title: Functional Remodeling of iNKT Cells by Sulfatide-Reactive Type II NKT Cells Reprograms Alveolar Macrophages to Alleviate Lung Ischemia-Reperfusion Injury

city: Wuhan

first: qingqing

last: li

address: No. 238 Jiefang Road, Wuchang District

department: Department of Respiratory and Critical Care Medicine

institute: Renmin Hospital of Wuhan University

summary: Lung ischemia-reperfusion injury (LIRI) is a serious complication in critical clinical situations. Despite its importance, the specific role of type II natural killer T (NKT) cells in LIRI remains unclear.

overall_design: In this study, we establish a LIRI mouse model and demonstrate that sulfatide-reactive type II NKT cells promote M2 polarization of alveolar macrophages (AMs) and alleviate LIRI through AMs-mediated mechanisms. This protective effect is absent in Jα18-/- mice, indicating the essential role of invariant NKT (iNKT) cells. Further analysis shows that interleukin-10 (IL-10) secreted by iNKT cells upregulates AT-rich interaction domain 3A (Arid3a) in macrophages, which then promotes the transcription of DNA damage inducible transcript 4 (DDIT4). This cascade enhances M2 polarization of macrophages, potentially contributing to lung protection and alleviating LIRI. These findings suggest that NKT cells may offer a therapeutic target for LIRI in the future.

first: Qingqing

last: Li


title: Androgen receptor-negative prostate cancer is vulnerable to SWI/SNF-targeting degrader molecules

status: Public on Dec 16 2025

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex becomes frequently deregulated in advanced castration-resistant prostate cancer (CRPC). Proteolysis targeting chimera (PROTAC) therapies degrading SWI/SNF ATPases offer a novel approach to interfere with androgen receptor (AR) signaling in AR-dependent castration-resistant prostate cancer (CRPC-AR). To explore the utility of SWI/SNF therapy beyond AR-sensitive CRPC, we investigated SWI/SNF-targeting agents in AR-negative CRPC. SWI/SNF targeting PROTAC treatment of cell lines and organoid models reduced the viability of not only CRPC-AR but also WNT-signaling dependent AR-negative CRPC (CRPC-WNT). We discovered that SWI/SNF ATPase SMARCA4 depletion interfered with the WNT master transcriptional regulator TCF7L2 (TCF4) in CRPC-WNT.

overall_design:
Patient-derived organoids (WCM1078) were treated with A947 (SMARCA2/SMARCA4 targeting PROTAC) and A858 (SMARCA-binder control).
RNA-seq: Organoids were treated with A858 or A947 (1µM) for 24h and 48h (3 biological replicates per condition).
ChIP-seq: Organoids were treated with A858 or A947 (1µM) for 4h (2 biological replicates per condition).
ATAC-seq: Organoids were treated with A858 or A947 (1µM) for 4h (3 biological replicates per condition).
scRNA: Organoids were treated for 72h with a control epimer (A858) or active compound (A947) at 1 µM.
PRO-cap: Organoids were treated for 24h with a control epimer (A858) or active compound (A947) at 1 µM.

first: Phillip

last: Thienger

first: Mark

middle: A

last: Rubin


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [CP-9mo-m-022]

status: Public on Dec 17 2025

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

overall_design: Apply snmC-seq3 to mouse brain regions to identify aging effects on epigenomics

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

middle: D

last: Lucero

first: Julia

middle: K

last: Osteen

first: Huaming

last: Chen

first: M

middle: M

last: Behrens


title: TAK1 is a key regulator of oncogenic signaling and differentiation blockade in rhabdomyosarcoma

city: Houston

first: Ashok

last: Kumar

state: Texas

address: 4349 Martin Luther King Blvd.

department: Pharmacological and Pharmaceutical Sciences

institute: University of Houston

summary: Rhabdomyosarcoma (RMS) is a malignant soft tissue sarcoma with a skeletal muscle phenotype, accounting for approximately 50% of all pediatric soft tissue sarcomas and 8% of all childhood cancers. Although RMS cells express myogenic regulatory factors, they fail to undergo terminal differentiation into mature muscle cells. Transforming growth factor β-activated kinase 1 (TAK1) is a major signaling protein that activates multiple intracellular pathways in response to growth factors, cytokines, and microbial products. Emerging evidence suggests that TAK1 is also an important regulator of self-renewal, proliferation, and differentiation of muscle progenitor cells. However, the role and mechanisms of action of TAK1 in RMS remain completely unknown. In this study, we demonstrate that TAK1 expression and activity are markedly elevated in a panel of RMS cell lines and in patient tumor specimens. Reverse phase protein array (RPPA) analyses revealed that TAK1 regulates the expression and activity of many molecules involved in cell cycle control, cell proliferation, and oncogenic signaling. Genetic knockdown or pharmacological inhibition of TAK1 suppresses RMS cell proliferation, migration, and invasiveness, while also promoting terminal myogenic differentiation. TAK1 inhibits differentiation in RMS, at least in part, through up-regulating YAP1 signaling. Our results also demonstrate that inducible knockdown of TAK1 in human RMS xenografts retards tumor growth and enhances myogenic differentiation in vivo. Collectively, these findings uncover a previously unrecognized role for TAK1 in RMS growth and differentiation, and suggest that TAK1 can be a potential therapeutic target for the treatment of RMS.

overall_design:
Bulk RNA-seq profiling of RD cells expressing Scrambled or TAK1 shRNA (n=3 each).

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The raw data are no longer available since the sequencing was performed 4 years ago. In addition,  NOVOGENE, the company who performed the sequencing,  does not have the data archived.
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first: Anh

middle: T

last: Vuong

first: Aniket

middle: S

last: Joshi

first: Anirban

last: Roy

first: Kavya

last: Mathukumalli

first: Phuong

last: Ho

first: Raksha

last: Bhat

first: Meiricris

last: Tomaz da Silva

first: Meghana

last: Trivedi

first: Bin

last: Guo

first: Benny

last: Kaipparettu


title: CALD1/IGF2BP1 complex mediates cisplatin resistance in bladder cancer via enhancing RFC4 mRNA stability in an m⁶A-dependent manner.

city: qingdao

first: Wenjie

last: Wei

address: 16 Jiangsu Road, Shinan District

department: Department of Urology

country: China

institute: The Affiliated Hospital of Qingdao University

summary: Cisplatin-based chemotherapy is the first-line treatment for muscle-invasive and metastatic bladder cancer, but most patients develop drug resistance within a short period. M⁶A modification (N⁶-methyladenosine) has been extensively validated as a key hallmark of multiple cancers, and its dysregulation may contribute to cisplatin resistance.

overall_design: Here, we established a cisplatin-resistant xenograft model of human bladder cancer through long-term intermittent chemotherapy and identified CALD1 as a critical determinant of cisplatin resistance. CALD1 was elevated in cisplatin-resistant bladder cancer cells, and loss of CALD1 conferred sensitivity to cisplatin. In patients, CALD1 was highly expressed in bladder cancer and associated with poor outcomes. Mechanistic investigations demonstrated that CALD1 interacts with the RRM1 domain of insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), which enhances the mRNA stability of the downstream gene RFC4 in an m⁶A-dependent manner, thereby increasing RFC4 expression. Elevated RFC4 protein levels subsequently enhanced tumor cell stemness and promoted cisplatin resistance. These findings suggest that targeting the CALD1/IGF2BP1–RFC4 axis may represent a novel strategy to reverse cisplatin chemoresistance.

first: Wei

last: Wenjie


city: Hangzhou

first: Da

last: Qian

state: Zhejiang

address: No. 158 Shangtang Road

department: Breast Surgery

institute: Zhejiang Provincial People's Hospital

summary: Icariin Ameliorates Exercise-Induced Fatigue by Promoting TFEB-Dependent Mitochondrial Clearance and Metabolic Re-programming, which reveals a novel molecular mechanism underlying icariin’s anti-fatigue efficacy and highlights its potential as a natural agent for enhancing exercise capacity.

relation:
Reanalysis of: GSM9351409
Reanalysis of: GSM9351410
Reanalysis of: GSM9351411
Reanalysis of: GSM9351412
Reanalysis of: GSM9351413
Reanalysis of: GSM9351414

overall_design:
Total RNA sequencing was performed on primary vascular smooth muscle cells (VSMCs) isolated from wild-type rats. The cells were first subjected to serum starvation and then treated with recombinant rat platelet-derived growth factor (PDGF). In contrast, control cells were cultured in fresh serum-free medium without the addition of any exogenous growth factors. Total RNA was extracted from the control group at 24 h post-treatment and from the PDGF-treated group at 48 h post-treatment, with three biological replicates set for each group.

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

last: Zheng


title: Regulation of the Yersinia pseudotuberculosis Type III Secretion System by the CpxAR Two-Component System

city: Santa Cruz

first: Victoria

last: Auerbuch

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California Santa Cruz

summary: The type III secretion system (T3SS) is a cell envelope-spanning injectisome found in many Gram negative pathogens. Expression of the T3SS is controlled by extracellular signals such as cell envelope stress. For example, the CpxAR two component system negatively regulates the Yersinia pseudotuberculosis Ysc T3SS, although the mechanism for this regulation remains unclear. As expected from previous studies, we found that mutations in Y. pseudotuberculosis that lock CpxR in its constitutively activated state (∆cpxA and cpxRD51E) led to decreased expression of the Ysc T3SS. CpxR did not bind to the regulatory regions of lcrF, encoding the Ysc T3SS master regulator. However, overexpression of LcrF protein rescued the T3SS expression defect of the ∆cpxA and cpxRD51E mutants, suggesting that CpxR represses lcrF through an indirect mechanism. Transcriptome analysis of Y. pseudotuberculosis showed that 101 genes were upregulated and 77 genes downregulated in both the ∆cpxA and cpxRD51E strains compared to wildtype, including seven genes known to modulate transcription. Individual deletion of these seven regulatory factors did not identify any single gene responsible for CpxR-dependent repression of LcrF, suggesting that the CpxAR system may act through multiple pathways to indirectly regulate the Ysc T3SS. However, this analysis led us to examine the role of the OmpR/EnvZ two component regulatory system, which is responsive to osmolarity, in LcrF regulation. Deletion of ompR led to a two-fold increase in LcrF and T3SS expression. These results suggest more complex regulation of the Ysc T3SS by two component regulatory systems than previously appreciated.

