title: Effects of NTHi on lung epithelial regeneration mechanisms in mouse-derived air-liquid interface cultures

city: Homburg

first: Felix

last: Ritzmann

address: Kirrberger Street

institute: Saarland University

summary: Bulk RNA sequencing was performed in mouse-derived EpCAM-positive lung epithelial cells cultured at air-liquid interface to assess NTHi-associated transcriptional changes during lung epithelial regeneration.

overall_design: EpCAM-positive lung epithelial cells isolated from C57BL/6J mice were cultured in transwells under air-liquid interface conditions. Freshly isolated cells, cells at airlift before NTHi exposure, and 4-day ALI cultures treated with NTHi or left untreated were subjected to bulk RNA sequencing.

first: Betül

last: Colakoglu

first: Christoph

last: Beisswenger


title: Na-dependent gene regulation in kidney and heart

status: Public on Jul 21 2026

city: New York

first: Evan

middle: C

last: Palmer-Young

state: NY

address: 525 E 68th St

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: We examined Na-dependent changes in gene expression in the renal papilla and heart ventricle of rats. Animals were conditioned with control or low-Na diets for 1 week. RNA isolated from kidneys or hearts was analyzed by RNAseq. In the renal papilla, notable genes upregulated in response to low dietary Na included alpha, betta, and gamma subunits of ENaC, alpha and beta subunits of the Na/K-ATPase, and the transcription factor Zbtb16.  Increases in mRNA for the ENaC were confirmed using qPCR and were strongly dependent on location within the kidney with papilla > outer medulla > cortex.   Differences in ENaC protein expression exhibited a similar dependence on location.  The effects of dietary Na+ on ENaC expression, as well as that of Zbtb16, in the papillae were not mimicked by treatment with aldosterone, indicating that other factors contribute to the adaptation to Na+ deprivation. In the heart, a smaller number of genes were affected by dietary Na+.  Effects clearly related to Na+ balance included downregulation of transcripts for the natriuretic peptides ANP and BNP. Enrichment analyses indicated that low dietary Na led to upregulation of many Gene Ontology (GO) gene sets related to growth and development in the kidney samples, but downregulation of such gene sets in the heart. Our results illustrate the profound site- and tissue-specific effects of changes in dietary Na+ on renal and cardiac gene expression and regulation of salt balance.

overall_design: Female Sprague-Dawley rats (120-200 g) were maintained on synthetic diets (Harlan Teklad) containing control Na (Na content 0.4%) or low Na (Na content 0.01 – 0.02%) for 7 d.  Some animals on control-Na diet were implanted with osmotic minipumps (Alzet model 2002) infusing aldosterone at a rate of 12 ug/day.  RNA isolated from kidney inner medulla (both low-salt and aldosterone experiments) and heart ventricle (low-salt experiment) of 4 rats per treatment was submitted for sequencing

first: Theresa

last: Rohan

first: Gustavo

last: Frindt

first: Lawrence

middle: G

last: Palmer


title: Localized PD-1 CAR T therapy reprograms neuroinflammation - mouse CAR T data.

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: B cell-depleting therapies are effective in multiple sclerosis (MS), yet many patients continue to accumulate disability, underscoring the need for more precise interventions. To identify new therapeutic targets, we generated a single-cell RNA-seq atlas of cerebrospinal fluid (CSF), brain, and blood from non-inflammatory controls and patients with MS or other neuroinflammatory diseases. We found disease-associated enrichment of class-switched IgG⁺ B cells and plasma cells in the CSF of patients with MS. Unbiased analysis further identified a rare subset of activated, TCR-restricted, PD-1⁺ T follicular helper-like cells with B-cell recruiting features that was enriched in the CSF of patients with MS. To target this population therapeutically, we developed PD-1-directed CAR T cells that selectively depleted pathogenic PD-1⁺ CD4 T cells and, in armored versions, released IL-10 at inflammatory sites. This strategy attenuated CNS inflammation, reprogrammed the local immune milieu, and improved clinical outcomes across murine neuroinflammation models. Together, these findings define a cellular framework for CNS-localized adaptive immunity in MS and nominate a selective strategy to disrupt it.

overall_design: All procedures were performed in accordance with protocols approved by the Instiututional Animal Care and Use Committee (IACUC). For EAE induction, 8-week-old C57BL/6 mice were immunized via 2 subcutaneous injections of emulsion above the hind legs. The emulsion for each mouse consisted of 200 µg of MOG₃₅₋₅₅ peptide (GeneScript Biotec, Singapore), or 200 µg of recombinant human MOG1-120 (rhMOG) produced as previously described, and 350 µg of Mycobacterium tuberculosis H37RA (BD, Cat. No. 231141) in Imject™ Freund's Incomplete Adjuvant (FIA) (Thermo scientific, France) to create a total volume of 200 µL of Complete Freund's Adjuvant (CFA) with MOG per mouse, and prepared by sonication. Immediately following immunization, mice received an intraperitoneal (i.p) injection of 250 µg of Pertussis toxin (EMD Millipore, Cat. No. 516560-50UG). A booster injection of Pertussis toxin was administered on day 2 post-immunization. EAE symptoms typically began to manifest 10-12 days post-immunization. According to the day of the specific experiment, transduced CAR T cells were taken from culture, washed in cold PBS and resuspended in 3x10⁶ cells per 100ul on ice. For each mouse, 4 days after EAE induction, 3x10⁶ cells in 100ul were injected retro-orbitally under isoflurane anesthesia, or 100ul of PBS for the control EAE untreated group. Tissues (spinal cord, brain, spleen, lung, CSF)  were harvested for scRNA-seq on day 14. Endogenous cells - CD45.2+; CAR T cells - CD45.1+ mCherry+.

first: Rotem

last: Shalita

first: Maya

last: Ben Yehuda

first: Chamutal

last: Gur

first: Yasmin

last: Frid

first: Sarah

last: McGrath

first: Roni

last: Suhler

first: Lihi

last: Bolokan

first: Vasyl

last: Eisenberg

first: Reut

last: Sharet Eshed

first: Shir

last: Shlomi-Loubaton

first: Adin

last: Tofield

first: Karin

last: Vardy

first: Mor

last: Zada

first: Anna

last: Kurilovich

first: Eyal

last: David

first: Diego

last: Jaitin

first: Kfir

last: Mazuz

first: Roberto

last: Avellino

last: Tzemach

first: Yuri

last: Kuznetsov

first: Liat

last: Fellus-Alyagor

first: Adva

last: Levy-Barda

last: Mundt

first: Rina

last: Rosenzweig

first: Bettina

last: Schreiner

first: Anneli

last: Peters

first: Christine

last: Stadelmann

first: Pascale

last: Zwicky

first: Adi

last: Wilf Yarkoni

first: Florian

last: Ingelfinger


title: Aspartic acid, cysteine, and glutamic acid prevent biofilm formation and disrupt mature biofilms of Candida albicans and Staphylococcus aureus

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

summary: Biofilms are surface-associated microbial communities that dominate natural and host-associated environments and serve as major reservoirs for infections. Current therapeutics primarily target planktonic cells and are often ineffective against biofilms, highlighting the need for biofilm-specific strategies. Here, we investigated non-toxic L-amino acids as antibiofilm agents against Candida albicans and Staphylococcus aureus. Administration of aspartic acid, cysteine, and glutamic acid inhibited biofilm formation and disrupted mature biofilms in both single- and dual-species settings. Moreover, these amino acids acted synergistically with fluconazole to enhance activity against C. albicans biofilms. These findings indicate that targeted amino acid administration, alone or in combination with existing antimicrobials, could provide a novel strategy for preventing and treating biofilm-associated infections.

overall_design: RNA-Seq profiling of Candida albicans SC5314, grown in sustained inhibition using 1.5% amino acids in RPMI for 24 hours and corresponding control grown in RPMI for 24 hours without amino acid.

first: James

middle: S

last: Goodwine

first: Megha

last: Gulati

first: Craig

middle: L

last: Ennis

first: Melanie

middle: A

last: Ikeh

first: Deepika

last: Gunasekaran

first: Hiram

last: Sanchez

first: Ashley

last: Valle Arevalo

first: Loyse

last: Martorano-Fernandes

first: Maria

middle: I

last: Madrigal

first: David

middle: R

last: Andes

middle: J


title: Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment [scRNA-seq]

city: Los Angeles

first: Sheng

last: Li

address: 1450 Biggy St

institute: University of Southern California

summary: Aging reshapes hematopoietic stem cell (HSC) behavior, yet how pre-existing heterogeneity forecasts clonal performance in aged microenvironments remains unclear. Using cellular barcoding and single cell-RNA-seq to longitudinally sample shared sister-clones across hetero- and homochronic transplants in mice, we quantify (i) intra- and inter-cellular transcriptional heterogeneity in young and old HSC, (ii) differential self-renewal and clonal fitness of HSC in reconstituted hematopoiesis, and (iii) clone-wise associations between pre-existing programs and fitness in aging contexts via predictive machine learning models. Old HSC exhibit greater heterogeneity and rates of generation of heterogeneity, driven by specific gene sets with known roles in HSC fitness. Old HSC exhibit higher self-renewal in old relative to young hosts, likely reflecting adaptation over life to the aged altered niche. Clones with higher fitness in aged mice are enriched for signatures of quiescence, genome integrity/DNA repair, and inflammaging when compared to lower-fitness clones before transplantation. Pre-existing heterogeneity predicts both higher clone fitness and higher self-renewal in the old hosts after transplantation, providing greater phenotypic variability for selection of adaptive clones. Together, these data argue that intrinsic aging encodes variable clonal ‘starting positions’ that interact with niche age to shape hematopoietic output. Our results contextualize recent clonal tracing studies in native hematopoiesis and aging—where lineage output is clonally restricted and age-expanded clones persist—and extend them by prospectively linking baseline HSC state variation to subsequent fitness under aged conditions. These findings nominate actionable, pre-transplant molecular predictors of clonal performance and suggest strategies to modulate aging programs to rebalance hematopoiesis.

overall_design: HSPCs (Lineage− Sca1+ c-Kit+ CD48− CD150+) were isolated from three young (2 months) and three old (20 months) C57BL/6J mice, named 1-3Ya, 4-6Oa. Cells were lentivirally barcoded using CellTag indexing to enable clonal tracking. Barcoded HSPCs were cultured in vitro for 15 days and analyzed, or transplanted into age-matched three recipient mice respectively in each age group, named as Y1-3B, O1-3B. Single-cell RNA-seq was performed to profile transcriptomes together with CellTag  barcode information.

first: Marco

last: De Dominici

last: De Gregori


title: Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment [celltag_cross_exp4]

overall_design: HSPCs (Lineage? Sca1+ c-Kit+ CD48? CD150+) were isolated from three young (2 months) and three old (20?22 months) C57BL/6J mice, named as Y_vitro, O_vitro. Cells were pooled after hashtag oligo antibodies to distinguish biological replicates, and lentivirally barcoded using CellTag indexing to enable clonal tracking. Barcoded HSPCs were cultured in vitro for 15 days and analyzed, and transplanted into age-matched or mismatched three recipient mice (YY: Young donor cells transplanted into young, OO: Old donor cells transplanted into old, YO: Young donor cells transplanted into old, OY: Old donor cells transplanted into young). For in vivo experiments,  cells were pooled from three recipient mice in each group and labeled with hashtag oligo antibodies to distinguish biological replicates. Single-cell RNA-seq was performed to profile transcriptomes together with CellTag and hashtag barcode information.


title: Single-cell analysis of mouse microglia carrying the mouse Nlrp3 wildtype locus, the human NLRP3 wildtype knock-in or the human NLRP3 D305N variant knock-in gene.

