title: Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq]

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Multiple myeloma (MM) is a hematological malignancy characterized by an expansion of malignant plasma cells in the bone marrow. For newly diagnosed MM (NDMM), standard three-drug treatment regimens—such as the combination of bortezomib, lenalidomide, and dexamethasone (VRd)—and the more recent inclusion of a fourth drug, anti-CD38 antibody immunotherapy, have significantly improved patient outcomes by targeting multiple mechanisms of tumorigenesis. This treatment approach typically involves several cycles of VRd induction therapy, followed by high dose melphalan (HDM) and autologous stem cell transplant (ASCT), and maintenance therapy. Treatment responses vary widely, with some patients requiring longer and more intense therapy and others exhibiting more rapid responses and longer relapse-free remission.This cycle of remission, maintenance, and eventual relapse persists despite advancements in treatment modalities, including immunotherapy, leaving MM incurable. This study characterizes the tumor state and immune microenvironment in MM patients across variable graded patient responses. Using a multimodal, longitudinal approach, we investigate immune and microenvironmental cellular changes during treatment in NDMM patients and in a second cohort of RRMM patients. For the NDMM cohort, longitudinal blood and bone marrow aspirate samples were collected at diagnosis, throughout induction therapy, following autologous stem cell transplant (ASCT), and at post-transplant intervals of 60 days, 90 days, and 1 and 2 years. Multi-omic profiling of these samples magnifies the individual heterogeneity between tumor and therapeutic response. The longitudinal aspect of the study allowed us to focus on individual-level longitudinal responses instead of cross-patient effects, enabling detailed insights into tumor and microenvironment dynamics. Using Olink proteomic analysis of plasma and bone marrow interstitial fluid (BMIF), and single-cell analyses (3’ CITE-seq, scRNA-seq, flow cytometry) of peripheral blood mononuclear cells (PBMC) and bone marrow mononuclear cells (BMMC) we longitudinally characterized tumor, the immune microenvironment, and therapeutic responses. This revealed distinct immune states and pathways associated with therapeutic response, and tumor survival, highlighting potential targets and therapeutic strategies to improve patient outcomes.

overall_design:
A cohort of patients aged 30 and older with newly diagnosed MM requiring systemic therapy was enrolled in Seattle, WA and had blood and bone marrow collected prior to receiving induction therapy, after two cycles of induction therapy (blood only), post-induction therapy, and 60 days post-transplant (blood only) and 90 days post-transplant (bone marrow biopsy is obtained between 60-100 days post-transplant at the clinical discretion of the treating physician). Additional blood and bone marrow samples were obtained at one- and two-years post transplant as well based on sample availability. This cohort was also followed for the flu vaccine perturbation and blood samples were collected at 0, 7, and 90 days post-vaccination during two consecutive flu years. b) A second cohort of patients over the age of 30 with suspected refractory MM receiving anti-CD38 MAb therapy were enrolled in Seattle, WA. Patients had bone marrow samples collected prior to receiving CD38 MAb therapy, after the 8th dose, and at progression. Patients will have blood collected after receiving 2, 4, 6, and 8 weeks of therapy, and after receiving 4, 6, 9, 12, 18, and 24 months of therapy. Patients may also have scheduled blood sampling before and after receiving influenza vaccination at 0, 7, and 90 days respectively. The 8-week bone marrow sample was collected after the 8th dose, but before biweekly dosing begins.

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Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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first: Aishwarya

last: Chander

first: Patrick

middle: I

last: McGrath

first: Love

last: Tätting

first: Yudong

middle: D

last: He

first: Emma

last: Kuan

first: Marla

last: Glass

first: Samir

last: Rachid Zaim

first: Palak

last: Genge

first: Medbh

last: Dillon

first: Cole

last: Phalen

first: Lauren

middle: Y

last: Okada

first: Zachary

last: Thomson

first: Christian

last: LaFrance

first: Tao

last: Peng

last: Wittig

first: Alexander

last: Heubeck

first: Julian

last: Reading

first: Charles

last: Roll

first: Veronica

last: Hernandez

first: Vaishnavi

last: Parthasarathy

first: Tyanna

last: Stuckey

first: Blessing

last: Musgrove

first: Elliott

last: Swanson

first: Cara

last: Lord

first: Morgan

last: Weiss

first: Regina

last: Mettey

first: Kevin

first: John

middle: B

last: Johanneson

first: Erin

last: Kawelo

first: Jessica

last: Garber

first: Upaasana

last: Krishnan

first: Xiaoling

last: Song

first: Philip

last: Greenberg

first: Lynne

last: Becker

first: Paul

last: Meijer

first: Ernest


title: Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [CITE-Seq]

status: Public on Jul 15 2026

first: Allen Institute

last: For Immunology

country: USA

type: Expression profiling by high throughput sequencing

first: Aishwarya

last: Chander

first: Patrick

last: McGrath

first: Love

last: Tätting

first: Yudong

last: He

first: Emma

middle: L

last: Kuan

first: Marla

middle: C

last: Glass

first: Samir

last: Rachid Zaim

first: Palak

last: Genge

first: Medbh

middle: A

last: Dillon

first: Cole

middle: G

last: Phalen

first: Lauren

last: Okada

first: Zachary

middle: J

last: Thomson

first: Christian

middle: M

last: LaFrance

first: Tao

last: Peng

first: Peter

last: Wittig

first: Alexander

middle: T

last: Heubeck

first: Julian

last: Reading

first: Charles

middle: R

last: Roll

first: Veronica

first: Vaishnavi

last: Lee

middle: K


title: Differences in miRNAs profile in pregnant women with preeclampsia compared with healthy pregnant women

city: Bangkok

first: Natthaya

last: Chuaypen

state: Select a State or Province

address: 1873 Rama 4 road, Pathumwan

department: Biochemistry

country: Thailand

institute: Chulalongkorn University, Faculty of Medicine

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 800 human miRNAs in serum samples of 12 pregnant women (4 samples from severe preeclampsia pregnancies, 4 samples from mild preeclampsia pregnancies and 4 samples from healthy pregnancies)

overall_design: In this study, we compared global miRNA expression profiling in 12 serum specimens obtained from pregnant women 3 group: severe preeclampsia pregnancies, mild preeclampsia pregnancies and healthy pregnancies, was used to expression profile of 800 human miRNAs, this may be a potential biomarker for the early diagnosis of preeclampsia.

first: Vorapong

last: Phupong


title: Exploring differential mRNA expression of colons in a mouse model of colitis

city: Zhangjiagang

first: Li

last: Zhou

address: No. 68 West Jiyang Road

country: China

institute: The Affiliated Zhangjiagang Hospital of Soochow University

summary: Ulcerative colitis (UC) is characterized with dysregulated chronic inflammation in the intestinal tract, accompanied with diarrhea and intestinal bleeding. To identify a pivotal factor in UC pathogenesis, we established experimental colitis models induced in mice with 3% DSS and performed gene expression profiling analysis.

overall_design: RNA_seq profiling of colons in control mice (fed with water) and 3% DSS treated mice (fed with 3% DSS in water).


title: Super-enhancer–mediated SMAD3–NR2F2–ID3 transcriptional complex orchestrates Osimertinib resistance in non-small cell lung cancer

city: Guangzhou

first: aochu

last: liu

state: Guangdong

address: No. 1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

summary: Osimertinib resistance remains a major challenge in the treatment of non–small cell lung cancer (NSCLC). Here, we identify an unconventional super-enhancer–driven transcriptional module, composed of SMAD3, NR2F2, and ID3, in which ID3 functions as a transcriptional co-factor to sustain resistance. Mechanistically, ID3 directly interacts with SMAD3 and NR2F2, inducing conformational rearrangements that enhance their DNA-binding affinity to enhancer regions, thereby increasing transcriptional activity. This ID3-SMAD3/NR2F2 complex selectively activates EPAS1, which in turn promotes neuroendocrine differentiation and suppresses ferroptosis, thereby maintaining the resistant phenotype. Disruption of this complex abrogates EPAS1 expression and restores Osimertinib sensitivity in preclinical models. Our findings uncover a previously unrecognized role of ID3 as a transcriptional co-factor and highlight the super-enhancer–driven SMAD3–NR2F2–ID3–EPAS1 axis as a promising therapeutic target to overcome Osimertinib resistance in NSCLC.

overall_design: RNA-seqprofiling of HCC827 cell line, the Osimertinib-resistant HCC827AR cell line and its knockdown derivatives (shID3, shNR2F2, shSMAD3).

first: Aochu

last: Liu

first: Zhenguo

first: Lizhen

last: Jiang

first: Andong

last: Huang

first: Bingyuan

first: Xinqing

last: Lin

first: Shiwen

last: Hu

first: Junjun

first: Liyuan

last: Yin

first: Yueyuan

last: Zheng

first: Xianping

last: Shi


title: Super-enhancer–mediated SMAD3–NR2F2–ID3 transcriptional complex orchestrates Osimertinib resistance in non-small cell lung cancer [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&Tag of the histone modification H3K27ac,H3K4me1, H3K4me3 and NSCLC TFs (SMAD3, NR2F2, ID3) in HCC827AR cells.


title: Super-enhancer–mediated SMAD3–NR2F2–ID3 transcriptional complex orchestrates Osimertinib resistance in non-small cell lung cancer [ChIP-seq]

overall_design: ChIP-seq of the histone modification H3K27ac in HCC827, PC9 with or without Osimertinib resistance.


title: Understanding rice responses to the combination of Bacterial Panicle Blight and High Nighttime temperatures

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary: The disease Bacterial Panicle Blight (BPB) caused by the bacterium Burkholderia glumae is one major constraint in rice production worldwide that has become more prevalent in years experiencing unusually high night temperatures (HNT). These observations suggest that BPB will be more devastating in the future with the increase in global temperatures; however, the relationship between BPB and HNT has not been investigated. This work sought to understand the interplay between BPB and HNT, by initially evaluating the phenotypic responses of 20 rice accessions from diverse geographic origins to B. glumae inoculation at two nighttime temperatures: normal nighttime temperature (NNT) (22oC) or high nighttime temperature (HNT) (28oC). The results revealed temperature-dependent and temperature-independent responses ranging from enhanced susceptibility to moderate resistance. To dissect the genetic basis of these differential responses, we used RNA-sequencing for comparative transcriptional profiling on two selected temperature-independent accessions with contrasting resistance (R) and susceptible (S) responses. Comparisons among accessions (R and S), treatments: Mock (M) and pathogen (P) and temperatures: NNT and HNT resulted in 6,346 differentially expressed genes (DEGs). Weighted gene co-expression network analysis of DEGs uncovered three modules showing contrasting expression patterns between the resistant and the susceptible accessions and MAPMAN analysis further identified 86 genes related to biotic stress. Those 86 genes were mapped to multiple functional categories and were evenly divided into upregulated in the resistant accession or upregulated in the susceptible accession after single stress (HNT or P) and combined stresses (HNT and P). We found enrichment in several functional categories including proteolysis, defense signaling, secondary metabolism and hormone regulation highlighting a complex transcriptional reprogramming involving multiple pathways. The results highlight the complex transcriptional reprogramming underlying stress responses and revealed that the genes responding to either HNT or P or the combination HNT/P are the same responses operating metabolism, proteolysis and secondary metabolites.  The results from this research will enable deeper understanding of rice differential responses to BPB when combined with high night temperatures while providing key candidate genes to develop rice varieties resilient to the combination biotic and abiotic stresses such as BPB and HNT.