overall_design: Yersinia pseudotuberculosis IP2666pIB1 strains with consitutive CpxR activation were generated, one lacking the cpxA gene (delta cpxA) and one posessing a cpxR allele coding for a phosphomemetic version of the protein (cpxRD51E). Mutant and wildtype strains were grown shaking at 26°C overnight in 2ml LB media and then subcultured to an OD of 0.2 in fresh low calcium LB supplemented with 20mM sodium oxalate and 20mM magnesium cholride. These cultures were grown shaking at 26°C for 1.5 hours and then shifted to 37°C shaking for 1.5 hours to mimic host infection conditions and induce Type III Secretion. Each sample was then pelleted and RNA extracted for sequencing.

first: Karen

last: Hug

first: David

last: Balderas


title: Inhibition of P2RX7 Protects Against Light-Induced Retinal Degeneration by Suppressing cGAS-STING Signaling I

city: Guangzhou

first: Haifeng

last: Cui

state: Guangdong

address: jinsui

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

summary: Using comprehensive transcriptomic data, this approach objectively and quantitatively links observable pathological phenomena (light damage, cell death) with underlying molecular mechanisms (activation of DNA damage pathways and innate immune pathways). Thereby, it uncovers the intrinsic logic of disease development and progression, providing the most direct molecular basis for identifying therapeutic targets (such as the STING protein).

overall_design: To investigate the protective mechanism of A74 on the retina, we designed experiments using Balb/c strain mice. Retinal tissues were harvested to establish a light-induced damage model. Subsequently, RNA was extracted from mouse retinas for sequencing analysis.


title: Inhibition of P2RX7 Protects Against Light-Induced Retinal Degeneration by Suppressing cGAS-STING Signaling II


title: Early-life NAD⁺ deficiency programs skeletal muscle aging via epigenetic downregulation of hyaluronic acid synthesis

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Nicotinamide adenine dinucleotide (NAD+) levels decline with age, which has been associated with the development of aging-associated diseases. However, it remains unknown whether low NAD+ levels in early life affect aging. This study demonstrates that deficiency of NAD synthetase (NADS), a critical enzyme of the deamidated NAD+ biosynthesis pathway, drastically reduced NAD+ levels in skeletal muscle and impaired muscle function at a young age. Intriguingly, NAD+ levels were restored to normal in middle-aged NADS knockout mice, whereas muscle function remained compromised. Gene expression analysis identified that hyaluronic acid synthase 2 (Has2) was downregulated in both young NADS knockout mice and aged wild-type mice. We also revealed that Has2 was epigenetically downregulated via the α-ketoglutarate-JMJD3 axis. Then, impaired hyaluronic acid signaling dampened muscle stem cell, leading to decreased locomotor activity. These results suggest that maintaining NAD+ levels during early life is important for promoting healthy aging in skeletal muscle.

overall_design: ChIP sequencing with anti-H3K27me3 antibody using the skeletal muscle samples from young WT and NADS KO mice.

first: Mariam

last: Karim

first: Takashi

last: Nakagawa


title: Systemic infections alter cortical transcriptional signatures in Alzheimer′s disease

city: Exeter

first: Giulia

last: Pegoraro

address: Barrack Road

country: United Kingdom

institute: University of Exeter

summary: Alzheimer′s disease (AD) is characterized by neuroinflammation, yet the impact of concurrent systemic infections on the AD brain remains poorly understood. We investigated the molecular mechanisms underlying the central nervous system response to systemic infections in AD by analyzing RNA sequencing data generated in the prefrontal cortex from 202 post-mortem donors (113 AD, 89 controls), where we stratified by the presence of a respiratory infection at the time of death. We identified 763 significantly differentially expressed genes (DEGs) between AD and controls without infection, which were enriched for oxidative phosphorylation and neurodegenerative pathways. In contrast, 122 DEGs distinguished AD from controls during infection, with 57 genes uniquely altered in AD in the presence of infection, including MAPK4 , VAV3 , and POU3F4 , implicating infection-dependent mechanisms of vascular and immune regulation. Pathway activity analysis revealed that infection in AD suppresses some immune and vascular pathways, while enhancing transcriptional and developmental programs. Weighted gene co-expression network analysis uncovered three key modules: one module strongly associated with AD, enriched for aging and signal transduction; one module linked to both AD and infection, highlighting cytoskeletal remodelling and host–pathogen interactions; and one module specific to infection, enriched in astrocytes, pericytes, and endothelial cells, implicating blood–brain–barrier dysfunction. These findings suggest that systemic respiratory infections reshape transcriptional programs in the AD brain, dampening immune effector pathways and engaging vascular and host–pathogen processes in blood–brain–barrier–associated cell types. Our results highlight the complex interplay between systemic infection, neuroinflammation, and vascular responses in AD.

overall_design: RNA profiling of human postmortem prefrontal cortex samples stratified by the presenence of Alzhimeir's Disease and respiratory infection.

first: Lachlan

middle: F

last: MacBean

first: Adam

last: Smith

first: Darren

last: Soanes

first: Rebecca

middle: G

first: Jennifer

last: Imm

first: Joshua

last: Harvey

first: Morteza

last: Koushar

first: Valentin

last: Roche

first: Luke

last: Weymouth

first: Isabel

last: Castanho

first: Winston

last: Hide

first: Laura

last: Palmer

first: Debra

middle: J

last: Lett

first: Andrew

middle: C

last: Robinson

first: Natalie

last: Woodman

first: Karina

last: McDade

first: Delphine

last: Boche

first: Ehsan

last: Pishva

first: Katie

last: Lunnon


title: Integrated omics revealed regulatory mechanisms governing potato (Solanum tuberosum L.) seedling growth during shade avoidance syndrome

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

summary:
Background: Potato (Solanum tuberosum L.) is the fourth largest food crop worldwide with significant economic value and importance for food security. Shade avoidance syndrome (SAS) considerably affects crop architecture and productivity in high-density planting systems; however, its molecular mechanisms in potato remain poorly understood.
Methods: Potato seedlings were subjected to four light treatments simulating different shade signals: white light (control, WL), low blue light (LBL, simulating blue light attenuation by plant canopies), low red:far-red ratio (WL+FR, simulating far-red reflection from neighboring plants), and their combination (LBL+FR, simulating complete plant shade environment). We conducted a comprehensive study integrating morphological characterization, leaf anatomical analysis, hormone quantification, transcriptome sequencing, and metabolite profiling.
Results: Morphological analysis revealed that WL+FR primarily induced internode elongation (+20.0%) and leaf hyponasty, while LBL promoted stem elongation through increased node production (+36.3%). When combined, these signals (LBL+FR) synergistically enhanced stem elongation by 79.3%. Anatomical examination showed that LBL-treated leaves formed thickened palisade tissue layers (176.34 μm) with 6-7 layers of spongy tissue, whereas WL+FR resulted in thinner leaves (151.22 μm). Transcriptomic analysis identified 6,057 differentially expressed genes enriched in photosynthesis, hormone signaling, and carbohydrate metabolism pathways. A total of 1,168 differentially accumulated metabolites were detected across treatments, particularly organic acids and lipids associated with TCA (tricarboxylic acid) cycle and starch-sucrose metabolism. Weighted gene co-expression network analysis (WGCNA) identified PHYTOCHROME A (PHYA) as the central hub gene coordinating SAS responses under combined light stress, significantly diverging from the PHYB-centric model established in Arabidopsis.

overall_design:
The experiment utilized 20-day-old potato plants (Solanum tuberosum L. cv. Atlantic) provided by the Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Sciences. This cultivar was selected for its vigorous growth and broad adaptability. Virus-free plantlets were obtained through tissue culture and subcultured for three generations before experiment. Only plants with uniform growth were selected and transferred to soil, where they were acclimated for 14 days under a 16-h light/8-h dark cycle at 60% relative humidity. The growth environment simulated artificial shading conditions, with temperature maintained at 23-25°C. The experiment was conducted with six plants per treatment group. Light treatments were implemented using combinations of different LED light sources, including white light, blue light (400-499 nm), red light (600-699 nm), and far-red light (700-750 nm). To establish low R:FR conditions, far-red light (peak wavelength 730 nm) was supplemented to white light. For low blue light conditions, white light was passed through two layers of yellow filter (#101, Lee Filters, CA, USA). Light quality and intensity were measured using a HiPoint HR-350 spectrometer (wavelength range: 380-780 nm, accuracy: ±2 nm), and R:FR ratios were calculated according to the method described by Lyu et al [30].
Four light treatments were established to assess plant responses under varying light conditions. The white light treatment (WL) applied full-spectrum white LEDs with peak wavelengths at 450 nm and 570 nm, simulating a daylight-like spectrum. In the low blue light treatment (LBL), white light filtered through yellow filters, reducing blue light intensity to 1.5 μmol·m⁻²·s⁻¹.  For low R:FR treatment (WL+FR), far-red light was added to the white light, resulting in an R:FR ratio of 0.41. The fourth treatment combined WL+FR and LBL, and was referred to as LBL+FR.
Photosynthetically active radiation (PAR) was maintained at 500 μmol m⁻²s⁻¹ to observe plant responses during the transition from etiolation to de-etiolation. Light quality parameters were monitored every 2 h throughout a 14-day treatment period， with detailed records of photon flux density (PPFD; 400-750 nm) under each treatment condition

first: Li

last: Zhang

first: Feng-Jie

last: Nie


title: Exercise Engages Coordinated Neuron–Glia Signaling to Shape Spinal Cord Plasticity

city: Basel

first: Shivani

last: Mansingh

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

summary: Physical activity induces systemic benefits for brain and muscle function, but how the healthy spinal cord adapts to exercise remains largely unknown. Here, we combine bulk proteomics, single-nucleus RNA sequencing, and cellular communication inference to map exercise-induced molecular adaptations in the mouse lumbar spinal cord. Endurance training elicited robust baseline remodeling, dominated by glial transcriptional changes. Acute exhaustive exercise triggered biphasic responses: widespread metabolic and synaptic gene upregulation at 6 h followed by balanced suppression at 24 h, with trained animals exhibiting enhanced amplitude and faster resolution. Cell–cell communication analysis revealed that exercise reshaped signaling networks in both magnitude and composition. While glia emerged as primary transcriptional responders, cholinergic neurons—despite minimal transcriptional changes—were central signaling hubs, engaging various pathways with astrocytes, oligodendrocyte precursor cells, and oligodendrocytes in a training-dependent and temporally restricted manner. Glial-derived communication further diversified these responses, with astrocytes, oligodendrocytes, and microglia shifting toward pathways supporting synaptic remodeling, axon guidance, and growth factor signaling while dampening inflammatory cues. Together, these findings identify neuron–glia communication as potential driver of spinal cord adaptation to exercise, suggesting pathways through which glial plasticity may serve as a key mechanism linking motor activity to spinal cord resilience.

