TOP1 and R-loops facilitate transcriptional DSBs at hypertranscribed cancer driver genes

DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employ several techniques to map DSBs, R-loops, and topoisomerase 1 cleavage complex (TOP1cc) to comprehensively investigate the interplay between transcription, DSBs, topoisomerase 1 (TOP1), and R-loops. Our findings reveal the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops. Remarkably, transcription-associated DSBs at these loci are significantly reduced upon depletion of R-loops and TOP1, uncovering the pivotal roles of TOP1 and R-loops in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development, highlighting the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations.

AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer

Anticancer therapies have been limited by the emergence of mutations and other adaptations. In bacteria, antibiotics activate the SOS response, which mobilizes error-prone factors that allow for continuous replication at the cost of mutagenesis. We investigated whether the treatment of lung cancer with EGFR inhibitors (EGFRi) similarly engages hypermutators. In cycling drug-tolerant persister (DTP) cells and in EGFRi-treated patients presenting residual disease, we observed upregulation of GAS6, whereas ablation of GAS6's receptor, AXL, eradicated resistance. Reciprocally, AXL overexpression enhanced DTP survival and accelerated the emergence of T790M, an EGFR mutation typical to resistant cells. Mechanistically, AXL induces low-fidelity DNA polymerases and activates their organizer, RAD18, by promoting neddylation. Metabolomics uncovered another hypermutator, AXL-driven activation of MYC, and increased purine synthesis that is unbalanced by pyrimidines. Aligning anti-AXL combination treatments with the transition from DTPs to resistant cells cured patient-derived xenografts. Hence, similar to bacteria, tumors tolerate therapy by engaging pharmacologically targetable endogenous mutators.

SIGNIFICANCE

EGFR-mutant lung cancers treated with kinase inhibitors often evolve resistance due to secondary mutations. We report that in similarity to the bacterial SOS response stimulated by antibiotics, endogenous mutators are activated in drug-treated cells, and this heralds tolerance. Blocking the process prevented resistance in xenograft models, which offers new treatment strategies. This article is highlighted in the In This Issue feature, p. 2483.

Programmed DNA Damage and Physiological DSBs: Mapping, Biological Significance and Perturbations in Disease States

DNA double strand breaks (DSBs) are known to be the most toxic and threatening of the various types of breaks that may occur to the DNA. However, growing evidence continuously sheds light on the regulatory roles of programmed DSBs. Emerging studies demonstrate the roles of DSBs in processes such as T and B cell development, meiosis, transcription and replication. A significant recent progress in the last few years has contributed to our advanced knowledge regarding the functions of DSBs is the development of many next generation sequencing (NGS) methods, which have considerably advanced our capabilities. Other studies have focused on the implications of programmed DSBs on chromosomal aberrations and tumorigenesis. This review aims to summarize what is known about DNA damage in its physiological context. In addition, we will examine the advancements of the past several years, which have made an impact on the study of genome landscape and its organization.

Pleiotropic tumor suppressor functions of WWOX antagonize metastasis

Tumor progression and metastasis are the major causes of death among cancer associated mortality. Metastatic cells acquire features of migration and invasion and usually undergo epithelia-mesenchymal transition (EMT). Acquirement of these various hallmarks rely on different cellular pathways, including TGF-β and Wnt signaling. Recently, we reported that WW domain-containing oxidoreductase (WWOX) acts as a tumor suppressor and has anti-metastatic activities involving regulation of several key microRNAs (miRNAs) in triple-negative breast cancer (TNBC). Here, we report that WWOX restoration in highly metastatic MDA-MB435S cancer cells alters mRNA expression profiles; further, WWOX interacts with various proteins to exert its tumor suppressor function. Careful alignment and analysis of gene and miRNA expression in these cells revealed profound changes in cellular pathways mediating adhesion, invasion and motility. We further demonstrate that WWOX, through regulation of miR-146a levels, regulates SMAD3, which is a member of the TGF-β signaling pathway. Moreover, proteomic analysis of WWOX partners revealed regulation of the Wnt-signaling activation through physical interaction with Disheveled. Altogether, these findings underscore a significant role for WWOX in antagonizing metastasis, further highlighting its role and therapeutic potential in suppressing tumor progression.

Mapping the breakome reveals tight regulation on oncogenic super-enhancers

DNA double-strand breaks (DSBs) could be deleterious and lead to age-related diseases, such as cancer. Recent evidence, however, associates DSBs with vital cellular processes. As discussed here, genome-wide mapping of DSBs revealed an unforeseen coupling mechanism between transcription and DNA repair at super-enhancers, as means of hypertranscription of oncogenic drivers.

Phylogeny of the order Phyllachorales (Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci

The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.

The BioGRID interaction database: 2017 update

The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical-protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.

Natural variability in Drosophila larval and pupal NaCl tolerance

The regulation of NaCl is essential for the maintenance of cellular tonicity and functionality, and excessive salt exposure has many adverse effects. The fruit fly, Drosophila melanogaster, is a good osmoregulator and some strains can survive on media with very low or high NaCl content. Previous analyses of mutant alleles have implicated various stress signaling cascades in NaCl sensitivity or tolerance; however, the genes influencing natural variability of NaCl tolerance remain for the most part unknown. Here, we use two approaches to investigate natural variation in D. melanogaster NaCl tolerance. We describe four D. melanogaster lines that were selected for different degrees of NaCl tolerance, and present data on their survival, development, and pupation position when raised on varying NaCl concentrations. After finding evidence for natural variation in salt tolerance, we present the results of Quantitative Trait Loci (QTL) mapping of natural variation in larval and pupal NaCl tolerance, and identify different genomic regions associated with NaCl tolerance during larval and pupal development.

