Background Neuroendocrine neoplasms (NENs) represent a heterogeneous class of rare tumors with increasing incidence. They are characterized by the ability to secrete peptide hormones and biogenic amines but other reliable biomarkers are lacking, making diagnosis and identification of the primary site very challenging. While in some NENs, such as the pancreatic ones, next generation sequencing technologies allowed the identification of new molecular hallmarks, our knowledge of the molecular profile of NENs from other anatomical sites is still poor. Methods Starting from the concept that NENs from different organs may be clinically and genetically correlated, we applied a multi-omics approach by combining multigene panel testing, CGH-array, transcriptome and miRNome profiling and computational analyses, with the aim to highlight common molecular and functional signatures of gastroenteropancreatic (GEP)-NENs and medullary thyroid carcinomas (MTCs) that could aid diagnosis, prognosis and therapy. Results By comparing genomic and transcriptional profiles, ATM-dependent signaling emerged among the most significant pathways at multiple levels, involving gene variations and miRNA-mediated regulation, thus representing a novel putative druggable pathway in these cancer types. Moreover, a set of circulating miRNAs was also selected as possible diagnostic/prognostic biomarkers useful for clinical management of NENs. Conclusions These findings depict a complex molecular and functional landscape of NENs, shedding light on novel therapeutic targets and disease biomarkers to be exploited.

BackgroundThe immune response to adenoviral COVID-19 vaccines is affected by the interval between doses. The optimal interval is unknown.AimWe aim to explore in-silico the effect of the interval between vaccine administrations on immunogenicity and to analyze the contribution of pre-existing levels of antibodies, plasma cells, and memory B and T lymphocytes.MethodsWe used a stochastic agent-based immune simulation platform to simulate two-dose and three-dose vaccination protocols with an adenoviral vaccine. We identified the model’s parameters fitting anti-Spike antibody levels from individuals immunized with the COVID-19 vaccine AstraZeneca (ChAdOx1-S, Vaxzevria). We used several statistical methods, such as principal component analysis and binary classification, to analyze the correlation between pre-existing levels of antibodies, plasma cells, and memory B and T cells to the magnitude of the antibody response following a booster dose.Results and conclusionsWe find that the magnitude of the antibody response to a booster depends on the number of pre-existing memory B cells, which, in turn, is highly correlated to the number of T helper cells and plasma cells, and the antibody titers. Pre-existing memory T cytotoxic cells and antibodies directly influence antigen availability hence limiting the magnitude of the immune response. The optimal immunogenicity of the third dose is achieved over a large time window, spanning from 6 to 16 months after the second dose. Interestingly, after any vaccine dose, individuals can be classified into two groups, sustainers and decayers, that differ in the kinetics of decline of their antibody titers due to differences in long-lived plasma cells. This suggests that the decayers may benefit from a tailored boosting schedule with a shorter interval to avoid the temporary loss of serological immunity.

