title: Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street, HITS 5001

institute: Indiana University School of Medicine

summary: Alcohol use disorder (AUD) induces complex transcriptional and regulatory changes across multiple brain regions including the caudate nucleus, which remains understudied. Using paired single-nucleus RNA-seq and ATAC-seq on caudate samples from 143 human postmortem brains, including 74 with AUD, we identified 17 distinct cell types. A significant portion of the alcohol-related differences in gene expression were accompanied by a corresponding difference in chromatin accessibility within the gene. We found novel transcriptional differences in medium spiny neurons that impact RNA metabolism and immune response pathways. A small cluster of D1/D2 hybrid neurons showed AUD-induced differences distinct from the D1 and D2 types, suggesting a unique role in AUD. Those with AUD had a higher proportion of microglia in an inflammatory state; astrocytes entered a reactive state partially regulated by JUND. Oligodendrocyte dysregulation was driven in part by OLIG2 activity and increased TGF-β1 signaling from microglia and astrocytes. We also observed increased microglia-astrocyte communication via the IL-1β pathway. These findings provide valuable insights into the genetic and cellular mechanisms in the caudate related to AUD. They also demonstrate the broader utility of large-scale multiomic studies in uncovering complex gene regulation across diverse cell types, which has implications beyond the substance use field.

overall_design: Single-nucleus RNA-seq and single-nucleus multiome (RNA+ATAC-seq) data from caudate tissue of human post-mortem brains, with and without alcohol use disorder. Multiple samples were pooled for sequencing, which were demultiplexed following sequence alignment, and each barcode in the pools were assigned to a sample. Raw data (bam) files include demultiplexed (sample-level) mapped snRNA-seq and snRNA-seq+snATAC-seq sequencing reads. Multiple files per sample indicate that the sample was sequenced multiple times. Processed data (.rds files) consist of Seurat objects for each sequencing pool (one for the RNA-seq assay, and one for the multiome assay), containing read counts for each cell and sample-level metadata. AUD-associated differences in gene expression and chromatin accessibility were investigated by comparing the RNA and ATAC data from individuals with AUD to those without.

first: Nick

last: Green

first: Hongyu

last: Gao

first: Xiaona

last: Chu

first: Quiyue

last: Yuan

first: Patrick

last: McGuire

first: Dongbing

last: Lai

first: Guanglong

last: Jiang

first: Xiaoling

last: Xuei

first: Jill

last: Reiter

first: Julia

last: Stevens

first: Greg

last: Sutherland

first: Alison

last: Goate

first: Zhiping

last: Pang

first: Paul

last: Slesinger

first: Ronald

last: Hart

first: Jay

last: Tischfield

first: Yue

last: Want

first: Zhana

last: Duren

first: Howard

middle: J

last: Edenberg


title: Mammary gland metabolism and its relevance to the fetoplacental expression of cytokine signaling in Caveolin-1 null mice

status: Public on Aug 04 2025

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

country: USA

institute: University of Missouri

type: Expression profiling by high throughput sequencing

summary: Mice lacking Caveolin-1 (Cav1), a major protein of the lipid raft of plasma membrane, show deregulated cellular proliferation of mammary gland and an abnormal fetoplacental communication during pregnancy. This study leverages multi-omics approach to test the hypothesis that the absence of Cav1 elicits a coordinated crosstalk of genes among the mammary gland, placenta and fetal brain in pregnant mice. Integrative analysis of metabolomics and transcriptomics data of mammary glands showed that the loss of Cav1 significantly impacted specific metabolites and metabolic pathways in the pregnant mice. Next, gene expression changes of the deregulated metabolic pathways of the mammary gland were compared with the gene expression changes of the placenta and fetus. The analysis showed that genes associated with specific metabolic and signaling pathways changed in a coordinated manner in the placenta, mammary gland and fetal brain in Cav1-null mice. The cytokine signaling pathway emerged as a key player of the molecular crosstalk among these tissues. By interrogating the single-nuclei gene expression data of placenta and fetal brain previously generated from Cav1-null mice, the study further revealed that these metabolic and signaling genes were differentially regulated in specific cell types of the placenta and fetal brain. Though a causal effect of mammary gland on the placenta and/or fetal brain can’t be inferred from this study, the findings show that the mammary gland, placenta and fetal brain show a coordinated molecular crosstalk in response to the absence of Cav1 in mice.

overall_design: Total RNA from mammary gland (in triplicates) from day-15 pregnant B6.Cg-Cav1tm1Mls/J (Cav1-null) and control (C57BL/6J) mice were used for RNA-seq. Placentae (in triplicates) of day-15 pregnant B6.Cg-Cav1tm1Mls/J (Cav1-null) were also included in the RNA-seq.

first: Shankar

middle: P

last: Poudel

first: Maliha

last: Islam

first: Erin

middle: M

last: Shangraw

first: Thomas

middle: B

last: McFadden

first: Susanta

middle: K

last: Behura


city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

summary: Gliomas are an incurable malignancy of the central nervous system. Patients that present with this disease have poor prognosis, necessitating the development of new therapeutic approaches. Glioblastoma is the most aggressive form of the disease and although lower grade gliomas have an intially better prognosis, they often progress to high grade glioma. Immunotherapy has been successful in other solid malignancies, but has not demonstrated efficacy in gliomas. Isocitrate dehydrogenase (IDH) is mutated in the majority of lower grade gliomas, and differences in the microenvironment between IDHmut and IDHwt disease contribute to differences in antitumor immunity. However, it remains unknown whether there are similiarites or differences between the immune landscape of IDHmut versus IDHwt gliomas. To address this question, we generated single-cell RNAseq data from 19 patients with grade II-IV glioma, of which 13 were IDHwt and 6 were IDHmut.

overall_design: Single-cell RNAseq analysis of peripheral blood and tumor infiltration immune cells in glioblastoma patients

middle: R

first: Nduka

last: Amankulor


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vivo RNA-Seq)

status: Public on Aug 03 2025

city: Beijing

first: Zexian (Davis)

last: Zeng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

summary: Despite the importance of tumor-associated macrophages (TAMs) in modulating anti-tumor immunity, the molecular determinants of their functional phenotypes remain elusive. Through a large-scale CRISPR screen, we discovered that tumor-derived lactic acid, PGE2, and GM-CSF collaboratively shape the highly conserved but mutually exclusive TAM phenotypes: MHC-II+ and angiogenic TAMs. Mechanistically, the dichotomous nature of these two phenotypes is driven by the antagonistic interactions between lactic acid/PGE2 and GM-CSF. Lactic acid and PGE2 coordinately induce the angiogenic gene program while suppressing the GM-CSF-induced MHC-II program at chromatin level. This mechanism leads to distinct spatial distribution of TAMs, with angiogenic TAMs in lactate-rich hypoxic regions and MHC-II+ TAMs outside these areas. Furthermore, in vivo genetic perturbation of TAMs showed that shifting TAMs to an interferon responsive program, triggered by Adar inactivation, substantially potentiates anti-tumor immunity. Our findings suggest a conserved mechanism of TAM polarization and a potential approach for reprogramming TAMs in immunotherapy.

overall_design: To explore the transcriptional profiles of pro-angiogenic and MHC-II TAMs in vivo, we sorted monocytes/neutrophils(DAPI-CD45+CD11b+Ly6C/G+), pro-angiogenic TAMs(DAPI-CD45+CD11b+Ly6C/G-CX3CR1-MHC-II-) and MHC-II(DAPI-CD45+CD11b+Ly6C/G-CX3CR1+MHC-II+) from 4T1 subcutaneous tumor model and followed by low-input RNA-seq library construction and sequencing.

first: Youxue

last: Lu

first: Ce

last: Luo

first: Lanxiang

last: Huang

first: Genyi

last: Wu

first: Lihan

last: Zhong

first: Jieyu

last: Chu

first: Fubin

last: Wang

first: Zexian

first: Deng

last: Pan


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vitro ATAC-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To explore the mechanism of lactic acid, PGE2 and GM-CSF in shaping TAM polarization, we performed ATAC-seq in BMDMs treated by 25mM lactic acid,100nM PGE2 or 2ng/mL GM-CSF alone and different combinational treatements of these molecules.


title: Controlling nephron precursor differentiation to generate proximal-biased kidney organoids with emerging maturity [scRNA-Seq]

city: Los Angeles

first: Nils

last: Lindström

state: CA

address: 1425 San Pablo Street Lab 409

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California (USC) -

summary: The kidney maintains fluid homeostasis by reabsorbing essential compounds and excreting waste. Proximal tubule cells, crucial for reabsorbing sugars, ions, and amino acids, are highly susceptible to injury, often leading to pathologies necessitating dialysis or transplants. Human pluripotent stem cell-derived kidney organoids offer a platform to model renal development, function, and disease, but proximal nephron differentiation and maturation in these structures is incomplete. Here, we drive proximal tubule development in pluripotent stem cell-derived kidney organoids by mimicking in vivo proximal differentiation. Transient PI3K inhibition during early nephrogenesis activates Notch signaling, shifting nephron axial differentiation towards epithelial and proximal precursor states that mature to proximal convoluted tubule cells broadly expressing physiology-imparting solute carriers including organic cation and organic anion family members. The “proximal-biased” organoids thus acquire function, and on exposure to nephrotoxic injury, display tubular collapse and DNA damage, and upregulate injury response markers HAVCR1/KIM1 and SOX9 while downregulating proximal transcription factor HNF4A. Here, we show that proximally biased human-derived kidney organoids provide a robust model to study nephron development, injury responses, and a platform for therapeutic discovery.

overall_design: Single-cell RNA-sequencing data from control and proximal-biased (treated with 10 uM Ly29 for 48 hours from differentiation days 10 to 12) kidney organoids. Single-cell data are from differentiation days 10 (untreated), 12, 14, and 18. Days 12, 14, and 18 include both control and proximal-biased cells. The supplementary file "sample_alignment.txt" is necessary to demultiplex the fastq files for the sublibraries (numbered 2 through 8) and properly separate individual samples. Raw data were aligned to hg38, annotation Ensembl 105, using splitpipe (Parse Biosciences), and these processed scRNA-seq data used in Figure S4 (all cells, nephrogenic and insterstitial) are provided as an .rds file.

first: Jack

last: Schnell


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vitro human macrophage RNA-Seq)

summary: Despite the pivotal role of tumor-associated macrophages (TAMs) in modulating anti-tumor immunity, the conserved patterns and molecular determinates for the formation of diverse TAM subsets remain largely elusive. In this study, we uncovered the exclusive distribution of pro-angiogenic and MHC-II programs of TAMs are well-conserved, and identified key genes and pathways required for macrophage polarization by tumor cells by CRISPR screen. Notably, we demonstrated that multiple TAM phenotypes were mainly shaped by the synergistic and antagonistic interactions between GM-CSF, PGE2, and lactic acid. We further found the inactivation of Adar, an RNA-editing enzyme, reprograms TAMs into an ISG+ phenotype characterized by the high expression of immune stimulatory genes, thereby enhancing the anti-tumor immune response. Thus, our study illuminates the molecular principles underlying the generation and rewiring of TAM functional phenotypes.

