Biology subjects

Benetti, C.

Publications and source records attributed to Benetti, C..

3 recordsLinked to original sources

bioRxiv2026

Characterization of Human Ectocentromeric Sites.

Centromeres are composed of DNA repeats within chromosomes primary constriction. CENP-B is the only centromeric protein known to bind a specific motif, the CENP-B box, promoting kinetochore stability. We recently uncovered degenerate CENP-B binding motifs outside centromeres, whose position and orientation defines chromosome specific banding patterns. Here, we leveraged telomere-to-telomere assemblies to map conservation of these ectocentromeric sequences (ECS) across hundreds of haplotypes. We found strong negative selection acting on their occurrence along chromosome arms, implying functional constraints incompatible with stochastic drift. We classified four categories: (i) ECSs that lack CENP-B binding ([~]84%); (ii) ECSs bound by CENP-B ([~]10%); (iii) ECSs near CENP-B-enriched accessible chromatin ([~]6%); (iv) we further identified [~]700 CENP-B binding sites outside centromeres without CENP-B boxes. Integrating chromatin conformation capture (HiC), neocentromeres and meiotic recombination mapping with CENP-B CUT&RUN, methylation and ATAC-seq data, we found heterogenous functionalities driven by distance-dependent enrichment and local contacts of boxes in inverted orientation on the same strand, analogous to ALU repeats affecting topological folding. CENP-B knockdown significantly reduced neighboring gene expression, revealing a moonlighting regulatory role outside centromeres. Our findings characterizes human ectocentromeric sites as evolutionarily constrained and functionally heterogeneous elements along chromosome arms with context-dependent roles in chromatin state. Graphical AbstractEctocentromeric sites exhibit heterogeneous CENP-B occupancy and context-dependent chromatin functions. Ectocentromeric sequences (ECSs) along chromosome arms fall into four categories: (i) CENP-B box motifs alone, lacking protein binding, embedded within repressed or boundary chromatin and contributing to TAD organization. Motifs with opposite orientation (forward and reverse complement) paired on the same strand may further promote self-complementary chromatin contacts analogous to Alu inverted repeats, reshaping topology with long-range looping contacts; (ii/iii) ECSs bound by CENP-B protein, associated with specific open chromatin state downstream of H3K27me3-marked compacted chromatin that modulate local accessibility and gene expression; and (iv) CENP-B binding peaks lacking a canonical box motif, located proximal to transcription start sites and linked to active gene expression. Together, ectocentromeric sites represent functionally heterogeneous elements with context-dependent roles spanning chromosome architecture, chromatin state, and transcription regulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/728588v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1683fb7org.highwire.dtl.DTLVardef@12f1c9dorg.highwire.dtl.DTLVardef@1ffc699org.highwire.dtl.DTLVardef@14790dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

TASC: A transcriptome-driven machine learning classifier to explore molecular heterogeneity and relapse-associated programs in T-cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia is a biologically heterogeneous malignancy characterized by diverse transcriptional and genomic alterations. Recent studies have defined a set of recurrent molecular subtypes associated with distinct differentiation stages and clinical outcomes. However, no unified framework currently exists for assigning these subtypes in a standardized and accessible manner. Existing approaches often rely on mutation or fusion detection and may overlook broader transcriptional programs. The lack of a comprehensive, transcriptome-based classification tool has hampered the use of subtype-specific insights in both research and clinical settings. Here, we present a machine learning-based classifier trained on transcriptomic data to predict previously defined multi-omic subtypes of T-cell acute lymphoblastic leukemia. The model accurately assigns subtype identity across patient samples and cell lines, and provides a practical tool for standardized molecular stratification, supporting future integration into diagnostic and translational workflows, as demonstrated by its ability to reveal subtype-specific patterns of relapse.

bioinformatics↗

bioRxiv2025

Macrophage-secreted Pyrimidine Metabolites Confer Chemotherapy Resistance in Acute Myeloid Leukemia (AML)

The tumor microenvironment (TME) programs cancer cells to influence therapeutic responses. Macrophages residing in TME switch from pro-phagocytic to tumor-promoting and immunosuppressive phenotypes as cancer develops. While these pro-tumor functions of macrophages are associated with poor outcomes, the underlying mechanisms by which bone-marrow (BM)-associated macrophages fuel myeloid malignancy and their precise contribution to relapse remain undissected. Here, we show expansion of monocyte/macrophage population in leukemia patients post-chemotherapy relapse, and spatial proximity of macrophages to leukemia blasts in the BM niche. This proximity proved functionally consequential--depletion of macrophages delayed leukemia relapse post cytarabine (AraC), a frontline chemotherapy, in patient-derived xenografts (PDX) and syngeneic leukemia models. Mechanistically, a pyrimidine metabolite, deoxycytidine (dC), secreted by BM macrophages, is taken up by leukemia cells to directly inhibit deoxycytidine kinase (DCK) to hamper AraC activation and subsequent resistance in a cell non-autonomous manner. Diagnosis AML patients exhibited significantly higher circulating dC levels than healthy donors, and dC levels further increased following chemotherapy. SAMHD1, which catalyzes deoxynucleoside triphosphates (dNTPs) into deoxynucleoside, was highly abundant in macrophages and mediated dC accumulation. Blockade of dC production in mouse and human macrophages via genetic and pharmacological inhibition of SAMHD1 or DHODH, a critical enzyme in pyrimidine synthesis, restored AraC sensitivity. Combination with DHODH inhibitors significantly delayed AraC relapse in human PDX and mouse syngeneic AML models. Collectively, we identify a metabolic immune-leukemia crosstalk in which SAMHD1high macrophages mediates chemoresistance by secreting pyrimidine metabolites and propose macrophage metabolic reprogramming as a tractable strategy to overcome TME-driven chemoresistance in myeloid leukemia.

cancer biology↗