The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation.

TIMELESS (TIM) in the fork protection complex acts as a scaffold of the replisome to prevent its uncoupling and ensure efficient DNA replication fork progression. Nevertheless, its underlying basis for coordinating leading and lagging strand synthesis to limit single-stranded DNA (ssDNA) exposure remains elusive. Here, we demonstrate that acute degradation of TIM at ongoing DNA replication forks induces the accumulation of ssDNA gaps stemming from defective Okazaki fragment (OF) processing. Cells devoid of TIM fail to support the poly(ADP-ribosyl)ation necessary for backing up the canonical OF processing mechanism mediated by LIG1 and FEN1. Consequently, recruitment of XRCC1, a known effector of PARP1-dependent single-strand break repair, to post-replicative ssDNA gaps behind replication forks is impaired. Physical disruption of the TIM-PARP1 complex phenocopies the rapid loss of TIM, indicating that the TIM-PARP1 interaction is critical for the activation of this compensatory pathway. Accordingly, combined deficiency of FEN1 and the TIM-PARP1 interaction leads to synergistic DNA damage and cytotoxicity. We propose that TIM is essential for the engagement of PARP1 to the replisome to coordinate lagging strand synthesis with replication fork progression. Our study identifies TIM as a synthetic lethal target of OF processing enzymes that can be exploited for cancer therapy.

Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection.

Poly(ADP-ribosyl)ation (PARylation), catalyzed mainly by poly(ADP-ribose) polymerase (PARP)1, is a key posttranslational modification involved in DNA replication and repair. Here, we report that TIMELESS (TIM), an essential scaffold of the replisome, is PARylated, which is linked to its proteolysis. TIM PARylation requires recognition of auto-modified PARP1 via two poly(ADP-ribose)-binding motifs, which primes TIM for proteasome-dependent degradation. Cells expressing the PARylation-refractory TIM mutant or under PARP inhibition accumulate TIM at DNA replication forks, causing replication stress and hyper-resection of stalled forks. Mechanistically, aberrant engagement of TIM with the replicative helicase impedes RAD51 loading and protection of reversed forks. Accordingly, defective TIM degradation hypersensitizes BRCA2-deficient cells to replication damage. Our study defines TIM as a substrate of PARP1 and elucidates how the control of replisome remodeling by PARylation is linked to stalled fork protection. Therefore, we propose a mechanism of PARP inhibition that impinges on the DNA replication fork instability caused by defective TIM turnover.

The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork.

DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.

Replisome dysfunction upon inducible TIMELESS degradation synergizes with ATR inhibition to trigger replication catastrophe.

The structure of DNA replication forks is preserved by TIMELESS (TIM) in the fork protection complex (FPC) to support seamless fork progression. While the scaffolding role of the FPC to couple the replisome activity is much appreciated, the detailed mechanism whereby inherent replication fork damage is sensed and counteracted during DNA replication remains largely elusive. Here, we implemented an auxin-based degron system that rapidly triggers inducible proteolysis of TIM as a source of endogenous DNA replication stress and replisome dysfunction to dissect the signaling events that unfold at stalled forks. We demonstrate that acute TIM degradation activates the ATR-CHK1 checkpoint, whose inhibition culminates in replication catastrophe by single-stranded DNA accumulation and RPA exhaustion. Mechanistically, unrestrained replisome uncoupling, excessive origin firing, and aberrant reversed fork processing account for the synergistic fork instability. Simultaneous TIM loss and ATR inactivation triggers DNA-PK-dependent CHK1 activation, which is unexpectedly necessary for promoting fork breakage by MRE11 and catastrophic cell death. We propose that acute replisome dysfunction results in a hyper-dependency on ATR to activate local and global fork stabilization mechanisms to counteract irreversible fork collapse. Our study identifies TIM as a point of replication vulnerability in cancer that can be exploited with ATR inhibitors.

The TIMELESS effort for timely DNA replication and protection.

Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.

A Machine Learning-Based Water Potability Prediction Model by Using Synthetic Minority Oversampling Technique and Explainable AI.

During the last few decades, the quality of water has deteriorated significantly due to pollution and many other issues. As a consequence of this, there is a need for a model that can make accurate projections about water quality. This work shows the comparative analysis of different machine learning approaches like Support Vector Machine (SVM), Decision Tree (DT), Random Forest, Gradient Boost, and Ada Boost, used for the water quality classification. The model is trained on the Water Quality Index dataset available on Kaggle. Z-score is used to normalize the dataset before beginning the training process for the model. Because the given dataset is unbalanced, Synthetic Minority Oversampling Technique (SMOTE) is used to balance the dataset. Experiments results depict that Random Forest and Gradient Boost give the highest accuracy of 81%. One of the major issues with the machine learning model is lack of transparency which makes it impossible to evaluate the results of the model. To address this issue, explainable AI (XAI) is used which assists us in determining which features are the most important. Within the context of this investigation, Local Interpretable Model-agnostic Explanations (LIME) is utilized to ascertain the significance of the features.

