ENDOMET database – A means to identify novel diagnostic and prognostic tools for endometriosis

Endometriosis is a common benign hormone reliant inflammatory gynecological disease that affects fertile aged women and has a considerable economic impact on healthcare systems. Symptoms include intense menstrual pain, persistent pelvic pain, and infertility. It is defined by the existence of endometrium-like tissue developing in ectopic locations outside the uterine cavity and inflammation in the peritoneal cavity. Endometriosis presents with multifactorial etiology, and despite extensive research the etiology is still poorly understood. Diagnostic delay from the onset of the disease to when a conclusive diagnosis is reached is between 7–12 years. There is no known cure, although symptoms can be improved with hormonal medications (which often have multiple side effects and prevent pregnancy), or through surgery which carries its own risk. Current non-invasive tools for diagnosis are not sufficiently dependable, and a definite diagnosis is achieved through laparoscopy or laparotomy. This study was based on two prospective cohorts: The ENDOMET study, including 137 endometriosis patients scheduled for surgery and 62 healthy women, and PROENDO that included 138 endometriosis patients and 33 healthy women. Our long-term goal with the current study was to support the discovery of innovative new tools for efficient diagnosis of endometriosis as well as tools to further understand the etiology and pathogenesis of the disease. We set about achieving this goal by creating a database, EndometDB, based on a relational data model, implemented with PostgreSQL programming language. The database allows e.g., for the exploration of global genome-wide expression patterns in the peritoneum, endometrium, and in endometriosis lesions of endometriosis patients as well as in the peritoneum and endometrium of healthy control women of reproductive age. The data collected in the EndometDB was also used for the development and validation of a symptom and biomarker-based predictive model designed for risk evaluation and early prediction of endometriosis without invasive diagnostic methods. Using the data in the EndometDB we discovered that compared with the eutopic endometrium, the WNT- signaling pathway is one of the molecular pathways that undergo strong changes in endometriosis. We then evaluated the potential role for secreted frizzled-related protein 2 (SFRP-2, a WNT-signaling pathway modulator), in improving endometriosis lesion border detection. The SFRP-2 expression visualizes the lesion better than previously used markers and can be used to better define lesion size and that the surgical excision of the lesions is complete.ENDOMET tietokanta – Keino tunnistaa uusi diagnostinen ja ennustava työkalu endometrioosille Endometrioosi on yleinen hyvänlaatuinen, hormoneista riippuvainen tulehduksellinen lisääntymisikäisten naisten gynekologinen sairaus, joka kuormittaa terveydenhuoltojärjestelmää merkittävästi. Endometrioositaudin oireita ovat mm. voimakas kuukautiskipu, jatkuva lantion alueen kipu ja hedelmättömyys. Sairaus määritellään kohdun limakalvon kaltaisen kudoksen esiintymisenä kohdun ulkopuolella sekä siihen liittyvänä vatsakalvon tulehduksena. Endometrioosin etiologia on monitahoinen, ja laajasta tutkimuksesta huolimatta edelleen huonosti tunnettu. Kesto taudin puhkeamisesta lopullisen diagnoosin saamiseen on usein jopa 7–12 vuotta. Sairauteen ei tunneta parannuskeinoa, mutta oireita voidaan lievittää esimerkiksi hormonaalisilla lääkkeillä (joilla on usein monia sivuvaikutuksia ja jotka estävät raskauden) tai leikkauksella, johon liittyy omat tunnetut riskit. Nykyiset ei-invasiiviset diagnoosityökalut eivät ole riittävän luotettavia sairauden tunnistamiseen, ja varma endometrioosin diagnoosi saavutetaan laparoskopian tai laparotomian avulla. Tämä tutkimus perustui kahteen prospektiiviseen kohorttiin: ENDOMET-tutkimuk-seen, johon osallistui 137 endometrioosipotilasta ja 62 terveellistä naista, sekä PROENDO-tutkimukseen, johon osallistui 138 endometrioosipotilasta ja 33 terveellistä naista. Tässä tutkimuksessa pitkän aikavälin tavoitteemme oli löytää uusia työkalujen endometrioosin diagnosointiin, sekä ymmärtää endometrioosin etiologiaa ja patogeneesiä. Ensimmäisessä vaiheessa loimme EndometDB –tietokannan PostgreSQL-ohjelmointi-kielellä. Tämän osittain avoimeen käyttöön vapautetun tietokannan avulla voidaan tutkia genomin, esimerkiksi kaikkien tunnettujen geenien ilmentymistä peritoneumissa, endo-metriumissa ja endometrioosipotilaiden endometrioosileesioissa EndometDB-tietokantaan kerättyjä tietoja käytettiin oireiden ja biomarkkeripohjaisen ennustemallin kehittämiseen ja validointiin. Malli tuottaa riskinarvioinnin endometrioositaudin varhaiseen ennustamiseen ilman laparoskopiaa. Käyttäen EndometDB-tietokannan tietoja havaitsimme, että endo-metrioositautikudoksessa tapahtui voimakkaita geeni-ilmentymisen muutoksia erityisesti geeneissä, jotka liittyvät WNT-signalointireitin säätelyyn. Keskeisin löydös oli, että SFRP-2 proteiinin ilmentyminen oli huomattavasti koholla endometrioosikudoksessa ja SFRP-2 proteiinin immunohistokemiallinen värjäys erottaa endometrioosin tautikudoksen terveestä kudoksesta aiempia merkkiaineita paremmin. Löydetyllä menetelmällä voidaan siten selvittää tautikudoksen laajuus ja tarvittaessa osoittaa, että leikkauksella on kyetty poistamaan koko sairas kudos