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: Mice with the humanized NLRP3 D305N gain-of-function mutation (hNLRP3_D305N) demonstrate peripheral immune cell infiltration into the brain. We used single cell RNA-sequencing to characterize the immune cell population of CD45+ cells in the brains of these mice, compared to hNLRP3_WT and mNlrp3_WT controls. We identified elevated peripheral immune cell populations in hNLRP3_D305N, with neutrophils, T cells, and monocytes as the most prevalent populations. hNLRP3_D305N microglia also showed broad transcriptional shifts towards more reactive profiles and the emergence of distinct subpopulations that were also defined by expression of proinflammatory genes.

overall_design:
CD45+ cells were isolated from whole brains of 18 mice (6 per genotype: mNlrp3 WT, hNLRP3 WT, hNLRP3 D305N) were processed for single-cell RNA-sequencing (scRNA-seq) in two batches of nine animals each. Cells from each animal within a batch were CMO-barcoded and combined for FACS to isolate CD45+ cells. CD45+ cells from each batch were captured on two GEMs, yielding pools 1A and 1B for the first batch of animals, and pools 2A and 2B for the second batch of animals.
**Single-cell RNA-seq experiment that includes cells from 18 mice; The cells were labelled with CMO tags and multiplexed for sequencing. There are 4 pools with samples from 9 mice each. Additional metadata about the composition of the pools the mapping between samples / cells and experimental metadata is included in the form of CSV files. The processed data file in HDF5 format contains results across the entire study (e.g. all cells from all pools).**

first: Lukas

last: Skuja

first: Sophia

middle: M

last: Guldberg

last: Joy

first: Kathryn

last: Monroe

first: Gilbert

last: Di Paolo


title: Transcriptional reprogramming by AP-1-bound cis-regulatory elements drives melanoma development

city: Deggendorf

last: Kappelmann-Fenzl

address: Dieter-Görlitz Platz 1

department: Applied Computer Science

country: Germany

institute: Deggendorf Institute of Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Malignant melanoma is characterized by high metastatic potential and cellular plasticity. Its progression is driven not only by genetic alterations but also by epigenetic repro-gramming and changes in the transcriptome, mediated by transcription factors. The AP-1 family favors an invasive cell state by facilitating processes such as angiogenesis and migration. However, the AP-1-driven regulatory landscape and its implications for melanoma plasticity remain poorly understood. Here, we further elucidate the role of the AP-1 members c-Jun and Fra-1 in enhancer-driven gene regulation during melanoma development. Integrative ChIP-seq and RNA-seq analyses revealed extensive enhancer reprogramming during tumor formation and significant upregulation of genes annotated to enhancers gained in melanoma cells. On average, half of these regions are directly bound by c-Jun/Fra-1, given a high AP-1 motif rate (~80%) and chromatin accessibility. Enhancer-regulated c-Jun/Fra-1 targets are functionally linked to an invasive phenotype and comprise well-known melanoma drivers involved in migration and EMT. Clinically, high c-Jun/Fra-1 and target gene expression correlate with poor survival in BRAF wild-type and NRAS mutant melanoma patients, highlighting c-Jun/Fra-1 as a potential biomarker and therapeutic target. Overall, our data identify c-Jun/Fra-1 as major drivers of melanoma development through enhancer-mediated transcriptional programs.

overall_design: ChIP-seq of H3K27ac and RNAPII in normal human epidermal melanocytes and melanoma cells

first: Anja-Katrin

last: Bosserhoff

first: Zubeir

last: El Ahmad


title: Drosophila Rumpelstiltskin alters Polycomb chromatin association and maintains proper 3D genome organization and barrier activity of the Homie insulator

city: Bethesda

first: Elissa

middle: P

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

summary: Three-dimensional genome organization is maintained in part by chromatin insulators, DNA-protein complexes that create boundaries between active and inactive chromatin and regulate enhancer-promoter interactions. In Drosophila, the Homing insulator at eve (Homie) sequence prevents repressive Polycomb (PcG) chromatin at even-skipped (eve) from spreading into the neighboring essential gene, TER94. Use of an in vivo reporter assay identified the requirement of the hnRNP M homolog, Rumpelstiltskin (Rump), for Homie barrier activity. Interestingly, Rump depletion resulted in no changes to chromatin insulator protein binding at Homie but extensive chromatin association changes to the Polycomb response element (PRE)-associated protein Crooked legs (Crol) at Crol-bound PREs. Furthermore, global chromatin association changes were detected for a subset of Polycomb repressive complex 1 and 2 (PRC1 and PRC2) components. Finally, we observed increased cis-compaction within the eve PcG domain and increased distances between eve and other PcG domains in trans after Rump depletion. These data suggest a regulatory role of Rump for both cis and trans interactions of PcG proteins, likely promoting Homie barrier activity independently of chromatin insulator proteins.

overall_design:
Hi-C libraries were prepared following the optimized Hi-C 2.0 protocol described by Belaghzal et al. 2017 and adapted for Drosophila cells. 4-5x107 control or Rump Kc167 cells were crosslinked with 1% formaldehyde to preserve chromatin interactions, quenched with 0.125 M glycine, and washed twice with cold PBS. Cells were snap-frozen in liquid nitrogen and stored at −80 °C until further processing. Crosslinked cells were lysed in cold lysis buffer for 30 min, and nuclei were isolated for subsequent restriction digestion. Chromatin was permeabilized in 1× NEBuffer 3.1 containing 0.1% SDS for 10 min at 65°C, followed by quenching with 1% Triton X-100. DNA was digested with the 4-base cutter DpnII (NEB) to generate frequent restriction fragments for high-resolution mapping. The resulting 5′ overhangs were filled in using Klenow DNA polymerase (NEB) in the presence of biotin-14-dATP (Invitrogen) to label fragment ends. Proximity blunt-end ligation was performed in situ using T4 DNA ligase (Invitrogen) to favor ligation of spatially proximal DNA ends. After ligation, crosslinks were reversed by incubation at 65°C with Proteinase K (NEB), and DNA was purified by repeated phenol:chloroform extraction followed by ethanol precipitation and concentration using 30 kDa Amicon columns. Biotin was removed from unligated ends using T4 DNA polymerase (NEB) in the presence of dATP and dGTP (Invitrogen) to enrich for valid ligation products. Free nucleotides including biotin-14-dATP were removed by repetitive concentration with Amicon columns. DNA was then sheared to ~200–300 bp fragments using the Bioruptor (Diagenode). Biotinylated ligation junctions were captured using Dynabeads MyOne Streptavidin C1 (Invitrogen). Sequencing libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina), and AMPure XP beads (Beckman Coulter) selection was used to remove adapter and primer dimers.
Libraries from 2 replicates of each condition were subjected to 50 bp paired-end sequencing for genome-wide contact mapping. This optimized protocol increases the fraction of valid intra-chromosomal interaction pairs and enables high-resolution characterization of chromatin architecture.

first: Savanna

middle: F

last: Lyda

first: Catherine

middle: E

last: McManus

first: Juan Manuel

last: Caravaca

first: Dagyeong

last: Yang

first: Yuejun

last: Wang

first: Hernan

last: Lorenzi

first: Fedor

last: Kouzine

last: Levens

first: Leah

last: Rosin


title: Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment

first: Sheng

last: Li

overall_design: Mice of different age groups (14-week to 95-week) were used . Samples were individually captured with Chromium 10x technology and libraies were prepared with Chromium GEM-X Single cell 3’ Chip Kit v4, then sequenced on Illumina Nova-seq 6000.


title: Time-Resolved Multi-Omics Identify Biomarkers of Immediate Reactions to mRNA Vaccination

city: Hamilton

first: Vincent

last: Munster

state: Montana

department: NIAID

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

overall_design: Refer to individual Series


title: Comparable Transcriptomic Profiles of HepaRG and HuH7 Cells Cultured in Chemically Defined and Serum-Based Media Using Primary Human Hepatocytes as Reference

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary: The composition of culture medium is a major, yet frequently undercontrolled, determinant of hepatic cell state in vitro. For decades, fetal bovine serum (FBS) has been routinely incorporated into liver cell culture. Its undefined and lot-to-lot variable composition can, however, confound cell identity and experimental reproducibility. Serum-free, chemically defined media (CDM) represent an alternative approach that can improve standardization, but the consequences of transitioning from FBS-supplemented media (FBS-SM) to CDM remain insufficiently characterized in hepatic models, particularly with respect to metabolic and detoxification programs that govern xenobiotic handling and hepatotoxicity readouts. Here, we systematically assessed how replacing FBS-SM with CDM remodels transcriptomic profiles in two widely used human hepatic cell lines (HepaRG and HuH7 cells) and compared the results to that obtained in primary human hepatocytes (PHH). Global transcriptomic analyses indicated that cell type was the primary driver of variance, whereas medium induced a model-dependent secondary effect. Functional interpretation showed preferential enhancement of xenobiotic metabolism and transport-associated programs in HepaRG cells, while HuH7 cells responses were dominated by lipid/sterol homeostasis and stress-linked processes. Benchmarking against PHH based on hepatic identity and detoxification gene panels further supported improved PHH alignment for HepaRG cells under CDM compared to cultures with FBS-SM, with limited improvement for HuH7 cells. Collectively, these findings address a key knowledge gap by defining how FBS-SM and CDM impact the transcriptomic profiles of HepaRG and HuH7 cells.

overall_design: RNA-seq profiling of HepaRG and HuH7 cells cultured in parallel under a chemically defined medium (CDM) or a serum-supplemented medium (FBS-SM) (n=3 biological replicates per cell line and medium). Pooled primary human hepatocytes (PHH; 10-donor pool) were included as a physiological reference (n=2 technical replicates), and HeLa cells were sequenced as a non-hepatic outgroup (n=3 per medium). Poly(A)-selected RNA libraries were sequenced as paired-end 2×150 bp reads on an Illumina NovaSeq 6000.

first: Ahmed S M

last: Ali

first: Albert

last: Braeuning

first: Jens

last: Kurreck


title: Comparative microarray analysis of skin transcriptomes from patients with atopic dermatitis and healthy controls

city: Seoul

first: Hye Li

last: Kim

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

summary: Microarray-based gene expression profiling was performed on skin samples from patients with atopic dermatitis and healthy controls to analyze disease-associated transcriptional differences.

overall_design: This study aimed to analyze differences in gene expression between atopic dermatitis and healthy control skin. Human skin samples were obtained under a protocol approved by the Institutional Review Board of Yonsei University College of Medicine (IRB No. 4-2013-0624).