Hepatic Abscess as Early Presentation of Perforated Diverticulitis.

A hepatic abscess is a rare condition which can have multiple etiologies, including biliary disease, intra-abdominal collections (appendicitis, diverticulitis, and inflammatory bowel disease), abdominal surgery, liver transplantation, and liver trauma. The diagnosis is primarily based on imaging findings of ultrasound and computed tomography scan. Management includes antibiotics and percutaneous drainage or surgical drainage of the abscess. Here, we present a case of a 43-year-old Hispanic female who initially presented with left lower quadrant and right upper quadrant abdominal pain for 1 week. She was found to have a hepatic abscess and pelvic abscess likely secondary to perforated diverticulum.

Assessing behavior in children aged 12-24 months using the Strengths and Difficulties Questionnaire.

Behavioral and emotional problems in infants and toddlers are common, often persist and put children at risk of later mental health problems. Reliable, efficient, and sensitive tools are needed to identify young children who may benefit from further assessment and support. The Strengths and Difficulties Questionnaire (SDQ), offers a brief, convenient means of screening for early problems, however, it lacks psychometric validation in infants. The aim of this study was to assess the validity and reliability of the SDQ in children aged 12-24 months. Ninety-three participants, with children aged 12-24 months, completed the SDQ and Child Behavior Checklist (CBCL) online. Concurrent validity of the SDQ was assessed through comparison with the CBCL. The results demonstrated that key subscales of the SDQ and CBCL were significantly correlated (r range= -.19 to -.57). Key SDQ subscales showed moderate reliability (Cronbach's alpha range = .38-.79, mean inter-item correlation range = .06-.43). The SDQ shows promising reliability and validity as a measure for rating the behavior of 12-24-months-old children, particularly for externalizing symptoms. Further research is needed to assess its predictive utility.

Validating TDP1 as an Inhibition Target for the Development of Chemosensitizers for Camptothecin-Based Chemotherapy Drugs.

Cancer chemotherapy sensitizers hold the key to maximizing the potential of standard anticancer treatments. We have a long-standing interest in developing and validating inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) as chemosensitizers for topoisomerase I poisons such as topotecan. Herein, by using thieno[2,3-b]pyridines, a class of TDP1 inhibitors, we showed that the inhibition of TDP1 can restore sensitivity to topotecan, results that are supported by TDP1 knockout cell experiments using CRISPR/Cas9. However, we also found that the restored sensitivity towards topoisomerase I inhibitors is likely regulated by multiple complementary DNA repair pathways. Our results showed that one of these pathways is likely modulated by PARP1, although it is also possible that other redundant and partially overlapping pathways may be involved in the DNA repair process. Our work thus raises the prospect of targeting multiple DNA repair pathways to increase the sensitivity to topoisomerase I inhibitors.

Pheochromocytoma Presenting as Testicular Pain: An Unusual Case Report.

Pheochromocytoma (PCC) is a rare catecholamine-secreting tumor that arises from chromaffin cells of the adrenal medulla which are derived from the neural crest. This report illustrates a 51-year-old Caucasian male with a history of hypertension diagnosed two years ago who presented to the hospital due to acute onset of right testicular pain of 3-day duration. Laboratory results and imaging revealed a presumptive diagnosis of PCC. The patient had undergone robot-assisted laparoscopic right adrenalectomy 14 days after being diagnosed with PCC due to perioperative management with phenoxybenzamine. The final pathology report revealed a PCC. At follow-up two weeks after discharge, the patient reported complete resolution of his testicular pain.

Gastric Cancer Presenting as Persistent Pneumonia: An Unusual Case Report.

Worldwide, gastric cancer is the fifth most common cancer and the third leading cause of cancer deaths, which carries a poor prognosis as only 28.3% are expected to survive after five years. The incidence varies depending on the geographical locations and dietary patterns. Here, we present a case of a 59-year-old Hispanic male with a 10-month history of recurrent bilateral pneumonia and dysphagia. Diagnostic workup revealed metastatic gastric adenocarcinoma.

Redox potential in human semen: Validation and qualification of the MiOXsys assay.