overall_design: Trained mice (6 weeks of voluntary running wheel access) and sedentary controls were compared following an acute bout of exhaustive treadmill exercise. Nuclei were isolated from lumbar spinal cord, PFA-fixed, and FACS-sorted based on DAPI staining to remove debris and duplets prior to snRNA-seq analysis using the 10X Genomics Flex assay.

first: Christoph

last: Handschin


title: Deciphering the immunopathogenesis of severe cutaneous adverse reaction

first: Gio

last: Wu

address: 3147 Biomedical Sciences Wy

institute: University of California San Diego

summary: Single cell sequencing with BD Rhapsody is performed to study reactive infectious mucocutaneous eruptions, DRESS syndrome and other severe cutaneous adverse reactions.

overall_design: PBMC, whole blood and blister fluid are analyzed during active disease, during treatment and upon recovery. Samples are analyzed using scRNAseq and VDJ sequencing.

first: Reid

last: Oldenburg

first: Ferhat

last: Ay

first: Hal

last: Hoffman

first: Ben

last: Croker

first: Daniela

last: Figueroa


title: Selective infection and loss of PRDM1+ LN Tfh cells in uncontrolled HIV infection precludes formation of Tfh reservoirs under ART

city: Philadelphia

first: Vincent

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

summary: The multifaceted and long-lived nature of HIV-1 reservoirs has proven to be a formidable obstacle in the development of a therapeutic cure of HIV-1. One of the major dimensions of the HIV-1 reservoir is its prevalence and persistence in  tissue environments, including in lymph nodes (LN). Within LN, T follicular helper (Tfh) cells are widely considered as the dominant sub-reservoir in viremic people with HIV (PWH). However, whether Tfh cells survive to establish a reservoir in PWH undergoing suppressive antiretroviral therapy (ART) has remained controversial. To address these issues, we deeply phenotyped over 500,000 cells and identified over 2,000 HIV-1 infected cells by employing single-cell multiomics on LN from PWH during viremia and suppressed on ART. While we detected HIV-1 infected Tfh cells, the majority of infected cells during viremia and ART had non-follicular phenotypes and were instead heterogeneously distributed between various CD4+ T-cell subsets. Within-subset comparisons of HIV+ and HIV- cells revealed heightened activation signatures and altered cell cycle states during viremia, but largely similar features during ART. Furthermore, the comparison between viremia and ART in PWH highlighted a noncanonical Tfh subset - defined by high locus accessibility and transcription of PRDM1 - that is selectively depleted during viremia, recovers after ART, and is highly susceptible to infection in vitro. Our work suggests a revised direction for the HIV-1 cure field where a mandate of any comprehensive strategy will be to address the high proportional burden of non-follicular cells towards the HIV reservoir.

overall_design: To establish a comprehensive and trimodal atlas of HIV+ cells from lymphoid tissue, we performed scDOGMAseq on sorted CD4+ T cells from inguinal or cervical LN of people without HIV (n = 4), viremic HIV (n = 12), and on ART (n = 10).

middle: H

first: Jayme

last: Nordin

first: Michael

last: Betts


title: Temporal modulation of gene expression in a controlled Schistosoma mansoni human infection model

city: Lubbock

first: Aravindan

last: Kalyanasundaram

address: 3601 4th Street

department: Immunology and Molecular Microbiology

institute: Texas Tech University Health Sciences Center

summary: Background Schistosomiasis is caused by parasitic blood flukes of the genus Schistosoma. Despite ongoing mass drug administration efforts, the disease remains a major public health burden in endemic regions. A better understanding of early host responses to schistosomiasis is critical for developing effective vaccines and therapeutics. Methods We conducted a longitudinal transcriptomic study of peripheral blood samples from 30 Schistosoma-naïve volunteers participating in two controlled human infection trials with male-or female-only S. mansoni cercariae. Blood was collected at six time points over 20 weeks post-infection. Whole-transcriptome RNA sequencing and integrative analyses, including differential gene expression, gene set enrichment, protein interaction networks, co-expression clustering, and immune module profiling, were employed to characterize temporal modulation of genes related to immune responses. Results Robust and highly time-dependent transcriptional responses were observed, peaking at Week 4 post-infection. Differential gene expression and pathway analyses revealed activation of immune responses, including type I and II interferon signaling, chemokine-mediated pathways, and antigen presentation. Notably, both Th1 and Th2 signatures were evident at Week 4. Key immune hubs included IFNG, TNF, and IL1B, along with transcriptional regulators such as STAT1 and IRF7. Blood transcription module analysis further highlighted transient activation of interferon and plasma cell-related responses. Conclusions This study provides a comprehensive transcriptional map of early host responses to S. mansoni infection in humans. The findings underscore the central role of interferon pathways, early mixed Th1/Th2 polarization, and inflammation-associated gene signatures in shaping host response to S. mansoni infection. These insights may inform the rational design of vaccines and biomarkers for schistosomiasis.

overall_design: The two controlled human Schistosoma infection dose escalation trials was performed at Leiden University Medical Center. Total RNA was extracted and purified from whole blood collected in PAXgene® Blood RNA tubes from 30 participants at six time points, including baseline (prior to exposure, Week 0) and every four weeks thereafter until Week 20 post-exposure (i.e.,Weeks 0, 4, 8, 12, 16, and 20). Paired-end whole-transcriptome sequencing (100 base pairs) was performed on the NovaSeq 6000 platform (Illumina,Inc., San Diego, CA).

first: Dawei

last: Li

first: Chuan

last: Jiang

first: Wenyu

last: Zhu

first: Emma

middle: L

last: Houlder

first: Koen

last: Stam

first: Jan Pieter

last: Koopman

first: Marijke

last: Langenberg

first: Ranmali

last: Kavishna

first: Sarah

last: Torkzadeh

first: Björn

last: Andersson

first: Josefine

last: Persson

first: Mumtaz

middle: Y

last: Balkhi

first: Desalegn

middle: W

last: Kifle

first: Aryandra

last: Arya

first: Hyon

last: Jeon

first: Birkneh

last: Tadesse

first: Sean

last: Gray

first: Darrick

last: Carter

first: Alison

last: Elliott

first: Florian

last: Marks

first: Ali

last: Harandi

first: Meta

last: Roestenberg

first: Afzal

last: Siddiqui


title: Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of Adam12CKO Mouse Model CD45- cells

city: Beijing

first: Qile

last: Guo

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

summary: Clinical trials targeting cancer-associated fibroblasts (CAFs)—crucial pro-tumoral factors in cancer—have almost all failed. This may be ascribed to their intrinsic functional plasticity and the opaque regulatory circuits underlying their heterogeneous phenotypes within tumors. We address these by developing a systematic screening approach for patient-derived fibroblasts using complementary CRISPR interference (CRISPRi) and activation (CRISPRa)-based perturb-seq. An anti-tumoral interferon (IFN)-I response-associated program is identified as the primary antagonism axis counteracting TGFβ-driven pro-tumoral myofibroblast activation. ADAM12 emerges as a molecular checkpoint mediating this relationship. Its ablation elicits IFN-I responsive programs, reconfigures myofibroblast population structures into progenitor-like states, revitalizes T cell-based immune responses, and induces tumor rejection across various murine models. Further combined with human genomics data analysis, our findings position ADAM12 as a potential target for fibroblasts, paving the way for actionable therapeutic interventions.

overall_design: ScRNA-seq of samples from Adam12 pCKO and littermate control mice bearing subcutaneous KPC, B16, and MC38 cells.


title: Systematic Bias Introduced by Ficoll-Based Isolation in AML Sample Composition and Downstream Analyses

city: Liege

first: Gregory

last: Ehx

address: Avenue de l'Hopital, 11

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: Acute myeloid leukemia (AML) is a heterogeneous malignancy whose characterization relies on immunophenotyping and molecular profiling. While red blood cell lysis is the recommended method for leukocyte isolation in clinical diagnostics, Ficoll-based density gradient centrifugation remains widely used in research and biobanking. Here, we systematically compare these two isolation approaches using paired primary AML samples. We show that Ficoll processing consistently enriches lymphocytes and AML blasts while depleting granulocytes. The increased T-cell content introduced by Ficoll impaired AML engraftment in immunodeficient NSG mice, as residual T cells in the graft triggered graft-versus-host disease, precluding reliable evaluation of leukemia-initiating activity. Although Ficoll had minimal impact on ex-vivo AML blast expansion or chemotherapy response, RNA sequencing identified 1,136 differentially expressed genes between isolation methods, with Ficoll samples exhibiting enrichment of proliferation-associated pathways and leukemic stem cell (LSC) transcriptional programs. Immunogenomic deconvolution further demonstrated that Ficoll artificially inflates estimated CD8⁺ T-cell and monocyte abundances while reducing inferred neutrophil frequencies. Mutation calling from RNA-seq data revealed substantial discrepancies between methods, including failure to detect a clinically relevant DNMT3A R882 mutation in a Ficoll-processed sample. These findings identify leukocyte isolation as a critical pre-analytical variable in AML research and support the systematic use of red blood cell lysis to preserve cellular diversity and avoid unpredictable biases introduced by Ficoll-based isolation.

