Differential expression of mRNA 3'-end isoforms in cervical and ovarian cancers.

Early diagnosis and therapeutic targeting are continuing challenges for gynecological cancers. Here, we focus on cancer transcriptomes and describe the differential expression of 3'UTR isoforms in patients using an algorithm to detect differential poly(A) site usage. We find primarily 3'UTR shortening cases in cervical cancers compared with the normal cervix. We show differential expression of alternate 3'-end isoforms of FOXP1, VPS4B, and OGT in HPV16-positive patients who develop high-grade cervical lesions compared with the infected but non-progressing group. In contrast, in ovarian cancers, 3'UTR lengthening is more evident compared with normal ovary tissue. Nevertheless, highly malignant ovarian tumors have unique 3'UTR shortening events (e.g., CHRAC1, SLC16A1, and TOP2A), some of which correlate with upregulated protein levels in tumors. Overall, our study shows isoform level deregulation in gynecological cancers and highlights the complexity of the transcriptome. This transcript diversity could help identify novel cancer genes and provide new possibilities for diagnosis and therapy.

Surgical mitral valve repair technique considerations based on the available evidence.

Mitral valve regurgitation is the second most common valve disease in the western world. Surgery is currently the best tool for generating a long-lasting elimination of mitral valve regurgitation. However, the mitral valve apparatus is a complex anatomical and functional structure, and repair results and durability show substantial heterogeneity. This is not only due to differences in the underlying mitral valve regurgitation pathophysiology but also due to differences in repair techniques. Repair philosophies differ substantially from one surgeon to the other, and consensus for the technically best repair strategy has not been reached yet. We had previously addressed this topic by suggesting that ring sizing is "voodoo". We now review the available evidence regarding the various repair techniques described for structural and functional mitral valve regurgitation. Herein, we illustrate that for structural mitral valve regurgitation, resuspension of prolapsing valve segments or torn chordae with polytetrafluoroethylene sutures and annuloplasty can generate the most durable results paired with the best achievable hemodynamics. For functional mitral valve regurgitation, the evidence suggests that annuloplasty alone is insufficient in most cases to generate durable results, and additional subvalvular strategies are associated with improved durability and possibly improved clinical outcomes. This review addresses current strategies but also implausibilities in mitral valve repair and informs the mitral valve surgeon about the current evidence. We believe that this information may help improve outcomes in mitral valve repair as the heterogeneity of mitral valve regurgitation pathophysiology does not allow a one-size-fits-all concept.

Cardiac Surgery 2021 Reviewed.

PubMed displayed more than 35,000 hits for the search term "cardiac surgery AND 2021." We used the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) approach and selected relevant publications for a results-oriented summary. As in recent years, we reviewed the fields of coronary and conventional valve surgery and their overlap with their interventional alternatives. COVID reduced cardiac surgical activity around the world. In the coronary field, the FAME 3 trial dominated publications by practically repeating SYNTAX, but with modern stents and fractional flow reserve (FFR)-guided percutaneous coronary interventions (PCIs). PCI was again unable to achieve non-inferiority compared with coronary artery bypass graft surgery (CABG) in patients with triple-vessel disease. Survival advantages of CABG over PCI could be linked to a reduction in myocardial infarctions and current terminology was criticized because the term "myocardial revascularization" is not precise and does not reflect the infarct-preventing collateralization effect of CABG. In structural heart disease, new guidelines were published, providing upgrades of interventional treatments of both aortic and mitral valve disease. While for aortic stenosis, transcatheter aortic valve implantation (TAVI) received a primary recommendation in older and high-risk patients; recommendations for transcatheter mitral edge-to-edge treatment were upgraded for patients considered inappropriate for surgery. For heart team discussions it is important to know that classic aortic valve replacement currently provides strong signals (from registry and randomized evidence) for a survival advantage over TAVI after 5 years. This article summarizes publications perceived as important by us. It can neither be complete nor free of individual interpretation, but provides up-to-date information for decision-making and patient information.

Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer.

