Institute of Genetics and Biophysics

Understanding how plants perceive and respond to environmental and developmental cues requires tools capable of monitoring molecular signals in vivo, across whole tissues, and in real time. Genetically encoded fluorescent indicators, coupled with fluorescence microscopy, have transformed plant biology, but their application remains largely confined to small model organisms and specialized microscopy instrumentation. Here, we present MAcro Plant Projection Imaging (MAPPI), an open-source, low-cost, and modular fluorescence imaging platform for soil-grown plants beyond the model organism or seedling stage. MAPPI enables wide field-of-view, dual-projection imaging of fluorescent reporters, supporting real-time visualization of systemic signals under near-physiological conditions. We validate MAPPI by tracking calcium and l-glutamate dynamics in adult Nicotiana benthamiana plants, revealing developmentally regulated long-distance calcium waves triggered by wounding, burning, or submergence, including bidirectional shoot-to-root and root-to-shoot signaling. By democratizing access to whole-plant functional imaging, MAPPI provides a scalable tool for dissecting signal propagation, stress adaptation, and systemic communication in both model and nonmodel species.

Myeloproliferative neoplasms (MPNs) are a heterogeneous group of diseases originating from hematopoietic stem cell transformation, characterized by the clonal proliferation of hematopoietic progenitors. A specific subset includes myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase (TK) gene fusions, particularly involving PDGFR A or B, which are sensitive to TK inhibitor treatment. We report a case of a 21-year-old patient with a myeloproliferative/myelodysplastic neoplasm, presenting with hyperleukocytosis, anemia, thrombocytopenia, and elevated LDH. The peripheral blood smear showed hypogranular neutrophils, eosinophils, basophils, and myeloid precursors. The absence of BCR::ABL1 and mutations in JAK2, CALR, and MPL excluded common MPNs. Cytogenetic analysis revealed a rearrangement between chromosomes 5 and 14. FISH analysis confirmed an inverted insertion from chromosome 5 to chromosome 14, involving the PDGFRB gene. WGS and RNAseq identified a fusion between PDGFRB and CCDC88C, causing the constitutive activation of PDGFRB. The fusion gene was confirmed by sequencing. This allowed for targeted therapy with a tyrosine kinase inhibitor (TKI), leading to molecular remission monitored by RT-qPCR. This case highlights how a multidisciplinary approach can identify atypical transcripts in MPN, guiding targeted therapy with TK inhibitors, thus resulting in effective treatment and molecular remission.

Abstract Background Recent evidence indicates that sex and genetic status significantly influence serum metabolic profiles in idiopathic Parkinson’s disease (iPD) and in patients carrying at least a mutation in GBA1, LRRK2, TMEM175, PARK2, PINK1 , or PARK7 genes. However, Parkinson’s disease patients (PD) may also carry rare genetic variants of uncertain significance, whose effects on systemic metabolism have yet to be studied. Methods We combined untargeted 1 H-NMR-based metabolomics to characterize serum metabolome profiles, with high-performance liquid chromatography (HPLC) to quantify D- and L-amino acids involved in neurotransmission, energy homeostasis, and oxidative stress. The study included 212 clinically and genetically well-characterized PD patients—121 with iPD and 91 with at least one rare genetic variant (rvPD) in PD-linked genes—and 140 sex-matched healthy controls (HCs). The same cohort was also investigated by targeted-association analysis of genes encoding key enzymes involved in glycine and serine metabolism, including SRR, DAO, DAOA, SHMT1, SHMT2, PHGDH, AMT, GCSH , GLDC , and N-methyl-D-aspartate receptor (NMDAR) subunits such as GRIN1 , GRIN2A , and GRIN2B. Data were replicated in independent case-control datasets. Results Notably, integrating untargeted NMR-based analysis, demographic and genetic information, our findings revealed substantial differences in serum metabolome profiles between the rvPD and HCs groups across sexes. Significantly, male patients showed more extensive metabolic disruption in amino acid metabolism, glutathione biosynthesis, and energy-related pathways. In contrast, female patients showed fewer metabolic changes, mainly affecting metabolites implicated in lipid-related pathways. Intriguingly, multivariate analysis did not distinguish serum metabolome profiles between individuals with iPD and rvPD in either sex, indicating shared biochemical abnormalities across patients with different genotypes. Noteworthy, consistent with NMR results, HPLC analysis substantiated a significant reduction in L-glutamate levels in male, but not female, rvPD patients compared to sex-matched HCs. Furthermore, we found that in male patients with rvPD, serum levels of L-serine, glycine, L-aspartate, and L-glutamate significantly correlated with MDS-UPDRS III scores. In the same way, L-serine and L-glutamine were associated with a worsening of motor symptoms in female patients. Finally, in line with prominent dysregulation of glycine-serine metabolism, association analyses identified SHMT1 , SHMT2 , and GCSH as potential genetic modifiers in sex-stratified rvPD. Conclusions In conclusion, we found that sex differences affect serum metabolomic changes and the relationships between amino acid levels and clinical characteristics in PD patients with rare variants. Trial registration The study protocols have been registered in clinicaltrial.gov with the numbers NCT02403765 (Release Date: 04/01/2015), NCT04620980 (Release Date: 11/03/2020), NCT05721911 (Release Date: 30/01/2023).