Non-Coding RNAs in Ovarian Cancer

Ovarian cancer (OC) is the most lethal form of gynaecological cancer, with high- grade serous ovarian carcinoma (HGSOC) being the most common and the deadliest subtype. Non-coding RNAs are a recently discovered species of RNAs that do not code for proteins, yet play a crucial role in both normal physiology and disease. The overall goal of this thesis was to apply the power of non-coding RNAs to OC with the following aims: (1) to identify novel small non-coding RNAs present in serum that could separate patients with HGSOC from healthy women as well as predict their surgical outcome, (2) to assess the role of long non-coding RNAs (lncRNAs) in promoting cisplatin resistance in cell line models of OC, and (3) to study the effects of mutant-p53 on mRNAs and lncRNAs using a small compound known as APR-246 as well as investigating the drug’s mechanisms of action. Firstly, the lethality of OC could partially be attributed to the lack of specific symptoms, leading this disease to be termed the ‘silent killer’, as well as low inci- dence rate of 9.4 cases per 100,000 individuals, both requiring a highly accurate test for population screening that remains an ongoing challenge. Measuring the levels of small non-coding RNAs, known as microRNAs, in serum, experiments described in this thesis aimed to identify novel microRNAs that could separate pa- tients with HGSOC from healthy women as well as predict their surgical outcome, one of the most important factors influencing overall patient survival. Because serum microRNAs can be affected by pre-analytical factors such as haemolysis, the sensitivity of four methodologies to detect low levels of haemolysis was first determined. This work is published in Plos One. The work described in this thesis identified a novel serum microRNA, miR-375, that could improve the accuracy of CA-125, a routinely used biomarker in diagnosing OC, in separating patients with HGSOC from healthy women. Next, serum microRNA miR-34a-5p was found to predict the surgical outcome of patients with HGSOC. In fact, miR-34a-5p was found to be superior to CA-125 for this purpose. Although the standard therapy for treating OC consists of surgical removal of the tumour followed by chemotherapy containing platinum/taxane agents, this regimen may be too aggressive for a sub- set of patients who might benefit from neoadjuvant chemotherapy, i.e. chemother- apy followed by the surgery. A pre-operative expectation of the the surgical out- come could help surgeons decide on optimal timing for surgery. Both miR-375 and miR-34a-5p were also unaffected by haemolysis. Secondly, although OC is initially sensitive to chemotherapy, most patients develop resistance within two years, resulting in recurrent disease that is difficult to treat. To identify novel lncRNAs that could promote drug resistance, expression of ninety lncRNAs was profiled in cell line models of cisplatin resistance. Five lncRNAs were found to have the potential to promote cisplatin resistance in vitro, and lncRNA Urothelial Cancer Associated 1 (UCA1) was selected for further investigations. Despite its role in promoting cisplatin resistance in bladder cancer, UCA1 was not found to promote cisplatin resistance in cell line models of OC. Lastly, the tumour suppressor TP53 plays a central role in the biology of cancer and it is almost universally mutated in HGSOC. Recent evidence suggests that p53, the protein encoded by TP53, can significantly influence the expression of both small and long non-coding RNAs. Experiments described in this thesis aimed to investigate the effect of mutant-p53 on protein-coding and non-coding RNAs by using a small compound known as APR-246 which has been reported to restore wild-type p53 activities in multiple cancers by stabilising the structure of mutant- p53. Despite currently undergoing a phase Ib/II clinical trial for potential treatment of recurrent HGSOC, the ability of APR-246 to restore wild-type p53 activities in HGSOC has not been tested. A global transcriptomic analysis conducted in this thesis discovered that p53-responsive mRNAs and lncRNAs were not robustly induced following APR-246 treatment in two cell line models of HGSOC, but indicated that APR-246 could function by inducing high levels of reactive oxidative species (ROS). Overall, data presented in this thesis demonstrated the utility of small non- coding RNAs in identifying patients with HGSOC from healthy women as well as predicting their surgical outcome. This thesis also implicated that lncRNAs, in general, could have a role in promoting cisplatin resistance in OC as well as suggested that APR-246 could, based on evidence obtained from the expression of p53-responsive mRNAs and lncRNAs, act independently of mutant-p53. Together, this research raises novel ways for clinical management of patients with HGSOC and addresses the challenge of drug resistance using non-coding RNAs, as well as questions the assumed mechanisms of action of the ‘p53-activating’ drug APR- 246

