

first: Chenjiang

last: You


title: Chil3+ immature neutrophils inhibit anti-tumor immunity and impede immune checkpoint blockade therapy in bone metastases [scRNA-seq]

city: 南京

first: shiji

last: ren

address: 南京鼓楼

institute: Nanjing University

summary: Bone metastases remain incurable and respond poorly to immune checkpoint blockade (ICB) therapy. The impact of neutrophil maturation in cancer remains largely unknown, especially in refractory tumors including bone metastases. Here, we observed the predominance of immature neutrophils in the bone metastasis microenvironment of both mouse models and cancer patients. DKK1 induces the immature-like functional state in neutrophils, which exert robust immunosuppressive capabilities to inhibit anti-tumor response of CD8+ T cells. Mechanistically, driven by the DKK1-CKAP4-STAT6 signaling, Chil3 expression is identified and required for the immune suppression mediated by immature neutrophils in bone metastases. Moreover, using multiple syngeneic and human immune system (HIS) mouse models, we found that DKK1 blockade efficiently allows neutrophil maturation to improve the immune microenvironment, controls tumor progression, and enhances ICB therapy response in bone metastases. Thus, our findings uncover an essential role for immature neutrophils in cancer, especially in bone metastases, and propose a potential strategy modulating neutrophils to improve cancer immunotherapy.

overall_design: 4T1 (TNBC model) cells  were injected into the caudal artery (CA) of mice using syringe needles immediately after anesthetization to construct syngeneic bone metastasis models. After CA inoculation of cancer cells, mice were randomized in groups and treated i.p. with  mDKN-01 or IgG2a (Isotype control for mDKN-01). Single-cell suspensions from mouse bone metastasis samples upon termination were isolated. CD45 positive cells were harvested from these tumors by CD45 MicroBeads and used for single cell sequencing analysis.

first: Tao

last: Shi

first: Wei

last: Liu

first: Yuting

last: Luo

first: Kaijie

last: Liang

first: Shiji

last: Ren

first: Taha

last: Merghoub

first: Yan

last: Li

first: Jia

last: Wei


title: Using fish models to understand the role of aryl hydrocarbon receptor (AHR)-interacting protein (AIP) in controlling sensitivity and resistance to dioxin-like compounds in vivo 5dpf

city: Woods Hole

first: Sibel

middle: I

last: Karchner

address: 45 Water St

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Humans are exposed to chemicals such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs) that cause toxicity through activation of the aryl hydrocarbon receptor (AHR). There is inter-individual variation in sensitivity to effects of AHR ligands, but it is not fully explained by variation in the human AHR, suggesting that other components of the AHR pathway are involved in controlling sensitivity. A clue to the genetic mechanisms underlying differential sensitivity to AHR agonists has emerged recently from studies of Atlantic killifish (Fundulus heteroclitus) populations with multi-generational exposure to PCBs, TCDD, and PAHs. Genomic studies of these populations identified the AHR chaperone AHR-interacting protein (AIP/Ara9/XAP2) as the strongest candidate resistance gene. However, the precise role of AIP in the mechanism of resistance is unknown. To understand the role of AIP in the toxicity of dioxin-like compounds and how variation in AIP may affect chemical sensitivity, we CRISPR-Cas9 to generate AIP loss-of-function alleles in killifish and zebrafish (Danio rerio). Homozygous mutant killifish and zebrafish die during larval development, while heterozygous mutants develop normally, survive to adulthood, and reproduce normally. Prior to death, homozygous mutant zebrafish exhibit reduced sensitivity to embryotoxic effects of exposure to 3,3',4,4',5-pentachlorobiphenyl (PCB126) and TCDD. Gene expression profiling of control and PCB126-exposed larvae at 3 days post-fertilization reveals some genes differentially expressed between mutant and wild-type larvae, but the induction of AHR-regulated genes is similar in aip-/-, aip-/+, and aip+/+ larvae. Understanding the role of AIP in controlling sensitivity to AHR agonists in fish models may shed light on the factors that determine differential susceptibility of humans to dioxin-like compounds and on the role of AIP in human disease.