overall_design: To investigate the effects of lactate, PGE2, and GM-CSF on the polarization of human macrophages, we isolated CD14+ monocytes from peripheral blood mononuclear cells (PBMCs) of healthy donors and differentiated them into macrophages. We then examined how these molecules influence human macrophage phenotypes and functions.

first: Lu

last: Youxue

first: Luo

last: Ce

first: Wu

last: Genyi

first: Huang

last: Lanxiang

first: Zhong

last: Lihan

first: Chu

last: Jieyu

first: Wang

last: Fubin

first: Zeng

last: Zexian

first: Pan

last: Deng


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (CROP-Seq, in vivo LGP pool)

first: Zexian (Davis)

last: Zeng

overall_design: To validate the effect of latic acid, PGE2 and GM-CSF in shaping TAM polarization in vivo, we characterize the phenotypes of TAMs pertubred the receptors of lactic acid, PGE2 and GM-CSF via pooled library(LGP pool). The experimental procedure was that we isolated CD117+ hematopoietic stem  cells(HSCs) from Loxp-Stop-Loxp-Cas9, Lyz2-Cre mice and delivered LGP pool into HSCs at MOI<0.3. Library cells were transplantated in lethally irradiated mice. After 6 weeks' reconstituion and LLC tumor inoculation, tumor associated macrophages(DAPI-CD45.2+CD11b+Ly6C-) were isolated for CROP-seq sequencing.

first: Youxue

last: Lu

first: Ce

last: Luo

first: Lanxiang

last: Huang

first: Genyi


title: Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

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

overall_design: Refer to individual Series

first: Jessica

last: St. Laurent

first: Alexander

middle: W

last: Ying


title: Controlling nephron precursor differentiation to generate proximal-biased kidney organoids with emerging maturity [snRNA-Seq]

first: Nils

last: Lindström

overall_design: SnRNA-sequencing was performed on differentiaton day 21 proximal-biased and differentiation day 27 proximal-biased kidney organoids. Proximal-biased kidney organoids are treated from differentiation days 10 to 12 (48 hours) with 10 µM LY294002. Organoids were flash-frozen in liquid nitrogen before nuclei isolation. SnRNA-sequencing libraries were constructed using 10X Genomics Chromium Next GEM Single Cell Multiome Reagents PN-1000283, following 10X Genomics CG000338 Rev E. Raw fastq files were processed using Cell Ranger (v9.0.0) and aligned to the human reference genome (GRCh38-2024-A). Feature-barcode matricies were read into Seurat 5.2 using the Read10X function.

first: Jack

last: Schnell


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vitro RNA-Seq)

overall_design: To explore the trabnscriptional changes of tumor educated macrophages perturbed by our screen hits, comparative gene expression profiling analysis of bulk RNA-seq data for tumor educated macrophages targeted by non-targeting control(sgNC) and sgLamtor1/Flcn/Adar/Ppp2r3c/Rreb1/Hif1a/Ptger4.

last: Wu

first: Lihan

last: Zhong

first: Jieyu

last: Chu

first: Fubin

last: Wang

first: Zexian

first: Deng

last: Pan


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [CROP-Seq, in vitro and in vivo pool]

overall_design: To characterize the whole transcriptional profiles targeted by our CRISPR screen candidates, we extended our tumor educated macrophage(TEM) system to CROP-seq, which is able to pair transcriptiome with sgRNA information. To validate the effect of these hits in vivo, we isolated CD117+ hematopoietic stem  cells(HSCs) from Loxp-Stop-Loxp-Cas9, Lyz2-Cre mice and delivered CROP-seq pool into HSCs at MOI<0.3. Library cells were transplantated in lethally irradiated mice. After 6 weeks' reconstituion and LLC tumor inoculation, tumor associated macrophages(DAPI-CD45.2+CD11b+Ly6C-) were isolated for CROP-seq sequencing.

first: Fubing


title: Controlling nephron precursor differentiation to generate proximal-biased kidney organoids with emerging maturity [bulk RNA-seq]

overall_design: Bulk RNA-sequencing data from control and proximal-biased (treated with 10 uM Ly29 for 48 hours from differentiation days 10 to 12) kidney organoids. Data are from differentiation days 10 (untreated), 12, 14, and 18. Days 12, 14, and 18 include both control and proximal-biased cells. There are n = 3 single organoid replicates for days 10, 12 control, and 12 Ly29-treated, and n = 2 replicates for each control and proximal-biased condition for days 14 and 18. Processed (raw feature counts table) data were aligned to hg38, Ensembl 105 annotation using STAR.


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages


title: A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation [dataset2]

status: Public on Aug 01 2025

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: Various SARS-CoV-2 viruses have caused the COVID-19 pandemic world-wide.  As the viruses evolve different mutations along their genomes, these mutations can impact virus RNA structures and their phenotypes.  Here we probe the RNA structures across Wuhan, alpha, beta, delta and omnicron strains of the SARS-CoV-2 viruses.  We observe that while the mutations impact RNA structures, it is not the main source of RNA structure changes (RBPs?). Structurally conserved structures are enriched for both long and short RNA pair-wise interactions.  We identified a conserved 17kb long range interaction that decreases the virus fitness when mutated. Additionally, this interaction binds to ADAR1 to alter editing levels on the virus. These studies reveal the importance of RNA structures along virus genomes to facilitate virus infectivity.

overall_design: A-to-I editing of WT SARS-CoV-2 in E6 TMPRSS2 Vero cells

first: S

middle: L

last: Yang

first: L

last: DeFalco

first: Y

middle: H

first: J

last: Han

first: CK

last: Mok

last: Zhang

first: H

first: A

last: Merits

first: R

last: Wan


title: HNF1A regulates a β-cell RNA splicing program that is disrupted in type 2 diabetes [ChIP-seq]

city: Barcelona

first: Edgar

last: Bernardo

state: Barcelona

address: C/ del Dr. Aiguader, 88,

country: Spain

institute: CRG

summary: Type 2 diabetes (T2D) is a complex chronic disease that results from pancreatic β-cell dysfunction and insulin resistance. Human genetic evidence supports a pivotal role of HNF1A, encoding hepatocyte nuclear factor 1A, in the pathophysiology of mendelian and type 2 diabetes. Recent single-cell genomic studies also reveal HNF1A as a key transcription factor underlying β-cell heterogeneity and disease progression. We now demonstrate that HNF1A-deficient diabetes is caused by β-cell-autonomous defects, and show that HNF1A governs not only β-cell transcription, but also a broad RNA splicing program. We uncover a regulatory hierarchy in which HNF1A controls transcription of A1CF, which in turn regulates splicing of genes important for membrane transport, lysosome, and secretory functions. Genetic variants that increase human pancreatic islet A1CF expression are associated with improved glycemia, increased insulin secretion, and decreased T2D susceptibility. Furthermore, β-cells from T2D individuals exhibit a profound disruption of A1CF-dependent splicing. These findings link HNF1A-deficiency to a β-cell RNA splicing defect that is impaired in Mendelian diabetes and T2D.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To investigate the role of HNF1A in β-cell functionality we create primary and cell line from mouse origin and human cell line and stem cell derived knock-out models of HNF1A and downstream target A1CF
We performed RNAseq and differential expression and splicing analysis on both mouse and human samples


title: Mapping enhancer-gene regulatory interactions from single-cell data

city: Stanford

first: Jesse

last: Engreitz

address: 450 Serra Mall

department: Genetics

institute: Stanford University

summary: We generated single-cell 10x Multiome data (ATAC-seq and RNA-seq) from various stages of hiPSC differentiation into hepatic progenitor cells. We used this dataset to benchmark the scE2G model and other single-cell enhancer–gene prediction models against a gold-standard CRISPR perturbation dataset.

first: Judhajeet

last: Ray

first: Jacob

last: Huang

first: Glen

last: Munson

first: Evelyn

last: Jagoda

first: Maya

last: Sheth


title: TGF-β1-dependent expression of FOXS1 attenuates adipogenic potential and enhances a myofibroblast cellular phenotype [hASC_RNAseq]

first: Matthew

last: Layne

address: 72 East Concord Street

institute: Boston University

summary: White adipose tissue (WAT) fibrosis is a major determinant of obesity-induced cardiometabolic dysfunction and is characterized by excessive extracellular matrix (ECM) deposition and myofibroblast activation. Transforming growth factor (TGF)-β1 is a profibrotic cytokine that potently induces myofibroblast activation in adipocyte stem cells (ASC). How TGF-β1 orchestrates ASC activation in WAT fibrosis is not completely understood. We identified FOXS1, a member of the forkhead box transcription factor superfamily, as a transcriptional target of TGF-β1 signaling in primary human WAT ASC (hASC). FOXS1 potentiated TGF-β1-dependent upregulation of several myofibroblast genes (e.g. Acta2, Col1a1, Fn1, Il11) in 10T1/2 fibroblasts. FOXS1 also mitigated the induction of several adipogenic factors (e.g. Pparg, Stat5a, Fabp4, Adipoq) in 10T1/2 fibroblasts and sensitized these cells to the anti-adipogenic effects of TGF-β1. Furthermore, loss of endogenous FOXS1 improved adipogenic permissiveness and activated proadipogenic gene programs in 10T1/2 cells, even after TGF-β1 stimulation. These results indicate that FOXS1 is a positive regulator of profibrotic TGF-β1-dependent cellular responses, orchestrating the regulation of molecular phenotypes that promote myofibroblast activation and block adipogenesis. These findings offer novel insight into the TGF-β1-dependent roles of FOXS1 in fibroblasts within the context of profibrotic ASC activation and provide a foundation for further investigation into the role of FOXS1 in WAT fibrosis and obesity-induced cardiometabolic dysfunction.

overall_design: RNA-seq profiling of primary human adipocyte stem cells (hASC) at 12 hours and 72 hours after TGF-β1 stimulation (1 nM)

first: Alexander

last: Tavares

first: Scott

last: Connelly

first: Daryn

last: Maskat

first: Jane

last: Zheng

first: Nabil

last: Rabhi

middle: D


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vivo ATAC-Seq)

first: Zexian (Davis)

last: Zeng

overall_design: To validate the chromatin accessibilities of pro-angiogenic and MHC-II TAMs regulated by lactic acid, PGE2 and GM-SCF in vivo, we sorted pro-angiogenic TAMs(DAPI-CD45+CD11b+Ly6C/G-CX3CR1-MHC-II-) and MHC-II(DAPI-CD45+CD11b+Ly6C/G-CX3CR1+MHC-II+) from MC38 subcutaneous tumor model and followed by ATAC-seq library construction and sequencing.

first: Youxue

last: Lu

first: Ce

last: Luo

first: Genyi

last: Wu

first: Lanxiang

first: Lihan

last: Zhong

first: Jieyu

last: Chu

first: Fubin

last: Wang

first: Zexian

first: Deng

last: Pan


title: Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta [RNA-Seq]