Modulation of RNA and protein expression to restore or normalize neuronal function has emerged as a powerful therapeutic strategy for neurodevelopmental disorders (NDDs) tailoring individual genetic mutations causing intellectual disability (ID), or autism spectrum disorder (ASD), or developmental epileptic encephalopathy (DEE). In recent years, diverse classes of RNA-based molecules have been developed with therapeutic potential, including antisense oligonucleotides (ASOs), oligonucleotides targeting natural antisense transcripts (antagoNATs), Short Interspersed Nuclear Element UP-regulating RNAs (SINEUPs), interfering RNAs (RNAi), Exon-Specific engineering U1 small nuclear RNAs (ExSpeU1s), and small-activating RNA (saRNA) This review highlights the promising advances of these RNA-based therapeutics in addressing syndromic ID, such as Fragile X syndrome, MECP2 duplication syndrome, FOXG1-gene related Rett syndrome and Angelman syndrome, which are characterized by well-defined genetic mutations with limited treatment options. Moreover, ASD-related condition linked to mutations in CHD8 is under investigation, extending the therapeutic landscape to complex behavioral and cognitive disorders. In the same way, several DEEs caused by mutations in CDKL5, DNM1, KCNT1, SCN1A, SCN2A, SCN8A, and UBA5 genes, which present severe pharmaco-resistant epilepsy, are increasingly becoming targets for RNA molecules that aim to restore neuronal excitability and network function. Together, these findings underscore the expanding therapeutic landscape enabled by RNA technologies, offering unprecedented specificity and flexibility for gene-targeted interventions in NDDs. As the field of RNA medicine continues to evolve across genomics and neuroscience, we aim to provide a resource for researchers and clinicians on promising innovative tools for molecular correction.

TBX1, a T-box transcription factor, is essential for pharyngeal apparatus development and marks cardiopharyngeal mesoderm (CPM) in various species. However, in mammals, we have an incomplete knowledge of the molecular pathways driving CPM diversification and of the role of TBX1 in this context. Using CPM-relevant in vitro differentiation of wild-type and Tbx1-/- mouse embryonic stem cells, we performed simultaneous single-nucleus RNA-seq and ATAC-seq at two stages, validated findings in embryos, and found that TBX1 loss affects gene expression and chromatin remodeling in a cell subpopulation-specific manner. TBX1 regulates chromatin accessibility and gene expression of distinct and evolutionarily conserved transcriptional modules for branchiomeric and cardiac development, and for tissue morphogenesis. Computational analyses predicted a feed-forward regulatory relationship between TBX1 and SIX factors. Notably, selected Tbx1 mutant CPM cell populations showed an altered differentiation trajectory, exhibiting activation of a mesothelial-like transcriptional program. We also observed cell death later in development. Thus, TBX1 is crucial for maintaining CPM transcriptional identity.

Parkinson’s disease (PD) represents one of the most frequent neurodegenerative disorders for which clinically useful biomarkers remain to be identified and validated. Here, we adopted an untargeted omics approach to disclose lipidomic, metabolomic and proteomic alterations in plasma and in dermal fibroblasts of PD patients carrying mutations in TMEM175 gene. We revealed a wide dysregulation of lysosome, autophagy, and mitochondrial pathways in these patients, supporting a role of this channel in regulating these cellular processes. The most significant altered lipid classes were Fatty acyls, Glycerophospholipids and Phosphosphingolipids. The plasma level of Phosphatidylcholines (PC) and Phosphatidylinositol (PI) 34:1 significantly correlated with an earlier age at onset of the disease in TMEM175 patients (p = 0.008; p = 0.006). In plasma we also observed altered amino acids metabolic pathways in PD patients. We highlighted that increased level of L-glutamate strongly correlated (p < 0.001) with the severity of motor and non-motor symptoms in PD_TMEM175 patients. In dermal fibroblasts, we disclosed alterations of proteins involved in lipids biosynthesis (PAG15, PP4P1, GALC, FYV1, PIGO, PGPS1, PLPP1), in the insulin pathway (IGF2R), in mitochondrial metabolism (ACD10, ACD11, ACADS) and autophagy (RAB7L). Interestingly, we quantified 43 lysosomal or lysosomal-related proteins, which were differentially modulated between TMEM175 patients and controls. Integrative correlation analysis of proteome and lipidome of PD_TMEM175 cellular models identified a strong positive correlation of 13 proteins involved in biosynthetic processes with PC and Ceramides. Altogether, these data provide novel insights into the molecular and metabolic alterations underlying TMEM175 mutations and may be relevant for PD prediction, diagnosis and treatment.

The KHDC3L gene encodes a component of the subcortical maternal complex (SCMC). Biallelic mutations in this gene cause 5%-10% of biparental hydatidiform moles (BiHM), and a few maternal deletions in KHDC3L have been identified in women with recurrent pregnancy loss (RPL). In this study, we had a patient with a history of 10 pregnancy or neonatal losses, including spontaneous abortions, neonatal deaths, and molar pregnancy. Whole-exome sequencing (WES) was performed for genetic diagnostic testing. We found a homozygous deleterious variant in the start codon of KHDC3L (c. 1A>G, p.M1V), which probably results in non-translation or the production of a truncated protein. This is the first report of a maternal loss-of-function variant in KHDC3L gene in a patient experiencing various types of pregnancy loss. This case report broadens the understanding of KHDC3L's pathogenic variants and phenotypic spectrum, consistent with its crucial role during human pre- and post-implantation development.