first: Chang Ook

last: Park


title: CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [RNA-Seq 3]

city: Orsay

first: Sabine

last: Druillennec

address: Bat 110 centre universitaire

country: France

institute: Institut Curie

summary: Medulloblastoma (MB) is the most common malignant pediatric brain tumor. The MYC‑amplified group 3 (G3) MB represents a high‑risk disease lacking effective therapies. A genetic screen identified the endoplasmic reticulum chaperone HSPA5 (BiP/GRP78) as a critical dependency in G3 MB. Its silencing induces apoptosis and suppresses tumor growth, with strong activation of the unfolded protein response (UPR). The UPR includes three branches, including the PERK–eIF2α axis, which transiently reduces global protein synthesis while enabling selective translation of stress‑responsive factors such as ATF4. We show that G3 MB requires sustained eIF2α activity for survival. Its inhibition triggers cell death through ATF4‑dependent and ‑independent transcriptional programs and translational reprogramming that deplete essential proteins and promote accumulation of detrimental factors. The eIF2α phosphatase PPP1R15B (CReP) maintains basal eIF2α activity and prevents apoptosis. These findings identify the eIF2α axis and its regulators as a crucial node and a targetable vulnerability in G3 MB.

overall_design: D458, D425, ONS and RPE cells transduced with shCtrl, shHSPA5#2 and shHSPA5#5 encoding lentiviral particles were seeded 72h after infection and total RNA was isolated 48h after.  RNA-sequencing data were used to compare gene expression profiles upon HSPA5 knockdown.

first: Liliana

last: Mirabal-Ortega

first: Magalie

last: Larcher

first: Dave Yong Xiang

last: Ng

first: Sara

last: Chabi

first: Marion

last: Le Grand

first: Kevin

last: Muller

first: Sofia

last: Gaid

first: Sophie

last: Leboucher

first: Bertrand

last: Duvillié

first: Franck

last: Bourdeaut

first: François

last: Doz

first: Véronique

last: Marsaud

first: Jacob

last: Torrejon

first: Olivier

last: Ayrault

first: Florence

last: Cavalli

first: Michael

middle: D

last: Taylor

first: Alain

last: Eychène

first: Rachid

last: Benhida

first: Eric

last: Chevet

first: Eddy

last: Pasquier

first: Celio

last: Pouponnot

first: Sandra

last: Majo

first: Lucie

last: Taunay

first: Laure

last: Lagaye

first: Coline

last: Kerjab

first: Moustapha

last: Ka

first: Cristele

last: Gilbert

first: Marine

last: Blanchard

first: Boris

last: Julien

last: Griscelli

first: Annelise

last: Bennaceur-Griscelli

first: Florent

last: Dingli

first: Damarys

last: Loew


title: Dual Immune Checkpoint Blockade Induces Distinct Systemic and Intratumoral Immune Activation in Recurrent Glioblastoma

first: Lu

last: Sun

address: 10833 Le Conte Avenue

institute: University of California, LA

summary: We conducted a surgical window-of-opportunity trial (NCT04606316) in 63 patients with relapsed, resectable glioblastoma. Participants received either dual PD-1+CTLA-4 immune checkpoint blockade (ICB) with nivolumab+ipilimumab (Arm 1), nivolumab alone (Arm 2), or placebo (Arm 3) before resection. Following surgery, Arms 1 and 3 received dual ICB, while Arm 2 received nivolumab until progression or unacceptable toxicity. Median overall survival was 402 days (95% CI, 265–543) in patients who received dual ICB and 276 days (95% CI, 166–698) for patients who received nivolumab alone.  Dual ICB elicited robust intratumoral and systemic immune activation characterized by the highest tumor-infiltrating lymphocyte (TIL) density and greater interferon-related gene expression in the blood. TIL density strongly correlated with survival outcomes, while tumor mutational burden did not. Blood transcriptional profiling revealed that early interferon signature upregulation after neoadjuvant therapy predicted improved survival, whereas sustained elevation during adjuvant treatment correlated with poorer outcomes.  Our results demonstrate the clear pharmacodynamic activity of dual ICB in glioblastoma, with survival outcomes comparing favorably to similar studies.

overall_design: RNA was extracted from resected tumor specimens from patients across all three trial arms. In addition, RNA was isolated from peripheral blood mononuclear cells (PBMCs) collected at multiple time points, including pre‑treatment (Baseline), after neoadjuvant dosing (PostNeo), following craniotomy (PostOp), and approximately three weeks after the first and second adjuvant doses (C2D1 and C3D1). All isolated RNA samples were submitted for RNA sequencing.

first: Sun

last: Lu

first: Markus

last: Lauren

first: Sanchez

last: Julio

first: Lai

last: Thomas

first: Lee

middle: Q

last: Eudocia

first: Li

last: Gang

first: Kim

last: Jiyoon

first: Zhuang

last: Zian

first: Reardon

last: David

first: Acevedo

last: Brenda

first: Everson

last: Richard

first: Mellinghoff

last: Ingo

first: Aquilanti

last: Elisa

first: Castro

last: Nicholas

first: McFaline-Figueroa

last: JR

first: Nayak

last: Lakshmi

first: Beroukhim

last: Rameen

first: Chong

last: Robert

first: Stone

last: Jacqueline

first: Kaley

first: Schaff

first: Wilcox

last: Jessica

first: Westergaard

last: Catarina

first: Reuss

last: Alyssa

first: Lavallee

last: Maria

first: Chukwueke

last: Ugonma

first: Van-den-Abbeele

last: Annick

first: Lim

last: Michael

first: Ellingson

last: Benjamin

first: Cloughesy

last: Timothy

first: Prins

first: Wen

middle: Y

last: Patrick


title: Time-Resolved Multi-Omics Identify Biomarkers of Immediate Reactions to mRNA Vaccination [RNA-Seq]

first: Vincent

last: Munster

summary: Background: Immediate vaccine reactions, including systemic allergic reactions (sARs) and immunization stress-related responses (ISRRs) require distinct management and contribute to vaccine hesitancy; improved molecular understanding may enhance patient care and vaccine implementations. Objective: To compare early immune and metabolic signatures and downstream immunity after vaccination in participants who experienced sARs, ISSRs, or no-reaction to second and booster doses of BNT162b2. Methods: We analyzed samples from a double-blind, placebo-controlled re-vaccination trial of BNT162b2 in individuals with suspected allergic reactions to a first dose of mRNA vaccine. Whole-blood transcriptomics, plasma proteomics, metabolomics, blood counts, and flow cytometry were measured 0.5–24 hours after second vaccine dose, booster, and placebo. Anti-spike antibodies were measured longitudinally; anti-nucleocapsid antibodies indicated intercurrent infection. Results: Interferon and antiviral transcriptional programs were conserved across reaction groups 24 h after vaccination. Early neutrophil activation and degranulation signatures peaked at 6 hours in no-reaction participants but were diminished in ISRR despite similar early neutrophil mobilization. ISRRs also showed reduced basophil activation and recruitment markers and early increases in norepinephrine with sustained elevations of bisphosphoglycerate and 2/3-phosphoglycerate. sARs showed opposite metabolite trajectories and trended towards early upregulation of neutrophil CD63. Anti-spike antibody responses after the second dose and booster were robust across reaction groups, although longer time intervals between the first and second vaccine dose were associated with lower anti-spike antibody levels. Conclusion: Time-resolved immune and metabolic signatures revealed candidate biomarkers that distinguished ISRRs from sARs. Vaccine-induced antiviral transcriptional responses and humoral immunity were preserved in all reaction groups.

overall_design: RNA-seq profiling of sixteen individuals 16 to 69 years of age who reported a systemic allergic reaction to their first dose of COVID-19 mRNA vaccine (either BNT162b2 from Pfizer-BioNTech or mRNA-1273 from Moderna) were consented and enrolled in the COVAAR trial. Recruited participants were then randomly assigned to receive a second dose of BNT162b2 vaccine (0.3-mL of 100 mg/mL of monovalent BNT162b2 mRNA vaccine targeting the original WH-1 strain) or saline placebo on consecutive days in a crossover fashion in the intensive care unit at the NIH Clinical Center. The interval between first and second doses varied between participants depending on when they were recruited, but all exceeded the recommended interval of primary series immunization at that time. The booster dose was administered open-label 5 months after the second dose.

first: Ana

last: Olivera

first: Benjamin

last: Schwarz

first: Brittany

last: Dulek

first: Ian

last: LaCroix

first: Min

last: Li

first: Lindsay

last: Chatman

first: Muhammad

middle: B

last: Khalid

first: Ellen

last: Zektser

first: Karen

last: Laky

first: Stella

last: Hartono

first: Eric

last: Bohrnsen

first: Cole

last: Kimzey

last: Chu

first: Roa

last: Harb

first: Pamela

last: Frischmeyer-Guerrerio


title: Localized PD-1 CAR T therapy reprograms neuroinflammation - human CSF data.

first: Ido

last: Amit

summary: B cell-depleting therapies are effective in multiple sclerosis (MS), yet many patients progress toward disability, highlighting the need for improved interventions. To identify new therapeutic targets, we generated a single-cell RNA-seq atlas of cerebrospinal fluid (CSF), brain, and blood from non-inflammatory controls and patients with MS or other neuroinflammatory diseases. We found disease-associated enrichment of class-switched IgG⁺ B cells and plasma cells in the CSF of patients with MS. Unbiased analysis revealed a rare subset of activated PD-1⁺, TCR-restricted, B-cell recruiting T follicular helper-like cells enriched in MS CSF. To therapeutically target this population, we developed PD-1-directed CAR T cells that selectively depleted pathogenic PD-1⁺ CD4 T cells. In a murine model of neuroinflammation, this approach attenuated CNS inflammation and improved clinical outcomes, particularly when using an IL-10-armored CAR construct. These findings establish a cellular framework for CNS-localized adaptive immunity in MS and outline a strategy for its selective disruption.

overall_design: Human CSF samples were obtained from 14 patients diagnosed with MS, and from 2 CSF inflammatory and 2 peripheral inflammatory donors at Rabin Medical Center hospital, Israel. All study protocols involving human participants were reviewed and approved by the Weizmann Institutional Review Board (IRB). The study was conducted in strict accordance with the ethical guidelines outlined in the Declaration of Helsinki and local regulations. Written informed consent was obtained from all participants prior to sample collection. All samples were de-identified to protect patient privacy and confidentiality. CSF samples were collected via lumbar puncture by trained medical personnel and were processed within 2-4 hours from collection. CSF samples were diluted with sterile PBS and centrifuged at 350 x g for 5 minutes at 4°C to pellet cells. The supernatant was washed, counted, and used immediately for FACS staining. Sorting gate was immune cells CD45+.

first: Rotem

last: Shalita

first: Maya

last: Ben Yehuda

first: Chamutal

last: Gur

first: Yasmin

last: Frid

first: Sarah

last: McGrath

first: Shir

last: Sarah

first: Roni

last: Suhler

first: Lihi

last: Bolokan

first: Vasyl

last: Eisenberg

last: Shlomi-Loubaton

first: Adin

last: Tofield

first: Karin

last: Vardy

first: Mor

last: Zada

first: Anna

last: Kurilovich

first: Eyal

last: David

first: Diego

last: Jaitin

first: Kfir

last: Mazuz

first: Roberto

last: Avellino

first: Reut

last: Tzemach

first: Yuri

last: Kuznetsov

first: Liat

last: Fellus-Alyagor

first: Adva

last: Levy-Barda

last: Mundt

first: Rina

last: Rosenzweig

first: Bettina

last: Schreiner

first: Anneli

last: Peters

first: Christine

last: Stadelmann

first: Pascale

last: Zwicky

first: Adi

last: Wilf Yarkoni

first: Florian

last: Ingelfinger


title: Reprogramming lineage-traced Müller glia for robust proliferation and neurogenesis in adult mammalian retinas

first: Ye

last: Xie

state: New York

address: 1468 Madison Ave

department: Ophthalmology

institute: Icahn School of Medicine at Mount Sinai

summary: In cold-blooded vertebrates such as zebrafish,  Müller glia (MG) act as endogenous retinal stem/progenitor cells upon retinal injury, which evokes a regenerative response that proceeds first with an symmetric division to generate a MG-derived multipotent progenitor cell robust proliferation of MG-derived multipotent progenitors (MGPCs) through that undergoes multiple rounds of cell division, followed by differentiation of MGPCs into new retinal neurons. By contrast, mammalian MG undergo reactive gliosis following retinal injury rather than cell-cycle re-entry for proliferation, hindering its capacity to replenish the lost retinal neuronal cells under pathological conditions. In this study, we treat the adult mouse retina with the combination of FGF2 (Fibroblast growth factor 2) and RA (retinoic acid) after AAV-mediated MG-specific gene transfer of Ascl1 (FAR), and scRNA-seq was employed to see whether the FAR treatment could induced robust MG proliferation and neural regeneration in adult mouse retina.