Systematic analysis of prognostic miRNAs and isomiRs in prostate cancer

There are no reliable prognostic indicators to distinguish between indolent and aggressive prostate cancer (PCa). Consequently, 42–66% of patients with indolent PCa are over-treated. Additionally, 15-45% of patients treated with radical prostatectomy (RP) experience biochemical recurrence (BCR) within 5-years, highlighting an urgent need for reliable prognostic biomarkers. MiRNAs (miRs) and isomiRs (miR isoforms) are non-coding regulatory RNAs that hold ideal biomarker properties such as detection in circulation, tissue and tumour specific expression profiles, and correlation with PCa development and progression. I hypothesised that miR species (canonical miRs and isomiRs) can be utilised as biomarkers for reliable PCa prognostication. A novel database of prognostic PCa miRs was built by performing a systematic review of relevant publications in the PubMed database. MiRs significantly associated with BCR were also identified following a meta-analysis of six datasets. MiR-148a-3p and miR-582-4p were identified as potential biomarker candidates as they were consistently prognostic in both the review and meta-analysis. The ability of miR species to predict BCR post-RP was tested with elastic net regularisation models using The Cancer Genome Atlas PCa dataset (recurrent=61, non-recurrent=330). Models based on a combination of isomiRs and clinical markers achieved marginally greater predictive power (AUC=0.795) than the model solely based on clinical markers (AUC=0.748), demonstrating that isomiRs could contribute additional prognostic value to the clinical markers currently used. The mechanism by which miR-27a-3p, a PCa-specific putative oncomiR, promotes tumour growth was investigated using RNA-seq data from LNCaP tumour xenograft models treated with a miR-27a-3p inhibitor (n=3) and control (n=3). 11 significantly dysregulated genes involved in apoptosis and oncogenic signalling were identified as likely mir-27a-3p targets. This study has not only furthered our understanding of the importance of miRs in PCa, but also identified potential prognostic miR biomarkers and showed the inclusion of miR species increases the utility of current markers.Open Acces

