A Multi-Faceted Analysis Showing CRNDE Transcripts and a Recently Confirmed Micropeptide as Important Players in Ovarian Carcinogenesis.

CRNDE is considered an oncogene expressed as long non-coding RNA. Our previous paper is the only one reporting CRNDE as a micropeptide-coding gene. The amino acid sequence of this micropeptide (CRNDEP) has recently been confirmed by other researchers. This study aimed at providing a mass spectrometry (MS)-based validation of the CRNDEP sequence and an investigation of how the differential expression of CRNDE(P) influences the metabolism and chemoresistance of ovarian cancer (OvCa) cells. We also assessed cellular localization changes of CRNDEP, looked for its protein partners, and bioinformatically evaluated its RNA-binding capacities. Herein, we detected most of the CRNDEP sequence by MS. Moreover, our results corroborated the oncogenic role of CRNDE, portraying it as the gene impacting carcinogenesis at the stages of DNA transcription and replication, affecting the RNA metabolism, and stimulating the cell cycle progression and proliferation, with CRNDEP being detected in the centrosomes of dividing cells. We also showed that CRNDEP is located in nucleoli and revealed interactions of this micropeptide with p54, an RNA helicase. Additionally, we proved that high CRNDE(P) expression increases the resistance of OvCa cells to treatment with microtubule-targeted cytostatics. Furthermore, altered CRNDE(P) expression affected the activity of the microtubular cytoskeleton and the formation of focal adhesion plaques. Finally, according to our in silico analyses, CRNDEP is likely capable of RNA binding. All these results contribute to a better understanding of the CRNDE(P) role in OvCa biology, which may potentially improve the screening, diagnosis, and treatment of this disease.

Allogenic Adipose-Derived Stem Cells in Diabetic Foot Ulcer Treatment: Clinical Effectiveness, Safety, Survival in the Wound Site, and Proteomic Impact.

Although encouraging results of adipose-derived stem cell (ADSC) use in wound healing are available, the mechanism of action has been studied mainly in vitro and in animals. This work aimed to examine the safety and efficacy of allogenic ADSCs in human diabetic foot ulcer treatment, in combination with the analyses of the wound. Equal groups of 23 participants each received fibrin gel with ADSCs or fibrin gel alone. The clinical effects were assessed at four time points: days 7, 14, 21 and 49. Material collected during debridement from a subset of each group was analyzed for the presence of ADSC donor DNA and proteomic changes. The reduction in wound size was greater at all subsequent visits, significantly on day 21 and 49, and the time to 50% reduction in the wound size was significantly shorter in patients who received ADSCs. Complete healing was achieved at the end of the study in seven patients treated with ADSCs vs. one treated without ADSCs. One week after ADSC application, 34 proteins significantly differentiated the material from both groups, seven of which, i.e., GAPDH, CAT, ACTN1, KRT1, KRT9, SCL4A1, and TPI, positively correlated with the healing rate. We detected ADSC donor DNA up to 21 days after administration. We confirmed ADSC-related improvement in wound healing that correlated with the molecular background, which provides insights into the role of ADSCs in wound healing-a step toward the development of cell-based therapies.

Analysis of short tandem repeat mutations in paternity cases from Masovian Voivodeship provinces form years 2018-2022 based on materials of the Department of Forensic Medicine, Medical University of Warsaw. / Analiza mutacji krótkich powtórzen tandemowych w sprawach spornego ojcostwa w woj. mazowieckim w latach 2018-2022 na podstawie materialów Katedry i Zakladu Medycyny Sadowej Warszawskiego Uniwersytetu Medycznego.

In paternity cases, genetic tests are of great importance as they allow to exclude or confirm paternity. As a result of paternity tests we can also obtain information on the frequency of short tandem repeat mutations, which are important in the statistical analysis of test results. A total of 468 cases of full paternity trios (mother, child and alleged father) were analysed from years 2018 - 2022 from the central part of Poland. For further analysis of the occurrence of the mutation 346 cases in which paternity was confirmed were qualified. DNA analysis was performed using the PowerPlex®Fusion 6C kit (Promega, USA). 36 mutations were observed in 13 of the 23 genetic markers analysed. 94.44% were one-step mutations and 5.56% were two-step mutations. Among those mutations, there were 18 insertions and 10 deletions, while in 8 cases it was not possible to determine whether an insertion or deletion occurred. There was also a significantly higher share of the father mutation in relation to the mother mutation at a ratio of 4.17:1.

Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population.

(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population.

A recurrent de novo variant supports KCNC2 involvement in the pathogenesis of developmental and epileptic encephalopathy.

