title: Generation and characterization of iPSC derived microglia from blood derived PBMCs for in vitro modeling of stimuli-specific neuroimmune responses

city: Indianapolis

first: Joshua

last: Kulas

address: 1210 Waterway Blvd Ste. 2000

institute: IBRI

summary: Microglia are highly specialized brain immune cells which express several genes known to influence the risk of developing Alzheimer’s disease. While interest in harnessing the potential neuroprotective functions of microglia using targeted therapeutics is high, it remains challenging to test emerging tool molecules for their potential biological effects in physiologically relevant model systems. Here we describe the generation of iPS cell lines from donor somatic cells (PBMCs) using non-integrating episomal reprogramming vectors for the downstream stepwise differentiation of iPSC-derived microglia (iMG). We find that our stepwise differentiation protocol reproducibly generates iMG expressing several microglia signature genes. Moreover, these iMG are highly morphologically and transcriptionally dynamic. We challenge iMG with diverse stimuli and find that iMG respond to myelin debris by robustly changing lipid metabolism and upregulating several chemokines including CXCL10. While iMG express both TREM2 and DAP12, neither Interleukin 4 mediated upregulation of TREM2 or TREM2 binding by an antibody tool molecule caused an increase in the phagocytosis of myelin debris. Interestingly, we find the TREM2 binding antibody induces a consistent transcriptional response resulting in the upregulation of several chemokines. We conclude iMG are a flexible model system which can be used to explore the biological response of human microglia-like cells to specific physiological stimuli and to test emerging tool molecules for their transcriptional and functional impacts.

overall_design: ultra low-total RNAseq of iMG stimulated with either the TREM2 agonist antibody (1 μg/mL), IgG antibody (1 μg/mL), myelin debris (5 μg/mL), TREM2 agonist antibody with myelin debris, or IgG with myelin debris, using untreated iMG as a control


title: JAX Study 10- RNA-seq of male KOLF2.2J hiPSC-derived endoderm and mesoderm homozygous null for three different transcription factors.

status: Public on Sep 01 2025

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

type: Expression profiling by high throughput sequencing

summary: This study aims to phenotype iPSC-derived early endoderm and mesoderm that contain homozygous null alleles for the following transcription factors: ISL1, NKX2-1, and EOMES. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1) in the case of ISL1 or full protein coding region deletion (KO) for NKX2-1 and EOMES. RNA-seq data was generated after 5 days of initiating differentiation from iPSCs. This analysis allowed the investigation of early embryonic development, cell fate mapping, and lineage analysis.

overall_design: The study involved the generation of RNA-seq on 15 samples. Two of the transcription factors were analyzed in the endoderm differentiation scheme and one in the early mesoderm scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions. This comprehensive design allowed the investigation of the effects of transcription factor manipulation during early embryonic development.

first: Juliana

middle: A

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: TFEB and TFE3 are key regulators of melanoma biology

status: Public on Sep 03 2025

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: Unlike MITF-M, the melanocyte-specific isoform of MITF, TFEB, TFE3 and non-melanocyte MITF isoforms are regulated primarily by mTORC1-mediated phosphorylation at the lysosome that promotes their cytoplasmic retention. As low levels of glucose or amino acids trigger down-regulation of MITF, it is likely that on nutrient limitation some MITF functions are assumed by TFE3 and TFEB, enabling MITFLow melanoma cells to survive and proliferate. The role TFEB and TFE3 in melanoma biology and their impact on MITF-driven proliferation is poorly understood.

overall_design: B16/F10-luc2 mouse melanoma cells were obtained from Caliper Life Sciences (Hopkinton, MA, USA). B16F10-luc2_Mitf_sKO were generated as described in PMID: 33789714. Tfeb and Tfe3 KO were generated using guides tfe3 CGTAGAAGCTGTCAGGATCG and tfeb TGGACACGTACTGTCCACCT. KO cells were clonally isolated and validated.

first: Diogo

last: Dias

first: Colin

middle: R

last: Goding


title: Treatment of prostate cancer with oncolytic virus OH2 [bulkRNA-seq_C4-2]

city: Wuhan

first: Jinzhou

last: Xu

state: Hubei

address: Jiefang Avenue

country: China

institute: Tongji Hospital

summary: Prostate cancer is a major challenge due to limited treatment options in advanced stages. Immunotherapy has shown promising prospects in various cancers, but it faces obstacles in prostate cancer due to its immunosuppressive microenvironment and low response rate to current therapies. Oncolytic virus therapy provides a new immunotherapy approach by stimulating anti-tumor immune responses. This study investigated the histological changes of the novel herpes simplex virus type II (HSV-II) oncolytic virus OH2 in prostate cancer tumors.

overall_design: Prostate cancer cell lines (C4-2, 3 vs. 3) were treated with oncolytic virus OH2 intervention

first: Ye

last: An

first: Guichen

last: Ye

first: Zhiyu

last: Xia

first: Shaogang

last: Wang

first: Qidong


title: Synergistic activity of caspofungin and posaconazole against Candida (Candidozyma) auris biofilms based on phenotypic, transcriptomic, and in vivo insights

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary:
Candida (Candidozyma) auris is an emerging multidrug-resistant fungal pathogen capable of establishing persistent skin colonization, contaminating the environment, and causing nosocomial outbreaks associated with high mortality rates. Conventional monotherapy frequently proves inadequate against biofilm-associated infections, underscoring the urgent need for novel therapeutic strategies. Therefore, we investigated the physiological and molecular responses of South Asian clade C. auris biofilms to treatment with a caspofungin–posaconazole combination. This regimen markedly reduced the median minimum inhibitory concentrations (4- to 32-fold for caspofungin; 8- to 64-fold for posaconazole) compared with monotherapies. Synergistic interactions were observed in all isolates, with fractional inhibitory concentration indices ranging from 0.078 to 0.31, and were further confirmed in vivo. Transcriptomic profiling
revealed activation of multiple stress-response pathways, driving adaptive changes such as enhanced extracellular matrix production and biofilm-forming capacity, maintenance of intracellular cation homeostasis, osmotic stress response, and extensive cell wall and
membrane remodeling affecting the mannan–glucan complex, chitin, sphingolipids, phosphatidylinositol- (4, 5)-bisphosphate, and ergosterol content. Additional responses included activation of RCT1 (fluconazole-inducible protein) and MDR1 (drug efflux
pump), collectively promoting survival under combined antifungal pressure. These findings demonstrate the potent synergistic activity of caspofungin and posaconazole against C. auris biofilms, thereby supporting the development of effective combination therapies for this high-risk pathogen.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of caspofungin and/or posaconazole treated and untreated Candida auris biofilms.

first: Fruzsina

last: Kovács

first: Andrea

last: Harmath

first: Dávid

last: Balázsi

first: Lajos

last: Forgács

first: Ágota

last: Ragyák

first: Noémi

last: Balla

first: Zoltán

last: Tóth

first: Aliz

last: Bozó

first: Andrew

middle: M

last: Borman

first: László

last: Majoros

first: Renátó

first: Ágnes


title: Treatment of prostate cancer with oncolytic virus OH2 [bulkRNA-seq_22-Rv1]

first: Jinzhou

overall_design: Prostate cancer cell lines (22-Rv1, 3 vs. 3) were treated with oncolytic virus OH2 intervention

first: Ye

first: Guichen


title: JAX Study 8- RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for nine different transcription factors.

first: MorPhiC

last: Consortium

summary: This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated by insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated after 6 days of initiating differentiation from iPSCs. The study included the homozygous null alleles for the following transcription factors: DLX3, MSX2, VGLL1, MAFB, NR2F2, ELF5, ASCL2, HIF1A, and TP63. Notably, the hypoxia-inducible factor HIF1A as well as ELF5, ASCL2, and TP63 were evaluated under both 20% oxygen and 3% (~ level present at peri-implantation) oxygen concentrations. This analysis provided insight into the impact of loss of function for these transcription factors in trophoblast lineage differentiation.

overall_design: The study involved the generation of RNA-seq on 53 samples. Eight of the transcription factors were analyzed in the primitive syncytium differentiation scheme and one in the extra-embryonic mesenchymal cell scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions and under both 20% and, in some cases, 3% O₂ concentrations. This comprehensive design allowed for a robust analysis on the effects of transcription factor manipulation on cell fate decisions within the extra-embryonic lineage.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: Inhibition of NLRP1 Inflammasome Activation by Tyrosine Kinase Inhibitors Restores Erythropoiesis in Diamond-Blackfan Anemia Syndrome

city: Elche

first: Alicia

last: Martinez Lopez

state: Alicante

address: Avenida Candalix 42, 5A

country: Spain

institute: IMIB

summary: Diamond-Blackfan Anemia Syndrome (DBAS) is characterized by impaired erythropoiesis due to dysfunctional ribosome biogenesis and aberrant cellular signaling. Here, we investigate how ribosomal stress-induced activation of the NLRP1 inflammasome modulates erythroid differentiation in DBAS. We demonstrate that FDA/EMA-approved tyrosine kinase inhibitors (TKIs) effectively mitigate defective erythropoiesis in Diamond-Blackfan anemia syndrome (DBAS) by inhibiting NLRP1 inflammasome activation. Specifically, nilotinib enhances erythroid differentiation in K562 cells through suppression of the ZAKα/P38/NLRP1/CASP1 axis, leading to increased GATA1 protein levels and upregulation of key erythroid genes involved in iron acquisition, hemoglobin synthesis, and erythrocyte structure. These effects were validated in human CD34+ hematopoietic stem and progenitor cells (HSPCs) and zebrafish models, where nilotinib, along with other TKIs (imatinib, dasatinib, and bosutinib), promoted erythropoiesis at the expense of myelopoiesis and reduced caspase-1 activity. Importantly, in RPS19-deficient zebrafish and human models and HSPCs from patients with DBAS, nilotinib, imatinib and dasatinib rescued defective erythroid differentiation and restored hemoglobin levels. These findings highlight the potential of TKIs to address the erythroid defects observed in ribosomopathies like DBAS. Given the limited treatment options available for DBAS and other congenital anemias, our study provides compelling evidence for repurposing TKIs as a novel therapeutic strategy to alleviate pathological NLRP1 activation and improve erythropoiesis. This work opens new avenues for managing ribosome-related disorders and advancing personalized medicine approaches for hematopoietic diseases.

overall_design: K562 cells were pretreated with 0.1 μM nilotinib, followed by differentiation with 50 μM hemin for 24 h. Three biological replicates (15 μl at 200 ng/μl)


title: Responses of intestinal organoids to infection by Mycobacterium avium resemble symptoms observed in Crohn’s disease