overall_design: RNA-seq profiling of the total leukocyte fraction isolated from five AML samples either through Ficoll or red blood cell lysis method

first: Bianca

middle: E

last: Silva


title: Importance of being non-triplet in alternative splicing

city: riverside

first: Shameerudeen

last: Athavudeen

address: 900 university ave

department: Biochemistry

institute: UC Riverside

summary: Alternative mRNA splicing can be used by a cell to regulate gene expression and to generate transcriptomic diversity. Most cases of alternative splicing studied to date are triplet in nature, meaning that both isoforms retain the same translational reading frame. Indeed, non-triplet alternative splicing is sometimes considered evidence of splicing errors or splicing noise. Nevertheless, some examples of functionally important non-triplet alternative splicing exist. We set out to determine the global prevalence, regulation, and function of non-triplet alternative splicing in vivo in C. elegans. We performed RNA-Seq on NMD-deficient mutants and bioinformatically categorized the molecular consequences of non-triplet alternative splicing into three categories: NMD-sensitive isoforms, alternative C-terminal length isoforms, and dual-coding isoforms. We identify hundreds of non-triplet alternative splicing events across these three categories. Genetic and molecular analysis reveals cases of developmental regulation, splicing factor autoregulation, cell-specific splicing patterns, and multiple non-triplet alternative splicing events with physiologically important functions. Together these experiments reveal the importance of non-triplet alternative splicing, a large but underappreciated class of alternative splicing events, for regulating gene expression and generating protein-coding diversity

overall_design: L4 staged animals from wild-type and mutant conditions. RNA extracted, and selected for polyA+ mRNA prior to library generation and short-read sequencing.

first: Adam

last: Norris


title: Transcriptome analysis (bulk RNAseq) of FlncKO-C2C12 during myogenic differentiation

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

summary: In this study we performed transcriptome analysis (bulk RNAseq) of WT-C2C12 immortalized mouse myoblasts and FlncKO-C2C12 cells during myogenic differentiation (day 0, 1, 2, 4 and 6).

overall_design: C2C12 cells were genetically modified using CRISPR/Cas9 guide RNA targeting the first exon of the mouse Flnc gene (NC_000072.6 (2933153.29461889)) as described in Klimenko et al., 2024. WT-C2C12 (wild type)and FlncKO-C2C12 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, 4.5 g/L d-Glucose, Gibco) supplemented with 10 % fetal bovine serum (FBS, Gibco), 2 mM l-glutamine, and 100 μg/ml penicillin-streptomycin (Pen-Strep, Gibco). Cells were re-plated every 48 h at a density of 100,000 cells per 100 mm dish. Myogenic differentiation was induced by culturing cells in low serum medium (DMEM, 2 mM l-glutamine, 100 μg/ml Pen-Strep) supplemented with 2 % horse serum (Gibco). During differentiation, the medium was refreshed daily. Total RNA was extracted on 0, 1, 2, 4 and 6 days after induction of myogenic differentiation. Total RNA was extracted using ExtractRNA reagent (Evrogen) according to the manufacturer's instructions. RNA-libraries from WT and FlncKO cells were prepared with TruSeq Stranded mRNA kit, samples were sequenced on Illumina NextSeq 2000, read length 51 bp.

first: Anna

last: Kostareva


title: Human bone marrow adipocytes drive prostate cancer bone metastasis progression via lipid-mediated induction of Angiopoietin-like 4

city: Toulouse

first: Camille

last: Attane

address: 205 route de Narbonne

country: France

institute: CNRS/IPBS

summary: Bone is the predominant metastatic site in advanced prostate cancer (PCa), and the role of bone marrow adipocytes (BMAds) which constitute over 70% of adult marrow remains poorly understood. Herein, we developed a physiologically relevant 3D culture model using primary human BMAds from red hematopoietic rich-areas (rBMAds). Using this model, we show that rBMAds engage in metabolic crosstalk with PCa cells by releasing free fatty acids (FFAs) through a non-canonical lipolytic pathway. These FFAs are taken up by PCa cells, and induce a transcriptional reprogramming that promotes motility. Among the responsive genes, Angiopoietin like 4 (ANGPTL4) is the most upregulated via a Peroxisome proliferator-activated receptor γ (PPARγ)-dependent mechanism, and its silencing abolishes the rBMAd-driven migratory and invasive phenotype. In bone metastases of patients with PCa, high ANGPTL4 levels correlated with poor survival. Together, our findings uncover a novel adipocyte-tumor interaction and identify ANGPTL4 as a key mediator and potential therapeutic target in bone-metastatic PCa.

overall_design: RNA-Seq profiling of PC3 cells cocultivated 3 days with human bone marrow adipocytes

first: Marine

last: Hernandez

first: Sauyeun

last: Shin

first: David

last: Rengel

first: Stéphanie

last: Dauvillier

first: Carine

last: Valle

first: Sarah

last: Pericart

first: Alessandro

last: Taccini

first: Mohamed

last: Moutahir

first: Justine

last: Bertrand-Michel

first: Nicolas

last: Reina

first: Catherine

last: Muller

last: Attané


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [ATAC]

first: Michael

last: Haney

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

summary: The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b led to reductions in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This was associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

overall_design: ATAC-seq of HSPCs in vitro including Tada2b KO HSPCs

last: Wilkinson

first: Christy

last: Munson

first: Ian

last: Hsu


title: Cell-specific effects of acute sleep deprivation on transcriptomic signatures of non-neuronal cells in the mouse hippocampus and prefrontal cortex

city: Iowa City

first: Junko

last: Kasuya

state: IA

address: 169 Newton Rd

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: Sleep is essential for maintaining cognitive, emotional, metabolic, and immune functions in animals. Although much research on sleep homeostasis has focused on neurons, non-neuronal cells are also critical. We performed transcriptomic analyses on nuclei isolated from non-neuronal cells in the hippocampus and prefrontal cortex of mice subjected to acute sleep deprivation (SD). We demonstrate that acute SD elicits robust, cell-type and region-specific transcriptional reprogramming in astrocytes and oligodrocytes. The most striking changes are in astrocyes, with reductions in cholesterol biosynthesis genes across both regions, but opposite changes in genes regulating mitochodrial and neurodegeneration-related pathways. Strikingly, we see the induction of genes associated with primary cilia in cortical astrocytes.  Within oligodendrocytes, genes encoding cell-adhesion molecules are down regulated.  This work highlights the importance of focusing our gene expression studies on specific cell populations and reveals new potential mechanisms for the regulation of sleep and sleep function by non-neuronal cells.

overall_design: Cell-specific effects of acute sleep deprivation on transcriptomic profiles were analyzed in non-neuronal cells from mice hippocampus using single nuclear RNAseq

first: Yutong

last: Wong

first: Yann

last: Vanrobaeys

first: Marcos

last: Frank

first: Ted

last: Abel


title: Rewiring STAT signaling from the cell surface with Trikine immunotherapeutics [RNAseq of IL21 Trikine]

city: Stanford

first: Yang

last: Zhao

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

summary: Cytokines dimerize two receptor chains to activate Janus kinases and STAT transcription factors that regulate immune cells but have therapeutic liabilities. We engineered “Trikines” to compel cis formation of three-chain cytokine receptor complexes at the cell surface that induce bespoke STAT transcriptional signaling programs optimized for therapeutic efficacy. Designed Trikines co-activated pSTAT5 and pSTAT3 signatures distinct from any natural cytokines, by assembling trimeric combinations of Interleukin-2 (IL-2), Interleukin-10 (IL-10), and Interleukin-21 (IL-21) receptors. IL-2-based-Trikines restrain terminal differentiation of T cells, promote stemness, and enhance durability of tumor control. Unexpectedly, an IL-10-based Trikine induced immune infiltration into poorly immunogenic tumors, showing striking efficacy in small cell lung cancer and pancreatic cancer models. Trikines obviate the need for cell engineering to customize STAT signatures for immunotherapy.

overall_design: Mouse T cells were pre-activated with IL-2 as described and rested in the absence of serum or cytokine overnight. Cells were then incubated with 100 nM IL-2 (GER110), IL-21(GER112), IL-1 + IL-21 (GERcombo) or 21/2-trikine(GER119) for 24 hours. Cell wee not stimulated (NS) as control. For each condition, we performed 3 technical replicates. Total RNA was extracted from 1-2.5million cells per condition using a RNeasy Micro Kit (Qiagen) followed by mRNA library preparation (poly-A enrichment) according to manufacturer instructions. Each library was sequenced on the NovaSeq X Plus PE150 resulting in approximately 12 x 106reads per sample.

first: Grayson

last: Rodriguez

first: Chris

last: Garcia


title: In vivo screen reveals specific roles of Hippo pathway components in development and regeneration

city: Edinburgh

first: Carsten

middle: Gram

last: Hansen

address: 4-5 Little France Dr

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: The Hippo signalling pathway is a major regulator of regeneration and development. However, the comparative importance and functional roles of individual Hippo pathway components in vivo is greatly unknown, particularly within the vertebrate lineage. To gain direct and comparable insights we took advantage of the zebrafish larvae model system. We generated individual and combined CRISPR/Cas9 F0 knockouts of a range of core Hippo pathway genes, including upstream regulators, the co-transcriptional regulators Yap1/Taz, and Yap1/Taz-target genes. We analysed and compared the resulting developmental and regenerative phenotypes. Our findings highlight that paralogues of core components have distinct, but in some instances overlapping, functions.  Intriguingly, we find that Yap and Taz have differential roles during development and regeneration. In addition, we characterise and compare two tail fin regenerative paradigms: after both severe and mild injury. These injury paradigms are drastically different and elicit diverse resolution processes. We confirm critical roles of the immune system in the regenerative process and identify that macrophages are recruited to lesser extent in tail fin regeneration upon Yap1 and Taz loss, suggesting defective regenerative macrophage function. This defective macrophage involvement might therefore be one of the mediators of the deficient regeneration in these two Crispants. Overall, our analysis emphasises distinct requirements and responses of the Hippo pathway during development and across different regenerative paradigms.

overall_design: Bulk RNA-seq of zebrafish tail fin tissue. Samples include uninjured and injured (severe tail fin injury paradigm tissue at 3dpf) tissue, from WT and Yap or Taz Crispant fish.

first: Susanna

last: Riley

first: Michaela

last: Noskova

first: Shijia

last: Xia

first: Richard

last: Cunningham

first: Justyna

last: Cholewa-Waclaw

first: Yi

last: Feng


title: Rewiring STAT signaling from the cell surface with Trikine immunotherapeutics [scRNAseq of IL10 Trikine]

overall_design: F1 mice were inoculated s.c. with 5 × 10⁵ KP1 cells and received i.p. administration of mono-IL-10(10) or IL-10/2-Trikine (trikine, 3 μg functional cytokine per dose) every other day from day 7 to day 19, along with anti-PD-1 antibody (Combo, 200 μg per dose, clone RMP1-14) on days 7, 11, 15, and 19. On day 19, mice were sacrificed and tumors were collected. Tumor-infiltrating leukocytes were enriched by density gradient centrifugation using Ficoll-Paque PLUS (Cytiva), followed by surface marker and DAPI staining (Thermo Fisher Scientific). Live CD45⁺ leukocytes were sorted using a Sony SH800 Cell Sorter (Sony Biotechnology) for Single cell RNA sequencing.