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Malassezia restricta and Staphylococcus epidermidis are dominant members of the human skin microbiome that interact closely, yet the molecular basis of their interaction remains unclear. In this study, we investigated how S. epidermidis-derived acetic acid (AcOH) influences chromatin organization in M. restricta. We generated the first high-resolution three-dimensional genome architecture map of M. restricta using in situ Hi-C and identified putative centromeric regions based on inter-chromosomal contact patterns. Exposure to AcOH, either by co-culture or direct treatment, led to large-scale chromatin decompaction and enhanced centromere clustering. These findings indicate that AcOH acts as an epigenetic modulator, inducing significant reorganization of nuclear architecture in M. restricta. This dataset provides a resource for understanding interkingdom interactions and the epigenetic effects of bacterial metabolites on fungal chromatin structure.

overall_design: This study explores how organic acid exposure and pH changes affect gene expression in M. restricta. RNA-Seq libraries were generated under the following conditions: 1) M. restricta cultured under normal conditions (untreated control), 2) M. restricta treated with HCl to adjust the medium to pH 5.0, 3) M. restricta treated with acetic acid to adjust the medium to pH 5.0. These datasets provide insights into the transcriptional responses of M. restricta to acidic stress by HCl and acetic acid.

first: Jae Min

last: Lee

first: Hyun Oh

last: Yang

first: Hideki

last: Tanizawa

first: Ken-ichi

last: Noma

first: Tae Kwon

first: Won Hee

last: Jung

first: Kyoung-Dong

last: Kim


title: HNF1A regulates a β-cell RNA splicing program that is disrupted in type 2 diabetes [RNA-seq]

first: Edgar

last: Bernardo


title: Differential gene expression in human keratinocytes cultured on different substrate topographies (S1 and S2) for 1h, 4h and 12h.

status: Public on Aug 02 2025

city: London

first: Sebastiaan

last: Zijl

address: 28th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond,

department: Centre for Gene Therapy and Regenerative Medicine,

country: United Kingdom

institute: King’s College London,

summary: Substrate topography has emerged as a novel regulator of cell fate behaviour in keratinocytes (Zijl, Acta Biomater, 2019). Specifically, small circular micropillars (S1) can induce the differentiation of spread cells, and larger triangular substrates (S2) can inhibit differentiation in kerinocytes. Here we investigated the potential molecular mechanisms behind these processes. We chose timepoints previously shown to be associated with differentiation in suspension cultures (Mishra, eLife, 2017), in order to find early regulators of the differentiation process. Our results show a delay in differentiation on S2 substrates and an upregulation of differentiation pathways on S1. Beyond this, no clear mechanistic regulators of the differentiation program were found.

overall_design: Bulk RNA sequencing on S1 and S2 substrates after 1h, 4h and 12h of culture on different substrate topographies.

first: Toru

last: Hiratsuka

first: Atefeh

last: Mobasseri

first: Mirsana

last: Ebrahimkutty

first: Mandy

last: Börmel

first: Sergi

last: Garcia-Manyes

first: Fiona

last: M. Watt


title: HybriSeq: Probe-based Device-free Single-cell RNA Profiling

city: San Francisco

first: Daniel

last: Foyt

address: 1700 4th Street, Floor 3

department: Department of Pharmaceutical Chemistry

institute: University of California San Francisco

summary: We have developed the HybriSeq method for single-cell RNA profiling, which utilizes in situ hybridization of multiple probes for targeted transcripts, followed by split-pool barcoding and sequencing analysis of the probes. We have shown that HybriSeq can achieve high sensitivity for RNA detection with multiple probes and profile entire transcripts without an end bias. The utility of HybriSeq is demonstrated in characterizing cell-to-cell heterogeneities of a panel of 196 genes in peripheral blood mononuclear cells and the detection of missed annotations of transcripts.

overall_design: HEK293, Do-11-10, and CD3/CD28-stimulated PBMC probed with HybriSeq.

first: David

last: Brown

first: Shuqin

last: Zhou

first: Brittany

last: Moser

first: Qin

last: Zhu

first: Zev

last: Gartner

first: Bo

last: Huang


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq]

first: Zexian (Davis)

last: Zeng

overall_design: Examine the transcription profile alterations of bone marrow-derived macrophages caused by tumor conditioned medium challenge and different combinational treatments of lactate, PGE2 and GM-CSF.   Comparative gene expression profiling analysis of RNA-seq data for tumor educated macrophages targeted by sgAdar and non-targeting control(sgNC).

first: Youxue

last: Lu

first: Ce

last: Luo

first: Lanxiang

first: Genyi

last: Wu

first: Lihan

last: Zhong

first: Jieyu

last: Chu

first: Fubing

last: Wang

first: Zexian

first: Deng

last: Pan


title: ER-resident CCDC134 safeguards TLR4 maturation by maintaining gp96 stability

city: Shanghai

first: Yang

last: Bai

address: Yueyang Road No.320

institute: Chinese Academy of Sciences

summary: Toll-like receptor 4 (TLR4), a pattern-recognition receptor located on the plasma membrane, senses extracellular danger signals to initiate inflammatory immune responses. It is initially synthesized in the endoplasmic reticulum (ER), undergoes N-linked glycosylation, and is subsequently transported to the Golgi before ultimately reaching the plasma membrane. However, the mechanisms underlying the processing and maturation of TLR4 in the ER remain elusive. Through whole genome-wide CRISPR screening, CCDC134 was identified as a critical and essential factor for TLR4-dependent inflammatory response. Localization of CCDC134 in the ER lumen rather than its exosome-mediated secretion is required for its role in TLR4 signaling. Loss of CCDC134 results in the retention of TLR4 in the ER for subsequent ER-associated degradation, and thus blockade of TLR4 maturation and plasma membrane trafficking. Defects in TLR4 processing and maturation in the ER in CCDC134-depleted cells are caused by aberrant hyperglycosylation and destabilization of glycoprotein 96 (gp96), a key chaperone of TLR4. These results suggest that CCDC134 controls gp96 glycosylation to facilitate TLR4 maturation in the ER.

overall_design: To test our hypothesis that CCDC134 is required for TLR4 signaling, we performed high-throughput RNA sequencing to analyze the gene expression profiles of WT and CCDC134-deficient iBMDMs treated with or without the TLR4 agonist LPS.

first: Fan

last: Deng

first: Shenglin

last: Mei

first: Judy

last: Lieberman

first: Jingxia

last: Zhao

first: Xing

last: Liu


title: Transcriptomic Profiling of Scleroderma Monocytes Reveals Links with Cardiovascular Complications, Implicating Notch and Interferon Pathways

first: Mehmed

last: Dinc

state: MA

address: One Boston Medical Center Pl

institute: Boston Medical Center

summary: Objectives: Recent research has highlighted the critical role of monocytes and macrophages in driving both inflammatory and fibrotic processes in systemic sclerosis (SSc). This study seeks to elucidate the gene expression profiles of SSc monocytes and their potential links to disease complications, with the ultimate goal of uncovering novel therapeutic targets. Methods: 48 SSc patients and 15 controls were recruited and monocytes were isolated using CD14+ magnetic beads. Total RNA was extracted and bulk RNA-seq analysis was performed. Differential gene expression followed by unsupervised hierarchical clustering and pathway analysis were conducted and correlations with clinical features were analyzed. Interferon signature score (IFN6) was calculated using the log transformed values of 6 genes (IFIT3, IFIT2, MX1, IFIH1, STAT2, and NCF1). Results: We identified four distinct patient subgroups, relative to normal, two with inflammatory and two with non-inflammatory gene profiles. The inflammatory subgroups exhibited high expression of interferon-related genes and included all SSc patients with pulmonary hypertension and most with cardiac involvement. In these patients, IFN6 was markedly elevated and showed a significant correlation with global longitudinal strain - GLS (r=-0.5, p=0.006), a key indicator of cardiac function. Furthermore, pathway analysis identified an enrichment of the Notch signaling pathway among genes whose overexpression correlated with impaired GLS. Conclusion: These findings unveil a potential new mechanistic link between interferon activity, Notch signaling, and cardiac complications in SSc, offering new insights into disease pathogenesis and potential therapeutic targets.

overall_design: Peripheral blood samples were obtained from 48 patients with systemic sclerosis (SSc) who met the 2013 ACR revised classification criteria and 15 healthy controls (HCs). Monocytes were isolated using CD14+ magnetic beads. Total RNA was extracted and bulk RNA-seq analysis was performed. RNA libraries were generated with the  Library Prep Kit (Illumina) and sequenced (paired-end, 2 × 50 bp) on an Illumina NextSeq 2000. Quality control was performed using FastQC; reads were aligned to the hg38 human reference genome with STAR, and gene-level counts were generated using featureCounts. Differential expression was assessed using DESeq2 with age as a covariate. Functional enrichment analysis was performed using clusterProfiler. Unsupervised hierarchical clustering was performed using Euclidean distance and complete linkage, with feature selection using elastic net regularization.

middle: T

first: Fatima

last: El-Adili

first: Justin

last: Lui

first: Kripesh

last: Subedi

first: Michael

last: York

first: Marcin

last: Trojanowski

first: Giovanni

last: Ligresti

first: Robert

last: Lafyatis

first: Maria

last: Trojanowska

first: Andreea

last: Bujor


title: Sipa1 Drives the Inflammatory Signature of Cardiac Fibroblasts and Aggravates Wound Healing Response After Myocardial Infarction

city: Tokyo

first: Seien

last: Ko

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

summary: Signal-induced proliferation-associated gene 1 (Sipa1) is known as a specific Rap1 GTPase-activating protein that negatively regulates Rap1 signaling. Although Sipa1 has been extensively studied in cancer research, its role in the wound healing response after myocardial infarction (MI) remains unexplored. To investigate the role of endogenous Sipa1 in MI, we performed permanent left anterior descending artery ligation in both Sipa1 knockout mice and their control littermates. Bone marrow transplantation, flow cytometry, cell sorting, and transcriptomic analysis were conducted to identify the cellular source of Sipa1 in the infarcted heart. The role of cardiac fibroblast-derived Sipa1 during MI was examined using Sipa1 deletion approaches, specifically in cardiac fibroblasts, in vivo and in vitro. Mice deficient in Sipa1 exhibited improved post-MI survival and cardiac function, along with attenuated expression of inflammatory mediators and diminished accumulation of Ly6Chigh monocytes and CCR2+ macrophages in the infarcted heart. Although Sipa1 was broadly expressed in the heart, cardiac fibroblasts were responsible for the Sipa1-induced deleterious phenotype as demonstrated by cardiac fibroblast-specific Sipa1 conditional knockout mice, which averted excessive inflammation and adverse cardiac remodeling following MI. Mechanistically, Sipa1 promotes the production of CCL2, CCL7 and granulocyte/macrophage colony-stimulating factor in the cardiac fibroblasts early after MI via a non-canonical RasGRP2-Ras-JNK signaling pathway, irrespective of canonical Rap1, thereby facilitating the accumulation and activation of inflammatory monocytes and macrophages. These results identify a previously unknown fibroblast-immune axis characterized by Sipa1, which initiates excessive inflammation and leads to poor outcomes after MI. Targeting Sipa1 offers a potential novel therapeutic strategy to optimize post-MI wound healing response, thereby preventing the development of chronic ischemic heart failure.

