title: Developmentally-inspired budding morphogenesis by optogenetic receptor tyrosine kinase signaling

status: Public on Apr 03 2026

city: Philadelphia

first: Ronald

last: Canlla

state: Pennsylvania

address: 107 Towne Building

institute: University of Pennsylvania

summary: The mammalian kidney relies on a branched network of collecting ducts for fluid transport and homeostasis. Replicating this network in vitro would parallelize function in synthetic replacement kidneys, yet current organoids have limited branching capacity. Here, we establish a developmentally-informed strategy to control organoid budding through optogenetic control of a receptor tyrosine kinase, RET. We first show pharmacological manipulation of RET signaling controls the extent of branching in mouse embryonic kidneys and human stem cell-derived kidney organoids. Next, we develop an optogenetic RET receptor (optoRET) that signals in a ligand-independent manner via blue light-mediated clustering. Epithelial cells expressing optoRET reproduce stereotyped RET signaling, scattering, and symmetry breaking in response to blue light. Human kidney organoids undergo budding with controllable orientation in response to spatially patterned optoRET stimulation. Our results establish ligand-free optogenetic control of branching and inspire new synthetic biology strategies for epithelial organoid design.

overall_design: RNA-seq was performed on human induced ureteric bud (iUB) organoids and iUB-optoRET organoids to characterize transcriptional responses to modulation of RET signaling. Day 12 iUB organoids were cultured under varying GDNF conditions (-GDNF, +GDNF, ++GDNF) or treated with a RET inhibitor (RETi). Day 11 iUB-optoRET organoids were cultured under combinations of presence or absence of GDNF and blue light stimulation (-GDNF/-Light, +GDNF/-Light, -GDNF/+Light, +GDNF/+Light) to assess ligand-dependent and optogenetic activation of RET signaling. Each condition includes 3 biological replicates.

first: Alex

last: Hughes

first: Louis

last: Prahl

first: Sandra

last: Shefter


title: Behavioral flexibility and gut microbiome as potential predictors of oral oxycodone self-administration

city: Stratford

first: Elizabeth

last: West

state: NJ

address: 2 Medical Center Dr

department: Neuroscience

country: USA

institute: Rowan University School of Osteopathic of Medicine

summary: Prescription opioids such as oxycodone have been widely used in the United States and have contributed to the ongoing opioid epidemic. While many individuals limit use to prescribed contexts, a subset transitions to misuse and, in some cases, to illicit opioid use. Identifying behavioral and biological factors that predict this vulnerability is critical for improving prevention and intervention strategies. Here, we investigated whether individual differences in behavioral flexibility and gut microbiome composition are associated with future oxycodone intake using a translationally relevant model of oral oxycodone self-administration in male and female Long-Evans rats. We established a model in which distinct intake phenotypes emerged, characterized by animals with high versus low oxycodone consumption. Behavioral flexibility, assessed using a contingency degradation task, was associated with oxycodone intake, identifying it as a potential behavioral biomarker of vulnerability. In parallel, oral oxycodone exposure altered gut microbiome composition, and microbiome features were associated with both behavioral flexibility and drug-taking behavior. These findings support a framework in which individual differences in opioid intake arise from the interaction of pre-existing behavioral traits and biological states, including gut microbiome composition which provides a foundation for identifying predictive biomarkers and developing individualized strategies to mitigate risk for opioid misuse.

overall_design: 16s rRNA sequencing of fecal samples from water exposed (control) and oxycodone exposed adult male and female Long-Evans rats at Pre (prior to self-administration) and Post (last days of self-administration, range: days 19 to 21) timepoints

first: Claire

middle: M

last: Corbett

first: Alexis

middle: E

last: O'Shall

first: Mark

last: Niedringhaus

middle: A


title: Aldosterone-induced gene expression changes in the brain [Multiomic]

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To uncover how aldosterone regulates gene expression in HSD2 neurons, we performed single-nucleus RNA sequencing on HSD2 neuron-enriched dorsal vagal complex samples from mice treated with vehicle or aldosterone for 24 hours. We then performed differential gene expression analysis on HSD2 neurons, comparing the vehicle and aldosterone-treated conditions.

overall_design: Male and female Hsd11b2-IRES-Cre mice were injected with AAV-DIO-H2b-mCherry to label HSD2 neurons. 10-14 days later, mice were then treated with vehicle or aldosterone (250 ng/hr) for 24 hours via mini osmotic pumps before brain harvesting. Single nuclei were isolated from the dorsal vagal complex of 1mm-thick coronal brainstem slices and samples were enriched for HSD2 neurons via fluorescence-activated nuclei sorting (FANS). Then, RNA profiling was performed on single nuclei from the dorsal vagal complex.

first: Miriam

middle: C

last: McDonough

first: Ahmet

last: Kuralay

first: Trevor

last: Butler

first: Silvia

last: Gasparini

first: Madelin

middle: R

last: Schwager

first: Christopher

middle: L

last: Jacobs

first: Anton

last: Gulko

first: Alysia

middle: B

last: Meyers

first: Linus

middle: T

last: Tsai

first: Joel

last: Geerling


title: Biomass Combustion Produces Hormone-like Pollutants: An Ignored Source

city: 南充市

first: ziru

last: zhou

state: 四川

address: 顺庆区涪江路234号

country: China

institute: 川北医学院

summary: Biomass burning, including household fuels and wildfires, affects billions globally, yet the unique health-related chemical components of PM2.5 emitted from these sources remain poorly understood. Here, we demonstrate that combustion of biomass—yak dung and pine—generates abundant hormone-like components within PM2.5, including natural, synthetic steroids and endocrine disruptors such as estradiol, testosterone enanthate and bisphenol A. Integrated network toxicology and whole-transcriptome sequencing reveal that these hormone compounds may exert distinct, fuel-specific respiratory toxicity by targeting critical genes (e.g., HIF1A or INHBA), functions (e.g., regulation of progesterone secretion or protein serine/threonine kinase activity) and pathways (e.g., vitamin digestion and absorption or RNA polymerase) via multi-level RNA regulation and mutagenic events. Our modelling estimates that mitigating this exposure could prevent ~66,000 premature deaths and yield economic benefits exceeding $11 billion annually. These findings uncover a previously unrecognized class of environmental hormonal pollutants generated by biomass combustion, redefine the health risks of air pollution, and provide a mechanistic foundation for advancing environmental justice and achieving Sustainable Development Goals in vulnerable populations worldwide.

overall_design: RNA-seq profiling of A549 cells under control (CK1, CK2, CK3) and experimental treatment (P1, P2, P3,Y1,Y2,Y3) conditions. The study includes three biological replicates per condition to investigate transcriptomic changes in response to the experimental treatment.


title: EpCAM identifies a developmentally poised DN thymocyte subset that drives T-cell production

status: Public on Apr 04 2026

city: chongqing

first: Debao

last: Li

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

institute: Chongqing International Institute for Immunology

summary: The age-related decline in thymic function is a major contributor to immune senescence. While stromal degeneration is a known cause, the intrinsic heterogeneity and regulatory mechanisms within early thymocyte progenitors are poorly understood. Here, we report that the epithelial cell adhesion molecule (EpCAM), conventionally a marker of thymic epithelial cells, identifies a functionally distinct subset within double-negative (DN) thymocytes. EpCAM⁺ DN cells are transcriptionally and epigenetically primed for T-cell lineage commitment, exhibit superior proliferative and differentiation potential in vitro, and serve as the dominant precursors for T-cell reconstitution in vivo. This progenitor pool expands acutely following thymic injury but undergoes pronounced contraction with age, a trajectory conserved in the human thymus. Our findings redefine EpCAM as a marker of a developmentally competent DN thymocyte state, whose erosion contributes to thymic involution and presents a potential target for regenerative strategies.

overall_design: EpCAM⁺ DN3 cells and EpCAM⁻ DN3 cells were lysed for ATAC-seq. After DNA fragmentation, purification, and amplification, the DNA products were sequenced by HaploX.

first: Xuemin

last: Sun

first: Yushi

last: Ran

first: Lang

last: Xiao

first: Weiwu

last: Gao

first: Yi

last: Zhang

first: Yuzhang

last: Wu


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [RNA-seq]

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: Depression is a globally prevalent disabling mental illness with serious social hazards. Previous studies suggest that neuroinflammation plays an important role in the pathogenesis of depression, but the underlying mechanism remains elusive. Endogenous retrovirus (ERVs) is a type of transposable elements (TEs), consists around 8% of human genome but are mostly silenced in vivo. Repressive histone modifications H3K9me3 mediated by the methyltransferase SETDB1 plays a key role in maintaining silencing of ERVs. In this study, we constructed Setdb1-CK-cKO (KO) transgenic mice. Behavioral tests showed that the KO mice exhibited anxiety-depression-like behaviors compared to wild type (WT). Cortex snRNA-seq analysis revealed significant changes in astrocytes in addition to excitatory neurons, with the emergence of a new sub cluster of astrocytes in the KO whose transcriptional profile exhibited specific ERVs activation. We observed a large number of GFAP-positive cells in the KO cortex and striatum by Immunostaining, suggesting reactive astrogliosis. Transcriptomic analysis of astrocytes revealed significant upregulation of genes associated with inflammation in the KO cortex, including multiple chemokine genes. To investigate the potential molecular mechanism underlying "endogenous" neuroinflammation in KO mice, we focused on the purinergic receptor P2X7R, which has been reported to play an important role in mediating neuroinflammation and emotional behaviors. Most importantly, we found that the expression of P2rx7 was significantly upregulated in the KO neuron. We applied multiple epigenomic methods (RNA-seq, ATAC-seq, H3K9me3 ChIP-seq) to analyze in detail the molecular mechanism by which SETDB1 regulates the P2rx7 gene expression, and identified a novel enhancer fragment, mE1. We further constructed a SETDB1 knockout human 293T cell line and examined chromatin accessibility by ATAC-seq. We found a regulatory fragment hE1 with enhancer activity, which was present at a similar location in the human P2RX7 locus, suggesting that this mechanism is conserved between human and mouse. Knockout of P2X7R effectively ameliorated neuroinflammation and partially alleviated neuronal dysfunction as well as behaviors in Setdb1-CK-cKO mice.

overall_design: Astrocyte specific RNA-seq in wildtype and Setdb1-CK-cKO mice, two animals combine to one sample, two samples per group. Neuronal nuclei RNA-seq in wildtype and Setdb1-CK-cKO mice, three animals per group. Cortex tissue RNA-seq in wildtype, Setdb1-CK-cKO and Setdb1-CK-cKO/P2rx7 knock out mice, three animals per group.

first: Yueyan

last: Zhu


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [ChIP-seq]

overall_design: H3K9me3 ChIP-seq of astrocyte in wildtype and Setdb1-CK-cKO mice cortex, three animals per group.


