Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias

Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used digital polymerase chain reaction to assess the frequency and spatial distribution of 10 different FGFR3 missense substitutions in the sexually mature male germline. Our functional assessment of the receptor signaling of the variants with biophysical methods showed that 9 of these variants resulted in a higher activation of the receptor´s downstream signaling, resulting in 2 different expansion behaviors. Variants that form larger subclonal expansions in a dissected postmortem testis also showed a positive correlation of the substitution frequency with the sperm donor's age, and a high and ligand-independent FGFR3 activation. In contrast, variants that measured high FGFR3 signaling and elevated substitution frequencies independent of the donor's age did not result in measurable subclonal expansions in the testis. This suggests that promiscuous signal activation might also result in an accumulation of mutations before the sexual maturation of the male gonad with clones staying relatively constant in size throughout time. Collectively, these results provide novel insights into our understanding of the mutagenesis of driver mutations and their resulting mosaicism in the male germline with important consequences for the transmission and recurrence of associated disorders.

High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing

The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.

Antimicrobial prescribing and antimicrobial resistance surveillance in equine practice

BACKGROUND

Antimicrobial resistance (AMR) is an increasingly serious threat to human and animal health, therefore responsible use of antimicrobials in equine practice is vital. There is a need to have accurate, up to date data on antimicrobial prescribing in equine practice in the UK.

OBJECTIVES

To characterise current antimicrobial prescribing practices by equine veterinarians and to describe surveillance, audit processes and identification of AMR.

STUDY DESIGN

Online cross-sectional, questionnaire-based survey.

METHODS

An online questionnaire targeting veterinarians who treat horses in the UK and Europe was distributed. The questionnaire collected data on participants' country of origin, practice policies, prescribing practices including use of high priority critical antimicrobials. Four common clinical case-based scenarios were included to further explore prescribing practice. Responses were compared using both descriptive statistics and multivariable logistic regression models.

RESULTS

Questionnaires were completed by 264 veterinarians from Europe (n=33/264) and the UK (n=231/264); 87% respondents worked only with horses and 67% worked at premises with hospitalisation facilities. Approximately half of respondents (54.4%) had a written antimicrobial use or stewardship policy within their practice. Over half of respondents did not perform any environmental surveillance (54.2%), audit of clinical infections (53.1%) or audit of infection control (57.1%). Potentiated sulphonamides were cited as the most used antimicrobial, although 44% reported using enrofloxacin in the last year and 66% used 3^rd or 4^th generation cephalosporins. Prophylactic antimicrobials before clean surgery were frequently/always prescribed by 48% respondents and 24% respondents frequently/always prescribed antimicrobials post-operatively in clean surgery.

MAIN LIMITATIONS

Potential selection bias of respondents, given individuals volunteered to take part in the survey.

CONCLUSIONS

Compared to a previous similar study conducted in 2009, overall antimicrobial usage appeared to be declining in clinical scenarios and a greater proportion of practices now have stewardship policies. However, the use of high priority critical antimicrobials is still relatively common in equine practice in the UK and Europe.

Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing

De novo mutations (DNMs) are important players in heritable diseases and evolution. Of particular interest are highly recurrent DNMs associated with congenital disorders that have been described as selfish mutations expanding in the male germline, thus becoming more frequent with age. Here, we have adapted duplex sequencing (DS), an ultradeep sequencing method that renders sequence information on both DNA strands; thus, one mutation can be reliably called in millions of sequenced bases. With DS, we examined ∼4.5 kb of the FGFR3 coding region in sperm DNA from older and younger donors. We identified sites with variant allele frequencies (VAFs) of 10-4 to 10-5, with an overall mutation frequency of the region of ∼6 × 10-7 Some of the substitutions are recurrent and are found at a higher VAF in older donors than in younger ones or are found exclusively in older donors. Also, older donors harbor more mutations associated with congenital disorders. Other mutations are present in both age groups, suggesting that these might result from a different mechanism (e.g., postzygotic mosaicism). We also observe that independent of age, the frequency and deleteriousness of the mutational spectra are more similar to COSMIC than to gnomAD variants. Our approach is an important strategy to identify mutations that could be associated with a gain of function of the receptor tyrosine kinase activity, with unexplored consequences in a society with delayed fatherhood.