overall_design: RNAseq profiling of 5 dpf zebrafish AIP CRISPR knock-out mutants (aipwh86) exposed to PCB126 (2 nM final concentration) or vehicle DMSO. WD: wildtype-DMSO, WP: wildtype-PCB, HED: Heterozygous-DMSO, HEP: Heterozygous-PCB, HOD: Homozygous-DMSO, HOP: Homozygous-PCB. Four biological replicates of each.

first: Neelakanteswar

last: Aluru

first: Diana

last: Franks

first: Chesna

last: Mandl

first: Jared

last: Goldstone

first: Tara

last: Burke

first: Denise

last: Champlin

first: Jane

last: La Du

first: Dante

last: Perone

first: Spencer

last: Stinson

first: Lisa

last: Truong

first: Bryan

last: Clark

first: Diane

last: Nacci

first: Robyn

last: Tanguay

first: Mark

last: Hahn


title: ELAV mediates circular RNA biogenesis in neurons [RNA-Seq]

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

summary: Circular RNAs (circRNAs) arise from back-splicing of precursor RNAs and accumulate in the nervous system of animals, where they are thought to regulate gene expression and synaptic function. Here, we show that neuronal circRNA biosynthesis is mediated by the pan-neuronal RNA-binding protein ELAV. In Drosophila embryos, we characterize the circRNA landscape in normal and elav mutant neurons. We find that neuronal circRNAs are globally depleted upon ELAV knockout, and induction of ELAV expression drives ectopic RNA circularization. In fly brains, ELAV binds to pre-mRNA introns flanking putative circRNAs and decreases efficiency of linear splicing in favor of intron pairing at reverse complementary matches, inducing circularization. Together, our data demonstrate that ELAV directly modulates splicing decisions to generate the neuronal circRNA landscape.

overall_design: RNA-seq from 18-20 hour old whole embryos from Drosophila melanogaster : 4 replicates of embryos, with (GFP-) Glut1 RCM deletion and control (GFP+), for two different mutations

first: Carlos

last: Alfonso-Gonzalez

first: Mengjin

last: Shi

first: Sakshi

last: Gorey

first: Sarah

last: Holec

first: Judit

last: Carrasco

first: Michael

last: Rauer

first: Stylianos

last: Tsagkris

first: Fernando

last: Mateos


title: Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RNA-Seq]

first: Han

last: Wang

first: Qiming

last: Wen

first: Minglei

last: Zhao

first: Hualong

last: He

first: Jie

last: Cui

first: Chenjiang

last: You


title: Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RIP-Seq]


title: Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana

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

overall_design: Refer to individual Series


title: In Vitro Modeling of Age-Related Methylation Changes with Intestinal Organoids [RNA-Seq]

city: Camden

first: Jean-Pierre

last: Issa

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: Intestinal organoids, three-dimensional cultures from intestinal stem cells, are a powerful model for studying aging, and DNA methylation is an accurate biological clock. Consequently, we hypothesized that organoid DNA methylation could serve as an aging metric and a valuable tool for in vitro aging research. Our initial study revealed significant DNA methylation changes, during organoid culture, with 27% of total CpG sites undergoing hypomethylation, and 11% gaining hypermethylation. Hypomethylation occurred predominantly in aging-associated genomic regions, including non-promoter, non-CpG island regions (e.g., transposable elements), while hypermethylation, in CpG islands, significantly (p < 0.001) correlated with aging. Comparison of aging-methylated sites with differentiation-specific CpG sites showed minimal overlap, indicating negligible association. Early-passage (P0 and P2) organoids, derived from 4- and 24-month-old mice, preserved aging-specific methylation patterns, with a correlation coefficient of 0.48 (p < 0.001) between methylation differences in old versus young primary cells. Conversely, long-term passaging revealed distinct methylation changes, specific to each organoid line. Some early passage organoids exhibited more hypomethylation, clustering with mid-passage (P10 - P13) organoids, while late-passage (P24 and P27) organoids entered a crisis stage with severe hypomethylation, growth arrest, and distant clustering. Transposable elements remained hypomethylated, compared to primary cells. Aging-related methylation sites continued to change with passage, and linear modeling predicted that organoids age at a rate of 0.46 months per week in culture. Treatment with decitabine reversed the methylation age of organoids, derived from 24-month-old mice. These findings suggest that organoids effectively model aging, with further research needed to assess culture-associated influences.