overall_design: RNA-seq profiling of cultured cardiac fibroblasts from adult C57BL/6 mice (6 weeks old), transfected with lentivirus containing either scramble or  short hairpin RNA targeting Sipa1 for knockdown, followed by LPS stimulation.

first: Xueyuan

first: Atsushi

last: Anzai


title: Cerebellar Dysfunction in a Mouse Model of Childhood-Onset Manganese-Induced Dystonia Parkinsonism

city: Miami

first: Tomas

last: Guilarte

state: FL

address: 11200 SW 8th Street

department: Environmental Health Sciences

institute: Florida International University

summary: Humans with pathogenic variants in the manganese (Mn) transporter gene SLC39A14 exhibit highly elevated brain Mn concentrations and childhood-onset dystonia-parkinsonism. Here we show that Slc39a14-knockout (KO) mice, a preclinical model of the disease, express deficits in physiological tremor implicating cerebellar (CB) dysfunction in the presence of elevated CB Mn levels. Imaging of intracellular Mn levels using synchrotron-based X-ray fluorescence microscopy revealed highly increased Mn concentrations in Purkinje cells (PCs). We performed RNAseq studies to determine biological pathways altered in the CB of Slc39a14-KO mice relative to wildtype (WT), which revealed an upregulation of pathways and genes responsible for immune response and cell death. To confirm these findings, we performed quantitative autoradiography of the neuroinflammation biomarker Translocator Protein 18kDa (TSPO) which was significantly increased in the CB of Slc39a14-KO mice relative to WT and was further confirmed with Iba-1 positive microglia activation and clustering in the CB cortex. Immunostaining for cleaved caspase-3 (cCASP3), a marker of apoptosis, revealed a widespread increase in cCASP3 immunoreactivity in PCs, which was supported by Hematoxylin and Eosin (H&E) staining demonstrating pyknotic PCs. Lastly, functional electrophysiological assessment of CB neurocircuitry revealed marked decrease in firing rates of cerebellar nuclei (CN) neurons and an increase in variability of PCs simple spikes firing.  These findings show, for the first time, Mn-induced PCs degeneration in the CB of Slc39a14-KO mice and provide a pathological substrate for the dystonia-like movement, balance, and gait abnormalities in SLC39A14 mutation carriers.

overall_design: RNA-seq profiling of gene expression in whole cerebellum of WT and Slc39a14-KO post natal day 60 male mice

first: Alexander

middle: N

last: Rodichkin

first: Amanda

last: Brown

first: Pavani

last: Devabathini

first: Jennifer

last: McGlothan

first: Si

last: Chen

first: Ajith

last: Pattammattel

first: Yong

middle: S

last: Chu

first: Tao

last: Lin

first: Daniel

last: Pontow

first: Karam

last: Abilmouna

first: Ritishka

last: Kapoor

first: Sarah

middle: E

last: Hardin

first: Yulia

last: Pushkar

first: Roy

middle: V

last: Sillitoe

first: Tomás


title: TGF-β1-dependent expression of FOXS1 attenuates adipogenic potential and enhances a myofibroblast cellular phenotype [10T_RNAseq]

first: Matthew

last: Layne

overall_design: RNA-seq profiling of wildtype (WT) or FOXS1 knockout (KO) C3H10T1/2 cells stimulated with TGF-β1 (1 nM) for 12 hours then stimulated with adipogenic differentiation media (DMII) for 48 hours.

last: Tavares

first: Scott

last: Connelly

first: Daryn

last: Maskat

first: Jane

last: Zheng

first: Nabil

last: Rabhi


title: Single cell astrocyte sequencing

city: New York

first: Elisa

last: Konofagou

state: NY

department: Biomedical Engineering

institute: Columbia University

summary: Male and female were isolated from 10 week old WT mice after exposure to Focused Ultrasound Blood-Brain Barrier opening or from the naïve sham gorup.

overall_design: Male and female astrocytes underwent focused ultrasound-induced blood-brain barrier opening either 2, 4 or 7 days prior to sacrifice for FACS and scRNA sequencing preparation.  A naïve sham group was also included.

first: Rebecca

last: Noel

first: Alina

last: Kline-Schoder


title: Complex interaction of tumor-derived factors instructs the spatially distinct phenotypes of tumor-associated macrophages [scRNA-Seq]

first: Zexian (Davis)

last: Zeng

overall_design: To investigate how ISG15+ tumor-associated macrophages(TAM)-based on Adar knockout affect the whole tumor microenvironment, we isolated CD117+ hematopoietic stem  cells(HSCs) from Loxp-Stop-Loxp-Cas9, Lyz2-Cre mice and generated control(sgNon-targeting control) and Adar myeloid specific conditonal knockout mice(mKO) by HSC recosntituion in lethally irradiated mice. Total tumor infiltrating immune cells(DAPI-CD45+) were isolated by Fluorescence-activated cell sorting(FACS) from Control and Adar mKO mice.

first: Youxue

last: Lu

first: Ce

last: Luo

first: Lanxiang

last: Huang

first: Genyi

last: Wu

first: Lihan

last: Zhong

first: Jieyu

last: Chu

first: Fubing

last: Wang

first: Zexian

first: Deng

last: Pan


title: Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages

overall_design: Refer to individual Series


title: Generation of modified cattle and sheep from spermatid-like haploid stem cells

city: Hohhot

first: Lei

last: Yang

state: Inner Mongolia Autonomous Region

address: 24 Zhaojun Rd.

department: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock

institute: Inner Mongolia University

type: Methylation profiling by high throughput sequencing

sample_organism:
Bos taurus
Ovis aries

platform_organism:
Bos taurus
Ovis aries


title: Age-impaired remyelination is associated with dysregulated microglial transitions.

city: Edmonton

first: Jason

middle: R.

last: Plemel

state: Alberta

address: 5-64 Heritage Medical Research Centre

department: Department of Medicine

country: Canada

institute: University of Alberta

summary: Multiple sclerosis (MS) is a chronic, inflammatory condition characterized by demyelination and neurodegeneration. Regeneration of lost myelin, or remyelination, occurs in people with MS but is prone to failure and impaired with age. Remyelination is facilitated by microglia but our understanding of the microglial response during remyelination is incomplete. Here, we profiled the microglial response in the lysolecithin mouse model of remyelination using single-cell RNA sequencing. We found several distinct microglial states during the early stages of remyelination that coalesced into a resolved microglial state defined by myelin transcripts. This resolved state was also present in MS brains. As remyelination becomes inefficient with age, we profiled microglia from both young and middle-aged mice during remyelination and found a delay in several microglial states, in concordance with delayed remyelination. Overall, microglia synchronously initiate a multi-faceted response during efficient remyelination in young mice, which becomes dysregulated with age.

overall_design: Live (Zombie Aqua negative), nucleated (DRAQ5 positive) myeloid (F4/80 positive) cells were isolated using Fluorescence-activated cell sorting, processed on the 10x chromium controller following the 10x Genomics Next GEM Single Cell 3’ GEM, library, and Gel Bead kit v3.1 and sequenced on the Illumina HiSeq P150 sequencer at Novogene corporation inc. Each sample contains spinal cords pooled from 10 male mice.


title: Prenatal adversity configures the transcriptome of a subpopulation of ventral dentate granule cells for recruitment to drive innate anxiety

status: Public on Jul 31 2025

first: Miklos

last: Toth

address: 525 E 68th St

department: Pharmacology

institute: Weill Cornell Medicine

summary: Adverse prenatal environment is a risk factor for the development of psychiatric disorders. Although studies have implicated epigenetic mechanisms, little is known about how epigenomic changes come about and lead to abnormal behaviors in affected individuals. We sought to identify epigenomic and transcriptomic signatures induced by a proinflammatory gestational environment in the ventral dentate gyrus (vDG), a hippocampal region linked to avoidance of threatening contexts, that persist and promote anxiety-like behavior in mice. Here we show that adversity shifted the methylation of enhancers and promoters with intermediate methylation and altered synapse-related gene expression, resulting in epigenetic and transcriptional heterogeneity in the vDG. Exposure to an anxiogenic environment recruited vDG neurons with the most transcriptional impact. Differentially expressed synapse-relevant genes in ensemble neurons tended to be differentially methylated. Finally, this ensemble exhibited higher activity in threatening than safe environment suggesting a prenatal adversity-induced epigenetic and neurobiological sequalae that leads to anxiety.

overall_design: Mice were placed on the EPM for 10 minutes. 1 hour later, the ventral hippocampus (vHPC) was dissected from each mouse brain. After isolation, nuclei were stained and sorted via FACS. Cells were sorted into active (FOS+ PROX1+) and inactive (FOS- PROX1+) dentate gyrus granule cells for 5HT1AR MIA and CON mice (n = 2 reps pooled from 6 mice).

first: Anika

last: Nabila

first: Rose

last: Sciortino

first: Nicole

last: Politowska

first: Elizabeth

last: Brindley

first: Peter

last: Hamor

first: Lia

last: Zallar

first: Judit

last: Gal Toth

first: Kristen

last: Pleil


title: A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation [SPLASH]

first: Roland

last: Huber

overall_design: SHAPE-MaP of 5 strains of SARS-CoV-2 in E6 TMPRSS2 Vero cells

first: S

first: L

last: DeFalco

first: Y

first: J

last: Han

first: CK

last: Mok

last: Zhang

first: H

middle: J

first: A

last: Merits

first: R

last: Wan


title: Comparative Molecular Analysis of IL-17A and IL-23 Pathway Inhibition in Moderate-to-Severe Psoriasis: 4-Week Results from IXORA-R

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: The purpose of this head-to-head study was to gain molecular insights into the MOA for IXE and GUS in PsO and to compare and contrast the gene expression profiles at early time-points for IXE targeting IL-17A and GUS targeting IL-23.

overall_design: IXORA-R enrolled adults with moderate-to-severe plaque psoriasis (static Physician’s Global Assessment [sPGA] ≥3, PASI ≥12, and BSA ≥10%). We generated longitudinal gene expression profiles of plaque psoriasis lesions from patients enrolled in the IXORA-R (NCT03573323) trial to directly compare the clinical responses with the sequential molecular and cellular events in the lesional skin and blood.

