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Biology subjects

Cerrato, C.

Publications and source records attributed to Cerrato, C..

5 recordsLinked to original sources

CISH, a novel intracellular immune checkpoint, in comparison and combination to existing and emerging cancer immune checkpoints

Over the past decade, Immuno-Oncology has largely focused on blocking inhibitory surface receptors like PD-1 to enhance T cell anti-tumor activity. However, intracellular immune checkpoints such as CISH, which function independently of tumor-expressed ligands, offer powerful and previously untapped therapeutic potential. As a downstream regulator of TCR signaling, CISH controls T cell activation, expansion, and neoantigen reactivity. Though historically considered undruggable, recent advances in CRISPR engineering have enabled functional interrogation of these targets. We demonstrate that CISH deletion enhances T cell activation and anti-cancer functions more effectively than other emerging intracellular checkpoints. In CAR-T cells, CISH inactivation significantly increased sensitivity to tumor antigen, enabling robust recognition and killing even at low antigen levels, conditions that often lead to treatment failure with conventional T cell therapies, mirroring antigen escape scenarios seen in solid tumors. Our findings further validate CISH as a potent and druggable intracellular checkpoint capable of boosting anti-tumor T cell responses across diverse cancer types, independent of PD-L1 status. The underlying mechanisms of CISH inhibition may help explain the positive outcomes reported in recent clinical studies of this approach in solid tumor immunotherapy.

cancer biology↗

Widespread transposon co-option in the Caenorhabditis germline regulatory network

The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. Here we show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one third of C. elegans germline-specific promoters have been co-opted from two related Miniature Inverted Repeat Transposable Elements (MITEs), CERP2 and CELE2. The promoters are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. Expansion of CERP2 occurred prior to radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in C. briggsae, we find evolutionary conservation of most CERP2 co-opted promoters, but a substantial fraction of events are species specific. Our work reveals the emergence of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.

genomics↗

DREAM represses distinct targets by cooperating with different THAP domain proteins

The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.

genomics↗

Tissue-specific profiling reveals distinctive regulatory architectures for ubiquitous, germline and somatic genes

Despite increasingly detailed knowledge of gene expression patterns, the regulatory architectures that drive them are not well understood. To address this, we compared transcriptional and regulatory element activities across five adult tissues of C. elegans, covering [~]90% of cells, and defined regulatory grammars associated with ubiquitous, germline and somatic tissue-specific gene expression patterns. We find architectural features that distinguish two major promoter types. Germline-specific and ubiquitously-active promoters have well positioned +1 and -1 nucleosomes associated with a periodic 10-bp WW signal. Somatic tissue-specific promoters lack these features, have wider nucleosome depleted regions, and are more enriched for core promoter elements, which surprisingly differ between tissues. A 10-bp periodic WW signal is also associated with +1 nucleosomes of ubiquitous promoters in fly and zebrafish but is not detected in mouse and human. Our results demonstrate fundamental differences in regulatory architectures of germline-active and somatic tissue-specific genes and provide a key resource for future studies.

genomics↗

Chromatin accessibility dynamics across C. elegans development and ageing

An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

genomics↗