title: DAP12 deficiency alters microglia-oligodendrocyte communication and enhances resilience against tau toxicity

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Pathogenic tau accumulation fuels neurodegeneration in Alzheimer’s disease (AD). The role of microglia in tau-driven neurodegeneration is intricate, with DAP12 (DNAX-activation protein 12) triggering microglial immune responses. Mice lacking DAP12 become resistant to tau-induced brain toxicity in tauopathy mice, yet the precise mechanism remains elusive. Our current study uncovers a novel resilience mechanism against tau toxicity conferred by Dap12 deletion. While inactivation of Dap12 elevates tau inclusions, potentially disrupting microglial tau processing, it curbs tau-induced brain inflammation and ameliorates myelin and synapse loss. Tau-induced disease-associated clusters in microglia (MG) and intermediate oligodendrocytes (iOli) are abolished by removal of Dap12. Additionally, AD brains exhibit mouse iOli-like cells spatially correlated with tau pathology. In summary, our study reveals that DAP12 signaling triggers toxic interactions between microglia and oligodendrocytes in tauopathy, mediating tau-induced damage to oligodendrocytes and synaptic loss. Targeting DAP12 signaling presents a promising therapeutic approach for enhancing resilience against tau toxicity in AD.

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus of WT, Dap12+/+ tau+ and Dap12–/–tau+.

first: Hao

last: Chen

last: Fan

first: Qi

last: Guo

first: Man

middle: Y

last: Wong

first: Fangmin

last: Yu

first: Nessa

last: Foxe

first: Winston

last: Wang

first: Aviram

last: Nessim

first: Gillian

last: Carling

first: Bangyan

last: Liu

first: Chloe

last: Lopez-Lee

first: Yige

last: Huang

first: Sadaf

last: Amin

first: Sue-Ann

last: Mok

first: Won-min

first: Bin

last: Zhang

first: Flint

last: Beal

first: Qin

last: Ma

first: Hongjun

last: Fu

first: Wenjie

last: Luo


title: Silencing of S100A11 Attenuates Murine Metabolic Dysfunction-associated Steatohepatitis

status: Public on Oct 22 2025

city: Rochester

first: Harmeet

last: Malhi

state: Mn

address: 200 1st SW

department: GI/Hep research

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: S100A11 is an alarmin known to be upregulated in MASH; however, its role in MASH pathophysiology remains incompletely defined. In MASH, insulin resistance and subsequent impaired hepatic carbohydrate and lipid metabolism significantly increase de novo lipogenesis causing hepatic steatosis and lipotoxicity. S100A11 promotes steatosis in cell lines. Therefore, we hypothesized that S100A11 drives MASH by upregulating lipid synthesis in the liver. We employed whole body S100A11 knockout (S100a11-/-) mice and liver specific knockdown mice and a MASH inducing diet to address this hypothesis. S100a11-/- mice demonstrated reduced steatosis, inflammation and fibrosis compared to wild type controls. Hepatotropic AAV8 mediated S100A11 silencing in mouse livers significantly attenuated steatosis, inflammation, and fibrosis. Significant dysregulation of carbohydrate and lipid metabolism was identified by Ingenuity Pathway Analysis of bulk-RNA sequencing of S100a11 silenced mouse livers. Candidate gene approach in these pathways identified hexokinase 2 (HK2) as significantly downregulated in the S100a11 knockdown mouse livers. Since hexokinases regulate the crucial stage of glucose flux into downstream metabolic processes, including de novo lipogenesis, we expressed exogenous HK2 in S100a11-/- mice. Overexpression of Hk2 was sufficient to upregulate steatosis under chow fed basal nutrition conditions in S100a11-/- mouse livers. These studies identify S100A11 and HK2 as potential therapeutic targets for MASH.

overall_design: Bulk RNA sequencing of mouse liver following silencing of S100A11 using an AAV8 construct in a dietary MASH model.

first: P. Vineeth

last: Daniel

first: Gyanendra

last: Puri

first: Yixing

first: Naresh

last: Golla

first: Takahito

last: Nishihara

first: Hanna

last: Erickson

first: George

last: Marek

first: Davide

last: Povero

first: Amy

last: Mauer

first: Jun


title: Methylome-driven regulation of miRNA expression and its relationship to cardiac dysfunction in idiopathic dilated cardiomyopathy

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

country: Spain

institute: Instituto de investigación Sanitaria La Fe

type: Non-coding RNA profiling by high throughput sequencing

summary: Idiopathic dilated cardiomyopathy (iDCM) is a multifactorial disease with a complex pathogenesis involving diverse molecular mechanisms. Among these, epigenetic mechanisms, including both DNA methylation and microRNAs (miRNAs)-mediated regulation, play an important role in determining the disease phenotype. However, the interplay between the DNA methylome and the miRNA transcriptome in iDCM remains largely unexplored. We conducted a cross-cohort multiomic integrative analysis of left ventricular (LV) tissue samples from iDCM patients and control (CNT) donors. DNA methylation profiling was performed using the Infinium MethylationEPIC BeadChip, whereas ncRNA-seq was used to assess transcriptomic changes. We identified a subset of 7 miRNAs exhibiting both differential methylation in their promoter regions and differential expression in their primary and mature forms. Notably, two of these miRNAs, hsa-miR-433-3p (r = 0.671, p < 0.01) and hsa-miR-493-5p (r = 0.585, p < 0.01), which are involved in fibrotic pathways appear to be significantly correlated with the left ventricular ejection fraction (LVEF), an established echocardiographic marker of cardiac function. Importantly, both miRNAs have predicted or validated target genes involved in fibrotic pathways, suggesting a potential link between DNA methylation, miRNA expression, cardiac remodeling, and the disease phenotype. This study enhances our understanding of the epigenetic mechanisms shaping the miRNA transcriptomic landscape in iDCM, revealing suggesting potential roles for these miRNAs in cardiac dysfunction and myocardial fibrosis.

overall_design: We analyzed 50 human heart samples from left ventricular apex of patients diagnosed with idiopathic dilated cardiomyopathy (n=20) and ischemic cardiomyopathy (n=22) undergoing heart transplantation, as well as from control donors (n=8).

first: Esther

last: Roselló-Lletí


title: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts [RNA-seq]

status: Public on Oct 23 2025

city: Guanzhou

first: dongmei

last: he

address: Yunpu Street

country: China

institute: University of Chinese Academy of Sciences

summary: Master transcription factors (MTFs) are key regulators in cell fate determination. However, an approach to profile MTF’s direct transcriptional targets together with their associated RNA-binding proteins (RBPs), is still lacking. Here, we applied 5-ethynyluridine RNA metabolic labelling and click chemistry to map the dynamics of the transcriptional targets and the RBPs interacting with the newly transcribed RNAs upon acute NANOG degradation in mouse embryonic stem cells (mESCs). We identified UTP15, a classic rRNA-biogenesis regulator, acts as a key activator of pluripotency-associated gene transcription independently of rRNA biogenesis. Importantly, NANOG-regulated transcription enhances UTP15 binding to transcription start sites (TSSs), associated with increased Pol II binding and more active transcription. Moreover, UTP15 promotes the assembly of Pol II biomolecular condensates, thereby potentially driving pluripotency gene transcription. Collectively, our study uncovers a NANOG-nascent transcript-UTP15 regulatory axis to activate pluripotency gene transcription, providing a distinct approach for studying MTF’s function during cell fate determination.

overall_design: To investigate the cooperative function NANOG/UTP15 in the regulation of pluripotency, we established NANOG-AID and UTP15-AID cell lines in which each target protein was allowed to be acute degradation.We then performed gene transcription profiling analysis using data obtained from nascent RNA-seq at different time points after target protein degradation.Comparative gene transcription profiling analysis of nascent RNA-seq data from NANOG-AID/UTP15-AID cells at different time points after target protein degradation

first: Mingqiang

last: Deng

first: Dongmei

last: He

first: Xiwei

last: Wang

first: Xichen

last: Bao


title: Contribution of macrophage subsets to scarless skin regeneration in Xenopus laevis frogs