overall_design: Intestinal crypts from 4-month-old and 24-month-old mice were isolated to generate organoids, which were then used for DNA and RNA extraction. These organoids underwent RRBS (Reduced Representation Bisulfite Sequencing) and RNA-seq analysis to investigate age- and passage-related changes in DNA methylation and gene expression. This approach allowed us to assess how aging and extended culturing influence the molecular landscape of the organoids


title: Rps15 mutation drives B cell malignancy through translational rewiring, oxidative stress and genomic instability

city: Boston

first: Catherine

middle: J.

last: Wu

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Ribosomal protein mutations are increasingly associated with cancer risk and thought to perturb ribosome function. At the same time, they reportedly activate p53, a critical anti-cancer barrier. To determine how these mutations overcome this protective block to enable tumorigenesis, we generated an in vivo model of the hotspot Rps15-S138F mutation identified as a putative driver of chronic lymphocytic leukemia. Under pre-leukemic conditions, this mutation induced protein instability, ribosome biogenesis defects and altered translation resulting in oxidative stress, DNA damage and induction of a p53-dependent response that promote initial cellular hypo-proliferation. However, aged mice with mutated Rps15 eventually developed B-cell leukemia (37% penetrance), which exhibited increased Myc activity with strong pro-survival and proliferation signatures. Mutant Rps15 thus induces both hypo- and hyper-proliferative signals, initially weighted towards cell cycle arrest; and that through translational rewiring, oxidative stress, DNA damage response defects and genomic instability set the stage for the acquisition of additional driving mutations, such as TP53 deletion, that can overcome this cell cycle block to trigger tumorigenesis.

overall_design: Paired RNA-seq and ribo-seq profiling of age-matched Rps15-S138F mutant and wildtype mice

last: Gutierrez

first: Marwan

last: Kwok

first: Neil

last: Ruthen


title: Differential response of human plasmacytoid pre-dendritic cells to SARS-CoV-2 variants

city: Paris

first: Okan

last: Ayas

address: 1 avenue Claude Vellefaux

institute: INSERM

summary: SARS-CoV-2 variants have been involved in various waves of the COVID19 pandemic and showed different pathogenicity and inflammatory potential. Whether they can induce different patterns of innate immune activation in antigen-presenting cells is poorly understood. Here, we investigated the ability of primary plasmacytoid pre-dendritic cells (pDC), type 2 dendritic cells (DC2), and monocytes isolated from healthy blood donors to respond to SARS-CoV-2 variants. Transcriptomic profiling using RNA sequencing revealed that pDC respond differentially to SARS-CoV-2 variants, while DC2 and monocytes do not. Functional studies showed that pDC undergo differential activation programs upon SARS-CoV-2 variant stimulation. The Alpha B220/95 and Delta variants induced P1-/P2-pDC effector phenotypes, characterized by strong IFN-α production. On the contrary, BA.1 variant turned pDC into a predominant T cell activating P3 phenotype, with less IFN-α and IFN-λ production, and stronger proinflammatory and CD4+T cell responses. Our results indicate that pDC activation and diversification pattern can be differentially controlled by SARS-CoV-2 variants, which may influence disease severity

overall_design: RNAseq profiling of blood pDCs and DC2s cultured for 20 hours with RNA copies of either SARS-CoV-2 Delta or Omicron BA.1 variant ; In parallel medium alone or TLR7/8 agonist resiquimod (R848) were used as negative and a positive control of pDC activation

first: Daria

last: Kartasheva-Ebertz

first: Dimitrios

last: Topalis

first: Claudia

last: Umana-Diaz

first: Laurine

last: Couture

first: Pierre

last: Tonnerre

first: Jasna

last: Medvedovic

first: Laurent

last: Meertens

first: Vassili

last: Soumelis

first: Ali

last: Amara


title: In Vitro Modeling of Age-Related Methylation Changes with Intestinal Organoids [RRBS]

type: Methylation profiling by high throughput sequencing


title: Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [Degradome-seq]

first: Han

last: Wang

first: Qiming

last: Wen

first: Minglei

last: Zhao

first: Hualong

last: He

last: Cui


title: Expression profiling of mouse testes on postnatal day 5 (P5) with conditional knockout of Mdm2 in pre-meiotic germ cells.