Mechanisms of cancer cell death by mutant p53-reactivating compound APR-246

Tumor suppressor TP53 is the most frequently mutated gene in cancer. A majority of TP53 mutations result in a mutant p53 that disrupts its DNA binding capabilities but may also acquire novel gain-of-function activities that contribute to tumor growth. The investigational drug APR-246 (Eprenetapopt) is the most clinically advanced compound to target mutant p53 and is being tested in a phase III clinical trial in mutant TP53 myelodysplastic syndrome (MDS). APR-246 is converted to its active product methylene quinuclidinone (MQ). MQ binds to cysteines in p53 promoting a folded structure and DNA binding, leading to cancer cell death. MQ also targets thiols or selenols in e.g. glutathione (GSH) or various enzymes. Depletion of glutathione and inhibition of antioxidant enzymes increase oxidative stress contributing to APR-246-induced cancer cell death. In Project I, combination treatment of APR-246 and multidrug resistance protein 1 (MRP1) inhibitor resulted in synergistic growth suppression in vitro in tumor cell lines, in vivo in esophageal cancer xenografts, and ex vivo in esophageal and colorectal cancer patient-derived organoids (PDO). We show that inhibition of MRP1 results in increased intracellular 14C- content after 14C-APR-246 treatment. This was attributed to retention of GSH-conjugated MQ (GS-MQ). We demonstrate that GS-MQ binding is reversible and that retention of GS-MQ creates an intracellular MQ pool that may target numerous thiols contributing to APR-246- induced growth suppression. In Project II we studied the spectrum of MQ-targeted cysteines in p53. This was enabled by first establishing a method utilizing the reducing agent NaBH4 to lock the MQ cysteine adducts into a stable form, overcoming reversibility. Cys182, Cys229 and Cys277 in the p53 core domain showed most prominent MQ modification. Additional modification at Cys124 and Cys141 was found in mutant p53. The electrophilic properties of MQ enables targeting of multiple cellular thiols. In Project III we identified novel MQ targets using CEllular Thermal Shift Assay (CETSA). Asparaginase synthetase (ASNS) was stabilized upon MQ treatment and thus is a potential MQ target. In acute lymphoblastic leukemia (ALL), ASNS is associated with resistance to standard treatment asparaginase. Asparaginase depletes extracellular asparagine which renders asparagine-auxotrophic ALL cells sensitive and therefore ASNS expression allows ALL cell survival. We found that combination treatment of APR-246 and asparaginase leads to synergistic growth suppression in ALL cells and may offer a novel treatment strategy for ALL. Lastly, in Project IV we assessed the functional activity of novel germline TP53 mutations identified in a Swedish cohort of families with Li-Fraumeni syndrome (LFS) or hereditary breast cancer (HrBC). Assessing the pathological outcome of TP53 mutations is important for understanding the cancer risk of these families. The first three projects are aimed at improving our understanding of mutant p53-reactivating compound APR-246. They suggest approaches for increasing treatment efficacy and novel combination strategies. The thesis has also addressed the role of mutant p53 in response to APR-246 and pathological properties in families with LFS or HrBC. All in all, these studies provide novel preclinical understanding of the role of mutant p53 in cancer and response to treatment, both highly relevant in the combat against cancer

Improving clinical outcomes for patients with locally advanced non-small cell lung cancer treated with photon and proton radiotherapy