city: Washington DC

first: Leon

last: Grayfer

address: 800 22nd ST NW

department: Biological Sciences

institute: George Washington University

summary: Xenopus laevis juvenile frogs are uniquely capable of scarless skin regeneration, but the cellular and molecular mechanisms guiding this process remain incompletely understood. Macrophages are known as key regulators of wound healing, yet how their phenotypes shift over time and influence downstream regeneration in X. laevis has not been previously defined. It is well established that macrophage functions are imperative to mammalian wound healing. In vertebrate biology, macrophage polarization is dictated by two colony-stimulating factor-1 (CSF1) receptor ligands: CSF1 and interleukin-34 (IL34). While IL34 in mammals is critical to the development of epidermal macrophages known as Langerhans cells, the contribution of CSF1- and IL34-derived macrophages to skin wound repair remains unexplored. Pertinently, using the X. laevis model, previous work from our lab showed that CSF1- and IL34- macrophages are functionally distinct, formulating our hypothesis that these subsets play distinct roles during different phases of cutaneous wound repair. We therefore characterized full-thickness (epidermis and dermis) skin wounds in juvenile X. laevis during regeneration, analyzing transcript levels reflecting: M( infiltration (csf1r) and phenotype abundance (csf1 and il34), fibroblast activation (αSMA/acta2), and wound bed collagen composition (Picrosirius red staining). To assess the functional roles of macrophage phenotypes, we enriched wounds with recombinant X. laevis CSF1, IL34, or a vector control 3 days post-wounding (dpw) and analyzed wound responses at 7 and 14 dpw. Normal scarless regeneration in these juveniles demonstrated that macrophages transiently accumulated in the wound bed, peaking at 7–14 dpw. This coincided with elevated csf1 expression, which later declined as il34 levels rose. Fibroblast activation into myofibroblasts as well as collagen deposition followed this cytokine shift and restored collagen to pre-wound levels by 60 dpw. Subcutaneous IL34 enrichment at 3 dpw led to significantly increased αSMA expression at 7 and 14 dpw, a higher type I:III collagen ratio at 7 dpw, and suppression of inflammatory mediators coupled with enhancement of other, anti-inflammatory mediators at 7dpw. CSF1 enrichment had no significant effect on αSMA expression or subsequent collagen deposition, but did show a bias towards inflammatory mediators and the suppression of resolving and pro-reparative transcripts at 7 dpw. These findings suggest that early IL34 supplementation promotes a pro-regenerative macrophage phenotype that enhances myofibroblast activation and matrix remodeling while early CSF1 supplementation may contribute to prolonged inflammation and impaired tissue regeneration. Temporal modulation of macrophage-derived signals, particularly IL34, plays a critical role in directing scarless skin regeneration in X. laevis. These findings identify a conserved immunoregulatory axis with potential relevance to improving wound healing in non-regenerative species. Xenopus laevis juvenile frogs are uniquely capable of scarless skin regeneration, but the cellular and molecular mechanisms guiding this process remain incompletely understood. Macrophages are known as key regulators of wound healing, yet how their phenotypes shift over time and influence downstream regeneration in X. laevis has not been previously defined. It is well established that M( functions are imperative to mammalian wound healing. In vertebrate biology, M( polarization is dictated by two colony-stimulating factor-1 (CSF1) receptor ligands: CSF1 and interleukin-34 (IL34). While IL34 in mammals is critical to the development of epidermal M(s known as Langerhans cells, the contribution of CSF1- and IL34-derived macrophages to skin wound repair remains unexplored. Pertinently, using the X. laevis model, previous work from our lab showed that CSF1- and IL34- M(s are functionally distinct, formulating our hypothesis that these subsets play distinct roles during different phases of cutaneous wound repair. We therefore characterized full-thickness (epidermis and dermis) skin wounds in juvenile X. laevis during regeneration, analyzing transcript levels reflecting: macrophage infiltration (csf1r) and phenotype abundance (csf1 and il34), fibroblast activation (αSMA/acta2), and wound bed collagen composition (Picrosirius red staining). To assess the functional roles of macrophage phenotypes, we enriched wounds with recombinant X. laevis CSF1, IL34, or a vector control 3 days post-wounding (dpw) and analyzed wound responses at 7 and 14 dpw. Normal scarless regeneration in these juveniles demonstrated that macrophages transiently accumulated in the wound bed, peaking at 7–14 dpw. This coincided with elevated csf1 expression, which later declined as il34 levels rose. Fibroblast activation into myofibroblasts as well as collagen deposition followed this cytokine shift and restored collagen to pre-wound levels by 60 dpw. Subcutaneous IL34 enrichment at 3 dpw led to significantly increased αSMA expression at 7 and 14 dpw, a higher type I:III collagen ratio at 7 dpw, and suppression of inflammatory mediators coupled with enhancement of other, anti-inflammatory mediators at 7dpw. CSF1 enrichment had no significant effect on αSMA expression or subsequent collagen deposition, but did show a bias towards inflammatory mediators and the suppression of resolving and pro-reparative transcripts at 7 dpw. These findings suggest that early IL34 supplementation promotes a pro-regenerative M( phenotype that enhances myofibroblast activation and matrix remodeling while early CSF1 supplementation may contribute to prolonged inflammation and impaired tissue regeneration. Temporal modulation of macrophage-derived signals, particularly IL34, plays a critical role in directing scarless skin regeneration in X. laevis. These findings identify a conserved immunoregulatory axis with potential relevance to improving wound healing in non-regenerative species.

overall_design: RNA-seq profiling of recombinant control, csf1, or il34 enriched healing outbred X. laevis skin wounds 7 and 14 days post wounding.

first: Christina

last: Garvey Griffith

first: Kelsey

last: Hauser

first: Bradley

last: Abramson

first: Katharine

last: Jennings

first: Elissa

middle: R

last: Chapkin

first: Elizabeth

last: Jones

first: Anju

last: Duttargi


title: Respiratory syncytial virus nonstructural protein 1 inhibits secretion of cytokines and chemokines by differentiated primary nasal epithelial cells cultured at air-liquid interface

city: Bilthoven

first: Amadeo

last: Muñoz

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

summary: Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in children and older adults. Several vaccines have recently been approved, which are all based on the RSV fusion (F) protein. Among the strategies to induce a broader immune response is the development of live-attenuated RSV vaccines, for example by disabling nonstructural protein 1 (NS1). RSV NS1 has been found to modulate the host immune response by repression of interferon (IFN) production. However, functional characterization of this protein was mainly performed in immortalized cell lines, which do not necessarily represent the in vivo situation.    Here, we assessed the effect of NS1 mutations on replication and host responses in differentiated primary human nasal epithelial cells (HNEC) cultured at air-liquid interface (ALI), which mimic several physiological properties of the human airways. Using a newly developed yeast-based RSV reverse genetics system, inactivating mutations in the NS1 gene were introduced. These mutations did not affect viral replication in Vero and A549 cells. However, in HNEC we observed a delayed replication of the NS1 mutants compared to the WT virus. Bulk RNA sequencing data from early post infection revealed a stronger antiviral signature in HNEC that were infected with NS1 mutants compared to WT, characterized by upregulation of IFN-β and IFN-λ1/2/3 and chemokines CXCL11 and CCL5. This signature was confirmed by analysis of the cytokines that were released into the HNEC basal medium. Finally, the basal medium containing these cytokines was used for an indirect immune cell migration assay. In this set-up, both WT and NS1 mutant viruses induce migration of mainly neutrophils.  In conclusion, this study shows that RSV NS1 supports viral replication not only via inhibition of the production of IFNs, but also by reducing early chemokine production and secretion by epithelial cells. Furthermore, our data highlight the suitability of the ALI transwell model for preclinical assessment of live-attenuated vaccine candidates.

overall_design: Cell source: well-differentiated primary nasal epithelial cells, cultured at Air-liquid interface 3 different nasal donors were used. Two transwells per condition were infected with the following RSV strains: RSV-X WT (wild-type virus) RSV-X NS1Y125A (Y125A point mutation in the NS1 protein) RSV-X NS1L132A/L133A (L132A/L133A point mutations in the NS1 protein) Mock: no virus Whole cell lysates were made at 20 hours post infection.  RNA was isolated from the cell lysates to perform RNA-seq profiling.

first: Rosanne

middle: W

last: Koutstaal

last: Munoz Garcia

first: Nadine

last: Ebert

first: Manon

middle: F

last: Licheri

first: Anke

middle: J

last: Lakerveld

first: Hendrik-Jan

last: Hamstra

first: Anne

middle: T

last: Gelderloos

first: Jørgen

last: de Jonge

first: Cécile

middle: A

last: van Els

first: Ronald

last: Dijkman

first: Volker

last: Thiel

first: Puck

middle: B

last: van Kasteren


title: Perturbation of multi-molecular complexes in skeletal muscle induces protective proteases in the CNS that degrade pathogenic proteins

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: ABSTRACT. Many cellular functions are ensured by the activity of multimolecular complexes and homeostatic mechanisms ensure their stoichiometric assembly. Disruption of individual complex components can perturb this process and induce local adaptive responses. In addition to cell-autonomous effects, such surveillance systems are also active at the organismal level: cellular stress in one tissue can be sensed systemically and lead to adaptive responses in other tissues during aging and disease, as found for muscle-to-central nervous system (CNS) stress signaling, Here, we have examined the local and systemic stress responses induced by the genetic perturbation of distinct molecular complexes, i.e. the sarcomere, mitochondrial complex I, proteasome, and VCP (valosin-containing protein) complex. Surprisingly, we find that a conserved stress response is induced locally in muscle and systemically following the muscle-specific RNAi for components of these diverse multimolecular complexes. These local and systemic responses are centered on the transcriptional induction of proteases and peptidases, many of which can degrade an aggregation-prone model protein, huntingtin-polyQ. The myokine Amyrel is a possible mediator of this muscle-to-CNS signaling because it was previously found to be triggered by proteasome stress in muscle and to regulate protease expression in the CNS. In agreement with this model, here we find that Amyrel expression is induced by perturbation of diverse multimolecular complexes. Moreover, Amyrel induction in muscle reduces pathogenic huntingtin-polyQ aggregates in the retina. These findings therefore suggest that Amyrel contributes to reshaping CNS proteostasis in response to perturbation of multimolecular complexes in skeletal muscle. Altogether, our study provides insight into a muscle-to-CNS systemic response that conveys the status of multimolecular complexes of skeletal muscle.

overall_design: Fly head and thorax samples compared across numerous RNAi tests, 3 replicates each

first: Mamta

last: Rai

first: Helen

last: Baddeley

first: Chia-Lung

last: Chuang

first: Anna

last: Platt

first: Michelle

last: Curley

first: Fabio

last: Demontis


title: Metformin inhibits IFN-g-mediated activation of macrophages in necrobiotic xanthogranuloma

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

country: Germany

institute: University of Cologne

summary: This study included lesional and non-lesional skin samples of patients diagnosed with NXG as well as control skin (non-involved, discarded skin obtained during dermatologic surgical non-melanoma skin cancer removal) from otherwise healthy donors. Skin samples of NXG were obtained for diagnostic purposes at the Department of Dermatology at the University Hospital of Cologne. Trained dermatologists histologically and clinically confirmed NXG or healthy skin. Skin tissues were immediately stored in RNAlater (invitrogen, AM7020). 30 µg of tissue stored in RNAlater was mechanically homogenized using a pre-cooled RETSCH MM 400 mixer mill (Thermo Fischer, 10573034). RNA from homogenized tissue was isolated using the RNeasy Fibrous Tissue Kit (Qiagen, 74704) according to the manufacturer´s protocol. This study was conducted according to the principles expressed in the Declaration of Helsinki and approved by the local Ethic Committee (Ethikkommission) of the University of Cologne (votes #20-1082 and #19-1146). All donors participated voluntarily and provided written informed consent for collecting samples and subsequent analyses.

overall_design: Tanscriptome profiling of two patients

first: Kerstin

last: Becker

first: Ahlem

last: Aloui

first: Muhammad

last: Sajid Hussain

first: Henning

last: Klapproth

first: Manuel

last: Huerta Arana

first: Mario

last: Fabri


title: Chemotherapy-driven intestinal dysbiosis and microbial indole-3-propionic acid rewire bone marrow myelopoiesis to promote anti-metastatic immunity [16S rRNA-Seq]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Chemotherapy induced intestinal mucositis drives microbial dysbiosis and IPA production.

overall_design: 16S rRNA gene sequencing of fecal samples from mice treated with vehicule or FO (5-FU + oxaliplatin) chemotherapy. Samples were collected 5 days post treatment.

first: Ludivine

last: Bersier

first: Tatiana

middle: V

last: Petrova


title: Spatially organized progenitors in the zebrafish heart field determine cardiovascular patterning [MERFISH]

city: Boston

first: Yunxia

last: Wang

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Progenitor cells expressing nkx2.5 are specified in the bilateral zebrafish heart field that give rise to distinct components of the cardiovascular system. We performed spatial transcriptomics (MERFISH) to profile 14-ss wildtype (TU) and Tg(nkx2.5:ZsYellow) zebrafish embryos as well as to determine their importance for heart development. Our data provide a blueprint of heart field organization that informs vulnerable aspects of cardiovascular development.

overall_design: 14-ss Tg(nkx2.5:ZsYellow) embryos for heart development were used for analysis.