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

summary: To investigate the transcriptomic changes of mouse testes after Mdm2 ablation in pre-meiotic germ cells, we collected Mdm2 sKO and normal control mouse testes on postnatal day 5 (P5) for RNA sequencing.

overall_design: We collected Mdm2 sKO and normal control mouse testes on postnatal day 5 (P5) for RNA sequencing, three replications for every group.

first: Mengcheng

last: Luo

first: Rong

last: Liu

first: Xinnai

last: Yu

first: Dupeng

last: Ma

first: Zhiyi

last: Chen


title: Transcriptional profiling of Wilms tumor via single nuclei RNA sequencing

city: Dallas

first: Keri

last: Drake

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatric Nephrology

institute: UTSW

summary: Wilms tumor, or nephroblastoma, is the most common pediatric kidney cancer, and is known to arise from renal precursor cells in the fetal kidney. Given that single nuclei RNA-sequencing generates gene expression profiles of diverse cell types within a heterogeneous tissue, here we sought to utilize this technology to profile blastema, stroma, and epithelial components of favorable histology Wilms tumor samples.

overall_design: Frozen, unfixed samples were biobanked at the time of surgical resection/nephrectomy. Nuclei isolation was performed for 10x genomics single nuclei RNA-seq, targeting 5000 nuclei with 50K reads/nuclei from each sample.

first: Drake

last: Keri

first: Ma

last: Yanru


title: Antibiotics driven gut microbiome perturbation alters the immune response to the rabies vaccine

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: The gut microbiome plays a crucial role in modulating human immunity. Previously, we found that antibiotic-induced microbiome perturbation affected influenza vaccine responses depending on pre-existing immunity levels. However, its impact on primary responses remains unclear. Here, we employed a systems biology approach to analyze the impact of antibiotic administration on primary and secondary immune responses to the rabies vaccine in humans. Antibiotic administration disrupted the microbiome, reducing gut bacterial load and causing long-lasting reduction in commensal diversity. This alteration was associated with reduced rabies-specific humoral responses. Multi-omics profiling revealed that antibiotic administration induced: 1) an enhanced pro-inflammatory signature early after vaccination, 2)  a shift in the balance of vaccine-specific T-helper 1(Th1) to T-follicular-helper response towards Th1 phenotype, 3) profound alterations in metabolites, particularly in secondary bile acids in blood. By integrating multi-omics datasets, we generated a multi-scale, multi-response network that revealed key regulatory nodes including the microbiota, secondary bile acids, and humoral immunity to vaccination.

overall_design: To determine the impact of antibiotics on the magnitude and kinetics of the transcriptional response, we performed bulk RNA-seq analysis on blood samples collected before and after vaccination.

first: Yupeng

last: Feng

first: bali

last: Pulendran


title: A collagenous extracellular matrix regulates germline gene expression in the sea star embryo

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: The sea star Patiria miniata uses cell-cell signaling mechanisms in the inductive process of germline formation and here we test if these cells require the extracellular matrix (ECM) in this process. The ECM is a network of proteins and long-chain sugar polymers necessary for structural support, cell signaling, and migration. Collagen is a fundamental component of the ECM network that provides tensile strength and structural integrity, in addition to interacting with other proteins such as laminin and integrins.  Here we used b-aminopropionitrile (BAPN), a well-known inhibitor of lysyl oxidase (LOX), an enzyme important for cross-linking mature collagen, a morpholino antisense oligonucleotide to LOX2A, and Col003, an inhibitor of collagen processing to test for a role of the ECM with cells that form the germ line. A DEG-RNA-seq approach was used to broadly test for genes responsive to the ECM at different times in development. A qPCR-based analysis of these resultant candidates show that some ECM responsive genes markedly increase gene expression, including eIF5A1, LvN1.2, ATF3, and the newly described BAPN-Associated Target with Malformed Archenteron (BATMAN), identified here. Furthermore, genes involved in germline formation in this embryo differentially respond to the ECM, including Nanos3, Vasa, PIWI, and the signaling factors BMP2/4, Nodal, and Wnt8. Our results show that disruption of the ECM dysregulates germline gene expression and normal gut morphogenesis during specific development stages. This paradigm adds to a growing list of mechanisms in how primordial germ cells use the ECM in an inductive mode

overall_design: Sea star embryos were treated with BAPN at different time points and at different concentrations. Total RNA was extracted using at least 200 embryos for each sample and sent to Novogene for next-generation bulk RNA sequencing following the manufacturer's instructions. Libraries were sequenced by Novogene in a paired-end stranded fashion.