PURPOSE: Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer that is frequently treated with chemotherapy. However, many patients exhibit either de novo chemoresistance or ultimately develop resistance to chemotherapy, leading to significantly high mortality rates. Therefore, increasing the efficacy of chemotherapy has potential to improve patient outcomes. METHODS: Here, we performed whole transcriptome sequencing (both RNA and small RNA-sequencing), coupled with network simulations and patient survival data analyses to build a novel miRNA-mRNA interaction network governing chemoresistance in TNBC. We performed cell proliferation assay, Western blotting, RNAi/miRNA mimic experiments, FN coating, 3D cultures, and ChIP assays to validate the interactions in the network, and their functional roles in chemoresistance. We developed xenograft models to test the therapeutic potential of the identified key miRNA/proteins in potentiating chemoresponse in vivo. We also analyzed several patient datasets to evaluate the clinical relevance of our findings. RESULTS: We identified fibronectin (FN1) as a central chemoresistance driver gene. Overexpressing miR-326 reversed FN1-driven chemoresistance by targeting FN1 receptor, ITGA5. miR-326 was downregulated by increased hypoxia/HIF1A and ECM stiffness in chemoresistant tumors, leading to upregulation of ITGA5 and activation of the downstream FAK/Src signaling pathways. Overexpression of miR-326 or inhibition of ITGA5 overcame FN1-driven chemotherapy resistance in vitro by inhibiting FAK/Src pathway and potentiated the efficacy of chemotherapy in vivo. Importantly, lower expression of miR-326 or higher levels of predicted miR-326 target genes was significantly associated with worse overall survival in chemotherapy-treated TNBC patients. CONCLUSION: FN1 is central in chemoresistance. In chemoresistant tumors, hypoxia and resulting ECM stiffness repress the expression of the tumor suppressor miRNA, miR-326. Hence, re-expression of miR-326 or inhibition of its target ITGA5 reverses FN1-driven chemoresistance making them attractive therapeutic approaches to enhance chemotherapy response in TNBCs.

A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions.

Eukaryotic translation initiates upon recruitment of the EIF2-GTP·Met-tRNAi ternary complex (TC) to the ribosomes. EIF2 (α, ß, γ subunits) is a GTPase. The GDP to GTP exchange within EIF2 is facilitated by the guanine nucleotide exchange factor EIF2B (α-ε subunits). During stress-induced conditions, phosphorylation of the α-subunit of EIF2 turns EIF2 into an inhibitor of EIF2B. In turn, inhibition of EIF2B decreases TC formation and triggers the internal stress response (ISR), which determines the cell fate. Deregulated ISR has been linked to neurodegenerative disorders and cancer, positioning EIF2B as a promising therapeutic target. Hence, a better understanding of the mechanisms/factors that regulate EIF2B activity is required. Here, combining transcript and protein level analyses, we describe an intronically polyadenylated (IPA) transcript of EIF2B's γ-subunit. We show that the IPA mRNA isoform is translated into a C-terminus truncated protein. Using structural modeling, we predict that the truncated EIF2Bγ protein has unfavorable interactions with EIF2γ, leading to a potential decrease in the stability of the nonproductive EIF2:EIF2B complex. While we discovered and confirmed the IPA mRNA isoform in breast cancer cells, the expression of this isoform is not cancer-specific and is widely present in normal tissues. Overall, our data show that a truncated EIF2Bγ protein co-exists with the canonical protein and is an additional player to regulate the equilibrium between productive and nonproductive states of the EIF2:EIF2B complex. These results may have implications in stress-induced translation control in normal and disease states. Our combinatorial approach demonstrates the need to study noncanonical mRNA and protein isoforms to understand protein interactions and intricate molecular mechanisms.

Identification of an mRNA isoform switch for HNRNPA1 in breast cancers.

Roles of HNRNPA1 are beginning to emerge in cancers; however, mechanisms causing deregulation of HNRNPA1 function remain elusive. Here, we describe an isoform switch between the 3'-UTR isoforms of HNRNPA1 in breast cancers. We show that the dominantly expressed isoform in mammary tissue has a short half-life. In breast cancers, this isoform is downregulated in favor of a stable isoform. The stable isoform is expressed more in breast cancers, and more HNRNPA1 protein is synthesized from this isoform. High HNRNPA1 protein levels correlate with poor survival in patients. In support of this, silencing of HNRNPA1 causes a reversal in neoplastic phenotypes, including proliferation, clonogenic potential, migration, and invasion. In addition, silencing of HNRNPA1 results in the downregulation of microRNAs that map to intragenic regions. Among these miRNAs, miR-21 is known for its transcriptional upregulation in breast and numerous other cancers. Altogether, the cancer-specific isoform switch we describe here for HNRNPA1 emphasizes the need to study gene expression at the isoform level in cancers to identify novel cases of oncogene activation.

A prelude to the proximity interaction mapping of CXXC5.