first: Hakan

last: Coskun

first: Xinlei

last: Gao

first: Kaifu

last: Chen

first: C

last: Geoffrey Burns

first: Caroline

middle: E

last: Burns


title: H3K36 Methylation - a Guardian of Epigenome Integrity [Hi-C]

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary: H3K36 methylation is a key epigenetic mark with critical roles in development and disease, yet its genome-wide functions remain incompletely understood. Here, we systematically dissect the role of H3K36 methylation using a series of CRISPR-engineered mouse mesenchymal stem cell lines with progressive knockouts of the five H3K36 methyltransferases: NSD1, NSD2, NSD3, SETD2 and ASH1L—culminating in quintuple knockout (QuiKO) cells entirely lacking H3K36me2/3. We demonstrate that H3K36me2 enriched at active cis-regulatory elements predominantly influences enhancer activity and supports the expression of enhancer-dependent genes. Within gene bodies, loss of H3K36me2/3 permits invasion by the repressive H3K27me2/3 modifications, thereby disrupting transcriptional fidelity. Unexpectedly, we uncover a previously undescribed relationship between H3K36me and H3K9me3: upon H3K36me2 depletion, SUV39H1-mediated H3K9me3 redistributes from large constitutive heterochromatic domains into euchromatin, leading to widespread epigenome restructuring and transcriptional changes. This redistribution is accompanied by a collapse of 3D genome organization, including weakened compartment boundaries and a profound loss of long-range interactions. Finally, we validate key findings in two human HNSCC cell lines overexpressing the H3K36M oncohistone, highlighting the conserved role of H3K36 methylation in maintaining epigenome integrity across species and cell types, and providing further mechanistic insights into the downstream consequences of this oncogenic mutation. Together, these data reveal that H3K36me is essential not only for local gene regulation but also for safeguarding the higher-order structure and functional balance of the genome.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Hi-C in C3H10T1-2 mouse mesenchymal stem cells and head and neck squamous cell carcinoma (HNSCC) cells to compare the chromatin structure between H3K36me-depleted cells and their respective parental controls.

first: Reinnier

last: Padilla

first: Gerald

last: Shipman

first: Cynthia

last: Horth

first: Michel

last: Gravel

first: Eric

last: Bareke


title: Differential Gene Expression During CAR T Cells Activation

city: Shen Zhen

first: Rui

last: Li

address: SZ

institute: BME

summary: Mechanical force generation at the immunological synapse is a hallmark of CAR T cell cytotoxicity and a key determinant of functional potency. However, the underlying mechanobiological mechanisms remain poorly understood. Here, we real-time measured the mechanical allostasis of single CAR T cells involving spatiotemporal dynamics of synaptic force and cellular metabolic activity upon CD19 antigen activation, and revealed that the CAR T cell activation is governed by sophisticated mechano-energetic mechanisms. We identify a Piezo1–Ca²⁺–Wnt axis that integrates force transduction with actin remodeling and metabolic reprogramming. Notably, functional heterogeneity across CAR T cell products from different patients as well as with different designs and manufacturing protocols correlates with variation in this mechano-metabolic program. Our findings revealed the reciprocal relationship between mechanosensation and metabolic switch, thus providing a new framework for (pre-)clinical screening of CAR T cell functional state and engineering CAR T cells with enhanced mechanical fitness, energetic resilience, and therapeutic efficacy.

overall_design: cells were treated with either CD19, ICAM-1, CD3e , or CD28 before testing.

first: Li

last: Rui

first: Luu

last: Bao Ngoc


title: Human retinal Mueller glial cell (HMG) response to Toxoplasma gondii infection

city: Adelaide

first: Feargal

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

summary: This experiment sough to understand the impact Toxoplasma gondii infection on the host transcriptome. We do this by sequencing both Total and Small RNA from 6 donors. Infection results is singificant alterations to both gene expression and miRNA experession. The GT1 strain of T. gondii induces different changes to that of GHPT strain.

overall_design: 6 donors with 3 samples from each. Exposed to 2 strains of T. gondii and 1 uninfected control.  Total RNA and small RNA were sequenced for each sample in order to profile both coding and non-coding expression in Mueller glial cells infected with Toxoplasma gondii. Total RNA was sequenced with paired end sequencing while Small RNA is single end.

first: David

last: Lynn

first: Justine

last: Smith


title: umami experiment-Analysis of the effect of amino-acids and humic substances on the transcriptome of Arabidopsis

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

summary: 2022_13_qs_umami- umami experiment-Analysis of the effects of biostimulants (amino-acids and humic substances) on plants-Analysis of transcriptomic variations in Arabidopsis seedlings grown in vitro with or without humic substances or amino acid solutions.

overall_design: 3 samples x 3 biological replicats with 1 control and 2 treated (amino-acids and humic substances)

first: Stéphanie

last: Pateyron

first: Christine

last: Paysant-LeRoux

first: Christian

last: Meyer


title: Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs [RNA-seq]

city: Charlottesville

first: Andrew

last: Miller

state: Virginia

address: 415 Lane Rd.

department: Biomedical Engineering

institute: University of Virginia

summary: Dysregulation of the cellular mechanisms that coordinate the interpretation and transduction of microenvironmental biophysical signals are a unifying feature of tissue remodeling pathologies such as fibrosis and cancer. While genomic regulation downstream of normal mechanotransduction (i.e. cases where cells sense soft and stiff appropriately) is well studied, significantly less is known about the consequences of abnormal mechanoperception and subsequent misinterpretation of the mechanical environment. Leveraging Thy-1 (a.k.a. CD90) loss as a model of impaired mechanoperception, we employed ATAC- and RNA-sequencing in parallel to characterize the changes in lung fibroblast genomic activity in response to a combination of substrate stiffness and culture time. Notably, we find perturbed mechanoperception elicits a near-complete shutdown of HOXA5, a transcription factor responsible for pattern specification and development in the nascent lung. In vitro investigation of HOXA5 expression reveals a potential mechanism connecting increased αv integrin signaling, cytoskeletal tension, and SRC kinase activity to HOXA5 silencing. These results establish novel links between integrin signaling and the expression dynamics of genes necessary for tissue formation and regeneration in the injured and/or developing lung, particularly HOXA5.

overall_design: RNA-sequencing of WT and CD90/Thy-1 CRISPR KO immortalized human lung fibroblasts cultured on 4kPa, 25kPa, and tissue culture plastic (TCP) substrates for periods of 24hr or 72hr. A 0-hr sample was collected from cell suspension as samples were seeded.

first: Ping

last: Hu

first: Rishi

last: Bhogaraju

first: Riley

last: Hannan

first: Daniel

last: Abebayehu

first: Mete

last: Civelek

first: Thomas

middle: H

last: Barker


title: H3K36 Methylation - a Guardian of Epigenome Integrity [CUT&RUN]

first: Jacek

last: Majewski

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&RUN sequencing for histone modifications H3K4me1, H3K27me3 and H3K9me3 in C3H10T1/2 mouse mesenchymal stem cells.

first: Reinnier

last: Padilla

first: Gerald

last: Shipman

first: Cynthia

last: Horth

first: Michel

last: Gravel

first: Eric

last: Bareke


title: Spatially organized progenitors in the zebrafish heart field determine cardiovascular patterning

first: Yunxia

last: Wang

summary: Progenitor cells expressing nkx2.5 are specified in the bilateral zebrafish heart field that give rise to distinct components of the cardiovascular system. We have employed a single cell sequencing approach using the inDrops platform to study progenitor cells expressing nkx2.5. After specification, these fields separate into two main sub-populations; a cardiac fraction that migrates to the midline and forms the ventricular myocardium, and a pharyngeal fraction that remains lateral before differentiating into the head muscles, outflow tract, and pharyngeal arch arteries.  This study represents the first multi-omics analysis of pre-migratory populations coordinate.

overall_design: 14- and 20-ss wildtype (TU) and Tg(nkx2.5:ZsYellow) embryos were dissociated by Fluorescence-activated cell sorting (FACSmax) cell dissociation solution and analyzed using scRNA-seq.

first: Hakan

last: Coskun

first: Xinlei

last: Gao

first: Kaifu

last: Chen

first: C

last: Geoffrey Burns

first: Caroline

last: Burns


title: Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs [ATAC-seq]

first: Andrew

last: Miller

overall_design: ATAC-sequencing of WT and CD90/Thy-1 CRISPR KO immortalized human lung fibroblasts cultured on 4kPa, 25kPa, and tissue culture plastic (TCP) substrates for periods of 24hr or 72hr. A 0-hr sample was collected from cell suspension as samples were seeded.

first: Ping

last: Hu

first: Rishi

last: Bhogaraju


title: Deep Learning Models for Cell Cycle Phase Prediction from Single-Cell RNA Sequencing Data

city: Morgantown

first: Halima Akhter

last: Akhter

state: West Virginia

address: 1 Medical Center Dr, Morgantown, WV 26506

department: Immunology, and Cell Biology

institute: West Virginia University

summary: Accurate prediction of cell cycle phases is important in understanding how certain diseases (e.g. cancer) develop and respond to treatment. It is also essential for reducing the confounding effects in single-cell RNA sequencing (scRNA-Seq) data analysis. We evaluated both traditional machine learning techniques and deep learning approaches for predicting cell cycle phases from scRNA-seq data. Models were trained on consensus predictions from four popular cell cycle analysis tools, namely, CellCycleScore, ccAF, Revelio, and Tricycle, then applied to unlabeled scRNA-seq data generated from human leukemia cell lines. We evaluated model performance using publicly available datasets, GSE146773 (human leukemia cells, 1,151 cells) and GSE64016 (human embryonic stem cells, 213 cells),  both labeled with their respective cell cycle phases through experiments. In addition to the four tools, we assessed traditional machine learning models (AdaBoost, Random Forest, and LightGBM), deep learning models including multiple dense networks DNN (2-5), CNN, Hybrid CNN-Dense, Feature embedding, and ensemble models. DNN 3 achieved the highest accuracy, reaching 75.16% on the GSE146773 dataset and 70.85% on GSE64016. This outperformed existing tools such as Revelio (68.34% on GSE146773, 68.2% on GSE64016), CellCycleScore (66.54% on GSE146773, 53.84% on GSE64016), ccAF (45% on GSE146773, 40% on GSE64016), ccAFv2 (47.23% on GSE146773, 43.72% on GSE64016), Tricycle (53.23% on GSE146773, 58.7% on GSE64016), and Cyclum (38.52% on GSE146773, 26.3% for GSE64016). These results signify the potential of deep learning models for robust cell cycle phase prediction in scRNA-seq data.