title: Widespread purine bias in bacterial genes driven by runaway transcription

city: Cambridge

first: K Julia

last: Dierksheide

state: MA

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

summary: Genes in many bacteria are rich in purine nucleotides and poor in pyrimidines. We show that this purine preference is critical for gene expression because it prevents premature transcription termination in species that exhibit runaway transcription. In contrast to coupled transcription-translation, runaway RNA polymerases that outpace trailing ribosomes have exposed nascent RNA and are vulnerable to the termination factor Rho. Using a massively parallel reporter assay in Bacillus subtilis, we found that Rho-dependent termination requires a high C-to-G skew and high T content. Consequently, purine-rich coding (sense) sequences escape premature termination, whereas the correspondingly pyrimidine-rich antisense sequences are targeted by Rho and transcriptionally silenced. This purine requirement drives biased codon usage in most bacterial species with runaway transcription, except in lineages that have lost Rho. Our results suggest that the avoidance of premature transcription termination imposes major constraints on nucleotide content during genome evolution and adaptation of foreign genes.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Antibiotic selection-based reporter assay was applied to assay for transcription termination sites encoded in gDNA fragments. Assay was performed in B. subtilis, on fragments of the B. subtilis 168 and E. coli MG1655 genomes. Antibiotic selection assay was performed in the presence and absence of the Rho inhibitor bicyclomycin-benzoate (BCM) to separate Rho-dependent termination events. Sequencing data was collected by gDNA sequencing of the B. subtilis library before (preselection) and after (postselection) selection at the site of the fragment integration to measure the representation of each genomic fragment in the library before and after antibiotic selection. Transcription termination drives antibiotic resistance, increasing representation in post-selection sample.

first: James

last: Taggart

first: Grace

last: Johnson

first: Gene-Wei


title: miR-200a-3p regulates gene expression of diabetic cardiomyopathy in murine cardiomyocytes

city: Changchun

first: Zhanchuan

last: Ma

state: Jilin

institute: First Hospital of Jilin University

summary: Hsa-miR200a-3p play a crucial role in regulating glycometabolism and diabetic progression. But how hsa-miR200a-3p impact diabetic cardiomyopathy development is sitill ill-defined. Here,we found that the expression of hsa-miR200a-3p was significantly reduced in mouse cardiomyocytes HL-1 cells after high glucose stimulation. And we systemically investigated the overall mRNA expression level under hsa-miR200a-3p mimics, or inhibitors treatment in HL-1 at high glucose conditions. High-throughput sequencing results showed that 744 genes were significantly differentially expressed by high glucose stimulation in mouse cardiomyocytes. And when compared with the control group, 414 genes were differentially expressed after hsa-miR200a-3p overexpression; 33 genes were differentially expressed after added hsa-miR200a-3p inhibitor. WGCNA analysis found that all DEGs could be divided into five modules, and the gene expression pattern in the yellow module was positively correlated with hsa-miR200a-3p overexpression group and negatively correlated with hsa-miR200a-3p inhibitor group.We observed that these DEGs were mostly enriched in RrRNA processing, translation, and RNA transport. Then, we further identified three DEGs (Gm13205, Flnc, and Ntmt1) were found to be commonly expressed in down-regulated DEGs of the hsa-miR200a-3p mimics group and up-regulated DEGs of the hsa-miR200a-3p inhibitor/ high glucose groups. In addition, we predicted that Srm andTspan4 were two main targets for hsa-miR200a-3p in HL-1 cells. These findings demonstrate that high glucose suppressed hsa-miR200a-3p in vitro, and hsa-miR200a-3p may involve in diabetic cardiomyopathy development.

overall_design: We transfected mimics or inhibitor of miR-200a-3p  in Hl-1 cell line, coupled with RNA-seq sequences, to comprehensively reveal the biological function of miR-200-3p in HL-1 cell and analyze the alterations of transcriptional profiles.

first: Yida

first: Huanfa

last: Yi

first: Zheng

last: Xu


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [ATAC-seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ATAC-seq of neuron in wildtype and Setdb1-CK-cKO mice, three animals per group. ATAC-seq of 293T cell line in control and SETDB1 knockout(sg-SETDB1) group, three replicate wells per cell line. ATAC-seq of astrocyte in wildtype and Setdb1-CK-cKO mice, two animals combine to one sample, two samples per group.


title: Chronic manganese exposure with and without latency period in hiPSC-derived cortical cultures

city: West Lafayette

first: Aaron

last: Bowman

state: IN

address: 700 Mitch Daniels Blvd

department: School of Health Sciences

institute: Purdue University

summary: Behavioral deficits encompassing motor, cognitive, and psychological domains can emerge after removal of manganese (Mn) exposures in humans and other mammals. While epidemiological studies provide substantial evidence supporting latent persistent Mn neurotoxicity, reproducing such effects in cellular and non-mammalian model systems has slowed mechanistic understanding. Here we report in human induced pluripotent stem cell (hiPSC)-derived cortical cultures that chronic Mn exposure elicits clear latent and persistent neurotoxic effects in gene expression and functional outcomes. To identify persistent and latent effects, and investigate underlying mechanisms, single-cell RNA sequencing was employed in the hiPSC model to provide a comprehensive cell-type specific comparison of transcriptomic changes immediately at the termination versus after a prolonged cessation of chronic Mn exposures. Transcriptomic alterations revealed clear latency of effects after Mn cessation that were not detected immediately following the 40-day exposure. Identified alterations support the linkage between the latent and persistent effects of chronic Mn exposure and a broad range of neurodegenerative pathogenesis and provide insight into the cellular pathways involved.

overall_design: An hiPSC line from a de-identified neurotypical male control (CD10) was derived into cortical culture following the dual-SMAD inhibition protocol. Cultures were maintained till differentiation day 110 before Mn exposures were applied. The before cessation group was exposed for 40 days at 0, 0.05, 0.5, and 5 µM MnCl2 directly added into the culture media. This group was harvested immediately after the termination of the exposure. The cessation group were further cultured in no-Mn containing media for another 10 days before harvested. Each group had 1 replicate. Harvested cells were processed for library preparation following instructions from 10X Genomics. Libraries sequencing was performed by the Purdue Genomic Facility on the NovaSeq X platform at a depth of 500 million reads per sample.

first: Xueqi

last: Tang

first: Anke

last: Tukker

first: Hyunjin

last: Kim

first: Phillip

middle: J

last: SanMiguel

first: Jyothi

last: Thimmapuram

first: Michael

last: Aschner


title: MicroRNA-224 Orchestrates the BMP Pathway and Represents a New Therapeutic Target for Pulmonary Arterial Hypertension

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Mice were maintained under hypoxic conditions for 3 weeks with weekly Sugen injections and were then randomized to receive an intratracheal injection of a chemically modified antisense oligonucleotide targeting miR-224 (LNA-224) or a control antimiR (LNA-Ctrl; 5 mg/kg each) at week 3. A separate group of mice was maintained under normoxic conditions and received an intratracheal injection of LNA-Ctrl at week 3 (Nox). All mice were sacrificed at week 6, and scRNA-seq analyses were performed.

overall_design: We collected  single nulcei in 9 mouse lungs and performed single nuclei sequencing with 10X 3' DE assay(V3).

first: Yassine

last: Sassi

first: Aymen

last: Halouani

first: Martin

last: Walsh

first: Lahouaria

last: Hadri


title: Genotoxicity profiling reveals distinct platform- and cell type–specific effects in therapeutic gene editing for genetic hyperinflammation

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Base editors enable precise correction of point mutations without requiring DNA double-strand breaks, yet platform– and cell type–specific genotoxicities remain incompletely characterized. Here, we applied cytosine base editing (CBE) to disrupt a cryptic splice-site mutation in the Unc13d locus of Jinx mice, a model of familial hemophagocytic lymphohistiocytosis type 3 (FHL3). Efficient editing (62–89%) in fibroblasts, T cells, and hematopoietic stem cells (HSCs) restored Unc13d splicing, reconstituted cytotoxic T cell function, and protected mice from virus-triggered hyperinflammation after transplantation of edited HSCs. Comparative genotoxicity profiling revealed distinct platform- and cell type–specific patterns: hyperactive CBE induced broader off-target activity and more structural variants than CRISPR–Cas9. While off-target sequence edits persisted, the stability of CBE-induced chromosomal translocations differed between cell types. These findings establish therapeutic base editing for a genetically predisposed hyperinflammatory syndrome and underscore the importance of context-specific safety profiling to guide clinical translation of genome editors.

overall_design: Murine T cells, HSCs and MEF cells were edited using Cas9 nuclease or evoCDA1-BE4max at the Unc13D locus. CAST-Seq was performed to assess the formation of chromosomal translocations between the on-target site and potential off-target sites.

first: Lei

last: Lei

first: Masako

last: M. Kaufmann

first: Jessica

last: Lao

first: Gudrun

last: Thoulass

first: Sandra

last: Ammann

first: Hui

last: Xiao

first: Manuel

last: Rhiel

first: Viviane

last: Dettmer-Monaco

first: Julian

last: Grünewald

first: Jamal

last: Alzubi

first: Bret

last: R. Miller

first: Kristoffer

last: Weißert

first: Linda

last: Gräßel

first: Christoph

last: Schell

first: Anna

last: Lena Illert

first: J. Keith

last: Joung

first: Melanie

last: Boerries

first: Tatjana

last: I. Cornu

first: Stephan

last: Ehl

first: Miriam

last: Erlacher

first: Peter

last: Aichele

first: Toni

last: Cathomen


title: Inhibition of inflammation and senescence with azole compound C7 enables expansion of hematopoietic stem and progenitor cells

city: Singapore

first: John

last: Ouyang

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

summary: Human hematopoietic stem and progenitor cells (HSPCs) derived from umbilical cord blood (UCB) are often insufficient in quantity for transplantation, necessitating efforts for ex vivo expansion. We previously developed a novel azole-based small molecule, C7, as a structural analog of the p38 mitogen-activated protein kinase inhibitor SB203580. C7 mediated robust ex vivo expansion of UCB HSPCs from unselected mononuclear cells, compared to its structural analogs and other published compounds. However, the molecular underpinnings of C7’s potency remained unclear. In this work, we demonstrate that C7 preferentially enhances the proliferation and viability of early HSPC subsets upon direct culture with pre-isolated HSPCs, while limiting mitochondrially-derived reactive oxygen species production linked to oxidative stress. C7 treatment enhances hematopoietic stem cell self-renewal and in vivo multilineage reconstitution without T- or myeloid lineage bias. Unlike existing p38 inhibitors, C7 targets multiple kinases and pathways to achieve superior HSPC expansion through suppression of NFκB and IL-10 inflammatory signaling and attenuation of stress/senescence‑associated markers (e.g., SERPINB2 and CDKN1A/p21). This mechanism of action of C7 is distinct from those of other existing compounds used for ex vivo HSPC expansion and has implications for application in other ex vivo culture platforms and clinical settings.

overall_design: UCB-CD34+ cells were cultured with C7 or DMSO as described previously for 3, 7 and 11 days. Harvested cells were then resuspended into single-cell suspensions into 1000-6000 cells/µl to be loaded into Chromium microfluidic chips with targeted cell recovery of 10,000 using the Chromium Controller (10x Genomics, USA). Single-cell RNA-seq libraries were prepared according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10 X Genomics, USA; PN-1000268). Captured libraries were sequenced on the Novaseq 6000 sequencer analyzer at PE150 and sequencing depth of 20,000 read pairs per cell (Novogene, China).