Processing Hundreds of SARS-CoV-2 Samples with an In-House PCR-Based Method without Robotics

The SARS-CoV-2 pandemic has required the development of multiple testing systems to monitor and control the viral infection. Here, we developed a PCR test to screen COVID-19 infections that can process up to ~180 samples per day without the requirement of robotics. For this purpose, we implemented the use of multichannel pipettes and plate magnetics for the RNA extraction step and combined the reverse transcription with the qPCR within one step. We tested the performance of two RT-qPCR kits as well as different sampling buffers and showed that samples taken in NaCl or PBS are stable and compatible with different COVID-19 testing systems. Finally, we designed a new internal control based on the human RNase P gene that does not require a DNA digestion step. Our protocol is easy to handle and reaches the sensitivity and accuracy of the standardized diagnostic protocols used in the clinic to detect COVID-19 infections.

Pathogenic postzygotic mosaicism in the tyrosine receptor kinase pathway: potential unidentified human disease hidden away in a few cells

Mutations occurring during embryonic development affect only a subset of cells resulting in two or more distinct cell populations that are present at different levels, also known as postzygotic mosaicism (PZM). Although PZM is a common biological phenomenon, it is often overlooked as a source of disease due to the challenges associated with its detection and characterization, especially for very low-frequency variants. Moreover, PZM can cause a different phenotype compared to constitutional mutations. Especially, lethal mutations in receptor tyrosine kinase (RTK) pathway genes, which exist only in a mosaic state, can have completely new clinical manifestations and can look very different from the associated monogenic disorder. However, some key questions are still not addressed, such as the level of mosaicism resulting in a pathogenic phenotype and how the clinical outcome changes with the development and age. Addressing these questions is not trivial as we require methods with the sensitivity to capture some of these variants hidden away in very few cells. Recent ultra-accurate deep-sequencing approaches can now identify these low-level mosaics and will be central to understand systemic and local effects of mosaicism in the RTK pathway. The main focus of this review is to highlight the importance of low-level mosaics and the need to include their detection in studies of genomic variation associated with disease.

Serum amyloid A and plasma fibrinogen concentrations in horses following emergency exploratory celiotomy

BACKGROUND

Acute-phase proteins may help assess the nature and severity of lesions and outcome in horses undergoing colic surgery.

OBJECTIVES

To compare serum amyloid A and plasma fibrinogen concentrations ([SAA] and [fibrinogen]) in the immediate post-operative period after exploratory celiotomy and determine their value in assessment of post-operative complications and survival to discharge.

STUDY DESIGN

Observational study.

METHODS

This study included horses over 1 year of age undergoing exploratory celiotomy. Surgical procedures, lesions, post-operative care, complications and survival to discharge were recorded. [SAA] and [fibrinogen] were measured prior to surgery and 5 days post-operatively. Statistical analyses included Yate's Chi-square test, linear mixed effects model, Mann-Whitney U test and logistic regression.

RESULTS

Of 300 horses, 52.0% developed post-operative complications and 83.7% survived to discharge, with significantly reduced chance of survival in horses that developed post-operative complications (P<0.01). Median [SAA] at days 1, 2, 3, 4 and 5 and median [fibrinogen] at days 3, 4 and 5 were significantly different between horses that did and did not develop post-operative complications (P<0.05). Median [SAA] at days 1, 4 and 5 were significantly different between horses that did and did not survive to discharge (P<0.05). Logistic regression revealed post-operative complications to be associated with strangulating lesions (OR 2.35, 95% confidence interval [CI] 1.41-3.91, P≤0.001) and higher [fibrinogen] at admission (OR 1.21, 95% CI 1.00-1.45, P<0.05), and survival to discharge to be associated with lower [SAA] at 5 days post-operatively (OR 0.965, 95% CI 0.94-0.99, P = 0.002).

MAIN LIMITATIONS

A large variety of lesions and complications prevented detailed analysis of associations between inflammatory markers, lesions and complications.

CONCLUSIONS

Horses that develop post-operative complications have acute-phase responses of greater magnitudes and durations compared with those that do not develop complications. This is also seen in horses that do not survive to discharge. Measuring [SAA] daily and [fibrinogen] at admission, may help predict the development of post-operative complications.

Clinical Research Abstracts of the British Equine Veterinary Association Congress 2015

REASONS FOR PERFORMING STUDY

Pleural effusion (PE) is reported to occur most commonly secondary to bacterial pneumonia or lung abscesses, with neoplastic effusions contributing the minority of cases. The majority of these reports originate from America and Australia, where long distance transport of horses, a recognised risk factor, appears to occur more frequently. Anecdotally, neoplastic PE is more commonly diagnosed in the UK.