overall_design: To profile the transcriptomes of reprogrammed MG after the FAR treatment, we performed single-cell RNA sequencing (scRNA-seq) analysis of Sun1-GFP+ MG dissociated from retinas of lineage-traced mice purified by fluorescence-activated cell sorting (FACS). To characterize the progression of the reprogramming process, we chose three time points for the transcriptomic analysis: an early time point (day 13) at the peak of MG proliferation, a middle time point (day 20) at the end of MG proliferation, and a late time point (day 90) to analyze the long-term states of reprogrammed MG. Untreated MG was set as the control for all time points.

first: Xin

last: Ying

first: Bo

last: Chen


title: KAS-CUT&Tag for direct mapping of transcription bubbles

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: We introduce KAS-CUT&Tag, a method that combines N3-kethoxal labeling of exposed guanines with CUT&Tag to directly map Pol II at transcription bubbles. Pol II-induced bubbles are enriched at many highly-expressed genes, but the highest enrichment is at canonical histone genes in all phases of the cell cycle.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration

first: Weifang

last: Wu

first: Jacob

last: Greene

first: Kami

last: Ahmad

first: Steven


title: B cell depletion with anti-CD20 promotes mucosal-originating regulatory IgA-secreting cells in multiple sclerosis

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: To investigate gut-mucosal IgA B cell trafficking during anti-CD20 treatment, we performed paired scRNA-seq and B cell receptor-seq (BCR-seq) on blood samples and gut biopsies from four anatomical sites of the intestine of one anti-CD20-depleted pwMS and one control patient.

overall_design:
scRNA seq profiling of blood and intestine samples of one control and one anti-CD20 depleted MS patient

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Anne-Katrin

last: Pröbstel

first: Tradite

last: Neziraj

first: Elisabeth

last: Pößnecker

first: Paul

last: Saary


title: CNS-penetrant NLRP3 inhibitor TN-783 achieves durable weight loss and reverses hypothalamic inflammation in diet-induced obesity

first: Thomas

last: Sandmann

summary: The NLRP3 inflammasome is a key mediator of innate immunity that integrates inflammatory and metabolic stress signals. Increased chronic activation of this critical pathway has been implicated in obesity, with increased hypothalamic neuroinflammation linked to dysregulation of energy balance. TN-783 is an investigational CNS-penetrant small-molecule NLRP3 inhibitor that potently suppresses inflammasome activation. In diet-induced obese (DIO) mice, TN-783 produced progressive and sustained weight loss. Transcriptomic profiling revealed partial reversal of obesity-associated molecular changes, particularly among genes involved in inflammation and neuronal signaling.

overall_design: Bulk RNA-seq profiling of hypothalamus microdissected from lean mice and diet-induced obese (DIO) mice administered with NLRP3 inhibitor TN-783 or its vehicle for 29 days (6 animals/group x 3 groups)

first: Ernie

last: Yulyaningsih

first: Jing

last: Guo

first: Dylan

last: Braun

first: Connie

last: Ha


title: Drosophila Rumpelstiltskin alters Polycomb chromatin association and maintains proper 3D genome organization and barrier activity of the Homie insulator [RNA-Seq]

first: Elissa

last: Lei

overall_design:
RNA-seq was performed in Drosophila Kc167 cells under control and Rump depletion conditions. Total RNA was extracted using the RNeasy Mini Kit and used to generate strand-specific RNA-seq libraries from 60–100 ng input RNA using the Ovation RNA-seq System.

Biological replicates were included for each condition. Sequencing reads were adapter-trimmed and aligned to the Drosophila dm6 genome. rRNA-derived reads, low-quality reads, and PCR duplicates were removed prior to analysis. Gene expression levels were quantified at the exon level, and differential expression analysis between conditions was performed using DESeq2.

first: Savanna

last: Lyda

first: Catherine

last: McManus

first: Juan Manuel

last: Caravaca

first: Dagyeong

last: Yang

first: Yuejun

last: Wang

first: Hernan

last: Lorenzi

first: Fedor

last: Kouzine

first: David

last: Levens

first: Leah

last: Rosin


title: Drosophila Rumpelstiltskin alters Polycomb chromatin association and maintains proper 3D genome organization and barrier activity of the Homie insulator [ChIP-Seq]

overall_design:
ChIP-seq was performed in Drosophila Kc167 cells under control and Rump depletion conditions. Cells were crosslinked with 1% formaldehyde, quenched with glycine, and chromatin was prepared using established protocols with modified sonication conditions. Immunoprecipitation was carried out using specific antibodies with either sepharose or magnetic beads.
Biological replicates were generated for each condition, along with corresponding input controls. Libraries were prepared using the NEB Ultra II DNA Library Prep Kit and sequenced on Illumina platforms (NovaSeq 6000 or HiSeq 2500) using 50 bp single- or paired-end reads, depending on the sample.
Sequencing reads were adapter-trimmed and aligned to the Drosophila dm6 genome. Low-quality, rRNA-derived, and duplicate reads were removed prior to analysis. Peaks were called using MACS2 on individual replicate IPs with corresponding inputs, and replicate peaks were merged based on overlapping regions.


title: Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma [Part 3 of 4: Illumina NovaSeq 6000; MARS_v2]

first: Ido

last: Amit

summary: Multiple myeloma (MM) is a plasma cell malignancy characterized by substantial genomic and biological heterogeneity, limiting disease classification and development of more targeted therapies. Here, we present a population-level single-cell atlas of MM and detailed clinical annotations from 342 patients representing MM disease and treatment continuum. Our analysis identifies five distinct malignant transcriptional archetypes (MM1–MM5), and a proliferative module variably expressed across archetypes. This proliferation signature emerges as a context-dependent program with independent prognostic value across archetypes. Combined archetype classification with proliferation scoring defines therapeutic resistance, genomic instability, and clinical outcomes. External validation using the CoMMpass cohort confirms the biological robustness and prognostic relevance of this stratification across platforms. Leveraging the resolution of our single-cell atlas, we applied a computational pipeline for therapeutic target discovery based on malignancy, cell-type specificity and tissue restriction. This approach highlights FCRL2 as a promising MM-specific therapeutic target, with selective expression in malignant plasma and B cells at both transcriptomic and protein levels. This integrative analysis provides a clinically actionable blueprint for patient-specific stratification and precision medicine in plasma cell malignancies.

overall_design: this submission includes single-cell RNA sequencing data from bone marrow aspirates collected from 322 multiple myeloma patients plus 20 healthy donors from hip surgery as controls. Samples represent patients with pre-myeloma stages (MGUS, SMM), newly diagnosed multiple myeloma (treatment-naive) and relapsed/refractory multiple myeloma with various prior treatment exposures, compared to normal bone marrow from healthy controls. Disease stage information is available for all samples, while additional clinical data including survival, FISH results, treatment response, and treatment history are available for subsets of samples. The study focuses on plasma cells, with tumor microenvironment cells captured but not analyzed in this dataset.

first: Mor

last: Zada

first: Anna

last: Kurilovich

first: Noam

last: Shapira

first: Shuang-Yin

first: Reut

last: Sharet-Eshed

first: Paulina

last: Chalan

first: Florian

last: Ingelfinger

first: Shlomit

last: Kfir-Erenfeld

first: Nathalie

last: Asherie

first: Chamutal

last: Gur

last: Gurevich-Shapiro

first: Iuliana

last: Vaxman

first: Rotem

last: Shalita

first: Maya

last: Ben Yehuda

first: Pascale

last: Zwicky

first: Michelle

last: von Locquenghien

first: Kfir

last: Mazuz

first: Eyal

last: David

first: Natan

last: Melamed

first: Irit

last: Avivi

first: Assaf

last: Weiner

first: Polina

last: Stepensky

first: Yael

last: Cohen


title: Targeting of Tripartite Neuron-Cancer-Immune Cell Crosstalk Augments Response to Chemotherapy and Immunotherapy

city: Faridabad

first: Avinash

last: Bajaj

state: Haryana

address: Faridabad-Gurgaon Expressway

country: India

institute: Regional Centre for Biotechnology

summary: Neurotransmitter-mediated crosstalk between nerve fibers, cancer cells, and immune cells in the tumor microenvironment (TME) have been shown to promote cancer progression and immunosuppression. While there are extensive reports on sympathetic nerve fibers, effect of parasympathetic neurons on cancer progression and immunosuppression still remains elusive. In colorectal cancer tissues, we observed presence of cholinergic parasympathetic nerve fibers near tumor stroma and elevated acetylcholine levels as compared to adjacent normal. To disrupt this crosstalk, we used Bupivacaine (BUP), an FDA-approved local anesthetic, delivered via a hydrogel (BUP-Gel) for localized release. BUP-Gel inhibited tumor growth across multiple murine models. Further, single cell RNA analysis revealed reshaping of TME, enhancing M1-like macrophages and cytotoxic T-cell activation. Additionally, BUP-Gel therapy amplified the efficacy of systemic chemotherapy, immune checkpoint blockade, and adoptive T-cell therapy. These findings highlight localized cholinergic inhibition as a promising therapeutic strategy.

overall_design: CT26 tumous were harvested from untreated and BUP-Gel treated groups. Single cells were prepared and stained for live/dead and CD45+ followed by FACS based sorting of CD45+ and CD45- cells. scRNA seq was performed after pooling 3 tumour per group and  CD45+ and CD45- were taken in 4:1 ratio.

first: Dolly

last: Jain

first: Nishant

last: Pandey

first: Somesh

middle: K

last: Jha

first: Shreya

last: Sinha

first: Ragini

last: Singh

first: Junaid

last: Alam

first: Bharti

last: Aggarwal

first: Neelam

last: Chauhan

first: Arunima

last: Acharya

first: Anu

last: V

first: Vandana

last: Dhangar

first: Ritika

last: Bhargava

first: Nikhil

last: Chourasiya

first: Ali

last: Khan

first: Arnab

last: Sahoo

first: Debasish

last: Nath

first: Lalita

last: Mehra

first: Kajal

last: Rana

first: Poonam

last: Yadav

first: Jahanvi

last: Ralhan

first: Saroj

last: Rajput

first: Ashish

last: Pal

first: Arindam

last: Maitra

first: Shantiswarup

last: Singha

first: Rajesh

last: Panwar

first: Satish

last: Khurana

first: Ujjaini

last: Dasgupta

first: Sandeep

last: Bhoriwal

first: Jyoti

last: Prabhu

first: Prasenjit

last: Das

first: Veena

last: Patil


title: T cell receptor γδ is a critical, real-time determinant of unique tissue surveillance mechanisms