CXXC5 is a member of the zinc-finger CXXC family proteins that interact with unmodified CpG dinucleotides through a conserved ZF-CXXC domain. CXXC5 is involved in the modulation of gene expressions that lead to alterations in diverse cellular events. However, the underlying mechanism of CXXC5-modulated gene expressions remains unclear. Proteins perform their functions in a network of proteins whose identities and amounts change spatiotemporally in response to various stimuli in a lineage-specific manner. Since CXXC5 lacks an intrinsic transcription regulatory function or enzymatic activity but is a DNA binder, CXXC5 by interacting with proteins could act as a scaffold to establish a chromatin state restrictive or permissive for transcription. To initially address this, we utilized the proximity-dependent biotinylation approach. Proximity interaction partners of CXXC5 include DNA and chromatin modifiers, transcription factors/co-regulators, and RNA processors. Of these, CXXC5 through its CXXC domain interacted with EMD, MAZ, and MeCP2. Furthermore, an interplay between CXXC5 and MeCP2 was critical for a subset of CXXC5 target gene expressions. It appears that CXXC5 may act as a nucleation factor in modulating gene expressions. Providing a prelude for CXXC5 actions, our results could also contribute to a better understanding of CXXC5-mediated cellular processes in physiology and pathophysiology.

OPCAB surgery with an alternative retraction method: a single-centre experience.

BACKGROUND: The off-pump coronary artery bypass (OPCAB) technique, which is used in order to avoid the side effects of cardiopulmonary bypass, is often questioned in terms of its efficacy and safety. Also, in this technique, surgeon experience plays a very important role. In this study, we share the results of our 606 OPCAB cases with an alternative retraction technique. METHODS: This study was a retrospective analysis of OPCAB operations performed between January 2014 and December 2018. Patients were evaluated and operated on by a surgical team led by an experienced OPCAB surgeon with over 200 prior OPCAB surgeries. RESULTS: The study included 606 OPCAB cases, and 21.8% (132) were female and 78.2% (474) were male. Our mortality rate was 1.7% (n = 10) and only two patients suffered a cerebrovascular incident. A statistically significant difference was found between pre-operative and six-month postoperative left ventricular ejection fraction values (p < 0.01). CONCLUSION: The OPCAB technique can be performed with similar results to on-pump surgery when conducted by an experienced surgeon, as in our study.

A New Arterial Cannulation Technique: Arterial Cannulation through Aortic Anastomosis ("Kaplan" Technique).

We performed Bentall procedure on a 65-year-old male patient. Cardiopulmonary bypass was initiated via cannulation of the aneurysmatic segment of the aorta. Distal anastomosis was performed with the open technique under deep hypothermic circulatory arrest at 18°C. We performed arterial recannulation through the anastomosis with a new technique, and cardiopulmonary bypass was reestablished. Cardiopulmonary bypass was terminated after rewarming and de-airing phases, and decannulation was performed without any problems. By this technique, the patient had no additional incisions for arterial cannulation, and there were no additional cannulation sutures left on the patient's arterial tree or the valved conduit.

Open Heart Surgery at Patient's Own Temperature Without Active Cooling.

BACKGROUND: Hypothermia is a method of myocardial protection in cardiac surgery. This protection occurs by decreasing the metabolic demands, however, it creates susceptibility to various problems. In this study, we investigated patients operated on under normothermia (at the patient's own temperature) and hypothermia for postoperative differences. METHODS: The study was conducted between June 2015 and September 2016 with 167 patients. The patients were divided into two groups in accordance with our routine clinical practice: the normothermic group (native temperature goup; intraoperative body temperature ≥ 34°C), and the hypothermic group intraoperative body temperature  < 34°C - ≥ 28°C). Preoperative and postoperative data of patients were recorded and the two groups were compared. RESULTS: There was no significant difference between the two groups in terms of cross clamp time, cardiopulmonary bypass time, awakening and extubation times, intensive care unit and hospital stay, drainage, mean serum lactate levels, arrhytmia, all causes infection, renal insufficiency, neurologic complications, myocardial infarction, or mortality (P > .05). Inotrope and transfusion requirements were found to be statistically significantly lower in the normothermic group than the hypothermic group (P < .05). CONCLUSION: Although hypothermia is commonly used in cardiac surgery, it has harmful effects. We believe that cardiac surgery can safely be performed at a patient's own temperature without active cooling to avoid these dangers.

An aortic valve papillary fibroelastoma: A case report.

Papillary fibroelastomas are rare tumors of the heart, mostly involving the valves. They can be asymptomatic and diagnosed incidentally or they can cause life-threatening clinic scenarios including cerebrovascular accidents, coronary arterial occlusions, or peripheral embolisms. Papillary fibroelastomas can be easily excised surgically using valve sparing techniques with low complication rates and without recurrence. In this report, we present a case of papillary fibroelastoma which was found incidentally before coronary artery bypass grafting operation and successful removal of the lesion with a valve sparing approach.