overall_design: We ran an experiment using two types of human leukemia cell lines. These include REH (ATCC #CRL-8286) and SUP-B15 (ATCC #CRL-1929). We prepared scMultiome libraries for each cell line for both gene expression (scRNA-seq) and chromatin accessibility (single-cell Assay for Transposase-Accessible Chromatin; scATAC-seq) at the same time at single-cell levels. In this study we focused only on scRNA-seq data.

first: Gangqing

first: Donald

last: Adjeroh

first: Debra

last: Piktel

first: Laura

last: Gibson

first: Halima


title: Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs

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

overall_design: Refer to individual Series


title: Transcriptional profile of B16-OVA cells with PUM1 knockout

city: chongqing

first: Xue

last: Zhang

address: 2 Chongwen Road, Nanan District, Chongqing

institute: Chongqing University of Posts and Telecommunications

summary: PUM1 is a highly conserved RNA-binding protein that plays a key role in  regulating mRNA stability. B16-OVA knockout PUM1 cell lines were constructed using CRISPR/CAS9 gene editing technology, and  it was found that the PUM1 knockout reduce  cell proliferation through indcuing G2/M phase arrest  and causing cell apoptosis. From RNA-seq sequencing results, GO enrichment analysis showed that differential expression genes were mainly enriched in the negative regulation of viral process, response to interferon-beta, defense response to virus, defense response to symbionts and other pathways closely related to immunity. KEGG enrichment analysis showed that differential genes were mainly enriched in JAK-STAT signaling pathway, TNF signaling pathway, NF-kappa B signaling pathway, PI3K-Akt signaling pathway, MAPK signaling pathway and NOD-like receptor signaling pathway.

overall_design: RNA-seq analysis of wildtype B16-OVA cells and their knockout derivatives (KO.3, KO.11) by CRISPR/CAS9 technique

first: Chenchen

last: Pan

first: Shuo

last: Song

first: Yaqi

last: Li

first: Defen

last: Zhou

first: Hanwei

last: Cui

first: Jiangan

last: Xie


title: the transcriptomic profiling of HCECs (PAI-2 knockout and control) exposed to PM2.5 for 3 hours

city: Hangzhou

first: Shengjie

last: Hao

address: 1 Xihu Avenue

institute: Zhejiang University

summary: We previously found that PAI-2 mediates long-term PM2.5 exposure-induced corneal damage in vivo and in vitro, while its role during subclinical stage remains unclear. In this study,we constructed PAI-2 knockout-human corneal epithelial cells (KO) and the negative control (NC).  Transcriptome analysis was performed in three groups: NC, PM2.5-exposed NC, KO and PM2.5-exposed KO. These analysis suggested cell-ECM interactions might play an important role in PAI-2-induced corneal injury upon PM2.5 exposure.

overall_design: PAI-2 KO and NC were exposed to PM2.5 for 3 hours and mRNA was isolated for RNA sequencing.

first: Ke

last: Yao

first: Qiuli

last: Fu


title: Dermal fibroblast cultures recapitulate differences between deermice and mice in their responses to Toll-like receptor agonists

city: Irvine

first: Jonathan

middle: Van

last: Duong

state: CA

address: 843 Health Sciences Rd

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: The white-footed deermouse Peromyscus leucopus is a primary reservoir for the agents of Lyme disease and other zoonoses in North America. These and other species of Peromyscus are tolerant of the infection by the bacteria, protozoa, and viruses they host. This is mainly by mitigating the damaging effects of the innate immune response. In previous studies we demonstrated differences between P. leucopus and either inbred or outbred M. musculus in the degree of sickness and profiles of biomarkers after exposure to bacterial lipopolysaccharide, a TLR4 agonist. With the objective of developing a method for broadly assessing of innate immunity of capture-release mammals in nature, we evaluated using bulk and single cell RNA-seq primary dermal fibroblast cultures of P. leucopus and M. musculus in their short-term responses to a lipopeptide that is a TLR2 agonist. As we had observed for experimental animals, the fibroblast cultures of the two species displayed both similarities and differences in their responses to the agonist. The notable differences included the greater magnitude of an anti-viral profile of cytokines and other effectors in the deermouse fibroblasts and the occurrence of an interleukin-11 response in the mouse cultures but not deermouse. We also observed in both species' cultures an increased transcription of several types of endogenous retrovirus (ERV) elements after exposure of the cells to the agonist. The P. leucopus cells were distinguished from M. musculus cells in the generally shorter retroviral open reading frames among the differentially expressed sequences. This was consistent with previous findings about ERV transcription in P. leucopus and M. musculus and suggests a greater suppression of ERV activity in P. leuocopus. The results affirm the feasibility of this in vitro model for both laboratory- and field-based studies without need for euthanasia and that inherent differences between deermice and mice in innate immune responses can be demonstrated in primary fibroblasts as well as the animals themselves.

sample_organism:
Peromyscus leucopus
Mus musculus

platform_organism:
Peromyscus leucopus
Mus musculus

overall_design: RNA-seq of primary skin cultures from ear of Peromyscus leucopus LL stock and Mus musculus CD-1 breed four hours after addition of TLR agonists to culture medium. Bacterial lipopolysaccharide at 1 microgram per milliliter, lipopeptide Pam3SK4 at 1 or 10 micrograms per milliliter final concentrations, or saline alone were used.

first: Aqsa

last: Motiwala

first: William

last: Hotz

first: Landen

last: Gozashti

first: Anthony

last: Long

first: Alan

last: Barbour


title: Genomic Dynamics of Patient Derived Parasites: Comparative Genomic Hybridization of Plasmodium vivax causing severe malaria

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

type: Genome variation profiling by genome tiling array

summary: Comparative Genomic Hybridization study of Severe vs Uncomplicated P. vivax malaria

overall_design: Agilent P. vivax 2x400K CGH microarray (AMADID: 25335)  designed by Genotypic Technology Private Limited

first: Ashis

last: Das


title: RNA sequencing profiling of circular RNA during during megakaryocyte maturation.

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

summary: To profile the landscape of circRNAs during megakaryocyte differentiation, we conducted circRNA expression profiling analysis on day 6 and day 13.

overall_design: By day 6 and 13, CD34+ cells differentiated into mature MKs to extract total RNA. RiboMinus/RNaseR-treated RNA sequencing (RNA-seq) was performed. Totaol RNA from MK cultures at days 6 and 13, RiboMinus/RNaseR-treated RNA -seq were performed.


title: Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22 [scRNA-seq]

city: CAMBRIDGE

first: Qiming

last: Zhang

state: MA

address: 88 Ames Street

institute: Koch institute

summary: A critical question in physiology is to understand how tissuesadaptand alter their composition in responsetodietary cues.The mammalian small intestine, avitaldigestive organ thatabsorbs nutrients, is maintainedby rapidly renewing Lgr5+ intestinalstem cells (ISCs) located attheintestinal crypt base. While Lgr5+ ISCs drive intestinal adaptation by altering self-renewing and differentiating divisions inresponse todiverse diets such as high-fat diets and fasting regimens, little is known about howmicronutrients, like amino acids, instruct Lgr5+ ISCfate decisions to control intestinal homeostasis and repair after injury. Here, we demonstrate that cysteine, an essential amino acid, enhances theability of Lgr5+ ISCs to repair intestinal injury.

overall_design: CD45+ immune cells were isolated from small intestine of cystine-fed samples and the matched control samples by fluorescence-activated cell sorting (FACS) and then scRNAseq experiments and analyses were performed.

first: Fangtao

last: Chi

first: Omer

last: Yilmaz


title: Chemotherapy-driven intestinal dysbiosis and microbial indole-3-propionic acid rewire bone marrow myelopoiesis to promote anti-metastatic immunity

first: Tania

last: Wyss

summary: We investigated how microbial derived product influence myeloid cell differentiation in vitro.

overall_design: To assess the effect of indole-3-propionic acid (IPA) on MDSC generation, we exposed bone marrow cells to MDSC-inducing media in the presence of vehicle, 10uM IPA or 50uM IPA.

first: Ludivine

last: Bersier

first: Tatiana

last: Petrova


title: Deletion of KLHDC3, an E3 ubiquitin ligase complex substrate receptor, leads to obesity in mice

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: WEHI

summary: Protein ubiquitination is a critical post-translational modification that regulates protein stability and cellular homeostasis. KLHDC3 is a substrate recognition receptor within the recently identified C-terminal degron-mediated DesCEND ubiquitination pathway. It has been characterised to selectively bind proteins with C-terminal RxxxG motifs, targeting them for degradation. Unlike the well-characterised N-terminal degron pathway, the physiological roles of C-terminal degrons remain poorly understood. To investigate KLHDC3 function in vivo, we generated Klhdc3-deficient (Klhdc3-/-) mice. These mice exhibited sub-Mendelian birth rates and progressive postnatal lethality, with a median survival of 136 days and maximum survival observed of ∼1 year of age. Early growth retardation was apparent, followed by a normalisation of body mass with age. However, as Klhdc3-/- mice aged they developed pronounced obesity at the expense of lean mass, with some individuals reaching fat mass exceeding 50% of total body weight. Combined transcriptomic and proteomic analyses of Klhdc3-/- embryonic fibroblasts revealed significant changes in protein expression with minimal impact on transcript levels, consistent with KLHDC3’s role in post-translational regulation. Among the upregulated proteins, HINT1 was identified as a novel KLHDC3 substrate, possessing a C-terminal degron motif. Protein stability assays and immunoblotting confirmed HINT1 as a direct target of KLHDC3. These findings establish a new in vivo physiological role for the DesCEND pathway and highlight KLHDC3 as a key regulator of development, survival, and adiposity in mice.

overall_design: 3'RNA-seq (methods used BRB-seq)

first: M

last: Smeets

first: P

last: Buco

first: Z

last: Liang

first: A

middle: M

first: S

last: Taylor

last: Gupte

first: J

last: Heraud-Farlow

first: C

last: Walkley


title: Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22

overall_design: Lgr5-high and Lgr5-low cell populations were isolated and RNA was then extracted and sequenced from small intestine of cystine-fed samples and the matched control samples.