Seminal oxidative stress (OS) is a major contributing factor to male infertility. Semen analysis cannot identify reactive oxygen species (ROS), which can be measured using a chemiluminescence assay. Measurement of redox potential provides a more comprehensive assessment of OS, although the test has yet to be fully validated. This study aimed to validate the MiOXsys analyser for measuring static oxidation-reduction potential (sORP). Results demonstrated that duplicate measurements must be taken, sensors must be batch tested, and sockets should be regularly changed to avoid inconsistency in measurement. Measurement of sORP using MiOXsys exhibited good reproducibility across different operators (p = 0.469), analysers (p = 0.963) and days (p = 0.942). It is not affected by mechanical agitation (p = 0.522) or snap freezing and thawing (p = 0.823). The stability of sORP over time requires further verification, particularly in samples with high initial sORP. Measurement is temperature sensitive between 2 and 37°C, significantly increasing with increasing temperature (p = 0.0004). MiOXsys is a more stable assay for assessing OS than chemiluminescence methods and permits greater flexibility for sample handling. MiOXsys could be implemented to complement semen analysis as part of routine diagnostic testing for male infertility and may be useful in identifying contributing factors to idiopathic infertility.

Cryptogenic Organizing Pneumonia Secondary to Mycoplasma pneumoniae Infection: A Case Report.

Cryptogenic organizing pneumonia (COP), previously known as bronchiolitis obliterans organizing pneumonia (BOOP), is a serious lung disease that can cause significant and long-term damage to the distal respiratory tract. Here we describe an unusual case in which an adult patient with recent mycoplasma pneumonia developed worsening lower airway disease despite initiation of multiple antibiotic therapies, illustrating the immunological effects related to Mycoplasma infections. It is critical that clinicians learn how to recognize early signs of COP in order to tailor appropriate therapy, reduce morbidity, and improve quality of life.

Comparative Profiling of Four Lignans (Phyllanthin, Hypophyllanthin, Nirtetralin, and Niranthin) in Nine Phyllanthus Species from India Using a Validated Reversed Phase HPLC-PDA Detection Method.

BACKGROUND: Phyllanthus species exhibit a wide range of in vitro and in vivo pharmacological activities; however, little is known about the compounds present in the extracts that are responsible for such actions. OBJECTIVE: Development and validation of a simple reversed phase HPLC-PDA method for profiling of phyllanthin, hypophyllanthin, nirtetralin, and niranthin in extracts of Phyllanthus species was carried out. METHODS: Separation was achieved using an XBridge column® (150 × 4.6 mm, 5.0 µm id) in an isocratic elution mode with mobile phase comprising of a mixture of acetonitrile and water with TFA (0.05%, v/v, pH = 2.15) at ambient temperature with a flow rate of 1 mL/min. RESULTS: Phyllanthin, hypophyllanthin, nirtetralin, and niranthin were eluted at mean retention times of 10.47, 11.10, 13.67, and 14.53 min, respectively. LOD and LOQ for all four analytes were 0.75 and 3.00 µg/mL, respectively. RSDr values for intraday and interday precision for phyllanthin, hypophyllanthin, nirtetralin, and niranthin were 0.38-1.32 and 0.45-1.77%; 0.22-3.69 and 0.24-3.04%, 0.73-2.37 and 0.09-0.31%, and 1.56-2.77 and 0.12-0.68%, respectively. CONCLUSIONS: The developed and validated HPLC-PDA method was applied for identification and quantification of phyllanthin, hypophyllanthin, nirtetralin, and niranthin in extracts of different plant parts of selected Phyllanthus species. The outcome of the present investigation could be useful for selection of best species to promote its commercial cultivation and suitable extraction solvent for preparation of lignan-enriched fractions. This HPLC-PDA method could be useful for quality control of herbal formulations containing plants from Phyllanthus species.

Hyperammonemic Encephalopathy: A Complication of Gastric Bypass Surgery.

Hyperammonemia is a metabolic abnormality characterized by elevated levels of ammonia in the blood. This case report illustrates a 72-year-old Caucasian female with a history of prior gastric bypass surgery done 15 years ago, who was admitted multiple times for acute encephalopathy over the course of a few months. The patient was found to have a gastro-gastric fistula seen on a CT scan of the abdomen, which was the culprit of her acute encephalopathy. The patient underwent fistula closure via esophagogastroduodenoscopy.

Cannabis Butane Hash Oil Dabbing Induced Lung Injury Mimicking Atypical Pneumonia.

"Dabbing" is the inhalation of concentrated marijuana, usually in butane solvent. This case report illustrates a previously healthy 25-year-old caucasian male with a 10-year history of cannabis butane hash oil (BHO) use. The patient presented with dyspnea and cough. The evaluation included a chest x-ray, basic laboratory investigations, computerized tomography angiogram of the chest and echocardiogram. Patient was diagnosed with acute lung injury mimicking atypical pneumonia. He was treated with steroids and had clinically improved and advised to stop dabbing. Further studies are needed to elucidate the full spectrum of the adverse effects of dabbing.

A Case Report of Babesiosis Seen Outside of its Endemic Area and Incubation Period.

