Biology subjects

Morelli, M. J.

Publications and source records attributed to Morelli, M. J..

4 recordsLinked to original sources

bioRxiv2026

Anonymized Somatic Tumor Twins (STTs) enable open genome data sharing and use in research and clinical oncology

The study of somatic variants from tumor genomes is fundamental to cancer research and clinical decision-making. However, existing data protection frameworks impose restrictions on the use and sharing of these variants in conjunction with sensitive germline information. To overcome these challenges, we developed GenomeAnonymizer, the first method to anonymize short-read DNA sequences from tumor-normal pairs. This generates Somatic Tumor Twins (STTs), an anonymized version of the original data that preserves the donors privacy while retaining somatic tumor information and sequencing noise. This method successfully removed all detectable germline variants from the 47 PCAWG-Pilot samples. We further demonstrate that Whole-Genome Sequencing (WGS) STTs preserve more than 98% of the original somatic variants, enabling reliable downstream analysis that replicates somatic-related findings from the original samples, including cancer driver genes, mutational signatures, and intratumor heterogeneity. Importantly, we also show that STTs can reproduce the identification of actionable genes and downstream clinical interpretations and decision-making. We generated a cancer cohort of STTs matched with synthetic clinical data that could be openly shared and used across projects and centers worldwide. This paradigm-shifting approach will accelerate discovery and clinical translation in oncology and enable the robust benchmarking of genome analysis and large-scale data infrastructures.

bioinformatics↗

bioRxiv2020

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity: how these binding modes are integrated to determine select transcriptional outputs remains unresolved. We designed mutants of the MYC transcription factor bearing substitutions in residues that contact either the DNA backbone or specific bases within the consensus binding motif (E-box), and profiled their DNA-binding and gene-regulatory activities in murine cells. Our data reveal that non-specific DNA binding is required for MYC to engage onto active regulatory elements in the genome, preceding sequence recognition; beyond merely stabilizing MYC onto select target loci, sequence-specific binding contributes to its precise positioning and - most unexpectedly - to transcriptional activation per se. In particular, at any given binding intensity, promoters targeted via the cognate DNA motif were more frequently activated by MYC. Hence, seemingly promiscuous chromatin interaction profiles actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.

molecular biology↗

bioRxiv2019

Cooperation between MYC and β-catenin in liver tumorigenesis requires Yap/Taz

Background & AimsActivation of MYC and CTNNB1 (encoding {beta}-catenin) can co-occur in liver cancer, but how these oncogenes cooperate in tumorigenesis remains unclear.\n\nApproach & ResultsWe generated a mouse model allowing conditional activation of MYC and WNT/{beta}-catenin signaling (through either {beta}-catenin activation or Apc loss) upon expression of CRE recombinase in the liver, and monitored their effects on hepatocyte proliferation, apoptosis, gene expression profiles and tumorigenesis. Conditional activation of WNT/{beta}-catenin signaling strongly accelerated MYC-driven carcinogenesis in the mouse liver. Both pathways also cooperated in promoting cellular transformation in vitro, demonstrating their cell-autonomous action. Short-term induction of MYC and {beta}-catenin in hepatocytes followed by RNA-seq profiling allowed the identification of a \"Myc/{beta}-catenin signature\", composed of a discrete set of Myc-activated genes whose expression increased in presence of active {beta}-catenin. Notably this signature enriched for targets of Yap and Taz, two transcriptional co-activators known to be activated by WNT/{beta}-catenin signaling, and to cooperate with MYC in mitogenic activation and liver transformation. Consistent with these regulatory connections, Yap/Taz accumulated upon Myc/{beta}-catenin activation and were required not only for the ensuing proliferative response, but also for tumor cell growth and survival. Finally, the Myc/{beta}-catenin signature was enriched in a subset of human hepatocellular carcinomas characterized by comparatively poor prognosis.\n\nConclusionsYap and Taz mediate the cooperative action of Myc and {beta}-catenin in liver tumorigenesis. This warrants efforts toward therapeutic targeting of Yap/Taz in aggressive liver tumors marked by elevated Myc/{beta}-catenin activity.

cancer biology↗

bioRxiv2019

An early Myc-dependent transcriptional program underlies enhanced macromolecular biosynthesis and cell growth during B-cell activation

Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue in primary mouse B-cells, based on conditional deletion of the c-myc gene, followed by LPS stimulation. Myc was rapidly induced, became detectable on virtually all active promoters and enhancers, but had no direct impact on global transcriptional activity. Instead, Myc contributed to the swift up- and down-regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc-activated promoters were enriched for E-box consensus motifs, bound Myc at the highest levels and showed enhanced RNA Polymerase II recruitment, the opposite being true at down-regulated loci. Remarkably, the Myc-dependent signature identified in activated B-cells was also enriched in Myc-driven B-cell lymphomas: hence, besides modulation of new cancer-specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.

cancer biology↗