Genomic, transcriptomic and RNA editing analysis of human MM1 and VV2 sporadic Creutzfeldt-Jakob disease

Creutzfeldt-Jakob disease (CJD) is characterized by a broad phenotypic spectrum regarding symptoms, progression, and molecular features. Current sporadic CJD (sCJD) classification recognizes six main clinical-pathological phenotypes. This work investigates the molecular basis of the phenotypic heterogeneity of prion diseases through a multiomics analysis of the two most common sCJD subtypes: MM1 and VV2. We performed DNA target sequencing on 118 genes on a cohort of 48 CJD patients and full exome RNA sequencing on post-mortem frontal cortex tissue on a subset of this cohort. DNA target sequencing identified multiple potential genetic contributors to the disease onset and phenotype, both in terms of coding, damaging-predicted variants, and enriched groups of SNPs in the whole cohort and the two subtypes. The results highlight a different functional impairment, with VV2 associated with higher impairment of the pathways related to dopamine secretion, regulation of calcium release and GABA signaling, showing some similarities with Parkinson’s disease both on a genomic and a transcriptomic level. MM1 showed a gene expression profile with several traits shared with different neurodegenerative, without an apparent distinctive characteristic or similarities with a specific disease. In addition, integrating genomic and transcriptomic data led to the discovery of several sites of ADAR-mediated RNA editing events, confirming and expanding previous findings in animal models. On the transcriptomic level, this work represents the first application of RNA sequencing on CJD human brain samples. Here, a good clusterization of the transcriptomic profiles of the two subtypes was achieved, together with the finding of several differently impaired pathways between the two subtypes. The results add to the understanding of the molecular features associated with sporadic CJD and its most common subtypes, revealing strain-specific genetic signatures and functional similarities between VV2 and Parkinson’s disease and providing preliminary evidence of RNA editing modifications in human sCJD

Sporadic Creutzfeldt-Jakob disease VM1: phenotypic and molecular characterization of a novel subtype of human prion disease

Creutzfeldt-Jakob disease; Prion disease; Prion strainsMalaltia de Creutzfeldt-Jakob; Malalties priòniques; Soques de prionsEnfermedad de Creutzfeldt-Jakob; Enfermedad priónica; Cepas de prionesThe methionine (M)-valine (V) polymorphic codon 129 of the prion protein gene (PRNP) plays a central role in both susceptibility and phenotypic expression of sporadic Creutzfeldt-Jakob diseases (sCJD). Experimental transmissions of sCJD in humanized transgenic mice led to the isolation of five prion strains, named M1, M2C, M2T, V2, and V1, based on two major conformations of the pathological prion protein (PrPSc, type 1 and type 2), and the codon 129 genotype determining susceptibility and propagation efficiency. While the most frequent sCJD strains have been described in codon 129 homozygosis (MM1, MM2C, VV2) and heterozygosis (MV1, MV2K, and MV2C), the V1 strain has only been found in patients carrying VV. We identified six sCJD cases, 4 in Catalonia and 2 in Italy, carrying MV at PRNP codon 129 in combination with PrPSc type 1 and a new clinical and neuropathological profile reminiscent of the VV1 sCJD subtype rather than typical MM1/MV1. All patients had a relatively long duration (mean of 20.5 vs. 3.5 months of MM1/MV1 patients) and lacked electroencephalographic periodic sharp-wave complexes at diagnosis. Distinctive histopathological features included the spongiform change with vacuoles of larger size than those seen in sCJD MM1/MV1, the lesion profile with prominent cortical and striatal involvement, and the pattern of PrPSc deposition characterized by a dissociation between florid spongiform change and mild synaptic deposits associated with coarse, patch-like deposits in the cerebellar molecular layer. Western blot analysis of brain homogenates revealed a PrPSc type 1 profile with physicochemical properties reminiscent of the type 1 protein linked to the VV1 sCJD subtype. In summary, we have identified a new subtype of sCJD with distinctive clinicopathological features significantly overlapping with those of the VV1 subtype, possibly representing the missing evidence of V1 sCJD strain propagation in the 129MV host genotype

Vibrationally resolved NEXAFS at C and N K-edges of pyridine, 2-fluoropyridine and 2,6-difluoropyridine: A combined experimental and theoretical assessment