title: Overexpressed PRR11-SKA2-miR301a/454 bidirectional transcription unit essentially and coordinately promotes PI3K-AKT pathway activation and lung cancer progression

first: youquan

last: bu

address: Medical College Road No.1

institute: Chongqing Medical University

summary: Gene pairing is a highly conserved and special mode of eukaryotic gene organization, and critically implicated in development and diseases including cancer. We previously found that PRR11 and SKA2 constitute a classic head-to-head gene pair. Here, we further demonstrate that PRR11, SKA2, and its intronic miR301a and miR454 constitute a more exquisite bidirectional transcription unit that are overexpressed in various types of cancers. Functional studies using lung cancer as a model system reveal that co-overexpression of PRR11, SKA2, miR301a and miR454 together remarkably accelerates cell growth, cell cycle progression and cell motility in lung cancer cells, and promotes tumor growth in mouse models in vivo, whereas CRISPRi-mediated repression of the entire transcription unit inhibits these malignant phenotypes. Mechanistically, the four component genes do not display any additive or synergistic effect, but rather compensate for each other for robustly sustained activation of PI3K-AKT pathway, with PRR11 interacting with GRB2, and SKA2 with EGFR. Notably, miR301a and miR454 exert their oncogenic functions at least partially via repressing PTEN translation. Moreover, the transcription unit presents as a prominent prognostic meta-marker for lung cancer. Collectively, these findings demonstrate the essential and coordinated roles of PRR11-SKA2-miR301a/454 bidirectional transcription unit in lung cancer progression, highlighting its potential diagnostic and therapeutic values in cancers.

overall_design:
To investigate the molecular mechanisms by which the PRR11/SKA2/miR301a/miR454 transcriptional unit promotes lung cancer development, we conducted four sets of experiments in A549 cells. In the first set, we established stable cell lines with suppressed bidirectional promoter transcriptional activity of PRR11/SKA2 using the CRISPRi system. In the second set, we established stable cell lines with individual overexpression of PRR11, SKA2, as well as co-overexpression of PRR11 and SKA2, using the Lenti-pCDH-CMV system. In the third set, we established stable cell lines with individual overexpression of miR301a, miR454, as well as co-overexpression of miR301a and miR454, using the Lenti-pCDH-CMV system. In the fourth set, we established cell lines with knockout of pre-miR301a and pre-miR454, respectively, using the CRISPRd system.
We subsequently conducted gene expression profiling analysis using RNA-seq data obtained from these four experimental groups.
Comparative gene expression profiling analysis was conducted on the RNA-seq data. For the first group, we compared the stable cell lines with suppressed bidirectional promoter transcriptional activity of PRR11/SKA2 (CRISPRi_PRR11+SKA2 promoter-sgRNA#1) with their corresponding control cell lines (CRISPRi_Mock sgRNA). In the second group, we compared the stable cell lines with individual overexpression of PRR11, SKA2, and co-overexpression of PRR11 and SKA2 (LV-PRR11, LV-SKA2, LV-P+S) with their respective control cell lines (LV-vector-PS). For the third group, we compared the stable cell lines with individual overexpression of miR301a, miR454, and co-overexpression of miR301a and miR454 (LV-miR301a, LV-miR454, LV-3+4) with their corresponding control cell lines (LV-vector-34). Lastly, for the fourth group, we compared the cell lines with knockout of pre-miR301a and pre-miR454 (CRISPRd_miR301a-#2, CRISPRd_miR454-#1) with their respective control cell lines (CRISPRd_Control).

first: Tao

last: Liu

first: Xiaofeng

last: Zuo

first: Shijie

last: Sun

first: Kailong

last: Du


title: Mapping Somatosensory Afferent Circuitry to Bone Identifies Neurotrophic Signals Required for Fracture Healing

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: A central feature of bone injury is the sensation of pain, transmitted by nociceptive sensory nerves that innervate the skeleton. Indeed skeletal-innervating peripheral neurons are known to regulate skeletal repair and pathophysiology.  Here, using retrograde peripheral nerve labeling and single cell RNA sequencing (scRNA-seq), we precisely identify the unique molecular signature of skeletal-innervating sensory neurons and the shifting neuronal transcriptomic landscape after bone fracture. Two methods to surgically or genetically denervate fractured bones were used in combination with scRNA-seq to implicate defective mesenchymal cell proliferation and osteodifferentiation as underlying the poor bone repair capacity in the presence of attenuated skeletal innervation. Multi-tissue scRNA-seq and interactome analyses implicated neuron-derived FGF9 as a potent regulator of fracture repair, a finding confirmed by in vitro assessments of neuron-to-skeletal mesenchyme interactions. Identification of FGF9 as a novel,  neuron-derived skeletal growth factor uncovers a potential target for improving tissue repair.

overall_design: To identify skeleton-innervating neurons, an engineered virus with enhanced tropism for peripheral neurons was injected into the midshaft of the  ulnar periosteum of 14-week-old mice (3.5μl AAV-PHP.S-tdTomato). 4 weeks after injection, retrograde labeling of dorsal root ganglion (DRG) neurons with  AAV-PHP.S-tdTomato was evaluated using whole-mount immunohistochemistry, scRNA-Seq and RNAscope (DRGs at C7, C8, T1 levels were used corresponding to the innervation pattern of the forelimb). To characterize temporal transcriptomic responses to ulnar stress fracture  retrogradely labeled whole DRGs were harvested and dissociated at 1-, 14- and 56- days post-stress fracture and subjected to scRNA-Seq. To uncover ulna callus resident cells that may interact with ulna-innervating sensory neurons, callus single-cell transcriptomics atlas from control and denervated callus were generated 14 days post fracture. Denervation of callus was achieved by two methods: surgical neurectomy of ulna neurectomy and chemical inhibition by administrating small molecule 1NMPP1 to TrkAF592A mice. Interaction modalities were performed to reveal potential skeleton-innervating neuron-derived ligands that are involved in fracture repair.

first: Mingxin

last: Xu

first: Zhao

last: Li

first: Masnsen

last: Cherief


title: High-Resolution Single-Cell RNA Sequencing Uncovers Disparate Neutrophil Populations within Metastatic Cancer Lesions Linked to Progression Free Survival in Multiple Myeloma Patients

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Understanding the myeloid cell biology of the tumor microenvironment (TME) will allow discovery of novel strategies to disrupt the local immunosuppressive milieu and to develop effective immune based therapies. Neutrophils are a major, understudied myeloid cell population in metastatic malignant tumors. Here, we studied myeloid cells freshly sorted from paired focal lesions (FL) (osteolytic lesions and plasmacytomas) and pelvic bone marrow (BM) from multiple myeloma (MM) patients. Using single cell RNA sequencing and functional assays, we discovered the emergence and expansion of distinct, late-stage neutrophil subsets with potent immunosuppressive signatures predominantly in FL. The most abundant late-stage neutrophil subset, MM_N_FL1, activates cytokine responses, the IL-8 CXCR2 pathway, and nitrogen compound metabolism while downregulating primary, secondary, and tertiary granule expression. FL neutrophils exhibit transcriptional and functional differences compared to their paired BM counterparts, displaying notably elevated immunosuppressive capacities independent of tumor cell percentage in FL and BM. Furthermore, the gene signature of the FL neutrophils was associated with significantly inferior progression-free survival (PFS) in a defined population of MM patients. The study provides an in-depth analysis of neutrophil dynamics, function, and imbalance in MM patient FL, suggesting promising targets for novel clinical immunomodulatory therapies.

overall_design: A total of 13 patients underwent biopsy: 10 had osteolytic lesions (OL) and 2 had extramedullary disease. These are grouped together as FL because the genetic analysis was the same for both populations. One OL had no cells recovered. We also included three healthy donors as basline control for patients. BM from healthy donors and BM or FL samples from MM patients were freshly collected using either standard blind aspiration (from healthy volunteers) or CT guided biopsy and aspiration (from patients) at the Roswell Park Comprehensive Cancer Center. The study was approved by the Roswell Park Institutional Review Board (protocol # I 66418). Informed consent was obtained from all patients and healthy volunteers before sampling. Ammonium–chloride–potassium (ACK) lysing buffer was used to exclude red blood cells (RBCs). CD11b+CD3-CD56-CD138- myeloid cells were freshly isolated using a SONY flow sorter. Selected cells were immediately used for scRNA-seq.

first: Hillengass

last: Jens

first: Mohammadpour

last: Hemn

first: McCarthy

last: Philip

first: Samur

last: Mehmet


title: Piezo1 balances the osteogenic-tenogenic plasticity of periosteal progenitor cells through the YAP pathway

city: ShangHai

first: Lijun

last: Wang

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: The extremity tendons and bones are derived from limb bud mesenchyme, which eventually become cells of different tissues. Despite their common origin, it was widely believed that tenocytes and skeletal cells are distinct lineages without interconversion. However, we found that periosteal skeletal progenitor cells could transform between osteogenic and tenogenic commitment. SCX can label the periosteal progenitor cell population. Loss of Piezo1 arrests the periosteal progenitor cells in a progenitor state. Piezo1 deficiency leads to upregulation of Scx expression due to the inhibited YAP nuclear localization. Loss of Piezo1 showed increased tenogenic marker genes and decreased osteogenic marker genes. The periosteal progenitor cells can regenerate the injured tendon more robustly when Piezo1 is absent. Taken together, our data reveal that periosteal SCX+ progenitor cells compromise the osteogenic ability and acquire the tenocyte-biased lineage commitment after loss of Piezo1, providing a strategy to modulate the periosteal progenitor cells for tissue regeneration.

overall_design: Periosteal cells were extracted from femurs and tibias of Prx1 Cre; Ai9/+ and Prx1 Cre; Ai9/+; Piezo1 fl/fl mice at 8 week.

first: Weiguo

last: Zou

first: Qian

last: Ren

first: Shuqin

last: Chen

first: Lixiang

last: Lou

first: Wenhui

last: Xing

first: Jun

first: Xuye

last: Hu

first: Miaomiao

first: Heng

last: Feng

first: Matthew

last: Greenblatt


first: Alistair

last: Chalk

first: P

last: Buco

first: M

last: Smeets

first: Z

last: Liang

first: A

first: S

last: Taylor

last: Gupte

first: J

last: Heraud-Farlow

first: C

last: Walkley


title: CEP290-deficiency disrupts ciliary axonemal architecture in human iPSC-derived cerebral organoids

city: Zurich

first: Ruxandra

last: Bachmann-Gagescu

address: Winterthurerstrasse 190

institute: University of Zurich

summary: Primary cilia are ubiquitous sensory organelles mediating various signaling modalities essential for development and cell homeostasis. Their dysfunction leads to ciliopathies, human disorders often affecting the central nervous system. CEP290 is a major ciliopathy-associated gene that encodes a centrosomal and ciliary transition zone protein. CEP290 has been implicated in different cellular functions, including cell cycle control, ciliogenesis, and control of ciliary membrane protein content. To investigate CEP290 dysfunction in human neurons, we generated human iPSC-derived cerebral organoids harboring CEP290 mutations. To quantitatively investigate the impact of CEP290 loss on cerebral organoid differentiation, we conducted single-cell RNA-sequencing. We found that CEP290 deficiency does not affect cell cycle progression or organoid formation, despite a tendency for less mature neuronal populations and formation of choroid plexus in mutant organoids.