Objectives To identify mechanisms improving clinical outcomes for patients with unresectable locally advanced non-small-cell lung cancer (LA-NSCLC) treated with photon and proton radiotherapy. Strategies explored include 1. Investigating using routine healthcare datasets to estimate survival outcomes for patients with LA-NSCLC treated with definitive radiotherapy, in order to assess the effectiveness of current strategies; 2. Assessing the physical advantages of protons by conducting a retrospective planning study comparing volumetric modulated arc therapy (VMAT) and pencil beam scanning (PBS) proton plans of superior sulcus tumours (SSTs), a rare subset of LA-NSCLC; 3. Exploring potential biological advantages of protons by examining major cell death pathways following XRT, high and low linear energy transfer (LET) proton irradiation of NSCLC cells. Methods Workflow 1: LA-NSCLC patients receiving definitive radiotherapy were identified. For each, key time points (date of diagnosis, recurrence, death or last clinical encounter) were used to calculate overall survival (OS) and progression free survival (PFS) from manual-data (hospital notes) and compared to estimated OS and PFS from routine-data (electronic databases). Dataset correlations were then tested to establish if routine-data were a reliable proxy measure for manual-data. Workflow 2: Patients with SSTs treated with 4D radiotherapy were identified. Tumour motion was assessed and excluded if >5 mm. Comparative VMAT and PBS plans were generated retrospectively. Robustness analysis was assessed for both plans involving: 1. 5 mm geometric uncertainty scenarios, with an additional 3.5% range uncertainty for proton plans; 2. verification plans at breathing extremes. Comparative dosimetric and robustness analyses were carried out. Workflow 3: Human NSCLC cell lines were irradiated with single doses of 2-15 Gy photon radiotherapy, high- or low-linear energy transfer (LET) protons (12 keV/µm and 1 keV/µm, respectively) and analysed 24-144 hours post-irradiation. DNA damage foci and cell death mechanisms were investigated. Results Workflow 1: In forty-three patients, routine data underestimated PFS by 0.09 months (p=0.86; 95% CI -0.86-1.03) and OS by 1.02 months (p=0.00; 95% CI 0.34-1.69) but there was good correlation with a Pearson correlation coefficient of 0.94 (p=0.00, 95% CI 0.90-0.97) for PFS and 0.97 (p= 0.00, 95% CI 0.95-0.98) for OS. Workflow 2: In ten patients, both modalities achieved similar target coverage with mean clinical target volume D95 of 98.1% + 0.4 (97.5-98.8) and 98.4% + 0.2 (98.1-98.9) for PBS and VMAT plans, respectively. The same four PBS and VMAT plans failed robustness. Proton plans significantly reduced mean lung dose (by 21.9%), lung V5, V10, V20 (by 47.9%, 36.4%, 12.1%, respectively), mean heart dose (by 21.4%) and vertebra dose (by 29.2%) (p<0.05). Workflow 3: XRT predominantly induced mitotic catastrophe, autophagy and senescence. Senescence, established via the p53/p21 pathway, was the major cell death pathway by which protons more effectively reduce clonogenic potential compared to XRT in NSCLC cell lines. High LET protons at a dose of 10 Gy(RBE) resulted in the lowest cell survival. The mechanisms driving the LET- and dose-dependent senescence was unclear but did not appear to be related to differential DNA repair machineries. Conclusions Proton radiotherapy could be pivotal in improving outcomes in select cases of LA-NSCLC. These studies demonstrate that 1. survival-outcomes are reliably estimated by routine data and such a methodology could enable rapid outcomes analysis to keep pace with trial development; 2. robust PBS plans are achievable in carefully selected patients and considerable dose reductions to the lung, heart and thoracic vertebra are possible without compromising target coverage; 3. Identification of LET- and dose-dependent proton-induced cellular senescence may guide radiotherapy optimisation and drug-radiotherapy combinations, maximising tumour cell kill. This work contributes to important preliminary research required to understand the physical and biological strengths and weaknesses prior to trials