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: Crohn’s disease (CD) is a chronic inflammatory bowel disease (IBD) in humans. Mycobacterium avium, which causes Johne’s disease in ruminants, has been suggested as a potential CD trigger due to similar pathology. However, early epithelial responses to M. avium and their relevance to CD remain unclear. This study aimed to establish a mouse small intestinal organoid (mSIO) model of M. avium infection and assess whether the resulting epithelial and immune responses resemble CD-related inflammation. M. avium-infected mSIOs were analyzed using confocal microscopy, serial block-face scanning electron microscopy, and a macrophage co-culture system to observe bacterial localization and immune cell behavior. RNA-seq and Gene Set Enrichment Analysis (GSEA) were performed to assess transcriptional changes. Comparative transcriptomic analysis was performed against a previous published RNA-seq dataset from gut tissues of germ-free mice colonized with microbiota from CD patients. M. avium efficiently infected mSIOs, disseminated through the tissue and triggered macrophage migration and clustering around infected organoids. Transcriptomic profiling revealed strong upregulation of inflammatory genes and enrichment of pro-inflammatory pathways such as TNF-α signaling. Comparative analysis revealed significant overlap in gene expression profile between M. avium-infected mSIOs and intestinal tissues of CD-humanized mice, including shared enrichment of the IBD signaling pathway. Notably, Mmp7, involved in epithelial remodeling and inflammation, emerged as a common marker in both models. This study presents a robust mSIO model of M. avium infection that replicates key features of CD-associated inflammation. The model presents a useful tool for studying host-pathogen interactions and identifies Mmp7 as a molecular link between bacterial infection and CD-like pathology.

overall_design: Mycobacterium avium-infected mouse small intestinal organoids and their uninfected control organoids were collected for RNAseq

middle: P

first: Wanbin

last: Hu


title: Transcriptional reprogramming in mantle cell lymphoma promotes BTK inhibitor resistance

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

country: USA

institute: Weill Cornell Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Resistance to Bruton’s tyrosine kinase inhibitors (BTKi) remains a major therapeutic challenge in B-cell malignancies, limiting treatment durability. We demonstrate BRG1-mediated chromatin remodeling as a major driver of BTKi resistance. We show that cancer-associated BRG1 ATPase domain mutations protect cells from BTKi-induced ferroptosis by limiting reactive oxygen species (ROS) production and labile iron. Mechanistically, the BRG1T910M mutation activates the unfolded protein response (UPR) via ATF4, leading to upregulation of MEF2B, a key suppressor of ferroptosis. MEF2B further inhibits mitochondrial respiration and thus prevent BTKi-induced mitophagy and ferroptosis. Pharmacological inhibition of BRG1 promotes ferroptosis by suppressing pro-survival B cell receptor (BCR) signaling and the ATF4-MEF2B axis. We show that a clinical stage BRG1 inhibitor restores ferroptosis in BTKi-resistant cells and synergizes with BTKi across various MCL models. Together we propose  for co-targeting BRG1 and BTK in treatment of B-cell malignancies.

overall_design:
MINO cells expressing wildtype or mutant BRG1 or treated with FHD-286 were analyzed by RNA-seq. JEKO cells ectopically expressing MEF2B were analyzed by RNA-seq. Primary MCL cells were analyzed by RNA-seq.
MINO cells expressing wildtype or mutant SMARCA4 or treated with FHD-286 were analyzed by ATAC-seq or BRG1/H2K27Ac Cut&Run. CCMCL1 cells expressing cas9-sgROSA or cas9-sgBRG1 were analyzed by ATAC-seq. JEKO cells ectopically expressing MEF2B were analyzed by Cut&Run.

first: Hwang

last: Sooyeon

first: Nikolli

last: Helgi

first: Paik

last: Jihye


title: Non-destructive transcriptomics via vesicular export (NTVE)

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

summary: Transcriptomics is a valuable technique for multiplexed monitoring of cellular states. Using an engineered RNA adapter, NTVE exports cellular transcripts from inducible human and murine reporter cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE allows monitoring of transcriptome changes in response to genetic and chemical perturbations (Interferon gamma; ASCL1 transactivation) in the same cells over time using standard sequencing workflows.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Samples originate either from cell lysates or were prepped from the supernatant by using a viral RNA preparation kit (see method section https://doi.org/10.1101/2024.11.11.622832)

first: Niklas

last: Armbrust

first: Martin

last: Grosshauser

first: Jeffery

last: Truong


title: Characterization of mouse melanocytes reveals ultrastructural and immunological insights into the inner ear function

status: Public on Aug 31 2025

city: Jinan

first: Jing

last: Cai

state: Shandong

address: 4 Duanxing West Road

department: Shandong Provincial ENT Hospital

institute: Shandong University

summary: Melanocytes are important components of the inner ear’s cellular architecture. However, limited morphological research has hindered a complete understanding of inner ear function. This study characterized the morphology of inner ear melanocytes and cells often misidentified as melanocytes. Immunofluorescence, Smart-seq, transmission/field emission scanning electron microscopy, and immunoelectron microscopy were used. Cells with a “black ball” appearance in the vestibule were identified as macrophages. We examined variation in melanocytes or macrophages with age, strain, and cisplatin injury. Kir4.1 expression and the greater noise resistance observed in pigmented mice suggest potential melanocyte functions. Based on melanin distribution in Pou3f4y/- mice, we hypothesize that melanocytes migrate from the modiolus along Reissner's membrane to the stria vascularis, following a base to apex gradient. These findings provide novel ultrastructural and immunological insights into inner ear function.

overall_design: Smart-RNA-seq profiling of Cells with a “black ball” appearance in the vestibule.

first: Lei

last: Xu

first: Yongdong

last: Song

first: Aizhen

last: Zhang

first: Zheng

last: Li

first: Boqin

first: Haibo

last: Wang


title: Blocking PD-1 engagement rapidly upregulates innate antiviral and immune functions that associate with HIV reservoir decay [bulkRNA-seq]

city: PHOENIX

first: Aarthi

last: Talla

state: ARIZONA

address: 2448 W ROWEL RD

institute: IMMUNASYST

summary: The HIV reservoir, a small pool of PD-1+CD4+ T cells that carry integrated HIV genomes, remains a formidable obstacle to HIV cure. The clinical use of PD-1 inhibitors has shown promising results in curbing the HIV reservoir in people with HIV (PWH) and cancer, but the underlying mechanisms are unknown. Here, we demonstrate that anti-PD-1 therapy leads to a decay in the frequency of cells harboring HIV DNA at the end of a two-year follow-up in 9 of 14 PWH receiving pembrolizumab within the CITN-12 clinical trial (NCT02595866). This reduction correlates with an innate immune response, characterized by increased monocyte frequencies and enhanced myeloid cell-specific transcription of interferon-stimulated genes (ISGs), chemokines, antiviral restriction factors, and TLR signaling. These changes emerge as early as 24 hours post-treatment and persist until the end of therapy. Within 24 hours of treatment, we also observe an increase in proliferating effector HIV-specific CD8+ T cells, increased expression of effector T cell genes, and a decline in plasma TGF-β levels. We validate the generalizability of these ISG expression modules across >1,000 publicly available scRNA-seq samples, revealing a consistent association between high ISG expression in peripheral blood mononuclear cells (PBMCs) and lower expression of WNT pathway and Treg gene sets - pathways known to regulate immune quiescence and persistence of the HIV reservoir - in PBMCs from uninfected controls, as well as in samples from individuals with cancer or infections. Furthermore, we demonstrate that ISGs triggered by TLR ligands protect CD4+ T cells from HIV infection in vitro. These findings support a mechanism by which ISGs restrict the HIV reservoir in vivo and define a set of immune signaling pathways that can be used to identify PWH in whom the HIV reservoir may decay upon anti-PD-1 therapy.

overall_design: Bulk RNA sequencing was performed on whole blood collected in PAXgene tubes from participants at the following timepoints: C01D01 (pre-treatment), C01D02 (hours after the first treatment cycle ), and EOT (end of therapy).

first: Joao

middle: L

last: Azevedo

first: Muhammad

middle: B

last: Latif

first: Ana

last: Enriquez

first: Gabriela

last: Sanchez

first: Ashish

last: Sharma

first: Rafick-Pierre

last: Sekaly


title: TGF-β induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis

status: Public on Aug 29 2025

city: New York

first: Zhenghan

address: 417 East 68th St

department: CBG

institute: Memorial Sloan Kettering Cancer Centerr

summary: The heterogeneity of epithelial-to-mesenchymal transition (EMT) programs is manifest in the diverse EMT-like phenotypes occurring during tumor progression. However, little is known about the mechanistic basis and functional role of specific forms of EMT in cancer. Here we address this question in lung adenocarcinoma (LUAD) cells that enter a dormancy period in response to TGF-β upon disseminating to distant sites. LUAD cells with the capacity to enter dormancy are characterized by expression of SOX2 and NKX2-1 primitive progenitor markers. In these cells, TGF-β induces growth inhibition accompanied by a full EMT response that subsequently transitions into an atypical mesenchymal state of round morphology and lacking actin stress fibers. TGF-β induces this transition by driving the expression of the actin-depolymerizing factor gelsolin, which changes a migratory, stress fiber-rich mesenchymal phenotype into a cortical actin-rich, spheroidal state. This transition lowers the biomechanical stiffness of metastatic progenitors, protecting them from killing by mechanosensitive cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Inhibiting this actin depolymerization process clears tissues of dormant metastatic cells. Thus, LUAD primitive progenitors undergo an atypical EMT as part of a strategy to evade immune-mediated elimination during dormancy. Our results provide a mechanistic basis and functional role of this atypical EMT response of LUAD metastatic progenitors and further illuminate the role of TGF-β as a crucial driver of immune evasive metastatic dormancy.

overall_design: To enable the simultaneous collection of samples exposed to different TGF-β treatment durations (0 h (control), 3 h, 1 d, 3 d, 5 d, and 7 d) for scRNA-seq analysis, the start of cell culture and TGF-β administration for these samples were correspondingly staggered. Specifically, H2087-BrM cells were plated in 10 cm petri dishes for each treatment condition and incubated overnight for attachment. Subsequently, the medium was replaced with fresh MLM medium supplemented with 10 pg/mL TGF-β for the specified durations, with the medium changed every 2 days, before being harvested for scRNA-seq analysis. Two experimental replicates (Samples 1 and 2) were collected and processed for scRNA-seq on consecutive days, following the same protocol as decribed. The two samples showed strong agreement, confirming their reproducibility as replicates, and were therefore combined for downstream analysis. In both samples, TotalSeq-A0251 and A0252 were used together to label cells following TGF-β treatment at 0 h (control), while A0253, A0254, A0255, A0256, and A0257 were used for the 3 h, 1 d, 3 d, 5 d, and 7 d time points, respectively.