overall_design: CEP290 CRISPR edited and WT cerebral organoids were harvested and dissociated with three organoids per sample. Samples were analysed using scRNA-seq.

first: Melanie

last: Eschment

first: Olivier

last: Mercey

first: Ellen

last: Aarts

first: Ludovico

last: Perego

first: Joana

last: Figueiro da Silva

first: Affef

last: Abidi

last: Generali

first: Paul

last: Guichard

first: Virginie

last: Hamel


title: Monitoring the complexity and dynamics of mitochondrial translation

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

summary: Eukaryotes house the additional protein synthesis system in mitochondria. Given the mitochondrial translation dictates OXPHOS complex abundance and then ATP level in cells, the exhaustive quantitative, and high-resolution delineation of mitoribosome traversal has been awaited. Here, we developed a high-resolution mitochondrial ribosome profiling and unveiled tight regulation of in organello translation. Our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the absolute mitoribosome numbers on a transcript, elongation rate, initiation rate, and lifetime translation round on a transcript. We also surveyed the impacts of all the 34th position modifications on mt-tRNAs, including f5C34, m5C34, τm5U34, τm5s2U34, s2U34, and Q34, as well as t6A37 by the responsible enzyme deletions. Moreover, retapamulin-assisted profiling and disome profiling unveiled cryptic translation initiation sites at sub-cognate codons and the programmed mitoribosome collision sites across the mitochondrial transcriptome, respectively. Our work provides a useful resource to delineate protein synthesis within the bioenergetic powerhouse.

sample_organism:
Homo sapiens
Mus
Mus musculus

platform_organism:
Homo sapiens
Mus
Mus musculus

overall_design: Ribo-Seq, RNA-Seq, Ribo-Calibration, MitoIP-Ribo-seq, MItoIP-Thor-Ribo-Seq, MitoIP-Thor-Disome-Seq.

first: Mari

last: Mito

first: Haruna

last: Yamashiro

first: Kotaro

last: Tomuro

first: Fan-Yan

last: Wei

first: Kazuhito

last: Tomizawa

first: Takeshi

last: Chujo

first: Asuteka

last: Nagao

first: Takeo

last: Suzuki

first: Yuichi

last: Shichino

first: Tsutomu

first: Shintaro

last: Iwasaki


title: Codon Specific Readthrough as a Mechanism of BRCA2 Restoration in Acquired PARP Inhibitor and Chemotherapy Resistance [RNA-seq]

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

summary: Deleterious alterations of the gene encoding BRCA2, a protein involved in homologous recombination (HR), contribute to the pathogenesis of a subset of ovarian, breast, prostate and pancreatic cancers as well as their increased sensitivity to platinating agents and poly(ADP-ribose) polymerase inhibitors (PARPis). While secondary mutations that restore a functional BRCA2 protein are detected in a fraction of cases that become drug resistant, the causes of resistance in other cases are poorly understood. Here we characterized clones derived from the BRCA2-mutant ovarian cancer line PEO1 by PARPi selection. Colony forming assays demonstrated cross-resistance of these clones to multiple PARPis, cisplatin and doxorubicin. Despite persistence of the signature 4965C>G (p.Y1655X) BRCA2 nonsense mutation, HR was restored in the resistant cells. Immunoprecipitation followed by immunoblotting or mass spectrometry demonstrated expression of low levels of BRCA2 protein, including peptides distal to the premature termination codon. Reporter assays demonstrated readthrough selective for the UAG stop codon in the resistant clones but not parental PEO1 cells. Mass spectrometry and immunoblotting provided evidence for readthrough of stop codons, particularly UAGs, in additional proteins in the resistant clones. BRCA2 gene interruption either 5’ or 3’ to the stop codon restored sensitivity of the resistant clones to PARPis and cisplatin, implicating the low level BRCA2 expression in resistance. Accordingly, the present results identify low level readthrough of nonsense codons as a potential mechanism of drug resistance that might need to be considered when assessing the impact of BRCA2 nonsense mutations.

overall_design: RNAseq data of 15 samples (PEO1 parental or and veliparib resistant ABTR clones (n=4) ) in three independent experiments. PEO1 resistant clones (ABTR) were generated by continuous exposurse to veliparib (ABT888) 40 uM.

first: Scott

last: Kaufmann

first: Hu

last: Li


title: miR-29 is an important driver of aging-related phenotypes

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

summary: Aging is a consequence of complex molecular changes, but the roles for individual microRNAs (miRNAs) in aging remain unclear.  One of the few miRNAs that is upregulated during both normal and premature aging is miR-29.  We confirmed this finding in our study in both mouse and monkey models.  Follow-up analysis of the transcriptomic changes during normal aging revealed that miR-29 is among the top miRNAs predicted to drive the aging-related gene expression changes.  We also showed that partial loss of miR-29 extends the lifespan of Zmpste-/- mice, an established model of progeria, which indicates that miR-29 is functionally important in this accelerated aging model.  To examine whether miR-29 upregulation alone is sufficient to promote aging-related phenotypes in vivo, we generated mice in which miR-29 can be conditionally overexpressed (miR-29TG).  We found that miR-29 overexpression in mice is sufficient to drive aging-related phenotypes including alopecia, kyphosis, osteoporosis and senescence, and leads to early lethality. Transcriptomic analysis of both young miR-29TG and old WT mice revealed shared downregulation of genes enriched in extracellular matrix and fatty acid metabolism, and shared upregulation of genes in pathways linked to inflammation.  Together, these results highlight the functional importance of miR-29 in controlling a gene expression program that drives aging-related phenotypes.

overall_design: RNA-seq of liver tissues from 2-month-old wild type B6 mice (n = 6), 2-year-old wild type B6 mice (n = 5) and 2-month-old miR-29 transgenic mice (n = 6) were performed.

first: Yu-Han

last: Hung


title: PyBo-seq of IVT RNA

status: Public on Oct 21 2025

city: Mainz

first: Alexandr

last: Gopanenko

address: Ackermannweg 4

institute: Institute of Molecular Biology gGmbH (IMB)

summary: The RNA modification 5-formylcytidine (f5C) is poorly explored in mammals. Low f5C levels reported in mRNA may reflect spurious 5-methylcytidine (m5C) oxidation or targeted demethylation by TET or ALKBH1 dioxygenases. Here we analyze f5C in RNA of mouse embryonic stem cells (mESCs) using LC-MS/MS and chemical-assisted sequencing. We reveal that the previously reported pyridine-borane-sequencing method misidentifies N4-acetylcytidine (ac4C) and unmodified, hyper-reactive cytidines in a CUMC context as f5C. To overcome these limitations, we developed FIBo-seq with enhanced specificity and sensitivity for f5C-sequencing. We find no evidence for a role of TET enzymes in generating f5C, unlike for ALKBH1. Moreover, no f5C sites are detectable in mRNA. Instead, the bulk of mammalian f5C resides in the well-established mitochondrial tRNA Methionine (mt-tRNAMet) and is mediated by ALKBH1. The results argue against an instructive function for f5C outside tRNA in mammals.

overall_design: Pyridine-borane-assisted RNA-sequencing (PyBo-seq) of synthetic, modification-free RNA generated by in vitro transcription (IVT) from poly(A)+ RNA of mESCs

first: Jasmin A.

last: Dehnen

first: Alexandr V.

first: Carola

last: Scholz

first: Michael U.

last: Musheev

first: Christof

last: Niehrs


title: Cell-specific delivery of GJB2 restores auditory function in mouse models of DFNB1 deafness and mediates appropriate expression in NHP cochlea

city: Boston

first: Erin

middle: Elizabeth

last: Duffy

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

summary: Mutations in the GJB2 gene cause DFNB1, the most common hereditary hearing loss. GJB2 is expressed by cochlear epithelial cells and fibrocytes, but not by sensory hair cells or neurons. Attempts to treat DFNB1 mouse models with gene therapy have not substantially restored function, as inappropriate expression in hair cells and neurons might compromise their electrical activity. Here, we use ATAC-seq to identify candidate gene regulatory elements (GREs) that can drive cell-type-specific expression of GJB2. HA-tagged GJB2, delivered to a conditional knockout mouse with AAV vectors carrying GREs, is expressed by the appropriate cells, prevents degeneration, and rescues hearing by only 10–20 dB. In a Gjb2 partial knockdown model, a vector lacking HA prevents degeneration and completely restores hearing. In cynomolgus monkey cochleas, human GJB2.HA delivered with similar vectors is located in the appropriate cell types and causes little or no compromise of hearing sensitivity. Together, these findings suggest that GRE-mediated expression of GJB2 can prevent hearing loss in DFNB1 patients.

overall_design: ATAC-seq of bilateral cochleae harvested from neonatal CD1 mice (P2, n=3; P5, n=3; P8, n=4) to determine developmentally relevant gene regulatory elements


title: BRMS1L promotes chemotherapy sensitivity by inhibiting autophagy in breast cancer

city: Guangzhou

first: Shaohua

last: Qu

state: Guangdong

address: No. 613, Huangpu West Avenue, Tianhe District, Guangzhou, Guangdong, P.R. China

institute: Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China

summary: BRMS1L (Breast cancer metastasis suppressor 1 like), a component of Sin3A-histone deacetylase (HDAC) co-repressor complex, has been shown to provide an epigenetic regulation ofWnt signal pathway and act as a metastasis suppressor in breast cancer. However, the role of BRMS1L in the progression and chemosensitivity has not been explored. In the present study, we for the first time showed that reduced BRMS1L expression correlates with poor response to neoadjuvant chemotherapy and poor prognosis in patients with breast cancer. Additionally, chemoresistant breast cancer cells exhibited decreased BRMS1L expression and increased autophagy levels. Furthermore, ectopic expression of BRMS1L significantly enhanced chemotherapy sensitivity via inhibiting protective autophagy in breast cancer cells. In vivo, the experiments in nude mice showed that BRMS1L strengthened the chemotherapy effects on xenografts. Collectively, these results revealed that BRMS1L enhances chemotherapy sensitivity via inhibiting autophagy. Our findings uncover a novel role of BRMS1L in drug sensitivity and highlight the potential clinical application of BRMS1L in the treatment of breast cancer.