Babesia microti is a parasitic alveolate that is usually transmitted by Ixodes scapularis tick, which also transmits Lyme disease. Babesiosis is endemic in the Northeast and Upper Midwestern regions of the United States. This case report illustrates a 29-year-old Hispanic male who presented to a Florida hospital emergency department with complaints of fever, generalized weakness, and flu-like symptoms over a duration of four days. Subsequently, he was diagnosed with babesiosis infection since he had a travel history to Cape Cod, Massachusetts about 10 weeks before presenting to the hospital. He was treated with atovaquone, clindamycin, and azithromycin. The importance of this report is to illustrate that babesiosis may occur outside its endemic area and incubation period.

Chronic stress-induced gut dysfunction exacerbates Parkinson's disease phenotype and pathology in a rotenone-induced mouse model of Parkinson's disease.

Recent evidence provides support for involvement of the microbiota-gut-brain axis in Parkinson's disease (PD) pathogenesis. We propose that a pro-inflammatory intestinal milieu, due to intestinal hyper-permeability and/or microbial dysbiosis, initiates or exacerbates PD pathogenesis. One factor that can cause intestinal hyper-permeability and dysbiosis is chronic stress which has been shown to accelerate neuronal degeneration and motor deficits in Parkinsonism rodent models. We hypothesized that stress-induced intestinal barrier dysfunction and microbial dysbiosis lead to a pro-inflammatory milieu that exacerbates the PD phenotype in the low-dose oral rotenone PD mice model. To test this hypothesis, mice received unpredictable restraint stress (RS) for 12 weeks, and during the last six weeks mice also received a daily administration of low-dose rotenone (10 mg/kg/day) orally. The initial six weeks of RS caused significantly higher urinary cortisol, intestinal hyperpermeability, and decreased abundance of putative "anti-inflammatory" bacteria (Lactobacillus) compared to non-stressed mice. Rotenone alone (i.e., without RS) disrupted the colonic expression of the tight junction protein ZO-1, increased oxidative stress (N-tyrosine), increased myenteric plexus enteric glial cell GFAP expression and increased α-synuclein (α-syn) protein levels in the colon compared to controls. Restraint stress exacerbated these rotenone-induced changes. Specifically, RS potentiated rotenone-induced effects in the colon including: 1) intestinal hyper-permeability, 2) disruption of tight junction proteins (ZO-1, Occludin, Claudin1), 3) oxidative stress (N-tyrosine), 4) inflammation in glial cells (GFAP + enteric glia cells), 5) α-syn, 6) increased relative abundance of fecal Akkermansia (mucin-degrading Gram-negative bacteria), and 7) endotoxemia. In addition, RS promoted a number of rotenone-induced effects in the brain including: 1) reduced number of resting microglia and a higher number of dystrophic/phagocytic microglia as well as (FJ-C+) dying cells in the substantia nigra (SN), 2) increased lipopolysaccharide (LPS) reactivity in the SN, and 3) reduced dopamine (DA) and DA metabolites (DOPAC, HVA) in the striatum compared to control mice. Our findings support a model in which chronic stress-induced, gut-derived, pro-inflammatory milieu exacerbates the PD phenotype via a dysfunctional microbiota-gut-brain axis.

Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy.

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an important DNA repair enzyme in humans, and a current and promising inhibition target for the development of new chemosensitizing agents due to its ability to remove DNA damage caused by topoisomerase 1 (Top1) poisons such as topotecan and irinotecan. Herein, we report our work on the synthesis and characterization of new Tdp1 inhibitors that combine the arylcoumarin (neoflavonoid) and monoterpenoid moieties. Our results showed that they are potent Tdp1 inhibitors with IC50 values in the submicromolar range. In vivo experiments with mice revealed that compound 3ba (IC50 0.62 µM) induced a significant increase in the antitumor effect of topotecan on the Krebs-2 ascites tumor model. Our results further strengthen the argument that Tdp1 is a druggable target with the potential to be developed into a clinically-potent adjunct therapy in conjunction with Top1 poisons.

New Hydrazinothiazole Derivatives of Usnic Acid as Potent Tdp1 Inhibitors.

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a promising therapeutic target in cancer therapy. Combination chemotherapy using Tdp1 inhibitors as a component can potentially improve therapeutic response to many chemotherapeutic regimes. A new set of usnic acid derivatives with hydrazonothiazole pharmacophore moieties were synthesized and evaluated as Tdp1 inhibitors. Most of these compounds were found to be potent inhibitors with IC50 values in the low nanomolar range. The activity of the compounds was verified by binding experiments and supported by molecular modeling. The ability of the most effective inhibitors, used at non-toxic concentrations, to sensitize tumors to the anticancer drug topotecan was also demonstrated. The order of administration of the inhibitor and topotecan on their synergistic effect was studied, suggesting that prior or simultaneous introduction of the inhibitor with topotecan is the most effective.