middle: F

first: Ze Hui

last: Kok

first: William

last: Hwang


title: Toll-Like-Receptor 5 Reduces Lung Dysbiosis and Protects Against Pulmonary Fibrosis

city: RTP

first: Thomas

last: Randall

state: NC

address: 101 TW Alexander

institute: NIEHS

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

overall_design: Refer to individual Series


title: Synovial sarcoma with prominent myxoid stroma and negative epithelial markers

city: Niigata City

first: Tomohiro

last: Miyazaki

address: 1-757 Asahimachi-Dori, ChuoKu

department: Orthopedics

country: Japan

institute: Niigata University Graduate School of Medical and Dental Sciences

summary: Bulk RNA sequencing was performed on two human synovial sarcoma specimens from a single patient: a primary thigh soft-tissue tumor and a recurrent subcutaneous thigh lesion.

overall_design: Two tumor samples from one patient were subjected to bulk RNA-seq. Sequencing reads were used for quality assessment, alignment/quantification, and fusion transcript screening.

first: Naoki

last: Oike

first: Takashi

last: Ariizumi

first: Hiroyuki

last: Kawashima


title: Dual antiviral and anti-inflammatory effects of BAY 11-7082 in SARS-CoV-2 infection via inhibition of the canonical NF-κB signaling pathway

city: Taipei

first: Po-Chih

last: Wu

address: No.109, Ln. 130, Sec. 1, Academia Rd., Nangang Dist., Taipei City 115, Taiwan

country: Taiwan

institute: TFDA

summary: The continued emergence of SARS-CoV-2 variants and persistent inflammatory complications of COVID-19 highlight the urgent need for therapeutics with both antiviral and anti-inflammatory properties. Despite intensive global efforts, no approved antiviral therapy with these dual functions has yet been developed, representing a significant gap in current COVID-19 treatment strategies. In this study, we identify BAY 11-7082 (BAY) as a dual–action compound that inhibits SARS-CoV-2 replication and the production of virus-induced proinflammatory cytokines and chemokines, including IL-6, IL-8, CXCL1, and CXCL2. BAY predominantly exerts its antiviral activity at the post-entry stage of the viral life cycle. Mechanistically, BAY potentially interacts with SARS-CoV-2 NSP14 and inhibits virus-induced phosphorylation and degradation of IκBα, suppressing NF-κB activation through the IKK-IκBα signaling axis. Furthermore, BAY exhibits potent antiviral activity against multiple SARS-CoV-2 variants of concern (VOCs). Collectively, these findings support the potential of BAY as a dual-action therapeutic candidate, combining antiviral and anti-inflammatory effects, against SARS-CoV-2 and its emerging variants.

overall_design: Transcriptomic changes were profiled in A549-ACE2 cells under four conditions: mock control, SARS-CoV-2 infection (MOI = 1), and SARS-CoV-2 infection treated with BAY 11-7082 at 10 µM or 20 µM. RNA-seq was performed to characterize host responses to viral infection and to assess dose-dependent transcriptional effects of BAY 11-7082, providing insight into drug-associated regulatory changes and potential antiviral mechanisms.

first: Chin-Mao

last: Hung

first: Meng-Chang

last: Lee

first: Ming-Sian

first: Chun-Hsi

last: Tso

first: Jia-Chuan

last: Hsu

first: Der-Yuan

last: Wang

first: Hao-Ai

last: Shui

first: Chi-Tun

last: Tang

first: Chia-Wen

last: Shih


title: Aldosterone-induced gene expression changes in the brain [scRNA-Seq]

first: Jon

last: Resch

first: Miriam

last: McDonough

first: Ahmet

last: Kuralay

first: Trevor

last: Butler

first: Silvia

last: Gasparini

first: Madelin

last: Schwager

first: Christopher

last: Jacobs

first: Anton

last: Gulko

first: Alysia

last: Meyers

first: Linus

last: Tsai

first: Joel

last: Geerling


title: Mechanotransduction unifies healthy non-diabetic wound healing over time by promoting a Cd14+/C1qa+ fibroblast subpopulation

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: Diabetes is a major growing public health concern, but the impact on cellular impairments in chronic wounds remains incompletely understood. Fibroblasts, key players in all phases of wound healing, are particularly responsive to mechanotransduction. Here, we characterize fibroblast heterogeneity in genetically induced and pathophysiological diabetic murine wounding models across all wound healing phases. Full-thickness excisional wounds were created on the dorsum of C57BL/6 non-diabetic wild-type (WT) mice (N-DB), WT-mice fed a high-fat diet to create pathophysiologic diabetes (P-DB), and leptin-receptor-deficient mice, a genetically induced diabetic model (G-DB). Tissue was submitted for single-cell RNA sequencing at postoperative days (PODs) 0, 2, 7 and 30. Both G-DB and P-DB significantly impaired wound healing compared to N-DB. N-DB expressed distinct myeloid-like Cd14+/C1qa+ angiogenic fibroblasts at PODs 2, and 7. Mechanotransduction pathways FAK and MAPK were consistently upregulated in N-DB fibroblasts and depleted in both diabetic models. G-DB upregulated WNT-activated Dpp4+ fibrotic fibroblasts at POD7 compared to N-DB. Thus, mechanotransduction pathways are present in physiologically healing fibroblasts and are selectively depleted in both pathophysiologic and genetically induced diabetes. In genetically induced diabetes, overactivation of canonical and non-canonical WNT pathways overwhelms cells and impairs healing processes. Transcriptomic insights into these mechanotransducive perturbations may lead to new therapies for diabetic wound repair.

overall_design: scRNA-seq was performed on murine cells collected from skin and wounded tissue .

first: Geoffrey

last: Gurtner

first: Abdelrahman

last: Alsharif

first: Katharina

last: Berryman


title: Aldosterone-induced gene expression changes in the brain


title: Refining NOA diagnosis: a dual approach through immunostaining subclassification and metabolic markers in Sertoli cells

city: beijing

first: KehKooi

last: Kee

address: 30 Shuangqing Road

institute: Tsinghua University

summary: Background Non-obstructive azoospermia (NOA) is a leading cause of male infertility, affecting approximately 1% of men worldwide. Accurate pathological diagnosis and subclassification of NOA remain challenging due to the lack of reliable markers for germ cells (GCs) and Sertoli cells (SCs) within seminiferous tubules. Current histopathological evaluation relies on Hematoxylin and Eosin (H/E) staining, which lacks molecular specificity and cannot precisely quantify GCs or identify the stage of spermatogenic arrest. This limits both prognostic accuracy and the development of targeted therapeutic strategies. The identification of robust cellular and molecular markers is therefore essential to improve diagnosis, subclassification, and clinical management of NOA. Methods We performed immunofluorescence staining for SOX9, DAZL, and SYCP3 on 146 testicular samples to refine NOA subtyping. Single-cell RNA sequencing (scRNA-seq) was conducted on samples from 5 NOA patients, integrated with data from healthy and obstructive azoospermia (OA) controls. Candidate markers identified from SC-specific transcriptional profiles were validated via immunofluorescence in human and mouse testicular tissues. Findings Immunostaining enabled a refined classification of NOA into three subtypes: Maturation Arrest-Meiotic Arrested (MA-MA), Maturation Arrest-Premeiotic Arrested (MA-PA), and Sertoli cell-only (SCO). The scRNA-seq revealed that SCs in adult NOA patients exhibit an immature transcriptional state resembling prepubertal SCs, characterized by a distinct metabolic profile. From this profile, we identified LDHB and PKM2 as significantly upregulated markers in NOA SCs. Immunofluorescence confirmed their elevated expression in human NOA samples and in immature mouse testes. Interpretation Our integrated approach establishes a novel immunostaining-based classification for NOA and identifies an immature SC state as a key pathological feature. The overexpression of LDHB and PKM2 in SCs provides two new candidate biomarkers for improving the pathological diagnosis and subclassification of NOA, with potential implications for future diagnostic and therapeutic strategies.

overall_design: The fresh human testis samples were minced with sterilized scissors after washing three times with PBS, then were digested in 1 mg/ml collagenase type IV at 37C for 15 min. During the process of digestion, the tissues were pipetted up and down once in every 5 minutes. The digestion process was stopped with DMEM (containing 10% FBS). The cell suspension was filtered through 40-μm nylon mesh. After centrifugation, the cells were suspended in DMEM (containing 10% FBS) to 800-1200 cells per microliter for immediate scRNA-seq

first: Defeng

last: Liu

first: Mengqing

last: Xie

first: Xiaoyu

last: Feng

first: Yu

last: Tan

first: Jianlin

last: Liang

first: Hui

last: Jiang


title: Inherent Specificity and Variation Sensitivity as Quantitative Metrics for RBP Binding

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

summary: Interactions between RNAs and RNA binding proteins (RBPs) regulate gene expression in eukaryotic cells. RNA-RBP affinity measurements in vitro reveal diverse binding preferences, yet approaches to directly compare motif specificities across RBPs are lacking. Here, we introduce two quantitative metrics: inherent specificity, which measures how selectively an RBP distinguishes its strongest binding motif from all possible motifs, and variation sensitivity, which assesses tolerance to single nucleotide variations within a preferred motif. Analyzing high-throughput sequencing datasets, we compared these metrics across 100 RBPs in vitro and 27 RBPs in cells, finding a strong correlation between in vitro and cellular measurements for RBPs that bind RNA independently of local structural context. Through RNA binding domain swap CLIP experiments between low-specificity RBM25 and high-specificity HNRNPC, we demonstrated that sequence specificity can be measurably transferred between protein contexts. Using these insights, we developed mathematical models to understand how inherent specificity and mutational sensitivity shape competitive RBP binding in ways not predicted by affinity alone. These models reveal that low-specificity RBPs can functionally enhance the specificity of high-specificity RBPs by occupying non-target sites. Overexpression of low-specificity RBM25 in cells recapitulates this effect, sharpening HNRNPC binding toward its preferred target motifs. Together, this work establishes inherent specificity and variation sensitivity as a quantitative basis for modeling how RBPs compete for RNA targets, complementing affinity-based descriptions of RNA-RBP interactions.

overall_design: To test whether a low-specificity RBP can focus the binding of a high-specificity RBP toward its preferred target sites in cells, we performed competition CLIP. HEK293 cells stably expressing V5-tagged wildtype or mutant RBM25 under doxycycline-inducible control were used. In these cells, both V5-RBM25 (via V5 IP) and endogenous HNRNPC (via anti-HNRNPC IP under V5-RBM25 overexpression) were profiled by CLIP-seq. To assess the contribution of endogenous HNRNPC tetramerization, V5-HNRNPC CLIP (wildtype and mutant) was performed with and without siRNA-mediated knockdown of endogenous HNRNPC. UV crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq) was performed to compare binding profiles across all conditions.

first: Joseph

last: Luna

first: Soon

first: Sashi

last: Singh

first: Rohan

last: Krishna

first: Vidusha

last: Kothwela


title: Transcriptomic analysis of therapy-naïve and alectinib-treated H3122 xenograft tumors from NSG and humanized HGF-NSG mice

city: Tampa

first: Bina

last: Desai

state: Florida

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

summary: To uncover the identity of the HGF-independent stromal-mediated resistance mechanism(s), we performed transcriptomic analyses of treatment-naïve and alectinib-treated H3122 xenograft tumors from NSG and humanized HGF-NSG (hHGF-NSG) mice. Xenograft tumors of H3122 cell model were used to perform bulk-RNA sequencing. Reads were mapped to both human and murine genomes, enabling simultaneous assessment of the tumor and stromal compartments. Our transcriptional analyses revealed the emergence of the HGF-dependent differences only after six weeks of alectinib treatment. Pathway enrichment analyses revealed marked changes in multiple pathways associated with extracellular matrix (ECM). Altogether, the transcriptomic analysis supported the potential involvement of tumor cell-ECM interactions in HGF-independent mediation of stromal-mediated resistance to alectinib.

