Biology subjects

Tenen, D.

Publications and source records attributed to Tenen, D..

8 recordsLinked to original sources

bioRxiv2026

AlphaGenome -enabled analysis of non-coding regulatory variants underlying RHD Expression

Systematic identification of functional non-coding regulatory variants remains a major challenge in human genetics. Conventional approaches such as large-scale CRISPR screening and genome-wide association studies (GWAS) are powerful but often prohibitively expensive, time-consuming, and experimentally intensive, limiting their scalability for locus-specific mechanistic studies. Recent advances in artificial intelligence offer the potential to partially replace or substantially augment these approaches by prioritizing regulatory variants with high functional likelihood. The RHD antigen, a major contributor to red blood cell alloimmunization, hemolytic transfusion reactions, and hemolytic disease of the fetus and newborn, serves as an excellent model for this paradigm, since coding variants alone do not fully account for differences in RHD expression. Here, we present an integrated artificial intelligence (AI)-guided and experimental framework to identify and validate functional non-coding regulatory variants governing RHD expression. We first applied AlphaGenome (AG), a deep-learning model released in 2025 for non-coding variant impact prediction, to systematically interrogate the RHD locus. By integrating multi-omics datasets, AG prioritized regulatory regions within the promoter, 5' untranslated region (5'UTR), and intragenic regions. In silico deletion- and Single Nucleotide Polymorphism (SNP)-based perturbation analyses consistently predicted that variants within the promoter and its proximal regions, as well as within intragenic regions, exert strong suppressive effects on RHD expression. To experimentally validate these predictions, we performed CRISPR-mediated base editing in K562 cells at AG-prioritized non-coding SNP sites. Editing of a high-score predicted variant (chr1:25272434 G>A) achieved efficient base conversion and was accompanied by additional nearby edits, all predicted by AG to downregulate RHD expression. In contrast, editing of low-score predicted sites (chr1:25272422 C>T) produced much smaller functional effects. Quantitative polymerase chain reaction (qPCR) analysis of full-length RHD transcripts, together with flow cytometry-based analysis of RHD expression, confirmed strong concordance between AI-based predictions and transcriptional as well as phenotypic outcomes. Taken together, our results demonstrate that the combination of AI-guided regulatory variant prioritization and targeted base editing provides a potentially scalable and cost-effective alternative to traditional CRISPR screening for decoding functional non-coding variants in blood group genes, with direct implications for genomics-based RHD typing and transfusion medicine. To our knowledge, this study also represents the first validation of AlphaGenome predictions at the phenotypic level using wet-lab experiments.

genomics↗

bioRxiv2023

SALL4B, not targeted by IMiD, is important for SALL4-mediated tumorigenesis

Immunomodulatory (IMiD) drugs have shown a prominent therapeutic activity in hematologic malignancies; however, their usage in solid tumors is limited. The oncofetal protein SALL4 is essential for cancer cell survival. While IMiDs can induce SALL4 degradation, they fail to induce cell death in SALL4-expressing cancer cell lines. Here, we observed that this inefficacy arose from their selective degradation of the long SALL4 isoform, while sparing the short SALL4B isoform. Selective silencing of SALL4B phenocopied total SALL4 depletion by inducing cancer apoptosis, underscoring the critical role of SALL4B in cancer maintenance. Recognizing that IMiDs cant degrade SALL4B, we performed a high-throughput screen to identify compound(s) that could achieve this. We identified a small molecule compound that degrades both SALL4 isoforms with enhanced potency towards SALL4B in a cereblon- and proteasome-dependent manner. This compound suppressed cancer cell proliferation and attenuated tumor development in both cell line and patient-derived xenograft models. Transcriptomic analyses further revealed convergent effects of genetic and pharmacologic SALL4B depletion on DNA damage response and replication pathways. Together, these findings identify SALL4B as the therapeutically relevant isoform in SALL4-dependent cancers and establish isoform-aware targeted degradation as a strategy to overcome the limitation of IMiDs in solid tumors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/548071v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@99670dorg.highwire.dtl.DTLVardef@13ca58forg.highwire.dtl.DTLVardef@998e7eorg.highwire.dtl.DTLVardef@15a1875_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract | Identification of QE: a non-IMiDs degrader capable of degrading both SALL4A and SALL4B, triggers anti-cancer effects beyond IMiDs, and Impacts of QE on Key Validated SALL4B Targets and Pathways C_FIG

