Integration and analysis of phenotypic data from functional screens

Motivation: Although various high-throughput technologies provide a lot of valuable information, each of them is giving an insight into different aspects of cellular activity and each has its own limitations. Thus, a complete and systematic understanding of the cellular machinery can be achieved only by a combined analysis of results coming from different approaches. However, methods and tools for integration and analysis of heterogenous biological data still have to be developed. Results: This work presents systemic analysis of basic cellular processes, i.e. cell viability and cell cycle, as well as embryonic stem cell pluripotency and differentiation. These phenomena were studied using several high-throughput technologies, whose combined results were analysed with existing and novel clustering and hit selection algorithms. This thesis also introduces two novel data management and data analysis tools. The first, called DSViewer, is a database application designed for integrating and querying results coming from various genome-wide experiments. The second, named PhenoFam, is an application performing gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. Both programs are accessible through a web interface. Conclusions: Eventually, investigations presented in this work provide the research community with novel and markedly improved repertoire of computational tools and methods that facilitate the systematic analysis of accumulated information obtained from high-throughput studies into novel biological insights

RUSSIA’S FALIN–KVITSINSKY ENERGY DOCTRINE: HISTORY AND EXPERIENCE APPLYING TO SELECTED CENTRAL EUROPEAN COUNTRIES

This article discusses the evolution of the energy security of Belarus, Estonia, Latvia, Lithuania, Poland and Ukraine since the collapse of the Union of Soviet Socialist Republics (USSR), in terms of natural gas supplies. Instead of framing energy dependencies on Russia in a descriptive way, this article shows the empirical validation of the Falin–Kvitsinsky doctrine, which includes the use of energy resources as tool in foreign policy. Therefore, the authors propose a three-element Falin–Kvitsinsky doctrine indicator to measure the power of this doctrine using the yearly data for 1991–2021. Authors argue that the impact of this doctrine should be assessed through the lens of energy supply security and then measured by appropriate indicators. This approach might be seen as opposite to the mainstream publications which are mostly descriptive in this field. In the article, the authors provided clear evidence of the Falin–Kvitsinsky doctrine existence until the end of 2021, which was applied during the Russian-Ukrainian war. Actions taken by Russia over the years were aimed at making Central European countries dependent on natural gas supply, which would then prompt these countries to limit their aid to Ukraine during the conflict that began in 2022. In conclusion, Russia is able to pursue its political goals in the manner suggested by the Falin–Kvitsinsky doctrine as long as each Central European country tries to ensure its own energy security. However, the Falin-Kvitsky doctrine did not fully meet its objectives, as Central European countries, as a result of the Russian-Ukrainian war, were able to quickly take steps to diversify the sources and directions of natural gas supplies by taking comprehensive measures and strengthening cooperation

Placenta percreta leading to uterine rupture at 18 weeks of pregnancy with consecutive hysterectomy: a case report

A 26-year-old woman in the fourth pregnancy with a history of two Cesarean sections and one dilation and curettage was admitted to the hospital at 18 weeks of gestation with acute abdominal pain. Life-saving laparotomy revealed uterine rupture and placental invasion into the uterine wall. Supracervical hysterectomy was performed. This case shows that pathological placentation due to previous cesarean sections may be the cause of uterine rupture

Prediction of designer-recombinases for DNA editing with generative deep learning

Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designerrecombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designerrecombinases. We gather the sequence information of over one million Crelike recombinase sequences evolved for 89 different target sites with whichwe train Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrates that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases

Embolizacja tętnic macicznych – zagadnienia kliniczne

The aim of the study was to present clinical issues concerning uterine artery embolization (UAE) in women with uterine fibromas. In order to ensure high clinical efficiency of UAE and prevent subsequent complications, it is necessary to carefully select patients eligible for the procedure. Patients with intramural fibromas, who do not plan to conceive, are the best candidates for the procedure. Fibroma necrosis, with following infection, and premature ovarian failure remain to be the most common complications after UAE. UAE may cause amenorrhea and increase FSH levels, what is typical for menopause. Thus, it may be responsible for problems with conception as well as optimal development of a pregnancy. It may also cause premature, iatrogenic menopause. This complication significantly more frequently occurs in women over the age of 45 as compared to younger patients. UAE is considered as an alternative therapeutic procedure, available to women who do not desire the surgery or wish to preserve the uterus. Patients subject to this procedure should be informed about the possible side effects.Celem pracy było przedstawienie zagadnień klinicznych związanych z zabiegami embolizacji tętnic macicznych (UAE) w przypadku objawowych mięśniaków macicy. Zwrócono uwagę, że odpowiednia kwalifikacja chorych do zabiegu ma kluczowe znaczenie dla wysokiej skuteczności klinicznej oraz zapobiegania powikłaniom po UAE. Kandydatkami powinny być kobiety z objawowymi mięśniakami położonymi śródściennie, które w przyszłości nie planują zachodzić w ciążę. Przedwczesne wygasanie czynności jajników, obok martwicy mięśniaka z następową infekcją stanowi jedno z najczęstszych powikłań embolizacji. Może być przyczyną przedwczesnej, jatrogennej menopauzy oraz trudności w zajściu i donoszeniu ciąży. UAE może niekorzystnie wpłynąć na funkcję jajników, powodując czasowe lub stałe zatrzymanie miesiączki, a także typowy dla okresu menopauzy wzrost poziomu FSH. Znacznie częściej to powikłanie UAE obserwuje się u kobiet po 45 roku życia, niż młodszych. Embolizacja tętnic macicznych przeprowadzana w celu leczenia objawowych mięśniaków macicy stanowi alternatywną opcję terapeutyczną, istotną dla kobiet, które nie chcą poddawać się operacji lub pragnących zachować macicę. Chore poddawane tego typu leczeniu powinny być poinformowane o możliwych skutkach ubocznych

Endovascular embolization as a treatment for symptomatic adenomyosis — results of preliminary study

Objectives: To present preliminary results of minimally invasive endovascular embolization as a treatment of symptomatic adenomyosis or adenomyosis with fibroids and to assess the long-term clinical outcome. Material and methods: Between 2015 and 2020 twelve patients with symptomatic adenomyosis or adenomyosis with fibroids underwent uterine artery embolization (UAE). All patients were evaluated in terms of patient’s overall satisfaction, relief of clinical symptoms, reintervention and hysterectomy as well as menopause rates. Results: Mean age on admission was 48 years. Reported symptoms included: dysmenorrhea with the mean VAS score of 7.8, menorrhagia and problems with urination. Successful embolization was achieved in all patients (100%). A reduction in pelvic pain intensity assessed using VAS was observed in 11/12 (92%) of the patients — pain decreased by 6.2 points on average (from 7.8 to 1.6 pts). In one patient (8%) the recurrence of pain was observed. All patients reported decrease of menstrual bleeding and consequently improvement of everyday life quality. Avoidance of hysterectomy was achieved in 83% of the women. Five patients experience absence of menstrual periods for at least 12 months after the embolization resulting in menopause rate of 42%. Ten patients (83%) reported to be very or fairly satisfied with the results and would recommend this treatment to a friend. Conclusions: Uterine artery embolization might be safe and effective method of treatment for patients with symptomatic adenomyosis with or without fibroids with very high rate of satisfied patients

Linzagolix therapy versus a placebo in patients with endometriosis-associated pain: a prospective, randomized, double-blind, Phase 3 study (EDELWEISS 3)