Developmental and epileptic encephalopathies (DEE) are a heterogenous group of conditions characterized by the co-occurrence of epilepsy and intellectual/developmental disability. Despite several known DEE-related genes, including these encoding ion channels, still many cases remain without molecular diagnosis. Here, we present a 2-year-old girl with severe DEE in whom whole exome sequencing revealed de novo p.(Val471Leu) variant in the KCNC2 encoding Kv3.2, a voltage-gated potassium channel. To the best of our knowledge, this is the third DEE case due to KCNC2 mutation. Our clinical and molecular findings, particularly the recurrence of p.(Val471Leu) in patient with similar clinical phenotype, further support KCNC2 as a novel DEE-associated gene.

Application of massively parallel sequencing (MPS) in paternity testing - case report.

Aim of the study: We present the application of massively parallel sequencing (MPS) to extend the scope of analysis in a disputed paternity case. Material and methods: A standard paternity test comprising 16 autosomal STRs was performed by capillary electrophoresis (CE) using 3130xl Genetic Analyzer. Additionally, MPS was performed with ForenSeq DNA Signature Prep Kit and Illumina MiSeq FGx™ Forensic Genomics System. Paternity index (PI) was calculated using DNAStat v.2.1 software. Results>: CE revealed two mismatches, at D21S11 and VWA, between the putative father and the child. Based on MPS results, the mismatches were analyzed and a nonconsensus sequence of allele 14 at the VWA locus in the mother - child pair was identified. Different sequence variants were also detected in 16-16 homozygote alleles at the D3S1358 locus in the child. Conclusions: MPS helped to formulate a definite conclusion regarding the paternity of the defendant and provided full information on intra-allelic polymorphism.

Polish population data on 15 autosomal STRs of AmpFlSTR NGM PCR kit.

The objective of the research was to provide a comprehensive database of autosomal microsatellite loci included in AmpFlSTR NGM PCR kit for a population of Poland considering possible genetic differentiation of a forensic interest. Fifteen STR markers were analyzed in 2041 unrelated individuals residing in eight geographically different regions. All the loci were found to be in Hardy-Weinberg equilibrium. The combined probability of match is 3.52 × 10(-19) and the combined Power of Exclusion is 0.9999998. The F(ST) estimate over all 15 STRs is 0.0051 for the Polish population. We established that a combined NGM database may be employed for a Polish population.

Genetic polymorphism of human Y chromosome and risk factors for cardiovascular diseases: a study in WOBASZ cohort.

Genetic variants of Y chromosome predispose to hypertension in rodents, whereas in humans the evidence is conflicting. Our purpose was to study the distribution of a panel of Y chromosome markers in a cohort from a cross-sectional population-based study on the prevalence of cardiovascular risk factors in Poland (WOBASZ study). The HindIII, YAP Y chromosome variants, previously shown to influence blood pressure, lipid traits or height, as well as SNPs defining main Y chromosome haplogroups, were typed in 3026, 2783 and 2652 samples, respectively. In addition, 4 subgroups (N~100 each) representing extremes of LDL concentration or blood pressure (BP) were typed for a panel of 17 STRs. The HindIII and YAP polymorphism were not associated with any of the studied traits. Analysis of the haplogroup distribution showed an association between higher HDL level and hg I-M170 (P = 0.02), higher LDL level and hg F*(xI-M170, J2-M172, K-M9) (P = 0.03) and lower BMI and hg N3-Tat (P = 0.04). Analysis of STRs did not show statistically significant differences. Since all these associations lost statistical significance after Bonferroni correction, we conclude that a major role of Y chromosome genetic variation (defined by HindIII, YAP or main Y chromosome haplogroups) in determining cardiovascular risk in Poles is unlikely.

Population genetics of 30 INDELs in populations of Poland and Taiwan.

The Investigator DIPplex(®) kit (Qiagen) contain components for the simultaneous amplification and analysis of 30 biallelic autosomal INDELs and amelogenin. The objective of this study was to estimate the diversity of the 30 markers in Polish (N P = 122) and Taiwanese (N T = 126) population samples and to evaluate their usefulness in forensic genetics. All amplicon lengths were shorter than 160 base pairs. The DIPplex genotype distributions showed no significant deviation from Hardy-Weinberg rule expectations (Bonferroni corrected) except for DLH39 in the Taiwanese population. Among the Poles and the Taiwanese the mean observed heterozygosity values are 0.4385 and 0.4079, and the combined matching probability values are 7.98 × 10(-14) and 1.22 × 10(-11), respectively. The investigated marker set has been confirmed as a potential extension to standard short tandem repeat-based kits or a separate informative system for individual identification and kinship analysis. Eight INDELs have been selected as possible ancestry informative single-nucleotide polymorphisms for further analyses.