overall_design:
Bulk RNA-sequencing profiling of therapy naïve and alectinib treated (2 weeks and 6 weeks) H3122 xenograft tumors from NSG and hHGF-NSG mice, mapped to human reference genome, to uncover changes in the tumor cell compartment.  See fpkm_hg38.txt.
Also mapped to murine reference genome.  See fpkm_mm10.txt.

first: Andriy

last: Marusyk

first: Sandhya

last: Prabhakaran


title: Integrative analysis reveals ciliary dysfunction and compartmentalized LCN2 expression as distinct features of COVID-19 [PBMC]

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

summary: The unique pulmonary pathophysiology of COVID-19 compared with other respiratory viral infections remains poorly understood. We performed integrative bulk and single-cell RNA sequencing on bronchoalveolar lavage fluid (BALF) from patients with COVID-19 (n=24) or influenza (n=10) and healthy controls (n=10). While influenza primarily induced conventional inflammatory responses, COVID-19 triggered distinct microenvironmental remodeling characterized by a specific cilium-related gene signature (e.g., DNAH9, FOXJ1) and expansion of ciliated and airway epithelial cells. Cross-tissue comparison with peripheral blood mononuclear cells uncovered a compartmentalized immune response, particularly for Lipocalin-2 (LCN2), which showed opposite expression trends between the lung and systemic circulation. This study identifies ciliary dysfunction and epithelial-immune crosstalk as key features distinguishing COVID-19 from influenza and highlights epithelial-derived LCN2 as a robust, compartmentalized biomarker for disease severity.

overall_design: This study utilized bulk RNA sequencing to characterize the transcriptomic landscape of the lower respiratory tract and systemic circulation during SARS-CoV-2 infection. BALF and PBMC samples were collected from COVID-19 patients, influenza patients (BALF only), and healthy controls. RNA was extracted using TRIzol reagent and sequenced via a commercial platform. Differential expression analysis was performed using the DESeq2 package, and batch effects across datasets were corrected using limma's removeBatchEffect function. The analysis focused on identifying COVID-19-specific signatures by comparing profiles against both healthy controls and influenza-infected samples.

first: Peiming

last: Huang

first: Haiqiong

last: Yu

first: Wenjuan

last: Cao

first: Yixin

last: Zhang

first: Jianteng

last: Zeng

first: Minghua

last: Chen

first: Jingjing

last: Luo

first: Xiaojun

last: Xiao

first: Shuangxin

last: Wu

first: Jianquan

first: Ting

last: Pan


title: Single-Cell Transcriptomic Profiling of Male Zebrafish hypothalamus: Investigating the Impact of CCK1/CCK2 Knockout on hypothalamus Function

city: Wuhan

first: Hangyu

last: Li

state: 湖北省

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: This study explores the effects of CCK1 and CCK2 knockout on the hypothalamus of male zebrafish using single-cell RNA sequencing (scRNA-seq). Two groups were analyzed: the CCK1/CCK2 knockout (KO) group and the wild-type (WT) group. hypothalamus tissues were dissociated into single cells, followed by RNA sequencing to examine changes in gene expression. The results show how CCK receptor loss impacts hypothalamus cell function and gene expression, providing insights into the role of CCK in zebrafish hypothalamus regulation and endocrine function.

overall_design: Male zebrafish (6 months old) from two groups, CCK1/CCK2 knockout (KO) and wild-type (WT), were used. hypothalamus tissues from 30 fish per group were collected for analysis.


title: The impact of KLF2-KLF3 regulated cellular localization on exhausted T cell differentiation [scMultiome-seq]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: During chronic viral infection, CD8 T cells lose effector function and acquire an exhausted phenotype, a process accompanied by changes in migratory behavior and tissue residency. Exhausted CD8 T cells differentiate from stem-like progenitor (Tpro) cells into either circulating, cytotoxic effector-like (Teff) cells or tissue-resident terminally exhausted (Texh) cells. However, whether these migratory changes passively reflect cell state or actively influence exhaustion trajectories remains unclear. Here, we identify a transcriptional circuit involving Krüppel-like factor 2 (KLF2) and its homolog KLF3 that links migratory program to CD8 T cell differentiation during exhaustion. Using multi-module approaches, we show that KLF2 primarily promotes the expression and chromatin accessibility of migratory genes in Tpro and Teff subsets, while KLF3 limits these programs by repressing Klf2 transcription and competing for shared genomic binding sites. Enhancing circulation through enforced S1PR1/S1PR5 expression or CD69 deletion biases differentiation toward effector-like fates and away from terminal exhaustion, suggesting that cellular localization can influence, not just reflect, CD8 T cell fate decisions. We further describe an integrated feed-forward and feedback loop in which KLF2 induces KLF3, which in turn constrains KLF2 transcription and binding to shared genomic loci. This reciprocal regulatory circuit modulates the balance between migration and tissue residency, thereby tuning the differentiation of CD8 T cells in chronic infection. These findings provide mechanistic insight into how transcriptional regulation of migratory behavior contributes to cell fate decisions during T cell exhaustion.

overall_design:
EXP-1: 10x single-cell Multiome-seq with sgCtrl and sgKlf2 P14 T cells sorted from spleen on day 21 post LCMV Clone 13 infection. sgCtrl data has been deposited and published as GSM6921318 and GSM6921319 in Series GSE222347 (Kharel, A. et al. Cell Rep. 2023). Only sgKlf2 data is deposited here.
EXP-2: 10x single-cell Multiome-seq with sgCtrl and sgKlf3 P14 T cells sorted from spleen on day 21 post LCMV Clone 13 infection.

first: Jian

last: Shen

first: Arjun

last: Kharel

first: Kexin

last: Gai


title: Nuclear envelope rupture causes RNA polymerase loss in LMNA cardiomyopathy

city: Cincinnati

first: Kohta

last: Ikegami

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Localized rupture of the nuclear envelope has been reported in various pathologies, including cancer, neurodegenerative disease, myocardial infarction, as well as dilated cardiomyopathy caused by Lamin A/C gene mutations (LMNA-DCM). Whether and how nuclear rupture contributes to disease remains unclear. Here, we report that nuclear rupture causes global transcriptional deficiency in a mouse model of LMNA-DCM. We observed that ruptured nuclei lost chromatin-bound RNA polymerase II, leading to downregulation of numerous genes essential for cardiomyocyte structure and function. Notably, over one third of ruptured nuclei resealed and regained transcription. Resealing involved the ESCRT-III membrane remodeling complex and was cardioprotective, as its blockade increased rupture frequency and accelerated cardiomyopathy. However, resealing was ineffective: resealed nuclei re-ruptured at twice the resealing rate and ten-fold faster than the de novo rupture rate. A mathematical model predicted a steady accumulation of ruptured nuclei despite ongoing resealing. Consistently, a human LMNA-mutant heart contained numerous ruptured nuclei at the time of disease presentation. These findings link nuclear rupture to organ deterioration through global transcriptional deficiency and suggested rupture repair as a critical modifier of nuclear rupture-associated conditions.

overall_design: RNA Polymerase II ChIP-seq was performed in mouse cardiomyocytes isolated from cardiomyocyte-specific Lmna knockout mice (Lmna F/F; Myh6MerCreMer) or wild-type control mice  (Lmna +/+; Myh6MerCreMer). Both mouse groups (n=3) were administered with tamoxifen, which induced Lmna knockout from the Lmna F/F allele. Cardiomyocytes were isolated at 2 weeks post tamoxifen. Cardiomyocyte chromatin extract was mixed with human BJ-5ta fibroblast chromatin, which served as a spike-in control, prior to ChIP. A fraction of the mixed chromatin was withdrawn as an input control. ChIP was performed with the anti-Rpb1 NTD(D8L4Y) antibody, which recognizes the largest subunit of the Pol II complex. Libraries from ChIP and input DNA were generated using the NEBNext Ultra II library preparation kit, and then sequenced using NovaSeqX with the paired-end 100-base mode.

first: Atsuki

last: En


title: Transcriptional profiling of immortalized human periodontal ligament cells subjected to compressive force

city: Seoul

first: Hanjin

last: Bae

address: 28 Yeongeon-dong

country: South Korea

institute: Seoul National University Hospital

summary: An immortalized human periodontal ligament cell line derived from cementifying fibroma cells was cultured in vitro and subjected to compressive force for 24 hours or maintained as untreated controls. Bulk RNA sequencing using a 3′ mRNA-seq (QuantSeq) approach was performed to characterize transcriptional responses to mechanical compression.

overall_design: Bulk RNA sequencing was conducted to compare gene expression profiles between control and compressive force–treated immortalized periodontal ligament cells.

first: Han-Jin


title: Transcriptomic profiling of bone marrow-derived mesenchymal stromal cells from patients with acquired idiopathic aplastic anemia.

city: Porto Salvo

first: Isabel

middle: Bogalho

last: Martins

address: Instituto Superior Técnico - Campus Taguspark Av. Prof. Doutor Cavaco Silva

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Técnico (IST)

summary: Acquired aplastic anemia (AA) is a rare disorder characterized by bone marrow (BM) failure, marked by a severe reduction in hematopoietic stem and progenitor cells (HSC/HPC) and BM microenvironment disruption, including BM replacement by adipocytes. While cytotoxic T-cell-mediated destruction of HSC/HPC is a key factor in AA pathogenesis, alterations in the stem cell niche are also implicated. Studies have reported dysfunctional mesenchymal stromal cells (MSCs) within the BM, although findings have been inconsistent. In this study, we performed bulk mRNA sequencing of BM-derived MSCs from patients with acquired idiopathic severe AA (SAA) and healthy controls to identify genes associated with disease pathophysiology and potential therapeutic targets. Using adjusted p-values (padj) < 0.05 and log2 fold-change (L2FC) cutoffs of <-1.5 for downregulated and >1.5 for upregulated genes in AA, we identified 306 differentially expressed genes (DEGs): 188 downregulated and 118 upregulated. Molecular patterns associated with altered immune response, adipogenesis, lipid metabolism, osteoblast differentiation, osteoclast activity, extracellular matrix (ECM) remodeling, cell interaction, hematopoietic support, angiogenesis, DNA repair/damage response, and stress response were observed in AA-derived MSCs compared to controls. Furthermore, gene expression profiles related to Wnt/β-catenin, MAPK, PI3K/AKT, JAK/STAT, and NF-κB signaling pathways were identified, although with variable results. This study seeks to provide new insights into the altered BM microenvironment in AA, advancing our understanding of disease mechanisms and facilitating the development of novel therapeutic strategies.

overall_design: Bulk RNA-Seq profilling of Human Bone Marrow-derived Mesenchymal Stromal Cells isolated from patient diagnosed with idiopathic acquired aplastic anemia in comparison with age-matched healthy controls.