first: Siting

last: Gan

first: Joan

last: Massagué


title: Treatment of prostate cancer with oncolytic virus OH2 [bulkRNA-seq_tumors]

status: Public on Aug 30 2025

first: Jinzhou

overall_design: Prostate cancer subcutaneous transplanted tumors (RM-1, 5 vs. 5) were treated with oncolytic virus OH2 intervention

first: Ye

last: An

first: Guichen

last: Ye

first: Zhiyu

last: Xia

first: Shaogang

first: Qidong


title: Therapeutic reduction of RAD23A extends lifespan and mitigates pathology in TDP-43 mice

city: London

first: Ravindra

middle: Singh

last: Prajapati

state: UK

address: 2nd floor, Maurice Wohl Clinical Neuroscience Inst, 5 Cutcombe Road

department: BCN, Maurice Wohl Clinical Neuroscience Ins

institute: King's College London

summary: Protein misfolding and aggregation are cardinal features of neurodegenerative disease (NDD) and they contribute to pathophysiology by both loss-of-function (LOF) and gain-of-function (GOF) mechanisms.  This is well exemplified by TDP-43 which aggregates and mislocalizes in several NDDs.  The depletion of nuclear TDP-43 leads to reduction in its normal function in RNA metabolism and the cytoplasmic accumulation of TDP-43 leads to aberrant protein homeostasis.  A modifier screen found that loss of rad23 suppressed TDP-43 pathology in invertebrate and tissue culture models.  Here we show in a mouse model of TDP-43 pathology that genetic or antisense oligonucleotide (ASO)-mediated reduction in the RAD23A confers benefits on survival and behavior, histological hallmarks of disease and reduction of mislocalized and aggregated TDP-43.  This results in improved function of the ubiquitin-proteasome system (UPS) and correction of transcriptomic alterations evoked by pathologic TDP-43.  RAD23A-dependent remodeling of the insoluble proteome appears to be the key event driving pathology in this model.  As TDP-43 pathology is prevalent in both familial and sporadic NDD, targeting RAD23A may have therapeutic potential.

overall_design: In order to gain insight into the mechanisms underlying RAD23A actions in a TDP-43-based mouse model of ALS/FTD (TDP-43Tg/+), we utilized antisense oligos to knock down Rad23a in the mouse motor cortex. Scrambled antisense oligos were used as a control. Both wild-type (WT) and TDP-43Tg/+ mice's motor cortex were treated with scrambled and rad23a knockdown ASOs. We used ten biological replicates for each condition. To identify genes associated with the disease, we compared WT scrambled with TDP-43Tg/+ scrambled, and to identify genes associated with the treatment, we compared TDP-43Tg/+ scrambled with TDP-43Tg/+ rad23a knockdown ASO-treated mice.

first: Xueshui

last: Guo

middle: S

first: Jiyeon

last: Chun

first: Insuk

last: Byun

first: Kamil

middle: K

last: Gebis

first: Yi-Zhi

first: Karen

last: Ling

first: Casey

last: Dalton

first: Jeff

last: Blair

first: Anahid

last: Hamidianjahromi

first: Jeffrey

middle: N

last: Savas

first: Min

middle: J

last: Lee

first: Jemeen

last: Sreedharan

first: Robert

last: Kalb


title: Single-cell RNA-seq of MMTV-PyMT mouse lungs treated with long-term systemic tamoxifen treatment

status: Public on Aug 28 2025

city: Incheon

first: Jong-Hyuk

last: Sung

address: 32 Songdogwahak-ro

country: South Korea

institute: Epi Biotech Co., Ltd.

summary: Estrogen receptor (ER)-positive breast cancer (BC) patients face constant threat of distant recurrence up to 20 years of diagnosis, reaching a total of 30% recurrence and a mortality rate of more than 25%. Here, we examined the influence of long-term tamoxifen treatment in metastatic niche formation in vivo. To test this, placebo or tamoxifen pellets were inoculateded in the 8-week old MMTV-PyMT mouse model and analyses were conducted 5-weeks after the treatment. Despite a reduction in primary tumor size compared to the placebo-treated group, lung metastasis was increased in the tamoxifen-treated mouse. At this point, scRNA-seq was also performed in mouse lungs of either placebo or tamoxifen-treated MMTV-PyMT mouse lungs, which revealed an increase in an interstitial macrophage subpopulation in the tamoxifen-treated group. This Prg4+ macrophages had enhanced lipid metabolic gene signatures and strongly interacted with fibroblasts via TGFβ1 signaling pathway, potentially contributing to lung fibrosis. This study identifies long-term tamoxifen treatment as a risk factor for promoting breast cancer cell resistance and altering the lung microenvironment, thereby facilitating lung metastasis.

overall_design: FVB/NJ mice mammary tumor virus–polyoma middle tumor-antigen (MMTV-PyMT; designated as PyMT) (RRID: IMSR_JAX:002374) at 8-weeks-old were separated randomly into two groups (n=2 for each group) and implanted with tamoxifen pellets (5 mg, 60-day release) (Innovative Research of America, SE-361) or placebo pellets (SE-111). Tumor diameter was measured with caliper two times a week, and tumor volumes were estimated using the following formula: tumor volume (cm3) = (length x width2) x 0.5. After 5 weeks of implantation, mice were sacrificed and lungs were removed after perfusion with sterile saline from the right to the left ventricle of the heart.

first: Mi-Ock

first: Minsoo

last: Noh

first: Seung-Su

last: Kim

first: Seungchan


title: Blocking PD-1 engagement rapidly upregulates innate antiviral and immune functions that associate with HIV reservoir decay [scRNA-seq]

first: Aarthi

last: Talla

overall_design: Single cell RNA sequencing was performed on Peripheral blood mononuclear cells (PBMCs) on a subset of participants that had bulk RNA sequencing data, at the following timepoints: C01D01 (pre-treatment), C01D02 (hours after the first treatment cycle ), and one week after the first cycle (C01D08).

first: Joao

last: Azevedo

first: Muhammad

last: Latif

first: Ana

last: Enriquez

first: Gabriela

last: Sanchez

first: Ashish

last: Sharma

first: Rafick-Pierre

last: Sekaly


title: Satellite Cells Choreograph an Immune Cell-Fibrogenic Cell Circuit During Mechanical Loading in Geriatric Skeletal Muscle

city: Lexington

first: Christopher

last: Fry

state: Kentucky

address: 900 S. Limestone

institute: University of Kentucky

summary: Muscle stem cells, or satellite cells, decline in number with age and may become senescent. Whether and how satellite cells contribute to muscle adaptation in the oldest-old is unclear. Using short-term mechanical overload in geriatric satellite cell replete and depleted mice (28 months of age) combined with single cell RNA-sequencing, we show: 1) subsets of geriatric satellite cells show signs of senescence as well as normal fate progression during overload, 2) satellite cells express markers that may contribute to the regulation of innervation, 3) the presence of satellite cells during overload globally enhances intercellular communication and causes upregulation of the cell surface receptor gene Cd74 in immune cells, 4) Mif, the primary ligand for CD74, is produced by fibrogenic cells and is more pronounced in the absence of satellite cells - perhaps to help normalize dysregulated fibrotic signaling, and 5) satellite cells drive fate directive transcript splicing that promotes the canonical macrophage response to hypertrophic loading. Our findings expose the behavior of satellite cells in response to mechanical loading in the oldest-old and reveal a satellite cell-macrophage-fibrogenic cell circuit in geriatric muscle that may promote extracellular matrix remodeling

overall_design: 28-month-old Pax7-DTA mice with satelite cells depleted via tamoxifen treatment  ("SC-" in study, "t" in file names) or satellite cells retained via sunflowerseed oil treatment vehicle ("SC+" in study, "v" in file names) 2-weeks prior to 96-hours of mechnical overlaod via removal of gastrocnemius and soleus muscles.

first: Nicholas

last: Thomas

first: Yuan

last: Wen

first: Kevin

last: Murach


title: Single cell RNA-sequencing of male and female dorsal root ganglia (DRG) following Bortezomib (BTZ) or vehicle (VEH) administration.

city: St. Louis

first: Valeria

last: Cavalli

state: MO

address: 1 Bookings Dr.

institute: Washington University in St. Louis

summary: Peripheral neuropathies are the most common neurodegenerative diseases affecting more than 20 million people in the USA alone. Chemotherapy, including treatment with the highly effective drug bortezomib (BTZ), is a frequent cause of peripheral neuropathy. We demonstrated recently that while some chemotherapeutics exert direct toxic effects on axons, BTZ leads to axon degeneration via signals from neuronal somata, which reside in the dorsal root ganglia (DRG). However, what these signals are and how they arise is unknown. To address this question, we treated mice intravenously with BTZ twice weekly for 8 weeks and determined the impact on DRG gene expression via single cell RNA-sequencing.

overall_design: In these experiments we used wild-type mice (Balb/cJ mice own colony, average age 13 weeks) to test the effects of bortezomib treatment on peripheral neuropathy. Vehicle (5% 100% EtOH, 5% Tween-80, 90% Sterile Saline) or bortezomib (2 mg/ml in 100% ethanol) (Millipore Sigma) dissolved in 5% Tween-80, 90% Sterile Saline (0.1 mg/ml) was administered intravenously by tail vein injection twice weekly at a dose of 0.8 mg/kg for 8 weeks. Following administration, DRG tissues were isolated and analyzed using scRNAseq.

first: Michael

last: Thomsen

first: Stefanie

last: Geisler

first: Oshri

last: Avraham


title: Hepatitis virus-associated B cell non-Hodgkin’s lymphoma involves dysregulated epigenetic and RNA-mediated regulatory gene expression and altered snoRNA transcription

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Infection with HBV and its satellite virus HDV remain a significant global health issue due to their involvement in hepatic and extrahepatic diseases, including B cell non-Hodgkin’s lymphoma (BNHL). Clinical and epidemiological evidence support a causal role for HBV in BNHL development, although mechanistic insight is lacking and the role of HDV infection in this process is unknown. We performed RNA-sequencing on peripheral B cells from patients with HBV mono-infection, HBV/HDV co-infection, BNHL, and HBV/HDV-associated BNHL to identify unique and shared transcriptional profiles associated with transformation. Our data suggest dysregulated epigenetic and miRNA-mediated regulatory gene expression may be a potential common pathway for lymphomagenesis among viral- and non-viral-associated lymphoma. We also observed wide-spread upregulation of snoRNAs in B cells from virally infected patients, supporting a role for these non-coding RNAs in viral infection and, potentially, viral-associated lymphomagenesis.