OBJECTIVES

To describe the causes of PE in horses resident in the UK, and to identify potential markers that can help differentiate between infectious and neoplastic causes of PE.

STUDY DESIGN

Retrospective clinical study.

METHODS

Medical records from 4 referral hospitals in southern England were searched for horses diagnosed with PE. Information gathered from medical records included signalment, diagnosis (infectious vs. neoplastic), admission physical examination and biochemical findings, and characteristics of the effusion (volume, cell count, total protein [TP] concentration). Statistical comparisons were made between the neoplastic and infectious group using appropriate testing.

RESULTS

Seventy horses were identified, of which 28 (40%) were neoplastic and 42 were infectious. Horses with infectious effusions were significantly younger (median 7 vs. 13 years; P = 0.002) and had significantly smaller volumes of pleural fluid drained at admission (9.8 vs. 32.3 l; P<0.001). Horses with infectious PE had a significantly higher rectal temperature (38.6 vs. 38.2°C; P = 0.03), fibrinogen concentration (7.8 vs. 5.7 g/l; P = 0.02) and serum amyloid A concentration (223 vs. 104 mg/l; P = 0.02). Pleural fluid characteristics identified a significantly greater cell count and TP concentration in horses with infectious PE (47 x 10(9)/l vs. 3.4 x 10(9)/l; P<0.001; 54 vs. 31 g/l; P = 0.001).

CONCLUSIONS

These results suggest that in the UK neoplastic effusions account for a greater proportion of PE than previously reported. A large volume of PE in an older horse with a low cell count and TP concentration should increase the index of suspicion of neoplasia. Ethical animal research: This was a retrospective study of clinical cases. Explicit owner informed consent for inclusion of animals in this study was not stated.

SOURCE OF FUNDING

None. Competing interests: None declared.

Deep erosions of the palmar aspect of the navicular bone diagnosed by standing magnetic resonance imaging

REASONS FOR PERFORMING STUDY

Erosion of the palmar (flexor) aspect of the navicular bone is difficult to diagnose with conventional imaging techniques.

OBJECTIVES

To review the clinical, magnetic resonance (MR) and pathological features of deep erosions of the palmar aspect of the navicular bone.

METHODS

Cases of deep erosions of the palmar aspect of the navicular bone, diagnosed by standing low field MR imaging, were selected. Clinical details, results of diagnostic procedures, MR features and pathological findings were reviewed.

RESULTS

Deep erosions of the palmar aspect of the navicular bone were diagnosed in 16 mature horses, 6 of which were bilaterally lame. Sudden onset of lameness was recorded in 63%. Radiography prior to MR imaging showed equivocal changes in 7 horses. The MR features consisted of focal areas of intermediate or high signal intensity on T1-, T2*- and T2-weighted images and STIR images affecting the dorsal aspect of the deep digital flexor tendon, the fibrocartilage of the palmar aspect, subchondral compact bone and medulla of the navicular bone. On follow-up, 7/16 horses (44%) had been subjected to euthanasia and only one was being worked at its previous level. Erosions of the palmar aspect of the navicular bone were confirmed post mortem in 2 horses. Histologically, the lesions were characterised by localised degeneration of fibrocartilage with underlying focal osteonecrosis and fibroplasia. The adjacent deep digital flexor tendon showed fibril formation and fibrocartilaginous metaplasia.

CONCLUSIONS

Deep erosions of the palmar aspect of the navicular bone are more easily diagnosed by standing low field MR imaging than by conventional radiography. The lesions involve degeneration of the palmar fibrocartilage with underlying osteonecrosis and fibroplasia affecting the subchondral compact bone and medulla, and carry a poor prognosis for return to performance.

POTENTIAL RELEVANCE

Diagnosis of shallow erosive lesions of the palmar fibrocartilage may allow therapeutic intervention earlier in the disease process, thereby preventing progression to deep erosive lesions.