first: Sandra

last: Garcet

first: Lam

middle: C

last: Tsoi

first: Johann

last: Gudjonsson


title: PYM1 controls non-canonical EJC occupancy and maintains homeostatic expression of membrance targeted transcripts

city: Columbu

first: Manu

last: Sanjeev

state: OH

address: 484 W 12th Ave

institute: The Ohio State University

summary: During pre-mRNA splicing in the nucleus, the spliceosome deposits the Exon Junction Complex (EJC) ~24 nucleotides upstream of exon-exon junctions. The EJC core thus deposited comprises of EIF4A3, RBM8A and MAGOH and remains stably bound to RNA to modulate mRNA fate at multiple post-transcriptional steps until its disassembly during translation. Such EJC disassembly is proposed to be mediated by PYM1, a factor that can bind both the ribosome and the RBM8A/MAGOH heterodimer of the EJC core. Here, we investigated the role of PYM1 in regulating EJC binding in human embryonic kidney 293 (HEK293) cells using a MAGOH mutant that assembles into EJC but is impaired in PYM1 interaction. We find that EJCs lacking PYM1 interaction show no defect in translation dependent disassembly. Surprisingly, PYM1 interaction deficient EJCs are enriched on sites away from the canonical EJC binding position including on transcripts without introns or fewer and longer exons. Additionally, acute reduction and elevation of PYM1 levels in HEK293 cells result in a modest NMD inhibition and stabilization of mRNAs that localize to endoplasmic reticulum associated TIS-granules and are characterized by fewer and longer exons. These gene expression changes are mirrored in flavivirus infected cells, suggesting a potential role for PYM1 in host-pathogen interactions, as flaviviruses are known to target this protein.

overall_design: RIPiT-Seq of EJC bound RNA from HEK293 cells expressing FLAG-tagged MAGOH and RNA-seq from cells depleted of PYM1, cells overexpressing PYM1, cells overexpressing PYM1 deltaN and control cells.

first: Guramrit

last: Singh

first: Lauren

last: Woodward


title: Hypoxia promotes airway differentiation in the human lung epithelium

city: Cambridge

first: Emma

last: Rawlins

address: Tennis court road

institute: University of Cambridge

summary: Human embryos develop under physiological hypoxia, but how hypoxia directly affects human organogenesis remains unknown. We have investigated the effects of hypoxia on human lung epithelia using organoids. First trimester lung epithelial progenitors remain undifferentiated under normoxia, but initiate spontaneous differentiation towards multiple airway cell types, and inhibit alveolar differentiation under hypoxia. Genetic and chemical manipulation experiments   showed that these effects were dependent on HIF (Hypoxia-Inducible Factor) activity, with HIF1α and HIF2α differentially regulating progenitor fate decisions. We identified the cell fate-determining transcription factors KLF4/KLF5 and ASCL1 as direct targets of the HIF pathway, promoting progenitor differentiation to basal and neuroendocrine cells respectively. Chronic hypoxia also induces transdifferentiation of human alveolar type 2 cells into airway cells via the HIF pathway, suggesting that the developmental response to hypoxia is conserved into adulthood and potentially contributes to chronic lung disease.

overall_design: Time series single cell RNA-seq of wild-type human lung progenitor organoids cultured under hypoxia for 0, 8, 16, 24, 32 days. Each time point has 2 biological replicates. Libraries prepared with Evercode Whole Transcriptome v2 kit. Each sublibrary is a mixture of all 10 barcoded samples (5 time points x 2 replicates). Sample loading information is attached for demultiplexing.

first: Ziqi

last: Dong


title: CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters [MeDIP-Seq]

city: Gandhinagar

first: Umashankar

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

summary: Human CGGBP1 has been attributed multiple function related to the regulation of gene expression, cytosine methylation (including non-CpG methylation), related epigenetic states of target gene promoter regions and somatic mutation rates. CGGBP1 has also been shown to be a prominent transcription repressor of protein coding genes as well as repetitive elements, mainly Alu-SINEs. There is a possibility that CGGBP1-regulated cytosine methylation affects base mutation rates (C-T transitions) thereby directing TFBS evolution in the human genome. Some recent data suggest that the DNA-binding activity of human CGGBP1 prevents TFBS from cytosine methylation and preserves their GC content. The DNA-binding domain of CGGBP1 is conserved more than its other segments which contain no identifiable domains. In this study we assay global cytosine methylation using MeDIP-seq on human cells (HEK293T) over-expressing only representative vertebrate species (Latimeria chalumnae (Lc), Anolis carolinenesis (Ac), Gallus gallus (Gg), Homo sapiens (Hs)) and perform comparative analyses. Our analyses encompass a parallel global expression profiling (using Agilent arrays, submitted separately to NCBI GEO) and a large-scale estimation of TFBS C-T transition mutation rates from orthologs of genes repressed by the various forms of CGGBP1 used in this study. We report that cytosine methylation restriction by CGGBP1 promotes GC retention in some GC-rich TFBSs.

overall_design: MeDIP-seq was performed on genomic DNA from HEK293T KD cells over-expressing vertebrate representative forms of CGGBP1 namely (Latimeria chalumnae Lc, Anolis carolinensis Ac, Gallus gallus Gg) and HEK293T CT cells over-expressing human CGGBP1 Hs and, HEK293T CT cells over-expressing empty pcDNA3.1(+) vector Ev as control.

first: Praveen

last: Kumar

first: Ishani

last: Morbia

first: Aditi

last: Satish

first: Subhamoy

last: Datta


first: Miklos

last: Toth

overall_design: The granule cell layer of the vDG was dissected from 4 individual mice per group (5HT1A-R MIA and Con). Following DNA extraction, RRBS was used to assess differential methylation between sample groups.

first: Anika

last: Nabila

first: Rose

last: Sciortino

first: Nicole

last: Politowska

first: Elizabeth

last: Brindley

first: Peter

last: Hamor

first: Lia

last: Zallar

first: Judit

last: Gal Toth

first: Kristen

last: Pleil


title: Combining MCL-1 Inhibition and CD37-directed CAR T Cells as an Effective Strategy to Target T-cell Lymphoma

status: Public on Jul 30 2025

city: Salt Lake City

first: Birgit

last: Knoechel

address: 2000 Circle of Hope

institute: HCI

summary: Chimeric antigen receptor (CAR) T cell therapy has not yet been realized for T-cell lymphomas (TCL), partially due to challenges in identifying tumor-specific antigens. We previously reported selective expression of CD37 on malignant T cells in a subset of TCL. Herein, we demonstrate CAR-37 T cells specifically target CD37-positive TCL in part by activating the intrinsic apoptotic pathway. To maximize therapeutic index, we identified selective/targetable BH3 dependences in individual TCL models and combined with CAR-37 T cells. We show that BH3 mimetics do not alter CD37 antigen binding capacity on TCL and have minimal effects on CAR-37 T-cell phenotype or function. In TCL models with dependence on MCL-1, combining CAR-37 T cells and the MCL-1 inhibitor AZD5991 increases anti-TCL response and prolongs survival of xenografted mice. These findings suggest that personalized selection of BH3 mimetic/CAR-T combinations could maximize the therapeutic index for patients with TCL and possibly other diseases.

overall_design: Splenic cells were harvested from DFTL-69579 engrafted mice on treatment day 14 from the vehicle and CAR-37 cohorts and on treatment day 15 from the AZD5991 and CAR-37+AZD5991 cohorts within 1 hour of receiving the final AZD5991 dose. Cells were stained with antibodies against human CD45, EGFR, and CD5. Cells were stained with DAPI to gate on viability. Tumor cells were gated as CD45+, CD5+, EGFR-. CART T cells were gated as CD45+, CD5+, EGFR+. Mixed plats/cells were gated as CD45+ and CD5+ and were later differentiated as tumor or CAR T cells during analysis. Single cells were sorted into 96-well plates using a Sony SH800, immediately centrifuged, and stored at -80°C until library preparation.


title: Hypoxia promotes airway differentiation in the human lung epithelium [Bulk RNA-seq]

first: Emma

overall_design: Bulk RNA-seq of human lung progenitor organoids transfected with CRISPRi and gRNA lentiviral constructs of non-targeting control or HIF1a-gRNA. Organoids cultured under normoxia or hypoxia for 9 days. In total 3 conditions: normoxia + NTC; hypoxia + NTC; hypoxia + HIF1a-targeting. Each condition has 2 different gRNA replicates and 3 biological replicates, in total 6 replicates.


title: Signaling Induced Plasticity Enables Transgene-Free Generation of Mouse Post-Gastrulation Whole Embryo Models Solely from Naïve ESCs and iPSCs (ii)

status: Public on Jul 29 2025

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: The ability to generate Synthetic mouse Embryo Models (SEMs) that can grow beyond gastrulation and early organogenesis has proven the plasticity of naïve Pluripotent stem cells (nPSC) to fully recapitulate the developmental dynamics of the mouse embryo. Existing protocols rely on  the induction of extraembryonic lineages by ectopically expressing master transcription factors that induce their differentiation to trophoblast (TE) or primitive endoderm (PrE) that latter will form the placenta and yolk sac, respectively. However, this approach brings technical difficulties related to the required genetic manipulation, separate lineage induction and mixing of nPSC. While several works have suggested efficient priming to extraembryonic lineages without the need of transgenes, they have not proven the capability of this cells to contribute to the formation of SEMs. In this study, we demonstrate that nPSCs can be co-induced in a single transgene free condition to give rise to both embryonic and extraembryonic lineages present in the preimplantation mouse embryo while preserving an epiblast compartment. Furthermore, this condition can be aggregated and cultured, resembling post-implantation egg cylinders, and by applying ex-utero growth technologies they progress to mimic features corresponding to E8.5 in-utero growth embryos. Moreover, by optimization of a  media termed Alternative Pluripotent Condition (APC), we provide ready to use condition that can be maintained long term and directly aggregated to generate TF-SEMs, eliminating the need of cell preinductions before aggregation.

overall_design: TFSEM (Transgene-Free Synthetic Embryo Models) were grown by the protocol described in the paper. Day 8 and Day 10 TFSEM, equivalent to E7.5 and E8.5 respectively, were pooled and trypsinized for 10 minutes. Trypsin was inactivated with serum containing media. Trypsinized cells were resuspended in PBS containing 400 μg/mL bovine serum albumin (BSA) and prepared for downstream processing according to the 10x Genomics Chromium v3.1 kit. and scRNA-seq was measured as described. Next, Day 10 TFSEM, equivalent to E8.5, were pooled and scRNA-seq was measured as described.

first: Alperen

last: Yilmaz

first: Gulben

last: Gurhan

first: Alejandro

last: Aguilera-Castrejon

first: Bernardo

last: Oldak

first: Jacob

last: Hanna


title: Recreating pathophysiology of CLN2 disease and demonstrating reversion by TPP1 gene therapy in hiPSCs-derived retinal organoid and retina-on-chip

city: Tuebingen

first: Kevin

last: Achberger

address: Oesterbergstrasse 3

department: Institute of Neuroanatomy and Developmental Biology

country: Germany

institute: University of Tuebingen

summary: Mutations in tripeptidyl peptidase 1 (TPP1) gene lead to late infantile neuronal ceroid lipofuscinosis CLN2, characterized by lysosomal accumulation of lipofuscins predominantly found in brain and retina. The ocular phenotype is characterized by bilateral outer retinal degeneration that leads to complete vision loss. CLN2 animal models struggle in recapitulating the retinal phenotype observed in patients. Here, we leveraged human induced pluripotent stem cell (hiPSC)-derived retinal organoids (ROs), retinal pigmented epithelial (RPE) cells, and retina-on-chip (RoC) technologies to model CLN2 disease in vitro in patient-specific microphysiological models of the human retina. Using these models, we were able to recreate the major clinical histological hallmark of CLN2 patients, namely the accumulation of lipofuscins containing subunit C of mitochondrial ATP synthase (SCMAS) and lipids mainly in the outer retina. Furthermore, single-cell RNA-sequencing of CLN2 ROs revealed a dysregulation of translational and mitochondrial function in cones. Finally, we demonstrate that an adeno-associated virus (AAV)-mediated TPP1 gene therapy was able to restore TPP1 expression and could decrease and even prevent SCMAS accumulations. In summary, our study produced novel human-relevant microphysiological retinal disease models, uncovered new mechanisms of CLN2 pathophysiology in the human retina, and demonstrated the immense potential of AAV9.hCLN2 gene therapy for CLN2 disease potentially treating and even curing blindness of affected individuals.