overall_design: RNA-sequencing of peripheral B cells isolated from patients with chronic HBV infection (n=4), HBV/HDV co-infection (n=7), B cell non-Hodgkin's lymphoma (n=6), HBV/HDV-associated B cell non-Hodgkin's lymphoma (n=3), and healthy donors (n=6)

last: De Giorgi


title: A fully iPSC-derived 3D model of the human blood-brain barrier for exploring neurovascular disease mechanisms and therapeutic interventions

status: Public on Aug 26 2025

first: Rainer

last: Malik

address: Feodor-Lynen-Str. 17

department: Institute for Stroke and Dementia Research

institute: Klinikum der Universität München

summary: Integrity of the blood-brain barrier (BBB) is critical for brain homeostasis, and its malfunction contributes to neurovascular and neurodegenerative disorders. So far, mechanistic studies on BBB function have been mostly conducted in rodent and non-physiological in vitro models, which recapitulate some disease features, but have limited translatability to humans and pose challenges for drug discovery. Here we report on a fully human iPSC-derived, microfluidic 3D BBB model consisting of endothelial cells (EC), mural cells, and astrocytes. Our model expresses typical cell fate markers, forms a barrier in vessel-like tubes, and enables perfusion, including with human blood. We optimized iPSC differentiations and validated cellular fates by comparison to published datasets and extensive benchmarking vs. primary cells with proteomic profiles provided in an online database. To demonstrate suitability for translational research, we applied the model to investigate deficiency of FOXF2, a major risk gene for cerebral small vessel disease. Deletion of FOXF2 in EC induced key features of BBB dysfunction, including compromised cell junction integrity and enhanced caveolae formation. Proteomic analysis further revealed dysregulation of endocytosis and cell junction pathways. Disease features phenocopied those seen in mice with endothelial cell-specific Foxf2 deficiency, validating the relevance of our in vitro model to investigate in vivo phenotypes of neurovascular disease. Moreover, lipid-nanoparticle-based treatment with Foxf2 mRNA rescued BBB deficits in our FOXF2 KO model, demonstrating its potential for drug development.

overall_design: bulk RNA-seq of human endothelial and mural cells derived from iPSCs, which were then compared to published datasets as described in the publication

first: Judit

last: González-Gallego

first: Katalin

last: Todorov-Völgyi

first: Martin

last: Dichgans

first: Dominik

last: Paquet


title: Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive

department: Cell Biology

institute: Duke University

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

overall_design: Refer to individual Series


title: Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells

status: Public on Aug 25 2025

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary:
This SuperSeries is composed of the SubSeries listed below.
Muscle stem cells (MuSC) are the cellular source for generation and regeneration of skeletal muscle. To ensure correct muscle growth, MuSC self-renewal and differentiation need to be tightly regulated. Several signaling systems have been implicated in the control of MuSCs, among them Bone Morphogenetic Proteins (BMPs) and Notch, both of which promote MuSC proliferation and suppress differentiation. To better understand the mechanisms of function and the target genes regulated by BMP signaling in myogenesis, we investigated the transcriptional responses of adult mouse MuSCs to BMP6/4 using RNA-sequencing. BMP6/4-stimulation of freshly isolated MuSCs for one hour rapidly increased the expression of classical BMP target genes like Id1 and strongly induced expression of genes of the Notch pathway (Hes1, Hey1, Lfng, Snai1). In parallel, using Cleavage Under Targets and Tagmentation (CUT&Tag), we generated whole-genome binding profiles for the BMP pathway effectors pSMAD1/5/9 and SMAD4 and detected binding in promoters and potential regulatory elements of BMP targets and Notch pathway genes (Hes1, Hey1, Lfng, Snai1) indicating that BMP signaling directly influences Notch and that crosstalk between the two pathways regulates myogenesis.

overall_design: Refer to individual Series.

first: Birthe

last: Lange

first: Ioanna

last: Polydorou

first: Viktoriia

last: Huryn

first: Helge

last: Amthor


title: STING induces ZBP1-mediated necroptosis independently of TNFR1 and FADD

status: Public on Aug 21 2025

city: Cologne

first: Gianmaria

last: Liccardi

address: Joseph Stelzmann strasse 52, Institute of Biochemistry

institute: Uniklinik, University of Cologne

summary: Conditional deletion of Caspase-8 in epidermal keratinocytes (Casp8E-KO) causes necroptosis-driven lethal dermatitis1-7. Here, we discover that Casp8 loss leads to accumulation of cytosolic DNA responsible for the activation of a cyclic-GMP-AMP synthase (cGAS)/stimulator of interferon (IFN) gene (STING)-mediated transcriptional program. Genetic and biochemical evidence indicate that STING upregulates both Z-DNA binding protein-1 (ZBP1), and mixed lineage kinase domain-like (MLKL). Combined Casp8-deficiency- and STING-activation-driven accumulation of Z-nuclei acids, activates ZBP1 and triggers formation of a ZBP1–RIPK1–RIPK3 complex independently of FADD-RIPK1-RIPK3 complex enabling necroptosis execution. Genetically, we reveal a functional overlap between STING and ZBP1 as drivers of lethal dermatitis independently of TNFR1, uncovering a novel aetiology of necroptotic inflammation. Since gain-of-function mutations in human STING cause STING-Associated Vasculopathy with onset in Infancy (SAVI), we assessed the role of STING-induced necroptosis in SAVI’s aetiology. Chronic activation of STING in patients orchestrates a necroptotic transcriptional program which is confirmed in the N153S-SAVI preclinical mouse model where immune cell–driven pathology and lethality are remarkably rescued by RIPK3 co-deletion. These findings establish STING-driven ZBP1-mediated necroptosis as a central pathogenic mechanism in both Casp8-deficient inflammation and SAVI and suggest that targeting the ZBP1-RIPK3-MLKL axis holds therapeutic potential for interferonopathies characterised by excessive necroptosis.

overall_design: Comparative gene expression from skin of p5 mice in Casp8E-KO , Casp8E-KO ;  Tnfr1-/- , Casp8E-KO ;  StingE-KO, Casp8E-KO ;  Sting-/-  , Casp8E-KO/wt. TP = Time point= P5.

first: Konstantinos

last: Kelepouras

first: Julia

last: Saggau

first: Debora

last: Bonasera

first: Christine

last: Kiefer

first: Federica

last: Locci

first: Hassan

last: Rakhsh-Khorshid

first: Louisa

last: Grauvogel

first: Ana

last: Abreu Varanda

last: Peifer

first: Elena

last: Loricchio

first: Antonella

last: Montinaro

first: Marijana

last: Croon

first: Aleksandra

last: Trifunovic

first: Giusi

last: Prencipe

last: Insalaco

first: Fabrizio

last: De Benedetti

first: Henning

last: Walczak


title: Ontogeny of the spinal cord dorsal horn [Xenium]

status: Public on Aug 22 2025

first: Brian

last: Roome

address: 35 Convent Drive

department: NINDS

summary: An exquisite example of form serving function is the dorsal horn of the spinal cord, the gateway  to the central nervous system for sensory information from the body. Each sensory input to the  dorsal horn targets a specific address within its laminated arrangement of diverse neuronal  populations. However, it is not known how this organization emerges during development from  an apparently homogenous pool of neural progenitors. Here, we found that both the excitatory  and inhibitory cell families of the mouse dorsal horn were born in successive waves as temporal  cohorts. The excitatory families then settled into a chronotopic map that transformed their birth  order into the dorsal laminae. Diversification of families into refined neuron types was mediated  by a dorsal-ventral progenitor gradient of Zic transcription factors. This work uncovered  fundamental temporal and spatial factors that establish the cell types and structure of the  spinal cord dorsal horn.

overall_design: Spinal cords taken from E16.5 mouse embryos were examined using the 10X Xenium v1 spatial transcriptomics platform, using the 247 gene mouse brain probe panel and with 100 additional custom gene probes.

first: R

first: Ariel

last: Levine


title: The effects of PD-L1 and SCE over-expression on CAR-NK cell cytotoxicity against tumor cells

status: Public on Aug 20 2025

city: Cambridge

first: Fuguo

last: Liu

address: 500 Main Street

department: Koch Institute For Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

summary: This experiment aims to investigate how the overexpression of PD-L1 and SCE enhances the cytotoxic activity of CAR-NK cells against tumor cells. Pathway enrichment analysis revealed that CAR-NK cells with reduced HLA-ABC and overexpressed PD-L1 showed enrichment in proliferation and pro-inflammatory pathways. In contrast, CAR-NK cells with reduced HLA-ABC and overexpressed SCE exhibited enrichment in homeostasis-related pathways. On the other hand, cellular stress pathways were more prominently enriched in HLA-ABC reduced CAR NK cells following co-culture with target cells.

overall_design: To elucidate the mechanisms underlying the enhanced NK cell cytotoxicity following PD-L1 and SCE overexpression, NK cells isolated from 4 unrelated donors were transduced with lentivectors expressing shRNA #1+MLSN CAR, shRNA #1+MLSN CAR+PD-L1, or shRNA #1+MLSN CAR+SCE. NK cells from the same donors but without transductions were used as controls. NK cells were labeled with CTV and then cocultured with OVCAR8 target cells or in the media alone for 18 hours in triplicates. The cocultured NK cells were purified by cell sorting and processed for RNAseq.

first: Yiming J

last: Zhang

first: Rizwan

last: Romee

first: Jianzhu

last: Chen


title: Ontogeny of the spinal cord dorsal horn


title: Chromatin profiling of the Harpegnathos saltator antennae

first: Bogdan

last: Sieriebriennikov

address: 100 Washington Sq E

institute: New York University

summary: We have profiled the antennae of Harpegnathos saltator for H3K27ac, H3K27me3, and H3K4me3.

overall_design: We have isolated nuclei from the antennae of Harpegnathos saltator and performed CUT&RUN against H3K27ac, H3K27me3, H3K36me3 and H3K4me3.