Open Cardiac Surgery without Blood and Blood Products Transplantation.

BACKGROUND: Blood transfusions are the most common type of tissue and organ transplantation. Perioperative and postoperative transfusions may cause morbidity and mortality and transfusion should based on only hematocrit values but also on hemodynamic and clinical parameters of the patient, which cannot be ignored. METHODS: A prospective study was conducted between January 2015 and October 2016 with adult patients undergoing elective open heart surgery. In these patients, a protocol was established, and patients were divided into two groups as transfusion (-) and transfusion (+). In the first 24 hours in the intensive care unit, patients' drainage, 24-hours urine output, awakening and extubation times, and lactate and bilirubin levels in arterial blood gases were recorded. Thirty-day mortality and morbidity, and hemodynamic and clinical data were compared between these two groups. RESULTS: We have performed a total of 138 cases; no blood and blood products were transfused in 71% (n = 98), and in 29.0% (n = 40) blood and blood products were transfused. Thirty-day mortality and morbidity (arrhythmia, infectious and pulmonary morbidity, myocardial infarction, cerebrovascular accident, renal dysfunction, sternal revision) were compared between these two groups and no statistically significant difference was observed. Patients' awakening, extubation time, cardiopulmonary bypass period, cross-clamp time, and days in intensive care unit and hospital were compared, and there was no statistically significant difference between the two groups. Conclusion: In this study, we conclude that open heart surgery without blood transfusion may be accomplished with decent peri/postoperative management. The patients who did not receive any blood or blood products were not compromised clinically or hemodynamically. No extra morbidity and mortality were seen in the non-transfusion group. Transfusion decision was based on clinical and hemodynamic parameters such as persistent hypotension or tachycardia, hyperlactatemia, low urine output, and anemic symptoms.

Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer.

Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. Therefore, we propose a pipeline to uncover patterns of alternative polyadenylation (APA), a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we analyzed expression data for 1045 cancer patients and found a significant shift in usage of poly(A) signals in common tumor types (breast, colon, lung, prostate, gastric, and ovarian) compared to normal tissues. Using machine-learning techniques, we further defined specific subsets of APA events to efficiently classify cancer types. Furthermore, APA patterns were associated with altered protein levels in patients, revealed by antibody-based profiling data, suggesting functional significance. Overall, our study offers a computational approach for use of APA in novel gene discovery and classification in common tumor types, with important implications in basic research, biomarker discovery, and precision medicine approaches.

Stent Embolism after Coronary Angiography: Case Report.

Endovascular interventions are widely performed of late; complications including stent embolism of arteries and veins, dislocation, or malposition of medical devices are frequently seen. Peripheral stent embolisms are generally asymptomatic, but when they cause acute ischemia or severe symptoms like claudication they must be removed. Stents can be removed not only with surgical techniques but also with endovascular maneuvers. In this case report, we state that in symptomatic peripheral arterial embolization cases, surgical intervention is the first choice for treatment due to the complexity and high risk of complications when using endovascular maneuvers.

Alternative Polyadenylation: Another Foe in Cancer.

Advancements in sequencing and transcriptome analysis methods have led to seminal discoveries that have begun to unravel the complexity of cancer. These studies are paving the way toward the development of improved diagnostics, prognostic predictions, and targeted treatment options. However, it is clear that pieces of the cancer puzzle are still missing. In an effort to have a more comprehensive understanding of the development and progression of cancer, we have come to appreciate the value of the noncoding regions of our genomes, partly due to the discovery of miRNAs and their significance in gene regulation. Interestingly, the miRNA-mRNA interactions are not solely dependent on variations in miRNA levels. Instead, the majority of genes harbor multiple polyadenylation signals on their 3' UTRs (untranslated regions) that can be differentially selected on the basis of the physiologic state of cells, resulting in alternative 3' UTR isoforms. Deregulation of alternative polyadenylation (APA) has increasing interest in cancer research, because APA generates mRNA 3' UTR isoforms with potentially different stabilities, subcellular localizations, translation efficiencies, and functions. This review focuses on the link between APA and cancer and discusses the mechanisms as well as the tools available for investigating APA events in cancer. Overall, detection of deregulated APA-generated isoforms in cancer may implicate some proto-oncogene activation cases of unknown causes and may help the discovery of novel cases; thus, contributing to a better understanding of molecular mechanisms of cancer. Mol Cancer Res; 14(6); 507-17. ©2016 AACR.