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

summary: γδ T cells are mediators of immunosurveillance used in the clinic. However, their status remains paradoxical.  While many display overt traits of adaptive immunity, several major γδ cell subsets including those in barrier tissues make rapid, seemingly TCR-independent responses phenocopying innate lymphoid cells (ILC).  While such uncertainty exists, the requirements for γδ T cell-mediated immunosurveillance will remain unclear.  This study resolves the paradox, showing that tissue-intrinsic γδ T cells share an absolute real-time dependence on the TCR for their phenotypes, including their so-called innate responses to tissue stress and carcinogenesis.  While different tissue-intrinsic γδsubsets showed distinct TCR-dependencies, they shared a core set of TCR-regulated molecules that was likewise disrupted by acute TCR ablation in human γδ T cells.  These findings unequivocally distinguish γδcells from ILC and set criteria for natural immunosurveillance that have clear implications for clinical γδ T cell-based immunotherapies.

overall_design:
Genetic deletion of human TCRγδ was achieved in human blood-derived Vδ1 cells by gene targeting using CRISPR at the exon 2 of TRDV1 gene.
TRDV1-deficient (KO) Vδ1 T cells were purified from the Vδ1 TCR expressing cell population by FACS using anti-Vδ1-PE antibody, and the Vδ1 TCR expressing cells were also sorted and used as controls. This was performed in two different samples coming from the same parental line D2, which were gene targeted using different gRNA sequences for TRDV1 exon 2. After sorting, cells were centrifudged and cell pellet resuspended in RLT plus Buffer from QIAGEN.
Transcriptomic analysis of TRDV1 KO cells was performed with bulk RNA-seq data to identify gene expression signatures affected by TCR deletion.

first: Nicolas

last: Veland

first: Miguel

last: Munoz-Ruiz

first: Adrian

last: Hayday


title: Integrated Transcriptomic and Functional Dissection of Reversible Liver-Heart Dysfunction in a Preclinical MASLD-HFpEF Model

city: La Jolla

first: Souradipta

last: Ganguly

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary:
Background
Metabolic dysfunction-associated steatotic liver disease (MASLD) and its advanced form, MASH, are closely linked to cardiac dysfunction, particularly heart failure with preserved ejection fraction (HFpEF). However, the mechanisms underlying MASLD-associated HFpEF and its reversibility remain poorly understood, largely due to the lack of robust preclinical models. Here, we established a translational model of MASLD-associated cardiac dysfunction that recapitulates the key features of human HFpEF. We applied functional and transcriptomic analyses of the left ventricle (LV) to define the pathways associated with cardiac dysfunction and its reversibility.
Methods
Alms1−/− (Foz/Foz) mice and wild-type littermates were fed normal chow (NC) or Western diet (WD) for up to 36 weeks (wk). Reversibility was modeled by switching WD-fed Foz/Foz mice at 12wk back to NC for 12wk. Cardiac assessment included echocardiography, invasive hemodynamics with dobutamine stimulation, histopathology, electron microscopy and isolated cardiomyocyte contractility. LV transcriptomes were profiled by bulk RNA sequencing and analyzed by differential expression and pathway enrichment.
Results
Foz/Foz mice on WD for 24wk developed metabolic syndrome and MASH with advanced liver fibrosis. Cardiac phenotyping showed LV hypertrophy, impaired cardiomyocyte contractility, reduced β-adrenergic reserve, elevated plasma BNP, and increased mortality while the ejection fraction was preserved (>50%), consistent with HFpEF. The progression of cardiac dysfunction was closely associated with liver fibrosis that developed during MASH. Switching WD-fed Foz/Foz mice at 12wk to normal chow diet reversed hepatic fibrosis, restored LV function, and reduced mortality, demonstrating plasticity of the liver-heart axis. LV transcriptomic analysis revealed that cardiac impairment in these mice was associated with mitochondrial dysfunction, altered substrate utilization, extracellular matrix remodeling, and metabolic stress; pathways that are similarly dysregulated in human HFpEF. Cardiac electron microscopy revealed swollen mitochondria with disrupted cristae, which improved following dietary intervention.
Conclusions
Mitochondrial dysfunction and fibroinflammatory remodeling are prominent features of MASLD-associated cardiac dysfunction. Reversal of hepatic and cardiac phenotypes with dietary intervention, together with elucidation of underlying pathways, establish the Foz/Foz model as a useful translational platform for studying liver-heart axis in MASLD.

overall_design: Alms1-deleted Foz/Foz mice, a model of metabolic syndrome (MetS), were used to study the impact of metabolic dysfunction-associated steatotic liver disease (MASLD) progression and regression on cardiac function. Mice were assigned to five groups: (1) Foz/Foz chow diet for 24 weeks; (2) Foz/Foz Western diet (WD) for 12 weeks; (3) Foz/Foz WD for 24 weeks; (4) Foz/Foz WD for 12 weeks followed by chow for 12 weeks (regression); and (5) wild-type controls on chow or WD for 24 weeks. Cardiac function was evaluated by echocardiography, hemodynamic measurements, and functional assays with isolated cardiomyocyte. Cardiac Left ventricular tissue was collected for transcriptomic profiling by bulk RNA sequencing.

first: Betul

last: Gunes

first: Yusu

last: Gu

first: Jorge

last: Suarez

first: Gautam

last: Gupta

first: Kei

last: Ishizuka

first: Rabi

last: Murad

first: Wolfgang

last: Dillmann

first: Tatiana

last: Kisseleva

first: Kirk

last: Peterson

first: Eric

last: Adler

first: David

last: Brenner

first: Debanjan

last: Dhar


title: Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma

first: Ido

last: Amit

overall_design: Refer to individual Series


title: Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma [Part 1 of 4: Illumina NovaSeq 6000; MARS]

first: Mor

last: Zada

first: Anna

last: Kurilovich

first: Noam

last: Shapira

first: Shuang-Yin

last: Wang

first: Reut

last: Sharet-Eshed

first: Paulina

last: Chalan

first: Florian

last: Ingelfinger

first: Shlomit

last: Kfir-Erenfeld

first: Nathalie

last: Asherie

first: Chamutal

last: Gur

last: Gurevich-Shapiro

first: Iuliana

last: Vaxman

first: Rotem

last: Shalita

first: Maya

last: Ben Yehuda

first: Pascale

last: Zwicky

first: Michelle

last: von Locquenghien

first: Kfir

last: Mazuz

first: Eyal

last: David

first: Natan

last: Melamed

first: Irit

last: Avivi

first: Assaf

last: Weiner

first: Polina

last: Stepensky

first: Yael

last: Cohen


title: RNA-seq result of human skin derived from patients with psoriasis and healthy controls.

first: Hye Li

last: Kim

summary: This study aimed to identify disease-specific transcriptomic signatures and compare them with those of psoriasis and healthy controls to distinct molecular markers. Differential expression analysis revealed key genes associated with epidermal barrier function and inflammation, including FLG, SPINK5, LOR, and SERPINB4, highlighting the unique molecular features of psoriasis in Asian populations. This dataset offers a valuable resource for advancing the understanding of psoriasis pathogenesis and exploring potential therapeutic targets.

overall_design: Skin biopsy samples from the lesional areas were obtained from Asian patients with psoriasis. All patients were clinically diagnosed by dermatologists. The study protocol was approved by the Institutional Review Board (N0. 4-2017-0782)

first: Tae-Gyun

first: Chang Ook

last: Park


title: GPR34 loss-of-function rescues TREM2 metabolic dysfunction and promotes responsive microglial states

first: Thomas

last: Sandmann

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Single-cell transcriptome analysis of wildtype, TREM2 knockout, GPR34 knock-out or TREM2/GPR34 double knock-out primary microglia from wildtype and APP knock-in mice (8 months)

summary: Microglia are broadly implicated in modifying disease risk in the central nervous system (CNS). Identifying regulators of microglia state is critical for elucidating their role in disease and identifying novel drug targets. GPR34 is a G-protein coupled receptor expressed in homeostatic microglia where its function is not well understood. Like TREM2, GPR34 detects lipid ligands. In both healthy and amyloid mouse models, Gpr34 KO accelerated microglial state transcriptionally and histologically consistent conversion of homeostatic microglia to a disease-associated microglia (DAM) state. Shifts in microglial state were accompanied by increased expression of multiple metabolic gene sets.

overall_design: 8 month old mice from one of four different genotypes were sacrificed: 1) Gpr34 WT/App WT (N=6), 2) Gpr34 WT/ App knock-in (N=6), 3) Gpr34 KO/ App WT (N=6), and 4) Gpr34 KO/ App-KI (N=6). Samples were processed on two different days (batches 1 and 2), with each batch containing animals from all four genotypes. For each batch, cells from each animal were first labeled separately with both 1) a unique Cell Multiplexing Oligo (CMO) and 2) stained with fluorescently labelled antibodies for FACS analysis. Afterwards, equal numbers of CMO-labelled cells from each animal were pooled. Next, we isolated CD11b+CD45−Ly6G− primary microglia from the pool of CMO-labelled cells using FACS. These primary microglia were loaded onto a Chromium G chip, targeting an estimated capture of 3,000 microglia per animal. To capture a sufficiently large number of cells, each pool was loaded onto 3 gem beads (for batch 1) or 2 gem beads (for batch 2), for a total of 5 channels / gems.

first: Karthik

last: Raju

first: Sophia

last: Guldberg

first: David

last: Tatarakis

first: Shan

middle: V

last: Andrews

first: Connie

last: Ha

first: Joseph

middle: W

last: Lewcock

first: Jim

last: Ray

first: Kathryn

last: Monroe


title: Single-cell transcriptome analysis of wildtype, TREM2 knockout, GPR34 knock-out or TREM2/GPR34 double knock-out primary microglia from wildtype and APP knock-in mice (17 months)

overall_design: 17 month old mice from one of four different genotypes were sacrificed: 1) Gpr34 WT/App WT (N=6), 2) Gpr34 WT/ App knock-in (N=6), 3) Gpr34 KO/ App WT (N=6), and 4) Gpr34 KO/ App-KI (N=6). Samples were processed on two different days (batches 1 and 2), with each batch containing animals from all four genotypes. For each batch, cells from each animal were first labeled separately with both 1) a unique Cell Multiplexing Oligo (CMO) and 2) stained with fluorescently labelled antibodies for FACS analysis. Afterwards, equal numbers of CMO-labelled cells from each animal were pooled. Next, we isolated CD11b+CD45−Ly6G− primary microglia from the pool of CMO-labelled cells using FACS. These primary microglia were loaded onto a Chromium G chip, targeting an estimated capture of 3,000 microglia per animal. To capture a sufficiently large number of cells, each pool was loaded onto 2 gem beads (for each batch), for a total of 4 channels / gems.