first: Paula

last: Kjöllerström

first: João

middle: S

last: Esteves

first: Joana

last: Santos

first: Ana

last: Fernandes-Platzgummer

first: Domingos

last: Henrique

first: Cláudia

last: Silva


first: Thomas

last: Randall

summary: TLR5 is a pathogen recognition receptor against flagellin that is expressed in various epithelial and immune cells. Mice pretreated with TLR5-agonist are protected against bleomycin-induced pulmonary fibrosis. However, the mechanisms by which TLR5-agonism protects against pulmonary fibrosis remains to be determined. Here, we found innate host defense gene sets to be selectively elevated in sorted type 2 alveolar epithelial.

overall_design: mRNA profiles of TLR5-agonist and vehicle-treated type 2 alveolar epithelial cells were generated by deep sequencing, in triplicate, using using BGI’s unique DNBseq™.

first: Yosuke

last: Sakamachi

first: Lecong

last: Zhou

first: Tom

first: Stavros

last: Garantziotis


summary: Idiopathic pulmonary fibrosis (IPF) is a devastating pulmonary disease with no curative treatment other than lung transplantation. IPF results from maladaptive responses to lung epithelial injury, but the underlying mechanisms remain unclear. Here, we show that deficiency in the innate immune receptor, toll-like receptor 5 (TLR5), is associated with IPF in humans and with increased susceptibility to experimental fibrosis in mice, while activation of lung epithelial TLR5 through a synthetic flagellin analog protects from experimental fibrosis. Mechanistically, epithelial TLR5 activation induces antimicrobial gene expression and ameliorates dysbiosis after lung injury.  In contrast, TLR5 deficiency in mice and IPF patients is associated with lung dysbiosis. Elimination of the microbiome in mice through antibiotics abolishes the protective effect of TLR5 and reconstitution of the microbiome rescues the observed phenotype. In aggregate, TLR5 deficiency is associated with IPF and dysbiosis in humans and in the murine model of pulmonary fibrosis. Furthermore, TLR5 protects against pulmonary fibrosis in mice, and this protection is mediated by effects on the microbiome.

overall_design: Experimental animals were euthanized using FatalPlus by intraperitoneal administration. Lungs were excised from animals under sterile conditions and were collected into DNA extraction buffer containing ATL buffer and proteinase K (Qiagen) and shaken in a FastPrep Instrument (MP Biomedicals) at 5.0ms-1 for 30s. Following bead-beating, genomic DNA (gDNA) was extracted using the DNeasy Blood and Tissue Kit (Qiagen) in accordance with the manufacturer protocol. The quality and quantity of the isolated gDNA was measured using a 4200 Tapestation System (Agilent). Bacterial DNA was quantified in experimental specimens with a QX200 droplet digital PCR (ddPCR) system (Bio-Rad). 16S V4 amplicon libraries were prepared following a modified Illumina library construction workflow developed by the Schloss Lab. The PCR amplification of the target region was performed using 515F (GTGYCAGCMGCCGCGGTAA) and 806R (GGACTACNVGGGTWTCTAAT) 16S primers. Amplicons were then purified using NGS clean-up and size-select (Macherey-Nagel) in accordance with the manufacturer protocol. For the Tlr5-/- dysbiosis study, wildtype and Tlr5-/- mice were treated with intratracheal bleomycin (3U/Kg) and were euthanized 7-days post administration. For the epithelial Tlr5 knockout dysbiosis study, Tlr5-/- and Tlr5fx/fx Spc-Cre mice were treated with intratracheal bleomycin (3U/Kg) and were euthanized 7-days post administration. For antibiotic (ABX)/bleomycin samples, animals were given a mixture of Ampicillin (1 g/L, Sigma, A1593-25G), Vancomycin (500 mg/L, Sigma, V2002-5G), Neomycin Sulfate (1 g/L, Sigma, N5286-25G), and Metronidazole (1 g/L, M1547-25G) in drinking water and in mash for 4-weeks prior to experimental use and throughout studies. Sucralose (1/50 dilution) was added for palatability. Mice were given bleomycin (3U/Kg), intratracheally, and euthanized at day 7. For TLR5-agonist/bleomycin samples, animals were dosed with 1.5 g of TLR5-agonist subcutaneously (200 L volume in normal saline with 0.01% Tween-80), 30-minutes prior to bleomycin administration. Mice were given bleomycin (3U/Kg), intratracheally, and euthanized at day 7. For the fecal microbiota transfer (FMT) donor samples, naïve wildtype and Tlr5-/- mice were euthanized for lung collection. For the FMT recipient samples, wildtype and Tlr5-/- mice were placed on ABX for 4-weeks and rested for 1-week prior to FMT from Tlr5+/+ or Tlr5-/- donors. FMT was employed in a 2-by-2 design, whereby microbiota-depleted Tlr5-/- and Tlr5+/+ mice (FMT recipients) received FMT from either Tlr5-/- or Tlr5+/+ mice (FMT donors) via 8 oral gavages in 2-weeks.

first: Thomas A

first: Brian

last: Papas

first: Jason

last: Malphurs

first: Benjamin G

last: Wu

first: Yonghua

last: Li

first: Leopoldo N

last: Segal


title: Tissue-specific mRNA m6A reprogramming unveils vitamin-driven post-transcriptional regulation in mice

city: Guangzhou

first: Xiaoyun

last: Wang

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Vitamins are critical regulators of cellular processes, yet their influence on mRNA modifications, particularly N6-methyladenosine (m6A), remains poorly understood. This study investigates the effects of various vitamins (VB2, VB6, and VB12) on the mRNA m6A epitranscriptome in multiple mouse tissues (brain, liver, and testis). Clustering analyses revealed closer similarity between brain and testis m6A profiles, while the liver exhibited a unique signature, reflecting tissue-specific regulatory dynamics. Notably, over 90% of vitamin-specific m6A sites did not correlate with mRNA abundance, highlighting the role of m6A as a post-transcriptional regulator. Pathway enrichment analyses further revealed tissue- and vitamin-specific adaptations. Key genes responsive to vitamin treatments emerged as central regulators of m6A dynamics, aligning with the known roles of vitamins in metabolism, neural plasticity, and gene expression.

overall_design: To explore the impact of vitamins on epigenetic regulation, we profiled the mRNA m6A epitranscriptome in mouse brain (representing the nervous system), liver (representing the digestive and defense system), and testis (representing the reproductive system). Using the m6A-seq2 protocol, we constructed MeRIP-seq libraries designed to profile m6A modifications. Both input and immunoprecipitation (IP) libraries were prepared from the three tissues (brain, liver, testis) treated with three different vitamins (VB2, VB6, and VB12) and subjected to sequencing.

first: Jia

first: Anrui

last: Liu


title: Dual antiviral and anti-inflammatory effects of BAY 11-7082 in SARS-CoV-2 infection via inhibition of the canonical NF-κB signaling pathway_[supplementary Fig.1]

first: Po-Chih

overall_design: Transcriptomic changes were profiled in A549 cells under three conditions: mock control, influenza A virus infection (MOI = 5), and influenza A virus infection treated with BAY 11-7082. RNA-seq was performed to characterize host responses to viral infection, enabling the identification of host pathways modulated by BAY 11-7082 that may also be relevant for controlling SARS-CoV-2 infection.

first: Chin-Mao

last: Hung

first: Meng-Chang

last: Lee

first: Ming-Sian

first: Chun-Hsi

last: Tso

first: Jia-Chuan

last: Hsu

first: Der-Yuan

first: Hao-Ai

last: Shui

first: Chi-Tun

last: Tang

first: Chia-Wen

last: Shih


title: Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and regulators of lung fibrosis (single-cell multiome sequencing)

city: Ann Arbor

first: Lu

last: Lu

state: MI

address: 100 Washtenaw Ave.

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan, Ann Arbor

summary: Chronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.

overall_design: MCs from patients who had a diagnosis of CLAD at the time of BAL (CLAD-MCs) were compared to the MCs obtained from control CLAD-free patients (non-CLAD MCs). The incidence of CLAD increases with time post-transplant, and CLAD diagnosis is generally made after the first year of lung transplantation. To investigate if transcriptional and epigenomic changes are inherent or acquired, MCs were also studied from BAL samples obtained early in the course (<6 weeks post-transplant). These patients were later clinically classified as having developed CLAD or remained CLAD-free.

first: Aidan

middle: P

last: McLinden

first: Natalie

last: Walker

first: Ragini

last: Vittal

first: Michael

last: Combs

first: Joshua

middle: D

last: Welch

first: Vibha

middle: N

last: Lama


title: Copper control of the suppressive capacity in regulatory T cells [CUT&Tag]

city: YI WU

first: Yage

last: Zhang

state: Zhejiang Province

address: No. 1575, Chouzhou North Road, Yiwu City, Zhejiang Province

institute: International Institutes of Medicine Zhejiang University

summary: Fine-tuning nutrient flow and energy production is required to sustain the functionality and survival of Tregs, yet key factors and pathways remain to be identified. Here, we show that, mitochondrial activity is a superior property over activation markers for Treg functionality. Through a screen of mitochondrial inhibitory compounds, we reveal that copper chelators/ionophores modulate mitochondrial activity. Tregs activated in vitro and from individuals with psoriasis and rheumatoid arthritis obscure a greater labile copper pool compared to controls. We characterize Slc31a1 as a major copper transporter in Treg, which supports oxidative phosphorylation, energy production and histone acetylation at the gene loci of suppressive genes to maintain the transcription of suppressive molecules and Treg functionality. This process is vital for peripheral immune tolerance. Our findings underscore the role of copper metabolism in Treg biology, which may offer therapeutic strategy for treating autoimmune diseases.

overall_design: TREG cells were fractionated by FACS sorting from different mice (ChiWT, ChiKO) for CUT&Tag seq (H3K27ac, H3K27me3)

first: Fan

last: Shi

first: Haoyu

first: Fudi

first: Songmin

last: Ying

first: Qian

last: Wu


title: NAD⁺ Augmentation by Nicotinamide Riboside Engages SLIT2/ROBO1 Signaling to Attenuate Th17 Inflammation in Psoriasis

city: Bethesda

last: Sack

state: MD

address: 10 Center Dr

institute: NHLBI/NIH

summary: BACKGROUND. Enhancing NAD+ level by Nicotinamide Riboside (NR) supplementation confer anti-inflammatory effects in human disease, yet the immunoregulatory mechanisms remain unclear. We previously demonstrated ex vivo study that NR blunts CD4+ T cell immune responsiveness in psoriasis. To explore whether these effects occur in vivo, we conducted a randomized, placebo-controlled NR supplementation study in participants with mild-tomoderate- psoriasis. METHODS. Psoriasis participants consumed oral NR supplementation (500 mg twice daily) or matching placebo for 4 weeks. Research bloods were drawn at baseline and at 4 weeks for analysis. In parallel, natural history cohorts of healthy controls and psoriasis participants donated research blood and skin punch biopsies for mechanistic analysis. RESULTS. Oral NR supplementation dampens Th17 immune responsiveness. Bulk RNA-seq of CD4+ cells identified that NR regulated the SLIT-ROBO signaling pathway. Participants on NR showed elevated circulating SLIT2 levels, and NR increased SLIT2 production in skin fibroblasts. Pharmacologic and genetic studies in CD4+ T cells and fibroblasts showed that SLIT2, acting through the ROBO1 receptor, inhibited Rho GTPase signaling, thereby reducing canonical Th17 polarization and fibroblast inflammatory activation. CONCLUSION. NAD+ augmentation confers anti-inflammatory effects in psoriasis through SLIT2/ROBO1-mediated crosstalk between dermal fibroblast and circulating CD4+ T cells, leading to attenuation of Th17-driven inflammation.