cancer biology↗

bioRxiv2021

A single cell atlas of human and mouse white adipose tissue

White adipose tissue (WAT), once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic, heterogenous, and involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control, and host defense1. High fat feeding and other metabolic stressors cause dramatic changes in adipose morphology, physiology, and cellular composition1, and alterations in adiposity are associated with insulin resistance, dyslipidemia, and type 2 diabetes (T2D)2. Here, we provide detailed cellular atlases of human and murine subcutaneous and visceral white fat at single cell resolution across a range of body weight. We identify subpopulations of adipocytes, adipose stem and progenitor cells (ASPCs), vascular, and immune cells and demonstrate commonalities and differences across species and dietary conditions. We link specific cell types to increased risk of metabolic disease, and we provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity. These data comprise an extensive resource for the exploration of genes, traits, and cell types in the function of WAT across species, depots, and nutritional conditions.

physiology↗

bioRxiv2021

Formation and recycling of an active epigenetic mark mediated by cell cycle-specific RNAs

The mechanisms by which epigenetic modifications are established in gene regulatory regions of active genes remain poorly understood. The data presented show that the establishment and recycling of a major epigenetic mark, the acetylated form of the replacement histone H2A.Z, is regulated by cell cycle-specific long noncoding RNAs encoded in regions adjacent to the promoters of active genes. These transcripts, termed SPEARs (S Phase EArly RNAs), are induced in early S phase: their expression precedes that of the downstream genes on which they exert their regulatory action. SPEARs drive the modification and deposition of the acetylated form of histone H2A.Z by bringing together the replacement histone and the histone acetyl transferase TIP60. This widespread bimodal pathway constitutes a novel RNA-mediated mechanism for the establishment of epigenetic marks and cell-specific epigenetic profiles, thereby providing a unifying explanation for the accuracy and persistence of epigenetic marks on chromatin.

genetics↗

bioRxiv2021

C/EBPα acts as an RNA binding protein essential for its chromatin recruitment and promotes Macrophage differentiation

C/EBP has known to be a transcription factor that involved in Neutrophil differentiation for decades. However, exploring the Chromatin RNA Immunoprecipitation Sequencing (RIP), we discover that C/EBP is a RNA binding protein mainly interacts with RNA introns. Structure study and RNA electrophoretic mobility shift assay (REMSA) show that C/EBP interacts with RNA through two novel RNA binding domains distinct from its DNA binding domain. Mouse bone marrow transplantation and in vitro cytokine assay reveal that C/EBP RNA binding is critical for Macrophage differentiation but not Neutrophil differentiation. Mechanically, RNA binding domains control specific gene transcription. In particular, PU.1 intron 4 RNA interacts with C/EBP and recruit C/EBP to its enhancer site, which facilitate PU.1 expression. Taken together, C/EBP is demonstrated to be a RNA binding protein with unique function distinct from its DNA binding activity. Our finding transforms our knowledge of transcriptional regulation by transcription factor. One-Sentence SummaryC/EBP interacts with RNA through novel RNA binding domains and regulates PU.1 expression during Macrophage differentiation.

cell biology↗

bioRxiv2020

Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia

Acute Myeloid Leukemia (AML) is a highly lethal blood cancer arising due to aberrant differentiation of haematopoietic stem cells. Here we obtained 3D genome organization maps by Hi-C in the CD34+ haematopoietic stem cells from three healthy individuals and eight individuals with AML, and found that AML have increased loops to oncogenes compared with normal CD34+ cells. The MEIS1 oncogenic transcription factor is regulated by a Frequently Interacting Region (FIRE). This FIRE is only present in normal bone marrow samples, and four of eight AML sample. FIRE presence is associated with MEIS1 expression. CRISPR excision of a FIRE boundary led to loss of MEIS1 and reduced cell growth. Moreover, MEIS1 can bind to the promoter of HOXA9, and HOXA9 shows gain of Acute Myeloid Leukemia-specific super-enhancers that loop to the HOXA9 promoter. SignificanceWe found that Acute Myeloid Leukemias have more chromatin loops to oncogenes compared with normal blood stem cells. We identified heterogeneity in chromatin interactions at oncogenes, and heterogeneity in super-enhancers that loop to oncogenes, as two key epigenetic mechanisms that underlie MEIS1 and HOXA9 oncogene expression respectively.