title: Time-Resolved Multi-Omics Identify Biomarkers of Immediate Reactions to mRNA Vaccination [SomaScan]

first: Vincent

last: Munster

overall_design: SomaScan proteomics profiling of sixteen individuals 16 to 69 years of age who reported a systemic allergic reaction to their first dose of COVID-19 mRNA vaccine (either BNT162b2 from Pfizer-BioNTech or mRNA-1273 from Moderna) were consented and enrolled in the COVAAR trial. Recruited participants were then randomly assigned to receive a second dose of BNT162b2 vaccine (0.3-mL of 100 mg/mL of monovalent BNT162b2 mRNA vaccine targeting the original WH-1 strain) or saline placebo on consecutive days in a crossover fashion in the intensive care unit at the NIH Clinical Center. The interval between first and second doses varied between participants depending on when they were recruited, but all exceeded the recommended interval of primary series immunization at that time. The booster dose was administered open-label 5 months after the second dose.

first: Ana

last: Olivera

first: Benjamin

last: Schwarz

first: Brittany

last: Dulek

first: Ian

middle: S

last: LaCroix

first: Min

last: Li

first: Lindsay

last: Chatman

first: Muhammad

last: Khalid

first: Ellen

last: Zektser

first: Karen

last: Laky

first: Stella

last: Hartono

first: Eric

last: Bohrnsen

first: Cole

last: Kimzey

last: Chu

first: Roa

last: Harb

first: Pamela

last: Frischmeyer-Guerrerio


title: Single-cell transcriptome analysis of wildtype, TREM2 knockout, GPR34 knock-out or TREM2/GPR34 double knock-out primary microglia from wildtype and APP knock-in mice (4 months)

first: Thomas

last: Sandmann

overall_design: 4 month old mice from one of four different genotypes were sacrificed: 1) Gpr34 WT/App WT (N=6), 2) Gpr34 WT/ App knock-in (N=5), 3) Gpr34 KO/ App WT (N=6), and 4) Gpr34 KO/ App-KI (N=6). Samples were processed in three separate batches (batches 3, 5, and 7), each containing animals from all four genotypes. For each batch, cells from each animal were first labeled separately with both 1) a unique Cell Multiplexing Oligo (CMO) and 2) stained with fluorescently labelled antibodies for FACS analysis. Afterwards, equal numbers of CMO-labelled cells from each animal were pooled. [Due to an operator error, cells from two animals (17931, 17932) were pooled before labeling; as these animals were from the same experimental group, they were treated as a single animal / replicate in the downstream analysis.] Next, we isolated CD11b+CD45−Ly6G− primary microglia from the pool of CMO-labelled cells using FACS. These primary microglia were loaded onto a Chromium G chip, targeting an estimated capture of 3,000 microglia per animal.

first: Karthik

last: Raju

first: Sophia

last: Guldberg

first: David

last: Tatarakis

first: Shan

last: Andrews

first: Connie

last: Ha

first: Joseph

last: Lewcock

first: Jim

last: Ray

last: Monroe


title: CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma.

first: Sabine

last: Druillennec

overall_design: D425Med cells transduced with shCtrl, shHSPA5#2 and shHSPA5#5 encoding lentiviral particles were seeded 72h after infection and total RNA was isolated 48h later. RNA-sequencing data were used to compare gene expression profiles upon HSPA5 knockdown.

first: Liliana

last: Mirabal-Ortega

first: Magalie

last: Larcher

first: Dave Yong Xiang

last: Ng

first: Sara

last: Chabi

first: Marion

last: Le Grand

first: Kevin

last: Muller

first: Sofia

last: Gaid

first: Sophie

last: Leboucher

first: Bertrand

last: Duvillié

first: Franck

last: Bourdeaut

first: François

last: Doz

first: Véronique

last: Marsaud

first: Jacob

last: Torrejon

first: Olivier

last: Ayrault

first: Florence

last: Cavalli

first: Michael

last: Taylor

first: Alain

last: Eychène

first: Rachid

last: Benhida

last: Chevet

first: Eddy

last: Pasquier

first: Celio

last: Pouponnot

first: Sandra

last: Majo

first: Lucie

last: Taunay

first: Laure

last: Lagaye

first: Coline

last: Kerjab

first: Moustapha

last: Ka

first: Cristele

last: Gilbert

first: Marine

last: Blanchard

first: Boris

last: Julien

last: Griscelli

first: Annelise

last: Bennaceur-Griscelli

first: Florent

last: Dingli

first: Damarys

last: Loew


title: CCR8 expression on regulatory T cells reveals trajectories of tissue adaptation and protects against myocardial infarction [bulk RNA-seq]

city: Wuhan

first: Hao

last: Panax

address: 1277# Jie-Fang Avenue

country: China

institute: Huazhong University of Science and Technology

summary: We employed single-cell RNA sequencing (scRNA-seq) in a mouse model of MI to gain a detailed analysis of heart and lymphoid Tregs, focusing on their developmental trajectories. Bulk RNA sequencing was used to further characterize the phenotype of CC motif chemokine receptor 8 positive (CCR8+) Tregs in the heart and lymph nodes. scRNA-seq of murine Tregs from the mediastinal lymph node (mLN) and heart after MI identified three Treg populations, one of which was mainly derived from the heart.

overall_design: mRNA profiles of injured heart CCR8+ and CCR8- Tregs ,and mediastinal lymph node (MLN) CCR8+ and CCR8- Tregs  isolated from 8-week-old Foxp3-GFP mice 7 days post-MI.

first: Nana

last: Li

first: Zhiheng

last: Hao

first: Ni

last: Xia

first: Xiang

last: Cheng


title: CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [D458]

first: Sabine

last: Druillennec

overall_design: D458Med cells transduced with shCtrl, shHSPA5#2 and shHSPA5#5 encoding lentiviral particles were seeded 72h after infection. RNA was isolated 6h after DMSO or ISRIB (0,5µM) treatment.  RNA-sequencing data were used to compare gene expression profiles upon HSPA5 knockdown and ISRIB treatment.

first: Liliana

last: Mirabal-Ortega

first: Magalie

last: Larcher

first: Dave Yong Xiang

last: Ng

first: Sara

last: Chabi

first: Marion

last: Le Grand

first: Kevin

last: Muller

first: Sofia

last: Gaid

first: Sophie

last: Leboucher

first: Bertrand

last: Duvillié

first: Franck

last: Bourdeaut

first: François

last: Doz

first: Véronique

last: Marsaud

first: Jacob

last: Torrejon

first: Olivier

last: Ayrault

first: Florence

last: Cavalli

first: Michael

last: Taylor

first: Alain

last: Eychène

first: Rachid

last: Benhida

first: Eric

last: Chevet

first: Eddy

last: Pasquier

first: Celio

last: Pouponnot

last: Majo


title: CCR8 expression on regulatory T cells reveals trajectories of tissue adaptation and protects against myocardial infarction [scRNA-seq]

first: Hao

last: Panax

overall_design: CD4+ T cells from the mLN of mice 7 days post-MI were collected for scRNA-seq.

first: Nana

last: Li

first: Zhiheng

last: Hao

first: Ni

last: Xia

first: Xiang

last: Cheng


title: Noncoding SNP rs17728461 regulates the malignant progression of lung cancer [ChIP-seq]

city: Tianjin

first: Xiaoling

last: Tian

state: Tianjin

address: Tianjin Medical University 22 Qixiangtai Road, Heping Distric

institute: Tianjin Medical University

summary: To study the effect of rs17728461 on histone modifications, we performed H3K27ac and H3K4me3 ChIP-seq in H1155(G/G) and H1155(C/C) cells.

overall_design: The H3K4me3 and H3K27ac ChIP-seq of H1155 cells carrying different genotypes of rs17728461.

first: Xinyue

last: Lei


title: Timestamp tracing delineates thymic regulatory T cell ontogeny in native conditions [RNA-seq]

city: Memphis

first: Mitchell

last: Weiss

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

summary: Thymic T-cell selection and regulatory T (Treg) cell development are executed via mechanisms that remain unclear. Here, we develop a timestamp tracing method using Rag1CreER knockin mice in combination with Rosa reporters to reveal the processes governing thymic Treg differentiation in native physiological conditions. It enables tracing of thymic T cells at the double negative and double positive stages upon tamoxifen administration. Following labeled cells over time, we define the processes, kinetics, and gene expression changes during thymic T-cell differentiation; specify thymic Treg maturation with CD73, gene expression changes, and Treg-specific DNA demethylation; characterize precursor cells with 4-1BB and/or CD25 expression that are induced by TCR signaling and differentiate to Treg cells in vitro and in vivo; and determine the features of recirculating or retained mature Treg cells. Thus, Rag1CreER–based timestamp tracing delineates thymic Treg ontogeny, proving the concept for exploring T-cell development and heterogeneity with age-resolved precision.

overall_design: Thymocytes were isolated from mice 7 days post tomaxifen injection, sort newly generated conventional T cells (CD4+tdTomato+GFP–CD73–), CD73– Treg cells (CD4+tdTomato+GFP+CD73–), CD73+ Treg cells (CD4+tdTomato+GFP+CD73+), and bulk Treg cells (CD4+tdTomato–GFP+) were then prepared for RNA sequencing, each has 3 replicates.

first: Menlin

last: Jiang

first: Xinying

last: Zong

first: Yichao

first: Yong

first: Yongqiang

last: Feng


title: Disease-Defining Catalytically Inactive Protein Kinase C alpha Mutation is a Driver in Chordoid Glioma by Dominant-Negative Mechanism

city: Paris

first: Franck

last: Bielle

address: 47-83 Bd de l'Hôpital

institute: Paris Brain Institute

summary: Chordoid glioma (ChG) is a rare low-grade brain tumor, characterised by a novel recurrent point mutation PRKCA p.D463H, a substitution in the kinase domain of Protein kinase C alpha (PKCα). This study demonstrates the role of this mutated kinase in the development of ChGs. Here we show the inactivation and dominant negative effect of PKCαD463H via in vitro and In cellulo activity assays. Our results show the mutation affects the tertiary structure, resulting in an open, unstable protein. Phosphoproteomic and Co-Immunoprecipitation mass spectrometry data from HEK cells overexpressing PKC⍺D463H show decreased phosphorylation and interaction with proteins involved in cell adhesion. We confirm genetically through single nuclei RNAseq that ChGs derive from specialised tanycytes. By understanding the cell context of tumorigenesis alongside the functional changes of this mutation on the activity and interactome of PKCα, we elaborated a model of the development of ChGs alongside the identification of a therapeutic approach.

overall_design: nuclear RNA were extracted from one chordoid glioma tumor and analysed using snRNAseq


title: Critical role for the TGF-β1/mTORC1 signalling axis in defining the transcriptional identity of CTHRC1+ pathologic fibroblasts in idiopathic pulmonary fibrosis

first: Manuela

last: Platé

state: Greater London

address: Rayne Institute, 5, University Street

department: UCL Respiratory

institute: University College London

summary: Fibroblasts represent key effector cells responsible for fibrogenesis during wound healing and pathological fibrosis, including idiopathic pulmonary fibrosis (IPF), the most rapidly progressive and fatal fibrotic lung disease. Single-cell RNA sequencing of fibrotic lung tissue has identified a novel population of high collagen-producing fibroblasts not present in non-diseased control lung, characterised by high expression of the marker, collagen triple helix repeat containing 1 (CTHRC1). The cardinal pro-fibrotic mediator TGF-β1 has been widely implicated in promoting fibrogenesis in multiple fibrotic conditions. In addition to the canonical Smad signalling pathway, TGF-β1-induced collagen I production is under critical regulatory control by the mTORC1/4E-BP1 signalling hub. Using pharmacological inhibition (dual ATP-competitive mTOR inhibitors and rapamycin) in combination with gene-editing approaches, we now demonstrate that the role of the mTORC1 axis extends to the regulation of over a third of all TGF-β1 regulated matrisome genes. We further show that the global transcriptome of TGF-β1-stimulated fibroblasts matches that of CTHRC1+ pathological fibroblast population in the IPF lung. In contrast, the TGF-β1 induced transcriptome of fibroblasts in which mTORC1-signalling is disrupted (by RPTOR gene editing using CRISPR-Cas9) does not map to any known fibroblast population. These data define, for the first time, a critical role for both TGF-β1 and the mTORC1 signalling hub in determining the transcriptional identity of CTHRC1+ pathological fibroblasts and provide strong scientific support for targeting mTORC1 as a therapeutic strategy in IPF and potentially other fibrotic conditions associated with dysregulated TGF-β1 profibrotic signalling.