overall_design: we recruited and consented 27 volunteers with mild-to-moderate psoriasis to participate in a randomized, oral, placebo-controlled study vs. NR (500 mg twice daily). The study protocol is schematized, with research blood drawn at baseline and after 4 weeks of supplementation

first: Kim

last: Han

first: Rachael

last: Klein

first: Thomas

last: Recupero

first: Anna Chiara

last: Russo

first: Rahul

last: Sharma

first: Anand

middle: K

last: Gupta

first: Shahin

last: Hassanzadeh

first: Rebecca

last: Huffstutler

first: Pradeep

last: Dagur

first: Bryan

last: Fisk

first: Neelam

last: Redekar


title: Copper control of the suppressive capacity in regulatory T cells [RNA-Seq]

first: Yage

overall_design: TREG cells were fractionated by FACS sorting from different mice

last: Tang

last: Wang


title: Copper control of the suppressive capacity in regulatory T cells

last: Zhang

overall_design: Mitotracker-labeled TREG cells were fractionated by FACS sorting into two distinct populations: Mitotracker-high (Mitohigh) and Mitotracker-low (Mitolow) Treg cells.

first: Fan

last: Shi


title: Developmental molecular signatures define de novo cortico-brainstem circuit for skilled forelimb movement

city: White Plains

first: Julia

last: Kaiser

state: NY

address: 784 Mamaroneck Avenue

institute: Burke Neurological Institute

summary:
Skilled motor control requires precise connections between subcerebral projection neurons (SCPN) in the cerebral cortex and their appropriate subcerebral targets in the brainstem or spinal cord. The brainstem has been widely recognized as a key integration and processing hub between “upper” motor centers and spinal circuits involved in execution of movements. Cortical input into the brainstem may fine-tune movement execution and support motor planning and is established by two SCPN supopulations: 1) cortico-brainstem neurons (CBN) that limit their axon extension to supraspinal levels, directly innervating brainstem nuclei, and 2) corticospinal neurons (CSN) that extend their axons into the spinal cord but additionally collateralize within the brainstem. Classical anatomical tracing approaches are not able to distinguish CBN from CSN, since these distinct subpopulations reside interdigitated in cortex, thus precluding the investigation of the function of CBN in skilled motor movement execution and planning until now.
We used a combination of transcriptomics, tracing, and imaging techniques to identify the molecular program that CBN vs. CSN at the time point of initial axon extension. We found that Neuropeptide Y (Npy) is specifically enriched in CBN in lateral cortex, while CART prepropeptide (Cartpt) delineates cervical-projecting CSN, which now provides, for the first time in the field, molecular access to specifically investigate direct cortical input into the brainstem. By using established Cre mouse lines for CBN / CSN specific markers, we now aim to investigate the function and connectivity of these CBN vs. CSN within the brainstem. Our preliminary results suggest a topographic organization of these subpopulations within the brainstem. Selectively silencing of Npy+ CBN within the lateral cortex will allow us to investigate the contribution of CBN to skilled motor movements in the single pellet reaching task and other selected motor tasks. Our results provide a foundation for future studies aiming to unravel the complexity of cortico-brainstem and cortico-spinal circuits, and their contribution to movement control in health and disease.

overall_design: retrograde labeling of SCPN (labeled form cerebral peduncles) vs CSN (labeled from spinal C2) at P0/P2 respectively, tissue collection and single cell dissociation at P1 vs. P3, FACS,  whole cell scRNA-Seq (10x Chromium SC 3')

first: Vibhu

last: Sahni

first: Dimitris

last: Konstantopoulos


title: Tomatidine is a senotherapeutic compound that improves cognitive function and reduces cellular senescence in aged mice

city: Rochester

first: Dominik

last: Saul

state: Minnesota

address: 200 First Street SW Rochester

institute: Mayo Clinic

summary: Cellular senescence contributes to aging and age-related dysfunction across multiple tissues, including the brain. Here, we identify tomatidine, an aglycone of tomatine naturally found in tomatoes, as a senotherapeutic agent. In vitro, tomatidine selectively suppressed SASP expression without affecting p16Ink4a or p21Cip1 levels in senescent human brain microvascular endothelial cells. In aged mice, dietary tomatidine reduced frailty and improved motor coordination and cognitive performance. These functional benefits were accompanied by a reduction in senescence markers (e.g., p16, p21, and telomere-associated DNA damage foci) in liver, skin, and hippocampal neurons, as well as decreased neuroinflammation and microglial activation. Tomatidine also reduced senescence in brain endothelial cells and increased the expression of tight junction–associated proteins. Together, these findings suggest that tomatidine is as a promising senotherapeutic with the potential to preserve cognitive and vascular function during aging. As a naturally occurring compound with oral bioavailability and a favorable safety profile, tomatidine holds strong translational promise for future therapeutic development.

overall_design: Hippocampus from control and treated mus musculus.

first: Daniela

middle: G

last: Costa

first: Lucy

last: Gee

first: Gung

last: Lee

first: Lilian

last: Gomez

first: Ana

last: Franco

first: Maria

last: Vizioli

first: Karla

last: Valdiviseo

first: Lei

first: Nick

last: Pirius

last: Porritt

first: Claudia

last: Cavadas

first: Scott

last: Ebert

first: Nathan

last: LeBrasseur

first: Sundeep

last: Khosla

first: Joao

last: Passos

first: Christopher

last: Adams

first: Paul

last: Robbins

first: Diana

last: Jurk


title: Eye-conic' spatial transcriptomics of keratoconus corneas

city: Poznan

first: Marzena

last: Gajecka

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

summary: The cornea is a transparent, avascular eye tissue composed of five layers: epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium, each of which, if affected by keratoconus (KTCN), may exhibit specific morphological changes. Due to the complexity of the tissue, the studies preserving the spatial location should be applied to identify the layer-specific molecular changes in KTCN, for further understanding of the mechanistic aspects of its cone formation.

overall_design: Eight corneas of 8 unrelated Polish male patients with KTCN were included in the study, as well as five normal/non-affected corneas collected postmortem from 5 deceased male donors. The 10 µm-thick corneal cryosections and Visium Spatial Gene Expression Libraries were prepared and processed according to manufacturer's protocol ‘for Fresh Frozen’ (v. 1, 10x Genomics, Pleasanton, CA, USA). The paired-end sequencing was performed using a NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA).

first: Alicja

last: Wysocka

first: Katarzyna

last: Jaskiewicz-Rajewicz

first: Jakub

last: Wozniak

first: Malgorzata

last: Rydzanicz

first: Rafal

last: Ploski

first: Monika

last: Udziela

first: Jacek

last: Szaflik


title: mRNA and lncRNA expression profiling of human atherosclerotic plaques

city: Shanghai

first: Yuanyuan

last: Wei

address: No. 130, Dong'an Road

institute: Fudan University

summary: To characterize transcriptional and post-transcriptional changes during human atherosclerosis development, we then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different stages of human carotid atherosclerotic plaques.

overall_design:
Comparative lncRNA and gene expression profiling analysis of RNA-seq data for early fibroatheromas (EFAs), late fibroatheromas (LFAs) with thick ﬁbrous caps, and thin-cap fibroatheromas (TCFAs).
>>>Raw data for human samples not available due to patient privacy concerns<<<

first: Yuhuai

last: Xie

first: Zhen

last: Zhao


title: Single-cell RNA-seq and TCR profiling of tissue-resident memory T cells in the fallopian tube and matched ovarian cancer samples

city: Oxford

first: luyao

last: wang

state: Oxfordshire

address: MRC Weatherall Institute of Molecular Medicine (Oxford University & John Radcliffe Hospital)

country: United Kingdom

institute: University of oxford

summary:
This study investigates the immune characteristics of tissue-resident memory T cells in the human fallopian tube in high-grade serous ovarian cancer (HGSOC). Single-cell RNA sequencing (scRNA-seq) and paired T-cell receptor sequencing (scTCR-seq) were performed on samples from non-cancerous fallopian tube tissue, metastatic omental tumors, and peripheral blood from HGSOC patients.

The dataset enables analysis of tissue-resident T cell populations, clonal relationships across tissues, and immune features associated with tumor progression. These data provide a resource for studying tissue-resident T cell heterogeneity, clonal expansion, and tumor-associated immune responses in ovarian cancer.

overall_design:
Samples were collected from four patients diagnosed with high-grade serous ovarian cancer. For each patient, matched non-cancerous fallopian tube tissue, metastatic omental tumor tissue, and peripheral blood mononuclear cells (PBMCs) were obtained.

Single-cell RNA sequencing (scRNA-seq) and paired single-cell T cell receptor sequencing (scTCR-seq) were performed to profile tissue-resident T cell populations across different tissue compartments. The dataset enables comparative analysis of tissue-resident T cell states and clonal relationships between non-cancerous and tumor-associated environments.

first: Luyao

last: Wang

first: Breeshey

last: Roskams-Hieter

first: Nancy

last: Zaarour

first: Ahmed

last: Ahmed


title: Transcriptome profiling of RNA from specific Hnrnpa2b1 overexpression in iWAT

first: Yu

last: Li

address: Minhang Dongchuan Road No.500

institute: East China Normal University

summary: Analysis of transcriptome from specific Hnrnpa2b1 overexpression in iWAT. Results provide insight into molecular mechanism underlying Hnrnpa2b1 function in iWAT.

overall_design: Total RNA were isolated from iWAT of adeno-associated virus (AAV) vector-mediated overexpression of CDS region of mouse Hnrnpa2b1 (AAV A2B1) or scrambled control (AAV GFP).Quantification of transcriptional gene expression and alternative splicing events detected in the iWAT overexpressing GFP and A2B1 samples.


title: Single-Cell Transcriptomic Profiling of Male Zebrafish Pituitary: Investigating the Impact of CCK1/CCK2 Knockout on Pituitary Function

first: Hangyu

summary: This study explores the effects of CCK1 and CCK2 knockout on the pituitary of male zebrafish using single-cell RNA sequencing (scRNA-seq). Two groups were analyzed: the CCK1/CCK2 knockout (KO) group and the wild-type (WT) group. Pituitary tissues were dissociated into single cells, followed by RNA sequencing to examine changes in gene expression. The results show how CCK receptor loss impacts pituitary cell function and gene expression, providing insights into the role of CCK in zebrafish pituitary regulation and endocrine function.

overall_design: Male zebrafish (6 months old) from two groups, CCK1/CCK2 knockout (KO) and wild-type (WT), were used. Pituitary tissues from 30 fish per group were collected for analysis.


title: lncRNA-mediated upregulation of MHC class II transactivator CIITA exacerbates atherosclerosis