Study questionCan small genetic variants detected in the whole genome sequencing of spontaneously aborted euploid embryos give insight into possible causes of pregnancy loss?Summary answerBy filtering and prioritizing genetic variants it is possible to identify genomic variants putatively responsible for miscarriage.What is known alreadyMiscarriage is often caused to chromosomal aneuploidies of the gametes but it can also have other genetic causes like small mutations, both de novo or inherited from parents. The analysis of genomic sequences of miscarried embryos has mostly focused on rare variation, and been carried out using criteria and methods that are difficult to reproduce. The role of small mutations has been scantily investigated so far.Study design, size, durationThis is a monocentric observational study. The study includes the data analysis of 46 embryos obtained from women experiencing pregnancy loss recruited by the University of Ferrara from 2017 to 2018. The study was approved by the Ethical committee of Emilia-Romagna (CE/FE 170475).Participants/materials, setting, methodsThe participants are forty-six women, mostly European (87%) diagnosed with first (n=25, av.age 32.7) or recurrent (n=21, av.age 36.5) miscarriage. Embryonic DNA was prepared form chorionic villi and used to select euploid embryos using quantitative PCR, comparative genomic hybridiztion and shallow sequencing of random genomic regions. Euploid embryos were whole-genome sequenced at 30X using Illumina short-reads technology and genomic sequences were used to identify genetic variants. Variants were annotated integrating information from Ensembl100 and literature knowledge on genes associated with embryonic development, miscarriages, lethality, cell cycle. Following annotation, variants were filtered to prioritize putatively detrimental variants in genes that are relevant for embryonic development using a pipeline that we developed. The code is available on gitHub (ezcn/grep).Main results and the role of chanceOur pipeline prioritized 439 putatively causative single nucleotide polymorphisms among 11M variants discovered in ten embryos. By systematic investigation of all coding regions, 47 genes per embryo were selected. Among them STAG2, known in literature for its role in congenital and developmental disorders as well as in cancer, TLE4 a key gene in embryonic development, expressed in both embryonic and extraembryonic tissues in the Wnt and Notch signalling pathways, and FMNL2, involved in cell motility with a major role in driving cell migration. Our analysis is fully reproducible (our code is open-source), and we take measures to increase its robustness to false positives by excluding genes with >5% chance to be selected in a control population.Limitations, reasons for cautionThis pilot study has major limitations in sample size and lack of integration of the parental genomic information. Despite being encouraging, the results need to be interpreted with caution as functional analyses are required to validate the hypotheses that have been generated. Although we have developed a robust and scalable methodology for prioritizing genetic variants, we have not yet extended it beyond the coding regions of the genome.Wider implications of the findingsThis pilot study demonstrate that analysis of genome sequencing can help to clarify the causes of idiopathic miscarriages and provides initial results from the analysis of ten euploid embryos, discovering plausible candidate genes and variants. This study provides guidance for a larger study. Results of this and following wider studies can be used to test genetic predisposition to miscarriages in parents that are planning to conceive or undergoing preimplantation genetic testing. In a wider context, the results of this study might be relevant for genetic counseling and risk management in miscarriagesStudy funding/competing interest(s)A.C. is a full time employee of Igenomix. A.D.M. was employee of Igenomix while working on this project. I.D.B., P.D.A., G.E., S.D.B. are full time employees of the MeriGen Research. All other authors declare that they have no conflicts of interest.

Miscarriage is the spontaneous termination of a pregnancy before 24 weeks of gestation. We studied the genome of euploid miscarried embryos from mothers in the range of healthy adult individuals to understand genetic susceptibility to miscarriage not caused by chromosomal aneuploidies. We developed gp , a pipeline that we used to prioritize 439 unique variants in 399 genes, including genes known to be associated with miscarriages. Among the prioritized genes we found STAG2 coding for the cohesin complex subunit, for which inactivation in mouse is lethal, and TLE4 a target of Notch and Wnt, physically interacting with a region on chromosome 9 associated to miscarriages.

BackgroundSmall supernumerary marker chromosomes (sSMC) occur in 0.072% of unselected cases of prenatal diagnoses, and their molecular cytogenetic characterization is required to establish a reliable karyotype-phenotype correlation. A small group of sSMC are C-band-negative and devoid of alpha-satellite DNA. We report the molecular cytogenetic characterization of a de novo analphoid sSMC derived from 18q22.1→qter in cultured amniocytes.ResultsWe identified an analphoid sSMC in cultured amniocytes during a prenatal diagnosis performed because of advanced maternal age. GTG-banding revealed an sSMC in all metaphases. FISH experiments with a probe specific for the chromosome 18 centromere, and C-banding revealed neither alphoid sequences nor C-banding-positive satellite DNA thereby suggesting the presence of a neocentromere. To characterize the marker in greater detail, we carried out additional FISH experiments with a set of appropriate BAC clones. The pattern of the FISH signals indicated a symmetrical organization of the marker, the breakpoint likely representing the centromere of an inverted duplicated chromosome that results in tetrasomy of 18q22.1→qter. The karyotype after molecular cytogenetic investigations was interpreted as follows:47,XY,+inv dup(18)(qter→q22.1::q22.1→neo→qter)ConclusionOur case is the first report, in the prenatal diagnosis setting, of a de novo analphoid marker chromosome originating from the long arm of chromosome 18, and the second report of a neocentromere formation at 18q22.1.