Transition from an excitable to an oscillatory state in dictyostelium discoideum

Under conditions of starvation, populations of the amoebae Dictyostelium discoideum aggregate are mediated by chemical excitation waves of cAMP. Two types of waves can be observed, either spiral or circular-shaped ones. We investigate transitions from rotating spirals to circular shaped waves (target patterns). Two different experiments demonstrating this phenomenon are presented. In the first case a continuous transition from the spiral type pattern to target waves was observed at the later stages of aggregation. In the second case the transition was induced by annihilation of waves by a spatially homogeneous cAMP pulse. Instead of the originally present spiral waves, oscillating spots bearing target patterns emerged. On the basis of a model for Dictyostelium aggregation, we provide a theoretical explanation for such transitions. It is shown that cell density can be an effective bifurcation parameter. Under certain conditions, the system is shifted from the excitable to the oscillatory state while the frequency of oscillations is proportional to the square root of the cell density. Thus, the regions with the highest cell density during the early stages of the spatial rearrangement of the cells become pacemakers and produce target patterns. The analytic results were confirmed in numerical simulations of the model.

Electrical stimulation of the energy metabolism in yeast cells using a planar Ti-Au-electrode interface

We report on the influence of dielectric pulse injection on the energy metabolism of yeast cells with a planar interdigitated electrode interface. The energy metabolism was measured via NADH fluorescence. The application of dielectric pulses results in a distinct decrease of the fluorescence, indicating a response of the energy metabolism of the yeast cells. The reduction of the NADH signal significantly depends on the pulse parameters, i.e., amplitude and width. Furthermore, the interface is used to detect electrical changes in the cell-electrolyte system, arising from glucose-induced oscillations in yeast cells and yeast extract, by dielectric spectroscopy at 10 kHz. These dielectric investigations revealed a beta(1)-dispersion for the system electrolyte/yeast cells as well as for the system electrolyte/yeast extract. In agreement with control measurements we obtained a glycolytic period of 45 s for yeast cells and of 11 min for yeast extract.

Comparison of glycolytic NADH oscillations in yeasts Saccharomyces cerevisiae and Saccharomyces carlsbergensis

The possible mechanism of synchronization of NADH oscillations in yeasts were studied. It was shown that the synchronization time depends on cell concentration in suspension. Synchronization of oscillations after acetaldehyde addition was found in Saccharomyces carlsbergensis whereas in S. cerevisiae oscillations were synchronized after adding potassium cyanide. It is possible, that synchronization of oscillations in S. cerevisiae requires low concentration of acetaldehyde and the high acetaldehyde concentration synchronizes oscillations in S. carlsbergensis. In addition, a possible mechanism of synchronization by acetaldehyde in proposed.

Antigen-specific IgG(T) responses in natural and experimental cyathostominae infection in horses

Equine clinical larval cyathostominosis is caused by simultaneous mass emergence of previously inhibited larvae from the mucosa of the colon. Clinical signs include diarrhoea, colic, weight loss and malaise, and in up to 50% of cases, the disease results in death. Cyathostominae spend a large part of their life cycle as larval stages in the intestinal mucosa. Definitive diagnosis is difficult due to the lack of diagnostic methods for pre-patent infection. In the present study, the enzyme-linked immunosorbent assay (ELISA) was used to investigate isotype responses to larval cyathostominae somatic antigen. Measurement of anti-larval IgG(T) responses appeared to have the most immunodiagnostic potential. An increase in IgG(T) response was detected to crude larval antigen by 5 weeks post-infection (PI) in individual infected ponies. Subsequently, IgG(T) responses to larval and adult somatic extracts were examined by Western blotting using sera from experimentally-infected horses and helminth-naive animals (n=6). Two antigen complexes, designated A and B, in larval somatic antigen were recognised specifically by the infected animals by 7 weeks PI. Sera taken from 23 endemically-infected animals, whose cyathostominae burdens had been enumerated, were also used to identify putative diagnostic antigens. Eighteen horses had positive mucosal worm burdens (range 723-3,595,725) and all but two of these animals had serum IgG(T) antibody specific to either complex. Moreover, IgG(T) responses specific to antigen complexes A and B were absent in all five parasite negative horses that were tested. Serum IgG(T) responses to either of the two complexes were identified in five clinical cases tested. IgG(T) responses to adult antigen somatic extracts were more heterogeneous, with no clear pattern between experimentally-infected ponies and helminth-free controls. The results indicate that increases in serum IgG(T) to mucosal larvae occur in the pre-patent period and that two antigenic complexes within somatic preparations of these stages have immunodiagnostic potential.

Spatio-temporal dynamics in glycolysis

During the glycolytic degradation of sugar in a thin layer of yeast extract, travelling waves of NADH and protons can be generated that carry a state of high enzymatic activity through the system. The controlled initiation of such waves with an activator of the enzyme phosphofructokinase (PFK) and the influence of various salts and co-factors on the propagation dynamics are investigated. Furthermore a first study of the dispersion of waves is presented. The experimental characterisation of this in vitro system contributes to unravelling the possible role of glycolysis for biological information processing. In this context, the provision of chemically available energy in the absence of compartmentation by glycolysis is of primary importance.