overall_design: iPSC-derived retinal organoids (ROs) at d192  of two control lines (CTRL1, CTRL2) and two CLN2 Patients lines untreated (CLN2-1, CLN-2) and treated with AAV9-hCLN2 (AAV9.hCLN2-treated CLN2-1 and AAV9.hCLN2-treated CLN2-2) were subjected to single cell sequencing analysis (10X Genomics). The six samples were distributed into 4 runs and demultiplexed by SNPs using SoupOrCell v2.0 (Heaton et al 2020). Run 1 contained CTRL1 and CLN2-1, Run2 contained CTRL1 and AAV9.hCLN2-treated CLN2-1, Run3 contained CTRL2 and CLN2-2, Run4 contained CTRL2 and AAV9.hCLN2-treated CLN2-2.

first: Serena

last: Corti

first: KwiHye

last: Kim

first: Ting

last: Chen

first: Virginia

last: Cora


title: Gene expression data from mouse inner medullary collecting duct cells expressing wild type ILK and missense variant T173I

city: Toronto

first: Norman

last: Rosenblum

address: 686 Bay Street

institute: The Hospital for Sick Children

summary:
Renal branching morphogenesis is regulated by a number of intracellular signalling pathways. ILK has been previously shown to be an important regulator of RBM. Missense Variant, ILK-T173I, within the ankyrin-repeat domain is associated with congenital abnormalities of renal and urinary tract.
We used microarray analysis to screen for differences in signalling pathway activity and gene target expression to identifity the underlying molecular mechanisms that contribute to renal and urinary tract malformations

overall_design: IMCD cells were transduced with a lentivirus expressing GFP and ILK under a bicistronic vector. Stable cell lines were generated expressing both wild type and ILK-T173I mutant and stimulated with EGF to look for differentially expressed genes in the samples.

first: Dana

last: Kablawi


title: Synthetic deconvolution of an auxin-dependent transcriptional code

first: Bruno

last: Guillotin

address: 12 Waverly Place, Floor 6

department: Biology

institute: NYU-Biology-CGSB

summary: How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.

overall_design: Single cell RNAseq approach on Arabidopsis thaliana, 7day old seedling, cultivated in vitro, MS/2, sucrose 1%, Agar 1%, and treated with IAA 1 μM for 16 h or Mock. Experiment was performed on 4 lines carrying the DR5, ER13, DR15 or IR8 synthetic promoters followed by a mTurquoise reporter.

first: Raquel

last: Martin-Arevalillo

first: Alice

last: Hugues

first: Marie-France

last: Gerentes

first: Jonas

last: Schön

first: Jeremy

last: Lucas

first: Emmanuel

last: Thevenon

first: Graeme

last: Vissers

first: Mohammed

last: Mohammed Ateequr

first: Carlos

last: Galvan-Ampudia

first: Coralie

last: Cance

first: Annick

last: Dubois

first: François

last: Parcy

first: Kenneth

last: Birnbaum

first: Matias

last: Zurbriggen

first: Renaud

last: Dumas

last: Roudier

first: Teva

last: Vernoux


title: Evolution of a transplantable cancer by adaptation

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

institute: University of Edinburgh

summary: The histocompatibility barrier prevents transmission of both normal and tumour cells between individuals 1, however clonally transmissible cancers in dogs, Tasmania devils and soft-shell clams can naturally transmit as allografts 2. To understand how tumours can escape the histocompatibility barrier, we have serially passaged a mouse melanoma first into syngeneic mice and then into progressively more mismatched mouse strains until a fully allo-transplantable tumour emerged. Here we show that tumour passaging selected for cells with an anti-viral inflammatory signature, characterised by expression of MHC-I, PD-L1, Qa-1 non-classical MHC molecules and the upregulation of intergenic endogenous retroviral elements (ERVs). Knock-out of RNA sensor RIG-I 3 in the transplantable tumour cells resulted in reduced expression of MHC-I, PD-L1 and Qa-1. Antibody-mediated blockade of both PD-L1 and Qa-1 induced tumour regression after transplantation. A similar inflammatory signature was found in human melanomas that respond to anti-PD1 antibody treatment. Thus, an inflammatory anti-viral signature likely induced by RIG-I sensing of ERVs facilitates escape of the mouse melanoma from allogeneic rejection. The results underscore the immunological plasticity of melanoma and reveal an unanticipated role for inflammation in allograft immune evasion.

overall_design: RNAseq profiling of tumours after serial passaging into mice. RNAseq was performed on polyA RNA extracted from tumours. Different tumours of the same passage are indicated with the letters A to C.

first: Ahmed

last: Rokan

first: Callum

last: Hall

first: Ariberto

last: Fassati


title: Quantitative CRACI reveals transcriptome-wide dynamics of tRNA and mRNA dihydrouridylation at base resolution

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

summary: D is an abundant RNA modification found in all kingdoms of life; yet our understanding of this modified base in mammals is lacking due to the lack of detecting methods. Until now, even for the most abundanct RNA speices with D, tRNA, we still do not have the profile of its sites. In this work, we introduce Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI), a powerful method that enables whole-transcriptome quantitative mapping of D modifications at single-base resolution.

sample_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus
synthetic construct

overall_design: The CRACI experiment was performed in RNA from mammal cells and plants.

first: Li-Sheng

last: Zhang

first: Chuan

last: He


title: Signaling Induced Plasticity Enables Transgene-Free Generation of Mouse Post-Gastrulation Whole Embryo Models Solely from Naïve ESCs and iPSCs (i)

first: Noa

last: Novershtern

summary: The ability to generate synthetic mouse embryo models (SEMs) that can grow beyond gastrulation and early organogenesis has proven the plasticity of naïve Pluripotent stem cells (nPSC) to fully recapitulate the developmental dynamics of the mouse embryo. Existing protocols rely on  the induction of extraembryonic lineages by ectopically expressing master transcription factors that induce their differentiation to trophoblast (TE) or primitive endoderm (PrE) that latter will form the placenta and yolk sac, respectively. However, this approach brings technical difficulties related to the required genetic manipulation, separate lineage induction and mixing of different cell lines. While several works have suggested efficient priming to extraembryonic lineages without the need of transgenes, they have not proven the capability of this cells to contribute to the formation of SEMs. In this study, we demonstrate that naive ESCs can be co-induced in a single transgene free condition to give rise to both embryonic and extraembryonic lineages present in the preimplantation mouse embryo while preserving an epiblast compartment. Furthermore, this condition can be aggregated and cultured, resembling post-implantation egg cylinders, and by applying ex-utero growth technologies they progress to mimic features corresponding to E8.5 in-utero growth embryos. Moreover, by optimization of a  media termed Alternative Condition (AC), we provide ready to use condition that can be maintained long term and directly aggregated to generate TF-SEMs, eliminating the need of cell preinductions before aggregation.

overall_design: Following iterative tests and optimizations, we formulated the following regimen and media compositions as most optimal to obtain Epi, PrE and TE cells within 4 days from 2i/LIF naïve ESCs (sample A). Our 4 day regimen consists of 24h treatment of Multilineage Promoting Media 1 (MLPM1) which contains N2B27 based media with CHIR – REPSOX – AM580 and NaB (sample B),  followed by 24h treatment of MLPM2 which is MLPM1 that lacks NaB, and has CHIR concentration reduced from 6 μM to 3 μM, and in which LIF is reintroduced (sample C). Next, the cells were then harvested and aggregated in AggreWell plates, with 30 cells per microwell as employed on previous transgene mediated SEM protocols, for 2 days in Multilineage Maturation Media (MLMM – N2B27 with FGF4, ACTIVIN A, XAV and TRULI) (sample D). Using the AC media, we maintained PrE, TE and Epi-like cells for 12 passages on mouse embryonic fibroblast layers and harvested these cells for sequencing.

first: Alperen

last: Yilmaz

first: Gulben

last: Gurhan

first: Alejandro

last: Aguilera-Castrejon

first: Bernardo

last: Oldak

first: Jacob

last: Hanna


title: Kcnj2 regulates electrical activity-induced gene networks in embryonic mouse palate shelves.

status: Public on Jul 28 2025

city: Aurora

first: Emily

middle: Anne

last: Bates

state: CO

summary: Cleft palate interferes with eating, drinking, breathing, and speech, causing significant human suffering. Fetal exposure to many medications that target ion channels increases the incidence of cleft palate. Cleft palate could be prevented by understanding how ion channels contribute to palatal development. Ion channels regulate the electrical properties of cells. We discovered that the mouse embryonic palate mesenchymal cells are electrically active, like neurons. In neurons, electrical activity regulates transcription cell-autonomously and regulates the secretion of chemical cues. We discovered that electrical activity regulates secretion of bone morphogenetic protein (BMP4) from mouse palate mesenchymal cells. The next important step is to determine how electrical activity affects transcription to control palate development. Loss of a potassium channel called Kcnj2 (Kcnj2KO/KO) alters electrical activity in palate mesenchyme cells and causes cleft palate in mice. We compared single cell RNA sequencing datasets from Kcnj2KO/KO and wildtype E13.5 mouse anterior palate shelves to define how electrical activity affects gene expression cell autonomously and in surrounding cells. Our data reveal that Kcnj2KO/KO alters a network of calcium-induced transcription factors and downstream effectors. These data also reveal that loss of Kcnj2 affects gene expression outside of the cells that express Kcnj2 consistent with disruption of BMP signaling.

overall_design: Kcnj2KO/+ (FVB.129-Kcnj2tm1Swz/J Stock No. 005057/Kcnj2, Jackson Labs) dams were bred to Kcnj2KO/+ males. Kcnj2KO/+ mice are maintained as a colony on a C57BL/6J background in accordance with IACUC protocol #0139 at the University of Colorado Anschutz Medical Campus. Observation of the vaginal plug was considered embryonic day 0.5. On embryonic day 13.5, pregnant dams were sacrificed with isoflurane followed by cervical dislocation and embryos were harvested. Heads were kept in ice-cold PBS for dissection. Two sequenced WT embryos were female and one WT was male while the two Kcnj2KO/KO embryos were male. Anterior palatal shelves were dissected and dissociated. Embryos were genotyped using the established Jackson Labs protocol. Single cell suspensions were submitted to the University of Colorado Anschutz Medical Campus Genomics Shared Resource for droplet derivation and library preparation with the Chromium single cell 3’ NextGen V3.1 chemistry (10X Genomics). Sequencing was performed on an Illumina NovaSeq6000 with V1.5 chemistry. 7976, 6994, and 7268 cells from 3 Wildtype embryos (22,238 cells in total across all embryos) and 7591 and 4067 cells from 2 Kcnj2KO/+ embryos (11,658 cells in total) were collected and sequenced at a depth of 100,000 reads per cell. Cells from different embryos were run separately and not pooled together during sequencing.