first: Gerardo

last: Reyes

first: Gary

last: Wessel


title: Using fish models to understand the role of aryl hydrocarbon receptor (AHR)-interacting protein (AIP) in controlling sensitivity and resistance to dioxin-like compounds in vivo

first: Sibel

last: Karchner

overall_design: RNAseq profiling of 3 dpf zebrafish AIP CRISPR knock-out mutants (aipwh239) exposed to PCB126 (10 nM final concentration) or vehicle DMSO. WD: wildtype-DMSO, WP: wildtype-PCB, HED: Heterozygous-DMSO, HEP: Heterozygous-PCB, HOD: Homozygous-DMSO, HOP: Homozygous-PCB. Four biological replicates of each.

first: Neelakanteswar

last: Aluru

first: Diana

last: Franks

first: Chesna

last: Mandl

first: Jared

last: Goldstone

first: Tara

last: Burke

first: Denise

last: Champlin

first: Jane

last: La Du

first: Dante

last: Perone

first: Spencer

last: Stinson

first: Lisa

last: Truong

first: Bryan

last: Clark

first: Diane

last: Nacci

first: Robyn

last: Tanguay

first: Mark

last: Hahn


title: NAT10 in Diabetic Cardiomyopathy in Exercise

first: Haobo

last: Li

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

summary: To investigate the role of NAT10 in diabetic cardiomyopathy in response to exercise, 6-week-old NAT10 floxed mice were fed a high-fat diet (HFD) for 18 weeks followed by low doses of STZ injections, some of the mice were then injected with AAV9-cTnT-Cre to knockout NAT10 in cardiomyocytes. There mice were then subjected to either sedentary or eight weeks of treadmill exercise. We then performed gene expression profiling analysis using data obtained from RNA-seq from RNAs pulldown with an ac4C antibody.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from RNAs pulldown with an ac4C antibody from heart tissues from mice treated with control or NAT10 knockout with exercise.


title: Sarcospan selectively interfaces with sarcoglycan subunits to stabilize the sarcolemma and prevent limb-girdle muscular dystrophy

city: Los Angeles

first: Daniel

last: Helzer

address: 610 Charles E. Young Drive East

institute: University of California, Los Angeles

summary: Gene duplication events provide redundancy to complex organisms, and homologous genes and their encoded proteins are potential replacements to treat loss-of-function genetic syndromes.  Skeletal muscle possesses redundant molecular mechanisms that partially or fully compensate for loss of gene function.  Within the dystrophin-glycoprotein complex (DGC), utrophin is known to substitute for dystrophin.  However, there has been little investigation of the orthologous relationships within the sarcoglycan subcomplex of the DGC.  In skeletal muscle, the sarcoglycan complex canonically consists of alpha-, beta-, gamma- and delta-subunits, with gamma- and delta-sarcoglycan showing the greatest homology but no functional redundancy.  We show that sarcospan, a transmembrane scaffolding protein, mediates assembly of a compensatory DGC with gamma-sarcoglycan replacement by zeta-sarcoglycan.  This alternative complex improved pathology ingamma-sarcoglycan muscular dystrophy, but not alpha- or beta-sarcoglycan muscular dystrophy where sarcospan was unable to form compensatory complexes.  Three-dimensional modeling of the compensatory DGC reveals that zeta-sarcoglycan maintains specific hydrophobic interactions with sarcospan and preserves overall quaternary arrangement.  This compensatory DGC protects the cell membrane from contraction-induced damage and all secondary consequences of disease.  These findings demonstrate a novel mechanism stabilizing the DGC by leveraging protein redundancy, with an important role for sarcospan in assembly and scaffolding of a compensatory DGC.

overall_design:
Quadriceps muscles form wildtype, Sgcg (gamma-sarcoglycan deficient), and SgcgTG (gamma-sarcoglycan deficient witih trangenic sarcospan expression) mice were scap frozen in liquid nitrogen (n = 1 female mouse per genotype). 7-AAD+ nuclei were isolated from snap frozen muscle by FACS and submitted for  RNA sequencing using the 10x genomics platform.