first: Olena

last: Kolumba

first: Aurore

last: de Beaurepaire

first: Jennifer

last: Wu

first: Eva

last: Bardol

first: Valentina

last: Fambri

first: Yuwei

last: Zhong

first: Ildar

last: Gainetdinov

first: Danny

last: Reinberg

first: Hua

last: Yan

first: Claude

last: Desplan


title: Pro-inflammatory c-Met+ CD4 T cells in multiple sclerosis

status: Public on Aug 19 2025

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Objective Hepatocyte growth factor (HGF) binds exclusively the c-Met surface receptor, and the HGF/c-Met axis regulates T-cell function in autoimmune diseases. We analyzed c-Met expression on human CD4 T cells in the blood and cerebrospinal fluid (CSF) from patients with multiple sclerosis (MS) versus non-inflammatory neurological disease (NIND), to better understand the role of CD4 T cells in MS. Methods We recruited 34 untreated MS patients (aged 28–43 years) and 10 NIND (aged 34–51 years) who underwent paired blood and CSF sampling at the time of diagnosis work-up. Phenotypic and functional CD4 T cells characterization was determined by flow cytometry and bulk RNA sequencing. Adhesion and transmigration capacities were studied to further characterize the function of c-Met+ CD4 T cells. Results c-Met+ memory CD4 T cells were detected at higher levels in both blood (median of 1.98%) and CSF (5.88%) in MS compared to NIND (0.37% and 0.68% respectively) (p<0.0001). Ex vivo c-Met+ CD4 T cells exhibited higher levels of GM-CSF, IL-17, IFN-γ and double positive IL-17+IFN-γ+ expression, compared with c-Met- CD4 T cells. c-Met+ CD4 T cells expressed increased levels of integrins – Itgα4β1 (VLA-4) and ItgαLβ2 (LFA-1) – compared with c-Met- CD4 T cells. Anti-Itgα4 (natalizumab) and anti-ItgαLβ2 (odulimomab) inhibited CD4 T cell transmigration with predominant inhibition of CD4 T cells expressing c-Met. Interpretation These results emphasize c-Met as an immune marker of highly pro-inflammatory and migratory CD4 T lymphocytes in both the periphery and central nervous system of MS patients.

overall_design: FACS-sorted T cell subsets were washed with PBS and resuspended in RNA lysis solution with 1% DTT. Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel). Complementary DNA was synthesized from total RNA using a reaction mix containing Tris-aminoMethane (200 mM), KCl (500 mM), MgCl2 (0.2 M; Sigma-Aldrich), DTT (100 mM; Invitrogen), random hexamers (50 mM; Invitrogen), oligo(dT) 15 primer (100 mg/ml; Promega), dNTP mix (10 mM; Promega), RNAsin (40 U/ml; Promega) and SuperScriptTM II (200 U/ml; Invitrogen). After incubation at 42°C for 50 min and inactivation at 99°C for 3 min, cDNA was diluted and stored at -20°C until use. On the FACS-sorted c-Met⁻ and c-Met⁺ CD4 T cells, we performed bulk-RNA sequencing. The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to the manufacturer’s specifications, starting with 1 ng of total RNA as input. Two hundred picograms of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High Sensitivity chip (Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads, generating an average of around 35,000,000 reads per sample. We employed GSEA to identify enriched biological themes within our dataset. Initially, differentially expressed genes (DEGs) were identified based on specific criteria (e.g., fold-change and p-value thresholds) and ranked based on their expression levels. Using the ranked list, GSEA was performed to determine whether sets of genes associated with specific biological processes, molecular functions, or cellular components were statistically overrepresented. We utilized the Molecular Signatures Database (MSigDB) for gene set annotations, and enrichment scores, nominal p-values, and false discovery rate (FDR) were calculated to assess the significance of gene set enrichment.

first: Gautier

last: Breville

first: Mahdia

last: Benkhoucha

first: Ayman

last: Rezk

first: Ngoc Lan

last: Tran

first: Isis

last: Senoner

first: Amit

last: Bar-Or

first: Patrice

middle: H

last: Lalive


title: Evolution of the human autopod skeleton

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

summary: We investigate the genetic architecture of autopod development at the regulatory and transcriptomic level.

overall_design: Examination of open chromatin regions (ATAC-seq) and differentially expressed genes (RNA-seq) in the developing autopod skeleton.

first: Alexander

last: Okamoto

middle: D


title: Gene expression and chromatin accessibility profiles at the single-nucleus level of the antennae of Harpegnathos saltator

first: Bogdan

last: Sieriebriennikov

summary: We performed multiome sequencing of the antennae of Harpegnathos saltator to identify potential regulatory element controlling the expression of odorant receptor genes.

overall_design: Nuclei were isolated from dissociated antennae and subjected to 10X multiome sequencing.

first: Olena

last: Kolumba

first: Aurore

last: de Beaurepaire

first: Jennifer

last: Wu

first: Eva

last: Bardol


title: Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease

city: Hamburg

first: Christian

last: Krebs

state: Hamburg

address: Martinistraße 52

institute: UKE

summary: Rapidly progressive glomerulonephritis (RPGN) is the most aggressive group of autoimmune kidney disease with the worst prognosis. Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis, anti-glomerular basement membrane (anti-GBM) and lupus nephritis are the most common causes of RPGN and are characterized by the formation of glomerular crescents and infiltration of leukocytes that eventually lead to glomerulosclerosis and kidney failure. In this work, we used high-resolution spatial transcriptomics of 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and 6 control patients to understand how intercellular signaling between immune and renal tissue cells leads to renal inflammation and glomerular injury. Using 3,218,210 immune and kidney cells, we observed that the biological pathways involved in the sequence of glomerular crescent formation are similar across the diseases. While innate immune cells infiltrated the glomerular compartment relatively early, later increases in adaptive immune cells were largely restricted to the periglomerular regions. These changes in immune cells temporally correlated with increases in glomerular parietal epithelial (PEC) and fibrotic mesangial cells, suggesting disease-relevant functional signaling between these immune and renal cells. Cell communication analysis revealed early disease PDGF signaling from epithelial and mesangial cells to PECs, causing their activation and proliferation. At later stages, TGF-β signaling from macrophages, T cells, epithelial cells, and mesangial cells to PECs triggered the expression of extracellular matrix components resulting in glomerulosclerosis. Our results highlight a spatio-temporally conserved progression into glomerular crescents and sclerosis for ANCA, lupus nephritis, and anti-GBM disease, which is driven by consecutive PDGF and TGF-β signaling to PECs.

overall_design: snRNA-seq of human samples from the kidney, specifically from individuals with ANCA-associated glomerulonephritis, was performed using Single Cell 3' v3.1 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 25,000 reads per cell on an Illumina NovaSeq 6000

first: Robin

last: Khatri

first: Saskia

last: Jauch-Speer

first: Ulf

last: Panzer

first: Stefan

last: Bonn

middle: F


title: Targeting Mediator MED23 inhibits HCC development by inhibiting compensatory proliferation and promoting ROS-mediated cell death [ChIP-seq]

status: Public on Aug 17 2025

city: Shanghai

first: zhang

last: yiyang

address: 2005 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan

summary: Hepatocellular carcinoma (HCC) is frequently linked to compensatory proliferating hepatocytes in damaged livers, yet the underlying molecular mechanisms remain elusive. The Mediator complex precisely coordinates multiple transcription factors and cofactors to regulate diverse physiological and pathological processes. Here we discovered that Mediator subunit MED23 is involved in the progression of HCC. Both constitutive and inducible liver-specific ablation of Med23 effectively inhibited HCC development in diethylnitrosamine (DEN)-induced HCC mouse models. Mechanistically, MED23 deficiency significantly compromised hepatocyte cell viability by reducing the stability of the NQO1 protein, thereby leading to an increase in reactive oxygen species (ROS) production. Furthermore, MED23 collaborates with the transcription factor RFX5 to regulate a novel enhancer function for IGF2 expression, which thus influences hepatocyte viability and HCC development. Consistently, overexpression of IGF2 in MED23-deficient HCC cells stabilizes NQO1 and partially restored cell growth and reduced apoptosis. Collectively, our findings underscore the significance of the MED23-IGF2-NQO1 axis in HCC progression and propose a novel therapeutic strategy for the treatment of HCC.

overall_design: CHIP-seq of H3K27ac and H3K4me1 in Tong cell with shRNA-mediated knockdown of Ctrl or MED23.

first: Zhichao

last: Wang

first: Xiaying

last: Zhao

first: Lihua

last: Min

first: Chonghui

last: Li


title: Transcriptomic profiling of oligodendrocytes, astrocytes, and microglia in an experimental autoimmune encephalomyelitis (EAE) model of demyelination

city: Sacramento

first: Hyun Kyu

last: Kim

state: CA

address: 2425 Stockton Blvd

department: Neurology

institute: UCDAVIS

summary: The experimental autoimmune encephalomyelitis (EAE) mouse model is widely used to study the pathophysiology of multiple sclerosis (MS), including brain inflammation and demyelination. This study investigates cell-type-specific transcriptional changes in oligodendrocytes, astrocytes, and microglia at day 30 post-induction of EAE using MOG peptide (amino acids 35–55) emulsified in complete Freund’s adjuvant (CFA) containing Mycobacterium tuberculosis, followed by pertussis toxin injections. CFA control mice received only CFA and pertussis toxin, without MOG peptide. Oligodendrocytes, astrocytes, and microglia were isolated using magnetic-activated cell sorting (MACS) from brain and spinal cord of CFA-treated and EAE-induced mice. Bulk RNA sequencing was conducted to uncover transcriptional changes associated with EAE-induced demyelination. These findings will enhance our understanding of glial cell contributions to MS pathogenesis and help identify potential therapeutic targets.

overall_design: Three-month-old C57BL/6 mice were received CFA and pertussis toxin (CFA control mice), or MOG peptide (35–55) emulsified in CFA and pertussis toxin to induce EAE. At day 30 post-induction,brain cell suspensions were prepared, and oligodendrocytes, astrocytes, and microglia were isolated using magnetic-activated cell sorting (MACS) with cell type-specific markers. Experimental groups for RNA sequencing: (1) Oligodendrocytes from CFA control mice (CFA_Ctrl_OL); (2) Oligodendrocytes from EAE mice (MOG_Ctrl_OL); (3) Astrocytes from CFA control mice (CFA_Ctrl_Astro); (4) Astrocytes from EAE mice (MOG_Ctrl_Astro); (5) Microglia from CFA control mice (CFA_Ctrl_MG); (6) Microglia from EAE mice (MOG_Ctrl_MG). Bulk RNA sequencing was performed for all cell types and conditions. Each group has 3 or 4 repeats.

first: Meina

last: Zhu

first: Yan

first: Fuzheng

last: Guo


title: Targeting Mediator MED23 inhibits HCC development by inhibiting compensatory proliferation and promoting ROS-mediated cell death [RNA-Seq]

overall_design: Whole liver tissues from Med23f/f and Med23Δli mice 48 hours after DEN treatment, used for RNA-seq profiling.


