Biology subjects

Cazzaniga, A.

Publications and source records attributed to Cazzaniga, A..

5 recordsLinked to original sources

bioRxiv2023

Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering

Technological advances in massively parallel sequencing have led to an exponential growth in the number of known protein sequences. Much of this growth originates from metagenomic projects producing new sequences from environmental and clinical samples. The Unified Human Gastrointestinal Proteome (UHGP) catalogue is one of the most relevant metagenomic datasets with applications ranging from medicine to biology. However, the lack of sequence annotation impairs its usability. This work aims to produce a family classification of UHGP sequences to facilitate downstream structural and functional annotation. This is achieved through the release of the DPCfam-UHGP50 dataset containing 10,778 putative protein families generated using DPCfam clustering, an unsupervised pipeline grouping sequences into multi-domain architectures. DPCfam-UHGP50 considerably improves family coverage at protein and residue levels compared to the manually curated repository Pfam. It is our hope that DPCfam-UHGP50 will foster future discoveries in the field of metagenomics of the human gut by the release of a FAIR-compliant database easily accessible via a searchable web server and Zenodo repository.

bioinformatics↗

bioRxiv2022

The geometry of hidden representations of protein language models

Protein language models (pLMs) transform their input into a sequence of hidden representations whose geometric behavior changes across layers. Looking at fundamental geometric properties such as the intrinsic dimension and the neighbor composition of these representations, we observe that these changes highlight a pattern characterized by three distinct phases. This phenomenon emerges across many models trained on diverse datasets, thus revealing a general computational strategy learned by pLMs to reconstruct missing parts of the data. These analyses show the existence of low-dimensional maps that encode evolutionary and biological properties such as remote homology and structural information. Our geometric approach sets the foundations for future systematic attempts to understand the space of protein sequences with representation learning techniques.

bioinformatics↗

bioRxiv2022

Adversarial Attacks on Protein Language Models

Deep Learning models for protein structure prediction, such as AlphaFold2, leverage Transformer architectures and their attention mechanism to capture structural and functional properties of amino acid sequences. Despite the high accuracy of predictions, biologically insignificant perturbations of the input sequences, or even single point mutations, can lead to substantially different 3d structures. On the other hand, protein language models are often insensitive to biologically relevant mutations that induce misfolding or dysfunction (e.g. missense mutations). Precisely, predictions of the 3d coordinates do not reveal the structure-disruptive effect of these mutations. Therefore, there is an evident inconsistency between the biological importance of mutations and the resulting change in structural prediction. Inspired by this problem, we introduce the concept of adversarial perturbation of protein sequences in continuous embedding spaces of protein language models. Our method relies on attention scores to detect the most vulnerable amino acid positions in the input sequences. Adversarial mutations are biologically diverse from their references and are able to significantly alter the resulting 3d structures.

bioinformatics↗

bioRxiv2022

The different effect of pharmacological or low-doses of IFN-γ in endothelial cells are mediated by different intracellular signaling pathways

Interferon (IFN)-{gamma} is a proinflammatory cytokine with a crucial role in intercellular communication during innate and acquired immune responses. IFN-{gamma} interacts with many cell types, among which endothelial cells. Here, we show that pharmacological and low-dose kinetically activated (SKA) IFN-{gamma} exert different effects on endothelial cells by activating different signal transduction pathways. Pharmacological concentrations of IFN-{gamma} activate JAK/STAT pathway, inducing the overexpression of the CDKN1A p21, which in turn inhibits cell growth. Conversely, low-dose SKA IFN-{gamma} does not activate the canonical JAK/STAT pathway but induces the phosphorylation of ERK. ERK activation is responsible for the induction of endothelial cell migration. Interestingly, ERK activation occurs only in the presence of kinetically activate low-dose IFN-{gamma}, underlying the importance of mechanical forces to potentiate IFN-{gamma} activity.

pharmacology and toxicology↗

bioRxiv2022

The presence of BBB hastens neuronal differentiation of cerebral organoids - the potential role of endothelial derived BDNF

Despite remaining the best in vitro model to resemble the human brain, a weakness of human cerebral organoids is the lack of the endothelial component that in vivo organizes in the blood brain barrier (BBB). Since the BBB is crucial to control the microenvironment of the nervous system, this study proposes a co-culture BBB and cerebral organoids. We utilized a BBB model consisting of primary brain microvascular endothelial cells and astrocytes in a transwell system. Starting from induced Pluripotent Stem Cells (iPSCs) we generated human cerebral organoids which were then cultured in the absence or presence of an in vitro model of BBB. We evaluated if the presence of the BBB influences the maturation of cerebral organoids. By morphological analysis, it emerges that in the presence of the BBB the cerebral organoids are better organized than controls in the absence of the BBB. This effect seems to be driven by Brain Derived Neurotrophic Factor (BDNF), a neurotrophic factor released by the endothelial component of the BBB, which is involved in neurodevelopment, neuroplasticity and neurosurvival. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/501119v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@483c47org.highwire.dtl.DTLVardef@6d5976org.highwire.dtl.DTLVardef@10c5545org.highwire.dtl.DTLVardef@b2610b_HPS_FORMAT_FIGEXP M_FIG C_FIG The current culture model of human cerebral organoids does not require the presence of a BBB (left side). However, the BBB is an important source of BDNF, which is crucial for neurodevelopment and brain health. The cerebral organoids co-cultured for 4 days in the presence of the BBB show a higher cortical organization than the organoids cultured in the absence of the BBB, as illustrated on the right.

cell biology↗