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title: Epithelial Transcription Factor Elf3 mediates host immune responses to microbiota and protects against aerocystitis in zebrafish

city: Durham

first: John

middle: F

last: Rawls

address: 213 Research Drive

institute: Duke University School of Medicine

summary: We identified Elf3 as a conserved microbially responsive transcription factor and generated an elf3 mutant  zebrafish allele to test whether it mediates host responses to microbes. We performed bulk RNA-sequencing of elf3 wildtype and mutant larvae reared without (germ-free) or with (conventionalized) the presence of microbes. We found that elf3 does mediate host-microbiota interactions in zebrafish and has an important role in the induction of many immune responsive genes.

overall_design: RNA-profiling of elf3 wildtype and mutant 6 days post-fertilization (dpf) zebrafish larvae reared in germ-free (GF) and conventionalized (CV) conditions

first: Briana

middle: R

last: Davis

first: Colin

last: Lickwar


title: Male germ cells-specific deletion of eukaryotic translation initiation factor 5 causes apoptosis of mouse progenitor spermatogonia by DNA repair defects and sustained endoplasmic reticulum stress [ Ribo-Seq]

city: China

first: hongwei

last: Wei

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

summary: Eukaryotic translation initiation factor 5 (eIF5) promotes protein translation by regulating the ternary complex (TC) of eIF2•GTP•Met-tRNAi. A previous study showed that eIF5 is closely associated with testicular germ cell tumors (TGCTs). However, the role of eIF5 in mouse spermatogenesis remains unclear. Our study found that eIF5 is highly expressed in the cytoplasm of germ cells compared to other cells in the mouse testis. To explore the role and mechanism of eIF5 in mouse spermatogenesis, we generated Eif5 conditional knockout mice by crossing Eif5fl/fl mice with Stra8-Cre mice. The deletion of Eif5 in male germ cells caused a reduction of progenitor spermatogonia and differentiating spermatogonia, eventually leading to the failure of meiosis initiation and male infertility. Further investigations demonstrated that the deletion of Eif5 in progenitor spermatogonia led to decreased cell proliferation, increased ROS level, DNA damage and apoptosis. These observed phenotypes can be attributed to decreased protein translation efficiency in DNA repair, ubiquitination, autophagy-related genes, and increased protein translation efficiency of endoplasmic reticulum stress-related genes. These findings underscore the indispensable role of eIF5 in the proliferation and differentiation of mouse progenitor spermatogonia.

overall_design: To determine whether eIF5 plays a crucial role in spermatogenesis, we generated germ cell conditional Eif5 knockout mice by crossing Eif5fl/fl mice with Stra8-Cre mice.


title: Male germ cells-specific deletion of eukaryotic translation initiation factor 5 causes apoptosis of mouse progenitor spermatogonia by DNA repair defects and sustained endoplasmic reticulum stress


title: CeRNA Microarray-Based Identification of Specific LncRNA Markers in Severe Tuberculosis for Early Diagnosis

first: Siyu

last: Yao

address: Tongzhou District, No.9 Beiguan Street, Yard 1

institute: Beijing Chest Hospital Affiliated toCapital Medical University

summary: Tuberculosis (TB) is still one of the leading causes of death from a single infectious agent in the world.The progression of tuberculosis to severe disease is the main cause of death of tuberculosis patients. Early identification of severe tuberculosis is very important. LncRNA can be used as a potential marker in the diagnosis of tuberculosis, but there is a lack of research on lncRNA in the field of severe tuberculosis.This study aims to use CeRNA Microarray analysis to identify specific lncRNAs as potential biomarkers for severe tuberculosis diagnosis.

overall_design: Genome-wide lncRNA profiling of peripheral blood mononuclear cells (PBMCs) from severe tuberculosis (STB) patients, mild tuberculosis patients (MTB), and healthy controls (HCs) was conducted using the Agilent microarray technique. STB:8 samples;MTB:12 samples;HC:10 samples