title: The role of microglia in demyelination: insights into the impact of oligodendrocyte-secreted Serpina3n

summary: Microglia, the primary immune cells of the central nervous system, play critical roles in demyelination process. This study investigates the transcriptional changes in microglia associated with demyelination and examines the role of oligodendrocyte-secreted Serpina3n in modulating microglial responses during this pathological process. Bulk RNA sequencing was conducted on microglia isolated from mice subjected to a 4-week cuprizone diet, a model of demyelination. The experimental groups included: (1) normal control mice (Norm_Ctrl), (2) cuprizone-treated wild-type mice (CPZ_Ctrl), and (3) cuprizone-treated Olig2-Cre Serpina3n flox/flox mice (CPZ_cKO). Microglia were purified from mouse brains using magnetic-activated cell sorting (MACS). The results of this study aim to deepen our understanding of olidodendroglial Serpina3n’s role in shaping microglial behavior during demyelination and could inform potential therapeutic strategies for demyelinating diseases.

overall_design: Experimental groups: Norm_Ctrl: Microglia isolated from wild-type mice fed with normal diet; CPZ_Ctrl: Microglia isolated from wild-type mice after 4 weeks of cuprizone diet; CPZ_cKO: Microglia isolated from Olig2-Cre Serpina3n flox/flox mice after 4 weeks of cuprizone diet. Microglia were isolated from mouse brains in each group using magnetic-activated cell sorting (MACS). Bulk RNA sequencing was performed on the purified microglia to profile transcriptional changes associated with demyelination and the loss of Serpina3n. Each group has 3 or 4 repeats.


title: Deciphering the role of oligodendroglial Serpina3n in EAE pathology using single-cell RNA sequencing

summary: This study employs single-cell RNA sequencing (scRNA-seq) to investigate cellular and transcriptional changes in the spinal cord at day 27 post-induction of experimental autoimmune encephalomyelitis (EAE). Samples were collected from three groups: (1) control mice treated with CFA only (Ctrl_CFA), (2) EAE-induced mice with MOG peptide administration (Ctrl_MOG), and (3) EAE-induced mice with oligodendrocyte-specific Serpina3n deletion (Olig2-Cre Serpina3n flox/flox, Serpina3n cKO_MOG). This approach aims to dissect the cellular diversity and molecular pathways affected by EAE, with a focus on the role of oligodendroglial Serpina3n in modulating neural cellular function and neuroinflammation. The findings provide insights into cell-specific contributions to spinal cord inflammation and demyelination, highlighting Serpina3n as a potential therapeutic target.

overall_design: Experimental Groups: (1) Ctrl_CFA: Spinal cord samples from control mice treated with CFA and pertussis toxin without MOG peptide. (2) Ctrl_MOG: Spinal cord samples from mice treated with MOG peptide (35–55) emulsified in CFA and pertussis toxin to induce EAE. (3) Serpina3n cKO_MOG: Spinal cord samples from EAE-induced mice with oligodendrocyte-specific Serpina3n deletion (Olig2-Cre Serpina3n flox/flox). At day 27 post-induction, spinal cords were extracted from mice in each group. Spinal cords from three mice were pooled and processed together for Single-cell RNA sequencing using the 10x Genomics Chromium platform.


title: Transcriptomic profiling of oligodendrocytes, astrocytes, and microglia in a cuprizone-induced demyelination model

summary: Demyelination is a central pathological feature of multiple sclerosis and many other neurodegenerative diseases, and the cuprizone diet is a widely used model for studying this process. This study examines the transcriptional changes in key glial cell types—oligodendrocyte and astrocytes—during demyelination induced by a 4-week cuprizone diet. Bulk RNA sequencing was performed on these cells isolated using magnetic-activated cell sorting (MACS) from mice on either a normal diet or a 0.3% cuprizone diet. The experimental groups included: (1) oligodendrocytes and astrocytes from mice on a normal diet, and (2) oligodendrocytes and astrocytes from mice on a cuprizone diet. This study provides a comprehensive transcriptomic view of how these glial cell types respond to demyelination and will enhance our understanding of their individual and collective roles in this pathological process.

overall_design: Two-month-old C57BL/6 mice were fed either a standard chow diet (Naive) or a 0.3% cuprizone-enriched diet (CPZ) for 4 weeks to induce demyelination. Brain cell suspensions were prepared, and oligodendrocytes, astrocytes, and microglia were isolated using magnetic-activated cell sorting (MACS) with cell type-specific MicroBeads. Experimental groups: (1) Oligodendrocytes from mice on a normal diet (Naive_OL); (2) Oligodendrocytes from mice on a cuprizone diet (CPZ_Ctrl_OL); (3)Astrocytes from mice on a normal diet (Naive_Ast); (4)Astrocytes from mice on a cuprizone diet (CPZ_Ctrl_Ast). Bulk RNA sequencing was performed for all cell types and conditions. Each group has 3 or 4 repeats.


title: Beta-catenin deletion and GSK3b inhibition in B-ALL cells

status: Public on Aug 08 2025

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: In most cell types, nuclear β-catenin functions as prominent oncogenic driver and pairs with TCF7-family factors for transcriptional activation of MYC. Surprisingly, B-lymphoid malignancies not only lacked expression and activating lesions of β-catenin but critically depended on GSK3b for effective b-catenin degradation. Our interactome studies in B-lymphoid tumors revealed that b-catenin formed repressive complexes with lymphoid-specific Ikaros and Lef1 factors at the expense of TCF7. While Lef1 was critical for nuclear β-catenin translocation, nuclear b-catenin enabled Ikaros-mediated recruitment of nucleosome remodeling and deacetylation (NuRD) complexes for transcriptional repression of MYC.

overall_design: To study gene expression changes induced by β-catenin deletion in B-ALL, BCR-ABL1 transformed Ctnnb1fl/fl cells were transduced with tamoxifen inducible Cre (Cre-ERT2) or control (ERT2) vectors. To induce deletion of β-catenin, cells were treated with 1μM 4-OHT for two days. For studying changes induced by small molecule induced activation of β-catenin, cells were treated with 40nM LY2090314 for 1 day. To assess whether β-catenin deletion reverts the LY2090314-induced transcriptional changes, cells were pre-treated 1μM 4-OHT 1 day before  LY2090314 treatment.

first: Kadriye

last: Nehir Cosgun

first: Markus

last: Müschen


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7) [I36]

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT36, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 7 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

overall_design: T cells were isolated from individual organs using mechanical dissociation, enzymatic digestion (collagenase I or DTE), and anti-CD45 intravenous labeling to distinguish tissue-resident from circulating cells. Sorted CD3e+ or IV- CD3e+ were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Giovanni

last: Galletti

first: Sara

last: Quon

first: Nicole

middle: E

last: Scharping

first: Kennidy

last: Takehara

first: Amir

last: Ferry

first: Ananda

last: Goldrath


title: Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age Associated Functional Decline

status: Public on Aug 13 2025

city: La Jolla

first: K. Garrett

last: Evensen

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Cellular senescence contributes to aging and age-related diseases by driving chronic inflammation through the Senescence Associated Secretory Phenotype (SASP) and interferon-stimulated genes (ISGs). Cyclin D1 (CCND1), a key cell cycle regulator, is paradoxically upregulated in these non-proliferating cells. We show that CCND1 and its kinase partner CDK6 drive SASP and ISG expression in senescent cells by promoting DNA damage accumulation. This leads to the formation of cytoplasmic chromatin fragments (CCFs) that activate pro-inflammatory CGAS-STING signaling. The tumor suppressor p53 (TP53) and its target p21 (CDKN2A) antagonize this CCND1-CDK6–dependent DNA damage accumulation pathway to suppress the SASP. In aged mouse livers, senescent hepatocytes show increased Ccnd1 expression. Hepatocyte-specific Ccnd1 knockout or treatment with the Cdk4/6 inhibitor Palbociclib reduces DNA damage and ISGs in aged mouse liver. Notably, Palbociclib also suppresses frailty and improves physical performance of aged mice. These findings reveal a novel role for CCND1/CDK6 in regulating DNA damage and inflammation in senescence and aging, highlighting it as a promising therapeutic target.

overall_design: In this study, we collected CosMx spatial transcriptomics data on young, old, and Pten KO mice using the 1,000 plex panel

first: Armin

last: Gandhi

first: Adarsh

last: Rajesh

first: K Garrett

first: Peter

last: Adams


title: Targeting the AKT–EphA2 Axis and Cell–Cell Adhesion Enhances Anoikis Sensitivity in Cancer Cells

status: Public on Aug 11 2025

city: Galveston

first: Nehal

last: Dwivedi

state: Texas

address: 301 University Blvd

institute: The University of Texas Medical Branch Galveston

summary: Rigidity sensing enables cells to respond to extracellular matrix stiffness and governs survival and apoptotic decisions. Tropomyosin 2.1 (Tpm2.1), a key actin-binding protein, is frequently downregulated in cancer. While re-expressing Tpm2.1 restores rigidity sensing and limits anchorage-independent growth, its ability to fully trigger anoikis, apoptosis induced by loss of matrix attachment, remains unclear. Here, we show that although Tpm2.1 overexpression reduces AKT activation and suppresses survival signaling in suspended breast cancer cells, most cells remain viable without matrix attachment. Time-resolved transcriptomic profiling of apoptotic and non-apoptotic suspended cells revealed compensatory survival programs, including reactivation of PI3K–Akt signaling and upregulation of intercellular adhesion molecules such as ICAM1. Importantly, anoikis resistance can be overcome. Pharmacological inhibition of AKT, EphA2, or ICAM1 in Tpm2.1-expressing cells significantly increases apoptosis under suspension conditions. These findings highlight that while rigidity sensing restoration alone may be insufficient to induce anoikis, it sensitizes cancer cells to targeted therapies, revealing actionable vulnerabilities to  eliminate detached tumor cells.

overall_design: RNA-seq profiling was performed on MDA-MB-231 cells expressing an empty vector (MDA-EV) and cells overexpressing Tropomyosin 2.1 (MDA-Tpm2.1), cultured under attached and suspension conditions for 5 hours, 1 day, 2 days, and 4 days. For each time point, MDA-Tpm2.1 cells in suspension were further separated into apoptotic and non-apoptotic fractions.