[Y-STR Poland--a database for evaluation of evidence value in forensic genetics]. / Y-STR Polska--baza danych do oceny wartosci dowodowej w genetyce sadowej.

The "Y-STR Poland" is a multicenter project, the aim of which is the construction of a widely available database of Y chromosome haplotypes determined in the Polish population in a range of sixteen loci in AmpFISTR Y-filer system. The database will be regularly updated and it will be used in assessment of evidence value in forensic genetics. The starting base "Y-STR Poland" contains 1600 Y-STR haplotypes and encompasses data collected in Lodz (two independent centers), Warsaw and Szczecin regions. The present report contains as an attachment the data in an Excel-type file, which serves as a tool in frequency determination of a given Y haplotype in the Polish population. The file will be updated on a regular basis along with updating the database, and will be freely available from www.genetyka-sadowa.pl.

Population data and sequence analysis of a 'new' microsatellite locus HumHUU (D16S3433).

This study reports sequence characteristics and population genetic data on a 'new' STR locus HumHUU (D16S3433) located in the non-coding region of chromosome 16q. Based on a population sample of 306 non-related Polish individuals 205 genotypes and 15 alleles with length range of 157-211bp were distinguished. No deviation from HWE was observed. The sequence analysis of each D16S3433 allele revealed a tetranucleotide repeat motif with a basic sequence structure (AAAA)(0-1)(AAAG)(11-22)(AAAAG)(AAAA)(AG)(AAAAAAG). The power of discrimination is 0.9538, showing a high degree of polymorphism. The presented results demonstrate that the D16S3433 is a useful genetic marker for forensic purposes and paternity testing.

Y-chromosomal haplotypes for the AmpFlSTR Yfiler PCR Amplification Kit in a population sample from Central Poland.

Haplotype and allele frequencies for 17 Y-STR loci (DYS456, DYS389I/II, DYS390, DYS458, DYS19, DYS385 I/II, Y GATA H4, DYS437, DYS438, DYS448, DYS393, DYS391, DYS439, Y GATA C4, DYS392) were determined in 255 unrelated males from central Poland using AmpFlSTR Yfiler PCR Amplification Kit. Two hundred and fifty-two different haplotypes were observed. The most common three haplotypes were shared by 0.8% of the sample, respectively. Two hundred and forty-nine haplotypes were encountered only once.

[STR polymorphism of the non-coding human growth hormone gene (HUMGHCSA) and its use in personal identification--a preliminary report]. / Polimorfizm STR niekodujacego regionu genu ludzkiego hormonu wzrostu (HUMGHCSA) i jego wykorzystanie w identyfikacji osobniczej--doniesienie wstepne.

The HUMGHCSA locus, located within the non-coding region of the human growth hormone gene on chromosome 17, exhibiting polymorphism of the number of repeats of two and four nucleotide motifs (CT and CTTT), but also polymorphism caused by nucleotide substitution, is one of the most polymorphic STR markers. The purpose of this study was to report the development of a system of fluorescent analysis for an automatic sequencer, to test its reliability and to develop biostatistical parameters of its usefulness in forensic examinations. The studies, carried out on a group of 200 non-related individuals, showed the presence of 24 different alleles, of 221 to 279 bp in length. Biostatistical calculations demonstrated that the expected heterozygosity was 0,898634 +/- 0,015091, PD - 0,980586, PIC - 0,887709, PE - 0,792767, PE for motherless cases - 0,6556701, and the average paternity index - 4,932625. Such results indicate a High usefulness of the studied HUMGHCSA locus for identification examinations.

[Polymorphism of the locus HUMHUU in the Polish population--a preliminary report]. / Polimorfizm locus HUMHUU w populacji polskiej--doniesienie wstepne.

The paper presents the results of a population study on the locus HUMHUU, which is a non-coding fragment of human DNA built of four nucleotide repeats (CTTT)n, localized on the 16th chromosome. The studies, carried out on a group of 200 non-related individuals, showed the presence of 14 different alleles, from 150 to 200 bp in length. Biostatistical calculations demonstrated that the expected heterozygosity was 0,830301 +/- 0,018768, PD - 0,949156, PIC - 0,806888, PE - 0,662444, PE for motherless cases - 0,491305, and the average paternity index - 2,946389. The results obtained during the studies of the locus HUMHUU allow for recognizing it as a marker of personal identification useful for the needs of both criminalistics and disputed paternity testing.