title: Deep longitudinal immune profiling reveals reprogramming of memory T cells that links to B cell dysregulation with age.

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Immune aging is a dynamic process shaped by time and external perturbation. Here, we sought to untangle the complexity of the healthy human immunity across age using deep molecular profiling. Applying our new Healthy Immune Cell Atlas, we profiled the transcriptional dynamics of peripheral immune cells in a longitudinal cohort of ~100 healthy young and older adults followed over 2 years, both under homeostasis and perturbation induced by vaccination, building a scRNA-seq dataset of more than 13.5 million PBMCs. From these data, we revealed that T cells exhibit substantially more age-related changes in transcription at homeostasis than other immune cell subsets, which persist both over time and across age and are distinct from those associated with biological sex or CMV infection status. B cells, which demonstrated few age-related differences at homeostasis, had numerous and persistent changes in vaccine-induced responses with age linked to an age- and GATA3-related transcriptional skewing in the central memory CD4 T cell compartment of older adults. Our study collectively highlights that gradual, age-related alterations in the homeostatic transcriptional networks in immune cells leads to shifts in the landscape of immune responsiveness as we age. This rich resource is further provided with data exploration tools at https://explore.allenimmunology.org/.

overall_design: A cohort of healthy participants aged 40-89+ was recruited for this study in the greater Palo Alto, CA area. A subset of 235 donors was selected from a larger pool of 800+ donors to represent our confirmatory cohort. This sample subset comprises 136 female and 98 male donors spanning ages 40-89+. The ethnicities of the donors include 132 Caucasians, 49 Asians, 12 African Americans, 4 American Indians, 2 Pacific Islanders, and 35 others. The population distribution was selected to be representative of Palo Alto, CA. Blood was collected from all participants at a single time point and PBMCs were isolated. PBMCs were assayed using the 10x flex scRNA-seq chemistry.

first: Qiuyu

last: Gong

first: Emma

middle: L

last: Kuan

first: Mehul

last: Sharma

first: Marla

last: Glass

first: Aishwarya

last: Chander

first: Mansi

last: Singh

first: Lucas

last: Graybuck

first: Zachary

last: Thomson

first: Christian

last: LaFrance

first: Samir

last: Zaim

first: Tao

last: Peng

first: Lauren

middle: Y

last: Okada

first: Palak

last: Genge

first: Cate

last: Speake

first: Thomas

middle: F

last: Bumol

first: Ananda

middle: W

last: Goldrath

first: Troy

last: Torgerson

first: Xiao-jun

last: Li

first: Peter

last: Skene

first: Jane

last: Buckner

first: Claire

last: Gustafson


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells [ChIC-ChIP]

status: Public on Sep 12 2025

city: Baltimore

first: Daniel

last: Ringwalt

state: MD

address: 3400N Charles St

department: Biology

country: USA

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Among the many factors influencing cell fate, epigenetic mechanisms, like histones, play a crucial role in regulating genomic programs like gene transcription and DNA replication, which are integral to a cell’s identity. However, the transcriptional, chromatin, and DNA replication timing profiles of stem cells within in vivo tissues remain poorly understood. The Drosophila testis serves as an excellent in vivo model for studying stem cells, as it contains two stem cell populations: the germline stem cells (GSC) and somatic cyst stem cells (CySC). Despite this, a comprehensive understanding of genome regulation in these cell types has been limited by the small number of stem cells and heterogeneity of the testis. In this study, we developed cell-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing profiles of GSCs and CySCs. Our single cell RNA-sequencing validated previous cell-biological and genetic studies on the role of intercellular communication between GSCs and CySCs while revealing high expression of chromatin regulators in GSCs. To characterize chromatin landscapes, we developed a cell-specific chromatin profiling assay to map H3K4me3, H3K27me3, and H3K9me3. These posttranslational modifications define euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determined the cell-specific replication timing profiles of GSCs and CySCs, integrating our in vivo datasets with published in vitro data. Our results reveal that the replication program of GSCs is distinct from somatic lineages and that these differences align with variations in chromatin patterns. Collectively, our integrated genomic datasets build a framework for understanding genome-wide regulatory differences in two in vivo stem cell populations, demonstrating the power of combining transcriptomic, chromatin, and replication datasets to uncover cell-specific features of genome regulation.

overall_design: Drosophila melanogaster testis tumors were produced by overexpressing the Unpaired (Upd) ligand via two genetic strategies. Upd was either overexpressed using the germline-specific nanos promoter or cyst cell-specific traffic jam promoter. From each genetic strategy, approximately 18-20 testis pairs were dissected and dissociated to create a single cell suspension. Replicates of each genetic type (combined samples of Input and Immunoprecipitation per histone modification) were proccessed for cell-specific sequential Chromatin Immunocleavage - Chromatin Immunoprecipitation (ChIC-ChIP).

first: Jennifer

middle: A

last: Urban

first: John

middle: M

first: Wingel

last: Xue

first: Ryan

last: Gleason

first: Keji

last: Zhao

first: Xin

last: Chen


title: Early cytokine and chemokine signals shape the anti-AML activity of bispecific engager-secreting T cells

first: Natalie

last: Holl

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Immunotherapies, including cell therapies, are effective anti-cancer agents. However, cellular product persistence can be limiting with short functional duration of activity contributing to disease relapse. A variety of manufacturing protocols are used to generate therapeutic engineered T-cells; these differ in techniques used for T-cell isolation, activation, genetic modification, and other methodology. We sought to determine how preselection affected the phenotype of T cells engineered to secrete a CD123xCD3 bispecific engager (ENG-T). These cells were designed to treat acute myeloid leukemia (AML). We evaluated the effect of T-cell selection on transduction efficiency, T-cell activation, short- and long-term anti-AML cytotoxicity, and gene transcription. Unselected, CD4, CD8, and CD4/CD8 pre-selected ENG-T cells have minor differences in T-cell subset components, equivalent activation, and equal cytotoxicity in short-term assays. While unselected and CD4/CD8-selected ENG-T cells have identical CD4:CD8 composition prior to target cell exposure, serial stimulation in vitro showed CD4/CD8 pre-selection supports ENG-T cell survival and long-term activity. Likewise, CD4 and CD4/CD8 pre-selected ENG-T cells display superior anti-tumor efficacy and prolong murine survival in AML xenografts. Unselected ENG-T cells are exposed to cytokines during early manufacture that imprint upregulation of intracellular inflammatory pathways. This early activation likely underpins long-term observed functional differences. Pre-selection of T cells from banked patient biospecimens decreased blast contamination, exposure to inflammatory cytokines, and may improve T-cell expansion during manufacture. Pre-selection of T-cell products should continue to be performed to enhance the quality of clinical cellular therapeutics.

overall_design: Bulk RNAseq was performed on T cells engineered to secrete a bispecific engager molecule. Engineered T cells were manufactured either from CD4/CD8-selected starting material or directly from whole peripheral blood mononuclear cells. Cells from 3 healthy donors were expanded and frozen on day 7 after activation for processing.

middle: J

first: Adam

last: Fearnow

first: Ilias

last: Christodoulou

first: Stamatia

middle: C

last: Vorri

first: Ruyan

last: Rahnama

first: Jun

last: Choe

first: Alokesh

last: Ghosal

first: Weng-Ian

last: Ng

first: Hannah

last: Song

first: Ravi

last: Varadhan

first: Vinay

last: Vyas

first: Challice

last: Bonifant


title: Differential gene expression between wild type (Col 0) and mutants (Atplh1, Atplh2, Atplh3)

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

summary: RNA sequencing of Arabidopsis 10 day old wild type and mutant seedlings (grown on MS media with and without ABA, NaCl for 5 days) using Illumina platform. Differential gene expression between wild type and mutants along with the effect of ABA and NaCl on gene expression was studied.

overall_design: Total RNA was extracted from all the samples using TRIzol followed by DNase1 treatment and purification. Sequencing was performed on Illumina HiSeq platform to generate 150bp long reads in paired-end mode. Adapter contamination and low-quality reads were removed using NGS QC Toolkit (v2.3.3). High-quality filtered reads were mapped on Arabidopsis reference genome using HISAT2. Differentially expressed genes were then identified using StringTie and cuffdiff.

first: Himanshi

last: Sharma


title: Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals

city: Seattle

first: Allen Institute

last: For Immunology

summary: Rheumatoid Arthritis is a chronic immune-mediated disease characterized by joint inflammation, autoantibodies, and systemic inflammatory features. Autoantibodies, including anti-citrullinated protein antibodies are highly predictive biomarkers that pre-date clinical disease and can be used to identify individuals “at-risk” for RA. We performed a prospective, longitudinal multi omic study of at-risk individuals at multiple timepoints to characterize their immune state. One-third of patients progressed to clinically active RA during the study. We show that at-risk RA subjects have systemic inflammation with features like those observed in active RA despite having no clinical disease. Progression to active disease was especially apparent in the T and B cells compartments, with pro-pathogenic features recognized in naive cells. We identify key molecular and cellular alterations in innate and adaptive immunity that accompany this inflammatory state.

overall_design:
A prospective, longitudinal study of individuals at-risk for RA was performed to define molecular and cellular changes that contribute to the development and onset of rheumatoid arthritis (RA). We enrolled 45 subjects with elevated anti-citrullinated protein antibodies (ACPA) but no clinical signs of arthritis and followed them up to 3 years post-enrollment. Peripheral blood and metadata were collected 2-3 times per year and at the time of onset of clinical RA. During the study, 16 subjects progressed to clinical RA and were diagnosed with inflammatory arthritis (IA) by a rheumatologist . For comparison, 38 site-matched ACPA- healthy controls (CON1) and 11 site-matched ACPA+ early RA patients (ERA), within 1 year of clinical diagnosis and naive to biological and targeted synthetic disease modifying anti-rheumatic drugs (DMARDs), were enrolled.