overall_design: CRISPR-Cas9 gene editing of the mTORC1 accessor protein RPTOR or the mTORC2 accessor protein RICTOR was performed in primary human lung fibroblasts. Gene-edited cells were treated with  TGF-β1 or vehicle control for 24h. Cells were harvested, RNA was extracted and used for library preparation and RNA-Sequencing. Each condition was done in triplicate, and a non-targeting guide RNA was used as CRISPR-Cas9 control.

first: Jo-Anne

last: Wilson

first: Delphine

last: Guillotin

first: Rachel

last: Walters

middle: C

last: Chambers


title: Timestamp tracing delineates thymic regulatory T cell ontogeny in native conditions [scRNA-seq]

overall_design: Thymocytes were isolated from mice treated with oil (serve as a control), tamoxifen (0.5 day, 2 days, 5 days and 12 days), or CsA ( 1 day, 2 days and 5 days) together with mock treated group. For timestamp labeled samples, tdTomato+CD4+CD8+ DP and tdTomato+ non-DP cells after Tam treatment  were FACS sorted. For profiling TCR signaling effects,  total DP and non-DP cells from Mock- and CsA-treated mice were FACS sorted. DP cells were partially depleted before laoding to increase the representation of non-DP cells.

first: Menglin


title: SUCLG1-deficiency causes hypersuccinylation and impairs leukemia development [RNA-seq]

city: Hefei

first: Mengqing

last: Gao

state: Anhui

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

summary: Succinyl-CoA synthetase was reported to sustain mitochondrial respiration and enhance leukemia proliferation. However, the biological mechanisms of mitochondrial metabolism and leukemia pathogenesis, beyond energy production, remains underexplored. Here we report that depletion of SUCLG1 causes hypersuccinylation in leukemia cell lines, which impairs cell proliferation and leukemia progression. We hypothesize that increased histone H3 succinylation attenuates bromodomain interaction with chromatin, hence disrupting BRD4-mediated leukemogenic genes transcription. To confirm the hypothesis, we performed RNA-seq analysis in SUCLG1 knockout cell lines, JQ1-treated cells, Ksuc high and low primary AML patients.

overall_design: To investigate the effect of SUCLG1 deletion, we generated SUCLG1 knockout (KO1, KO2) and non-targeting (NT) U937 cell lines using CRISPR-Cas9 lentiviral system. Total RNAs from NT and knockout cells (KO1, KO2) were subjected to RNA-seq analysis. To characterize BRD4-mediated gene transcription, we treat U937 cells with 0.5 μM JQ-1 for 24 hours before being harvested for RNA extractions. To understand the effect of succinylation on transcriptomic profiles in AML patients, RNA from Ksuc high and low groups of primary bone marrow mononuclear cells (n=4 per group) were subjected to RNA-seq analysis.

first: Domenico

last: Iuso

first: Xiaoyu

last: Zhu


title: Gene expression data from white adipose tissue (WAT) treated with Vigna Umbellata extract (VE).

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

country: Japan

institute: UNIVERSITY OF TSUKUBA

summary:
Gene expression profiling reveals DEGs in WAT.
We evaluated the effects of Vigna Umbellata on WAT of ob/ob mice through an untargeted whole-genome transcriptome analysis.

overall_design: The microarray analysis was conducted on control ob/ob mice group and VE treated group with comparison to wild type (WT) group using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer’s instructions. Firstly, about 100 ng of RNA from each sample was obtained to synthesize complementary DNA (cDNA) for complementary RNA (cRNA) synthesis. cRNA was purified and reverse transcribed for single-stranded cDNA (ss-cDNA) synthesis, purification, fragmentation and labelling. ClariomTM S Array (Mouse; ThermoFisher Scientific) were hybridized with samples extracted from WAT. Tissue samples were prepared from control groups, including ob/ob mice (n = 3) and, when applicable, wild-type mice (n = 3), as well as from VE-treated groups receiving 100 mg/kg BW (n = 3). All of the samples were hybridized for 16 hours in a 45 degree celcius incubator, washed and stained on the GeneChip™ Fluidics Station (ThermoFisher Scientific). The scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data was obtained using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific) and raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value <0.05 (one-way between-subjects ANOVA) and fold change >1.1 (in linear space) were considered as differentially expressed genes (DEGs).

first: Elda Nurafnie

last: Ibnu Rasid


title: Knockdown and knockout of the Integrated Stress Response (ISR) and ATF4  in cultures of adult mouse dorsal root ganglia

city: San Francisco

first: Trent

middle: A.

last: Watkins

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

summary: The Activating Transcription Factor-4 (ATF4) contributes to pro-regenerative transcriptional responses following optic axon damage. Here we use an in vitro model of axon regeneration to investigate the contributions of ATF4 to the transcriptional injury response of adult mouse sensory neurons of the dorsal root ganglion (DRG). We find that, in contrast to optic axon injury, the upregulation of the pro-regenerative transcription factor ATF3 is not ATF4-dependent, and without that contribution, ATF4 instead limits adult DRG axon regrowth in collaboration with C/EBPgamma. Knockout or knockdown of ATF4 enhances axon regeneration in this model while regulating a collection of genes strongly overlapping with those regulated by C/EBPgamma. We find that overexpression of ATF4 suppresses axon regeneration in a C/EBPgamma-dependent manner. This effect, however, is not a simple reciprocal of ATF4 knockout, as it is also correlated with suppression of ATF3- and c-Jun-dependent transcription. Together these findings suggest that axon injury induces an ATF4-dependent transcriptional program that limits regeneration in parallel with pro-regenerative responses.

overall_design: RNA-seq profiling of neuron-enriched cultures of adult mouse dorsal root ganglion (DRG) 42 h after cell isolation and immediate transfection with ON-TARGETplus siRNA targeting factors involved in the Integrated Stress Response (ISR): the kinase Perk/Eif2ak3, the transcription factor Atf4, and Atf4's potential binding partner Cebpg. DRGs were isolated from wildtype mice or each of two transgenic lines: (1) Atf4 conditional knockout (Atf4.cKO) mice heterozygous for Cre recombinase knock-in to the Advillin (Avil) locus for sensory neuron-specific knockout; or (2) "ISR.cKO" mice homozygous for the embryonic lethal S51A phosphorylation-defective mutation in Eif2s1 (eIF2alpha); homozygous for the CMV-loxp-Eif2s1-loxp-EGFP conditional rescue transgene; and heterozygous for Cre recombinase knock-in to the Advillin (Avil) locus for sensory neuron-specific knockout of the rescue transgene.

middle: A


title: SUCLG1-deficiency causes hypersuccinylation and impairs leukemia development [ChIP-seq]

summary: Succinyl-CoA synthetase was reported to sustain mitochondrial respiration and enhance leukemia proliferation in acute myeloid leukemia (AML). However, the biological mechanisms of mitochondrial metabolism and leukemia pathogenesis, beyond energy production, remains underexplored. Here we report that depletion of SUCLG1 causes hypersuccinylation in leukemia cell lines, which impairs cell proliferation and leukemia progression. We hypothesize that increased histone H3 succinylation attenuates bromodomain interaction with chromatin, hence disrupting BRD4-mediated leukemogenic genes transcription. To confirm the hypothesis, we performed ChIP-seq analysis on BRD4 in SUCLG1 knockout cell lines.

overall_design: Chromatin immunoprecipitation sequencing for BRD4 was performed on U937 KO1, KO2, and NT cells.


title: Transfer RNAs, not microRNAs, are linked to ischemic stroke and major bleeding in patients with end-stage kidney disease

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Patients with end-stage kidney disease (ESKD) are at very high risk for thromboembolism and bleeding. This study aimed to identify small non-coding RNAs (sncRNAs), specifically microRNAs and transfer-RNA (tRNA)-derived fragments (tRFs), as potential novel biomarkers for predicting thromboembolism and bleeding in this high-risk population.
Methods: In this sncRNA discovery research, we leveraged the VIVALDI cohort, consisting of 625 ESKD patients on hemodialysis, to conduct two nested case-control studies, each comprising 18 participants. The primary outcomes were ischemic stroke in the first study and major bleeding in the second. Plasma samples were processed using the mIND pipeline for RNA-seq analysis to investigate differential expression of microRNAs and tRNA/tRFs between cases and their respective matched controls, with results stringently adjusted for false discovery rate (FDR).
Results: No significant differential expression of microRNAs for either ischemic stroke or major bleeding outcomes was observed in the two nested case-control studies. However, we identified four tRNAs significantly differentially expressed in ischemic stroke cases and seven in major bleeding cases, compared to controls (FDR<0.1). Coverage plots indicated that specific tRNA fragments (tRFs), rather than full-length tRNAs, were detected, however. Alternative mapping approaches revealed challenges and technical limitations that precluded in-depth differential expression analyses on these specific tRFs. Yet, they also underscored the potential of tRNAs and tRFs as markers for thromboembolism and bleeding.
Conclusion: While microRNAs did not show significant differential expression, our study identifies specific tRNAs/tRFs as potential novel biomarkers for ischemic stroke and major bleeding in ESKD patients.

overall_design: small non-coding RNA sequencing of two nested case-control ESKD cohorts.

first: Stephan

last: Nopp

first: Oliver

last: Königsbrügge

first: Sabine

last: Schmaldienst

first: Marcus

last: Säemann

first: Ingrid

last: Pabinger

first: Anne Yaël

last: Nossent

first: Cihan

last: Ay


title: Genome evolution during domestication of an antibiotic-producing lineage of Streptomyces clavuligerus

city: Glasgow

first: Paul

last: Hoskisson

state: Glasgow

address: Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street

department: SIPBS

institute: University of Strathclyde

summary: RNA-seq analysis of industrial lineage to determine transcriptional changes in late vs early lineage memebers.  Compartitive transcriptomics experiment comparing adapted lineage strains (SC3-SC6) to industrial progenitor strain (SC2).