cancer biology↗

bioRxiv2020

Obesity-linked PPARγ S273 phosphorylation promotes insulin resistance through Growth Differentiation Factor 3

Overnutrition and obesity promote adipose tissue dysfunction, often leading to systemic insulin resistance. The thiazolidinediones (TZDs) are a potent class of insulin-sensitizing drugs and ligands of PPAR{gamma} that improve insulin sensitivity, but their use is limited due to significant side effects. Recently, we demonstrated a mechanism by which TZDs improve insulin sensitivity distinct from receptor agonism and adipogenesis: reversal of obesity-linked phosphorylation of PPAR{gamma} at Serine 273. However, the role of this modification has not been tested genetically. Here we demonstrate that mice encoding an allele of PPAR{gamma} which cannot be phosphorylated at S273 are protected from insulin resistance, without exhibiting differences in body weight or TZD-associated side effects. Indeed, hyperinsulinemic-euglycemic clamp experiments confirm improved insulin sensitivity, as evidenced by increased whole-body glucose uptake. RNA-seq experiments reveal PPAR{gamma} S273 phosphorylation specifically enhances transcription of Gdf3, a BMP family member. Ectopic expression of Gdf3 is sufficient to induce insulin resistance in lean, healthy mice. We find that Gdf3 can impact metabolism by inhibition of BMP signaling. Together, these results highlight the diabetogenic role of PPAR{gamma} S273 phosphorylation and focuses attention on a putative target, Gdf3.

cell biology↗

bioRxiv2018

Thermoneutrality induces skeletal muscle myopathy via brown adipose tissue in an IRF4- and myostatin-dependent manner

Skeletal muscle and brown adipose tissue (BAT) share a common lineage and have been functionally linked, as exercise increases browning through the actions of various myokines. It is unknown, however, whether BAT can affect skeletal muscle function. Our prior work has shown that loss of the transcription factor IRF4 in BAT (BATI4KO) reduces adaptive thermogenesis. Here, we note that these mice also have reduced exercise capacity relative to wild-type littermates, associated with diminished mitochondrial function, ribosomal protein synthesis, and mTOR signaling in muscle, in addition to the signature ultrastructural abnormalities of tubular aggregate myopathy. Within brown adipose tissue, loss of IRF4 caused the induction of a myogenic gene expression signature, which includes an increase in the secreted factor myostatin, a known inhibitor of muscle function. Reduction of myostatin activity by the injection of neutralizing antibodies or soluble ActRIIB receptor rescued the exercise capacity of BATI4KO mice. Additionally, overexpression of IRF4 in brown adipocytes reduced serum myostatin and increased mitochondrial function and exercise capacity in muscle. A physiological role for this system is suggested by the observation that mice housed at thermoneutrality show lower exercise capacity with increased serum myostatin; both of these abnormalities are corrected by surgical removal of BAT. Collectively, our data point to an unsuspected level of BAT-muscle cross-talk driven by IRF4 and myostatin.\n\nHighlightsO_LIMice lacking IRF4 in BAT have a decrease in exercise capacity, accompanied by histological, ultrastructural, signaling, gene expression, and bioenergetic evidence of myopathy in white vastus.\nC_LIO_LILoss of IRF4 promotes the expression of a myogenic signature in BAT, including the myokine myostatin.\nC_LIO_LINeutralization of serum myostatin rescues the ability of BATI4KO mice to exercise normally, while overexpression of IRF4 in BAT allows mice to run better than wild-type counterparts.\nC_LIO_LIThermoneutrality reduces the level of IRF4 in BAT of WT mice, resulting in a myopathic phenotype that can be reversed by surgical excision of BAT.\nC_LI

physiology↗