first: Xiuxiu

last: Ji

first: Ruize

last: Wang

first: Liping

last: Pan

first: Qiuyue

last: Liu


city: Fukuoka

first: Shota

last: Inoue

address: 744 Motooka Nishi-ku Fukuoka

department: Graduate School of Systems Life Sciences

country: Japan

institute: Kyushu University

summary:
Previously, we reported that mammalian cells, specifically human dermal fibroblasts (HDFs), could be transdifferentiated by lactic acid bacteria (LAB). Later, we observed that HDFs incorporated LAB-derived ribosomes, forming the ribosome-induced cell clusters (RICs) and transdifferentiating into cells derived from all three germ layers. Based on this insight, we hypothesized that incorporating ribosomes into non-mammalian cells could reveal the universality of this mechanism and open the door to commercial applications. Our current study demonstrates that ribosome incorporation can transdifferentiate chick primary muscle-derived cells (CMCs) into adipocytes, osteoblasts, and chondrocytes. Furthermore, the culture medium supernatant from ribosome-incorporated CMCs was found to significantly enhance CMCs proliferation. RNA-seq analysis revealed that RICs-CMC exhibit increased expression of genes related to multi-lineage cell growth. In addition, we developed a novel technological shift in meat production—the "CulNet System"—which replicates organ interactions within mechanical systems for cell-cultured meat production. While significant efforts are still required to implement this technology in a cost-effective manner, we believe that combining the "CulNet System" with ribosome-incorporated multipotent cells that have prolonged culture capability could substantially improve the scalability and cost-effectiveness of cultured chicken meat production. This report highlights a promising approach for cell-culture-based meat production, offering a sustainable alternative to traditional methods.

Type of manuscript: Article
Title: Ribosome incorporation transdifferentiates chick primary cells and
induces their proliferation by secreting growth factors
Authors: Shota Inoue, Arif Istiaq, Anamika Datta, Mengxue Lu, Shintaro
Nakayama, Kousei Takashi, Nobushige Nakajo, Shigehiko Tamura, Ikko Kawashima, Kunimasa Ohta
Journal: Journal of Developmental Biology
issue and page numbers: Volume 13, Issue 2,19
DOI: 10.3390/jdb13020019

overall_design: RNA-seq profiling of wildtype Chicken primary Muscle-derived Cells (CMCs) and ribosomes incoporated CMCs (RICs-CMC) at Day 14 in stem cell medium (ESGRO).

first: Arif

last: Istiaq

first: Anamika

last: Datta

first: Mengxue

last: Lu

first: Shintaro

last: Nakayama

first: Kosei

last: Takashi

first: Nobushige

last: Nakajo

first: Shigehiko

last: Tamura

first: Ikko

last: Kawashima

first: Kunimasa

last: Ohta


title: ParBF DNA binding profiles from variants of the CTP binding motif

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

institute: CNRS

summary: We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli, investigates the impact of mutations in the CTP binding motif BoxIII on ParBF DNA binding profiles in vivo. We found that ParBF-N153A allele binds to parS as WT but is impaired in clamp formation thus abolishing the long distance DNA binding on parS-proximal DNA. By contrast, ParBF-R156A DNA binding profile reveals that it binds to parS, converts to clamps that diffuse over several Kb and unbinds non-specific DNA in a similar way as WT. However, the reduction in ParB binding at proximity of parS revealed that ParBF-R156A is impaired in ParB-ParB interaction, thus preventing the assembly of ParB condensates.

overall_design: Chromatin immunoprecipitation DNA-sequencing for ParB of plasmid F (ParBF) in Escherichia coli. Biological replicates are labelled IP1 and IP2. Anti ParBF antibody is affinity purified before used.

first: Perrine

last: Revoil

first: Jerome

last: Rech

first: Delphine

last: Labourdette

first: Hicham

last: Sekkouri Alaoui


title: GmMEKK2 enhanced mosaic virus resistance in soybean (Glycine max L.)

city: Hangzhou

first: Xuanbo

last: Zhong

address: 866 Yuhangtang Road

institute: Zhejiang university

summary: Mitogen-activated protein kinase kinase kinase (MAPKKK) assume a pivotal position within the MAPK cascade signaling pathway that converts external stimuli into intracellular responses, and plays a central role in adaptation and resistance to biotic and abiotic stress. Only a limited number of researches have reported that MAPKKK conducted on regulating the resistance to soybeans mosaic viruses (SMV). Here, we identified a MAPKKK 2-like gene named as GmMEKK2 from SMV resistance cultivar. Overexpression of GmMEKK2 in soybean not only reduced SMV content but also decreased the disease index of virus. Importantly, overexpression of GmMEKK2 mitigated the yield loss after SMV inoculation and improved the yield-related traits of soybean. These demonstrated that GmMEKK2 had a favorable role in SMV resistance. This study explored the functions of GmMEKK2 in soybean and provided an assertive solution for effectively improving SMV resistance.

overall_design: The top trifoliate leaves of wildtype and the GmMEKK2 overexpression line at 7 dpi and 14 dpi SMV were sampled, and the leaves before inoculation were used as controls.

first: Guixiang

last: Tang


title: Defining pathogenic IL-17 and CSF-1 gene expression signatures in chronic graft-versus-host disease [IL-17]

city: Seattle

first: Julie

last: Boiko

state: Washington

address: 1101 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Chronic graft-versus-host disease (cGVHD) remains the leading cause of non-relapse morbidity and mortality after allogeneic hematopoietic cell transplantation (HCT). Effective therapeutics agents targeting dysregulated cytokines including IL-17 and CSF-1 have been defined in preclinical models of cGVHD, and efficacy in subsequent clinical trials has led to their recent FDA approval. Despite this, these agents are effective in only a subset of patients, expensive, difficult to access outside the US, and used in a trial-and-error fashion. The ability to readily discern druggable, dysregulated immunity in these patients is desperately needed to facilitate the selection of appropriate treatment and to potentially identify high-risk individuals for preemptive therapy. We used single cell sequencing-based approaches in our informative preclinical cGVHD models to “reverse engineer” temporal IL-17 and CSF-1 signatures in mouse blood that could be used to interrogate patients. We defined distinct, non-intuitive IL-17 and CSF-1 signatures in mouse blood monocytes that could be identified in relevant monocytes within 70% of patients at diagnosis of cGVHD and in half of patients at day +100 post-HCT who subsequently developed cGVHD. These signatures can now be evaluated prospectively in clinical studies to help delineate potential responder and non-responders to relevant therapeutics targeting these pathways.

overall_design: scRNAseq profiling of peripheral blood in a graft-versus-host disease model of mice transplanted with WT vs IL17A KO vs IL17RC KO donors' bone marrow + T cells, as well as mice transplanted with WT donor T cell depleted bone marrow only. Timepoints are serially collected from the same mice at days 14, 21, and 28 days post-transplant, with four mice per group.


title: Defining pathogenic IL-17 and CSF-1 gene expression signatures in chronic graft-versus-host disease [CSF-1]

overall_design: scRNAseq profiling of peripheral blood in a graft-versus-host disease model of mice transplanted with donors' bone marrow + T cells, as well as mice transplanted with WT donor T cell depleted bone marrow only. Mice receiving T cells + bone marrow received M279 antibody or antibody isotype control starting at day +7 post-transplant and continuing three times weekly through the end of the experiment. Timepoints are serially collected from the same mice at days 14, 21, and 28 days post-transplant, with four mice per group.


title: CD157+ vascular endothelial cells derived from human induced pluripotent stem cells have high angiogenic potential

city: Suita-shi

first: Yukika

last: Tanabe

state: Osaka

address: 3-1 Yamada-ok

institute: Research Institute for Microbial Diseases, Osaka University

summary: We previously reported that a vascular endothelial stem cell population resides in pre-existing blood vessels in mice and may contribute to vascular endothelial cells in liver injury or hind limb ischemia models in the long-term. However, whether such stem cells exist in humans and can differentiate specifically into vascular endothelial cells have not been determined. We hypothesized that CD157+ vascular endothelial cells in humans may also possess high angiogenic potential.  First, human-derived induced pluripotent stem cells were differentiated into vascular endothelial cells, and the expression of CD157 was monitored during the differentiation process. We found that CD157 emerged 11 days after the induction of differentiation, peaked at 14 days, and then declined by 24 days. WNext, we also evaluated blood vessel formation by 14- and 24-day-old vascular endothelial cells.It was found that 14-day-old cells, when CD157 expression was at its peak, formed more blood vessels than 24-day-old cells.These results suggest that vascular endothelial cells expressing CD157 have high angiogenic potential and may exist as vascular endothelial stem cells.

overall_design: iPS cells

first: Ami

last: Takii


title: Defining pathogenic IL-17 and CSF-1 gene expression signatures in chronic graft-versus-host disease [Naïve]

overall_design: scRNAseq profiling of peripheral blood in WT and IL-17RC KO B6 mice, with three mice per group.