overall_design: In brief (full methods section below).  Triplicate Samples were grown under the same conditions, RNA extracted and sequenced and compared using primarily  DEseq2.  Full methods: S. clavuligerus SC2-SC6 were grown in 250 ml Erlenmeyer flasks in 50 ml Tryptone soy broth (TSB; Oxoid) from ~1x 108 spore stocks, in triplicate, at 26 oC with shaking at 250 rpm.  After 48 hrs, cells were centrifuged at 4000 x g, and resuspended at an OD600nm of 0.4 and 2 ml inoculated into fresh medium.  Samples were grown to late exponential phase (~48 hrs).  Samples (1 ml of culture) were centrifuged at max speed (16,160 x g) in 2 ml screw capped tubes and resuspended in 1 ml of RNA-later (~5 volumes to 100-200 µL of biomass) and stored at -20oC until extraction (a minimum of 30 minutes). Samples were centrifuged, supernatant removed and resuspended in 300 µL TE buffer (Tris-HCl 50 mM, EDTA 20 mM) with 100 mg\mL lysozyme and incubated at 30oC for 30 minutes.  To each sample, 50 µL 10% SDS was added and mixed, then 85 µL of 5M NaCl and mixed.  Trizol was added (1 mL) to each, vortexed for 15 seconds and centrifuged for 10 minutes.  The top, clear, colourless aqueous phase was removed and combined with 300 µL chloroform, vortexed and centrifuged.  The upper aqueous phase was removed and passaged through Qiagen RNeasy kit following the manufacturers instructions.  On column DNase treatment (using Qiagen RNase free DNase) following manufacturers instructions (in brief: following first was with RW1, 10 µL DNase was added to 70 µL RDD buffer and incubated on column at RT for 20 minutes). Samples were resuspended in 90 µL RNase free water and an off column DNase Treatment carried out (following manufacturers instructions: to each sample, add 7.5 (in brief: following first was with RW1, 10 µL DNase was added to 70 µL RDD buffer and incubated on column at RT for 20 minutes) RDD buffer and 2.5 µL DNase, incubate at room temperature for 20 minutes, add 100 µL RLT buffer and 100 µL 90% EtOH and apply to fresh column).  Samples were passed through a second round of RNeasy kit extraction minus DNase steps.  Samples were then submitted to Novogene for sequencing and the following broad steps taken.  Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was then end repaired, poly A-tailed, adapters ligated, size selected, amplified, and purified and sequenced.

first: John

middle: T

last: Munnoch


title: NAT10 as an acetyltransferase to  promote erythropoiesis

city: Beijing

first: Yanran

last: Wang

address: No.5, Dongdan Sanjiao, Dongcheng District, Beijing

department: State Key Laboratory of Medical Molecular Biology

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary: Understanding erythropoiesis involves comprehending the process of erythroid differentiation, yet there are still numerous mysteryin this field.The purpose of this research was to look at NAT10-mediated regulation of gene expression during erythroid differentiation. NAT10, an acetyltransferase, has been shown to be highly expressed in the early stages of erythroid differentiation and to play an important role in stimulating erythroid differentiation.We identified ac4C modification on RAC2 and GDF15 mRNAs by acetylated RNA immunoprecipitation sequencing (acRIP-seq) and ribosome profiling sequencing (Ribo-seq) combined with RNA sequencing,  which are significant downstream targets of NAT10 to improve erythropoiesis . Collectively, our data suggest that NAT10 promotes erythropoiesis by acetylating RAC2 and GDF15 mRNA associated with erythroid progenitors, thereby promoting erythroid differentiation by increasing RNA stability and translation efficiency. This study reveals unexpected patterns in the regulation of erythroid differentiation, advances our understanding of the regulatory network for erythroid differentiation from multiple perspectives, and identifies potential clinical targets for controlling erythroid regeneration.

overall_design:
To investigate the mechanism of NAT10 in erythroid differentiation, we constructed k562 cell lines by using CRISPR-cas9 to knock out exon 5 of NAT10.Analysis of the comparative gene expression from data of RNA-seqin the parental k562 cells and their knockdown derivatives.Ribo-seq to determine translational efficiency alterations from NAT10 knockout and parental k562 cells and acRIP-seq to identify NAT10 mediates mRNA ac4C modification.
Pelase note that the *merged.bam.RPKM.bw file generated from both replicates is linked to the corresponding *_1 sample records.

first: Gaoyuan

last: Li

first: Fang

first: Jia

last: Yu


title: Candida albicans adapts to toxic levels of the quorum sensing molecule farnesol through cell wall remodeling

city: Merced

first: Clarissa

last: Nobile

address: 5200 N Lake road

institute: University of California MERCED

summary: In this study, we discover that Candida albicans tolerates farnesol by actively remodeling its cell wall to generate a thicker, less permeable cell wall. Using RNA seq, we found that C. albicans cells respond to exogenous farnesol by mounting a stress response that involves the upregulation of genes involved in drug efflux, protein folding, redox homeostasis,and cell wall assembly.

overall_design: Examination of Candida albicans cells exposed to farnesol versus control cells. 2 biological replicates containing two technical replicates were sequenced to determine the effect of farnesol on the transcriptome.

first: Melanie

last: Ikeh

first: Deepika

last: Gunasekaran

first: Cen

last: Jiang


title: Native DNA methylation profiling of human prefrontal cortex neuronal nuclei by Oxford Nanopore sequencing

status: Public on Jul 20 2026

first: Eran

last: Mukamel

address: 9500 Gilman Dr

institute: University of California San Diego

summary: Native DNA Oxford Nanopore sequencing was used to profile DNA methylation in Glu and MGE-GABA nuclei from human prefrontal cortex.

overall_design: Fifteen libraries representing Glu or MGE-GABA neuronal populations were analyzed by native DNA Oxford Nanopore sequencing.

first: Heng

last: Xu

first: Jo-Fan

last: Chien

first: Alexey

last: Kozlenkov

first: Ramu

last: Vadukapuram

first: Junhao

last: Liu

first: Jinyoung

last: Jung

first: Yu

last: Wei

first: Andrew

middle: J

last: Dwork

first: Chunyu

first: Stella

last: Dracheva


title: Single-cell RNA sequencing of liver non-parenchymal cells from hepatocyte-specific ADK-overexpressing and control mice

city: College Station

first: Chaodong

last: Wu

state: TX

address: 373 Olsen Blvd

department: Nutrition

institute: Texas A&M University

summary: Adenosine kinase (ADK) regulates adenosine metabolism and cellular methylation reactions. This study investigated how hepatocyte-specific ADK overexpression affects the transcriptomic states of liver non-parenchymal cells. Liver non-parenchymal cells were isolated from 5-month-old male hepatocyte-specific ADK-overexpressing mice (Hep-ADKTg) and control mice (Hep-ADKWT) maintained on a standard chow diet. Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform to characterize liver cell populations and evaluate transcriptional changes in immune and stromal cells. The analysis showed that hepatocyte ADK overexpression promoted proinflammatory transcriptional changes in liver macrophages and monocytes.

overall_design: Five-month-old male Hep-ADKTg and Hep-ADKWT mice were maintained on a standard chow diet. Liver non-parenchymal cells were isolated by collagenase digestion and processed using the 10x Genomics Chromium Controller with v3 chemistry. Libraries were sequenced on an Illumina NextSeq 500 platform. Single-cell reads were processed using Cell Ranger v6.1.2. After mapping, 15,663 cells from the Hep-ADKWT dataset and 17,462 cells from the Hep-ADKTg dataset were retained. Ambient RNA was removed using SoupX v1.5.2, and downstream analyses were performed using Seurat v4.0.2 and Harmony v0.1.0.

first: Wu

last: Chaodong

first: Li

last: Honggui

first: Guo

last: Xinlei


title: Short Title: 53bp1 supports p53-family transcriptional program

city: Milan

first: Mario

last: Faretta

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology (IEO)

summary: Understanding how molecular mechanisms regulate cell function in tissues requires approaches that link phenotypes to mechanisms across different spatial scales. Here, we present Automated Multimodal Multiplexed Microscopy for Image CytOmetry (A.M3.I.CO), a correlative imaging platform that combines multiscale resolution, from millimeters to nanometers, with automated workflows for high-throughput phenotypic profiling and targeted single-molecule analysis in-situ. Applying A.M3.I.CO, we observed that 53BP1 is recruited at transcribed p53-target genes independently of the activating stimuli, with evidence for a putative complex formation involving 53BP1, p53, and the basal transcription machinery, as also demonstrated by in-vivo observations in tumor models. This localization extends to p63- and p73-targeted transcription sites, suggesting a broader role for 53BP1 in participating to p53 family–dependent transcription. These findings extend genome surveillance pathways to transcriptional control for the execution of extremely different cell functions and establish A.M3.I.CO as a platform for spatially resolved functional analysis.

overall_design: ChIPseq of 53bp1, Pol2S2p, Pol2S5p and Input performed on MCF10A cells growing in normal conditions.

first: Simone

last: Pelicci

first: Laura

last: Furia

first: Lorenzo

last: Ciacci

first: Teresa

last: Gravina

first: Pier Giuseppe

first: Gaetano Ivan

last: Dellino


title: Characterizing circular and linear non-coding RNA in human aging brains and their association with dementia

city: Boston

first: Alexander

last: Knyshov

address: 72 E Concord St

department: Medicine

institute: Boston University

summary: Total RNA, depleted for ribosomal RNA, is commonly used for RNA sequencing to capture both polyadenylated and non-polyadenylated transcripts, while the poly(A) tail targeting protocols can either enrich (Poly(A)-selection) or deplete (Poly(A)-depletion) the polyadenylated fraction. To ascertain the best library strategy for capturing long non-coding RNAs (lncRNAs, >200nt) and circular RNAs (circRNAs) in aged brains, we applied three protocols (total ribo-depleted, poly(A)-selected, and poly(A)-depleted) to 128 human hippocampus samples. Our results show that both ribo-depleted and poly(A)-depleted perform well for lncRNA and circRNA profiling, with poly(A)-depleted protocol generally having a slightly higher number of non-coding RNAs detected. Additionally, we compared poly(A)-selected and -depleted data for predicting the poly(A) status of hippocampus transcripts. The proportion of non-polyadenylated transcripts was higher than previously found. This study demonstrates how the choice of library construction impacts the outcomes, helping to make informed methodological choices when studying brain non-coding RNAs. In addition, we for the first time examined whether the poly(A) status of protein-coding mRNAs is associated with AD and AD-related dementias.

overall_design: linear non-coding and circular RNA profiling in human hippocampus using RNA-Seq of three library types: total ribo-depleted RNA, polyA-enriched RNA, and polyA-depleted RNA

first: Junming

last: Hu

first: Mintao

last: Lin

first: Benyu

last: Zhou

first: Sasha

last: Bacot

first: Jenny

last: Empawi

first: Sambhavi

last: Puri

first: Thor

last: Stein

first: Lindsay

last: Farrer

first: Benjamin

last: Wolozin

first: Xiaoling

last: Zhang


title: Spatial transcript analysis of gene expression in paired gastric cancer tissue sections of 10 patients

city: Chapel hill

first: Brent

last: Hanks

state: North Carolina

address: 450 West Dr

institute: UNC at Chapel Hill

summary: We investigated changes in gene expression and the corresponding spatial distribution of different types of myeloid cells in baseline and treatment tissues from patients with gastric cancer. Our findings indicated that higher levels of NLRP3 are negatively correlated with genes related to the MHC class I antigen. In patients who are resistant to treatment, we observed increased NLRP3 activity alongside lower levels of MHC-1

overall_design: Baseine FFPE tissue specimens were collected from 10 patients with unresectable stage III or stage IV GE adenocarcinoma at Duke Cancer Institute prior to initiating pembrolizumab on the IRB-approved KeyLARGO clinical trial (NCT03342937)

first: Balamayooran

last: Theivanthiran

first: Nagendra

last: Yarla

first: Kyra

last: Majors