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

overall_design: Refer to individual Series


title: The impact of KLF2-KLF3 regulated cellular localization on exhausted T cell differentiation [CUT&Tag]

first: Weiguo

last: Cui

summary: During chronic viral infection, CD8 T cells lose effector function and acquire an exhausted phenotype, a process accompanied by changes in migratory behavior and tissue residency. Exhausted CD8 T cells differentiate from stem-like progenitor (Tpro) cells into either circulating, cytotoxic effector-like (Teff) cells or tissue-resident terminally exhausted (Texh) cells. However, whether these migratory changes passively reflect cell state or actively influence exhaustion trajectories remains unclear. Here, we identify a transcriptional circuit involving Krüppel-like factor 2 (KLF2) and its homolog KLF3 that links migratory program to CD8 T cell differentiation during exhaustion. Using multi-module approaches, we show that KLF2 primarily promotes the expression and chromatin accessibility of migratory genes in Tpro and Teff subsets, while KLF3 limits these programs by repressing Klf2 transcription and competing for shared genomic binding sites. Enhancing circulation through enforced S1PR1/S1PR5 expression or CD69 deletion biases differentiation toward effector-like fates and away from terminal exhaustion, suggesting that cellular localization can influence, not just reflect, CD8 T cell fate decisions. We further describe an integrated feed-forward and feedback loop in which KLF2 induces KLF3, which in turn constrains KLF2 transcription and binding to shared genomic loci. This reciprocal regulatory circuit modulates the balance between migration and tissue residency, thereby tuning the differentiation of CD8 T cells in chronic infection. These findings provide mechanistic insight into how transcriptional regulation of migratory behavior contributes to cell fate decisions during T cell exhaustion.

overall_design:
EXP-1: KLF2 CUT&Tag assay on P14 CD8 T cells isolated from LCMV Clone 13 infected mice on day 8 post-infection.
EXP-2: KLF2 and ER-KLF3 CUT&Tag assay on tamoxifen treated ER-KLF3 expressing CD8 T cells (in vitro).

first: Jian

last: Shen

first: Kexin

last: Gai


title: Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae [Biofilm, AKI]

city: Memphis

first: Deepak

last: Balasubramanian

state: TN

address: 262 Danny Thomas Pl Rm D2037

department: Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary: The sole gain of laterally acquired virulence genes does not fully explain the transition of environmental strains into human pathogens. To date, the specific molecular drivers and fitness trade-offs that enable some strains within a population to undergo this process remain enigmatic. Here, we describe a small RNA (sRNA) with a unique modular structure that shapes the evolution of toxigenic Vibrio cholerae, the agent of cholera. The sRNA comprises of a highly variable 5’ module located within the ompU ORF and a conserved 3’ one downstream from the gene. The bimodular nature of the OmpU-encoded sRNA (OueS) generates allelic variants that differentially contribute to the emergence of virulence potential in some strains and associated fitness trade-offs between human infection and environmental survival. Unlike environmental counterparts, the OueS allele from toxigenic strains controls phenotypes essential during host colonization: a) stringently inhibits biofilm formation by suppressing the iron-responsive sRNA RyhB, and b) confers resistance against intestinal bacteriophages by activating the CBASS phage defense system. Toxigenic OueS is also required for successful intestinal colonization and acts as a functional surrogate of the master virulence regulator ToxR, controlling over 84% of its regulome. On the other hand, strains encoding environmental alleles of OueS exhibit higher competitive fitness than those harboring toxigenic ones during colonization of natural reservoirs such as crustaceans (Artemia salina) and phytoplankton (Microcystis aeruginosa). These results uncover the fitness trade-offs between human infection and environmental survival and costs associated with pathogen emergence.

overall_design: To investigate the allele specific role of the small RNA OueS in regulation of virulence, we generated isogenic mutants of the clinical Vibrio cholerae El Tor C6706 strain expressing either the clinical (C6706) or environmental (GBE1114) OueS alleles, expression driven under the ParaBAD inducible promoter. The strains were then grown under conditions inducing virulence gene expression (AKI conditions) or as biofilms and total RNA isolated for transcriptome analysis by Illumina NovaSeq.

first: Salvador

last: Almagro-Moreno


title: Adipose Stromal Cells in the Human Rotator Cuff are Resistant to Fibrotic Microenvironmental Cues

city: St. Louis

first: Dakota

last: Kamm

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

summary: Rotator cuff tears are the most common upper extremity orthopaedic injury, causing degenerative changes within the bone, tendon, joint capsule, bursa, and muscle. These degenerative changes are linked to poor rehabilitative and surgical outcomes, which has launched investigations into co-therapeutic biologics. Specifically, Mesenchymal Stem Cells (MSCs) have shown promise in mitigating degenerative changes in animal models of RC tears, however reports of their impact on clinical outcomes remain mixed.  Here we describe an alternative source of MSCs in the human shoulder, adipose stromal cells (ASCs) from the subacromial fat (SAF) pad. Compared to the gold-standard subcutaneous (SQ) fat, we show that SAF ASCs are less sensitive to chemical and mechanical fibrotic cues, 1) retaining smaller cell area with reduced actin stress fiber alignment across a range of physiological and pathological stiffnesses, 2) reduced traction forces and ECM production and 3) reduced myofibroblastic conversion in response to cytokine challenge.  Furthermore, we show that SAF ASCs enhance fusion of primary human myoblasts via paracrine signaling.  Despite a fibrotic signature in SAF from rotator cuffs with tendon tears, SAF ASCs sourced from torn rotator cuffs were equally effective at resisting fibroblastic conversion and promoting myogenesis as those from intact rotator cuffs, further supporting autologous clinical use of these cells. In conclusion, this study describes human SAF ASCs as an alternative, and potentially superior, cell source for rotator cuff therapies.

overall_design: RNA-seq profiling of subacromial fat and subcutaneous fat derived from intact rotator cuffs and torn rotator cuffs. Subacromial fat samples are referred to as "RCA" and subcutaneous fat samples are referred to as "SQ".

first: Kamm

last: Dakota R.

first: Meyer

last: Gretchen A.


title: SPECIFIC REACTIVITY OF ABASIC SITES WITH POLYAMINES ENABLES THEIR GENOMIC MAPPING

status: Public on Apr 02 2026

city: Paris

first: Anton

last: Granzhan

address: 45 rue des Saints-Pères

department: UMR8601 LCBPT

country: France

institute: Université Paris Cité

summary: Apurinic/apyrimidinic (AP) sites are among the most abundant DNA lesions and represent key intermediates in the base excision DNA repair pathway. Knowing their genomic distribution is important for understanding the mechanisms of genotoxic agents. Although several methods exist for genomic mapping of AP sites, some of them suffer from limited specificity and/or complex multi-step workflows. Here, we present APX-seq, a novel method based on the recently discovered reaction of AP sites with 1,2-diamines, for highly specific chemical labelling, isolation and enrichment of AP site-containing genomic fragments for subsequent DNA sequencing. Following in vitro optimization and validation, we applied APX-seq to the genome of cultured HepG2 cells. Our finding reveal that AP sites are broadly distributed in the genome and are enriched in euchromatin, consistent with the prior studies. Moreover, we show that treatment with genotoxic agents such as a DNA-alkylating chemical or X-ray radiation, barely alters the genomic landscape of AP sites.

overall_design: APX-seq and AP-seq were performed in HepG2 cells subjected to four conditions: untreated (control), 5 mM MMS treatment, 10 mM MMS treatment, and 6 Gy X-ray radiation (XRD). Cells were harvested at defined time points following treatment for subsequent genomic DNA extraction and AP site profiling.

first: Eka Putra

last: Gusti Ngurah Putu

first: Laurent

last: Cattiaux

first: Nicolas

last: Servant

first: Sophie

last: Bombard


title: Impaired BCAA metabolism exacerbates vascular calcification by decreasing histone H3K23 propionylation

first: Liyun

last: Feng

address: 253 Industrial Avenue, Guangzhou, Guangdong province

institute: Zhujiang Hospital, Southern Medical University

summary: In this study,we report the protective effect of BCKDHA on vascular calcification in chronic kidney disease (CKD). To explore the underlying mechanism of BCKDHA's protective effect on vascular calcification, we performed high-throughput RNA sequencing to identify the target genes of BCKDHA.

overall_design: Human vascular smooth muscle cells were transfected with either Ad/GFP or Ad/BCKDHA and cultured in calcifying medium (CM). RNA-seq was performed to identify the downstream target genes of BCKDHA.

first: Jianyun

last: Yan


title: Transcriptome profiling of human PDLSC under GM/OM with BMP2/BMP9 at days 1, 7, and 15

city: Seoup

first: Dong Woo

last: Lee

address: 174, Yulgok-ro, Jongno-gu

institute: Seoul National University

summary:
We investigated the gene expression changes in human periodontal ligament stem cells (PDLSCs) cultured in growth medium (GM) or osteogenic medium (OM) with various treatments (NT, BMP2, BMP9) over three time points (1d, 7d, 15d).
Each group has two biological replicates. Total 12 groups, 24 samples. Affymetrix Human Gene 2.0 ST arrays were used.

overall_design: PDLSCs were divided into 12 conditions: (GM_NT, OM_NT, OM_B2, OM_B9) × 3 time points (1d, 7d, 15d). Two biological replicates per condition. cDNA was synthesized using the GeneChip WT kit, labeled with biotin, and hybridized to the HuGene 2.0 ST array. Data were processed using RMA background correction, quantile normalization, PM-only median polish summarization.

first: Jue Yeon

first: Yoon Jeong

last: Park

first: Yoon Shin

first: Chong Pyung

last: Chung


title: Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae

first: Deepak

overall_design: To investigate the allele specific role of the small RNA OueS in regulation of virulence, we generated isogenic clinical strains expressing either the clinical-like (C6706, GBE1194) or environmental-like (GBE1114, GBE1116) OueS alleles, expression driven by the PompU promoter, integrated at its native ompU locus. The strains were then grown under conditions inducing virulence gene expression (AKI conditions) and their transcriptomes were analyzed by Illumina NovaSeq.


title: MiRNA profiling of CD8+ T cells, CD14+ monocytes and neutrophils from patients with multiple sclerosis (MS), type 1 diabetes (T1D) and healthy controls (HCs)

city: Monza

first: Jacopo

last: Ronchi

state: MB

address: Via Cadore 48

department: School of Medicine and Surgery

country: Italy

institute: University of Milano-Bicocca

summary:
Autoimmune diseases (AIDs) arise from complex immune dysregulations involving multiple immune cell types, cytokines and molecular mediators. Among these, microRNAs (miRNAs) have recently emerged as key regulators of leukocyte processes and are frequently dysregulated in AIDs. However, their role in disease pathophysiology remains poorly understood. In this study, we performed a comprehensive analysis of miRNA expression in three immune populations, namely CD14+ monocytes, neutrophils and CD8+ T cells, in multiple sclerosis (MS) and type 1 diabetes (T1D), two prototypical AIDs. Our results reveal distinct patterns of miRNA dysregulation in each cell type, with monocytes from T1D patients showing enhanced M1 polarization and inflammatory vascular damage. On the other hand, CD8+ T cells from MS patients show profound alterations related to Tc17 and CD8+ Treg differentiation, apoptosis regulation and migratory capacity. Notably, we identified miRNAs that regulate key transcription factors such as FOXP3, IRF4, and RORC, potentially shaping pathogenic T cell responses. Our results suggest that miRNA networks play a central role in orchestrating disease-specific dysregulation in AIDs. By elucidating these intricate regulatory mechanisms, our study provides a foundation for future therapeutic strategies targeting miRNAs in autoimmunity.
MiRNA microarrays were employed to assess the impact of miRNA dysregulations in CD8+ T cells, CD14+ monocytes, and neutrophils, in two AIDs, namely multiple sclerosis and type 1 diabetes.