first: Anat

last: Galis-Vivante

first: Michael

last: Sheetz

first: Guy

last: Nir


title: Conservation of chromatin states and their association with transcription in land plants

city: Vienna

first: Vikas

last: Shukla

state: Vienna

address: Dr.Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: The complexity of varied modifications of chromatin composition is reduced to archetypal combinations called chromatin states that broadly define the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. We have identified and characterized chromatin states in the flowering plant Arabidopsis thaliana and the bryophyte Marchantia polymorpha, showing a large degree of functional conservation over more than 450 million years of land plant evolution. We analyzed the interplay between transcription factors and chromatin states to understand their influence on gene regulation. Combining binding sites with activity of transcription factors, we have shown their preferential association with specific chromatin states in both species. These associations define three main groups of transcription factors that bind in the promoter 5’ of the transcription start site, at the +1 nucleosome or inside the gene body downstream of the transcription start site. These groups broadly associate with distinct functions, such as house-keeping genes, putative pioneer factors, development, and response to the environment, suggesting co-evolution of the chromatin regulatory mechanisms with transcription factors.

overall_design: ChIP-seq for histone H2A variants: H2A.Z, H2A.X.1, H2A.X.2, H2A.M.2 performed in 14 days old thalie of Marchantia polymorpha (wt-Tak1). ChIP-seq for histone modifications H3K27me3, H2AKUb, H3K4me3, H3K27me1, and H3K9me1 in wild type and Mpez1,Mpknox2 double mutant of of Marchantia polymorpha.

first: Tetsuya

last: Hisanaga

first: Frederic

last: Bereger

first: Elin

last: Axelsson


title: Characterization of DNA methylation and transcriptomics during early pregnancy in dairy cows

status: Public on Aug 09 2025

city: shihezi

first: shiyi

last: li

address: shibei 4th road

institute: shihezi university

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an essential epigenetic mechanism involved in cell differentiation, proliferation, apoptosis, and metabolism. However, the DNA methylation changes of related genes during early pregnancy in dairy cows remain unclear . The purpose of this study was to study DNA methylation-related changes in early pregnancy cows and construct gene pools associated with pregnancy. In this study, we used peripheral blood samples from 15 healthy, productive and similar cows at 30 days post-breeding (Pre30) and 10 non-pregnant cows (Ctrl) and association analysis was performed using Reduced Representation Bisulfite Sequencing (RRBS) and transcriptomic sequencing methods. Targeted bisulfite sequencing (TBS) and Quantitative Real-time PCR (RT-qPCR) method are used to verify the Methylation differential genes. Our findings showed that DNA methylation majorly occurred in the cytosine-guanine (CG) range, and the amount of hypomethylation was higher than that of hypermethylation in 3Utrs, introns and promoters. A total of 76530 differentially methylated sites (DMCs) and 16411 differentially methylated regions (DMRs) were identified. RNA-seq identified 8858 differentially expressed genes (DEGs), with 4499 down-DEGs and 4359 up-DEGs. However, there were 44 significant differentially expressed genes, including 25 up-DEGs and 19 down-DEGs. DMC gene ontology (GO) analysis revealed significant enrichment in developmental process, cell differentitaion and nevous system development in biological processes (BP)；Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant enrichment in cancer overview and cellular and Gastric cancer and Immune disease signaling pathways. DMRs GO analysis highlighted significant enrichment in the developmental process, cell differentiation and nervous system development; KEGG the results showed that significant enrichment in Signaling pathways regulating pluripotency of stem cells, Systemic lupus erythematosus，Transcriptional misregulation in cancer，Spliceosome，Herpes simplex virus 1 infection, Maturity onset diabetes of the young. DEG GO analysis results show that the main enrichment in BP differentiation of bone marrow cells, red blood cell differentiation and erythrocyte steady-state and anion during transportation and transshipment; KEGG analysis mainly concentrated in retinol metabolism, purine metabolism, cAMP signaling pathway and Gap junction pathway. Through a comprehensive analysis of RRBS and transcriptomics, 12 genes, including HBB, HBA 1, GPR 4, CPXM 2, SLC20A2, AFAP 1 and DOK 7, were different both in the methylome and the transcriptome. Early pregnancy changes in DNA methylation were significant and mainly down-regulated. These results can be the epigenetic changes in early pregnancy for cows provide new insights.

overall_design: To investigate the changes in methylation associated with early pregnancy in cows, we used peripheral blood from 15 cows 30 days post-breeding (Pre30) and 10 non-pregnant cows (Ctrl).There were two groups, each with three biological replicates.


title: Changes in Ikaros binding and histone-modifications upon oncogenic β-catenin activation [ChIP-Seq]

first: Mark

last: Robinson

summary: We find that, in contrast to most cancer types, beta-catenin activation in preB-ALL cells supresses proliferation and leads to cell death. Proteomic analyses indicate that unlike in solid tumors beta-catenin interacts with Ikaros factors (IKZF1 and IKZF3) in pre-B cells. In order to examine the interaction between IKZF1/IKZF3 and beta-catenin we performed ChIPseq to assay chromatin state and TF binding in CTNNB1-GOF and IKZF1/3-LOF conditions.

overall_design: IKZF1, IKZF3, H3K27ac and H3K4me3 ChIP-seq was performed in pre-B cells from Ctnnb1Ex3fl/+ mice transformed with BCR-ABL1 and transfected with either non-targeting or IKZF1 and IKZF3 CRISPR/Cas9-RNP in order to study the effect of beta-catenin activation on IKZF1/3 binding and histone modifications in both IKZF1/3-WT and IKZF1/3-KO conditions.

first: Kadriye

last: Cosgun

first: Markus

last: Muschen


title: Ribosome biogenesis in embryo-like grand states as potential therapeutic target for KRAS mutant CRC

status: Public on Aug 10 2025

city: Ariake

first: Ryoji

last: Yao

state: Tokyo

country: Japan

institute: Cancer Institute, JFCR

summary: KRAS signaling is a promising target for cancer treatment, and the development of molecular targeted therapies has significantly improved the treatment outcome. However, cancer cells often adopt drug tolerant state to impede efficacy of chemotherapeutic agents. In colorectal cancer (CRC), therapeutic agents targeting KRAS have often failed to demonstrate a significant benefit, and the elucidation of its mechanism has been major clinical challenge. Here we show that MEK inhibitor, trametinib, and allele specific KRAS inhibitor, AMG510, induce the cellular state resembling the pluripotent naïve grand state of embryonic stem cells (ESCs). These cells are characterized by elevated ribosome biogenesis with Myc expression profile, yet global protein synthesis rate is low. We found they were vulnerable to the inhibition of ribosome biogenesis, and RNA polymerase I (RNA PolI) inhibition showed synergistic anti-tumor effects with trametinib and AMG510 in the autochthonous mouse model of intestinal tumors and in human patient-derived organoids with KRAS G12C mutation, respectively. These observations in PDOs demonstrated that CRC cells are equipotent to enter the pluripotent stem-like state by exploiting the cellular program of early embryogenesis and become tolerant to KRAS inhibition. High ribosome biogenesis is indispensable to maintain this cell state and is a potential therapeutic target of these cells. Our findings uncover previously unrecognized mechanisms of drug tolerance of CRC to KRAS inhibition, and provide the clue for the development of therapeutic strategies.

overall_design: PDO established from colorectal cancer patients were subjected to scRNA-seq analysis.


title: Ontogeny of the spinal cord dorsal horn [scRNA-seq]

first: Brian

last: Roome

institute: National Institutes of Health

summary: An exquisite example of form serving function is the dorsal horn of the spinal cord, the gateway to the central nervous system for sensory information from the body. Each sensory input to the dorsal horn targets a specific address within its laminated arrangement of diverse neuronal populations. However, it is not known how this organization emerges during development from an apparently homogenous pool of neural progenitors. Here, we found that both the excitatory and inhibitory cell families of the mouse dorsal horn were born in successive waves as temporal cohorts. The excitatory families then settled into a chronotopic map that transformed their birth order into the dorsal laminae. Diversification of families into refined neuron types was mediated by a dorsal-ventral progenitor gradient of Zic transcription factors. This work uncovered fundamental temporal and spatial factors that establish the cell types and structure of the spinal cord dorsal horn.

overall_design: Spinal cords taken from E14.5 and E16.5 mouse embryos at three axial levels were run on the 10X Chromium 3' gene expression assay. All spinal cord cells were indiscriminately collected, and neurons were selected post-sequencing for further analysis. The goals of this work were to identify hierarchical organization of dorsal horn neurons, and to use described axes of variation to uncover basic ontogenic principles.

first: Robert

first: Archana

last: Yadav

first: Lydia

last: Flores

first: Amrit

last: Puarr

first: Diana

last: Nardini

first: Alexander

last: Richardson

first: Ronald

last: Waclaw

first: Ruth

last: Arkell

first: Vilas

last: Menon

first: Jane

last: Johnson

first: Ariel

last: Levine


title: Gene expression changes in B-ALL upon oncogenic β-catenin activation [RNA-Seq]

summary: We find that, in contrast to most cancer types, beta-catenin activation in preB-ALL cells supresses proliferation and leads to cell death. Proteomic analyses indicate that unlike in solid tumors beta-catenin interacts with Ikaros factors (IKZF1 and IKZF3) in pre-B cells. We performed RNA-seq in order to examine changes in expression upon beta-catenin activation in the presence and absence of Ikaros factors.

overall_design: RNA-seq was performed in pre-B cells from Ctnnb1Ex3fl/+ mice transformed with BCR-ABL1 and transfected with either non-targeting or IKZF1 and IKZF3 CRISPR/Cas9-RNP in order to study the effect of beta-catenin activation on gene expression in both IKZF1/3-WT and IKZF1/3-KO conditions.


title: Evolution of the human autopod skeleton [ATAC-seq]

first: Terence

last: Capellini

summary: We investigate the genetic architecture of autopod development at the regulatory and transcriptomic level.

overall_design: Examination of open chromatin regions (ATAC-seq) and differentially expressed genes (RNA-seq) in the developing autopod skeleton.

last: Okamoto


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain [MPRA]

status: Public on Aug 07 2025

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Here, we generated a multiomic data from post-mortem cortex tissue across nine mammals and identified candidate CREs (cCREs) in a cell type–specific manner. We developed a multidimensional framework of conservation, integrating sequence, chromatin accessibility, and enhancer–gene linkage. Using massively parallel reporter assays (MPRA) in human neural progenitor cells and neurons, we measured activity of cCREs spanning conserved to human-specific regions. CRISPR interference (CRISPRi) validated conserved enhancer function, including at neurodevelopmental loci like FAM181B. Motif enrichment and chromBPnet revealed transcription factors distinguishing conserved versus recent cCREs. Linkage disequilibrium  score regression showed both conserved and human-specific cCREs were enriched for neuropsychiatric GWAS risk, while neurodegenerative risk was confined to conserved elements. Our findings define functional dimensions of enhancer conservation and demonstrate how regulatory evolution shapes human brain biology and disease susceptibility.