3'UTR shortening and EGF signaling: implications for breast cancer.

Alternative polyadenylation (APA) plays a role in gene expression regulation generally by shortening of 3'UTRs (untranslated regions) upon proliferative signals and relieving microRNA-mediated repression. Owing to high proliferative indices of triple negative breast cancers (TNBCs), we hypothesized APA to cause 3'UTR length changes in this aggressive subgroup of breast cancers. Our probe-based meta-analysis approach identified 3'UTR length alterations where the significant majority was shortening events (∼70%, 113 of 165) of mostly proliferation-related transcripts in 520 TNBC patients compared with controls. Representative shortening events were further investigated for their microRNA binding potentials by computational predictions and dual-luciferase assay. In silico-predicted 3'UTR shortening events were experimentally confirmed in patient and cell line samples. To begin addressing the underlying mechanisms, we found CSTF2 (cleavage stimulation factor 2), a major regulator of 3'UTR shortening to be up-regulated in response to epidermal growth factor (EGF). EGF treatment also resulted with further shortening of the 3'UTRs. To investigate the contribution of CSTF2 and 3'UTR length alterations to the proliferative phenotype, we showed pharmacological inhibition of the EGF pathway to lead to a reduction in CSTF2 levels. Accordingly, RNAi-induced silencing of CSTF2 decreased the proliferative rate of cancer cells. Therefore, our computational and experimental approach revealed a pattern of 3'UTR length changes in TNBC patients and a potential link between APA and EGF signaling. Overall, detection of 3'UTR length alterations of various genes may help the discovery of new cancer-related genes, which may have been overlooked in conventional microarray gene expression analyses.

Open distal anastomosis technique for ascending aortic aneurysm repair without cerebral perfusion.

BACKGROUND: This study aimed to report the outcomes of patients who underwent proximal thoracic aortic aneurysm surgery with open distal anastomosis technique but without cerebral perfusion, instead under deep hypothermic circulatory arrest. METHODS: Thirty patients (21 male, 9 female) who underwent ascending aortic aneurysm repair with open distal anastomosis technique were included. The average age was 60.2±11.7 years. Operations were performed under deep hypothermic circulatory arrest and the cannulation for cardiopulmonary bypass was first done over the aneurysmatic segment and then moved over the graft. Intraoperative and early postoperative mortality and morbidity outcomes were reported. RESULTS: Average duration of cardiopulmonary bypass and cross-clamps were 210.8±43 and 154.9±35.4 minutes, respectively. Average duration of total circulatory arrest was 25.2±2.4 minutes. There was one hospital death (3.3%) due to chronic obstructive pulmonary disease at postoperative day 22. No neurological dysfunction was observed during the postoperative period. CONCLUSION: These results demonstrate that open distal anastomosis under less than 30 minutes of deep hypothermic circulatory arrest without antegrade or retrograde cerebral perfusion and cannulation of the aneurysmatic segment is a safe and reliable procedure in patients undergoing proximal thoracic aortic aneurysm surgery.

Identification of novel reference genes based on MeSH categories.

Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds.

Estrogen-induced upregulation and 3'-UTR shortening of CDC6.

3'-Untranslated region (UTR) shortening of mRNAs via alternative polyadenylation (APA) has important ramifications for gene expression. By using proximal APA sites and switching to shorter 3'-UTRs, proliferating cells avoid miRNA-mediated repression. Such APA and 3'-UTR shortening events may explain the basis of some of the proto-oncogene activation cases observed in cancer cells. In this study, we investigated whether 17 ß-estradiol (E2), a potent proliferation signal, induces APA and 3'-UTR shortening to activate proto-oncogenes in estrogen receptor positive (ER+) breast cancers. Our initial probe based screen of independent expression arrays suggested upregulation and 3'-UTR shortening of an essential regulator of DNA replication, CDC6 (cell division cycle 6), upon E2 treatment. We further confirmed the E2- and ER-dependent upregulation and 3'UTR shortening of CDC6, which lead to increased CDC6 protein levels and higher BrdU incorporation. Consequently, miRNA binding predictions and dual luciferase assays suggested that 3'-UTR shortening of CDC6 was a mechanism to avoid 3'-UTR-dependent negative regulations. Hence, we demonstrated CDC6 APA induction by the proliferative effect of E2 in ER+ cells and provided new insights into the complex regulation of APA. E2-induced APA is likely to be an important but previously overlooked mechanism of E2-responsive gene expression.