Does linzagolix administered orally once daily for up to 3 months at a dose of 75 mg alone or 200 mg in combination with add-back therapy (ABT) (1.0 mg estradiol; 0.5 mg norethindrone acetate, also known as norethisterone acetate [NETA]) demonstrate better efficacy than placebo in the management of endometriosis-related dysmenorrhea and non-menstrual pelvic pain? Combining 200 mg linzagolix with ABT was found to significantly reduce dysmenorrhea and non-menstrual pelvic pain at 3 months of therapy, while a daily dose of 75 mg linzagolix yielded a significant decrease only in dysmenorrhea at 3 months. A previously published Phase 2, dose-finding study reported that at a dose of 200 mg daily, linzagolix promotes full suppression of estradiol secretion to serum levels below 20 pg/ml and noted that the addition of ABT may be needed to manage hypoestrogenic side effects. At lower doses (75 mg and 100 mg/day), linzagolix maintains estradiol values within the target range of 20-60 pg/ml, which could be ideal to alleviate symptoms linked to endometriosis. EDELWEISS 3 was a multicenter, prospective, randomized, placebo-controlled, double-blind, double-dummy Phase 3 study to evaluate the safety and efficacy of linzagolix for the treatment of moderate-to-severe endometriosis-associated pain. Treatment was administered orally once daily for up to 6 months. In the EDELWEISS 3 trial, 486 subjects with moderate-to-severe endometriosis-associated pain were randomized at a 1:1:1 ratio to one of the three study groups: placebo, 75 mg linzagolix alone or 200 mg linzagolix in association with ABT. Pain was measured daily on a verbal rating scale and recorded in an electronic diary. At 3 months, the daily 200 mg linzagolix dose with ABT met the primary efficacy objective, showing clinically meaningful and statistically significant reductions in dysmenorrhea and non-menstrual pelvic pain, with stable or decreased use of analgesics. The proportion of responders for dysmenorrhea in the 200 mg linzagolix with ABT group was 72.9% compared with 23.5% in the placebo group (P < 0.001), while the rates of responders for non-menstrual pelvic pain were 47.3% and 30.9% (P = 0.007), respectively. The 75 mg linzagolix daily dose demonstrated a clinically meaningful and statistically significant reduction in dysmenorrhea versus placebo at 3 months. The proportion of responders for dysmenorrhea in the 75 mg linzagolix group was 44.0% compared with 23.5% in the placebo group (P < 0.001). Although the 75 mg dose showed a trend toward reduction in non-menstrual pelvic pain at 3 months relative to the placebo, it was not statistically significant (P = 0.279). Significant improvements in dyschezia and overall pelvic pain were observed in both linzagolix groups when compared to placebo. Small improvements in dyspareunia scores were observed in both linzagolix groups but they were not significant. In both groups, hypoestrogenic effects were mild, with low rates of hot flushes and bone density loss of <1%. A daily dose of 200 mg linzagolix with ABT or 75 mg linzagolix alone was found to significantly reduce dysmenorrhea and non-menstrual pelvic pain also at 6 months of therapy. Efficacy was compared between linzagolix groups and placebo; however, it would be useful to have results from comparative studies with estro-progestogens or progestogens. It will be important to ascertain whether gonadotropin-releasing hormone antagonists have significant benefits over traditional first-line medications. Linzagolix administered orally once daily at a dose of 200 mg in combination with add-back therapy (ABT) demonstrated better efficacy and safety than placebo in the management of moderate-to-severe endometriosis-associated pain. The quality of life was improved and the risks of bone loss and vasomotor symptoms were minimized due to the ABT. The 75 mg dose alone could be suitable for chronic treatment of endometriosis-associated pain without the need for concomitant hormonal ABT, but further research is needed to confirm this. If confirmed, it would offer a viable option for women who do not want to wish to have ABT or for whom it is contraindicated. Funding for the EDELWEISS 3 study was provided by ObsEva (Geneva, Switzerland). Analysis of data and manuscript writing were partially supported by ObsEva (Geneva, Switzerland), Theramex (London, UK) and Kissei (Japan) and grant 5/4/150/5 was awarded to M.-M.D. by FNRS. J.D. was a member of the scientific advisory board of ObsEva until August 2022, a member of the scientific advisory board of PregLem, and received personal fees from Gedeon Richter, ObsEva and Theramex. J.D. received consulting fees, speakers' fees, and travel support from Gedeon Richter, Obseva and Theramex, which was paid to their institution. C.B. has received fees from Theramex, Gedeon Richter, and Myovant, and travel support from Gedeon Richter-all funds went to the University of Oxford. He was a member of the data monitoring board supervising the current study, and served at an advisory board for endometriosis studies of Myovant. H.T. has received grants from Abbvie and was past president of ASRM. F.C.H. has received fees from Gedeon Richter and Theramex. O.D. received fees for lectures from Gedeon Richter and ObsEva and research grants for clinical studies from Preglem and ObsEva independent from the current study. A.H. has received grants from NIHR, UKRI, CSO, Wellbeing of Women, and Roche Diagnostics; he has received fees from Theramex. A.H.'s institution has received honoraria for consultancy from Roche Diagnostics, Gesynta, and Joii. M.P. has nothing to declare. F.P. has received fees from Theramex. S.P.R. has been a member of the scientific advisory board of Gedeon Richter and received fees from Gedeon Richter. A.P. and M.B. are employees of Theramex. E.B. was an employee of ObsEva, sponsor chair of the data monitoring board supervising the current study, and has been working as a consultant for Theramex since December 2022; she owns stock options in ObsEva. M.-M.D. has received fees and travel support from Gedeon Richter and Theramex. NCT03992846. 20 June 2019. 13 June 2019

Correction of a Factor VIII genomic inversion with designer-recombinases

Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct the 140 kb inversion of the F8 gene frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we develop a coupled heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient-derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, results in 12% correction of the inversion and restores Factor VIII mRNA expression. In this work, we present designer-recombinases as an efficient and specific means towards treatment of monogenic diseases caused by large gene inversions