overall_design: MPRA of candidate CREs evaluated in triplicate in HEK293s, NPCs, and Neurons.

first: Ashlyn

last: Anderson

first: Brianne

last: Rogers

first: Nicholas


title: Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli [mutagenesis]

status: Public on Aug 06 2025

city: Beverly

first: Hoong Chuin

last: Lim

address: 44 Dunham Ridge Road

institute: New England Biolabs

summary: Some phages and microbes employ Diversity-Generating Retroelements (DGRs) to achieve rapid targeted adaptation. DGRs mutagenize a specific gene without harming the rest of the genome. Mutagenesis relies on the DGR reverse transcriptase (dRT), which is highly error-prone when transcribing adenines of an RNA template. The resulting mutagenized cDNA then alters the target gene through a poorly understood mechanism. Transplanting DGRs into a tractable organism, like Escherichia coli, holds promise for creating a powerful system for gene-targeted editing. Here, we successfully reconstituted the archetypal BPP DGR in E. coli, demonstrating that DGRs are "plug-and-play" systems adaptable to non-native hosts. Systematic analysis of reconstituted DGR established principles for target mutagenesis. Our results revealed that cytosine misincorporation is the most common error when dRT transcribes adenines. However, error rates peak in 5'-AAC-3' and 5'-ACC-3' contexts, driven by elevated adenine and guanosine misincorporations, respectively. Using high-throughput genetics, we discovered that cells lacking the single-stranded DNA exonuclease ExoI exhibit 15-fold higher DGR activity. Our evidence indicates that ExoI inhibits DGRs by binding a limited cellular factor, rather than through direct cDNA degradation. Finally, by profiling DGR targets across thousands of chromosomal loci, we discovered that DGRs preferentially edit targets near the replication origin and oriented in the same direction as replication. We showed that the directionality of replication underlies this bias, possibly through unwinding the target to facilitate base-pairing with incoming cDNA. These findings establish a reconstituted DGR system in E. coli and provide a foundation for optimizing targeted gene-editing applications in the future.

overall_design: cDNA sequencing of newly synthesized and mutagenized cDNA by DGRs. Arranged all 16 possible NAN tri-nucleotides in different orientations for templates and sequenced resulting cDNA to understand if sequence context matters for DGR mutagenesis.

first: Irem

last: Unlu

first: Marina

last: Smiley

first: Vladimir

last: Potapov

first: Yoan

last: Renoux-Martin

first: Zhi-Yi

last: Sun


title: Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli [TranscriptionalStrength]

type: Genome variation profiling by high throughput sequencing

overall_design: DGR reporter integrated in the chromosome at 3758105 under the control of either a strong (J23118) or weak (J23112) promoter. Activated DGR repair to and sequence for mutagenesis rates to test whether the strength of the target's promoter affects repair frequency.


title: Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Transposon sequencing data to identify cellular factors that influence diversity generating retroelements (DGR). Transposon library sequenced before and after selection by DGR specific reporter. Reporter represents a defective kanamycin resistance gene and DGR targeting sequences at 4088112 on the genome.


title: Enhancer distance matters: forced linear recruitment of a super-enhancer strongly reactivates the developmentally silenced fetal HBG globin genes [ATAC]

status: Public on Aug 05 2025

city: Utrecht

first: Richard

last: Gremmen

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: The human genome contains regulatory DNA elements (enhancers, silencers, insulators) that can recruit proteins to activate or repress transcription of distal genes. Interspersed are DNA intervals without any known coding or regulatory capacity. Here, we show that these intrinsically non-regulatory DNA stretches can allow gene silencing by keeping enhancers at distance. During development, the fetal globin HBG genes recruit activated repressor proteins to their promoters. This enables the HBG genes to silence and ignore the distal super-enhancer, which subsequently acts on and activates the downstream adult HBD and HBB genes. We found that forced linear recruitment of the super-enhancer, bringing it immediately upstream of the otherwise intact HBG gene promoters, results in significant HBG reactivation and partial HBB inactivation in adult erythroid cells and ex vivo differentiated human hematopoietic stem and progenitor cells. Forced HBG reactivation is accomplished by CRISPR-Cas9 deletions of the intervening 25 kilobases sequence interval. Additionally, it can be achieved by inversions that leave this interval intact and proximal, but no longer situated between the enhancer and HBG genes. We conclude that the HBG genes must be at substantial linear distance to bypass activation by the super-enhancer and activate their promoter-encoded silencing program in adulthood. Overall, this assigns a functional role to seemingly non-regulatory segments in our genome: by providing linear separation they may support genes to autonomously control their transcriptional response to distal enhancers.

overall_design: CRISPR/Cas9 edits in the Beta-Globin locus were performed in Hudep-2 cell line. ATAC-seq was performed in two idenpendant clones to investigate changes in accessibilty in the Beta-Globin locus. Published control guides and WT were used as controls.

first: Anna-Karina

last: Felder

first: Rezin

last: Majied

first: Han

last: Verhagen

first: Marjon

last: Verstegen

first: Thijs

last: Verheul

first: Rebecca

last: Mohnani

first: Peter

last: Krijger

first: Sjaak

last: Philipsen

first: Emile

last: van den Akker

first: Wouter

last: de Laat


title: Enhancer distance matters: forced linear recruitment of a super-enhancer strongly reactivates the developmentally silenced fetal HBG globin genes [CutnRun]

overall_design: CRISPR/Cas9 edits in the Beta-Globin locus were performed in Hudep-2 cell line. CutnRun with an antibody against H3K4me3 was performed in two idenpendant clones to investigate changes in the histone mark in the Beta-Globin locus. Published control guides and WT were used as controls.


title: Oncogenic β-catenin activation

first: Mark

last: Robinson

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of Debaryomyces hansenii reveals detoxification and stress responses to benzo(a)pyrene exposure

status: Public on Aug 04 2025

city: Ciudad de México

first: Francisco

last: Padilla-Garfias

state: Ciudad de México

address: Cto. Exterior s/n, C.U., Coyoacán, 04510 Ciudad de México, CDMX

department: Genética Molecular

country: Mexico

institute: Instituito de Fisiologia Celular, UNAM

summary: The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs), such as benzo(a)pyrene (BaP), poses significant threats to ecosystems and public health due to their persistent nature, mutagenic potential, and well-documented carcinogenicity. In this study, we investigated the ability of the extremophilic yeast Debaryomyces hansenii to activate specialized detoxification mechanisms for BaP degradation, even under nutrient-deprived conditions. When exposed to 100 ppm BaP, D. hansenii eliminated over 70% of the contaminant within three days while maintaining normal growth dynamics. RNA-Seq analysis revealed widespread transcriptional remodeling, with 1179 genes upregulated and 1031 downregulated under BaP-only conditions, and 1067 upregulated and 977 downregulated genes during co-metabolic exposure (2% glucose + 100 ppm BaP), from a total of 6506 annotated genes. Gene Ontology (GO) and KEGG enrichment analyses highlighted the activation of xenobiotic degradation pathways, notably involving cytochrome P450 monooxygenases (CYPs), epoxide hydrolases (EHs), and glutathione S-transferases (GSTs), alongside an enhanced antioxidant response and finely tuned glutathione homeostasis. This work provides the first comprehensive transcriptomic profile of BaP detoxification in D. hansenii, revealing an intricate and highly adaptive stress response. Collectively, these findings position D. hansenii as a promising eukaryotic platform for bioremediation in saline and contaminated environments, especially where conventional microbial candidates fall short due to environmental extremes or nutrient scarcity.

overall_design: Transcriptomes of Debaryomyces hansenii were analyzed under carbon-limited conditions with or without 100 ppm benzo[a]pyrene (BaP). Two independent experiments were performed, each with three biological replicates per condition. Samples were collected on days 0 and 3 for total RNA extraction.

first: Augusto Cesar

last: Poot-Hernández

first: Minerva

last: Araiza-Villanueva

first: Martha

last: Calahorra

first: Norma Silvia

last: Sánchez

first: Antonio

last: Peña


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 60) [I40]

first: Liang

last: Yang

summary: This study is part of the immgenT Open Source Project, specifically from IGT40, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 60 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

overall_design: T cells were isolated from individual organs using mechanical dissociation, enzymatic digestion (collagenase I or DTE), and anti-CD45 intravenous labeling to distinguish tissue-resident from circulating cells. Sorted CD3e+ or IV- CD3e+ were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Giovanni

last: Galletti

first: Sara

last: Quon

first: Nicole

last: Scharping

first: Kennidy

last: Takehara

first: Amir

last: Ferry

first: Ananda

last: Goldrath


title: Transcriptomic analysis of lipase TLL during the lipid expression process of Aspergillus niger at different time points.

status: Public on Aug 01 2025

city: kunming

first: le

last: yang

state: yunnan

address: cuihubeilu

institute: yunnan university

summary: Aspergillus Niger CICC2629 was used as the host strain to express Thermomyces lanuginosus lipase. The enzyme activity and enzymatic properties of the lipase were measured, and the expression ability of exogenous protein in the host strain was investigated using transcriptomics.

overall_design: The WT and lipase TLL expressing strains were collected at different time points (0,24, 48 and 72  hours) when the lipase was produced. Wild-type mycelial samples were collected and cDNA libraries were constructed for each sample for sequencing.

first: Le

first: Xiao yan

last: Shang

first: Zun xi

last: Huang


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. [scATAC-Seq]

status: Public on Aug 03 2025

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, while cone-differentiation factors Thrb, Rxrg, and Mef2c are expressed precociously in cone specification. Functional analyses reveal that Zic3 and Mef2c promote cone specification, acting through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that evolutionary modifications to gene regulatory networks underlie the development of cone-dominant retinas, providing insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

overall_design: In 13LGS, retinal neurogenesis begins around embryonic day 18 (E18), with birth occurring at E27 (blue-dotted line in Fig. 1A), and concludes by postnatal day 17 (P17)27. To comprehensively profile cellular-level changes in gene expression and chromatin accessibility, we conducted scRNA-Seq and scATAC-Seq analyses across ten developmental time points, spanning the full course of neurogenesis and the immediate post-neurogenesis period (E18–P21).

first: Kurt

last: Weir

first: Sangeetha

last: Kandoi

first: Roujin

last: An

last: Pannullo

first: Isabella

last: Palazzo

first: Jared A.

last: Tangeman

first: Jun

last: Shi

first: Steven H.

last: DeVries

first: Dana K.

last: Merriman

first: Jiang

last: Qian

first: Seth

last: Blackshaw