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [scRNA]

first: Michael

last: Haney

overall_design: Single Cell-seq of HSPCs in vitro including Tada2b, Taf5l KO HSPCs

first: Adam

last: Wilkinson

first: Haney

last: Michael


title: Transcriptomic Signature-Guided Depletion of Intermediate Alveolar Epithelial Cells Ameliorates Pulmonary Fibrosis in Mice

city: New Orleans

first: Yong

last: Zhou

state: LA

address: 333 S Liberty St

department: Medicine - Pulmonary Diseases

institute: Tulane University

summary: scRNA-seq was used to profile transitional AT2 cells in bleomycin-injured mouse lungs. Using an RNA-sensing strategy, Sprr1a-expressing cells corresponding to Krt8⁺ alveolar differentiation intermediates (ADIs) were selectively labeled and analyzed. scRNA-seq revealed that Sprr1a+ cells display transcriptomic features of transitional epithelial states. These datasets provide a resource to study the role of transitional epithelial populations in lung fibrosis.

overall_design: C57BL/6 mice were treated with bleomycin to induce lung fibrosis. At the fibrotic stage, AAV6.2FF vectors encoding Sprr1a sensor RNAs fused to EGFP were delivered to label Sprr1a+ transitional AT2 cells. Labeled (EGFP+) and unlabeled cells were isolated for scRNA-seq using the 10x Genomics Fixed RNA Profiling platform with a custom EGFP probe. Libraries were sequenced on an Illumina NextSeq 2000 and analyzed with Cell Ranger and Scanpy to define Sprr1a+ cell states and compare them with known Krt8+ ADIs.

first: Fei

last: Peng

first: Chun-sun

last: Jiang

first: Zhen

last: Zheng

first: Shaharam

last: Aliyari

first: Dan

last: Shan

first: Aaryan

last: Sabharwal

first: Qinyan

last: Yin

first: Shigeki

last: Saito

first: Chao

last: He

first: Ivan

middle: O

last: Rosas

first: Joseph

middle: A

last: Lasky

first: Victor

last: Thannickal


title: Transient Sprr1a expression defines a population of border zone cardiomyocytes that survive ischemic injury

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Cardiomyocytes in the border zone (BZ) of a myocardial infarction (MI) reside directly adjacent to the ischemic core, a niche characterized by tissue necrosis, immune cell infiltration, and altered mechanical properties. Very few tools exist to study the BZ, limiting the development of strategies to prevent cardiomyocyte death and infarct expansion or promote heart regeneration. Here, we describe two novel mouse lines to visualize, track, and isolate BZ cardiomyocytes, which has revealed their transcriptional signature and surprising longevity.

overall_design: We subjected Sprr1a-GFP mice to MI at 12 weeks of age.  5 days after MI, we isolated cardiomyocytes by langendorff digestion. We separated GFP+ border zone myocytes from GFP- remote zone myocytes by flow cytometry using  a 130um nozzle and slow flow rate. RNA was isolated from the cell pellets and subjected to RNA-sequencing. n= 5 mice.

first: Eric

last: Small

first: Emily

last: Marshall

first: Daniel

last: Zuppo

first: Kimberly

middle: N

last: Burgos Villar


title: Spatiotemporally Controlled Restoration of GAS6 Signaling via mRNA Therapy Promotes Scarless Healing in Preclinical Models

city: hangzhou

first: Yan

state: 浙江省

address: hangzhou

institute: 浙江大学医学院附属第二医院

summary: Deep cutaneous injuries in adult mammals often lead to fibrotic scarring, a process exacerbated by inflammatory fibroblasts that amplify immune recruitment. Early modulation of immune–fibroblast crosstalk represents a promising therapeutic strategy. Here we show that GAS6 is a key regulator of this interaction and can be therapeutically targeted using a spatiotemporally controlled lipid nanoparticle (LNP)–mRNA hydrogel platform. We engineer LNP-GAS6 mRNA to enhance macrophage efferocytosis and suppress inflammatory fibroblasts, then encapsulate it in a thermosensitive hydrogel for localized delivery. In murine, rabbit ear, and Bama minipig wound models, this treatment significantly accelerated wound closure and reduced fibrotic scarring. These results demonstrate that restoring GAS6 signaling via mRNA-based delivery promotes scarless healing and offers an effective therapeutic approach for fibrotic skin disorders.

overall_design: Male C57BL/6 mice (6-8 weeks) underwent dorsal full-thickness 6-mm circular excisions under intraperitoneal injection anesthesia, stabilized with silicone rings and 3M Tegaderm film (inhibiting wound contraction). Treatments included hydrogel + LNP and hydrogel + GAS6 mRNA-LNP. Peri-wound tissues were harvested at day 3.


title: PTEN regulates vagal-insulin signaling to optimize autonomic output determining peripheral inflammatory and metabolic homeostasis

city: Toronto

first: Minna

last: Woo

state: Ontario

address: 10-601D, College Street

department: Department of Medicine

country: Canada

institute: University of Toronto

summary: The vagus nerve (VN) is a major component of the parasympathetic nervous system that regulates glucose and energy homeostasis. However, the specific molecular signaling pathways mediated by the VN that regulates homeostasis remain unclear. Here, we show that vagal neuron-specific deletion of phosphatase and tensin homolog (Pten), the endogenous negative regulator of PI3K, led to increased vagal output. Intriguingly, dopaminergic signaling genes were upregulated, correlating with elevated sympathetic nerve density and increased norepinephrine levels in adipose tissue of Pten-deficient mice. These mice were also protected against high-fat diet-induced obesity, insulin resistance, and systemic inflammation. To investigate insulin-specific PI3K signaling within the VN, we generated mice with vagal neuron-specific insulin receptor deletion that resulted in exacerbation of metabolic defects, which was rescued by concomitant Pten deletion. In summary, we show that insulin-PI3K-PTEN axis within vagal neurons is essential in optimizing the autonomic output that determines peripheral inflammatory and metabolic homeostasis.

overall_design: Overall experimental design: P-PTEN WT and P-PTEN KO animals were weaned at 4 weeks of age and allowed to acclimatize to newly separated littermates for 2 weeks prior to performing baseline insulin/glucose tolerance tests. Following the 2 weeks, the animals and subsequently separated into chow or high fat diet consisting of 60% fat content cohorots and were maintained on their respective diets for 3 months. Following the 3 months, the animals were assessed for their vagal output , endpoint itt/gtts and metabolic parameters via metabolic caging. Animals were then subsequently euthanized and their adipose, liver and muscle tissue were collected for molecular analysis including western blot, real-time PCR alongside histological analysis Single-nucleus rna-sequencing design: Animals were fed for 2 weeks of HFD after 6 weeks of age where the body weights start to diverge between our P-PTEN WT and P-PTEN KO. Animals were subsequently euthanized and both their left and right cervical vagus nerves which contained the nodose ganglion were collected. 14 vagus nerves collected from 7 animals were then subsequently pooled into a single sample from both cohorts of mice. Nuclei were then extracted per sample and single nucleus rna-sequencing was performed. The Seurat and Harmony programs were used in RStudio version 4.2.2 to annotate and cluster different cell populations and to generate the list of genes enriched within the different cellular populations. The samples are separated into WT and KO data respectively

first: Yu Zhe

last: Li

first: Joe Eun

last: Son

first: Nathaniel

last: Vo

first: Catherine

last: Bellisimo

first: Ju Hee

last: Lee

first: Joshua

last: Rapps

first: Evan

last: Pollock-Tahari

first: Martha

last: Ghebreselassie

first: Chuck Tsu

last: Chen

first: Richard P

last: Bazinet

first: Fillio

last: Billia

first: Akira

last: Suzuki

first: Chi-Chung

last: Hui

first: Tak W

last: Mak

first: Hoon-Ki

last: Sung

first: Paul

last: Yoo


title: Single nucleus tanscriptomic analysis of the mouse enteric nervous system

city: New York

first: Robert

last: Lovelett

state: New York

address: 430 E 29th Street, 10th Floor

institute: Kallyope

summary: Enteric neurons are present throughout the GI tract where they integrate local and external signals to regulate GI function and are key modulators of multiple GI diseases. Here, we dissected each layer of the enteric nervous system along the GI tract, and used single nucleus sequencing to identify and characterize neuronal populations.

overall_design: The myenteric and submucusal layers of the mouse enteric nervous system were dissected and homogenized. A neuron-specific antibody (HuC/D, Abcam, ab237235; Clone EPR19098) was used to enrich the homogenates for neuronal nuclei. Nuclei were sorted and sequenced using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1.

first: Bernadette

last: Bracken

first: Sunny

last: Jones

first: Rijul

last: Singhal

last: Muller


title: Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing [snRNA-seq, ssRNA-seq]

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

summary: Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods constrained by an inherent trade-off between throughput and synaptic precision. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and single-compartment sequencing to map neuronal connectivity at single-synapse resolution. We validate this approach in the mouse pontocerebellar circuit, successfully identifying thousands of connections including the predominant excitatory projections from pontine neurons to cerebellar granule cells, while also revealing potentially novel synaptic partnerships. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.

overall_design:
Pons and cerebellum tissue was obtained from Sun1-sfGFP-Myc mice, and nuclei and synaptosomes were subsequently isolated via fluorescence-activated cell sorting, selecting based on GFP, HA, or V5 signals, before undergoing single-nucleus and single-synaptosome RNA sequencing (snRNA-seq, ssRNA-seq) analysis.
mRNA library: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: ChIP-seq of PAX5 in H526 small cell lung cancer cell

first: ailing

last: wu

address: yuhangtang street

institute: hangzhou normal university

summary: To investigate the mechanisms gene regulation of PAX5, we performed ChIP-seq on H526 cell, a human small cell lung cancer cell.

overall_design: H526 cells were divided into two groups: control group and PAX5 group. Each group consisted of two biologically independent replicates.


title: VEGF-Induced Transcriptomic Alterations in A549 Cells

summary: To investigate the mechanisms of cellular transformation, we performed transcriptome sequencing (RNA-seq) on VEGF-treated A549 non-small cell lung cancer (NSCLC) cells, with a focus on profiling changes in key target genes.

overall_design: A549 cells were divided into two groups: a vehicle control group and a VEGF treatment group. Each group consisted of two biologically independent replicates. Following the treatment, total RNA was isolated from all samples. The integrity and quantity of the RNA were verified. Subsequently, RNA-seq libraries were constructed from the high-quality RNA and sequenced on an Illumina platform to generate transcriptome profiles for subsequent analysis.