overall_design: Blood samples were collected from a total of 61 subjects, divided into two cohorts. Individuals in the first cohort were recruited at San Gerardo Hospital (HSG) in Milan, comprising 20 RRMS patients and 15 age-matched controls. The second cohort was enrolled at San Raffaele Hospital (HSR) in Milan, and included 12 patients with T1D and 14 age-matched controls. \textbf{Table 1} summarizes the number of subjects used in the analysis along with the main clinical characteristics. CD14+ monocytes, neutrophils, and CD8+ T cells were then isolated from each individual donor. After discarding 15 samples due to low RNA quality, a total of 168 miRNA expression profiles were obtained through microarray technology.

first: Roberta

last: Rigolio

first: Davide

last: Trevisan

first: Angela

last: Papagna

first: Martina

last: Gallinaro

first: Maria

last: Fusco

last: Cogo

first: Guido

last: Cavaletti

first: Giovanni

last: Malerba

first: Emanuela

last: Battaglia

last: Foti


title: Gene expression profile at single cell level of cerebrospinal fluid (CSF) cells from lung adenocarcinoma leptomeningeal metastases patients (LUAD LM)

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: Lung adenocarcinoma (LUAD)-derived leptomeningeal metastases (LM) represent a predominant subtype among all LM cases. Nevertheless, the cerebrospinal fluid (CSF) profile of LUAD-LM patients remains poorly characterized and reliable CSF diagnostic biomarkers for LUAD-LM have yet to be established. Using single-cell RNA sequencing data of CSF cells from six LUAD-LM patients, we drew a systematic transcriptomic atlas of the CSF cellular landscape. Our analysis revealed that LUAD-LM reprograms CSF into an immunosuppressive state, marked by the emergence of pro-tumoral LGMN-SELENOPhigh macrophages and proliferating CSF circulating tumor cells (CSF-CTC). Cell-cell communication analysis showed that CSF-CTC reinforces immunosuppression by co-inhibitory checkpoint axis NECTIN2_TIGIT axis with the CD8+T/NK cells, and via CD47_SIRPA axis with antigen-presenting cells. Furthermore, we identified the single-cell transcriptomic difference between CSF-CTC and tumor cells of parenchymal brain metastases (PBM). Notably, Trophoblast cell surface antigen 2 (TROP2) levels in CSF were significantly elevated in LUAD-LM patients versus both normal controls (NC) and LUAD patients without LM (Non-LM). It showed strong diagnostic accuracy for distinguishing LUAD LM from Non-LM or NC, and PBM did not influence the CSF TROP2 level. Collectively, our findings advance the understanding of LUAD-LM pathogenesis and highlight the potential of CSF TROP2 as a diagnostic biomarker for LM.

overall_design: The whole CSF cells from LUAD LM patients were performed scRNA-seq by 10× genomics method

first: Haoyu

last: Ruan

first: Zhe

last: Wang


title: Pediatric Cancer Dependencies Accelerator

status: Public on Apr 07 2026

first: Pediatric Cancer Dependencies

last: Acclerator

address: 262 Danny Thomas Blvd


title: Spatial transcriptomics reveals immune-stromal crosstalk within the synovium of patients with juvenile idiopathic arthritis

city: Aurora

first: Kentaro

last: Yomogida

state: Colorado

address: 1775 Aurora Ct

department: Pediatrics

institute: University of Colorado

summary: Juvenile idiopathic arthritis (JIA) is the most prevalent chronic inflammatory arthritis of childhood, yet the spatial organization in the synovium remains poorly understood. Here, we perform subcellular-resolution spatial transcriptomic profiling of synovial tissue from patients with active JIA. We identify diverse immune and stromal cell populations and reconstruct spatially defined cellular niches. Applying a newly developed spatial colocalization analysis pipeline, we uncover microanatomical structures, including endothelial-fibroblast interactions mediated by NOTCH signaling, and a CXCL9/CXCR3 signaling axis between inflammatory macrophages and CD8+ T cells, alongside the characterization of other resident macrophage subsets. We also detect and characterize tertiary lymphoid structures marked by CXCL13/CXCR5 and CCL19-mediated signaling from Tph cells and immunoregulatory DCs, analogous to those observed in other autoimmune diseases. Finally, comparative analysis with rheumatoid arthritis reveals JIA-enriched cell states, including NOTCH3+ and CXCL12+ sublining fibroblasts, suggesting potentially differential inflammatory programs in pediatric versus adult arthritis. These findings provide a spatially resolved molecular framework of JIA synovitis and introduce a generalizable computational pipeline for spatial colocalization analysis in tissue inflammation.

overall_design: Synovial tissue samples were obtained via ultrasound-guided biopsy using a Quick-Core needle. Six to eight tissue fragments were fixed in formalin for subsequent paraffin embedding and 4 histological processing.

first: Yomogida

last: Kentaro


title: Cell-Inspired Dual-Tandem Catalytic Nanoreactors Drive Targeted Hearing Protection

first: baoying

last: xu

address: No. 333, Nan Chen Road, Baoshan District

department: School of Life Sciences

institute: Shanghai University

summary: Sensorineural hearing loss is driven by irreversible disruption of cochlear homeostasis, where dysregulated redox balance, ionic regulation, and metabolic exhaustion are important factors that trigger hair cell degeneration and synaptic injury. Current antioxidant strategies lack the capacity to restore the coordinated enzymatic ROS-clearance pathways or effectively penetrate the blood–labyrinth barrier, limiting their therapeutic efficacy.

overall_design: Here, we develop a cell-inspired dual-tandem catalytic nanoreactor (HSC@Se) that integrates a GPx-mimetic diselenide crosslinker with superoxide dismutase and catalase to reconstruct a physiological detoxification cascade (O2•⁻→H2O2→H2O). Human serum albumin scaffolding stabilizes the nanoarchitecture and enables active BLB penetration through synergistic engagement of neutrophil-adhesive transport and megalin-mediated uptake at the vascular plexus, thereby facilitating precise cochlear delivery to sensory hair cells and spiral ganglion neurons, which are cell populations highly vulnerable to oxidative injury. In noise-induced hearing loss models, HSC@Se restored redox equilibrium, suppressed lipid-peroxidation-driven ferroptosis, normalized intracellular iron handling, preserved hair-cell integrity, maintained ribbon synapses, and significantly reduced auditory threshold shifts. Transcriptomic profiling further revealed the activation of antioxidative and metabolic repair pathways. This work establishes a biomimetic catalytic platform in which cell-inspired dual-tandem nanoreactors emulate natural antioxidant networks to rebalance cochlear redox homeostasis and drive targeted functional hearing protection.

first: Baoying

last: Xu


title: RBMXL3 drives transcriptome changes in human TCam-2 cells (RNA-seq data)

first: Joanna

last: Zyprych-Walczak

address: Wojska Polskiego 28

department: Department of Mathematical and Statistical Methods

institute: Poznan University of Life Sciences

summary: RBMXL3 is a primate-specific gene localized on the X chromosome, which expression is detectable mainly in the male gonad. So far, very little is known about RBMXL3 protein function and its molecular network but recent reports mention the RBMXL3 gene in the context of human spermatogenesis, cancer, and also a breathing disorder that affects newborns. In this study, we investigate the RBMXL3’s molecular network on a genome-wide scale using the human seminoma cell line (TCam-2) as a male germline in vitro model. Our transcriptomic (RNAseq, eCLIP) and proteomic (Co-IP coupled with MS) data show that RBMXL3 is an important player involved in RNA metabolism in human cells. Moreover, we report for the first time that primate-specific RBMXL3 protein restricts human LINE-1 (L1) retrotransposition. Our data indicate that RBMXL3 could play a decent function in controlling transcriptome fate in germ cells and beyond.

overall_design: The RNA-seq experiment was done in duplicate and performed using TCam-2 cells transduced with RBMXL3_FLAG, GFP_FLAG and non-transduced WT. Cells transduced with GFP_FLAG and non-transduced WT TCam-2 cells were used as negative controls in order to perform analysis of differentially expressed and differentially spliced genes upon RBMXL3 overexpression.

first: Natalia

last: Rozwadowska

first: Agata

last: Barszcz

first: Katarzyna

last: Tutak

first: Erik

last: Dassi

first: Erkut

last: Ilaslan


title: Ca2+ influx through ER-plasma membrane contacts is required for brown fat thermogenesis and metabolic health

city: Berkeley

first: Gunes

last: Parlakgul

state: CA

address: 119 Morgan Hall

department: Metabolic Biology and Nutrition

institute: University of California, Berkeley

summary: Brown adipose tissue (BAT) exhibits exceptional metabolic plasticity, rapidly increasing energy expenditure to sustain thermogenesis during cold exposure. This high metabolic activity imposes substantial demands on cellular systems, requiring robust adaptive mechanisms to maintain homeostasis and prevent cellular stress. Yet, the pathways that support and coordinate these adaptive responses in brown adipocytes remain incompletely understood. Here, we identify a cold- induced adaptive program in BAT characterized by the formation of endoplasmic reticulum- plasma membrane (ER-PM) contact sites and the activation of store-operated calcium entry (SOCE), which is essential for maintaining brown adipocyte health during thermogenic activation. Cold exposure enhances ER-PM contacts and upregulates the expression of STIM and Orai proteins, key mediators of SOCE. Loss of STIM in brown adipocytes disrupts intracellular Ca2+ homeostasis and induces aberrant aggregation of ER membranes. STIM deficiency also impairs cold-induced mitochondrial fission resulting in hyperfused mitochondria with reduced oxidative capacity, independently of UCP1 abundance. Importantly, mice lacking STIM in BAT exhibit impaired lipid oxidation, are cold intolerant and develop exacerbated peripheral insulin resistance when challenged with a high-fat diet. Together, these findings identify ER-PM remodeling and STIM-mediated SOCE as a central regulator that links organelle architecture to brown adipocyte function and contributes to whole-body metabolic homeostasis.

overall_design: Bulk RNA-sequencing of brown adipose tissue samples obtained from mice exposed to 6hours of cold (4C) temperature or housed in room temperature from wild type control or adipocyte specific Stim1/2 knockout mice (under adiponectin promoter).

first: Jiamin

last: Zhou

first: Cansu

last: Dogan

first: Leonardo

last: Artico

first: Karina

last: Rodrigues

first: Sophia

last: Hakam

first: Tony

last: Kim

first: Vivian

first: Kalina

last: Lapenta

first: Misun

last: Kang

first: Danielle

last: Jorgens

first: Scott

last: Widenmaier

first: Ana

last: Arruda


title: Simultaneous orthogonal cell engineering by a single CRISPR-Cas9 polyfunctional editor

city: Milano

first: Sara

last: Valsoni

address: via Olgettina 60

department: TIGET

institute: SR-TIGET

type: Methylation profiling by high throughput sequencing