In the present work, the near edge X-ray absorption spectroscopy (NEXAFS) spectra at both C and N K-edges of pyridine, 2-fluoropyridine, and 2,6-difluoropyridine have been studied both experimentally and theoretically. From an electronic point of view, both transition potential density functional theory and time-dependent density functional theory approaches lead to reliable results provided that suitable basis sets and density functionals are employed. In this connection, the global hybrid B3LYP functional in conjunction with the EPR-III basis set appears particularly suitable after constant scaling of the band positions. For the N K-edge, vertical energies obtained at these levels and broadened by symmetric Gaussian distributions provide spectra in reasonable agreement with the experiment. Vibronic contributions further modulate the band-shapes leading to a better agreement with the experimental results, but are not strictly necessary for semi-quantitative investigations. On the other hand, vibronic contributions are responsible for strong intensity redistribution in the NEXAFS C K-edge spectra, and their inclusion is thus mandatory for a proper description of experiments. In this connection, the simple vertical gradient model is particularly appealing in view of its sufficient reliability and low computational cost. For more quantitative results, the more refined vertical Hessian approach can be employed, and its effectiveness has been improved thanks to a new least-squares fitting approach

The ionic states of iodobenzene studied by photoionization and ab initio configuration interaction and DFT computations

New valence electron photoelectron spectra of iodobenzene obtained using synchrotron radiation have been recorded. Ionization energies (IEs) determined using multi-configuration SCF calculation (MCSCF) procedures confirmed the adiabatic IE order as: X2B1 < A2A2 < B2B2 < C2B1. Although it is convenient to retain C2v labelling, there is an evidence that minor distortion to CS symmetry occurs at the MCSCF level for the C state. The fifth ionization process shown to be D2A1 exhibits dissociation to C6H5+ + I both in the experimental and theoretical studies. The calculated Franck- Condon vibrational spectral envelopes, including hot band contributions, for the first four ionic states reproduce the observed peak positions and intensities with reasonable accuracy. In order to simulate the observed spectra, different bandwidths are required for different states. The increase in the required bandwidths for the A2A2 and B2B2 states is attributed to internal conversion to lower-lying states. The presence of relatively high intensity sequence bands leads to asymmetry of each of the X2B1 state bands

Combined theoretical and experimental study of the valence, Rydberg, and ionic states of chlorobenzene

New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV) spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-cooled sample. Both the VUV and REMPI spectra have enabled identification of a considerable number of Rydberg states for the first time. The use of ab initio calculations, which include both multi-reference multi-root doubles and singles configuration interaction (MRD-CI) and time dependent density functional theoretical (TDDFT) methods, has led to major advances in interpretation of the vibrational structure of the ionic and electronically excited states. Franck-Condon (FC) analyses of the PE spectra, including both hot and cold bands, indicate much more complex envelopes than previously thought. The sequence of ionic states can be best interpreted by our multi-configuration self-consistent field computations and also by comparison of the calculated vibrational structure of the B and C ionic states with experiment; these conclusions suggest that the leading sequence is the same as that of iodobenzene and bromobenzene, namely: X2B1(3b1 121) < A2A2(1a2 121) < B2B2(6b2 121) < C2B1(2b1 121). The absorption onset near 4.6 eV has been investigated using MRD-CI and TDDFT calculations; the principal component of this band is 1B2 and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. The other low-lying absorption band near 5.8 eV is dominated by a 1A1 state, but an underlying weak 1B1 state (\u3c0\u3c3 17) is also found. The strongest band in the VUV spectrum near 6.7 eV is poorly resolved and is analyzed in terms of two \u3c0\u3c0 17 states of 1A1 (higher oscillator strength) and 1B2 (lower oscillator strength) symmetries, respectively. The calculated vertical excitation energies of these two states are critically dependent upon the presence of Rydberg functions in the basis set, since both manifolds are strongly perturbed by the Rydberg states in this energy range. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene and bromobenzene

Two novel PRNP truncating mutations broaden the spectrum of prion amyloidosis

Truncating mutations in PRNP have been associated with heterogeneous phenotypes ranging from chronic diarrhea and neuropathy to dementia, either rapidly or slowly progressive. We identified novel PRNP stop-codon mutations (p.Y163X, p.Y169X) in two Italian kindreds. Disease typically presented in the third or fourth decade with progressive autonomic failure and diarrhea. Moreover, one proband (p.Y163X) developed late cognitive decline, whereas some of his relatives presented with isolated cognitive and psychiatric symptoms. Our results strengthen the link between PRNP truncating mutations and systemic abnormal PrP deposition and support a wider application of PRNP screening to include unsolved cases of familial autonomic neuropathy