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [RNA-seq]

city: Frederick

first: Sandra

last: Wolin

state: MD

address: FDC 560 BG RM 11-82C / 560 CHANDLER STREET

institute: NCI

summary: Although most efforts to understand the functions of RNAs packaged in extracellular vesicles (EVs) have focused on mRNAs and miRNAs, recent studies using less-biased sequencing techniques have revealed that tRNAs and other noncoding RNAs (ncRNAs) are far more abundant. However, the extent to which EV ncRNAs resemble overall cellular RNAs and the benefits to host cells of packaging them into EVs remain unknown. Here, we purified EVs from the culture media of mouse and human cells and characterized their RNA components using high throughput sequencing and Northern blotting. We report that EVs are enriched for numerous aberrant ncRNAs, many of which contain oligouridine tails, a modification associated with degradation by Dis3l2, a cytosolic exoribonuclease that degrades defective structured ncRNAs. Both the numbers of EVs released and the fractions of tailed RNAs in EVs increase on Dis3l2 depletion, indicating that packaging of aberrant ncRNAs into EVs occurs in competition with Dis3l2 decay. Upregulation of multiple type I interferon stimulated genes (ISGs) occurs on Dis3l2 depletion, and cells treated with a neutral sphingomyelinase inhibitor that reduces exosome biogenesis also show moderate ISG upregulation, an effect that is enhanced in Dis3l2-depleted cells and accompanied by the accumulation of aberrant ncRNAs in cellular RNA. Thus, Dis3l2 degradation and packaging of aberrant RNAs into vesicles may prevent these RNAs from activating innate immune sensors and triggering an interferon response.

overall_design: Total RNA-seq profiling of  RNA purified from RAW 264.7 cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2).

last: Williams

first: Soyeong

last: Sim

first: Wilfired

last: Guiblet

first: Jubin

last: George

first: Jennifer


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA profiling of total RNA purified from RAW 264.7 whole cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2)


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [THP TGIRT-seq]

overall_design: TGIRT-sequencing profiling of total RNA purified from THP1 whole cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2), as well as extracellular vesicles derived from these cells and shDis3l2 cells.


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [TGIRT-seq]

overall_design: TGIRT-sequencing profiling of total RNA purified from RAW 264.7 whole cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2), as well as extracellular vesicles derived from these cells and shDis3l2 cells also expressing an shRNA-resistant Dis3l2 transgene (Dis3l2r), catalytically inacitve Dis3l2 transgene (Dis3l2 D389N), and an empty vector (vector).


title: Dgat1 detoxifies androgen receptor signaling to promote antitumor CD8+ T cell responses

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: The role of fatty acid (FA) oxidation 31 in T cell responses has been extensively studied, but whether FA esterification to triacylglycerol (TAG) regulates T cell exhaustion is unknown. Dgat1 catalyzes the rate-limiting step in TAGsynthesis. Here,we showthat deficiency in Dgat1 improvedmitochondrial metabolic fitness and expanded the pool of progenitors of CD8+ exhausted T (Tex) cells to sustain antitumor responses in femalemice. Inmalemice, however, Dgat1 deficiency synergized with androgen receptor (AR) signaling to cause FA peroxidation, endoplasmic reticulum (ER) stress, and Tex cell death. Deletion of Ar, overexpression of glutathione peroxidase 4 (Gpx4), or inhibition of ER stress-induced cell death rescued Dgat1-deficient CD8+ T cell survival and promoted antitumor responses in male mice. This study suggests that Dgat1 detoxifies AR signaling to protect against ER stress-induced cell death and maintain T cell stemness in males, and highlights sex-specific metabolic adaptations in the tumormicroenvironment.

overall_design: Male and female C57BL/6N mice (6-8 weeks old) were subcutaneously inoculated with 3e5 B16-GP33 cells. On day 15 post-inoculation, P14 WT and Dgat1 KO mice were sacrificed, and splenocytes were isolated and cultured for 72 hours with GP33 peptide (10 ng/mL) and IL-2 (10 ng/mL). Activated splenocytes from KO and WT mice were mixed while maintaining equal numbers of CD8+ T cells in both groups. The mixture was intravenously injected into tumor-bearing mice. Four days later, mice were euthanized. TILs were enriched by gradient centrifugation, and WT and KO P14 donor cells were FACS-sorted.

first: Alaa

last: Madi

first: Guoliang

last: Cui


title: Vaginal and gut microbiome pilot in the Carolina Endometrial Cancer

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

summary: Characterization of the microbiome in vaginal and stool samples self-sampled from endometrial cancer survivors enrolled in the Carolina Endometrial Cancer Study.

overall_design: Observational Cohort

first: Hazel

middle: B

last: Nichols

first: Mu

last: Jin


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (10X Chromium v3 multiplexed)

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

summary: The paraventricular hypothalamus (PVH) controls many behavioral and physiologic processes, including appetite, social behavior, autonomic outflow, and pituitary hormone secretion. However, molecular markers for functionally-specific PVH neuron projections remain largely undefined, and a complete census of PVH cell types has not been established. Therefore, we performed extensive single-cell/nucleus RNA sequencing to identify unique neuronal subtypes and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to validate and map them spatially. Our spatial transcriptomic atlas resolved 26 Sim1+ and 29 GABAergic neuron populations from the PVH and surrounding areas, revealing multiple subtypes not described previously and distinct transcriptional programs between neuroendocrine and centrally-projecting neurons. Additionally, projection-based profiling determined neuronal subtypes that project to the parabrachial region (PB) and spinal cord, helping to identify PVH populations that regulate satiety and sympathetic nervous system activity, respectively. Notably, PB-projecting PVH neurons expressing bombesin-like receptor 3 (Brs3) induce satiety, and their silencing causes obesity. Together, this atlas fills a critical gap by contributing high-resolution PVH spatial and circuit-based gene expression profiles, representing a valuable resource for the field of homeostasis.

overall_design: Single cells and single nuclei were isolated from dissections of mouse PVH tissue from 1mm-thick coronal brain slices. The transcriptional profile of individual cells and nuclei were then measured using a combination of Drop-seq, DroNc-seq, and 10X Chromium v3 assays. Data were collected from both male and female mice aged 6-12 weeks across 11 batches (Drop-seq = 7 batches, DroNc-seq = 2 batches, and 10X Chromium-v3 = 2 batches). Additionally, we completed targeted projection-specific sequencing of PVH nuclei fluorescently-labeled with retrograde AAV-cre injections into either the spinal cord or parabrachial region of H2B-TRAP mice. Fluorescently-labeled nuclei were then sequenced with either 10X Chromium v3 or Smart-Seq2 sequencing technologies.

first: Yuxi

last: Li

first: Trevor

last: Butler

first: Stefano

last: Nardone

first: Christopher

last: Jacobs

first: Amelia

middle: M

last: Douglass

first: Joseph

last: Madara

first: Miriam

last: McDonough

first: Jenkang

last: Tao

first: Elijah

middle: D

last: Lowenstein

first: Luhong

first: Deepti

last: Pant

first: Samuel

last: Walker

first: Annette

first: Harini

last: Srinivasan

first: Zongfang

last: Yang

first: John

last: Campbell

first: Linus

last: Tsai

first: Bradford

last: Lowell


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (10X Chromium v3)

first: Jon

last: Resch

first: Yuxi

first: Trevor

last: Wang

middle: T


title: Differential expression of VA opsin transcript variants in tissues linked to photoperiodic time measurement in Svalbard rock ptarmigan

city: Tromsø

first: Jana

last: Kalinova

address: Postboks 6050 Stakkevollan

country: Norway

institute: UiT The Arctic University of Norway

summary: Photoperiodic time measurement is the process through which annual changes in daylength are integrated to synchronize seasonal physiological and behavioral responses. Unlike mammals, which detect light exclusively through the eyes, birds possess multiple photoreceptive sites including the eyes, pineal gland, and deep brain photoreceptors (DBPs) located within the hypothalamus. The cellular and molecular identity of the DBPs mediating avian photoperiodic time measurement remains a matter of debate, however. Vertebrate ancient opsin (VA opn) is considered a strong DBP candidate, based on its anatomical localization and spectral response characteristics. Here, we used three different RNA profiling methods to evaluate VA opn expression across photosensitive structures in the Svalbard rock ptarmigan, a highly photoperiodic galliform species adapted to the extreme light conditions of the High Arctic. In the pineal gland, over 60% of transcripts encoded a full-length VA opn, containing all seven transmembrane domains considered necessary for photoreceptor function. In vitro analysis demonstrated that the full-length VA opn has peak spectral sensitivity at approximately 500 nm, consistent with published work in other galliform species. By contrast, in the hypothalamus and retina, the majority of VA opn transcripts are predicted to encode non-functional proteins lacking at least 2 out of 7 transmembrane domains. In the hypothalamus, single-nuclei RNA-sequencing analysis showed that VA opn transcript variants are predominantly expressed in cells of the oligodendrocyte lineage. These data support a model in which, in the Svalbard rock ptarmigan, VA opn contributes to the photosensitivity of the pineal gland, but not to hypothalamic DBP function.