*_ARI: At Risk Individual Sample
*_LONG: Longitudinal At Risk Sample
*_ERA: Early RA Sample
*_CON1: ACPA -ve Control Sample
*_CON2: Healthy Controls

***Submitters state that raw data is subject to controlled access and thus will be submitted to dbGaP***

middle: K

last: Savage

first: Alexander

middle: T

last: Heubeck

first: Ananda

last: Goldrath

first: Blessing

last: Musgrove

first: Cara

last: Lord

first: Charles

middle: R

last: Roll

first: Christian

last: LaFrance

first: Christy

middle: E

last: Bennett

first: Claire

last: Gustafson

first: Cole

middle: G

last: Phalen

first: Elisabeth

last: Dornisch

first: Elliott

last: Swanson

first: Emma

last: Kuan

first: Erin

last: Kawelo

first: Jessica

last: Garber

first: Julian

last: Reading

first: Kevin

last: Lee

first: Lauren

last: Okada

first: Lucas

last: Graybuck

first: Lynne

last: Becker

first: Mark

last: Gillespie

first: Marla

last: Glass

first: Morgan

middle: D

last: Weiss

first: Nhung

last: Tran

first: Padmapriyadarshini

last: Ravisankar

first: Palak

last: Genge

first: Peter

last: Skene

first: Pravina

last: Venkatesan

first: Qiuyu

last: Gong

first: Regina

last: Mettey

first: Samir

last: Zaim

first: Tao

last: Peng

first: Thomas

last: Bumol

first: Troy


title: Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens [scRNA-seq]

city: Pamplona

first: Laura

last: Pilar Aguado Alvaro

address: Av. de Pío XII, 55

country: Spain

institute: Center for Applied Medical Research (CIMA)- University of Navarra

summary: Cardiac fibrosis is mediated by the persistent activity of myofibroblasts, which differentiate from resident cardiac fibroblasts in response to tissue damage and stress signals. The signaling pathways and transcription factors regulating fibrotic transformation have been thoroughly studied. By contrast, the roles of chromatin factors in fibroblast differentiation and their contribution to pathogenic cardiac fibrosis remain poorly understood. Here, we have combined bulk and single-cell CRISPR screens to characterize the roles of chromatin factors inex vivofibroblast differentiation. We uncover strong regulators of fibrotic states including Srcap and Tip60 chromatin remodelers, the NSL complex and the co-factors Hcfc1 and Wdr82. We confirm these factors are required for cellular processes underlying fibrosis including collagen synthesis and cell contractility. We use epigenetic profiling to demonstrate these chromatin factors facilitate the activity of pro-fibrotic transcription factors. Finally, using chemical perturbation in primary human cardiac fibroblasts we suggest Tip60 inhibition as a potential therapeutic approach for cardiac fibrosis.

overall_design: Primary Cas9 cardiac fibroblasts transduced with Lentiviral-CRISPR library containing sgRNAs targeting specific Chromatin factors were isolated by Fluorescence-activated cell sorting (FACS) according to the presence Cas9 (GFP signal) and sgRNA (BFP signal) and analyzed using Single-Cell 3' (Dual Index) with CRISPR Feature Barcode

middle: P

last: Alvaro

first: Nerea

last: Garitano

first: Wolfgang

last: Esser-Skala

first: Judy

last: Sayers

first: Cynthia

last: del Valle

first: Daniel

last: Alameda

first: Julen

last: Mendieta-Esteban

first: Maria

last: Cervantes

first: Ainhoa

last: Goñi-Salaverri

first: Jon

last: Zazpe

first: Anna

last: de Vito

first: Francesco

last: Marchese

first: Diego

last: Alignani

first: Juliana

last: Cudini

first: Torsten

last: Gross

first: Gregorio

last: Rábago

first: Nisha

last: Narayan

last: Martinez

first: Sonia

first: Arantxa

last: Miqueo

first: Brian

last: Huntly

first: Paul

last: Riley

first: Nikolaus

last: Fortelny

first: Jake

last: Taylor-King

first: Beatriz

last: Pelacho

first: David

last: Lara-Astiaso


title: Deiodinase type-3 establishes the period of circannual interval timing in mammals

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

country: United Kingdom

institute: University of Glasgow

summary: Animals respond to environmental cues to time phenological events, but the intrinsic mechanism of circannual timing remains elusive. We used advanced transcriptomic sequencing and high frequency resolution during the initiation, maintenance and recovery of circannual timing for Siberian hamster energy balance to delineate the molecular architecture of a neuroendocrine seasonal clock. Three distinct phases of transcript changes were identified, and deiodinase type-3 (Dio3) expression was activated during the initiation phase. Targeted mutation of Dio3 resulted in a shortening of the circannual interval timer period. Hamsters that exhibit a form of naturally occurring disruption in Dio3 eliminated circannual interval timing. Our work demonstrates that the evolutionary conserved changes in hypothalamic tanycytes expression of Dio3 is critical for timing seasonal life history traits in chordates.

overall_design: To investigate molecular changes occuring in the distinct regions of the hypothalamus. Siberian hamsters were held in long days (LD) or short days (SD) for up to 32-weeks. At 4-week intervals, animals were sacrificed and the piutiary and hpyothalamic nuclei were dissected. Microdissections were homogenised and RNA was extracted using the RNEasy plus mini kit. following this transcript abundance was assesed using the cDNA-PCR sequencing kit (SQK-PCB109, Oxford Nanopore).

first: Callum

first: Tyler

last: Stevenson


title: Specific oncogenic drivers differently shaped the composition and functional diversity of immune cells in the microenvironment of experimental gliomas

city: Warsaw

first: Karol

last: Jacek

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: We performed spatial transcriptomics to profile spatial localization and intercations of cell populations within GL261 glioma mouse model.

overall_design: Two healthy (sham operated) and two GL261 bearing hemispheres from C57BL/6 male mice were used for the analysis using 10X Visium Spatial Transcriptionics kit.

first: Anna

last: Lenkiewicz

first: Salwador

last: Cyranowski

first: Aleksandra

last: Ellert-Miklaszewska

first: Mitrajit

last: Ghosh

first: Szymon

last: Baluszek

first: Paulina

last: Pilnac

last: Szadkowska

first: Zuzanna

last: Łuczak-Sobotkowska

first: Iwona

last: Ciechmoska

first: Bartłomiej

last: Gielniewski

first: Paweł

last: Segit

first: Maria

last: Castro

first: Bozena

last: Kaminska


title: Deep longitudinal immune profiling reveals reprogramming of memory T cells that links to B cell dysregulation with age

first: Allen Institute

last: For Immunology

overall_design:
The SoundLife cohort comprised of healthy young adults aged 25–35 years old and older adults aged 55–65 years old were recruited from the greater Seattle, WA area. Longitudinal visits were collected from these subjects prior to (Day 0) and following seasonal influenza vaccination (Day 7, Day 90) for two years. An additional Immune Variation series was collected over the course of 3 months (Day 0, 7, 90) and served as a baseline comparison of no vaccination/perturbation. A single stand-alone blood draw was also collected from these participants over the course of the two year study. Blood was drawn and PBMCs were isolated. PBMCs were assayed for flow cytometry and 10x 3' scRNA-seq (v3.1).

***************************************************************
Submitter states that missing raw data are being made available for controlled access in dbGaP.
***************************************************************

first: Qiuyu

last: Gong

first: Emma

last: Kuan

first: Mehul

last: Sharma

first: Marla

last: Glass

first: Aishwarya

last: Chander

first: Mansi

last: Singh

first: Lucas

last: Graybuck

first: Zachary

last: Thomson

first: Christian

last: LaFrance

first: Samir

last: Zaim

first: Tao

last: Peng

first: Lauren

last: Okada

first: Palak

last: Genge

first: Cate

last: Speake

first: Thomas

last: Bumol

first: Ananda

last: Goldrath

first: Troy

last: Torgerson

first: Xiao-jun

last: Li

first: Peter

last: Skene

first: Jane

middle: H

last: Buckner

first: Claire

last: Gustafson


title: Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (ChIP-Seq)

first: Laura

last: Pilar Aguado Alvaro

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variant H2Az-acetylated in primary cardiac fibroblasts unstimulated and stimulated with TGFb

last: Aguado Alvaro

first: Nerea

last: Garitano

first: Wolfgang

last: Esser-Skala

first: Judy

last: Sayers

first: Cynthia

last: del Valle

first: Daniel

last: Alameda

first: Julen

last: Mendieta-Esteban

first: Maria

last: Calleja Cervantes

first: Ainhoa

last: Goñi-Salaverri

first: Jon

last: Zazpe

first: Anna

last: Rosaria de Vito

first: Francesco

last: Marchese

first: Diego

last: Alignani

first: Juliana

last: Cudini

first: Torsten

last: Gross

first: Gregorio

last: Rábago

first: Nisha

last: Narayan

last: Martinez

first: Sonia

first: Arantxa

last: Gonzalez Miqueo

first: Brian

last: Huntly

first: Paul

last: Riley

first: Nikolaus

last: Fortelny

first: Jake

last: Taylor-King

first: Beatriz

last: Pelacho

first: David

last: Lara-Astiaso


title: Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens

first: Laura

last: Pilar Aguado Alvaro

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Sensory neurons imprint local macrophage identity via TGF-β [RNA-seq_in_vitro]

city: Freiburg

first: Julia

last: Kolter

address: Breisacher Str. 115b

country: Germany

institute: University of Freiburg

summary: Macrophages play integral roles in maintaining homeostasis and function in their tissues of residence. In the skin, prenatally seeded and highly specialized macrophages physically interact with sensory nerves and contribute to their regeneration after injury. However, mechanisms underlying the development and maintenance of this paradigmatic, potentially lifelong commitment of macrophages to nociceptors remain largely elusive. Here, we found that infiltrating myeloid progenitor cells approached the sprouting axons of sensory nerves and gradually adopted a nerve-associated macrophage-like profile. This change in identity was steered and maintained by the immediate microenvironment, in particular TGF-β, which was produced by neurons and locally activated by the physical interaction with nerves and integrin-mediated cleavage. Following injury, TGF-β driven specification of macrophages essentially supported nerve regeneration. Overall, we identified TGF-β as a central mediator governing local imprinting and long-term specialization of macrophages in the skin, providing insights into the bidirectional communication between macrophages and sensory nerves.

overall_design: BMDM were cultured alone or together with DRG-derived sensory neurons for 5 days or in the presence of 0.02ng/ml TGF-β and afterwards purified by cell sorting. All samples were taken from 3 different mice (triplicates) and analyzed by RNAseq.

first: Clarissa

last: Döring

first: Sebastian

last: Baasch

first: Philipp

last: Henneke


title: S ensory neurons shape local macrophage identity via TGF-β signaling


title: Sensory neurons imprint local macrophage identity via TGF-β [RNA-seq_in_vivo]

overall_design: CX3CR1-creERT2/gfp R26-tdT/+ mice were induced with Tamoxifen, and 3 weeks later, left ears were punched. After 10 days, macrophages were sorted from left ear (injury) and right ear (homeostasis) for interstitial macrophages (GFP-/Tomato-), resident nerve-associated macrophages (GFP+/Tomato+) and recruited nerve-associated macrophages after injury (GFP+/Tomato-). All samples were taken from 3 different mice and analyzed by RNAseq.


title: CRISPRi screen to identify genes critical for the shear stress activation of non-adherent monocyte.

first: Vishal

last: Nigam

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: Seattle Childrens Research Institute

summary: Circulating blood cells, such as leukocytes, experience significant hemodynamic stresses. These stresses are significantly higher when a patient requires mechanical support of the circulation, such as cardiopulmonary bypass. To identify molecular mechanisms by which cells sense these stresses, we utilized genome wide CRISPRi and phosphoproteomics data. These screens identified non-erythroid spectrin 1 (SPTAN1) and RAF1 as effectors of  hemodynamic stress in monocytes. We show that fluid stress induces SPTAN1/RAF1 signaling to promote STIM1 and ORAI1 interaction resulting in Store-Operated Calcium Entry (SOCE) thereby driving inflammation and cell death.