Role of Distal Regulatory Elements in Cancer Progression and Therapy

Enhancer elements comprise of regions of DNA that are distal to gene promoters with a characteristic capacity to affect and regulate gene transcription. Enhancers are enriched in a highly context-specific manner allowing for intricate control of gene expression. Current studies endeavor to elucidate the mechanisms underlying enhancer activation and function to ultimately exploit their specificity in targeted therapeutics. Due to the reported addiction of cancer to aberrant gene transcription, targeting enhancer elements is a promising therapeutic target in various malignancies. In this project, we conduct a series of studies with the general aim of extending the knowledge about the molecular mechanisms by which enhancers drive aberrant transcription in cancer. We focus on epigenetic modulation to exploit enhancer elements as therapeutic or prognostic targets. In the first study included in our project, we evaluated the importance of the super enhancer subcategory of distal regulatory elements in a breast cancer cell line where estrogen plays an important role in driving gene expression through enhancers. Super enhancers are claimed to be a highly active subgroup of distal regulatory elements that is abundantly enriched with transcription factors, span long stretches of DNA, and exhibit preferential efficacy in driving major transcriptional programs in cancer. We identified super enhancers related to estrogen in this system using the standard algorithm and failed to observe a distinct high efficacy of super enhancers compared to typical enhancers. By varying the settings of this algorithm, we also uncovered biases in enhancer identification that extensively influence the results. On the other hand, we observed that major targets of estrogen activation showed a preference for association with super enhancers and concluded that they may indeed tend to regulate the transcription of master regulators. Accordingly, we concluded that the focused attention given to super enhancers should not lead to disregarding typical enhancers which also play a significant and important role in gene transcription regulation. Consequently, in the second study we reviewed the role of enhancers in pancreatic cancer, a malignancy with exceptionally low survival rates. We focused on the application of epigenetic modulators, such as bromodomain and extraterminal proteins inhibitors and histone deactylase inhibitors, in targeting enhancer elements and speculated about mechanisms underlying the reported synergy between these two inhibitors. Interestingly, we used publicly available data to further study the context-specificity of enhancers. Notably, we observed a tendency where the same oncogenic target gene is activated by different enhancers in various systems due to differential expression of transcription factors. Accordingly, we expanded our studies in pancreatic cancer and uncovered a group of subtype-specific super enhancers that drive the cells into a squamous phenotype which correlates with a particularly poor prognosis. Studying the general activation epigenetic profiles of different pancreatic cancer cell lines identified deltaNp63 as a major driver of the squamous molecular identity in cells and patient-derived xenografts. Moreover, extensive analysis of the role of deltaNp63 in driving a more aggressive phenotype uncovered the implication of super enhancers which are supported by a network of interconnected and differentially expressed transcription factors. This pattern resembles the reports of transcription factor regulatory circuitry driving the pluripotent molecular identity of embryonic stem cells. Identification of the same pattern governing differentiation into specific molecular subtypes in pancreatic cancer opens the door to precision-based medicine approaches targeting this circuitry in this particular subtype. Finally, we further investigated the role of enhancer elements in the context of chemotherapeutic resistance in pancreatic cancer. Interestingly, we observed that pro-inflammatory and migratory programs are activated in paclitaxel-resistant cells via activation of BET-dependent enhancers. Furthermore, we observed that BET inhibition sensitizes resistant and sensitive cells to paclitaxel. Notably, super enhancers that we observed to be enriched in resistant cells were associated with genes that correlate with poor prognosis. This study confirmed the patterns we uncovered in the other studies where enhancers and super enhancers drive aberrant transcription activation in cancer and present a promising target for patient treatment. Altogether, this project resulted in 2 peer-reviewed publications in the journals of Transcription and Epigenomes, one manuscript that has been peer-reviewed and is currently under revision in Proceedings of the National Academy of Sciences of the United States of America (PNAS), and another manuscript in preparation for submission. These publications/manuscripts join the growing body of literature investigating the role of enhancers in malignancy and aim to guide new approaches for precision-based medicine.2019-12-1

An investigation into the effects of commencing haemodialysis in the critically ill

&lt;b&gt;Introduction:&lt;/b&gt; We have aimed to describe haemodynamic changes when haemodialysis is instituted in the critically ill. 3 hypotheses are tested: 1)The initial session is associated with cardiovascular instability, 2)The initial session is associated with more cardiovascular instability compared to subsequent sessions, and 3)Looking at unstable sessions alone, there will be a greater proportion of potentially harmful changes in the initial sessions compared to subsequent ones. &lt;b&gt;Methods:&lt;/b&gt; Data was collected for 209 patients, identifying 1605 dialysis sessions. Analysis was performed on hourly records, classifying sessions as stable/unstable by a cutoff of &gt;+/-20% change in baseline physiology (HR/MAP). Data from 3 hours prior, and 4 hours after dialysis was included, and average and minimum values derived. 3 time comparisons were made (pre-HD:during, during HD:post, pre-HD:post). Initial sessions were analysed separately from subsequent sessions to derive 2 groups. If a session was identified as being unstable, then the nature of instability was examined by recording whether changes crossed defined physiological ranges. The changes seen in unstable sessions could be described as to their effects: being harmful/potentially harmful, or beneficial/potentially beneficial. &lt;b&gt;Results:&lt;/b&gt; Discarding incomplete data, 181 initial and 1382 subsequent sessions were analysed. A session was deemed to be stable if there was no significant change (&gt;+/-20%) in the time-averaged or minimum MAP/HR across time comparisons. By this definition 85/181 initial sessions were unstable (47%, 95% CI SEM 39.8-54.2). Therefore Hypothesis 1 is accepted. This compares to 44% of subsequent sessions (95% CI 41.1-46.3). Comparing these proportions and their respective CI gives a 95% CI for the standard error of the difference of -4% to 10%. Therefore Hypothesis 2 is rejected. In initial sessions there were 92/1020 harmful changes. This gives a proportion of 9.0% (95% CI SEM 7.4-10.9). In the subsequent sessions there were 712/7248 harmful changes. This gives a proportion of 9.8% (95% CI SEM 9.1-10.5). Comparing the two unpaired proportions gives a difference of -0.08% with a 95% CI of the SE of the difference of -2.5 to +1.2. Hypothesis 3 is rejected. Fisher’s exact test gives a result of p=0.68, reinforcing the lack of significant variance. &lt;b&gt;Conclusions:&lt;/b&gt; Our results reject the claims that using haemodialysis is an inherently unstable choice of therapy. Although proportionally more of the initial sessions are classed as unstable, the majority of MAP and HR changes are beneficial in nature

Alternations of microRNAs, the microbiome, and gut-host interactions in gastrointestinal diseases

Over the past few decades, an ageing population combined with a shift towards a Western lifestyle has predisposed many individuals towards inter-connected gastrointestinal (GI) diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), gastric cancer (GC) and Clostridioides difficile (C. difficile) infection (CDI). anti-TNF-α treatment for IBD patients has a high unresponsive rate, by using bioinformatics approaches, I identified neutrophil chemotaxis may contribute to the treatment resistance and IL13RA2 is the best predictor to identify treatment unresponsive patients. On the other hand, in the intestinal tract, colonocytes consistently exfoliate and shed into the lumen, affecting gut microbiota composition. These molecular/microbial changes involved in disease pathogenesis can be detected in faeces. By using Taqman probe-based real-time polymerase chain reaction (RT qPCR) assay, several non-coding microRNAs (such as miR-18a, miR-20a, miR-221 and miR 135b) and gut microbes (including Fusobacterium nucleatum, Parvimonas micra, Gemella morbillorum, Peptostreptococcus anaerobius, Clostridium hathewayi and Lachnoclostrium sp.) are highly expressed/enriched in faeces in CRC individuals compared to control subjects. The use of a faecal immunological test (FIT) in combination with these biomarkers may improve the non-invasive CRC screening accuracy. Furthermore, Epstein-Barr virus (EBV) is an oncogenic virus and EBV-driven GC accounts for roughly 10% of total GC cases. GC cells infected with EBV alter the molecular aspect at whole-genome, transcriptome, and epigenome levels. For instance, AKT2 activated by mutation in EBV-positive GC cells affecting downstream MAPK and focal adhesion signalling pathways; AKT2 mutation associates with poor patient survival in EBV-positive GC. Furthermore, once patients have received GI treatments, it may suppress/interfere with the patients’ immune system, disrupt the gut flora homeostasis and trigger CDI. Faecal microbiota transplantation (FMT) has been demonstrated as an effective and alternative treatment strategy for CDI patients. However, it is still in clinical trials due to safety concerns. My study revealed that serum miRNAs such as miR-23a-3p, miR-150-5p, miR-26b-5p and miR-28-5p could be used to monitor FMT treatment in CDI patients, and these markers inversely correlate with IL-12B, IL-18, FGF21 and TNFSRF9 at serum protein and mRNA levels, respectively. Furthermore, miR-23a and miR-150 showed cytoprotective effects against C. difficile Toxin B (TcdB)