overall_design:
RNA-profiling of photosensitive tissues (hypothalamus, retina, pineal gland) of the Svalbard rock ptarmigan across 4 seasonal states.
For further details see: https://doi.org/10.1016/j.jpap.2025.100272


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (DroNc-Seq)

last: Li

last: Butler

first: Stefano

last: Nardone

first: Christopher

first: Amelia

first: Joseph


title: Diurnal Light Transitions in Chlamydomonas reinhardtii

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: For the model alga Chlamydomonas, acclimation to diurnal low light (LL) or high light (HL) results in changes in photosynthetic complexes, chlorophyll content, thylakoid membrane architecture, and nonphotochemical quenching capacity that are maintained through the intervening night phases. To determine how diurnal photoacclimation influences algal fitness and document the molecular events during reacclimation upon a change in daylight intensity, we transitioned LL-acclimated populations to diurnal HL and HL-acclimated populations to diurnal LL and performed an RNA-Seq timecourse over two diurnal periods.

overall_design: Cells were grown photoautotrophically in turbidostat photobioreactors under diurnal cycles of 12 h light at 28°C and 12 h dark at 18°C for a minimum of two weeks in order to establish population synchrony and acclimate them to either LL (50 PFD) or HL (1000 PFD). Then, the LL-acclimated populations were subjected to diurnal HL conditions, and the HL-acclimated populations were subjected to diurnal LL conditions. Cell physiology (cell number, size, pigments, photosynthetic parameters), the transcriptome, and the proteome were monitored for two diurnal periods. Samples were collected for RNA-Seq every 2 h.

first: Sunnyjoy

last: Dupuis

first: Victor

last: Zhong

first: Sabeeha

middle: S

last: Merchant


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Smart-Seq2)

last: Jacobs

last: Douglass

last: Madara

first: Miriam

last: McDonough

first: Jenkang

last: Tao

first: Elijah

last: Lowenstein

first: Luhong

first: Deepti

last: Pant

first: Samuel

middle: J

first: Annette

first: Harini


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Drop-Seq)

first: Jon

last: Resch

first: Yuxi

first: Trevor

middle: C

last: Walker

last: Srinivasan

first: Zongfang

last: Yang

first: John

last: Campbell

first: Linus

last: Tsai

first: Bradford

last: Lowell


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types

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

overall_design: Refer to individual Series


title: Neuronal Idol deletion ameliorates amyloid pathology

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

summary: Earlier studies demonstrated that overexpression of the low-density lipoprotein receptor (LDLR) decreases apolipoprotein E (APOE) levels in the brain and alleviates amyloid-beta (Aβ) pathology. We hypothesized that inhibiting the Inducible Degrader of LDLR (IDOL)- an E3 ubiquitin ligase that ubiquitinates LDLR for degradation- would increase endogenous LDLR levels and decrease amyloid pathology. Previously, we demonstrated that the deletion of Idol increased LDLR levels and reduced amyloid deposition in a transgenic mouse model of Aβ-amyloidosis. However, the cellular mechanisms underlying these beneficial effects were unknown. Here, we investigate the cell-type-specific contribution of Idol deletion to amyloid pathology by generating Idol conditional knock-out mouse models. We demonstrate that deletion of neuronal, but not microglial, Idol reduces amyloid accumulation in the 5XFAD transgenic mouse model. Furthermore, only neuronal Idol deletion alters brain LDLR and APOE levels, pointing to the critical role of the neuronal LDLR-APOE axis in modulating Aβ accumulation.

overall_design: Quant-seq (3' mRNA-seq) analysis of cerebral cortices of female 5xFAD mice with Camk2a-Cre Idol WT vs. cKO genotypes at 4 months of age

first: Hande

last: Karahan

first: Kelly

last: Hartigan

first: Md Mamun

last: Al-Amin

first: Sutha K

last: John

first: Brianne

last: McCord

first: H.R. Sagara

last: Wijeratne

first: Dominic J

last: Acri

first: Daniel C

last: Smith

first: Luke C

last: Dabin

first: Hannah M

last: Rondon Cordero

first: Byungwook

first: Do-Hun

last: Lee


title: Rewiring STAT signaling from the cell surface with Trikine immunotherapeutics [scRNAseq of IL21 Trikine]

first: Yang

last: Zhao

state: CA

summary: Cytokines dimerize two receptor chains to activate Janus kinases and STAT transcription factors that regulate immune cells but have therapeutic liabilities. We engineered “Trikines” to compel cis formation of three-chain cytokine receptor complexes at the cell surface that induce bespoke STAT transcriptional signaling programs optimized for therapeutic efficacy. Designed Trikines co-activated pSTAT5 and pSTAT3 signatures distinct from any natural cytokines, by assembling trimeric combinations of Interleukin-2 (IL-2), Interleukin-10 (IL-10), and Interleukin-21 (IL-21) receptors. IL-2-based-Trikines restrain terminal differentiation of T cells, promote stemness, and enhance durability of tumor control. Unexpectedly, an IL-10-based Trikine induced immune infiltration into poorly immunogenic tumors, showing striking efficacy in small cell lung cancer and pancreatic cancer models. Trikines obviate the need for cell engineering to customize STAT signatures for immunotherapy.

overall_design: For the low dose regimen of super IL-2(2), sIL-2 + IL-21 (2Pos21), or IL-2/21-trikine(2-trikine) treatment in the B16F10 +pmel ACT model, tumors from mice were harvested on day 18 following tumor injection. Tumorswere minced and dissociated using a gentleMACS Octo Dissociator. TILs were collected forsequencing by sorting for live, single cell, Thy1.1+CD8+ cells on a Sony Cell Sorter SH800S.

first: Grayson

last: Rodriguez

first: Chris

last: Garcia


title: HIV-1 expression is heterogeneous among clones of CD4+ T cells carrying authentic intact latent proviruses

city: NEW YORK

first: Thiago

last: Oliveira

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Antiretroviral therapy suppresses HIV-1 infection but is not curative because it fails to eliminate a reservoir of intact latent proviruses that reside primarily in CD4+ T cells. This compartment is composed of rare T cells that predominantly express memory and effector memory markers. The lack of precise understanding of the latent compartment has made it challenging to develop curative strategies for HIV-1 infection. Here we report on the properties of CD4+ T cells clones carrying intact latent proviruses, expanded in vitro from single cells obtained from the reservoir of people living with HIV-1. The latent proviruses in the clones were integrated into ZNF genes, non-genic satellite and centromeric regions, frequently associated with latency. Notably, the transcriptome of the cultured clones resembled their cells of origin. Despite their descent from single cells, only a fraction of the cells ranging from 0.4-14% expressed relatively low levels of HIV-1 that did not measurably alter host gene transcriptome. Latency reversing agents (LRAs) variably increased the number and amount of expression per cell, but the effects were modest and clone and LRA specific. The results suggest that pharmacologic and immunologic approaches to clear the reservoir should be optimized to accommodate intra- and inter-clonal diversity.

overall_design: CD4+ T cells harboring intact latent proviruses were obtained from single cells from 7 ART-suppressed individuals and expanded in vitro. These expanded clones were analyzed at baseline (resting) and after 24 hours of stimulation (activated) with anti-CD3/CD28 + IL-2. We performed 5' single-cell RNA sequencing (scRNA-seq) and T-cell receptor (scV(D)J-seq) using the 10X Genomics platform to characterize proviral expression and the host cell transcriptome.

first: Cintia

last: Bittar

first: Ana

middle: R

last: Teixeira

first: Gabriela

last: Santos

first: Klara

last: Lenart

first: Marcilio

last: Fumagalli

first: Noemi

last: Linden

first: Isabella

last: Ferreira

first: Marina

last: Caskey

first: R. Brad

last: Jones

first: Mila

last: Jankovic

first: Michel

last: Nussenzweig


title: TopBP1 controls conventional dendritic cell development and Flt3L-driven cDC1 differentiation via PU.1 and IRF8 [ChIP-Seq]

city: Suwon-si

first: Minsuk

last: Cha

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

summary: DNA topoisomerase II-binding protein 1 (TopBP1) plays a vital role in V(D)J recombination during B and T cell development. However, its role in the development of conventional dendritic cells (cDCs) remains unexplored. Mice with DC-specific depletion of TopBP1 (TopBP1cKO) showed accelerated tumor progression due to impaired anti-tumor immunity, characterized by cDC deficiency and pre-DC accumulation. Notably, Flt3 ligand (Flt3L)-mediated tumor immunotherapy was ineffective in TopBP1cKO tumor-bearing mice. Our study demonstrates that TopBP1 is required not only for the steady-state differentiation of total cDCs, including both cDC1 and cDC2, but also for the terminal differentiation of XCR1⁻CD24⁺ emergency progenitors (EPs; CD11c⁺cKit⁺) into XCR1⁺CD24⁺ cDC1s in response to Flt3L. Furthermore, we revealed that TopBP1 directly interacts with PU.1 and IRF8, key transcription factors (TFs) required for cDC development, triggering the expression of their downstream target genes. These findings identify TopBP1 as a crucial factor for cDC development and Flt3L-driven EP differentiation into cDC1s, revealing that the function of key TFs for cDC development is mediated via interaction with TopBP1. Our work underscores the importance of TopBP1 in promoting cDC development and the therapeutic efficacy of Flt3L-mediated tumor immunotherapy.

overall_design: ChIP-seq profiling of CD24⁺ EP(Emergency progenitor; CD11c+CD117+)s from the spleen of TopBP1^fl/fl (littermate) mice on day 9 after Flt3L-Ig injection.

first: Min-Suk

first: Yong-Soo

last: Bae


title: Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1/2 Mutations, dataset 1