overall_design: IL8-GFP THP-1 cells were transduced with Brunello CRISPRi lentivirus library at multiplicity of infection (MOI) of 1. Cells were sheared in an in vitro system at 2 million cells/mL at a rate of 10mL/min for 2 hours. After shear, cells were prepared for flow cytometry and fluorescence-activated cell sorting (FACS). The 10% brightest GFP cells (LH2) were collected as the experimental group. The next 25% brightest cells (LH3) and unsheared transduced cells were collected. DNA was isolated and sequenced for the gRNAs. MAGeCKFlute was used to analyze the sequencing data.

first: Lance

last: Hsieh


title: Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: We report a new but determining pathway of mRNA quality control by transcription-translation coupling (TTC), which inhibits the generation of untranslatable mRNAs from the promoter-proximal region when transcription is decoupled from translation. Single-molecule mRNA FISH shows that the 5’ end-proximal regions of mRNA, of which amount reflects transcription initiation, are not generated without translation. The decoupling between transcription and translation results in the occupancy of RNAPs only within 250 base pairs from the transcription start site. It is further supported by the observation that RNAP decoupled with translation elongates mRNA only 80-90 bp on average in vivo. We show that the length of RNAP elongation before coupling with the ribosome (i.e., 5’-UTR length) determines the mRNA expression level. Our results demonstrate that the ribosome-coupling near the promoter-proximal region, within 100 bp from the transcription start site, functions as an mRNA-quality control, critical for the efficient synthesis of translatable mRNAs by RNAPs. The limited processivity of RNAP before coupling with ribosome provides a potential explanation of the natural distribution of 5’-UTR lengths in E. coli, where longer than 100 bp 5’-UTRs are rare.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We performed chromatin immunoprecipitation with exonuclease sequencing (ChIP-exo) on E. coli strains harboring either wild-type or dRBSdATG (ribosome binding site- and start codon-removed) genes. The target proteins for ChIP-exo were the RNA polymerase beta subunit and a synthetic 8-myc-tagged NusG.

first: Sora

last: Yang

first: Jina

first: Soojin

last: Park

first: Yong Hee

last: Han

first: Nam Ki

last: Lee


title: Characterization of Zearalenone-Induced Hepatotoxicity and its Mechanisms by Transcriptomics in Zebrafish Model

city: Jinan

first: Chenqinyao

last: Li

state: shandong

address: jinshidongroad, 1009, jinan, shandong, china

country: China

institute: Qilu University of Technology

summary: Zearalenone is a mycotoxin produced by several species of Fusarium fungi, which contaminates crop and cereal products worldwide. It mainly has estrogenic, immunotoxic and xenogenic effects on various organisms. Though its hepatotoxicity has been reported by few studies, the underlying mechanisms are yet to be investigated. This study aimed to comprehensively evaluate the hepatotoxic effects of zearalenone and its molecular mechanism in the zebrafish model system.

overall_design: First, we found that zearalenone exposure can specifically cause liver injury, as evidenced by reduced liver size, decreased liver-specific fluorescence, increased AST activity, delayed yolk sac absorption, and lipid accumulation. Then, RNA-seq was performed using dissected zebrafish fry liver. The experiment included a control group,  2000 and 4000 ng/mL zearalenone exposure group. Each treatment group had 3 biological replicates. Each replicate experiment consists of 80-100 pooled fish livers.

first: Changqing

last: Zhang

first: Yun

first: Kechun

last: Liu


title: Role of MicroRNA-30a on Pulmonary Angiogenesis and Alveolarization  in neonatal hyperoxia

city: Philadelphia

first: Krithika

last: Lingappan

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: miR-30a -/- neonatal mice were exposed to hyperoxia [95% FiO2, postnatal day (PND) 1-5] or room air before being euthanized on PND 21.

overall_design: Examination of the effect of hyperoxia on the lung transcriptome in WT and miR30a -/- mice and sex-specific differences

first: Cristian

last: Coarfa


title: RNA-seq data of Ly6Chigh CD11c+ MHC-II+ and Ly6C low cells FACS-sorted from Mock-LLC and SULT2B1b-LLC tumors

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

summary: This study reports a differential expression of LXR and cholesterol synthesis transcripts in immune cells infiltrating Mock- or SULT2B1b-LLC tumors

overall_design: Analysis of transcriptomes of Ly6Chigh CD11c+ MHC-II+ and Ly6C low cells infiltrating 10-day established Mock- or SULT2B1b-LLC tumors

first: Laura

last: Raccosta

first: Vincenzo

last: Russo


title: Progressive neuroinflammation and deficits in motor function in a mouse model with an Epg5 pathogenic variant of Vici syndrome

status: Public on Sep 11 2025

city: Kansas City

first: Jay

last: Vivian

state: MO

address: 2401 Gillham Road

department: Clinical Genetics

institute: Children's Mercy Hospital

summary: Transcriptomic profiling was performed on CNS tissues of 7 month old sibling control or homozygous mutant mice carrying a genetically engineered truncating W860X mutation recapitulating a pathogenic variant of Vici Syndrome. Analysis revealed robust neuroinflammatory signatures, implicating the activation of both microglia and astrocytes. Notably, the molecular profiles of Epg5-deficient mice share features with disease-associated microglia observed in other models of neurological disease and injury.

overall_design: Total RNA isolated from anterior spinal cord or cerebellum of 7 month old wildtype control or W860X homozygous mutant mice (four mice each; two male, two female) was used in an Illumina-based bulk RNA sequencing for whole transcriptomic analyses.


title: Activation of mtDNA transcription by mitochondrial RNA polymerase overexpression enhances stress-induced exercise capacity

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: POLRMT is the sole RNA polymerase in human mitochondria, where it generates primers for mitochondrial DNA (mtDNA) replication and transcribes the mtDNA to express genes encoding essential components of the oxidative phosphorylation (OXPHOS) system. Elevated POLRMT levels are found in several cancers and in mouse models with severe mitochondrial dysfunction. Here, we generated and characterized mice over-expressing Polrmt to investigate the physiological and molecular consequences of elevated POLRMT levels. Increasing POLRMT levels did not result in any pathological phenotype but led to increased exercise performance in male mice under stress conditions. Polrmt overexpression increased de novo transcription initiation, resulting in higher steady-state levels of the promoter-proximal L-strand transcript 7S RNA. Surprisingly, the abundance of mature mitochondrial RNAs was not affected by the elevated POLRMT levels. Furthermore, ubiquitous simultaneous overexpression of Polrmt and Lrpprc, which stabilizes mitochondrial messenger RNAs, did not increase steady-state levels of mitochondrial transcripts in the mouse. Our data show that POLRMT levels regulate transcription initiation, but additional regulatory steps downstream of transcription initiation and transcript stability limit OXPHOS biogenesis.

overall_design: RNA-Seq profiling of Polrmt overexpressor, Lrpprc overexpressor and double Polrmt/Lrpprc overexpressor mice against wild type

first: Maria

last: Miranda

first: Andrea

last: Mesaros

first: Nathalie

last: Scrima

first: Louise

last: Pérard

first: Irina

last: Kuznetsova

first: Martin

last: Purrio

first: Ilian

last: Atanassov

first: Aleksandra

last: Filipovska

first: Arnaud

last: Mourier

first: Nils-Goran

last: Larsson

first: Inge

last: Kühl


title: snRNAseq for Modeling long QT syndrome using gene-edited pigs

city: hangzhou

first: jiuxiao

last: zhao

state: zhejiang

address: Yuhangtang Road, Hangzhou 310058

institute: zhejiang university

summary: To date, KCNH2 mutations identified in patients with long QT syndrome type 2 (LQT2) have been extensively studied using heterologous expression systems. While these systems allow for the evaluation of the pathogenicity of specific hERG mutations through the overexpression of mutant channels, they fail to recapitulate the full spectrum of electrophysiological alterations and ion channel remodeling that occur in cardiomyocytes under physiological conditions in LQT. Existing zebrafish and rodent models are also limited in their ability to faithfully model human QT interval abnormalities due to substantial differences in lifespan, size, anatomy, and physiology. For instance, rodents exhibit a much higher heart rate and significantly shorter action potential duration (APD) than humans. Moreover, IKr is the major repolarizing current in human ventricles, whereas its inhibition in rodents has minimal impact on ventricular repolarization, rendering genetic mouse models inadequate for the study of LQT2. Thus, there is a critical need to develop animal models that can more accurately mimic human inherited arrhythmias. To address this gap, we generated a miniature pig model of LQT2, capitalizing on the physiological similarities to humans, as well as advantages in breeding and genome editing compared to non-human primates. To investigate the mechanisms by which KCNH2 mutations lead to LQT, we performed single-nucleus RNA sequencing to compare the transcriptomes of ventricular tissues from KCNH2-mutant pigs and wild-type controls.

overall_design: To investigate the underlying mechanisms, single-nucleus transcriptomic analysis was performed on ventricular myocardial tissue from WT and LQT(L5) pigs. Tissue samples were dissected from multiple layers—including the left and right ventricular endocardium, myocardium, epicardium, and the interventricular septum—then pooled for subsequent sequencing. After rigorous quality control, a total of 22,342 genes were analyzed across 8,103 cells from WT and 9,691 cells from the L5 group.


title: Integrating single-cell and bulk transcriptome analysis of fibroblast growth factor 23 (FGF23)-producing mesenchymal tumors reveals molecular basis of its secretory phenotype.

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Tumor-induced osteomalacia (TIO) is a rare disorder caused by a phosphaturic mesenchymal tumor (PMT) secreting fibroblast growth factor 23 (FGF23). The aim of this study was to analyze PMTs for their transcriptomic characteristics. We performed single-cell RNA sequencing of PMTs (n=3) and resulting in total of 22449 cells divided into 13 clusters. We identified clusters #1 and #2 as the PMT tumor cells and characterized by different epithelial-mesenchymal states, by different FGF23 expression levels, by various SNPs and CNVs.  We further identified tumor cell differentiation trajectory and tumorigenesis associated regulon driven by ERG and EGR3. In both single-cell and bulk transcriptomes (GSE261162) we found upregulation of vesicle-specific and exocytosis associated genes (SLC30A3, SYT1, STX1A and SNAP25) which most likely represent molecular mechanisms of active secretion in PMT. We report transmembrane protein coding genes expressed in all PMT samples specifically in tumor cell clusters (PHEX, ERBB4, PCDH7, LRRFIP2) which are suggested as potential diagnostic targets. In addition, we confirmed the presence of FN1-FGFR1 fusion genes and Klotho expression in scPMT-8 and scPMT-6 samples, respectively. Conclusion:  specific SNARE proteins gene upregulation along with transcriptional signatures of PMT offer new insights into its pathogenesis which may be further studied for diagnostic and therapeutic interventions.

overall_design: Single cell RNA sequencing of three PMT samples.

first: Gronskaia

last: Sofia

first: Deviatiiarov

last: Ruslan

first: Chekhonin

last: Vladimir

first: Dedov

last: Ivan

first: Buklemishev

last: Yuriy

first: Boulytcheva

last: Irena

first: Utkina

last: Marina

first: Popov

last: Sergei

first: Rodionova

last: Svetlana

first: Rozhinskaya

last: Liudmila

first: Gusev

last: Oleg

first: Belaya

last: Zhanna


title: Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (ATAC-Seq)

first: Laura

last: Pilar Aguado Alvaro

overall_design: Here we have used ATAC-seq to analyse the chromatin accessibility patterns of primary cardiac fibroblasts knocked-out for specific Chromatin Factors ex vivo differentiated under TGFb stimulation.

last: Aguado Alvaro

first: Nerea

last: Garitano

first: Wolfgang

last: Esser-Skala

first: Judy

last: Sayers

first: Cynthia

last: del Valle

first: Daniel

last: Alameda

first: Julen

last: Mendieta-Esteban

first: Maria

last: Calleja Cervantes

first: Ainhoa

last: Goñi-Salaverri

first: Jon

last: Zazpe

first: Anna

last: Rosaria de Vito

first: Francesco

last: Marchese

first: Diego

last: Alignani

first: Juliana

last: Cudini

first: Torsten

last: Gross

first: Gregorio

last: Rábago

first: Nisha

last: Narayan

last: Martinez

first: Sonia

first: Arantxa

last: Gonzalez Miqueo

first: Brian

last: Huntly

first: Paul

last: Riley

first: Nikolaus

last: Fortelny

first: Jake

last: Taylor-King

first: Beatriz

last: Pelacho

first: David

last: Lara-Astiaso


title: Transcriptomic analysis of monocytes stimulated with M-CSF in the presence or absence of PFM037 or TNF or TNF +PFM037

first: Michela

last: Riba

summary: in vitro stimulation of monocytes with the LXR antagonist PFM037, TNFa or the combination.

overall_design: Cells stimulated for 24 hours and then processed for RNA extraction

first: Laura

last: Raccosta

first: Vincenzo

last: Russo


title: Hypoxia promotes BCMA loss and a suppressive secretome thereby hindering CAR T cell therapy in multiple myeloma

city: Brussels

first: Eline

last: Menu

address: Bd de la Plaine 2

country: Belgium

institute: Vrije Universiteit Brussel

summary: Multiple myeloma (MM) develops in a hypoxic bone marrow (BM) microenvironment, which alters tumor behavior and immune responses. While hypoxia is known to directly suppress immune function, its effect on immunotherapy-relevant antigen expression and the MM secretome remains underexplored. Here, we investigated how hypoxia affects BCMA expression and BCMA-targeted CAR T cell responses. MM cells cultured under hypoxia (1% O₂) showed reduced BCMA surface and total protein expression, resulting in reduced CAR-mediated signaling. Importantly, the hypoxic tumor secretome further reduced BCMA levels and significantly impaired CAR T cell killing and cytokine production, which was partially reversible by γ-secretase inhibition. To dissect the suppressive nature of the hypoxic secretome, we identified an increase in small extracellular vesicle (sEV) release under hypoxia. RNA profiling of sEVs revealed a hypoxia-induced RNA signature with potential immunomodulatory roles. In conclusion, hypoxia diminishes BCMA expression and enhances secretion of immunosuppressive factors, including sEVs, thereby limiting the efficacy of BCMA CAR T cell therapy in MM.

overall_design: RNAseq of extracellular vesicles derived from RPMI-8226 and HS5 cells, placed in normoxia or hypoxia for 48 hours

first: Arne

last: Van der Vreken

first: Chenggong

last: Tu

first: Fien

last: Meeus

first: Lauren

last: van den Broecke

first: Jack

last: Brons

first: Karine

last: Breckpot


title: Organ-on-a-chip reveals the synergistic effect of mregDC and Treg in non-small cell lung cancer

city: Harbin

first: Qiming

last: Shen

address: Thoracic Surgery, The First Hospital Of China Medical University, No.155 North Nanjing Road, Heping Area, Shenyang

summary: Since the introduction of the first lung alveolus organ-on-a-chip, organ-on-a-chip technology has evolved over 15 years and is now widely applied in disease modeling, drug development, toxicological assessment, and personalized precision medicine due to its high biomimicry, dynamic and mechanical microenvironment simulation, and multi-cellular co-culture capabilities. Here, we utilized and developed a tumor metastasis organ-on-a-chip (TMOC) model to systematically investigate how modulating mregDC-Treg interactions can alleviate T cell exhaustion and tumor metastasis. To precisely study how mregDCs shape T cell exhaustion in the NSCLC TME, our TMOC spontaneously generates a hypoxia gradient from the tumor periphery to the center, mimicking the real TME, while enabling real-time observation of fluorescently labeled tumor cells metastasizing to adjacent tissue niches via a pump-driven self-circulating blood flow system. This TMOC model is suitable for the study of tumor immune microenvironment and has potential application prospects in other tumor metastasis studies.

overall_design: RNA-seq: This study included six TMOC samples, of which three are non-small cell lung cancer TMOCs and three are non-small cell lung cancer TMOCs with mregDC infiltration

first: Jie

last: Liang

first: Xinwen

last: Zhong


title: Mitochondrial-encoded peptide MOTS-c prevents pancreatic islet cell senescence to delay diabetes

city: Cambridge

first: Byung Soo

last: Kong

state: MA

address: 655 Huntington Avenue, Building 1, Room 512

department: Molecular Metabolism

institute: Harvard University

summary: To understand the mechanism underlying the role of MOTS-c in protecting pancreatic islets from senescence, we performed gene microarray analyses in pancreatic islet cells treated with either MOTS-c or a scrambled peptide

overall_design: Pancreatic islet cells were treated with either MOTS-c or a scrambled peptide from four littermates of 60-week-old C57BL/6 mice (n=2/group)


title: AoMbp1 interacts with AoSwi6 and plays pleiotropic roles in mycelial development, trap morphogenesis, and stress respone in the nematode-trapping fungus Arthrobotrys oligospora [RNA-Seq]

city: Kunming

last: Bai

address: No. 2 Cuihu North Road, Huashan Street, Wuhua District

institute: Yunan University

summary: The fungal specific APSES family proteins involve in regulating fungal growth, development, and multiple biological processes. In this study, AoMbp1, an ortholog of Saccharomyces cerevisiae APSES-type transcription factor Mbp1, was functionally analyzed in a representative nematode-trapping fungus Arthrobotrys oligospora. Inactivation of Aombp1 caused a severe affect on the mycelial growth and development, the mycelial growth rate of ∆Aombp1 mutant was remarkably decreased, the hyphal septa were increased whereas the number of nuclei were significantly reduced, and the lipid droplet accumulation was remarkably increased. Meanwhile, the deletion of Aombp1 resulted a considerable reduction in the number of conidiophores and spore yield, which also caused abnormal spore morphology. In addition, the ∆Aombp1 mutants became more sensitive to several chemical stressors, especially to hyperosmotic reagents. Importantly, disruption of Aombp1 caused the number of traps and nematode-trapping ability were significantly reduced, and most of the traps have changed from their original three-dimensional structure to a planar shape. RNA-Seq, DAP-Seq and Y2H assay showed that AoMbp1 interacted with AoSwi6, and involved in regulating cell cycle, meiosis, lipid metabolism, DNA replication, mismatch repair and nucleotide excision repair. Our study elucidated the functions and potential regulatory mechanism of APSES protein Mbp1 in the mycelial development and trap morphogenesis of nematode-trapping fungi.

overall_design: WT (represented by AO) and ΔAombp1 (represented by AoMbp1) strains were cultured in PD broth at 28℃ with agitation (180 r/min) for 5 days. Mycelia were collected, washed three times with 0.1 M phosphate buffer (pH 6.8–7.2), divided into four groups, and induced with approximately 600 nematodes for 0, 12, and 24 h, respectively; three replicates were used for each sample. RNA was extracted using the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China) and sequenced using the Illumina MiSeq platform at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). High-throughput sequencingdata were analyzed using the OmicShare online platform.

first: Xioali

last: Li

first: Lirong

last: Zhu

first: Meihua

last: Xie

first: Jinkui

last: Yang


title: Integrated biochemical and transcriptomic analyses elucidate the physiological mechanisms in rainbow trout (Oncorhynchus mykiss) head kidney under hypoxia stress

city: Lanzhou

first: QI

last: Wang

state: Gansu

address: Yintan Road Street

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: Hypoxia has emerged as a critical threat to the stability of aquatic ecosystems and the sustainability of aquaculture industries. Rainbow trout (Oncorhynchus mykiss), a globally significant economic fish species, exhibits remarkable sensitivity to hypoxia. However, the physiological mechanisms of head kidney in rainbow trout under hypoxia stress, especially under acute and severe hypoxia conditions, remain largely unexplored. This research explored the transcriptomic responses of rainbow trout head kidney to moderate hypoxia (4.5 ± 0.1 mg/L) and severe hypoxia (3.0 ± 0.1 mg/L) for 12 h, alongside dynamic changes in biochemical parameters during hypoxia exposure (0, 4, 8, 12, 24 h, and 1 month) and reoxygenation (R12 h and R24 h). The results showed that compared with the control group, the activities of T-AOC, CAT, T-SOD, GOT, GPT, and ACP were decreased under moderate and severe hypoxia conditions, while the content of MDA and the activity of AKP were increased. In RNA-seq analysis, we identified several hypoxia-related, immune-related and metabolism-related genes (hif-1α, fih1, vhl, ddit4, egln1/2/3, cxcr1/3/4/5, ccr5/7, clec4e/m, tlr2, socs2/3, ighv3-43, ighv3-53, g6pc3, pk, ldha, hk2, and foxo1a) from 20,399 significantly differentially expressed genes, which were enriched in insulin signaling pathway, glycolysis/gluconeogenesis, FcγR-mediated phagocytosis, hematopoietic cell lineage and B cell receptor signaling pathway. Additionally, the expression levels of cxcr1, ddit4, egln2, egln3, fih1 and foxo1a in rainbow trout were significantly up-regulated under hypoxia stress and returned to normal after reoxygenation. These findings provide new insights into the physiological and molecular responses of rainbow trout under hypoxia stress and contribute to developing effective strategies for fish to cope with environmental hypoxia.

overall_design:
Full-sib rainbow trout (average weight of 130 ± 5.0 g) were obtained from a farm located in Yongjing, Gansu Province, China. Prior to experimentation, fish were divided into three groups (normoxic control, moderate hypoxia, and severe hypoxia) and acclimatized for two weeks at the Fisheries Science Training Center of Gansu Agricultural University. During acclimatization, DO was maintained at 8.5 ± 0.1 mg/L, and water temperature was controlled at 12.0 ± 0.1°C. Following an acclimation period, the DO levels of the moderate and severe hypoxia groups were rapidly reduced to 4.5 ± 0.1 mg/L and 3.0 ± 0.1 mg/L by nitrogen gas. Sampling was conducted at specified intervals throughout hypoxia exposure (0, 4, 8, 12, 24 h, 1 month) and subsequent reoxygenation (R12 h, R24 h, DO restore to 8.5 ± 0.1 mg/L), with rainbow trout randomly sampled at each stage. Head kidney tissues from MS-222-anesthetized fish were harvested into freezing tubes and flash-frozen in liquid nitrogen for later analyses. All experimental procedures strictly adhered to the Animal Ethics Committee of Gansu Agricultural University (GSAU-Eth-AST-2021-004).
**National Natural Science Foundation of China (Grant No. 32060823) and Discipline Team Project of Gansu Agricultural university (NO: GAU-XKTD-2022-23).

first: Jinqiang

last: Huang

first: Zhijia

last: Guo


title: Conserved gene expression plasticity in development is more pervasive than expression divergence between species of Caenorhabditis nematodes

city: Toronto

first: Athmaja

last: Viswanath

state: Ontario

address: 25 Willcocks Street, Room 3055

department: Department of Ecology & Evolutionary Biology

country: Canada

institute: University of Toronto

summary: Diverse regulatory mechanisms enable precise spatio-temporal control of gene expression across developmental stages, tissues, and sexes, contributing to the proper development of the organism. Evolutionary divergence leads to species-specific gene expression patterns, even in preserved developmental structures, due to regulatory changes that can disproportionately influence subsets of developmental genetic networks. Here we quantify the evolution of sex-biased and tissue-biased transcriptomes from two tissue types (gonad and soma) for each of two sexes (male and female) from two of the closest known sister species of Caenorhabditis nematodes (C. remanei and C. latens). Differential gene expression and co-expression network analyses identify gene sets with distinct transcriptomic profiles, revealing widespread divergence between these morphologically and developmentally cryptic sister species. The transcriptomic divergence occurs despite most genes showing conserved expression across tissues and sexes. These observations implicate shared selection pressures related to tissue and sex differences as outweighing species-specific selection and developmental system drift in shaping overall transcriptome profiles. Although developmentally-plastic tissue-biased expression profiles are mostly conserved between species, we find that sex-biased genes, particularly male-biased genes, contribute disproportionately to species-differences in gene expression, consistent with a disproportionate role for male-biased selection driving gene expression divergence.

sample_organism:
Caenorhabditis remanei
Caenorhabditis latens

overall_design: We generated RNA-Seq data from two Caenorhabditis species—C. remanei (strain VX0003) and C. latens (strain VX0088)—including both males and females. For each sex and species, we dissected two tissue types: the soma and the gonad. All dissections were performed on wild-type individuals

first: Daniel

last: Fusca

first: John

last: Calarco

first: Asher

last: Cutter


title: AoMbp1 interacts with AoSwi6 and plays pleiotropic roles in mycelial development, trap morphogenesis, and stress respone in the nematode-trapping fungus Arthrobotrys oligospora

summary: DAP-Seq analysis revealed that AoMbp1 was involved in cellular growth and diverse metabolic processes.

overall_design: The cDNA sequence encoding protein AoMbp1 is constructed in Halo Tag plasmid, the construct vector pAoMbp1-halo was identified by sequencing, then the vector and the genome DNA of A. oligospora were send to Genedenovo Biotechnology (Guangzhou, China) for DAP-seq analysis. The AoMbp1 protein binds to the target genome fragment, thus the DNA fragment of the genome bound by the target protein can be enriched. Through the combination with high-throughput sequencing technology, DNA products after DAP were sequenced and analyzed, DNA binding sites of target proteins were searched from the whole genome, and high-throughput data results were obtained by efficient sequencing methods. The DNA libraries were sequenced on the Illumina sequencing platform by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).


title: Exercise sensitizes the pressure diuresis response: shifting immune landscapes underlie renal adaptations to exercise

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

summary: Background: Exercise benefits several physiological systems to confer health; however, the mechanisms by which exercise impacts renal health remain poorly understood. Studies show moderate intensity exercise slows the age-related decline in kidney function. Additionally, exercise protects against AKI in several rodent models. We hypothesize that exercise triggers adaptative responses, which preserve hemodynamic balance in the kidneys under stress. Methods: We evaluated exercise-induced adaptations in 10–14-wk-old C57BL/6J male and female mice subjected to either 4 wk of voluntary wheel running or up to 2 wk of forced treadmill running (70% capacity for 40 min/d). Additionally, we evaluated endpoints 24 h after a single bout of exhaustive exercise to discern acute responses from chronic adaptations. We evaluated renal perfusion with contrast-enhanced ultrasound and assessed kidney function by measuring the ability to clear a volume load. Additionally, we performed flow cytometry, cytokine array, histopathology, and bulk mRNA sequencing to evaluate exercise-induced changes in the kidney. Results: We found a significant increase in the maximum steady state tissue contrast intensity in the kidneys of exercised male mice vs sedentary controls. Additionally, exercised male, but not female, mice excreted significantly more urine in the first hour after administration of a saline bolus. At the cellular level, we observed a significant increase in kidney resident macrophages (KRMs; CD45+CD11b+F4/80hi) after exercise training in male, but not female, mice. Because the macrophages were primarily CX3CR1+CCR2-, this suggests expansion of KRMs as the source of the increase. Lastly, bulk mRNA sequencing suggested exercise induces changes relating to water and sodium handling as well as angiogenesis and wound healing. Conclusions: These data suggest that exercise alters the immune landscape of the kidney, which may promote angiogenesis to increase renal microvasculature and improve sensitivity of the pressure diuresis response. Future studies will identify if macrophages cause the functional adaptations observed.

overall_design: Exercised mice were subjected to either 1 day, 1 week, or 2 weeks of forced treadmill running at 70% capacity for 40 minutes. Kidney cortex pieces were flash frozen at time of euthanisia.

first: Sophia

last: Sears


title: Gut microbiota dysbiosis affects intestinal sensitivity through epithelium-to-neuron signaling: novel insights from colon organoid-based model to improve visceral pain therapy

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

institute: Università degli Studi di Firenze

summary: Chronic gastrointestinal pain is a hallmark of most intestinal pathologies, yet effective treatments remain elusive given the complexity of the underlying mechanisms. Aiming to investigate the intestinal epithelium contribution to visceral pain modulation in dysbiosis context, we first demonstrated that intracolonic instillation of microbe-free faecal supernatants from mice with post-inflammatory dysbiosis induced by dextran sodium sulfate (FS DSS ) provokes visceral hypersensitivity in recipient mice. Epithelium involvement in the response to FS DSS was thoroughly analyzed through a novel in vitro approach comprising murine epithelial colon organoids and primary dorsal root ganglia (DRG) neurons. FS DSS treatment induced growth and metabolic impairment in colon organoids, which reveals a dysbiosis-driven epithelial dysfunction. Notably, the combination of FS DSS and conditioned medium from FS DSS -treated colon organoids increased DRG neuron excitability, implicating a synergism between microbial and epithelial products in visceral sensitivity regulation. By investigating the underlying signaling, metabolomic analysis revealed reduced levels of short chain fatty acids in FS DSS whereas transcriptomic analysis of FS DSS - treated colon organoids showed the dysregulated expression of several signaling factors. These findings provide novel insights into the role of gut epithelium in the modulation of sensory neuron excitability under dysbiosis conditions, emphasizing that targeting epithelial-neuronal signaling might represent a promising therapeutic strategy for visceral pain management.

overall_design: RNA-seq profiling of wildtype C3H10T1/2 cells and their knockdown derivatives (shKDM4D, shNFIB, and shTNFα) at Day0 and Day5 of adipogenic differentiation.

first: Francesco

last: Margiotta

first: Elena

last: Lucarini

first: Alessandra

last: Toti

first: Lorenzo

last: Curti

first: Alessio

last: Masi

first: Tommaso

last: Mello

first: Gwenaelle

last: Le Gall

first: Alberto

last: Magi

first: David

last: Vauzour

first: Guido

last: Mannaioni

last: Di Cesare Mannelli

first: Carla

last: Ghelardini


title: CpG ODN-functionalized gold nanorods for better immune activation and its potential mechanism

city: kunming

first: Shiwen

last: Zhang

address: kunming

institute: Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University, Peking University Cancer Hospital Yunnan)

summary: Background: Immune escape in the treatment by functionalized gold nanorods (Au NRs) should not be ignored. Whether CpG ODN, an immune adjuvant, can synergize with Au NRs to activate the immune response and its potential mechanism is not clear. Methods: The expression of CD8+ T cells, macrophage, NK cells, Th17, and Treg was detected by flow cytometry. Expression levels of IL-1, IL-6, IL-17, and TNF-α were assessed by ELISA. Subsequently, transcriptome sequencing analysis was performed to identify DEGs. GO, KEGG and PPI analyses explored the mechanism. The immune activation properties of antibody functionalization-associated Au NR were then compared. Results: Flow cytometry and ELISA analyses indicate that both Au NRs and CpG ODN promote the proliferation of inflammatory factors and immune activation. However, the CpG ODN-coupled Au NRs (Au NRs-C) demonstrated superior immune activation potential. Furthermore, Au NRs stimulate the expression of Treg, while Au NRs-C significantly inhibited this effect. This suggests that the conjugation of CpG ODN with Au NRs not only greatly enhances the immune activation but also compensates for their deficiencies in eliciting immune responses. Transcriptome sequencing uncovered DEGs mainly localized to immune and pro-inflammatory cytokine pathways. PPI analysis identified six hub genes: FOXM1, HMOX1, UBE2C, E2F1, PECAM1, and FCGR3A. Moreover, CpG conjugation with antibody-associated Au NRs enhances immune stimulation. Conclusion: Au NRs-C may upregulate the E2F1 and downregulate the PECAM1, which promotes MHC antigen presentation and Toll-like receptor-mediated immune processes while inhibiting CXCR receptor binding and immune negative regulation, thereby resulting in a stronger immune activation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBS, Au NRS and Au NRs-C groups.

first: Changqiang

last: Wang


title: Multidimensional Deep Receptor Scanning Reveals Constraints on GPCR Biosynthesis [Ribo-Seq]

city: Lafayette

first: Austin

last: Tedman

state: IN

address: 716 Brown St Apt 4

department: Chemistry

institute: Purdue University

summary: G protein-coupled receptors (GPCRs) mediate a variety of signaling pathways and are among the most common pharmacological targets. While advances in structural biochemistry have provided deep functional insights into dozens of key receptors, many of the 800+ human GPCRs remain understudied. In the following, we introduce a versatile “deep receptor scanning” platform that can be used to experimentally characterize 767 human GPCRs and 174 known GPCR splice variants in parallel. We quantitatively characterize the relative abundance of receptor transcripts, their translational efficiency, and the plasma membrane expression of each receptor in the context of a recombinant pool of HEK293T cells expressing individual GPCRs. We then employ machine learning to identify specific structural features that modulate GPCR expression. This experimental platform and informatic approach are compatible with a variety of assays and can be used to efficiently explore the biochemical and pharmacological properties of the GPCRome.

overall_design: Total RNA-seq of both mock and stably transfected HEK 293T cells where each cell encodes one of 767 single stably expressed GPCRs


title: Natural plant-derived superoxide dismutase nanoenzyme for sepsis-induced liver injury therapy.

city: JiNan

first: chonglei

last: zhong

address: huaiyin district

institute: Shandong First Medical University

summary: Sepsis-induced liver injury is an important cause of septicemia deaths, this injury is characterized by an overproduction of reactive oxygen species (ROS) within the liver, which activates the inflammatory response and results in the release of numerous inflammatory factors, ultimately leading to liver damage. Thus, the development of medicines capable of eliminating ROS and reducing inflammatory factors holds significant prospects. In this study, we synthesized and characterized a natural superoxide dismutase-mimicking carbon dots (G-CDs) form a greenery Glycyrrhiza with distinctive ROS scavenging ability for SILI therapy. The abundant surface unsaturated groups especially oxhydry and carbonyl groups enable G-CDs to exhibit excellent SOD-like enzyme activity exceeding 10000 U/mg and significantly reduce the excessive production of ROS and inflammatory factors. In addition, G-CDs reduced inflammation, oxidative damage, and tissue damage in the liver of lipopolysaccharide (LPS) induced SILI mice model. Mechanistically, G-CDs protect liver tissue by activating Keap-1/Nrf-2 mediated antioxidant signaling and inhibiting NF-κB-dependent inflammatory responses. In conclusion, this study establishes the potential of G-CDs as a promising therapeutic agent for the treatment SILI.

overall_design: RAW264.7 cells were cultured in a 6 wells plate in LPS (1 μg/ml) containing medium for 6 h supplemented with or without G-CDs (400 μg/ml), and total RNA was extracted using the TRIzol reagent. RNA sequencing was conducted using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

first: Chonglei

last: Zhong


title: Single cell map of the adult female mouse urethra reveals epithelial and stromal macrophages with distinct functional identities

city: Dallas

first: Douglas

last: Strand

state: TX

address: 5323 Harry Hines Blvd JA5.150 JA5.150

department: Urology

institute: UT Southwestern Medical Center

summary: The epithelial lining of the urethra is an understudied mucosal barrier with emerging roles in antimicrobial defense during urinary tract infections. Here, we present a comprehensive cellular atlas of the adult female mouse urethra, focusing on epithelial and resident immune cells which act in concert at mucosal sites to direct host defense. Single cell RNA-sequencing revealed two distinct macrophage populations compartmentalized within the epithelium and stroma. Epithelial-associated macrophages display a highly dendritic morphology and populate the urethral lining in increasing numbers over the course of development. Epithelial-associated macrophages, express Cx3cr1, MHCII genes, Cd74 and Aif1/Iba-1, representing an activated macrophage type (Mac-Activated) and also express genes involved in antigen presentation and inflammatory response. In contrast, stromal macrophages express the scavenging receptors Mrc1/Cd206, Lyve1, Cd163 and Mgl2/Cd301b and display a signature enriched for endocytic function, vasculature development and tissue homeostasis (Mac-Endocytic). We identified epithelial cells in the urethral lining and associated glands expressing the monocyte chemoattractant genes Cx3cl1 and Cxcl17. Chemoattractant gene expression in the urethral epithelium follows a proximal-distal gradient which correlates with the increasing density of epithelial-associated macrophages expressing the receptor Cx3cr1, along the proximal-distal axis of the urethra. The study delineates spatially compartmentalized macrophage subsets in the urethra and implicate epithelial-derived chemokines in the establishment of macrophage positioning and functional specialization along the urethral axis.

overall_design: 5 µm sections mouse female urethra were prepared from FFPE tissue and mounted on a Xenium slide (10x Genomics). Manufacturer recommendations for sample processing and operation of the Xenium analyzer were followed for downstream sample preparation and data collection.

first: John

last: Lafin

first: Diya

middle: B

last: Joseph


title: The impact of CXCL13 and IL-9 expression on CAR T cell functionality

city: Guangzhou

first: yang

last: zhou

address: South Shatai Road, Baiyun District

institute: Southern Medical University

summary: CXCL13 expression is highly elevated in T cells from patients who respond to PD-1 blockade, suggesting that CXCL13 may play a role in boosting T cell antitumor responses. Compared to conventional Th1/Tc1 cells, Th9/Tc9 cells exhibit stronger antitumor functions, and IL-9 plays a critical role in mediating their antitumor efficacy. Therefore, we investigate the respective effects of CXCL13 and IL-9 on CAR T cells.

overall_design: CD3+ T cells were extracted from C57BL/6J mouse splenocytes and cultured on plates coated with anti-CD3 (5 mg/mL) in the presence of soluble anti-CD28 (1 mg/mL) and IL-2 (100 U/mL) to induce differentiation. CD3+ T cells were then cultured with different viruses (control CAR, CXCL13 CAR, IL-9 CAR) and polybrene (10 µg/mL), then incubated for 24 hours. After three days, CAR T cells were carefully removed from the plates, centrifuged to remove the supernatant, and grown in fresh media with IL-2 (100 U/mL). RNAex Pro RNA Reagent was used to obtain total RNA of CAR T cells on day 5 for RNAseq.

first: Yang

last: Zhou

first: Wenli

last: Zhao

first: Yihan

last: Zhu

first: Enguang

last: Bi


title: Self-assembled hyaluronic acid nanoparticles target TLR2 to regulate macrophage M1 polarization and alleviate psoriasis

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

summary: Self-assembled hyaluronic acid nanoparticles (HANPs) possess unique biocompatibility and receptor-binding properties, making them widely studied as drug delivery systems. Notably, empty HANPs alone have demonstrated therapeutic and ameliorative effects in various inflammatory diseases. In this study, we conjugated hyaluronic acid and 5βcholanic acid to create self-assembled nanoparticles (HACNs). We then investigated the effects of HACNs on macrophage polarization towards the pro-inflammatory M1 phenotype using mouse primary bone marrow-derived macrophages and the human monocyte cell line THP-1 cells. Our findings reveal that HACNs directly interact with Toll-like receptor 2 (TLR2) and effectively suppress the expression of pro-inflammatory mediators by competitively inhibiting ligand-receptor interactions in macrophages. This inhibitory effect on TLR2 signaling is mainly due to the spherical structure of the selfassembled hydrophilic hyaluronic acid (HA) shell, rather than to free HA or the hydrophobic core component, 5β-cholanic acid. Furthermore, the protective effects of HACNs against IMQ-induced epidermal hyperplasia and elevated pro-inflammatory cytokine levels were significantly diminished in TLR2-defecient mice. These results highlight the potential of empty HACNs as effective therapeutic agents for TLR2- mediated inflammatory disorders.

overall_design:
Seven-week-old female C57BL/6 mice and TLR2 knockout mice were housed in groups of five per cage and allowed to acclimate for one week prior to the study.
To induce psoriasis, 62.5 mg/cm² of 5% imiquimod (IMQ) cream (Aldara; 3M Pharmaceuticals) was applied topically to the shaved dorsal skin for four consecutive days. The dorsal skin was shaved using an electric clipper and treated with depilatory cream.


title: Time-restricted feeding provides limited microglial immunometabolic improvements in diet-induced obese rats

city: Amsterdam

first: Han

last: Jiao

address: 9 Meibergdreef, Endocrine Laboratory, Clin. Chemistry

country: Netherlands

institute: University of Amsterdam, Amsterdam, The Netherlands.

summary: Time-restricted eating has shown great promise for improving metabolic health in humans with obesity, but its mechanism is still not completely resolved. In this study, we investigated how time-restricted feeding (TRF) affects microglial immunometabolism using Wistar rats. High-fat diet (HFD)-fed animals became obese, but restricting food intake to the active phase reduced fat mass, reinforced the rhythmicity of the microglial transcriptome, and prevented an increase of hypothalamic microglial cell numbers. However, TRF failed to reverse HFD-induced microglial immune dysfunction and metabolic disturbances, including suppressed electron transport chain activity, increased lipid metabolism gene expression, and impaired metabolic flexibility. These findings suggest that obesity-driven microglial immunometabolic reprogramming persists despite TRF-induced weight loss and may contribute to obesogenic memory and weight regain after weight loss induced by dietary interventions.

overall_design: RNA-seq profiling was performed on isolated microglia from adult male Wistar rats to investigate the impact of diet and feeding schedule on circadian transcriptional dynamics. Animals were maintained on either standard chow or a high-fat diet (HFD) and were subjected to one of three feeding regimens: ad libitum, dark-phase feeding, or light-phase feeding. Microglia were collected at six Zeitgeber times (ZT02, ZT06, ZT10, ZT14, ZT18, and ZT22), resulting in 6 experimental groups × 6 circadian time points. This design enables the comparison of microglial transcriptional responses to diet, feeding schedule, and circadian phase.

first: Jarne

last: Jermei

first: Xian

last: Liang

first: Hendrik JP

last: van der Zande

first: Frank

last: Vrieling

first: Valentina

middle: S

last: Rumanova

first: Milan

last: Dorscheidt

first: Anhui

first: Ewout

last: Foppen

first: Bob

last: Ignacio

first: Dirk Jan

last: Stenvers

first: Tiemin

last: Liu

first: Kimberly

last: Bonger

first: Rinke

last: Stienstra

first: Zhi

first: Andries

last: Kalsbeek

first: Chun-Xia

last: Yi


title: Epigenetic, ribosomal, and immune dysregulation in Paediatric Acute Neuropsychiatric Syndrome [RNA-Seq]

city: Westmead

first: Brian

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

institute: Westmead Institute of Medical Research

summary: Paediatric Acute Neuropsychiatric Syndrome (PANS) is characterised by abrupt onset obsessive compulsive disorder and regression in neurodevelopmental skills, triggered by infection or stress. Whether PANS is a distinct entity or part of a neurodevelopmental spectrum is uncertain, and its pathophysiology unclear. We show that children with PANS and other non-PANS neurodevelopmental disorders have higher reported early childhood infections and loss of previously acquired developmental skills compared to neurotypical controls. Children with PANS have normal routine immune testing, however bulk RNA-sequencing revealed upregulated pathways in ribosomal biogenesis and RNA methyltransferases, and downregulated pathways in diverse cellular functions such as mitochondrial activity, cell signalling, endocytosis, and immune responses. Single-cell RNA-sequencing confirmed these findings but showed heterogeneity across immune cell types. Toll-like receptor stimulation assay using peripheral blood mononuclear cells revealed reduced TNF and interleukin-6 responses in PANS patients compared to controls. RNA sequencing before and after intravenous immunoglobulin treatment in PANS patients revealed reversal of the dysregulated ribosomal, epigenetic,  and cell signaling pathways. Given the central role of the immune system in synaptic pruning and neurodevelopment, these insights provide rationale for novel epigenetic and immune modulating therapies to optimize neurodevelopmental trajectories and minimize neuropsychiatric impairment.

overall_design: We performed bulk blood transcriptomic analyses in PANS, and then further explored these findings in PANS via single cell transcriptomics and functional immune assays. We also conducted blood transcriptomic analysis on children with PANS both before and after intravenous immunoglobulin administration, aiming to define the biological effect of IVIg in these individuals.

first: Velda

middle: X

last: Han

first: Shrujna

last: Patel

first: Russell

last: Dale


title: MicroRNA-372-3p impairs fatty acid metabolism in hepatocellular carcinoma cells by targeting CPT1A and ACSL4

city: Pathumwan

first: Archittapon

last: Nokkeaw

state: Bangkok

address: Padtayapatana Building, 1873, Henri Dunant Road

department: Biochemistry

country: Thailand

institute: Chulalongkorn university, faculty of medicine

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, with limited effective treatment options. Recent studies highlight the emerging role of microRNAs in HCC biology, including microRNA-372-3p (miR-372-3p), but its precise function in HCC remains controversial. Here, we investigated the role of miR-372-3p in HCC using a transcriptomic approach. Overexpression of miR-372-3p in HCC cell lines significantly impaired proliferation, migration, invasion, and colony formation, indicating a tumor-suppressive function. RNA sequencing and Gene Set Enrichment Analysis (GSEA) revealed downregulation of genes involved in fatty acid metabolism, specifically fatty acid oxidation (FAO). Consistently, miR-372-3p overexpression increased lipid droplet  accumulation and triglyceride levels while inhibiting FAO, leading to impaired lipid utilization under glucose deprivation and compromised interactions of lipid droplets with mitochondria and lysosomes. Mechanistically, we identified CPT1A and ACSL4 as direct targets of  miR-372-3p using bioinformatics and dual luciferase assays. These findings demonstrate that miR-372-3p acts as a tumor suppressor in HCC by inhibiting FAO and disrupting lipid metabolism, suggesting a potential therapeutic target for HCC treatment.

overall_design: A human HCC cell line with control and hsa-miR-372-3p overexpressed using a pri-miRNA plasmid. Three technical replicates were performed for each group.

first: Chinnatam

last: Phetkong

first: Thammachanok

last: Boonto

first: Pannathon

last: Thamjamrassri

first: Chaiyaboot

last: Ariyachet

first: Pisit

last: Tangkijvanich


title: Epigenetic, ribosomal, and immune dysregulation in Paediatric Acute Neuropsychiatric Syndrome [scRNA-Seq]


title: Gene expression profiles in fibroblast growth factor 23 (FGF23)-producing tumors provide new insights on diagnostic and therapeutic intervention.

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

institute: Juntendo University

summary: Tumor-induced osteomalacia (TIO) is a rare disorder caused by phosphaturic mesenchymal tumor (PMT) that secrete fibroblast growth factor 23 (FGF23). There is limited data regarding the genetic of PMT. Fusion genes with FN1-FGFR1, FN1-FGF1, NIPBL-BEND2  have been reported , yet they are absent in 30-40% of PMTs. We conducted RNA sequencing on PMT and surrounding control tissue samples obtained during tumor resection in 5 patients, where PMTs were confirmed histologically. We identified 3261 differentially expressed (DE) genes between tumors and control tissues. Such DE genes were associated with musculoskeletal system diseases, mineralization, and pathways in cancer. We found de novo SNPs in regulatory regions of genes exhibiting statistically significant expression changes between control and PMT samples - ELOVL6, GM2A, NUDT4, that hold diagnostic and therapeutic relevance . We identified FN1-FGF1 fusion genes in 1 out of 5 PMT samples, confirming previous studies. We found that PMT overexpressed genes associated with osteoblast activity and differentiation, such as OPG/RANKL, highlighting tumor development.

overall_design: Healthy and PMT tissue samples from six patients.

first: Sofia

last: Gronskaia

first: Yuriy

last: Buklemishev

first: Vladimir

last: Chekhonin

first: Sergei

last: Popov

first: Roman

last: Fedotov

first: Svetlana

last: Rodionova

first: Liudmila

last: Rozhinskaya

first: Oleg

last: Gusev

first: Zhanna

last: Belaya


title: Viral rebound in SHIV-infected infant macaques is predicted by immunovirologic features measured before and after antiretroviral therapy

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Evaluation of HIV cure strategies requires antiretroviral therapy (ART) interruption, but ethical and clinical considerations make this difficult in children. Uncovering predictors of time to viral rebound (TTR) and post-treatment control (PTC) of rebound viremia in a pediatric preclinical model may inform the design of studies testing novel cure interventions in these populations. We thus assessed 141 variables in SHIV-infected infant rhesus macaques (RMs) where ART initiation was staggered then followed by analytical treatment interruption (ATI). Viral rebound occurred in 25/30 RMs within 7-98 d of ATI, with TTR significantly delayed in the Early ART group compared to the Intermediate and Late ART groups (median TTR  84, 18, and 17 d, respectively; p<0.001). Peak plasma viral load pre-ART best described TTR, with increased predictive strength through the successive inclusion of six additional variables. Increased peak viral load pre-ART decreased the odds of no rebound and elevated Ki67+ effector memory CD8+ T cells in lymph nodes pre-ATI increased the odds of PTC. RNA sequencing of CD4+ T cells pre-ATI showed heme metabolism and IFNg response pathways were most upregulated in RMs with sustained suppression of viremia during ATI. Analysis of only the Early ART group also implicated TGFb pathway genes in lack of viral rebound off ART. This comprehensive investigation reveals major determinants of viral rebound dynamics following ART interruption that should be validated and explored as biomarkers to screen children with HIV being considered for ATI.

overall_design: 18 infant Indian rhesus macaques infected with SHIV.C.CH505.375H.dCT at 4 weeks of age divided into three groups (n=6) differing in timing of antiretroviral therapy (ART) initiation following infection: 8 wpi for Late ART, 2 wpi for Intermediate ART, and 4 or 7 dpi for Early ART. Animals were maintained on daily ART for a minimum of 52 weeks prior to treatment interruption. RNA sequencing was perfomed on CD4+ T cells isolated from blood and lymph nodes prior to treatment interruption.

first: Veronica

last: Obregon-Perko

first: Achal

last: Awasthi

first: Richard

last: Barfield

first: Stella

last: Berendam

first: Bhrugu

last: Yagnik

first: Tiffany

last: Styles

first: Greg

first: Prachi

last: Kumar

first: Mithra

first: Emily

last: Fray

first: Fan

last: Bu

first: Janet

last: Siliciano

first: Bob

first: Maud

last: Mavigner

first: Rama

last: Amara

first: Steve

last: Bosinger

first: Genevieve

last: Fouda

first: Sallie

last: Permar

first: Cliburn

last: Chan

first: Ann

last: Chahroudi


title: A TrkB and TrkC partial agonist prevents synaptic plasticity deficits and elicits activity-dependent synaptic and microglial transcriptomic changes in a late-stage Alzheimer’s disease mouse model

city: Stanford

first: Robert

middle: Raymond

last: Butler

state: CA

address: 3172 Porter Dr., MC 5475

department: Neurology & Neurological Sciences

institute: Stanford University School of Medicine

summary: Introduction: TrkB and TrkC receptor signaling promotes synaptic plasticity and interacts with pathways affected by amyloid-β (Aβ)-toxicity. Upregulating TrkB/C signaling could reduce Alzheimer’s disease (AD)-related degenerative signaling, memory loss, and synaptic dysfunction. Methods: PTX-BD10-2 (BD10-2), a small molecule TrkB/C receptor partial agonist, was orally administered to aged London/Swedish-APP mutant mice (APPL/S) and wild-type controls (WT). Effects on memory and hippocampal long-term potentiation (LTP) were assessed using electrophysiology, behavioral studies, immunoblotting, immunofluorescence staining, and RNA-sequencing. Results: Memory and LTP deficits in APPL/S mice were attenuated by treatment with BD10-2. BD10-2 prevented aberrant AKT, CaMKII, and GLUA1 phosphorylation, and enhanced activity-dependent recruitment of synaptic proteins. BD10-2 also had potentially favorable effects on LTP-dependent complement pathway and synaptic gene transcription. Conclusions: BD10-2 prevented APPL/S/Aβ-associated memory and LTP deficits, reduced abnormalities in synapse-related signaling and activity-dependent transcription of synaptic genes, and bolstered transcriptional changes associated with microglial immune response.

overall_design: To investigate transcriptional changes associated with LTP and BD10-2 treatment in the context of an amyloid model (Thy1-hAPPLond/Swe [Line 41] mice) of Alzheimer's, we conducted RNA sequencing on eight experimental groups. All mice were either Wildtype (B6) or T41B mice, dosed via oral gavage with BD10-2 or vehicle for 3 months from 13-16 months of age. Afterwards, right hippocampal slices were rapidly dissected for ephysiology (stimulated or unstimulated control), subjected to 3 times theta burst stimulation consisting of 10 bursts of 4 stimuli at 100 Hz separated by 200 ms each. Unstimulated slices experienced sham procedure of the same duration without TBS. Immediately after slices were flash frozen for RNAseq processing.

first: Amira

last: Latif-Hernandez

first: Tao

last: Yang

last: Butler III

first: Patricia

last: Moran Losada

first: Paras

last: Minhas

first: Halle

last: White

first: Kevin

last: Tran

first: Harry

last: Liu

first: Danielle

last: Simmons

first: Vanessa

last: Langness

first: Tony

last: Wyss-Coray

first: Frank

last: Longo


title: Nucleotide-Binding Oligomerization Domain 1 (NOD1) Positively Regulates microglia-driven inflammatory response during Pseudorabies Virus Infection

city: Wuhan

first: Xiuxiu

last: Sun

address: Shizishan Street

institute: Huazhong Agricultural University

summary: The main cause of viral encephalitis is that the virus invades the central nervous system (CNS) and causes neuroinflammation, which poses a serious threat to the world’s public health. Microgliaare CNS-resident macrophages that playanimportantroleinneuroinflammation and thus often identified as target of choice for the prevention or treatment of viral encephalitis. Nucleotide-binding oligomerization domain 1 (NOD1) is a type of pattern recognition receptor and has been associated with many inflammatory diseases in humans. Here, we used pseudorabiesvirus (PRV) as a model to examine the regulation of microglia responses during viral encephalitis and discuss whether NOD1 suppressed neuroinflammation by regulating microglial activation. Cellular experiments indicated that microglia activation accompanying by cell migration, characteristic morphological changes, phagocytosis, inflammatory cytokine production and antigen presentation. We then investigated the effect of NOD1 on the PRV-induced microglia activation. Theresultsinvitro and in vivoshowedthat PRV infection upregulated the mRNA and protein expression of NOD1. Inhibition or overexpression of NOD1 can reduce or enhance the activation JNK and NF-κB signal pathway to regulate the microglia activation and inflammatory response induced by PRV.

overall_design: Comparative gene expression profiling analysins of RNA-seq data for BV2 cells with or without PRV

first: Guofu

last: Cheng

first: Xinxin

last: Jin


title: Mitotic endosomes regulate spindle organization and function via Occludin and FIP5 binding

city: Shanghai

first: Zichao

last: Zhang

address: No.2005, Husong Road

institute: Fudan University

summary: The genetic basis of vertebrate emergence is a major unanswered question in metazoan evolution. Understanding vertebrate-specific genes, such as Occludin (Ocln), may help answer this question. Here, we show that mammary glands lacking Ocln exhibit retarded branching, resulting from reduced cell proliferation. Interestingly, Ocln regulates spindle orientation and function, and its loss leads to a range of phenotypes, including prolonged prophase and failed nuclear and/or cytoplasmic division.

overall_design: Luminal cells were extracted from control and Ocln-/- mice at 7-week stage. Then, RNA was isolated using RNA extraction kit.


title: Sensory neuron gene expression changes in response to type 2 skin inflammation after recovery

city: St. Louis

first: Aaron

last: Ver Heul

address: 660 S Euclid Ave.

institute: Washington University School of Medicine

summary: Type 2 inflammation contributes to the pathology of skin diseases such as atopic dermatitis and urticaria. Itch is a common symptom accompanying type 2 skin inflammation. Yet how chronic type 2 inflammation affects itch sensory neurons innervating the skin is poorly understood. The goal of this study was to characterize long term transcriptional changes in sensory ganglia innervating the skin in the setting of chronic type 2 skin inflammation after resolution of inflammation.

overall_design: 8-10 week old wild type C57BL6 mice were treated with topical application of calcipotriol or vehicle daily for 12 days to induce chronic atopic-dermatitis-like inflammation. Mice were then allowed to recover without treatment for 30 days until skin inflammation has visibly resolved, after which trigeminal ganglia innervating the treated cheek areas were harvested and total RNA was extracted for sequencing.

first: Brian

last: Kim


title: Single nuclei RNA sequencing of mouse dorsal root, nodose, and trigeminal ganglia from humanized JAK1 gain-of-function mice

summary: Janus kinase 1 (JAK1) critically mediates downstream signaling from a variety of immune receptors. Gain-of-function mutations in JAK1 in humans lead to immune dysregulation and exaggerated type 2 immune responses, including atopic dermatitis. We have previously shown that JAK1 expressed in neurons mediates cytokine-enhanced itch signaling in atopic dermatitis. We generated a novel mouse expressing human JAK1 with the gain-of-function mutation p.A634D. To better understand how enhanced JAK1 signaling my impact sensory neurons, we performed single nuclei RNA sequencing on different sensory ganglia from JAK1 gain-of-function mice and littermate controls.

overall_design: 10-12-week-old C57BL6 mice heterozygous for an allele where the mouse Jak1 gene was replaced by human JAK1 with the p.A634D mutation, or homozygous for wild type mouse Jak1, were used. Thoracic dorsal root ganglia, nodose ganglia, and trigeminal ganglia were dissociated into single nuclei preps and sequenced using the 10X Genomics multiome pipeline.

first: Masato

last: Tamari

first: Lydia

last: Zamidar


title: Single nuclei RNA sequencing of mouse dorsal root and nodose ganglia in the setting of asthma-like airway inflammation.

summary: Type 2 inflammation contributes to the pathology of airway diseases such as asthma and eosinophilic pneumonia. Yet how sensory neurons innervating the airways respond to type 2 airway inflammation is poorly understood. The goal of this study was to characterize transcriptional changes in sensory ganglia innervating the lungs in the setting of type 2 airway inflammation induced by Alternaria allergen treatment.

overall_design: 8–10-week-old C57BL6 mice with the Jak1 gene conditionally deleted in Nav1.8-expressing neurons (homozygous for a floxed mouse Jak1 allele and crossed to Nav1.8-Cre = del-Jak1) or Cre-negative littermates (LM) were treated with 2 ug of Alternaria extract daily for four days to induce asthma-like airway inflammation. At day 5, nodose ganglia and thoracic dorsal root ganglia were harvested and the tissue was dissociated to yield single nuclei suspensions for downstream single-nuclei sequencing.


title: Single nuclei RNA and ATAC sequencing of mouse trigeminal ganglia at baseline and in atopic dermatitis-like disease.

summary: Type 2 inflammation contributes to the pathology of skin diseases such as atopic dermatitis and urticaria. Itch is a common symptom accompanying type 2 skin inflammation. Yet how chronic type 2 inflammation affects itch sensory neurons innervating the skin is poorly understood. The goal of this study was to characterize transcriptional changes in sensory ganglia innervating the skin in the setting of chronic type 2 skin inflammation.

overall_design: 8–10-week-old wild type C57BL6 mice were treated with topical application of calcipotriol or vehicle daily for 12 days to induce chronic atopic-dermatitis-like inflammation. At day 4, day 13, or day 43 (30 days post-treatment recovery), trigeminal ganglia innervating the treated cheek areas were harvested and the tissue was dissociated to yield single nuclei suspensions for downstream single-nuclei sequencing using the 10C Genomics multiome pipeline.


title: Sensory neuron gene expression changes in response to type 2 skin inflammation

overall_design: 8-10 week old wild type C57BL6 mice were treated with topical application of calcipotriol or vehicle daily for 12 days to induce chronic atopic-dermatitis-like inflammation. At day 13, trigeminal ganglia innervating the treated cheek areas were harvested and total RNA was extracted for sequencing.


title: Genome-wide CRISPR screening reveals a PKA-driven resistance mechanism to metformin for oral cancer prevention that can be exploited by combination with NSAIDs

status: Public on Sep 10 2025

city: La Jolla

first: Kuniaki

last: Sato

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

summary: Head and neck squamous cell carcinoma (HNSCC) is among the ten most common cancers worldwide and is associated with high morbidity and poor survival. Diminished HNSCC outcomes are often related to delayed diagnosis and treatment of occult progression of premalignant lesions, underscoring the need for effective and low risk chemoprevention strategies. In this regard, metformin has shown promising clinical activity for HNSCC prevention. Here, we performed a genome-wide CRISPR/Cas9 screen of metformin-treated HNSCC cells and identified activation of PKA signaling as the top resistance pathway.

overall_design: LentiCas9-Blast plasmid was used to generate Cas9-expressing Cal33 HNSCC cells. The human Brunello whole-genome CRISPR pooled library DNA was transformed by electroporation using electrocompetent cells, and the amplified library DNA was then extracted and purified using the QIAGEN Midi Prep Kit. The high-titer VSV- G pseudotyped lentiviral vector was generated and purified by VectorBuilder. The screen was performed by culturing Cal33-Cas9 cells divided into two treatment arms: vehicle or 1mmol/L metformin treatment. The cells were cultured until the population doubling level reached 18. The entirety of isolated genomic DNA extracted from cells was used for subsequent amplification through PCR to ensure capturing the full representation of the libraries. PCR products were sequenced on a HiSeq4000 instrument.

first: Thomas

last: Hoang

first: Jorge Silvio

last: Gutkind


title: Comparing PBMCs from patients with atopic dermatitis pre- and post-treatment with dupilumab

summary: Atopic dermatitis (AD) is an inflammatory skin condition characterized in part by elevations in type 2 immune cytokines such as IL-4 and IL-13. Dupilumab is a monoclonal antibody that targets the shared receptor for these cytokines and has shown remarkable efficacy in reducing inflammation in AD. The goal of this study was to study the changes that occur in circulating immune cells in AD at the single cell level in response to dupilumab treatment.

overall_design: After giving informed consent, patients with moderate to severe AD provided whole blood samples prior to starting on therapy with dupilumab. At a subsequent visit (around 4 months after initiating therapy), patients provided a second whole blood sample. PBMCs were isolated from whole blood and the 10X Genomics Chromium platform was used to generate single cell RNA-sequencing libraries, which were sequenced on an Illumina NovaSeq 6000.

first: Madison

last: Mack


title: Comparing PBMCs from patients with different pruritic conditions

summary: Chronic pruritis is a common and debilitating symptom that can manifest in multiple conditions. The goal of this study was to examine populations of circulating immune cells at the single cell level from patients with different pruritic conditions and compare them to healthy controls to identify possible biomarkers or therapeutic targets for chronic pruritis.

overall_design: After giving informed consent, patients with moderate to severe atopic dermatitis, chronic pruritis of unknown origin also known as chronic idiopathic pruritis, cutaneous T cell lymphoma, or healthy controls provided whole blood samples. Peripheral blood mononuclear cells were isolated from whole blood and the 10X Genomics Chromium platform was used to generate single cell RNA-sequencing libraries, which were sequenced on an Illumina NovaSeq 6000.


title: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [snRNA-seq]

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that critically regulates many behaviors related to reward and motivation. The NAc is implicated in several neuropsychiatric disorders, including major depressive disorder, schizophrenia, and substance use disorder. Rodent studies have identified spatial organization of heterogeneous medium spiny neuron (MSN) subtypes across the NAc core and shell, but the extent to which this cellular diversity and spatial organization is conserved in the human brain remains unclear. Here, we generated a spatiomolecular atlas of NAc cell types and spatial domains by integrating spatial transcriptomics and single-nucleus RNA sequencing data from postmortem NAc tissue from 10 neurotypical adult donors. We identified 20 transcriptionally unique cell populations and 8 spatial domains, including specialized D1 islands composed of distinct dopamine receptor 1 (DRD1) MSN subtypes, which were enriched for OPRM1. In contrast to a discrete core vs. shell division, we observed continuous spatial gradients of gene expression across MSN domains, suggesting a more complex organization of DRD1 and DRD2 MSNs. Cross-species comparisons demonstrated conservation of MSN subtypes and spatial features between human, rodent, and nonhuman primate NAc. Genetic enrichment analysis with stratified linkage disequilibrium score regression revealed specific spatial domains associated with risk for psychiatric and addiction-related traits. To investigate this further, we spatially mapped ligand-receptor interactions involving neuropsychiatric risk genes. Finally, we leveraged existing rodent NAc data to identify drug-responsive transcriptional programs and predict their spatial distribution in the human NAc. Collectively, we provide a spatiomolecular framework for understanding the human NAc and its relevance to neuropsychiatric disease.

overall_design: Ten neurotypical control postmortem human brain donors were selected for the single-nucleus and spatial transcriptomic study of the nucleus accumbens (NAc). We generated an integrated atlas with the two datasets of the human postmortem NAc to better understand the anatomical organization of heterogeneous medium spiny neuron (MSN) cell types. We identified multiple transcriptionally-distinct populations of MSNs that were organized in continuous gradients across the NAc.

first: Prashanthi

last: Ravichandran

first: Svitlana

middle: V

last: Bach

first: Robert

last: Phillips III

first: Madeline

last: Valentine

first: Nicholas

last: Eagles

first: Yufeng

last: Du

first: Ishbel

last: del Rosario

first: Ryan

last: Miller

first: Heena

last: Divecha

first: Madhavi

last: Tippani

first: Kelsey

last: Montgomery

first: Joel

last: Kleinman

first: Stephanie

last: Page

last: Hyde

first: Leonardo

last: Collado-Torres

first: Alexis

last: Battle

last: Hicks

first: Kristen

last: Maynard


title: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [Spatial Transcriptomics]

first: Keri

last: Martinowich

last: Ravichandran

last: Bach

middle: A

first: Thomas