Traveling waves in yeast extract and in cultures of Dictyostelium discoideum

Biological self-organization was investigated in a biochemical and a cellular system: yeast extract and cultures of the slime mold Dictyostelium discoideum. In both systems traveling reaction-diffusion waves occur in response to oscillatory reactions. Glycolytic degradation of sugar in a yeast extract leads to the spontaneous formation of NADH and proton waves. Manipulation of the adenine nucleotide pool by addition of purified plasma membrane ATPase favors the formation of both reaction-diffusion waves and phase waves. The results indicate that the energy charge has an important impact for the dynamics of glycolytic patterns. When affecting the lower part of glycolysis by pyruvate addition the frequency of wave generation was increased with concomitant formation of rotating NADH and proton spirals. During morphogenesis of the cellular system Dictyostelium discoideum, circular and spiral shaped aggregation patterns of motile amoeboid cells form in response to traveling cAMP waves. Velocity analysis of the cell movements reveals that the cAMP waves guide the cells towards the site of wave initiation along optimized trajectories. The minimization of aggregation paths is based on a mechanism exploiting general properties of excitation waves. The resulting aggregation territories are reminiscent of Voronoi diagrams.

In vitro model for the evaluation of inferior vena cava filters: effect of experimental parameters on thrombus-capturing efficacy of the Vena Tech-LGM filter

PURPOSE

To determine the experimental parameters in an in vitro model that influence the thrombus-capturing efficacy of the Vena Tech-LGM filter.

MATERIALS AND METHODS

The Vena Tech-LGM filter was evaluated in an in vitro model of the vena cava with a computer-controlled flow system with a total of 5,200 thrombi. The influences of the following experimental parameters on the capture rate were analyzed with a multiple logistic regression model: type of testing (single, double, and multiple shot testing), thrombus diameter and length, IVC diameter and orientation, flow quality and quantity, flow velocity, and the length of the prepositioned thrombus.

RESULTS

A significant influence on the capture rate could be demonstrated for the type of testing, the thrombus diameter and length, the IVC diameter, and with double shot testing for the length of the prepositioned thrombus and the IVC orientation. The flow quality and the peak velocity were not significant. Based on these results, a protocol for in vitro testing of IVC filters was designed.

CONCLUSIONS

Experimental parameters influence the thrombus-capturing efficacy of the Vena Tech-LGM filter and should be taken into account when in vitro testing is performed.

A physiologic in vitro model of the inferior vena cava with a computer-controlled flow system for testing of inferior vena cava filters

RATIONALE AND OBJECTIVES

The authors develop a physiologic in vitro model of the inferior vena cava (IVC) for testing of filters.

METHODS

The model is driven by a centrifugal pump. A computer-controlled electromagnetic valve is used for generation of different flow patterns. Limitation of the pressure increase in case of IVC occlusion is achieved by a bypass circuit. A glycerin solution is used for perfusion. Artificial clots are made from polyacrylamide gel. Data acquisition includes continuous monitoring of flow and difference pressure over the filter and video recording of the testing events.

RESULTS

The model can generate constant and pulsatile flows. The pressure increase can be limited to 70 mm Hg in case of occlusion. Calculation of the flow velocities in the IVC is possible. A classification of thrombus capturing is presented. The testing of most of the results are reproducible.

CONCLUSIONS

The in vitro model simulates the physiologic conditions in the IVC. It can be used for comparative testing of different filters and the evaluation of new filter designs.

Traveling NADH and proton waves during oscillatory glycolysis in vitro

Propagation and mutual annihilation of circular and spiral NADH and proton waves were detected by spatially resolved spectrophotometry and fluorescent proton indicators in a biological in vitro system: an organelle-free yeast extract. Spontaneous wave generation during glycolytic sugar degradation is established after an induction period of about 1 h. Controlled wave initiation could be performed by local injection of the strong activator of phosphofructokinase, fructose 2,6-bisphosphate. A crucial role for wave initiation and control of pattern dynamics is attributed to the key enzyme of glycolysis, the allosterically regulated phosphofructokinase. An overall increase in the concentration of its positive effector AMP leads to the formation of rotating spirals. The dynamics of the observed wave patterns resemble that of self-organized calcium waves as recently found in frog eggs and heart cells.