first: Yunus

last: Ozekin

first: Rebecca

last: O’Rourke

middle: A


title: Hypoxia promotes airway differentiation in the human lung epithelium [DamID-seq]

first: Emma

last: Rawlins

overall_design: Targeted DamID-seq of human lung progenitor organoids transfected with empty vectors, Dam-HIF1a or Dam-HIF2a. Organoids cultured under hypoxia for 6 days. 4 biological replicates.

first: Ziqi

last: Dong

first: Niek

last: Wit

first: Dnyanesh

last: Dubal

first: Jelle

last: van den Ameele

first: James

last: Nathan


title: A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation [dataset1]

city: Singapore

first: Roland

last: Huber

address: 30 Biopolis Street

institute: Agency for Science, Technology and Research (A*STAR)

summary: Various SARS-CoV-2 viruses have caused the COVID-19 pandemic world-wide.  As the viruses evolve different mutations along their genomes, these mutations can impact virus RNA structures and their phenotypes.  Here we probe the RNA structures across Wuhan, alpha, beta, delta and omnicron strains of the SARS-CoV-2 viruses.  We observe that while the mutations impact RNA structures, it is not the main source of RNA structure changes (RBPs?). Structurally conserved structures are enriched for both long and short RNA pair-wise interactions.  We identified a conserved 17kb long range interaction that decreases the virus fitness when mutated. Additionally, this interaction binds to ADAR1 to alter editing levels on the virus. These studies reveal the importance of RNA structures along virus genomes to facilitate virus infectivity.

overall_design: SHAPE-MaP of 5 strains of SARS-CoV-2 in E6 TMPRSS2 Vero cells

first: S

last: Wang

first: SL

last: Yang

first: L

last: DeFalco

first: YH

first: J

last: Han

first: CK

last: Mok

first: Y

last: Zhang

first: HJ

last: Chu

first: A

last: Merits

first: RG

last: Wan


title: Study of Immunological and Inflammatory gene response in Indian Cohort of Covid-19 Patients by NanoString Technology

city: Bengaluru

first: Sudarson

last: Sundarrajan

address: Sri Shankara Research Centre 1st Cross, RM hospital, Shankara Matt Premises, Shankarapuram, Basavanagudi

department: Molecular Biology

institute: Cancyte Technologies Private Limited

summary:
The Nanostring nCounter gene expression assay was used to investigate the molecular signalling of host to Covid-19 infection, from Indian Cohort.
The study revealed several biomarkers with strong predictive performance to differentiate Covid-19 infection from healthy controls and markers to differentiate between Covid-19 infection from other flu like symptoms.

overall_design: The experiment included samples from 4 different groups, Covid-19 infection at time of diagnosis, Covid-19 infection after 14 days, Negative controls or other flu-like symptoms and healthy controls. Sufficient amount of RNA was extracted suitable for NanoString custom assay and after subjecting to quantity and quality check it was proceeded for NanoString nCounter gene expression profiling assay. Total samples- 11 with each group having 2 biological replicates except for healthy control which had 3 biological replicates..

first: K

last: Sridhar


title: Multi-omics analysis of thermogenic lipolysis in brown adipocytes

city: Copenhagen

first: Matthias

last: Anagho-Mattanovich

address: Blegdamsvej 3B

department: SUND

country: Denmark

institute: University of Copenhagen

summary: The integration of omics technologies into molecular biological research has transformed it into a field where a system can be investigated as a whole by combining information from multiple biochemical layers. This extension of traditional molecular biology, where various data sources are considered independently, offers novel insights into complex molecular interactions. Here, we present a multi-omics analysis of murine brown adipocytes undergoing thermogenic lipolysis, which is part of the non-shivering response to cold. Through combining information from multiple types of biomolecules, we describe what is important for each biochemical layer, and the coordinated molecular responses across different layers at the system level, at different time points. Furthermore, a classification of data integration approaches for multi-omics data analysis is presented, and their applications in our study are compared, providing insights into the focus and effectiveness of these methods.

overall_design: RNA-seq profiling of BMC cells, murine brown adipocytes, before- and at different time points after induction of thermogenic lipolysis by norepinephrine stimulation

first: Holda

first: Lidia

last: Argemi-Muntadas

first: Michael

last: Lund Nielsen

first: Qian

last: Gao

first: Thomas

last: Moritz


title: CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters [Array]

first: Umashankar

last: Singh

summary: Human and other vertebrate representative forms of CGGBP1 have been used in this study to assay global gene expression. HEK293T cells with endogenous CGGBP1 knocked down were used to over-express other vertebrate representative forms of CGGBP1 (Latimeria chalumnae (Lc), Anolis carolinensis (Ac), Gallus gallus (Gg)) followed by RNA extraction and one-coloured global gene expression analysis (Agilent). HEK293T cells with normal level of endogenous CGGBP1 were used to over-express Human CGGBP1 (Hs) or pcDNA3.1(+) empty vector (Ev). Overexpression of CGGBP1 forms resulted in the repression of specific gene sets at two different temperatures (37 degrees and 40 degrees Celsius). The proximal promoters of these repressed genes exhibit a marked difference in the occurrence of GC-rich transcription factor binding sites (TFBSs). Through additional studies on these samples we have separately assayed global cytosine methylation patterns (submitted separately to NCBI GEO) and reported that the GC content of these promoters is determined by a combination of motif occurrence as well as motif GC contents. Notably, the within these gene promoters human CGGBP1 was found to restrict cytosine methylation at certain GC-rich TFBSs. A high-throughput analysis of the GC compositional bias across these CGGBP1-regulated TFBSs, using orthologous sequences from over 100 species, revealed a strong link between CGGBP1-induced cytosine methylation restriction and GC retention at specific TFBSs. Further, orthology analysis showed that this regulatory mechanism of CGGBP1 is conserved in higher amniotes (birds and mammals) and exhibits lineage-specific variations in lower amniotes (reptiles).

overall_design: To investigate gene expression, HEK293T cells were transfected with various CGGBP1 forms, including those from Latimeria chalumnae (Lc), Anolis carolinensis (Ac), Gallus gallus (Gg), and Homo sapiens (Hs), as well as with the pcDNA3.1(+) empty vector control. Gene expression was assessed 72 hours post-transfection. In parallel, heat stress conditions were applied by first incubating the cells at 37°C for 24 hours, followed by 48 hours of continuous heat stress at 40°C. Gene expression changes were subsequently analysed to evaluate the impact of heat stress. All experiments were performed in triplicate to ensure statistical reliability.

first: Praveen

last: Kumar

first: Ishani

last: Morbia

first: Aditi

last: Satish

first: Subhamoy

last: Datta


title: A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkTCR_Trilateral_similarity]

status: Public on Jul 25 2025

city: Noda-shi

first: Mikiya

last: Tsunoda

state: Chiba

department: Molecular Preventive Medicine

institute: The University of Tokyo

summary: Effective cancer immunotherapy relies on the clonal proliferation and expansion of CD8+ T cells in the tumor.  However, our insights into clonal expansions are limited, owing to an inability to track the same clones in tumors over time. Here, we developed a multi-site tumor mouse model system to track hundreds of expanding and contracting CD8+ T cell clones over multiple timepoints in tumors of the same individual. Through coupling of clonal expansion dynamics and single-cell RNA/TCR-seq data, we identified a transcriptomic signature in PD-1+Ly108+ precursor exhausted cells that strongly predicts rates of intratumoral clone expansion. The signature correlates with expansion in mice, both with and without immunotherapies, and in patients undergoing PD-1 blockade therapy. Expression of the signature during treatment corresponds with positive clinical outcomes. Downregulation of the signature precedes clone contraction – a phase in which clones contract but maintain revivable precursor exhausted cells in the tumor. LAG-3 blockade re-activates the expansion signature, re-expanding pre-existing clones, including previously contracted clones. These findings reveal how the study of clonal expansion dynamics provide a powerful ‘pan-immunotherapy’ signature for monitoring immunotherapies with implications for their future development.

overall_design: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank, right flank and the left hip of C57BL/6 mice (untreated : n=5, aLAG3 : n=6). Tumors were excised on day 14 and devided into two pieces, and the TCR repertoire of CD4+ and CD8+ tumor infiltrating lymphocytes (TILs) in each piece were analyzed independently. T cells obtained from each tumor were analyzed by bulk TCR-sequencing.

first: Munetomo

last: Takahashi

first: Hiroyasu

last: Aoki

first: Masaki

last: Kurosu

first: Haru

last: Ogiwara

first: Shigeyuki

last: Shichino

first: David

last: Bending

first: Shumpei

last: Ishikawa

first: James

last: Thaventhiran

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Stereo-random Oligonucleotides Enable Efficient Recruitment of ADAR in vitro and in vivo

first: Laura

middle: Sophia

last: Pfeiffer

address: Auf der Morgenstelle 15

summary: Site-directed RNA editing is a promising and potentially safer alternative to genome editing. Previous methods have been developed that recruit the endogenously and ubiquitously expressed ADAR enzymes to initiate site-specific A-to-I edits, but often suffer from low efficacy or dependency on viral delivery. Chemically modified oligonucleotides may be a promising alternative, but the approach still lacks systematic in-depth studies. Furthermore, the best characterized platform uses stereo-pure backbone chemistry, which is not widely used, commercially unavailable and challenging to manufacture. Here, we report on single-stranded oligonucleotides of 30-60 nt length, which are fully chemically stabilized by applying commercially available, classical RNA drug modifications, like 2´-O-methyl, 2´-fluoro, and DNA on a stereo-random phosphate/phosphorothioate backbone. We demonstrate our so-called RESTORE 2.0 oligonucleotides to induce the correction of pathogenic point mutations, efficacy after GalNAc-mediated uptake into human primary hepatocytes, and proof of in-vivo efficacy in mice upon lipid nanoparticle-mediated delivery. The discovered design principles may increase the accessibility of site-directed RNA base editing to expand and support further research in this field. Here, the transcriptome-wide precision of our RNA editing ONs is tested by RNA Seq of treated NHA cells.

overall_design: RNA Seq profiling of NHA cell transcriptome 24h after RNAiMAX Lipofectamine transfection with RNA editing ONs v117.19 (minimally modified) and v117.28 (pyrimidines modified).