overall_design: RNA sequencing (RNA-seq) on MCF-7 and MCF-7/ADR cells

first: Yuan

first: Dian

last: Zhang

first: Junhao

last: Zhao

first: Mei

last: Yang

first: Yiping

last: Wang

first: Peiyao

last: Lee


title: HTGTS-TCR-seq for profiling of mouse and human T-cell receptor α and β gene rearrangements and diversity

city: Shanghai

first: Haiqiang

last: Dai

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell  Science

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

overall_design: Refer to individual Series


title: Regulatory T cells in skin utilize the Cxcr4-Cxcl12 axis to promote hair follicle regeneration

city: San Francisco

first: Jarish

last: Cohen

address: 513 Parnassus Ave, HSW12 Room 1201B

department: Dermatology

institute: University of California, San Francisco

summary: We have employed a fixed single nuclear RNA sequencing using the 10X Genomics FLEX assay to characterize the cellular constituents in healthy human scalp skin. Hair follicles are microanatomic niches that attract immune cells. Therefore, we generated this dataset to gain further insight into the chemokines kerotinocytes in skin express, and expression their cognate receptors on skin lymphocytes.

overall_design: Two formalin-fixed paraffin-embedded healthy human scalp skin specimens were retrieved, and underwent tissue microtomy to generate three 50 micron thick tissue scrolls. The thick tissue scrolls underwent deparaffinization, rehydration, and mechanical and enzymatic dissocation using a Miltenyi GentleMacs Octodissociator with heaters. The resulting suspension was passed through a 30 micron strainer. Nuclei were counted using a Cellaca cell counter and submitted for standard 10X Genomics Flex assay.

first: Cohen

last: Jarish

first: Rosenblum

last: Michael


title: Transcriptomics of mouse oligodendrocyte precursor cells treated with microglia-derived extracellular vesicles

city: Milano

first: Stefano

last: Raffaele

state: -- Please Select (only U.S. / Can / Aus)

address: Via Balzaretti 9

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli Studi di Milano

summary:
Myelin loss due to oligodendrocyte degeneration is a central feature of various neurodegenerative disorders and contributes significantly to neurological disability. Promoting endogenous myelin repair by enhancing oligodendrocyte precursor cell (OPC) differentiation represents a promising therapeutic strategy. Extracellular vesicles (EVs) secreted by pro-regenerative microglia have been shown to support OPC maturation and remyelination, yet the underlying molecular mechanisms remain incompletely understood.
In this study, we performed transcriptomic profiling of primary murine OPCs undergoing differentiation in the presence of EVs derived from donor microglia exposed to pro-inflammatory cytokines (i-EVs), interleukin-4 (IL4-EVs), or mesenchymal stem cells (MSC-EVs). This dataset provides insights into the transcriptional changes associated with EV-mediated modulation of OPC differentiation.

overall_design: Primary OPCs were isolated from P2 mouse brains using anti-CD140a microbeads and MACS-sorting. After 48h of proliferation, OPCs were switched to differentiation medium and exposed to different types of EVs derived from primary mouse microglia (i-EVs, IL4-EVs, MSC-EVs) or medium alone (CTRL). After 24h of treatment, OPCs were lysed for RNA extraction and hybridization on Affymetrix Clariom D mouse microarrays.

first: Claudia

last: Verderio

first: Marta

last: Fumagalli


title: GDF-11 stimulates human extravillous trophoblast cell invasion by upregulating ANGPTL4 expression

city: Zhengzhou

first: Jung-Chien

last: Cheng

state: Henan

address: 40, Daxue Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: Proper regulation of extravillous trophoblast (EVT) cell invasion is critical for normal placental development and function. Growth differentiation factor 11 (GDF-11), a member of the transforming growth factor-β (TGF-β) superfamily, has been shown to promote EVT cell invasion, yet the underlying molecular mechanisms remain largely unclear. In this study, RNA sequencing identified angiopoietin-like 4 (ANGPTL4), a multifunctional secreted protein, as a novel downstream target of GDF-11. In vitro experiments demonstrated that GDF-11 significantly upregulated ANGPTL4 expression in both HTR-8/SVneo cells and primary human EVT cells. Mechanistically, we found that the type I TGF-β receptors ALK4 and ALK5 were essential for mediating the stimulatory effect of GDF-11 on ANGPTL4 expression. Further analysis revealed that SMAD3, but not SMAD2, was the key transcription factor involved in this process. Using both loss- and gain-of-function approaches, we demonstrated that ANGPTL4 was required for GDF-11-induced EVT cell invasion. Importantly, serum levels of GDF-11 were markedly reduced in patients with preeclampsia (PE), a pregnancy disorder associated with shallow trophoblast invasion and poor placentation. Together, our findings uncover a previously unrecognized GDF-11-ANGPTL4 signaling axis that regulates EVT cell invasion and provide new insight into the pathophysiology of PE.

overall_design: HTR-8/SVneo cells were treated with 30 ng/mL GDF-11 for 3 hours

first: Ze

last: Wu

first: Lanlan

last: Fang

first: Xuan

last: Dang

last: Yu

first: Beibei

last: Bi

first: Xiaoyu

last: Han

first: Ying-Pu

last: Sun


title: Evaluation of an Anti-thyroid Mode of Action for Thyroid Follicular Cell Adenomas in Female Mice Exposed to Tertiary Butyl Alcohol

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

summary: Chronic exposure to high concentrations of tertiary butyl alcohol (TBA) in drinking water is associated with, low, but increased (15% vs 3% in controls) thyroid follicular cell (TFC) adenomas in female mice. The U. S. Environmental Protection Agency (EPA) developed linear cancer toxicity criteria on this endpoint. This study evaluates whether TBA, a nongenotoxic alcohol, induces TFC adenomas in female B6C3F1 mice through a nonlinear anti-thyroid mode of action (MOA). Female mice were exposed to TBA either by oral gavage (500 and 1000 mg/kg) for 5 days or via drinking water (5, 10, 20, or 40 mg/mL) for 14 or 28 days. Key events (KEs) within an anti-thyroid MOA framework—including activation of CAR/PXR, induction of phase I and II liver enzymes, changes in serum thyroxine (T4) and thyroid-stimulating hormone (TSH), and histopathological and proliferative alterations in the thyroid—were evaluated. TBA exposure was found to activate CAR/PXR and induce hepatic phase I and II enzymes; however, it did not produce consistent alterations in T4 or changes in TSH levels, nor did it cause histological changes in the thyroid or increased TFC proliferation in these short-term exposure studies. Considered together with the TBA chronic study demonstrating TFC hyperplasia, there is some evidence to support an anti-thyroid MOA. The data, herein demonstrate TBA activates upstream KEs (CAR/PXR signaling, with upregulation of UGT and SULT transcripts, enzymes that can influence T4 serum levels) in the MOA while downstream events (serum TSH changes nor histopathological changes in the thyroid) were not demonstrated in these short-term studies. The inability to unequivocally demonstrate downstream KEs is likely a consequence of the overall weak tumor response following chronic exposure to high-dose levels (~2110 mg/kg-bw/day) of TBA. Notably, the EPA considered the evidence for thyroid adenomas as “suggestive”, a level that would typically not support a dose-response assessment. The MOA analyses herein highlight an important consequence of conducting risk assessments on weak, suggestive tumor data.

overall_design: Comparative gene expression profiling analysis of TempO-Seq data from FFPE liver tissue of female B6C3F1 mice exposed to various dose levels of TBA (0, 10, 20, or 40 mg/mL) in drinking water for 14 or 28 days.

first: Susan

last: Borghoff

first: Brianna

last: Rivera

first: Laurie

middle: C

last: Haws

first: Chad

last: Thompson


title: SELEX-seq of AP1 homodimer

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

summary: These datasets represent the results of a SELEX-seq experiment to identify the DNA binding specificity of Arabidopsis thaliana AP1-AP1 dimers

overall_design: Starting from a set of DNA oligos with random sequence, 4 rounds of enrichment were done using the AP1 proteins

first: Peilin

last: Chen

first: Cezary

last: Smaczniak

first: Kerstin

last: Kaufmann


title: Differential expression analysis in single cell and spatial RNASeq without model assumptions

city: Bethesda

first: Sergey

last: Leikin

department: NICHD

institute: National Institutes of Health

summary: Gene up(down)regulation findings in single cell and spatial RNASeq can be inconsistent despite remarkable progress in technology. False findings in high-quality samples raise concerns about assumptions behind widely accepted data analysis approaches. We have developed a weighted averaging approach for data analysis without assuming anything besides randomness of technical noise. This approach is closely related to prior work on statistics of cluster-randomized experiments. We show that weighing transcript counts based on measured noise variances and utilizing weighted rather than standard unweighted tests reduces both false positive and false negative findings. Our approach eliminates the need for parametrizing data distributions and/or rescaling transcript counts, which may cause artifacts by distorting and biasing the data. The resulting analysis is less complex and produces more consistent differential gene expression. The present dataset is a Visium HD slide with 3 sections from the same E18 mouse tibia. Comparison of proliferating chondrocytes in the growth plates of these sections based on commonly used differential expression analysis methods produced numerous false positive findings, initiating our study. Our weighted averaging appproach eliminated these false positive findings. This dataset is used as an example in the paper for illustrating application of the weighted averaging approach to high-resolution spatial transcriptomics.

overall_design: Tibias from untreated, wild type C57BL/6J mouse embryo at embryonic day E18.5 were dissected, fixed in freshly prepared 4% methanol-free formaldehyde solution in phosphate-buffered saline for 24 h at room temperature, and embedded into paraffin. Three sections from the same tibia were utilized for the experiment.

first: Leikin

last: Sergey


title: Acute session of three endurance exercise intensities alters subcutaneous adipose tissue transcriptome in regular exercisers

city: Ann Arbor

first: Jeffrey

last: Horowitz

state: MI

address: 830 N University Ave

department: School of Kinesiology

institute: University of Michigan

summary: The primary aim of this study was to compare the acute effects of three exercise intensities on abdominal subcutaneous adipose tissue (aSAT) transcriptome in regular exercisers. A total of 45 adults who exercise regularly were assigned to perform a single session of either low-intensity continuous (LOW; 60min at 30% VO2max; n=15), moderate-intensity continuous (MOD; 45min at 65% VO2max; n=15), or high-intensity interval exercise (HIGH; 10x1min at 90% VO2max interspersed with 1min active recovery; n=15). aSAT biopsy samples were collected before and 1.5hours after the exercise session for bulk RNA sequencing and targeted protein immunoassays. HIGH upregulated genes involved in cytokine secretion, insulin signaling, and proteolysis while MOD and LOW upregulated genes regulating ECM remodeling, ribosome biogenesis, and oxidative phosphorylation pathways. Exercise-induced changes in aSAT angiogenic, MAPK cascade, and clock genes, ERK protein phosphorylation, and circulating cytokines were similar after all three exercise treatments. Network analysis identified exercise-responsive gene clusters linked to cardiometabolic health traits. Cell-type analysis highlighted a heterogeneous response of aSAT cell types to exercise, with distinct patterns observed across exercise intensities. Collectively, our data characterizes early responses in aSAT after a single session of exercise. Because adaptations to exercise training stem from an accrual of responses after each session of exercise, these early responses to exercise are likely important contributors to the long-term structural and functional changes that occur in adipose tissue in response to exercise training.