overall_design: Two temperature-independent accessions, one BPB resistant (R) (GSOR 310131) and one BPB susceptible (S) (GSOR 311383) were selected for transcriptomic analysis. The selected accessions were grown until heading stage in the greenhouse and emerging panicles were inoculated with B. glumae (Pathogen, P) or treated with water (Mock, M) and maintained at NNT and HNT conditions for 3 days. Three replicates per treatment/temperature combination for each accession were harvested in liquid nitrogen for RNA-Sequencing, for a total of 24 samples.

first: Sapana

last: Ghimire

first: Shilu

last: Dahal

first: Chia-Sin

last: Liew

first: Laura

last: Ortega

first: Kumar

last: Shrestha

first: Clemencia

last: Rojas


title: Long FAM13A isoforms regulate human lung epithelial development in vitro

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: We performed single cell transcriptomic profiling of induced human pluripotent stem cells (iPSCs)-derived anterior foregut progenitors (D6) and lung progenitors (D15). FAM13A-long isoforms were knocked out of iPSCs prior to differentiation. Prior to capture, cells were labelled with hashing antibodies (HTO). Cells were captured for 10x Genomics Single cell capture (V3 protocol), and GEX and HTO libraries were sequenced. HTODemux function was used to demultiplex the samples. FAM13A-long KO changed clustering of D15 NKX2-1+ lung progenitors

overall_design: Single-cell transcriptomic analysis of iPSC-derived anterior foregut progenitors and lung progenitors comparing wild-type cells with FAM13A-long KO

first: Rhiannon

last: Werder

first: Carlos

last: Villacorta-Martin

first: Andrew

last: Wilson


title: ACLY-driven metabolic reprogramming promotes histone acetylation and inflammation-associated fibrosis in chronic kidney disease

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

institute: Dalian medical university

summary: Conducted chromatin accessibility by ATAC-seq in tubule-specific Acly knockout and WT mice. The dataset includes raw sequencing files.

overall_design:
To assess the role of ACLY in regulating chromatin accessibility during kidney injury, we performed ATAC-seq on kidney tissues from wild-type (n=5) and tubule-specific Acly knockout (n=3) mice. Two wild-type datasets (GSM4752171 and GSM4752172) were retrieved from the GEO database, whereas the additional three wild-type replicates and all knockout samples were generated in our laboratory.

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

last: Mukhi

first: Katalin

last: Susztak


title: RNA-seq detection of primary neural stem cells with knockdown of RPLP2 and exogenous supplementation

city: 西安市

first: Wu

last: Wei

state: 雁塔区

address: 小寨西路西安交通大学第一附属医院

institute: The First Affiliated Hospital of Xi'an Jiaotong University

summary: This study aims to investigate genes regulated by RPLP2

overall_design: "Primary neural stem cells were isolated and cultured from embryonic mouse brain tissue, followed by RNA-seq analysis of cells cultured with AAV vectors or rRPLP2 protein

first: Peiyu

last: Luo

first: Wei

last: Wu

first: Huan

last: Peng

last: Wang


title: Regulatory logic of neuronal differentiation in the Drosophila visual system

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

summary: Combinations of terminal selector transcription factors (tsTFs) are thought to establish and maintain the unique identities of the numerous cell types found in nervous systems. However, it remains largely unclear how tsTF combinations are specified during development, and how they then coordinate the type-specific differentiation programs of each neuron. To investigate these regulatory mechanisms, we performed simultaneous single-cell RNA and ATAC sequencing on the Drosophila optic lobes at four stages of their development and identified over 250 distinct cell types. We characterized the common cis-regulatory features of neuronal enhancers and performed comprehensive inference of gene regulatory networks across cell types and stages. Our results reveal cell-type and stage-specific enhancers of many neuronal genes and the cooperative actions of tsTFs, pan-neuronal and ecdysone-responsive TFs on these enhancers. We show that the same effector genes are often regulated by different tsTF combinations in different neurons. During neurogenesis, tsTF codes are established within a brief critical period in newborn neurons, often through lineage-specific enhancers that are not accessible in their progenitors. Accordingly, when neuroblast temporal patterning TFs are re-utilized as tsTFs in neurons, they are regulated independently through separate enhancers before and after the terminal cell division. Therefore, neuronal identity specification and differentiation is a multi-step regulatory program, wherein the same TFs enact distinct regulatory codes at different steps and across cell types.

overall_design: We performed simultaneous RNA and ATAC sequencing on developing Drosophila optic lobe cells using a genetic multiplexing strategy with 12 DGRP lines crossed to Canton S. For each of four developmental stages (P0, P24, P48, Adult), a single female from each cross was dissected and processed together for nuclei isolation and 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kits library prep.


title: Tumor cell intrinsic dsRNA innate immune response triggered by PARP inhibitor is compromised in BRCA1 deficient breast cancer by repressing IRF3

city: Macau

first: Cuiting

last: Zhang

address: Taipa

institute: University of Macau

summary: Poly (ADP-ribose) polymerase 1 (PARP1) inhibition represents promising targeted therapy for BRCA deficient cancer patients based on synthetic lethality theory. Recent evidence shows that efficacy of DNA damage drugs depends on two aspects, DNA repair signaling and immune response. Applying a functional proteomics approach, we find that the function of spliceosome is perturbed by PARP inhibitors via enhancing interaction between PARP1 and SF3B1, a key factor of spliceosome. We demonstrate that differential alternative spliced mRNA and accumulation of double strand RNA (dsRNA) are induced by perturbation of spliceosome upon PARP inhibitors treatment, resulting in triggering dsRNA antiviral mimicry innate immune response. Moreover, we identify a novel function of BRCA1, through which BRCA1 regulates innate immune response leading to compromising of the innate immune signaling by downregulation of IRF3 in BRCA1 deficient breast cancer cells, which reduces the sensitivity to PARP inhibitors and causes intrinsic resistance. Polyinosinic-polycytidylic acid (poly(I:C)) is a dsRNA synthetic analog sensitizing PARP inhibitors through further triggering dsRNA signaling. Finally, we show that the combination of PARP inhibitors and poly(I:C) enhances antitumor efficiency in vivo. Overall, our study reveals BRCA1 deficiency impedes tumor cell intrinsic innate immune response, inducing intrinsic resistance to PARP inhibitors that can be overcome when poly(I:C) is combined.

overall_design: RNA-seq of HCC1937-EV (a BRCA1 mutated cell line HCC1937 carrying an empty vector) and HCC1937-OE-BRCA1 (wild type BRCA1 overexpressed HCC1937) cells upon olaparib treatment for 12h or 24h.

first: Chu-Xia

last: Deng

first: Jing-Bo

last: Zhou


title: Arginase-1 dependent Insulin-like Growth Factor-1 from myofibroblasts and endothelial cells facilitates kidney tubular proliferation after ischemic injury

city: New Haven

first: Bhavya

last: Bharathan

state: CT

address: 300 Cedar Street

department: Nephrology

institute: Yale University School of Medicine

summary: Following acute kidney injury, successful regeneration of tubular epithelium is essential to restore normal kidney function. We have previously reported that alternatively activated (Arg1+) macrophages in the outer medulla promote tubular proliferation following ischemic injury, however the specific growth factor(s) mediating this effect remained unidentified.

overall_design: Single-cell RNA (scRNA-seq) sequencing was performed in the Pdgfrβ+ cells from mouse injured kidney outer medulla. To identify the growth factor that is present downstream of Arg-1, we performed contralateral nephrectomy/IRI (IRI/CL-NX) in 8-week old male mice and harvested the injured kidney on Day 2  post-IRI and dissected outer medulla, which was enzymatically digested using Liberase-DNase mix at 37°C to obtain single-cell suspensions. Cells were filtered through a 70 µm mesh, washed with 1X PBS, followed by Fc receptor blocking and incubated with fluorophore-conjugated antibodies targeting CD140b (PDGFRB) Antibody. The viable cells which were positive for Pdgfrβ were submitted for sequencing.

first: Bismark

last: Frimpong

first: Lloyd

last: Cantley

first: Leyuan

last: Xu


title: Obstetric complications in pregnant people with Fontan Circulation: identifying candidate pathologic pathways in the placenta

city: Ann Arbor

first: Ashley

last: Hesson

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

summary: Pregnant people with Fontan circulation have high rates of fetal growth restriction (FGR) and preterm birth. The mechanisms underlying these complications are poorly understood. We performed targeted sampling of FGR and non-FGR placentas from pregnancies in individuals with Fontan circulation to characterize the differential expression across pathology-dense regions in these two conditions.

overall_design: Six placentals from pregnancies complicated by maternal Fontan circulation were selected based on 1) having been delivered pretermwith a liverbirth (reflecting the outcomes of this population) and 2) representing N=3 with FGR based on fetal ultrasound criteria versus N=3 that were well-grown on ultrasound (non-FGR). Areas of high density pathology were identified for all six samples by a sub-specialized placental pathologist for spatial transcriptomic analysis.

first: Alexa

last: Pinsky

first: Angela

last: Quain

first: Caroline

last: Simon

first: Levi

last: Anderson

first: Michael

last: Joynt

first: Elizabeth

last: Langen


title: Nanostring analysis of Extracellular vesicles and other particles in lung cancer

city: Milan

first: Orazio

last: Fortunato

address: Via Venezian 1

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Lung cancer is still the deadliest cancer worldwide, mostly as a consequence of metastatic dissemination. In this context, extracellular vesicles (EVs) have emerged as key players acting as cell to cell communicators through the delivery of cargo’s molecules (as miRNAs and proteins) to recipient cells. However, little is known about the role of circulating plasma EVs from lung cancer patients in pMN formation. For this reason, we aim to  identify new prognostic biomarkers for early relapse in lung cancer by Nanostring analysis

overall_design: Plasma EVPs were obtained from patients with resectable early-stage (I-II) lung cancer who died within two years of diagnosis (ESD; n=20), and patients alive at five years post-diagnosis (ESA; n=20)

first: Francesca

last: Pontis

first: Mattia

last: Boeri

first: Silvia

last: Brich


title: RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair

city: Zurich

first: Charles

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

summary: DNA double-stranded breaks (DSBs) are an especially toxic form of damage that can be reversed without loss of genetic information by homology-directed repair (HDR), which copies from an intact template molecule. Finding a correct template within millions to billions of other DNA bases is termed homology search and is mediated by the protein RAD51. A major challenge in understanding homology search is the lack of tools to monitor search itself, rather than the end-stage outcome of HDR. We developed RAD51 proximity identification sequencing (RaPID-seq), a highly sensitive in cellulo method that marks all DNA searched by RAD51, regardless of whether it is chosen as the final template. We find that HDR in human cells is hierarchical. Only DSB-proximal sequences are searched, and even identical sequences outside the proximal window are not efficiently interrogated. Final recombination is unlocked by template homology but only at proximal sequences. We further find that RAD51 efficiently searches exogenously introduced DNA templates, such as those commonly used during genome editing, even those with no homology to the DSB site.  Such highly abundant exogenous templates compete with search of endogenous genome templates. Our data reveal the invisible process of homology search and shed new light on fundamental mechanisms underlying genome editing.

overall_design:
DISCOVER-seq identification of CRISPR/Cas9 genome editing off-targets (DSBs) by MRE11 ChIP-seq. Detailed protocol at (https://www.nature.com/articles/s41596-020-0309-5).
Targeted genes are HBB (sgHBB) or a conserved abundant genomic sequence (sgMulti1).

first: Jacob

middle: E

last: Corn


overall_design: Chromatin immunoprecipitation for DNA repair factors in the context of DNA double-strand breaks (DSBs) from CRISPR/Cas9 genome editing experiments, including non-DSB conditions as a negative control/background condition. DNA repair factor is RAD51, including tagged a V5-tagged RAD51 fusion protein (Dam-V5-RAD51).


title: Neural Cell Models of Specific Reading Disabilities: Identification of Migration and Transcriptome Alterations

city: Toronto

first: Cathy

last: Barr

state: ON

address: 399 Bathurst St

country: Canada

institute: UHN

summary: Based on post-mortem studies, a long-standing hypothesis on the biological bases of specific reading disabilities (RD) has been that alterations in neuronal migration alter language neural circuits. However, this idea has not been strongly supported by current genetic studies. In this study, we test neural cell migration using cells derived from two pairs of siblings strongly discordant for reading – probands with severe RD and their strong readers siblings. We observed significant differences in migration in the neurosphere assay with the neural precursor cells (NPCs) from the probands migrating significantly further than their strong reader siblings. Transcriptome analyses of NPCs and excitatory neurons identified genes differentially expressed between the probands and siblings, including genes previously identified in neurodevelopmental disorders. Of note was the overexpression of the hormone IGF1 and the transcription factor OTX2, responsible for the opening and closing of critical windows in development and predicted to be involved in critical windows for language acquisition. Our results support altered migration in RD and point to specific genes contributing to the altered cell phenotypes.

overall_design: iPSC-derived neural precursor cells and neurons were generated from four human donors forming two sibling pairs. Each pair consisted of one child with a reading disability (based on standardized reading assessments) and a high-performing sibling control (strong reader). Donors included both males and females aged 8, 10, and 16 years. Six biological replicates were generated per donor per cell type. Total RNA was extracted from both neural precursor cells and differentiated neurons and used to prepare RNA-seq libraries. Sequencing was performed at the UC San Diego IGM Genomics Center using an Illumina NovaSeq 6000 with paired-end reads.

first: Barr

last: Cathy L.

first: Wigg

last: Karen

first: Feng

last: Yu

first: Benassi

last: Simone

first: Marchetto

last: Maria C.


title: Induction of mitochondrial DNA compaction limits innate immune memory

city: Shanghai, China

first: Cheng

last: Peng

state: Shanghai (31)

address: Zhengmin Road

institute: Tongji University

summary: Implication of innate immune memory in host defense and pathogenesis of diverse inflammatory diseases is usually characterized by chromatin modification that leads to more effective transcription of cytokine genes. Mitochondrial DNA (mtDNA) is compacted by mitochondrial transcription factor (TFAM) and plays a crucial role in maintaining mitochondrial function.  Here, we demonstrate that Bacillus Calmette-Guérin (BCG) PE18 induced mtDNA compaction through enhancing TFAM level. Mechanistically, PE18 interacted with SLC25A5 and reduced mitochondrial ATP level, thus blocking the degradation of TFAM by protease AFG3L2. Accumulated TFAM restricted mtDNA accessibility, which inhibited transcription of mitochondrial encoded NADH dehydrogenase subunit 1 (mtNd1), leading to reduction of oxidative phosphorylation (OXPHOS) activity and mtROS production. Moreover, deletion of pe18 from BCG conferred better and longer protection against Mycobacterium tuberculosis (Mtb) infection, and higher safety in immunocompromised mice than did parental BCG. These findings suggest that targeting mtDNA accessibility for immune memory may provide prevailing protective immunity.

overall_design:
RNA-seq profiling of mouse BCG- and BCGΔpe18-trained BMDMs infected with Mtb H37Rv for 6 h

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Submitter states "our mouse RNA-seq dataset is subject to institutional data governance restrictions that prevent public deposition of raw sequence files"
***************************************************************


title: A Liquid biopsy-RNAseq Method for Monitoring the Expression of Genes Involved in Drug Disposition: Proof-of-Concept Application to Cholestatic Disease

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Between-patient variability in metabolism and disposition of therapeutic drugs is associated with variable expression and activity of enzymes and drug transporters. Direct measurement of the expression of such proteins in relevant organs is limited by access to tissue biopsies. Characterization of such pathways in plasma-derived extracellular vesicles (EVs) as liquid biopsy is proposed herein as a minimally invasive and widely accessible alternative to tissue biopsy. This report provides a technical account for the extraction, characterization and RNAseq of EVs from two sets of healthy and cholestatic plasma samples (n = 3). Quality controls (QCs) implemented at different stages of the protocol ensured quality of the EVs and extracted RNA for downstream analysis. These QCs included visualization, size distribution, protein content and RNA quality and yield. Extracted EVs were a mixture of small and large vesicles (35-350 nm). Replicate RNAseq data reflected strong correlation (Pearson r = 1, p < 0.001), low bias (average fold error = 1), and limited scatter (absolute average fold error = 1.34) across replicates. The method was able to monitor cfRNA expression of 656 pharmacologically relevant genes, including 199 xenobiotic-metabolizing enzymes, 444 transporters, and 11 transcription factors. Disease perturbation in expression from healthy baseline was estimated for 93% of monitored pharmacokinetic pathways. The data, along with demographic and plasma albumin changes, were used to generate a Cholestasis Population pharmacokinetic model. The model reflected exposure to budesonide and cyclosporine consistent with early-stage cholestasis. The model also reflected increased serum bilirubin, likely due to hepatobiliary transport dysregulation.

overall_design: Extracellular vesicles were extracted using ExoQuick reagent and gentle centrifugation. Cell free RNA was isolated using a bead based method. Sequencing was done with Ampliseq (Illumina). RNAseq was conducted by Illumina NovaSeq X Plus.

first: Brahim

last: Achour


overall_design: RAD51 proximity Identification sequencing (RaPID-seq) of DNA double-stranded break (DSB) homology directed repair (HDR) marking for homology search events by DNA-protein proximity labelling (DamID).  Dam protein is fused to RAD51, the key mediator of homology search or no fusion (control condition). Cells are then treated with ±DSB using CRISPR/Cas9, and differential comparison between the ±DSB conditions is used to perform background subtraction, enabling high sensitivity detection of search events. Except in cell line K562-RaPID-BFP, sgBFP corresponds to the non-targeting control (sgNTC).


title: Role of plasma extracellular vesicles in lung cancer pre-metastatic niche formation

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Lung cancer is the deadliest cancer worldwide, primarily due to metastatic spread. Tumor-derived extracellular vesicles (EVs) play a crucial role in the formation of pre-metastatic niches (pMNs), facilitating the spread and expansion of circulating cancer cells. So far, little is known about the role of plasma EVs in lung cancer pMN formation. We aim to elucidate the EV role in pMN formation and identify new prognostic biomarkers for early-stage lung cancer.Plasma-derived EVs were obtained by ultracentrifugation from early-stage lung cancer patients who survived at 5 years (ESA-EVs) and patients who died within two years (ESD-EVs). Heavy-smokers cancer free individuals were used as control (HS-EVs). Functional in vitro experiments on endothelial cells were carried out using 15ug of EVs from different groups for 48h. We observed that ESD-EVs significantly induced a “pro-inflammatory” endothelial phenotype. Characterization of ESD-EV revealed higher levels of miR-29 and C4a compared to ESA and HS-EVs. Concomitant miR-29 transfection and C4a administration in endothelial cells recapitulated the pro-inflammatory activation observed with EVs. In conclusion, we showed that plasma EVs could drive lung pMN formation, conferring a pro-inflammatory phenotype to endothelial cells to favour metastasis outgrowth

overall_design: 1x105 Human Umbilical Vein Endothelial Cells (HUVEC) were treated for 48h with 15ug of ESD, ESA or HS-EVs. Untreated cells (NT) were used as control. After 48h the cells were harvested for RNA extraction.  To demonstrate the effect of synergism between miR-29 and C4a, HUVEC were transfected with mirVana™ miR-29a-3p or the negative sequence SCR 5 nM) using Lipofectamine 2000 (Thermo Fisher Scientific) according to manufacturer's protocol. After 4 hours, medium was changed to complete medium for 48-hour incubation alone or with recombinant C4A (300 nM, Origene).


title: Scalable Generation of Hematopoietic Stem Cells Engineered Off-the-Shelf Mono-Specific Cytotoxic T Cells Targeting Solid Tumors

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

summary: Adoptive T cell therapy has emerged as a promising strategy for treating solid tumors. However, its clinical application remains constrained by major limitations, including manufacturing complexity in autologous settings and risks of graft-versus-host disease (GvHD), HLA restriction and donor variability in allogeneic contexts. To address these challenges, we present a scalable platform for the generation of hematopoietic stem and progenitor cell (HSPC)-derived, mono-specific cytotoxic T cells targeting the NY-ESO-1 antigen. Using an ex vivo, feeder-free, serum-free culture system, we differentiate gene-engineered HSPCs into allogeneic T cells (AlloESO-T) with a uniform cytotoxic phenotype and robust antitumor activity. These cells employ dual tumor-targeting strategies by antigen-specific killing via a transgenic TCR, and antigen-independent cytotoxicity via natural killer receptors. Compared to conventional PBMC-derived TCR-T cells, Allogeneic ESO-T cells display superior cytotoxic potency, selective solid tumor homing, durable killing persistence, and resilience against immune evasion. Notably, they exhibit a favorable safety profile, with low risks of graft-versus-host disease (GvHD) and cytokine release syndrome (CRS), alongside stable hypoimmunogenic features. Collectively, our findings demonstrate the feasibility, universality, and therapeutic potential of HSPC-engineered, off-the-shelf mono-specific cytotoxic T cells. This work lays a foundation for next-generation T cell immunotherapies that are scalable, safe, and broadly applicable to diverse solid tumors.

overall_design: Gene expression profiling of therapeutic cells in an in vivo study using an A375 human melanoma xenograft NSG mouse model

first: Jiaji

first: Yan-Ruide

last: Li

first: Lili

last: Yang


title: DXO1 involves in ABA regulation through m7G capping

city: Hong Kong

first: Shumin

last: LIANG

address: 224 Waterloo Road, Kowloon Tong, HK

department: Biology

institute: Hong Kong Baptist University

summary: Eukaryotic mRNA typically features the N7-methylguanosine (m7G) moiety as a 5' cap, which is essential for mRNA function and stability. While m7G capping was once considered a constitutive housekeeping process, emerging evidence suggests that it is dynamically regulated to influence gene expression in response to stimuli, although the underlying mechanisms remain largely unknown. The recent discovery of NAD-capped RNAs (NAD-RNAs) adds complexity to the role of RNA capping in gene regulation. Arabidopsis DXO1 has been identified as a decapping enzyme for NAD-RNAs (deNADding), and its loss-of-function mutation has been reported to cause pleiotropic phenotypes, including reduced sensitivity to ABA. Recently, we found that DXO1 is also a crucial component of m7G capping, acting as an activator of RNMT1, which methylates the unmethylated guanosine cap of mRNA to produce the m7G cap. In this study, we demonstrate that DXO1 contributes to the ABA response not through its role as a deNADding enzyme, but rather through its function in m7G capping. Additionally, loss-of-function mutations in RNMT1 result in an ABA-insensitive phenotype similar to that of dxo1. RNA sequencing and phenotypic analyses further reveal comparable regulatory roles for DXO1 and RNMT1 in influencing gene expression in response to ABA treatment and in response to certain abiotic stresses. Our findings highlight the significant role of m7G capping in mediating the ABA and stress responses.

overall_design: RNAseq profiling of wildtype col-0,  mutants (dxo1, rnmt1) and transgenic plants (Cd and Nd).

first: Shangwei

last: WU

first: Chen

last: XIAO

first: Yiji

last: XIA


title: MeCP2 binding and genome-lamina reorganization precede long neuronal gene

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: During corticogenesis, neural gene expression is tightly coordinated by changes in chromatin state and epigenetic regulation. However, the role of spatial genome organization—particularly interactions with the nuclear lamina—during these developmental programs remains poorly understood. Here, we combined in utero electroporation with scDam&T-seq to jointly profile genome-lamina contacts and transcriptomes in single cells of the mouse embryonic cortex. We uncover a large cohort of long, neuronal function-related genes that undergo spatial genome-lamina repositioning during neurogenesis. Notably, detachment of these genes frequently precedes transcriptional activation, positioning lamina disengagement as an early gene regulatory event. We further identify the methyl CpG binding protein 2 (MeCP2)—mutated in Rett syndrome—as a candidate mediator of this process. MeCP2 binds lamina-associated, hydroxymethylated long genes before their repositioning, suggesting that MeCP2 may prime genome-lamina reorganization. These findings suggest a link between prevalent genome-lamina reorganization and MeCP2 regulation to ensure proper spatiotemporal activation of neuronal genes during corticogenesis.

overall_design: scDam&T-seq, mapping genome-lamina contacts (scDamID; Dam-Lamin B1) and transcription (CEL-seq2) was perfomed after in utero electroporation on E15.5, E16.6 and E18.5 mouse embryos


title: Spatial transcriptomics of the human first trimester decidua

city: Graz

first: Julia

last: Feichtinger

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical University of Graz

summary: Understanding how extravillous trophoblasts (EVTs) reshape the maternal uterine environment (decidua basalis) is critical for deciphering early human placental development. To study the impact of EVT invasion on the distribution of immune cells and the restructuring of the decidual tissue, we performed spatial transcriptomic profiling using the Visium platform (10x Genomics) on first trimester decidua.

overall_design: To investigate the spatial organization of the human decidua, we applied spatial transcriptomics using the Visium platform (10x Genomics) to four tissue sections. Experimental design: matched samples from both the first trimester decidua basalis and decidua parietalis of two independent donors.

first: Gerit

last: Moser

first: Martin

last: Gauster


title: Transcriptome regulation in T-cells and monocytes in patients with Common Variable Immunodeficiency

city: Oslo

first: Mingyi

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

summary: A large subgroup of Common Variable Immunodeficiency (CVID) patients has autoimmune and inflammatory complications, associated with T cell and monocyte pathology, but the molecular mechanism for this CVID-subgroup is still elusive. To identify novel molecular pathways impacted in CVID T cells and monocytes, we examined the transcriptomic profiles in these cells from healthy control and the CVID patients in the subgroup with inflammatory complications.

overall_design: RNA sequencing T cell (CD3+) and monocyte cells (CD14+) from blood PBMC in both CVID patient  and healthy control.

first: Mari

last: Kaarbø

first: Vegard

last: Myhre

first: Børre

last: Fevang

first: Pål

last: Aukrust

first: Mirta

last: Sousa

first: Animesh

last: Sharma

first: Torbjørn

last: Rognes

first: Magnar

last: Bjørås

first: Silje

middle: F

last: Jørgensen


title: BIRC3 (encoding cIAP2) variants are associated with Crohn’s Disease.

first: Aleixo

last: Muise

address: 686 Bay Street, 19-9400 I-M PGCRL

department: Cell Biology

institute: The Hospital for Sick Children

summary: The baculoviral IAP repeat-containing 3 (BIRC3) gene encodes the Cellular Inhibitor of Apoptosis Protein 2 (cIAP2) a regulator of innate immune pathways including TNFα receptor signaling. We identified 5 heterozygous and 3 homozygous rare damaging BIRC3 variants in 13 patients from 9 independent families who presented with Crohn’s Disease (CD) between 2 months and 31 years of age. A knock-in mouse model of the BIRC3 variant (cIAP2H312Y/+) identified in two independent CD families had increased susceptibility to DSS-induced colitis and ciap−/+ zebrafish developed spontaneous colitis. Transcriptome analysis showed that reduced BIRC3 expression led to the induction of several TNFa responsive genes including NFKB2. Functional studies showed that all cIAP2 variants had impaired inhibition of NFκB2 activity and increased cell death when induced by TNFa. Finally, cIAP2H312Y/+ mice treated with apoptosis or RIPK1 inhibitors had improved clinical outcomes. Our study demonstrates that BIRC3 variants results in dysregulation of NFκB2 signaling leading to in CD.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: For mus musculus: Organoids were derived from wild-type (WT), cIAP2 H312Y/+, and cIAP2 knockout (−/−) mice, and were either treated with TNF-α or left unstimulated.  For danio rerio: To investigate the role of birc3 in the development of very early onset inflammatory bowel disease,we generated zebrafish birc3 knock out line using CRISPR/Cas9 technology.    We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line, birc 3(-/+)  and birc 3(-/-) line, at two timepoints (3 dpf and 8 dpf).    Comparative gene expression profiling analysis between wt , birc3het and birc3 homo zebrafish mutant were performed to examine the transcriptomic alterations caused by birc3 deficiency.

first: Qi

last: Li

first: Ryusuke

last: Nambu

first: Yaqiang

last: Hu

first: Xiang

last: Shen

first: Carmen

last: Argmann

first: Rei

last: Guan

first: Erin

last: Janssen


title: Lsp2 links mTORC1 to TOP mRNA translation and lifespan in Drosophila

city: changsha

first: cai

last: zixin

email: 964530737@qq.com, cangjie@hnu.edu.cn

state: 湖南Hunan

address: yuelu district tianma road

institute: Hunan university

summary: Mechanistic target of rapamycin complex 1 (mTORC1) senses amino acid availability to orchestrate metabolic processes critical for physiological homeostasis and organismal ageing 1. While mTORC1 preferentially regulates the translation of 5′-terminal oligopyrimidine (TOP) motif-containing mRNAs that predominantly encode ribosomal proteins (RPs) via the translational repressor 4E-BP 2, this mTORC1 function is resistant to rapamycin inhibition 3. TOP mRNAs are exceptionally abundant, thus imposing a major translational burden on cells; yet how their translation is physiologically tuned and linked to longevity remain unexplored. Here we identify Lsp2, originally known as a storage protein 4, as an adipose effector of mTORC1 that modulates lifespan in Drosophila. Lsp2 is induced by essential amino acids (EAAs) via mTORC1. Genetic ablation of Lsp2 to blunt organismal response to protein diets drives robust lifespan extension without compromising key life-history traits such as reproduction. Translatomic profiling reveals that loss of Lsp2 selectively reduces global TOP mRNA translation in a 4E-BP-dependent manner, thereby extending lifespan via a mechanism distinct from rapamycin inhibition. Finally, Lsp2 adipokine promotes 4E-BP phosphorylation and acts systemically across tissues to shape the lifespan responses to dietary protein. Collectively, our findings establish Lsp2 as a novel translational regulator of TOP genes that mechanistically couples physiological ribosomal protein synthesis with organismal longevity.

overall_design: This study included RNA-seq, monosome-seq, and polysome-seq analyses of whole-body samples from Drosophila melanogaster with different genotypes and ages. For 15-day-old flies, Lpp[TS]>Lsp2, Lpp[TS]>Rheb, and Lpp[TS]>w1118 samples were analyzed, with two biological replicates for each genotype and sequencing fraction. In addition, 15-day-old Lsp2[A10], Lsp2[B14], Thor[2]; Lsp2[A10], and Thor[2]; Lsp2[B14] flies were analyzed, with three biological replicates for each genotype and sequencing fraction. To examine age-related differences, 2–3-day-old Lsp2[A10] and Lsp2[B14] flies were also analyzed, with three biological replicates for each genotype and sequencing fraction. For each experimental group, total RNA, monosome-associated RNA, and polysome-associated RNA were sequenced to assess transcript abundance and translational regulation. A total of 72 sequencing libraries were included in this study.

first: Jun

last: Wang

first: Zixin

last: Cai

first: Yirong

first: Zongzhao

last: Zhai


title: AATF silencing suppresses tumor progression by reprogramming the microenvironment  in hepatocellular carcinoma

city: Mysore

first: Divya

middle: P

last: Kumar

state: Karnataka

address: SS Nagar

country: India

institute: JSS Medical College

summary: Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and a leading cause of cancer-related mortality worldwide. It is characterized by a highly heterogeneous and immunosuppressive tumor microenvironment (TME) that promotes disease progression and therapeutic resistance. The TME plays a crucial role in the progression of HCC by regulating immune response, extracellular matrix remodeling, and angiogenesis. We previously elucidated that apoptosis antagonizing transcription factor (AATF) drives angiogenesis in HCC. However, its role in TME remains unexplored. Here, we studied the effect of AATF silencing in TME on HCC progression using an orthotopic xenograft model. Mice were injected with liver-specific AAV8 carrying siAATF or siControl and monitored for tumor growth. Whole transcriptomics and molecular analyses were carried out. AATF silencing reduced tumor growth and invasion. Species-specific transcriptomic analysis showed that the TME signatures like inflammation, immune response, angiogenesis, and ECM remodeling were altered in siAATF mice compared to the siControl. Mechanistically, TGF-β signaling was markedly suppressed in the TME affecting the cell cycle and metabolic activity of tumor cells, leading to tumor regression. These findings highlight AATF as a critical regulator of the TME, offering novel insights into potential therapeutic targets for HCC.

overall_design: We performed the liver-specific silencing of AATF using adeno-associated vectors (AAV)  in a BALB/c (nu/nu) orthotopic HCC model. The human HCC cells were injected directly into the liver of the mice, and the development of the tumor was observed. After one week of implantation, AAV8 contaning siAATF was injected through the tail vein, and mice were observed further for 3 weeks. Gene expression analysis was done using RNA sequencing in liver tissues obtained at the end of the study from four groups. Three replicates were used in the analysis. Comparisons were made between  AAV8-siAATF and AAV8-siControl.

first: Kumar

last: Divya Prasanna


title: Transcriptomic profiling of  HTR-8/SVneo cells under normal and MLEC knockdown conditions

city: Xuzhou

first: Yunlong

last: Si

state: --- Select One ---

address: Jiangsu Key Laboratory of Brain Disease and Bioinformation

institute: Xuzhou medical university

summary: This dataset comprises the gene expression profiles of HTR-8/SVneo cells under WT and MLEC knockdown conditions. RNA sequencing (RNA-seq) was conducted to examine the effects of MLEC depletion on gene expression, with the goal of elucidating its role in trophoblast function, including unfolded protein response (UPR), endoplasmic reticulum stress (ER Stress) and ER Stress-induced apoptosis. This dataset offers valuable insights into the molecular mechanisms governed by MLEC in trophoblast biology and its potential relevance to pregnancy-related disorders.

overall_design: RNA-seq profiling of MLEC knockdown (Mal-Sh) and their corresponding control (Mal-Sh-Con) in HTR-8/SVneo cells (H8)

first: Jiahui

last: Zhu


title: Analysis of the role of RPS26 during translation in HEK293T RPS26 p.100_M115 del cells by 48S footprinting (TCP-seq)

city: Rehovot

first: Benjamin

last: Weiss

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

summary: The ribosome mRNA channel is central for translation, but its role in specific regulatory mechanisms remains unexplored. Using Cryo-EM ribosomal complexes bound to Kozak and TISU mRNAs from WT and RPS26dC mutant cells, we demonstrate that RPS26 adopts distinct conformations, providing the basis for its opposing effects on their activity. Translatome studies of the RPS26dC mutant revealed sequence-dependent rearrangements of the 48S and 80S and slower scanning. Downregulated mRNAs are enriched with AUG upstream nucleotides and a -1C that contacts 18S G1207, a contact that is lost in the mutant structure. The top downregulated mRNAs are replication-dependent histones. Despite very short 5’UTRs and suboptimal Kozak, histones 5’UTRs exhibit strong translation activity that is RPS26-dependent. We identified a translational enhancer in H2B 5’UTR spanning nucleotide -16 to -9, matching RPS26 binding sites. Intriguingly, the H2B-ribosome complex adopts a different conformation compared to Kozak and TISU. Exploiting these features, we designed a translational cassette with high efficiency and minimal leaky scanning, improving efficacy and safety for mRNA therapy. These findings underscore the importance of the ribosome mRNA binding channel for selective regulation and therapeutic applications.

overall_design: 48S footprints from HEK293T WT and RPS26 delta C-terminus mutant cells (RPS26 p.R100_M115 deletion) were isolated, sequenced and analysed.

first: Davide

last: Fraticelli

first: Rivka

last: Dikstein


title: Limb cell-fate commissioning is guided by widespread coordinated genome detachment from the nuclear lamina [scDam&T-seq]

first: Jop

last: Kind

summary: Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate remains a key open question. Here, we address this by mapping a prevalent heterochromatic feature - genome-lamina interactions - relative to transcription in single-cells during mouse embryogenesis. We find that lamina-genome interactions remain relatively uniform following gastrulation but are extensively reconfigured during organogenesis in diverse tissues. Focusing on limb development, we demonstrate that genome-lamina interactions are selectively released at key developmental genes and their surrounding regulatory domains in early multipotent progenitors. Strikingly, this “lamina-release” often precedes later gene expression, suggesting it primes regulatory domains for future potential activation. Lamina-release also coincides with the putative binding of crucial limb transcription factors and so is closely intertwined with the regulatory machinery that drives limb formation. Conversely, we show that CTCF-defined boundaries of topologically-associated domains (TADs) constrains the spread of lamina-release at a limb gene locus. This ensures independent heterochromatin dynamics between neighbouring domains. Together, this suggests a previously unrecognised process where genome-lamina interactions are selectively dismantled at regulatory domains to transition loci toward more permissive chromatin states, thereby potentiating cell-type specific activation. Our work thus reveals how systematic heterochromatin reorganization links to developmental multipotency, providing mechanistic insight into how progenitors traverse diverse cell-fates in vivo.

overall_design: To profile LADs and corresponding gene expression read-out in single cells, Dam-LMNB1 was induced and embryonic tissue from E8.5 to E13.5 was dissociated and processed using scDam&T-seq. mESCs were also collected and processed using scDam&T-seq.

first: Konrad

last: Chudzik

first: Isabel

last: Guerreiro

first: Samy

last: Kefalopoulou

first: Alex

last: Abraham

first: Magdalena

last: Schindler

first: Mario

last: Nicodemi

first: Irina

last: Solovei

first: Andrea

last: Chiariello

first: Stefan

last: Mundlos

first: Michael

middle: I

last: Robson


title: Limb cell-fate commissioning is guided by widespread coordinated genome detachment from the nuclear lamina [Multiome]

overall_design: ATAC and gene expression single-cell read-outs were obtained from dissociated embryonic tissue of E8.5 to E13.5 and processed according to 10x Genomics guidelines.


title: Human microglia remove intraneuronal a-synuclein aggregates in a stem cell model of Parkinson’s disease

city: Oxford

first: HungJu

last: Chueh

address: Dorothy Crowfoot Hodgkin Building

department: Nuffield Department of Clinical Neuroscience

country: United Kingdom

institute: University of Oxford

summary: Microglia are the primary immune cells of the brain but their role in Parkinson’s disease is not fully understood. Although most studies suggest that chronic microglial activation is toxic to neurons, they also exert beneficial functions in the early stages of neuronal pathology that are not yet well defined. We used iPSC modelling to investigate how human microglia respond to α-synuclein aggregation that forms de novo in human dopaminergic neurons with α-synuclein gene triplication or is triggered by fibrils.  We found that microglia cleared Ser129 phosphorylated α-synuclein aggregates without exacerbating neurotoxicity, using a contact-dependent mechanism involving selective phagocytosis (i.e. trogocytosis) of neuronal sub-compartments that is independent of TREM2 or phosphotidylserine. In the presence of intraneuronal α-synuclein aggregates, microglia exhibited morphological changes and transcriptomic profiles indicative of activation. Using single cell sequencing, we identified a sub-cluster of disease-associated microglia (DAM) in association with this phenotype, and GPNMB as a key effector of a-synuclein aggregate clearance by microglial lysosomes. Importantly, our secretome analysis suggests that the identified DAM sub-cluster is negatively regulated by an autocrine loop mechanism involving IL-10 and blocking this pathway using antibodies promotes the phagocytic response. Taken together, our study identifies a specific microglial subtype that exerts beneficial trogocytic effects on human dopaminergic neurons containing α-synuclein aggregates and suggests that stabilisation of such subpopulations during the neurodegenerative process could be a useful therapeutic strategy.

overall_design: scRNA-seq of hiPSC-derived healthy control microglia (OX3-9) co-cultured with hiPSC-derived dopaminergic neuron with SNCA Triplication (SFC831-03-05). This was done to indentify pathways involved in the microglial response to intraneuronal α-synuclein aggregation.

first: Hung-Ju

first: Antigoni

last: Katsikoudi

first: Ana Aragon

last: Gonzalez

first: Liezel

last: Tamon

first: Chor Lai

last: Lam

first: Sally

last: Cowley

first: David

last: Sims

first: George K

last: Tofaris


title: Enhancement of hepatic artery blood flow improves tuft cell selenoamino acid metabolism and alleviates biliary injury in liver transplantation (130 characters)

city: 重庆

first: cc

last: z

address: 沙坪坝区高滩岩正街30号

institute: 陆军军医大学

summary: Biliary injury in liver transplantation (LT) determined postoperative graft survival. Tuft cells regulate inflammation but are reduced in biliary injury. Sufficient arterial blood is indispensable for biliary repair. We aimed to propose a strategy of biliary repair through hepatic artery flow enhancement and investigate its mechanism, particularly in tuft cells.

overall_design: We established a rat LT model with ischemic injury (control) and administrated an arterial flow elevation by ligating the splenic and gastric-duodenal arteries (treatment). Histological and functional alternations were assessed. Single-cell RNA sequencing of bile duct was performed on both groups at days 1, 3, and 7 post-LT.


title: Bulk RNA-seq of striatum of 6-OHDA lesioned rats exposed to levodopa/benserazide and trapidil

city: San Diego

first: Aarash

last: Bordbar

state: CA

address: 3210 Merryfield Row

institute: Sinopia Biosciences

summary: Gene expression changes in striatum of 6-OHDA lesioned female Sprague Dawley rats due to 14 days of daily dosing of levodopa/benserazide with or without trapidil.

overall_design: 25 female Sprague Dawley rats were lesioned with 6-OHDA and then randomly split into three treatment groups. Animals were dosed for 14 days with treatment and behaviorally assessed. On day 15, 1 hour of test articles administration, animals were sacrificed striatum ipsilateral to the lesion were collected for RNA-seq.  Treatments groups were leveodopa (6mg/kg, QD) (n=5), levodopa (6 mg/kg, QD) & trapidil (7.5 mg/kg, BID) (n=10), levodopa (6 mg/kg, QD) & trapidil (15 mg/kg, BID) (n=10).


title: Tonicity drives maturation of the collecting ducts in the mammalian kidney

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: Organ maturation is a fundamental question in biology and a key requisite for organoid maturation in regenerative medicine. As the kidney matures, the osmolality in the renal medulla increases for urine concentration, but how this extreme environment conversely contributes to kidney maturation is unclear. Here we show that high tonicity, i.e. high salt concentration, promotes the maturation of mouse embryonic kidneys and human kidney organoids. Exposure of mouse embryonic collecting ducts (CDs) to high tonicity induces morphological changes in the epithelia, upregulates maturation-associated genes, and confers responsiveness to antidiuretic hormone, which mainly depend on the transcription factor NFAT5 (nuclear factor of activated T cells 5). Based on these findings, we have established a robust maturation protocol for human CD organoids that allows recapitulation of disease states caused not only by NFAT5 deletion, but also by a missense mutation of the antidiuretic hormone receptor reported to cause congenital nephrogenic diabetes insipidus. Collectively, high tonicity is a driving force for mammalian kidney maturation, not only for urinary concentration. Our study uncovers a novel principle of organ maturation triggered by environmental cues, and offers a promising path to maximize the potential of organoids for future therapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: These datasets contain transcriptional profiles of the followings at single cell resolution: mouse collecting ducts at normal and high tonicity, mouse collecting ducts at high tonicity in the presence of hormones, mouse WT and Nfat5 KO collecting ducts at high tonicity, mouse ES-derived nephron and stroma progenitors, embryonic day 15.5, postnatal day 0 and Day7 kidneys, human CD organoids at normal and high tonicity, and adult human kidney.

first: Daisuke

last: Inoue

first: Koichiro

last: Miike

first: Keiichiro

last: Yasunaga

first: Tomomi

last: Kamba

first: Ryuichi

last: Nishinakamura


title: D-lactate derived from bacteria drives lysine D-lactylation to modulate transcription in liver cells

city: tianjin

first: yong

last: zang

address: Heping District qixiangtailu22hao

institute: Tianjin Medical University

summary: Emerging evidence suggests that accumulated D-lactate (D-la) induces diverse effects in human intestinal injury diseases. However, the regulatory mechanism remain elusive. Here, we discover the lysine D-lactylation (D-Kla) induced by D-la and reveal the molecular mechanism underlying D-la-driven D-Kla for transcription regulation. We first discovered D-Kla in HepG2 cells stimulated by D-la from E. coli secretions. Next, we validated the existence of D-la-driven D-Kla by four approaches, especially including metabolic labelling experiments. Additionally, we uncover that SCOT1 catalyzes the transformation of D-la to D-lactyl-CoA, serving as a key donor for D-Kla. Furthermore, we identify the D-Kla landscape with 2895 sites by proteomics analysis and 34 histone D-Kla sites activated by D-la and further indicate the regulation of H3K18-Dla in transcription by CUT&Tag and RNA-seq assays. Finally, we show the effect of D-Kla on inhibiting the hepatocellular carcinoma cells proliferation. In summary, we uncover the D-la-driven D-Kla and reveal a D-Kla-mediated transcription regulation for tumor suppression, providing new insight into the protein modifications induced by microbiota secretions.

overall_design: To explored the function of D-lactate in HepG2 cells, RNA-seq and CUT&Tag-seq for D-lactylation in HepG2 cells stimulated by 20 mM  or 0 mN D-lactate for 48 hours

first: Yong

last: Zang

first: Jianji

last: Zhang

first: Aiyuan

last: Wang

first: Mingxin

last: Xia


title: G9a/DNMT1 co-targeting inhibits non-small cell lung cancer growth and reprograms tumor cells to respond to cancer-drugs through SCARA5 and AOX1

city: Pamplona

first: Francisco

last: Exposito

state: Navarra

address: Irunlarrea SN, Research Building

department: Department of Pathology, Anatomy and Physiology, School of Medicine

country: Spain

institute: University of Navarra

summary: Treatment of non-small cell lung cancer (NSCLC) patients has greatly improved with recent therapeutic strategies but many patients do not benefit from them. Therefore, new treatment strategies are highly needed. Here we have assessed the antitumor efficacy of co-targeting G9 and DNMT1 enzymes and its potential as a cancer-drug sensitizer. We found co-expression and overexpression of G9a and DNMT1 in NSCLC, in association with poor prognosis. G9a/DNMT1 co-targeting with the drug CM-272 reduced proliferation and increased apoptosis in a panel of human and murine NSCLC cell lines. Moreover, reprogramming of the transcriptome of these cells to become highly responsive to chemotherapy (cisplatin), targeted therapy (trametinib) and epigenetic therapy (vorinostat) was observed. In vivo, CM-272 decreased tumor volume in human and murine cell-derived cancer models, an effect synergistically enhanced by cisplatin. Expression of SCARA5 and AOX1 was induced by CM-272 and both proteins were found to be essential for the antiproliferative response, as gene silencing reduced cytotoxicity. Expression of SCARA5 and AOX1 was positively correlated among themselves and inversely correlated with that of G9a and DNMT1, in NSCLC patients. SCARA5 and AOX1 DNA promoters were hypermethylated in NSCLC, and SCARA5 methylation was found as an epigenetic biomarker in tumors and liquid biopsies from NSCLC patients. Therefore, we demonstrate that G9a/DNMT1-co-targeting is a promising strategy to enhance the effect of cancer-drugs and that SCARA5 methylation could be used as a non-invasive biomarker to monitor tumor evolution.

overall_design: We treated H358 and A549 lung cancer cell lines with CM272 a novel first-in-class dual reversible inhibitor of G9a (GLP) and DNMTs for 48h with half-maximal inhibitory concentration (IC50).  The transcriptomic profiles of H358 and A549 cells treated with CM-272 was compared to that of untreated cells.

first: Alfonso

last: Calvo


title: 3D porous microscaffold promoted hPSC-macrophage large-scale production by facilitating proliferation and self-renewal gene network

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

summary: Macrophages play crucial roles in various physiological and pathological processes, including immune response and tissue homeostasis. Therefore, the importance of macrophages in preclinical study and clinical application is increasing, necessitating the development of more efficient human pluripotent stem cell(hPSCs) derived macrophage(iMac) differentiation methods to meet the growing demand. Utilizing three-dimensional porous microscaffold (PMS), we have devised a novel approach to induce hPSCs to generate a substantial number of macrophages. This method differs from existing hematopoietic differentiation methods for iMacs. Interestingly, it leads to the formation of a vascular-like hematopoiesis structure resembling the early aorta-gonad-mesonephros(AGM) during embryogenesis. The subsequent event involved the generation of a substantial quantity of macrophages undergoing robust proliferation. Multi-omics data analysis revealed that the 3D microenvironment may generate numerous ligands that promote macrophage proliferation and activate the expression of proliferation and self-renewal genes during iMac generation stage. The subsequent functional experiments demonstrated iMacs can serve as off-the-shelf products for the treatment of infection symptoms caused by drug-resistant Streptococcus pneumoniae infections, and may allow for further innovative cell-based treatment strategies.

overall_design: Differentiate macrophage in 3D porous niche, and perform bulk/single-cell RNA-seq,ATAC-seq and CHIP-seq to get their transcriptomic and epigenetic profile, then compare with 2D differentiated macrophages.

first: Peiliang

first: Hui

last: Qiu

first: Xia

last: Chen

first: Wenjing

last: Li

first: Tianjie


title: Single Nuclei sequencing of mouse model of MBL1 and 2 KD

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

summary:
This study looks at a new model of MBL1 and MBL1 KD to understand how these proteins funciton in muscle development and contribute for DM1 pathology. Animals were injected into the tibialis anterior (TA) muscle at 10 weeks of age. Sampling was performed approximately 10 weeks after injection, i.e. at around 20 weeks of age.
The left TA was injected with an AAV encoding shmir directed against Mbnl1 and Mbnl2, and the left TA was injected with an AAV encoding shmir directed against LacZ (control). Both muscles were therefore injected with AAV.

overall_design: Wildtype mice were injected with an AAV vector containing the shRNA for either MBL1 or MBL2. The TA was collected for single- nucleus RNA-sequencing after verfying the downregulation by qPCR. snRNA-seq was perfromed using thr 10x 3' Gene Expression kit.

first: Xavière

last: Lornage

first: Piera

last: Smeriglio

first: Denis

last: Furling


title: Gene expression of aquaporin genes in roots of Sri Lankan Indica II rice cultivars

city: Aberdeen

first: Elaina

last: Collie-Duguid

address: 23 St Machar Drive

institute: University of Aberdeen

summary: Molecular variation in the roots of Sri Lankan Indica II rice cultivars was examined.

overall_design: Gene expression in root tissue was examined in five strains, Azucena, Bala, Moddai Karuppan (MK), Niyan Wee (NW) and Sarali. RNA-sequencing was performed for 4 samples of each genotype.

first: Poornima

last: Herath

first: Adam

middle: H

last: Price

first: Louie

middle: N

last: van de Lagemaat

first: Zeynab

last: Heidari

first: Ewan

last: Campbell


title: USP10-mediated PFKFB4 deubiquitination induces lung cancer radioresistance by activating the fumarate/Rad51 axis

city: Wuhan

first: Yunshang

address: No. 1277 Jiefang Avenue

institute: Wuhan Union Hospital

summary: Radioresistance is a major cause of radiotherapy failure in lung cancer, and its mechanism has not been fully elucidated. Glucose metabolism is closely related to radioresistance, and targeting key molecules in glucose metabolism is expected to increase radiosensitivity. Our study demonstrated that the expression of the gluconeogenic enzyme PFKFB4 was upregulated in lung cancer. Genetic silencing and pharmacological inhibition of PFKFB4 significantly enhanced lung cancer radiosensitivity. Mechanistically, the fumaric acid/Rad51 axis is crucial for PFKFB4-induced radioresistance. PFKFB4 inhibits histone demethylase KDM1A by upregulating fumaric acid, which in turn increases the level of H3K4me1 at the Rad51 promoter region and induces Rad51 transcriptional activation, and ultimately leads to lung cancer radioresistance. Furthermore, by constructing a library of ubiquitinated compounds, the deubiquitinating enzyme USP10 was identified as a key upstream molecule for stabilizing PFKFB4 expression, and USP10 silencing downregulated fumaric acid and Rad51 in a PFKFB4-dependent manner, which in turn increased lung cancer radiosensitivity. In conclusion, the present study reveals that USP10-mediated PFKFB4deubiquitination promotes lung cancer radioresistance through activation of the fumaric acid/Rad51 axis and provides important evidence for the clinical translation of PFKFB4.

overall_design: H1299 cells transfected with Scrambled or SiRNAs targeting PFKFB4 for 48 hours were analyzed by RNA-seq.

first: Xiaohua

last: Jie

first: Gang

last: Wu


title: Translational regulation of chaperone-mediated autophagy by the RNA-binding protein IMP2

city: New York

first: Jeetayu

last: Biswas

state: NY

address: 417 East 68th St

department: Molecular Pharmacology

institute: Memorial Sloan Kettering Cancer Center

summary: Chaperone-mediated autophagy (CMA) selectively targets proteins for lysosomal degradation. During aging, levels of LAMP2A (lysosome-associated membrane protein 2A), a limiting CMA component, decline. Here we show that insulin-like growth factor 2 mRNA-binding protein 2 (IMP2), is a post-transcriptional regulator of CMA that binds Lamp2a mRNA and inhibits its translation, leading to decreased CMA activity and that IMP2 depletion or pharmacological inhibition effectively upregulate CMA. We identified a fraction of IMP2 at the lysosomal surface and using single-molecule fluorescence in situ hybridization, demonstrated its contribution to the lysosomal degradation of Lamp2a mRNA. IMP2 levels and distribution change with age and in response to dietary lipid challenges, both conditions known to reduce CMA activity. We propose that the increase in IMP2 levels under these conditions enhances Lamp2a RNA degradation, thereby contributing to the decline of CMA. Our data highlight IMP2 as a physiological regulator of CMA activity and potential target for gerotherapeutic interventions.

overall_design: We identify the targets of RNA binding proteins by fusing the proteins of interest to the hyperactive variant of the RNA-editing enzyme adenosine deaminase (RBP-ADAR). Fusion plasmids containing a fluorescent protein reporter are transfected into cell lines of interest. FACS sorted cells are used for standard RNA sequencing library preparation. Targets are read out by RNA sequencing, where two replicates are compared to an mCherry-ADAR control (as detailed in Rahman et al, Nature Protocols 2018 and Biswas et al, STAR Protocols 2021).

first: Robert

last: Singer


title: Sequencing of C.elegans at different time points treated with Black Rice Extract and controls

first: Dan

middle: Yang

last: Wang

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: Comparison of gene expression profiles from C. elegans at different time points after OP50 and Black Rice Extract (BRE) treatment. The RNA-seq data comprise 5 time points (1, 6, 11, 15 and 17 days) treated with OP50 and BRE as well as 4 time points (6, 11, 15 and 17 days).

overall_design: L4 stage worms were exposed to OP50 or BRE for different time and total RNA was extracted for 3 biological replicates. 27 samples in 9 groups: 1 day OP50 (3 Samples), 6 day OP50 (3 Samples), 11 day OP50 (3 Samples), 15 day OP50 (3 Samples), 17 day OP50 (3 Samples), 6 day BRE (3 Samples), 11 day BRE (3 Samples), 15 BRE OP50 (3 Samples), 17 BRE OP50 (3 Samples)

first: Danyang

first: Shanshan

last: Yu

first: Chenxi

last: Lin


title: RNA-seq of mouse tissue samples from animal model: Effects of MMP9 on gene expression.

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

summary: In the present study, RNA-seq technique were performed to explore biological significance of MMP9 in the neuro-cutaneous signaling network of chronic itch. We performed high-throughput sequencing of mouse cheek tissue samples from MMP9 animal models (the MMP9 protein or its vehicle was injected into the right cheek of mice).

overall_design: Mouse cheek tissue were from MMP9 model mice.The gene expression of these cells were investigated utilizing DNBSeq platform.

first: Ruizhen

first: Jianghui

last: Meng


title: Co-option of CENP-A for activity-induced neuronal plasticity

city: Zürich

first: Ana

last: Stankovic

address: Winterthurerstrasse 190

department: Brain research institute

institute: University of Zurich

summary: We report that CENP-A plays a pivotal role in neuronal activation and subsequent memory formation in rodent hippocampus. More specifically, we find that CENP-A containing chromatin controls expression of Immediate Early Genes (IEGs); a set of transcriptional factors crucial for neuronal firing, long-term potentiation and memory formation. Downregulation of CENP-A impairs IEGs expression and causes memory defects. Furthermore, we show that this behavior of CENP-A is evolutionary conserved between rodents and humans, whereby human forebrain organoids display a similar dependency on CENP-A expression for neuronal activation. Therefore, we attribute a novel, mitotic-independent role to CENP-A in hippocampal neurons, thus providing direct evidence that a distinct chromatin state is a necessary requirement for memory formation. CENP-A Chip seq on dissected hippocampi from C57BL/6 mice. Paired experiement includes 4 mice per condition, total of 3 replicate experiments. Each experiment contains control group (Untreated) and PTZ-treated group.

overall_design: Dentate gyri from C57BL/6 wild-type mice were microdissected and processed for nuclei isolation. Isolated nuclei were subjected to micrococcal nuclease digestion to generate chromatin fragments, followed by chromatin immunoprecipitation using an anti–CENP-A antibody. Immunoprecipitated and input DNA were purified, prepared into sequencing libraries, and analyzed by paired-end high-throughput sequencing. Experiments were performed with three independent biological replicates per condition.

first: Izaskun

last: Mallona

first: Vladyslav

last: Korobeynyk

first: Sebastian

last: Jessberger


title: Single-cell RNA sequencing of PBMCs from convalescent COVID-19 patients compared to healthy controls

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: WI

address: 8727 W Watertown Plank Road

institute: Versiti Blood Research Institute

summary: We compared the immune response to COVID-19 in symptomatic and asymptomatic patients when compared to healthy controls after recovery from infection. We observed active interferon signaling in symptomatic patients even after recovery.

overall_design: We performed single-cell RNA sequencing on PBMCs from healthy persons as well as recovered symptomatic and asymptomatic COVID-19 patients.

first: Poojitha

last: Sitaram


title: Transcriptomic profiling of PBMCs from healthy persons and persons recovered from COVID-19 infection by bulk RNA-seq

overall_design: We performed bulk RNA sequencing on PBMCs from healthy persons (n=2) as well as recovered symptomatic (n=2) and asymptomatic (n=2) COVID-19 patients.


title: Single-cell RNA-seq of out-of-thaw bone marrow-derived mesenchymal stromal cells (BM-MSCs)

status: Public on Jul 14 2026

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

summary: Human mesenchymal stromal cells (MSCs) used in cell therapy are frequently administered directly out of thaw, yet the single-cell transcriptomic landscape of out-of-thaw MSC products is poorly defined. Here, cryopreserved bone marrow-derived MSCs from six healthy donors (seven lots) were characterized immediately after thawing using droplet-based single-cell RNA-sequencing on the Illumina-Bio-Rad ddSEQ platform. After SureCell-based UMI counting and knee filtering, profiles were analyzed with SC3 and Seurat. Donor-level clusters were identified that differ in immune-signaling, cell-surface, cell-cycle and metabolic gene programs, with low within-sample heterogeneity; cell-cycle status emerged as a major axis of inter-donor variation. Only the bone marrow samples are included in this submission.

overall_design: Droplet-based single-cell RNA-sequencing (Illumina-Bio-Rad ddSEQ) of out-of-thaw human bone marrow-derived MSCs from six donors (seven samples: BM1, BM2a, BM2b, BM3, BM4, BM5, BM6; BM2a and BM2b are the same donor expanded in two laboratories). Samples were sequenced in three batches.

first: Camila

last: Medrano-Trochez

first: Paramita

last: Chatterjee

first: Pallab

last: Pradhan

first: Hazel

middle: Y

last: Stevens

first: Molly

last: Ogle

first: Edward

last: Botchwey

first: Joanne

last: Kurtzberg

first: Carolyn

last: Yeago

first: Greg

last: Gibson


title: Isogenic Human Stem Cell Models Reveal Mutation-Dependent Protective Mechanisms of APOE3 Christchurch

city: Tempe

first: David

last: Brafman

state: Arizona

address: ECG RM346/ISTB4

department: SBHSE

institute: Arizona State University

summary: The rare APOE3 Christchurch (APOE3ch) variant has been linked to exceptional resilience against Alzheimer’s disease (AD), yet its protective mechanisms remain unclear. Here, we examined how APOE3ch modulates AD-related phenotypes across distinct autosomal-dominant AD mutations using isogenic human induced pluripotent stem cell (hiPSC)–derived neural cultures. Using prime editing, we introduced APOE3ch into hiPSC lines carrying PSEN1 E280A or APP duplication (APPdp) mutations and differentiated them into neuron–astrocyte cultures. APOE3ch did not affect neural differentiation or APOE secretion but produced mutation-dependent effects on disease-relevant pathways. In APPdp cultures, APOE3ch reduced amyloidogenic APP processing, Aβ40/42 production, and tau phosphorylation. In contrast, PSEN1 E280A cultures showed enhanced non-amyloidogenic processing and extensive transcriptional remodeling without reduced Aβ. Transcriptomic analyses revealed convergent activation of Wnt and cadherin signaling across both genetic backgrounds, alongside mutation-specific pathway changes. Together, these findings establish APOE3ch as a context-dependent modifier of AD pathology.

overall_design: RNA-seq profiling of hiPSC derrived neural cultures for isogenic lines of WT, APOEch mutation, and APOEch mutation with PSEN1 E280A or APP duplication mutations.

first: Carlye

last: Frisch

first: Gayathri

last: Srinivasan

first: Lauren

last: Baker

first: Morgan

last: Pedroza

first: Brooke

last: Galyon


title: Shared PRAME epitopes are T-Cell Targets in NUT Carcinoma

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

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

institute: University of North Carolina at Chapel Hill

summary: NUT carcinoma is a rare but highly lethal solid tumor without an effective standard of care. NUT carcinoma is caused by bromodomain-containing NUTM1 fusion oncogenes, most commonly BRD4::NUTM1. BRD4::NUTM1 recruits p300 to acetylate H3K27 forming expansive stretches of hyperacetylated chromatin called “megadomains” with the overexpression of corresponding oncogenes, including MYC. We hypothesized that transcriptional dysregulation caused by BRD4::NUTM1 would lead to the generation of cancer-specific antigens that could be therapeutically actionable. We integrated genomics, computational antigen prediction software, targeted immunopeptidomics using single- and double-labeled peptide standards, and gain/loss-of-function genetic experiments on a panel of cell lines (N=5), a patient derived xenograft, a tissue microarray (N=77), and patient samples from the Tempus AI Sequencing Database harboring evidence of NUTM1 fusions (N=165). We identified PRAME as the most commonly expressed cancer/testis antigen in patient samples harboring the three canonical NUT carcinoma fusions (BRD4::NUTM1, BRD3::NUTM1, and NSD3::NUTM1). Additionally, 56% (43/77) of NUT carcinoma tissue microarray samples stained positive for PRAME. BRD4::NUTM1 expression in HEK 293T cells enhanced PRAME levels and BRD4::NUTM1 knockout in NUT carcinoma cells reduced PRAME levels. Immunopeptidomics detected more PRAME-derived HLA ligands (N=9) than all other cancer/testis antigens combined (N=5). Targeted mass spectrometry detected the HLA-A*02:01/SLLQHLIGL (PRAME425) epitope in 100% (4/4) of HLA-A*02+, PRAME+ NUT carcinoma samples at higher levels (>0.01 fM) than HLA-A*02:01/RLDQLLRHV (PRAME312) or HLA-A*02:01/YLHARLREL (PRAME462). The anti-PRAME425 T-cell receptor x SP34 anti-CD3 bispecific molecule and  anti-PRAME425 TCR T-cells each exhibited potent, T-cell mediated cytotoxicity against PRAME+ NUT carcinoma cells. PRAME is highly and frequently expressed in NUT carcinoma and the most common oncoprotein causing NUT carcinoma, BRD4::NUTM1, contributes to these high PRAME levels. PRAME epitopes presented by HLA Class I are a previously unrecognized therapeutic vulnerability for NUT carcinoma that warrant clinical trials testing PRAME targeted immunotherapies in this neglected patient population.

overall_design:
To investigate BRD4::NUTM1 driven cancer testes antigen gene expression, we completed bulk RNA sequencing in established NUT carcinoma cell lines as well as long-read RNA and DNA sequencing
***Raw data is not provided as the informed consent does not include language permitting submission to national repositories.***

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

first: Benjamin

last: Vincent

first: Alex

last: Rubinsteyn

first: Jared

last: Weiss

first: Sara

last: Peterson

first: Jeffrey

middle: L

last: Jensen


title: Effect of VEGF on miRNA profile in miR-1 overexpressing HUVECs for isomiR analysis study

city: New Haven

first: Asawari

last: Korde

state: CT

address: 300 Cedar street, TAC S440, PO Box 208057

department: Internal Medicine, PCCSM section

institute: Yale University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: MiRNAs are generated through a finely tuned multi-step process that includes precise cropping and cleavage of their precursors. The mature miRNA is then loaded onto an argonaute (Ago) protein to form an RNA-induced silencing complex (RISC) and target messenger RNAs.  Most of the mechanisms of miRNA regulation target one of the steps in the biogenesis. However, through analysis of miR-1 precursors, we demonstrate that VEGF stimulation induces degradation (decay) of mature miR-1-3p without affecting its precursors. This analysis also identified a specific miRNA 3’-adenylation pathway that targets the guide strand after RISC loading. In this study we detected miRNA sequences which are modified at their 3' end.

overall_design: We transduced HUVECs with a miR-1 overexpression vector before treating the cells with VEGF or vehicle control (PBS/no VEGF). Transduced cells (3 per group) were treated with VEGF (10ng/ml) or vehicle control for 24 hours before RNA extraction. Total RNA (1ug/sample) were sent for miRNA sequencing.

first: Giovanni

last: Nigita

first: Shervin

last: Takyar


title: 吡咯喹啉醌改善了自然衰老小鼠与增强线粒体生物能量相关的认知相关行为表现

first: di

last: deng

address: No. 11, Beisanhuan East Road, Chaoyang District, Beijing

institute: Beijing University of Chinese Medicine

summary: We investigated whether pyrroloquinoline quinone (PQQ) could improve cognitive performance in twenty-month-old naturally aged mice and explored the potential mechanisms involved. Results showed that PQQ supplementation improved spatial working memory and recognition memory without inducing anxiety-like behavior, and was associated with better preservation of hippocampal neuronal integrity. In HT-22 hippocampal neuronal cells, PQQ reduced reactive oxygen species (ROS) accumulation, restored mitochondrial membrane potential, and enhanced mitochondrial respiratory capacity. Hippocampal transcriptomic analysis and upstream regulator prediction identified SIRT1 as a major regulator associated with the PQQ-induced transcriptional response, while uncoupling protein 2 (UCP2) emerged as a candidate downstream mitochondrial effector. Consistently, PQQ increased hippocampal SIRT1 protein expression and downregulated UCP2 at both mRNA and protein levels. Pharmacological inhibition of SIRT1 attenuated the PQQ-induced increase in ATP production and partially weakened the regulatory effect of PQQ on UCP2, supporting the involvement of SIRT1 in PQQ-associated mitochondrial bioenergetic regulation. Collectively, these findings indicate that PQQ improves cognitive-related behavioral performance in naturally aged mice and is associated with mitochondrial bioenergetic regulation, and suggest that modulation of a SIRT1–UCP2-associated pathway may contribute to its neuroprotective effects.

overall_design: The animal experimental procedures involved in this study have been approved by the Ethics Committee for Animal Experimentation of Beijing University of Chinese Medicine (Approval No.BUCM-2024032503-1181). Twenty-month-old male C57BL/6J mice were purchased from Hangzhou Ziyuan Laboratory Animal Technology Co., Ltd. (license number: SCXK [Zhe] 2024-0004) and housed in the SPF animal facility of Beijing University of Chinese Medicine under stable environmental conditions (temperature, 20-24 °C; humidity, 40-70%; 12 h light/dark cycle). A total of eighteen mice were randomly assigned to three groups (n = 6 per group): control (0.2 mL normal saline, CON), low-dose PQQ (5 mg/kg/day in 0.2 mL normal saline, PQQ-L), and high-dose PQQ (10 mg/kg/day in 0.2 mL normal saline, PQQ-H). The intervention lasted 14 days with oral gavage.

first: 云

last: 燕

first: 迪

last: 鄧

first: 春霞

last: 棕褐色


title: Cannabidiol reverses microglial exhaustion in aged Gulf War Illness mice

city: Irvine

first: Kwang-Mook

last: Jung

address: 3105 Gillespie NRF

department: Anatomy&Neurobiology

institute: University of California, Irvine

summary: Gulf War Illness (GWI) affects up to one-third of 1990–1991 Gulf War veterans and is associated with chronic low-grade neuroinflammation, yet its cellular substrates remain unclear and targeted pharmacological therapies are still limited. By using bulk RNA-seq analyses of FACS-purified microglia in an established GWI mouse model, we uncovered a multi-lineage primed neuroimmune signature in aged GWI mice. Systemic lipopolysaccharide (LPS) elicited an amplified pro-inflammatory response in the brains of GWI mice compared to age-matched controls, yet paradoxically, microglia were transcriptionally hyporesponsive to LPS, with inverted antigen presentation module score indicative of a microglial exhaustion phenotype. Chronic cannabidiol (CBD) attenuated neuroimmune priming at baseline, reshaping microglial translational and energetic states. Under immune-stimulated conditions, CBD partially restored GWI-associated deficits in microglial antigen presentation and oxidative phosphorylation, defining a therapeutic axis amenable to pharmacological intervention.

overall_design: Male C57BL/6J mice (10‑week‑old) were exposed to Gulf War chemicals by intraperitoneal injection of 0.7 mg/kg pyridostigmine bromide and 200 mg/kg permethrin, or vehicle, once daily for 10 days. Following exposure, animals were aged to 17.5 months and assigned to a 2 × 2 × 3 factorial design: Ctrl-Veh-PBS, Ctrl-Veh-LPS, GW-Veh-PBS, GW-Veh-LPS, GW-CBD-PBS, GW-CBD-LPS (n = 3–4 per condition). CBD-arm animals received daily i.p. administration of CBD (30 mg/kg in 5% Tween 80/PBS) for 28 consecutive days, followed by maintenance dosing once every 2 days for an additional 2 weeks; vehicle-arm animals received an equal volume of vehicle. On the morning after the final dose, LPS-arm mice received a single intraperitoneal injection of 0.33 mg/kg LPS from Escherichia coli; PBS mice received an equal volume of sterile PBS. After 24 hours, mice were anesthetized with isoflurane, and the brains were quickly isolated and were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec). Myelin was removed, and microglia were purified by flow cytometry cell sorting (FACS) as live CD45mid /CD11b⁺/CD11a⁻ cells. Total RNA was extracted from the microglia using a Trizol/RNeasy hybrid method. RNA sequencing was conducted at Novogene (Bejing, People’s Republic of China) using the Illumina NovaSeq platform with paired-end 150 bp (PE 150) sequencing strategy. Poly(A)-enriched stranded libraries were prepared and sequenced, and reads were aligned to GRCm38/mm10 to produce gene-level counts.

first: Hye-Lim

last: Lee

first: Daniele

last: Piomelli


title: Cannabidiol reverses neuroimmune priming in aged Gulf War Illness mice

summary: Gulf War Illness (GWI) affects up to one-third of 1990–1991 Gulf War veterans and is associated with chronic low-grade neuroinflammation, yet its cellular substrates remain unclear and targeted pharmacological therapies are still limited. By using bulk RNA-seq analyses of whole-brain in an established GWI mouse model, we uncovered a multi-lineage primed neuroimmune signature in aged GWI mice. Systemic lipopolysaccharide (LPS) elicited an amplified pro-inflammatory response in the brains of GWI mice compared to age-matched controls. Chronic cannabidiol (CBD) attenuated neuroimmune priming at baseline, and suppressed the parenchymal hyper-response, defining a therapeutic axis amenable to pharmacological intervention.

overall_design: Male C57BL/6J mice (10‑week‑old) were exposed to Gulf War chemicals by intraperitoneal injection of 0.7 mg/kg pyridostigmine bromide and 200 mg/kg permethrin, or vehicle, once daily for 10 days. Following exposure, animals were aged to 17.5 months and assigned to a 2 × 2 × 3 factorial design: CtrlVeh, CtrlVehLPS, GWVeh, GWVehLPS, GWCBD30, GWCBD30LPS (n = 3–4 per condition). CBD-arm animals received daily i.p. administration of CBD (30 mg/kg in 5% Tween 80/PBS) for 28 consecutive days, followed by maintenance dosing once every 2 days for an additional 2 weeks; vehicle-arm animals received an equal volume of vehicle. On the morning after the final dose, LPS-arm mice received a single intraperitoneal injection of 0.33 mg/kg LPS from Escherichia coli; vehicle control mice received an equal volume of sterile PBS. After 24 hours, mice were anesthetized with isoflurane, and the brains were removed. Total RNA was extracted from the whole brain using a Trizol/RNeasy hybrid method. Total RNA was extracted. RNA sequencing was conducted at Novogene (Bejing, People’s Republic of China) using the Illumina NovaSeq platform with paired-end 150 bp (PE 150) sequencing strategy. Poly(A)-enriched stranded libraries were prepared and sequenced, and reads were aligned to GRCm38/mm10 to produce gene-level counts.


title: Dissection of Poly(A)-binding protein (PABPC) cellular function using degron-mediated depletion with replacement

city: Cambridge

first: Ryan

middle: Yue

last: Muller

state: Massachusetts

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

summary: Cytoplasmic poly(A)-binding proteins (PABPCs) are essential and highly abundant regulators of mRNA stability and translation, but their cellular functions have been difficult to dissect due to slow turnover and the lethality observed upon loss of both major paralogs, PABPC1 and PABPC4. To enable structure–function analysis of PABPC in human cells, we developed a protein-replacement platform that couples rapid auxin-inducible degradation of endogenous PABPC1 and PABPC4 with doxycycline-controlled expression of engineered PABPC variants. This approach enables acute removal of native PABPC and real-time assessment of how specific domains, paralogs, and sequence alterations support cellular fitness, shape transcriptome profiles, and regulate poly(A)-tail length. Using this system, we show that the RRM4 domain of PABPC1 is essential for growth, whereas post-translationally modified lysines within RRM4 are individually dispensable. Paralogs and variants with heterologous RRM4 domains vary in their ability to substitute for PABPC1, revealing functional divergence among PABPCs. Transcriptome profiling identifies variant-specific regulatory signatures, and dose-controlled rescue further delineates the relationship between PABPC variant abundance and global poly(A) tail lengths in vivo. Together, this platform provides a generalizable strategy for dissecting PABPC biology in the cellular context using rationally designed variants.

overall_design: RNA-seq profiling following replacement of endogenous PABPC1 and PABPC4 protein with transgenically-expressed PABPC variants. HCT116 polyclonal cell lines were constructed with endogenous mAID degron tags on PABPC1 and PABPC4 and multi-copy transposon-mediated integration of PABPC variant expression constructs. PABPC replacement was induced with 1μg/mL doxycycline and 0.5 mM indole-3-acetic acid (IAA) for 25 days if the PABPC replacement variant rescued growth or 48 hours if the replacement variant did not rescue growth.

first: Kiara

middle: X

last: Wang

first: David

last: Bartel


title: Neuroimmune priming and microglial exhaustion in aged Gulf War Illness mice

summary: Gulf War Illness (GWI) affects up to one-third of 1990–1991 Gulf War veterans and is associated with chronic low-grade neuroinflammation, yet its cellular substrates remain unclear and targeted pharmacological therapies are still limited. By using hippocampal single-nucleus RNA sequencing (snRNA-seq) in an established GWI mouse model, we uncovered a multi-lineage primed neuroimmune signature in aged GWI mice.

overall_design: Male C57BL/6J mice (10‑week‑old) were exposed to Gulf War chemicals by intraperitoneal injection of 0.7 mg/kg pyridostigmine bromide and 200 mg/kg permethrin, or vehicle, once daily for 10 days. Following exposure, animals were aged to 19 months, anesthetized with isoflurane, killed by decapitation, and brains were removed. For each condition (Control, GWI), hippocampi from three mice (three biological replicates) were dissected, pooled, and rapidly frozen; pooled hippocampi per condition were processed as a single nuclei suspension, yielding one 10x Genomics single‑nucleus RNA‑sequencing library per group from three biological replicates.