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary: Paired serum and plasma samples from 23 patients were analyzed using a custom qPCR panel comprising 182 miRNAs. Since this experiment is part of a broader study on miRnome alterations associated with BRCA mutations or BRCA-related cancers (particularly ovarian and breast cancer), 17 of the analyzed samples came from patients with BRCA1/2 mutations. This analysis was preceded by sequencing-based quantification on a larger set subset of the samples, the results of which are submitted separately to GEO under accession number GSE299150. The generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury, and by the National Science Centre (Poland) OPUS grant “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

overall_design: miRCURY LNA miRNA PCR Custom panel with 182 miRNA was used. miRNAs detected in at least 50% of the samples of either serum or plasma were included in the final analysis. Normalization was based on the mean of Cq values of miRNAs detected in all samples in a set. dCq values were calculated as the difference between the global mean Cq of a given sample and the Cq of the miRNA of interest. Differential expression and correlation analyses were used to assess similarities and differences in miRNA abundance between plasma and serum.

last: Smyczyńska

first: Wojciech

last: Fendler

first: Dipanjan

last: Chowdhury

first: Aleksander

last: Rycerz


title: Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1/2 Mutations, dataset 2

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

summary: Serum samples from 94 healthy women were analyzed using a custom qPCR panel comprising 182 miRNAs. Since this experiment is part of a broader study on miRnome alterations associated with BRCA mutations or BRCA-related cancers (particularly ovarian and breast cancer), 37 of the analyzed samples came from patients with BRCA1 mutations and 19 from BRCA2 mutation carriers. This analysis was preceded by sequencing-based quantification on the same set of the samples, the results of which are submitted separately to GEO under accession number GSE299787. The generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury, and by the National Science Centre (Poland) OPUS grant “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

overall_design: A custom PCR panel comprising 186 miRCURY LNA miRNA PCR Custom assays was used. miRNAs detected in at least 50% of the samples were kept in analysis. Normalization was based on the mean of Cq values of miRNAs detected in all samples in a set. dCq values were calculated as the difference between the global mean Cq of a given sample and the Cq of the miRNA of interest. Correlation analyses were used to assess similarities and differences in miRNA abundance between qPCR and sequencing.


title: Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1 or BRCA2 Mutations - dataset 3 part 1

summary: This dataset consists of miRNA expression in plasma of 78 women with germline BRCA1/2 mutations and expression in serum of 11 of them. Serum samples of remaining 67 women have been already submitted to GEO in GSE226445 dataset and to SRA as Bioproject PRJNA898621, while counts generated in re-mapping for this project are deposited as GSE299846 data set. MicroRNA abundance was quantified with sequencing in both biological materials. Data was analyzed with the aim of assessing the impact of blood processing steps on quantified miRNA abundance. Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

overall_design: The experiment was performed in 78 pairs of human plasma and serum samples. All plasma samples belong to this submission, while in the case of serum 67 samples have been submitted previously, while the remaining 11 belong to this submission. All patients were female carriers of BRCA1/2 mutations, among them 1 had breast cancer at sample collection, 3 had ovarian cancer, 74 were healthy.


title: The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine


title: The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma [ChIP-seq]

summary: Deregulation of proteins involved in chromatin regulation is common in pancreatic ductal adenocarcinoma (PDAC). Lysine demethylase 4C (Kdm4C) is one of the chromatin-modifying proteins frequently overexpressed across multiple solid cancers and is linked to chromatin instability, increased cell proliferation, and enhanced stem cell-like behavior. We observed upregulation of Kdm4C protein in a panel of human PDAC cell lines and patient samples compared to non-neoplastic controls. CRISPR/Cas9-mediated deletion of KDM4C in human and murine PDAC cells reduced proliferation, clonogenicity and increased survival of orthotopically implanted murine PDAC allografts. Transcriptomic and proteomics analyses revealed that loss of Kdm4C in both human and murine PDAC cell lines was associated with reduction of activated phospho-Erk, a pivotal effector downstream of mutant Ras. Using proximity labeling, we identified the histone deacetylase SIRT1 as a novel interacting protein with Kdm4C via the latter’s Tudor reader domain. SIRT1-mediated deacetylation leads to repression of downstream targets, including the dual specificity phosphatase DUSP2, which is known to inactivate Erk via dephosphorylation. In vitro propagation of KDM4C-null PDAC lines eventually led to adaptation and restitution of Erk signaling via compensatory upregulation of other KDM4 family members. To bypass this genetic compensation, we tested a preclinical pan-KDM4 inhibitor TACH107 and confirmed its efficacy in in vitro and in vivo PDAC models including those resistant to the covalent KRASG12D inhibitor MTRX1133.  Our studies identify Kdm4C as an oncogenic molecule that sustains Erk signaling in KRAS-mutant PDAC and can be broadly targeted via small molecule inhibitors.

overall_design: H3K27Ac and H3K36me3 ChIP-seq profiling of wildtype AsPC1 cells, and their early passage KDM4C knockout derivatives.

first: Mennatallah

last: Shaheen

first: Sarah

last: Dhebat

first: Kimal

middle: I

last: Rajapakshe

first: Bidyut

last: Ghosh

first: Benson

last: Selvanesan

first: Shariq

last: Ansari

first: Cara

last: Haymaker

first: Dorsay

last: Sadeghian

first: Huamin

last: Wang

first: Haoqiang

last: Ying


title: The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma [RNA-Seq]

overall_design: RNA-seq profiling of wildtype AsPC1 cells, and their early passage KDM4C knockout, or late passage KDM4C knockdown derivatives.


title: Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1 or BRCA2 Mutations - dataset 3 part 2

summary: This dataset consists of miRNA expression in serum of 69 women. This data is the result of remapping raw sequencing FASTQ files being a part of the GSE226445 dataset and the SRA Bioproject PRJNA898621. MicroRNA abundance was quantified by sequencing. Data was analyzed together with plasma samples of those same patients with the aim of assessing the impact of blood processing steps on quantified miRNA abundance. Plasma data belongs to a separate submission (accession will be added when issued). Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

overall_design: The whole experiment was performed in 78 pairs of human plasma and serum samples. This submission contains data from 69 serum samples with raw FASTQ files already deposited to SRA as Bioproject PRJNA898621. The difference between this dataset and previous one lays in data processing procedures, namely here sequencing data was mapped with version 2.3.0 of nf-core/smrnaseq for compatibility with newer plasma dataset, while GSE226445 contains counts generated by version 1.1.0. Remaining serum and plasma samples belong to separate submission. All 69 sample donors were healthy, female carriers of BRCA1/2 mutations.


title: Gut resident T-bet expressing Tr1 cells driven by dietary signals dominate the small intestinal immune landscape I

city: San Diego

first: Eduardo

last: Ansaldo

address: 15550 Torrey Pines Rd

department: IMM

institute: Scripps Research

summary: Intestinal immunity provides defense against enteric pathogens, mediates symbiotic relationships with the resident microbiota, and provides tolerance to food antigens, safeguarding critical nutrient absorption and barrier functions of this mucosal tissue. Despite the large abundance of tissue resident activated T cells, how T cell immunity contributes to these various roles remains poorly understood. Here we describe a previously uncharacterized dominant T-bet expressing Tr1 T cell population in the small intestine lamina propria present at homeostasis. Importantly, this IL-10 secreting CD4^+^T-bet^+^ T cell population appears in the small intestine at the time of weaning independently of the resident microbiota, presenting similar accumulation, functional capacity, and TCR repertoire in germ free conditions. Instead, small intestinal T-bet^+^ Tr1 T cells respond to dietary signals driving their accumulation, suppressive program, and clonal selection; and depend on cDC1s, IL-27 signaling, and T-bet, but not IL-12. Altogether, this work uncovers a previously unappreciated dominant player in homeostatic small intestinal immunity with the potential to play critical suppressive roles in oral tolerance to dietary antigens, raising important implications for the understanding of food allergy and celiac disease.

overall_design: SILP CD4 T cells (Live, CD45+CD90.2+, TCRb+, CD4+) from 4 SPF and 4 GF T-bet-ZsGreen mice (adult , steady state) were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 32000 cells per lane (total of 8 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq2000 platform (NextSeq 1000/2000 P2 reagents).

first: Eduard

first: Daniel

last: Yong

first: Nathan

last: Carrillo

first: Taryn

last: McFadden

first: Mahnoor

last: Abid

first: Dan

last: Corral

first: Claudia

last: Rivera

first: Taylor

last: Farley

first: Nicolas

last: Bouladoux

first: Inta

last: Gribonika

first: Yasmine

last: Belkaid


title: Inhibition of cancer stem cell self-renewal by a platinum(II) complex suppresses metastasis in gastrointestinal cancer

city: Madrid

first: Luis

last: del Peso

email: luis.peso@uam.es, lpeso@iib.uam.es

state: Madrid

address: Arturo Duperier 4

country: Spain

institute: Universidad Autonoma de Madrid

summary: Cancer stem cells (CSCs) drive therapy resistance, metastasis, and relapses in gastrointestinal cancers, highlighting the need for novel strategies to target this subpopulation. Here, we characterize the platinum(II) complex trans-[PtI₂(isopropylamine)₂] (I5) as a potent inhibitor of CSC-associated pathways and functions in gastric and pancreatic cancer models. Transcriptomic and functional analyses reveal that I5 markedly suppresses Hedgehog, NOTCH, and JAK/STAT signaling, leading to reduced expression of pluripotency markers (NANOG, SOX2, OCT3/4), CSC surface antigens (CD133, CXCR4), and diminished tumorosphere formation. I5 also induces mitochondrial dysfunction, oxidative stress, and metabolic impairment in CSC-enriched populations. In vivo, I5 pre-treatment significantly impairs tumor initiation and metastatic potential in xenograft models. Unlike cisplatin, I5 overcomes platinum resistance by targeting core self-renewal and survival mechanisms in CSCs. These findings position I5 as a promising therapeutic.

overall_design: Human gastric and pancreatic cancer cell lines were challenged in vitro with different concentrations of the platinium(II) compounds I5 or I6 for 24h. The experiment was repeated twice.

first: Isabel

last: Sanchez-Perez

first: Jorge

last: Melones-Herrero

first: Bruno

last: Sainz Jr

first: Sonia

last: Alcalá


title: Gut resident T-bet expressing Tr1 cells driven by dietary signals dominate the small intestinal immune landscape II

first: Eduardo

overall_design: SILP CD4^+^ T cells (Live, CD45+CD90.2+, TCRb+, CD4+) from SPF or GF T-bet-ZsGreen mice that received aCD3 or isotype as described in the corresponding methods section were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 40000 cells per lane (total of 4 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents).