The PRECISE European initiative for cancer-vulnerability mapping and prediction

Francesco Iorio, Mathew J. Garnett, Pedro Beltrao, Maximilian Billmann, Larissa Bless, Christoph Bock, Michael Boutros, Alejandra Bruna, Piero Carninci, Giovanni Ciriello, Isidro Cortés-Ciriano, Giuseppina D’Alessandro, Roberta Esposito, Stefania Faletti, Emanuel Gonçalves, Syed Haider, Nereo Kalebic, Manuel Kaulich, Giuseppe Leuzzi, Nuria Lopez-Bigas, Christopher J. Lord, Evangelia Petsalaki, Stephen Pettitt, Ludovica Proietti, Roland Rad, Nevenka Radic, Colm J. Ryan, Jonathan L. Schmid-Burgk, Sumana Sharma, Andrea Sottoriva, Christopher Tape, Livio Trusolino, Jolanda van Leeuwen, David Walter, Lodewyk Wessels & the PRECISE consortium

Together with 30 other research groups, the Kalebic Lab is part of PRECISE (Predictive Relationships Explaining Cancer Genetic Interactions and Synthetic Essentiality), a pan-European network coordinated by Francesco Iorio from Human Technopole, that aims to combine high-throughput perturbation biology, multimodal profiling and AI-driven inference to predict cancer vulnerabilities in disease-relevant models. The vision and the mission of PRECISE have now been presented in a Nature Genetics commentary.

Human basal radial glia morphotypes are transcriptionally distinct and exhibit different cell fate determination

Kaluthantrige Don F., Barelli C., Bonfanti M., Passi M., Bosotti R., Wagner L., Capra E., Bertani I., Ricca D., Casagrande F., Fasciani A., Peano C. and Kalebic N.

Using human cortical organoids, live imaging and CellShape-seq, we show that basal radial glia morphotypes differ in morphodynamics, proliferative capacity and transcriptional identity. Multipolar bRG are the most proliferative and progenitor-like, whereas bifurcated bRG are less proliferative and enriched for YBX1. Inhibiting YBX1 alters bRG composition, reduces neurogenesis, and promotes glial commitment, linking progenitor morphology to gene expression and fate in human cortical development.

Lysergic acid diethylamide reverses aging- and neurodegeneration-associated brain transcriptional programs

Savino A., Liaci C., Bertani I., Rando S., Camera M., Merlo G.R., Avalle L., Poli V., Kalebic N. and Iorio F.

Adducins regulate morphology and fate of neural progenitors during neocortical neurogenesis

Ossola C.*, Cokorac N.*, Capra E.*, Faletti S.*, Bertani I., Ambrosini C., Restelli E., Casagrande F., Fasciani A., Bosotti R., Maghelli N., Faga G., Taverna E. and Kalebic N. *, co-first authors

Here we show that adducin proteins (ADD1–3) emerge as key morphoregulatory factors controlling neural progenitor abundance across mammals. They regulate basal progenitor morphology, mitotic spindle orientation and cell fate decisions during neurogenesis in mouse, ferret and human models. In human cortical organoids, adducins are required for proper neurogenesis, highlighting their conserved role in cortical development.

Shaping the Neocortex: Radial Glia and Astrocytes in Development and Evolution

Mosti F., Kawasaki H., Babbit C., Di Benedetto B., Silver D.L., Kalebic N., and Falcone C.

In this review, we examine how radial glia and astrocytes contributed to mammalian neocortical expansion and evolution, particularly in primates. We highlight how species-specific genes, epigenetic regulation, radial glia morphology, cortical folding and astrocyte diversity shaped cortical complexity. Together, these insights provide a framework for understanding how cellular innovations contributed to the emergence of the modern primate and human brain.

Human-specific morphoregulatory signatures in basal radial glia characterize neocortex evolution

Schütze T., Ditzer N., Vangelisti S., Kolodziejczyk A., Capra E., Chiaradia I., Peters J., Krause M., Eugster C., Derihaci R.P., Birdir C., Martin U., Wimberger P., Long K.R., Lancaster M., Kalebic N., Bonev B. and Albert M.

Stem cell morphology defines functional heterogeneity and therapeutic vulnerabilities in glioblastoma

Barelli C., Bonfanti M., Mirabella F., Ricca D., Alizadehmohajer N., Bosotti R., Bertani I., Sokolova V., Campione A., Sicuri G.M., Peano C., Faletti S., Stefini R. and Kalebic N.