first: Pfeiffer

last: Laura

first: Merkle

last: Tobias

first: Vogel

last: Paul

first: Jarmoskaite

last: Inga

first: Geisinger

middle: M

last: Jonathan

first: Latifi

last: Ngadhnjim

first: Herrera-Barrera

last: Marco

first: Zhang

last: Feijie

first: Gross

last: Lisa

first: Schlitz

last: Carolin

first: Hofacker

last: Daniel

first: Lochmann

last: Clemens

first: Fumagalli

last: Davide

first: Gackstatter

last: Stefanie

first: Deisling

last: Vanessa

first: Kay

last: Mark

first: Li

middle: B

last: Jin

first: Stafforst

last: Thorsten


title: GNAS/PKA pathway promotes aberrant osteochondral differentiation of Gli1+ tendon  sheath progenitors

city: Hefei

first: Chao

last: Peng

state: 安徽Anhui

address: 81 Meishan Road

institute: Anhui Medical University

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study the identity and fate determination of Gli1+ tendon sheath progenitors in heterotopic ossification(HO) formation following tenotomy. Gli1 is a signature gene for several tissue-specific Mesenchymal stem cells (MSCs). Aberrant osteochondral differentiation of MSCs in soft tissues leads to incorrect tissue regeneration into HO. This study demonstrated a subpopulation of Gli1+ tendon sheath cells that function as tendon stem/progenitors and can initially differentiate into normal or osteochondral tendon-lineage progenitors, with the latter subsequently giving rise to chondrocytes and osteocytes in development of tendon HO.

overall_design: Gli1+ cells from uninjured and injured tendon(7-, and 21-days post-injury) of Gli1-CreERT2; Ai9 reporter mice with tamoxifen induction (n=24, equal sex distribution) were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Lijun

last: Chen

first: Lanyi

last: Chai

first: Renjie

last: Zhang

first: Chen

last: Kan


title: Single-cell sequencing WT and PADI4 cKO skin, P1

city: Stockholm

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: Tissue formation requires a coordinated balance of progenitor cell proliferation and differentiation. Posttranslational protein modifications have emerged as a mechanism utilized to regulate progenitor cell state transitions. Herein, we exploit the well characterized and stereotyped hair follicle development to delineate the function of PADI4; an enzyme converting peptidylarginine to citrulline. Single cell-sequencing places Padi4 in both progenitor and differentiated hair lineage cells during hair follicle development. We show that the absence of PADI4 induces gene expression across hair follicle cell clusters, suggesting that PADI4 acts to negatively impact transcription. In addition, we establish PADI4 as a negative regulator of proliferation, acting of LEF1-positive hair shaft committed progenitor cells. Mechanistically, PADI4 citrullinates proteins associated with mRNA-processing and ribosomal biogenesis, and lack of PADI4 promotes protein synthesis and rRNA transcription in vivo, in both hair follicle progenitor and committed lineage cells. Characterizing key translational effectors, we demonstrate that PADI4 interacts with 4E-BP1 and reveal a crosstalk between PADI4 activity and 4E-BP1 phosphorylation. We report that PADI4 contributes to hair follicle development by repressing progenitor cell proliferation and translational activity. This work sheds new light on how posttranslational modifications impact progenitor cell states and tissue formation.

overall_design: At postnatal day 1, K14-Cre Padi4 fl/fl, tdTOMATO  mouse back skins were dissected and used for single-cell preparation. tdTOMATO cells were isolated and used for library preparation.

first: Kim

last: Vikhe Patil

last: Campamà Sanz

last: Kasper


title: Mitochondrial activity tunes cellular resilience to excitotoxicity

city: San Francisco

first: Lin

last: Yuan

institute: UCSF

summary: The capsaicin receptor, TRPV1, mediates the detection of noxious chemical and thermal stimuli by nociceptors, primary sensory neurons of the pain pathway. Overactivation of TRPV1 leads to cellular damage or death through calcium entry and excitotoxicity. We have exploited this phenomenon to conduct a systematic analysis of excitotoxicity through a genome-wide CRISPRi screen, thereby revealing a comprehensive network of regulatory pathways. We show that decreased expression of mitochondrial electron transport chain (ETC) components protects against capsaicin-induced toxicity and other challenges by mitigating both calcium imbalance and the generation of mitochondrial reactive oxygen species via distinct pathways. Moreover, we confirm the regulatory roles of the ETC in sensory neurons through gain-of-function and loss-of-function experiments. Interestingly, TRPV1+ sensory neurons maintain lower expression of ETC components and can better tolerate excitotoxicity and oxidative stress compared to other sensory neuron subtypes, implicating ETC tuning as an intrinsic cellular strategy that protects nociceptors against excitotoxicity.

overall_design: For the CRISPRi screen, we engineered a TRPV1+ K562 clonal cell line expressing the required CRISPRi machinery. These cells were transduced with a well-validated genome-scale single-guide RNA (sgRNA) library that targets 18905 genes with 5 sgRNAs/gene and 1895 non-targeting (NT) sgRNA controls (hCRISPRi_v2, Horlbeck et al., 2016). Samples were collected from two biological replicates at the outset of the experiment (T0) and from either untreated or capsaicin treated cells at day 14, the experimental endpoint .  For comparative transcriptomics, RNA was extracted from triplicated samples (TRPV1+ K562 cells) that were pretreated with either vehicle (Veh) or Piericidin A (PierA) for 3 days then treated with either vehicle (Veh) or capsaicin (Cap) for 4 hours. cDNA libraries were prepared from RNA and sequenced.

first: David

last: Julius


title: A dual TGF-β-driven immunosuppressive mechanism controls T cell recruitment and expansion in metastatic colorectal cancer

city: Barcelon

first: Lidia

last: Mateo

address: C/ Baldiri Reixac 10

institute: Institute for Research in Biomedicine (IRB Barcelona)

summary: Poor prognosis colorectal cancer (CRC) is characterized by an immune suppressive TGF-β-activated tumor microenvironment (TME). Pharmacological inhibition of TGF-β signaling promotes T cell infiltration and synergizes with immune checkpoint blockade (ICB) to eliminate metastatic disease in experimental models. Through genetic dissection in model systems and analysis of patient datasets, here we uncover a network of genetic programs regulated by TGF-β signaling in liver metastasis. We show that productive immune responses require both continuous recruitment of tumor-specific CD8+ T cells and subsequent clonal expansion in the TME. TGF-β signaling prevents the recruitment of memory CD8+ T cells by enforcing residence in the lymph nodes. In the absence of newly arrived T cells, the response of tumor-resident T cells to immunotherapy is insufficient to eradicate metastases. We further unveil a genetic program induced by TGF-β in macrophages, which characterizes CRC patients with a high risk of developing metastatic disease. TGF-β-activated macrophages prevent the clonal expansion of newly arrived T cells in the TME through the extracellular matrix protein osteopontin. Overall, our findings reveal how TGF-β signaling integrates immune-suppressive responses in the innate and adaptive immune systems to enable metastatic outgrowth.

overall_design: C57BL/6J mice, were purchased from Janvier Labs at six weeks of age, and injected at 7-8 weeks. Sex was matched with the origin of the tumor. Intrasplenic injections were used for liver colonization by the introduction of dissociated organoids (small 3-4 cell clusters) into the portal circulation. Galunisertib (also known as LY2157299) was synthesized in house and prepared as previously described (Tauriello et al, 2018). Galunisertib or vehicle control was administered by oral gavage in a 0.15 ml volume, twice per day, starting 12-15 days after cell injection for metastasis-initiation experiments, unless otherwise indicated. An 800 mg/kg dose per treatment was used for all experiments. For checkpoint immunotherapy or dual immunotherapy, we used rat anti-PD-L1 (10F.9G2; BioXCell BE0101) or rat anti-IgG2b (LTF-2; BioXCell BE0090) isotype-control antibodies. Whole individual metastases were excised from livers ex vivo and mechanically disaggregat¬ed in 1 ml of Trizol (Life Technologies, 15596018) using a tissue disruptor. Disaggregat¬ed tissues in Trizol were stored in -80ºC until processing. For RNA extraction, samples in Trizol were thawed. 200μl of chloroform (Sigma, 372978) was then added and samples were vigorously mixed for 15 seconds. Mixed samples were centrifuged at 12.000 g for 15 minutes at 4ºC, after which a colorless upper phase containing the RNA was transferred into a new Eppendorf, and mixed with one volume of 70% ethanol. The mix was then processed using a PureLink® RNA Mini Kit (Life Technologies, 12183025) following the manufacturer’s specifications. RNA was eluted using distilled water (Invitrogen, 10977-035) and the concentration was determined using the Nanodrop 1000 spectrophotometer (ThermoFisher).

first: Ana

last: Henriques

last: Salvany

first: Paula

last: Nieto

first: Sergio

last: Palomo-Ponce

first: Marta

last: Sevillano

first: Xavier

last: Hernando-Momblona

first: Emily

last: Middendorp-Guerra

first: Sebastien

last: Tosi

first: Theresa

last: Suckert

first: Adria

last: Caballé

first: Daniele

last: Tauriello

first: Elena

last: Sancho

first: Camille

last: Stephan-Otto Attolini

first: Alejandro

last: Prados

first: Holger

last: Heyn

first: Eduard

last: Batlle


title: Remodeling of the immune microenvironment is linked to adverse outcome in pediatric T cell acute lymphoblastic leukemia

first: Birgit

last: Knoechel

summary: Changes in the immune microenvironment are frequent in cancers occurring in adult patients, yet our understanding of the pediatric cancer immune microenvironment and its clinical relevance is limited. We investigate the immune microenvironment in pediatric T cell acute lymphoblastic leukemia (T-ALL), using single-cell CITE-seq and immune repertoire analyses. We identify a T-ALL subgroup characterized by a remodeled immune microenvironment, which is associated with adverse clinical outcome in minimal residual disease low patients. This adverse immune landscape is dominated by the presence of a population of non-malignant CD4-CD8-TCRab T cells that interact with CXCL16 expressing non-classical monocytes. Leukemia cell intrinsic transcriptional rewiring in these patients is associated with activation of Rap1 signaling. Inhibiting Rap1 signaling results in increased sensitivity to the BCL2/BCL-XL inhibitor navitoclax. Our study provides insights into the immune microenvironment of pediatric hematologic malignancies, forming the basis for identifying novel (immuno)therapeutic targets and risk stratification for treatment.

overall_design:
Single-cell multi-omics (CITE-seq (RNA-seq + ADT-seq), TCR-seq and BCR-seq (5' 10x Genomics)) of primary human bone marrow and peripheral blood CD45+ mononuclear cells of 4 normal donors and 15 pediatric T-ALL patients at diagnosis (n=15), short-term treatment (n=8) and remission (n=6). T-ALL patient samples were separated into CD45++ immune cells and CD45+CD7+ leukemia cells by flow-based sorting and subsequently pooled to increase immune-leukemia cell ratio. This study is registered under dbGaP: phs004269.v1.p1.

Low-input RNA-seq (Smart-seq2) of CD8+ T-cells cultured in the absence and presence of 100ng/ml CXCL16.

first: Caroline

middle: R

last: Wiggers

first: Jens

middle: G

last: Lohr