Prion-related peripheral neuropathy in sporadic Creutzfeldt-Jakob disease

OBJECTIVE: To assess whether the involvement of the peripheral nervous system (PNS) belongs to the phenotypic spectrum of sporadic Creutzfeldt-Jakob disease (sCJD). METHODS: We examined medical records of 117 sCJDVV2 (ataxic type), 65 sCJDMV2K (kuru-plaque type) and 121 sCJDMM(V)1 (myoclonic type) subjects for clinical symptoms, objective signs and neurophysiological data. We reviewed two diagnostic nerve biopsies and looked for abnormal prion protein (PrP(Sc)) by western blotting and real-time quaking-induced conversion (RT-QuIC) in postmortem PNS samples from 14 subjects. RESULTS: Seventy-five (41.2%) VV2-MV2K patients, but only 11 (9.1%) MM(V)1, had symptoms or signs suggestive of PNS involvement occurring at onset in 18 cases (17 VV2-MV2K, 9.3%; and 1 MM(V)1, 0.8%) and isolated in 6. Nerve biopsy showed a mixed predominantly axonal and demyelinating neuropathy in two sCJDMV2K. Electromyography showed signs of neuropathy in half of the examined VV2-MV2K patients. Prion RT-QuIC was positive in all CJD PNS samples, whereas western blotting detected PrP(Sc) in the sciatic nerve in one VV2 and one MV2K. CONCLUSIONS: Peripheral neuropathy, likely related to PrP(Sc) deposition, belongs to the phenotypic spectrum of sCJDMV2K and VV2 and may mark the clinical onset. The significantly lower prevalence of PNS involvement in typical sCJDMM(V)1 suggests that the PNS tropism of sCJD prions is strain dependent

Cognitive profile in idiopathic autonomic failure: relation with white matter hyperintensities and neurofilament levels

To disclose the nature of cognitive deficits in a cohort of patients with idiopathic autonomic failure (IAF) by exploring the relation among cognitive functions, cardiovascular autonomic failure (AF) and clinical progression to another α-synucleinopathy (phenoconversion)

In vivo assessment of Lewy body and beta-amyloid copathologies in idiopathic normal pressure hydrocephalus: prevalence and associations with clinical features and surgery outcome

Background: Idiopathic normal pressure hydrocephalus (iNPH) is a clinico-radiological syndrome of elderly individuals likely sustained by different neurodegenerative changes as copathologies. Since iNPH is a potentially reversible condition, assessing neurodegenerative pathologies in vitam through CSF biomarkers and their influence on clinical features and surgical outcome represents crucial steps.Methods: We measured a-synuclein seeding activity related to Lewy body (LB) pathology by the real-time quaking-induced conversion assay (RT-QuIC) and Alzheimer disease core biomarkers (proteins total-tau, phospho-tau, and amyloid-beta) by immunoassays in the cerebrospinal fluid (CSF) of 293 iNPH patients from two independent cohorts. To compare the prevalence of LB copathology between iNPH participants and a control group representative of the general population, we searched for a-synuclein seeding activity in 89 age-matched individuals who died of Creutzfeldt-Jakob disease (CJD). Finally, in one of the iNPH cohorts, we also measured the CSF levels of neurofilament light chain protein (NfL) and evaluated the association between all CSF biomarkers, baseline clinical features, and surgery outcome at 6 months.Results: Sixty (20.5%) iNPH patients showed alpha-synuclein seeding activity with no significant difference between cohorts. In contrast, the prevalence observed in CJD was only 6.7% (p= 0.002). Overall, 24.0% of iNPH participants showed an amyloid-positive (A+) status, indicating a brain co-pathology related to A beta deposition. At baseline, in the Italian cohort, a-synuclein RT-QuIC positivity was associated with higher scores on axial and upper limb rigidity (p=0.003 and p =0.011, respectively) and lower MMSEc scores (p =0.003). A+ patients showed lower scores on the MMSEc (p =0.037) than A- patients. Higher NfL levels were also associated with lower scores on the MMSEc (rho = -0.213; p= 0.021). There were no significant associations between CSF biomarkers and surgical outcome at 6 months (i.e. responders defined by decrease of 1 point on the mRankin scale).Conclusions: Prevalent LB- and AD-related neurodegenerative pathologies affect a significant proportion of iNPH patients and contribute to cognitive decline (both) and motor impairment (only LB pathology) but do not significantly influence the surgical outcome at 6 months. Their effect on the clinical benefit after surgery over a more extended period remains to be determined