Here we link glioblastoma stem cell morphology with clinically relevant functions. We developed CellShape-seq which integrates cell morphology with transcriptomics, revealing three distinct morphoclasses of glioblastoma stem cell linked to invasion, intercellular networking and therapy response. We further show that chemoresistance has morphotype-specific vulnerabilities. Targeting these morphoclass-specific mechanisms sensitizes resistant GSCs to temozolomide, supporting morphology-informed therapeutic strategies for GBM.

Morphoregulatory ADD3 underlies glioblastoma growth and formation of tumor–tumor connections

Barelli C., Kaluthantrige Don F., Iannuzzi R.M., Faletti S., Bertani I., Osei I., Sorrentino S., Villa G., Sokolova V., Campione A., Minotti M.R., Sicuri G.M., Stefini R., Iorio F. and Kalebic N.

We show that glioblastoma stem cells (GSCs) display morphological heterogeneity that influences tumor–tumor communication, proliferation, survival and therapy resistance. We identify the neurodevelopmental morphoregulator ADD3 as a key regulator of GSC morphology, tumor–tumor connections, cell cycle progression and chemoresistance through actin cytoskeleton stability. These findings suggest that GSC morphology and its regulators may provide new therapeutic targets and diagnostic markers.

Serialized on-grid lift-in sectioning for tomography (SOLIST) enables a biopsy at the nanoscale

Nguyen H.T.D., Perone G., Klena N., Vazzana R., Kaluthantrige Don F., Silva M., Sorrentino S., Swuec P., Leroux F., Kalebic N., Coscia F. and Erdmann P.S.

DOT1L activity affects neural stem cell division mode and reduces differentiation and ASNS expression

Appiah B., Fullio C.L., Ossola C., Bertani I., Restelli E., Cheffer A., Polenghi M., Haffner C., Garcia-Miralles M., Zeis P., Treppner M., Bovio P., Schlichtholz L., Mas-Sanchez A., Zografidou L., Winter J., Binder H., Grun D., Kalebic N., Taverna E. and Vogel T.

Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals

Pinson A., Xing L., Namba T., Kalebic N., Peters J., Eugster Oegema C., Traikov S., Reppe K., Riesenberg S., Maricic T., Derihaci R., Wimberger P., Pääbo S. and Huttner W.B.

Forebrain Organoids to Model the Cell Biology of Basal Radial Glia in Neurodevelopmental Disorders and Brain Evolution

Kaluthantrige Don F. and Kalebic N.

Roots of the Malformations of Cortical Development in the Cell Biology of Neural Progenitor Cells

Ossola C. and Kalebic N.

Inheritance and flexibility of cell polarity: a clue for understanding human brain development and evolution

Kalebic N. and Namba T.

In this hypothesis article, we propose that the inheritance and flexibility of cell polarity are key mechanisms contributing to neocortical evolutionary expansion. We suggest that polarity features can be transmitted across progenitor lineages and ultimately to neurons, while flexible polarity in basal progenitors and neurons supports progenitor amplification and neuronal dispersion.

The Ferret as a Model System for Neocortex Development and Evolution

Gilardi C. and Kalebic N.

In this review, we discuss the ferret as a valuable model for studying neocortex development, expansion and folding. We highlight the molecular, cellular and histological features of the ferret cortex, focusing on neural stem cell proliferation, neuronal differentiation, visual system development and neurodevelopmental pathologies. We also compare ferret neocortical development with other model organisms and discuss advances enabling in vivo genetic manipulation.

Basal Progenitor Morphology and Neocortex Evolution

Kalebic N. and Hutner W.B.

Basal progenitors are central to mammalian neocortical expansion because their increased proliferative capacity enhances neuronal production during development. We propose that BP morphology, particularly the presence and complexity of cellular processes, is a key feature supporting proliferation by enabling access to pro-proliferative signals and transmission of self-renewing capacity. Changes in BP morphology may also contribute to neuronal migration and the transition of progenitors toward different fates.

Serotonin Receptor 2A Activation Promotes Evolutionarily Relevant Basal Progenitor Proliferation in the Developing Neocortex

Xing L., Kalebic N., Namba T., Vaid S., Wimberger P. and Huttner W.B.

Extracellular matrix-inducing Sox9 promotes both basal progenitor proliferation and gliogenesis in developing neocortex

Guven A., Kalebic N., Long K.R., Florio M., Vaid S., Brandl H., Stenzel D. and Huttner W.B.

In Vivo Targeting of Neural Progenitor Cells in Ferret Neocortex by In Utero Electroporation

Kalebic N., Langen B., Helppi J., Kawasaki H. and Huttner W.B.