overall_design: Bulk RNA-seq profiling and targeted protein analysis on abdominal subcutaneous adipose tissue (aSAT) biopsy samples from regular exercisers before and 1.5 hours after one exercise session of three different intensities.

first: Cheehoon

last: Ahn

first: Tao

last: Zhang

first: Thomas

last: Rode

first: Gayoung

last: Yang

first: Olivia

middle: K

last: Chugh

first: Sierra

last: Ellis

first: Sophia

last: Ghayur

first: Shirya

last: Mehta

first: Ryan

last: Salzman

first: Hui

last: Jiang

first: Stephen

last: Parker

first: Charles

last: Burant


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

sample_organism:
Pseudomonas aeruginosa
Escherichia coli
Bacillus subtilis
Acetivibrio thermocellus
Haloferax volcanii
Pyrococcus furiosus
Sulfolobus acidocaldarius
Thermoplasma acidophilum
Saccharomyces cerevisiae
Homo sapiens
Salmonella enterica
Pyrodictium abyssi
Thermococcus kodakarensis
Planococcus halocryophilus


title: Massively parallel functional screen identifies thousands of regulatory differences in human versus chimpanzee postcranial skeletal development

city: Cambridge

first: Terence

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

summary: Every element of the human skeleton exhibits some differences in comparison to our closest living relatives. Many of these skeletal modifications underpin key events in human evolution, enabling our species to walk upright, manipulate tools with precision, and support enlarged brains. Accordingly, many derived human features related to changes in the brain, locomotion, diet, and life history have been under natural selection since our last common ancestor with chimpanzees. Other changes result from random processes such as genetic drift. Identifying the genomic changes that underlie human-specific features of the skeleton (and other tissues) remains an outstanding challenge due to the substantial number of differences between the human and chimpanzee genomes. Approximately 3,000 of these changes are human accelerated regions (HARs) or regions that have accumulated more nucleotide changes than expected by chance, while others are single base-pair substitutions or other genomic signals. For the most part, a comprehensive functional analysis of all such changes as they pertain to the skeleton, let alone any tissue, remains lacking. Therefore, to identify human-chimp sequence differences that modulate gene expression in the developing postcranial skeleton, we used a massively parallel reporter assay (MPRA) to screen the human and chimp versions of 70,000 regulatory elements present in the prenatal cartilage template for differential activity. After testing our library in two cartilage and one bone marrow-derived lymphoblast line, we identify 30,736 regions (45.2%) with activity in our assay. Of the active regions, we find that 11,542 (37.6%; or 17% of the entire pool) regions exhibited differential activity between the human and chimpanzee. We find that human ancestor quickly evolved regions (HAQERs) were predictive of differential activity while HARs were not and both sets failed to predict the magnitude of effect, unlike the total number of base pair differences between species, which was weakly correlated with effect size. These findings reveal that human skeletal evolution involves widespread regulatory changes distributed across thousands of elements rather than concentrated effects at a few key loci, supporting a polygenic model for the evolution of complex morphological traits. This comprehensive dataset provides a large resource for understanding the regulatory basis of human skeletal adaptations and demonstrates the necessity of large-scale functional validation for interpreting evolutionary genomic comparisons.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: MPRA testing the regulatory potential of 70,000 regulatory elements active in the prenatal cartilage template for differential activity between humans and chimpanzees. Five replicates were performed in K562, TC28a2, and CHON002 cells.

first: Alexander

middle: S

last: Okamoto

first: Clarissa

middle: R

last: Coveney

first: Danalaxshmi

last: Ganapathee

middle: D


title: HIV-1 transcription dominates over host gene activity at the HIV-1 integration site [ATAC-seq]

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: 295 Congress Ave

institute: Yale University

summary: HIV-1 persists as an integrated DNA provirus in infected cells. Antiretroviral therapy (ART) does not inhibit HIV-1 promoter activity. It is often assumed that HIV-1 reactivation versus latency passively follows host gene activation and repression near the HIV-1 integration site. HIV-1 proviruses integrated into active genes are then transcriptionally active, typically resulting in immune clearance of infected cells. HIV-1 proviruses integrated into repressive chromatin conversely escape immune surveillance. To understand how host gene activity affects HIV-1 transcription, we examined how CRISPR-mediated activation and inhibition of host genes affected HIV-1 nearby chromatin accessibility and RNA transcription using qPCR, ATAC-seq, and strand-specific RNA-seq, in seven Jurkat T cell clones having known HIV-1 integration site. We further examined host CRISPR-mediated HIV-1 activation and inhibition effects on host chromatin accessibility and RNA transcription. We found that host gene activation at the integration site decreased HIV-1 transcription, while host gene inhibition frequently increased HIV-1 transcription. Changes to transcription occurred in both HIV-1 orientations relative to the host gene. Particularly at same-orientation integration sites, reductions in HIV-1 transcription were accompanied by reduced chromatin accessibility at the HIV-1 promoter. However, when HIV-1 integrated in close proximity to host transcription start site, host gene activation increased HIV-1 transcription. When HIV-1 integrated into a non-genic region, we found that HIV-1 increased host chromatin accessibility, remained transcriptionally active, and drove high level of aberrant host RNA transcription. Overall, we found that instead of passively following host gene activity, HIV-1 shapes host chromatin accessibility while an interplay of host factors and transcriptional interference modulate its expression.

overall_design: Triplicate ATAC-seq profiling of Jurkat T cells infected with a single copy of replication-defective HIV-GFP, transduced with CRISPRa (dCas9-VP64 and MS2-P65-HSF1 transcription activator) or CRISPRi (dCas9-KRAB). Cell lines contain either nontargeting gRNA, HIV-targeting gRNA, or gRNA targeting the host gene containing the HIV integration site. Genomic DNA was prepared via ATAC-seq protocol and isolated by Qiagen MinElute PCR cleanup kit, (#28004) and library prep performed with NEBNext Ultra II Q5 master mix (NEB #M0544X) and Nextera indexed according to NEBNext Ultra II (NEB #E7645). Following baseline amplification, typically 8 cycles, SYBR qPCR was used to determine total cycle numbers needed. Typically, a total of 12 additional PCR cycles of library amplification were added, depending on qPCR results. After validating library size on an Agilent TapeStation, 150-bp paired-end sequencing was performed by NovaSeq 6000 at Yale Center for Genome Sequencing.

first: Samuel

last: Weissman

first: Yang-Hui

middle: J

last: Yeh

first: Miriam

last: Viazmenski

first: Rachel

last: Kim

first: Jack

middle: A

last: Collora

first: Savannah

last: Steinhauser


title: HIV-1 transcription dominates over host gene activity at the HIV-1 integration site

overall_design: Triplicate RNA-seq profiling of Jurkat T cells infected with a single copy of replication-defective HIV-GFP, transduced with CRISPRa (dCas9-VP64 and MS2-P65-HSF1 transcription activator) or CRISPRi (dCas9-KRAB). Cell lines contain either nontargeting gRNA, HIV-targeting gRNA, or gRNA targeting the host gene containing the HIV integration site. RNA was isolated using Zymo Research Direct-zol kits (#R2056) and sequenced using NEB's rRNA-depletion and adapter ligation/Illumina sequencing protocol. Of note, the sequenced molecule is rRNA-depleted RNA.


title: A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors

city: Rende

first: Rosamaria

last: Lappano

state: Cs

address: via P. Bucci

institute: University of Calabria

summary:
Background. Male breast cancer (BC) is rare, accounting for only approximately 1% of all cases of BC, and poorly characterized. In contrast, prostate cancer is the most prevalent cancer in men and serves as a model for understanding male-specific tumor biology. The advent of high-throughput technologies has enabled the development of gene expression signatures for both breast and prostate tumors that could inform prognosis and guide treatment. In this respect, the role of the tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), remains largely underexplored. Here, we sought to identify a CAF-related gene signature in male patients with BC and prostate cancer to reveal specific protumorigenic mechanisms and identify novel therapeutic targets for both malignancies.
Methods. RNA sequencing was performed to analyze and compare the transcriptomes of CAFs isolated from female and male BC patients. Differentially expressed genes (DEGs) between female and male breast CAFs were identified and subjected to enrichment analyses. Using a set of candidate upregulated genes in male breast CAFs, K-means clustering of prostate cancer patients was performed using multiple datasets to define a prognostic gene signature. Kaplan‒Meier curves and log-rank tests were conducted to assess differences in patient outcomes and other clinical variables between groups of patients with high or low prognostic gene expression. The clustering results were then validated using decision tree analysis, and boosted calculations were employed to increase the classifier performance.
Results. Transcriptomic profiling revealed 775 DEGs between female and male breast CAFs. Owing to the limited transcriptomic data from male BC patients, we leveraged large prostate cancer cohorts to investigate the relevance of the genes expressed by male breast CAFs. A six-gene signature (ASPN, COL4A1, COL4A2, COL5A3, COMP and FN1) that could predict patient outcomes in multiple independent cohorts of prostate cancer patients was identified.
Conclusions. We identified a novel gene signature with strong prognostic value in prostate cancer and potential relevance to male BC. This gene signature represents a complementary tool to standard clinical parameters for improving patient stratification and management.

overall_design: Identification of a novel CAFs-related gene signature for male breast and prostate cancer patients.


title: Effects of α- and β-amylin on gene expression in mouse embryonic fibroblasts (MEFs)

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

institute: National Center for Geriatrics and Gerontology

summary: α- and β-amyrin exhibit senolytic activity in MEFs. This study aimed to investigate the underlying pathways involved in this anti-senescent effect.

overall_design: Non-senescent (passage 1) and senescent (P6) MEFs were stimulated with α-amyrin (20 μM) or β-amyrin (20 μM) for 3 days. RNA expression was analyzed by RNA-sequencing.

first: Mikako

last: Hirose


title: PyBo-seq in Tet1/2/3 CTRL and TKO and Alkbh1 CTRL and KO mESCs,  Mal-seq in Alkbh1 CTRL and KO mESCs

first: Alexandr

last: Gopanenko

overall_design:
Pyridine-borane-assisted RNA-sequencing (PyBo-seq) of Tet1/2/3 control (CTRL) mouse embryonic stem cells (mESCs) and their corresponding Tet1/2/3 triple knockout (TKO) mESCs.
PyBo-seq and malononitrile-assisted RNA-seq (Mal-seq) of Alkbh1 CTRL mESCs and their corresponding knockout (KO) mESCs.

first: Jasmin A.

last: Dehnen

first: Alexandr V.

first: Carola

last: Scholz

first: Michael U.

last: Musheev

first: Christof

last: Niehrs