No evidence for loss of hippocampal neurons in non-Alzheimer dementia patients

OBJECTIVE

To use stereological methods for estimating the total number of neurons in hippocampi of non-Alzheimer demented patients.

MATERIAL AND METHODS

Hippocampi from six women with severely impaired memory but without Alzheimer pathology were compared with six mentally intact age-matched female controls. The total number of neurons was estimated in the granule cell layer of the dentate gyrus, the hilus of the dentate gyrus, the pyramidal cell layer of CA3 and CA2, the pyramidal cell layer of CA1 and the cellular layer of subiculum using the optical fractionator.

RESULTS

The total neuron number was the same in the dementia cases, 22.4 x 106, compared with 22.7 x 106 in the controls (P = 0.85). No region-specific group differences or side difference were found. Two cases without clinical signs of dementia but with abundant plaques and tangles in hippocampus and neocortex had total neuron numbers within normal limits.

CONCLUSION

Our results indicate that severely impaired memory can occur in the presence of intact numbers of hippocampal neurons in non-Alzheimer dementia and that nerve cell loss in the hippocampus might be characteristic for Alzheimer's disease, and perhaps other forms of primary cortical dementia.

Tiaprofenic acid-induced cystitis--three cases and a literature review

Tiaprofenic acid is a non-steroidal anti-inflammatory drug that may cause severe non-bacterial cystitis. Three cases are described and the literature is reviewed.

[Toxoplasma encephalitis with atypical manifestation and normal CT]

A case of cerebral toxoplasmosis in a HIV-positive man with unusual clinical manifestations and a normal computed tomographic (CT) scanning is presented. Even though most patients with cerebral toxoplasmosis have focal neurological deficits on physical examination, the patients can also present with more diffuse symptoms. Neither the lack of antitoxoplasma antibodies nor normal findings at CT scanning exclude the diagnosis of toxoplasma encephalitis. The sensitivity is higher with magnetic resonance than with CT scanning. We present a case story that demonstrate how delusive cerebral toxoplasmosis can be in HIV positive patients. It is recommended that the possibility of cerebral toxoplasmosis be considered in every HIV-positive patient with neurological symptoms and empirical therapy be instituted on wide indications.

Six billion neurons lost in AIDS. A stereological study of the neocortex

Human immunodeficiency virus type 1 (HIV1) is neurotropic. One of the morphological changes that is seen in patients with acquired immunodeficiency syndrome (AIDS) is cerebral atrophy affecting various structures including the neocortex. The cause of atrophy is not known. The total number of neocortical neurons was estimated in formalin fixed brains of 12 males with AIDS and 12 male controls matched for age and height. The mean number of neocortical neurons was 16.0 x 10(9) (coefficient of variation = 0.11) in the AIDS patients compared with 21.9 x 10(9) (coefficient of variation = 0.22) in the controls, a difference of approximately six billion (p < 0.005, 2-tailed). The global neuronal loss was 37%, and affected all four neocortical lobes. Ten patients did not have a history of central nervous system symptoms; two patients had a history of dementia. The number of neurons in the AIDS cases was not associated with dementia. AIDS is the first disease in which a global loss of neocortical neurons has been demonstrated using unbiased stereological methods. The loss of more than one third of the neurons may partly explain the cortical atrophy. Focal neuron loss has been reported by several authors, but none have been based on unbiased methods. In this group of AIDS patients the severe loss of neurons did not correspond to neurological deficits.

Cerebral atrophy in AIDS: a stereological study

Stereological estimates of mean volumes, surface areas, and cortical thicknesses were obtained on formalin-fixed brains from 19 men with AIDS and 19 controls. Volumes of neocortex, white matter, central brain nuclei, ventricles and archicortex were estimated using point counting and Cavalieri's unbiased principle for volume estimation. In AIDS, the mean volume of neocortex was reduced by 11%, and that of the central brain nuclei by 18%. Mean ventricular volume was increased by 55%. Mean neocortical thickness was reduced by 12%. The mean volume of white matter was reduced by 13%. The findings in 6 clinically demented AIDS patients were not statistically different from the rest of the group.

A randomized trial of cefepime (BMY-28142) and ceftazidime for the treatment of pneumonia

Cefepime is a new cephalosporin with a broad antimicrobial spectrum that includes Staphylococcus aureus and Pseudomonas aeruginosa. To study the efficacy and safety of cefepime for treatment of pneumonia, 65 patients were randomized to therapy with either cefepime or ceftazidime at a two to one ratio. Of the 57 evaluable patients, 89% of the cefepime patients and 84% of the ceftazidime patients were cured clinically or improved. Haemophilus spp., Streptococcus pneumoniae, and Neisseria spp. were common pathogens. Bacteriological cure was achieved in 31 (91%) of cefepime patients and 17 (100%) ceftazidime patients. Adverse clinical and laboratory reactions possibly due to study drug occurred in 9 (21%) cefepime patients and in 1 (5%) ceftazidime patient. Most reactions were mild and resolved with discontinuation of study drug. In this study, cefepime appeared as effective as ceftazidime for the treatment of pneumonia.

Juvenile ceroid-lipofuscinosis and calcifications of the CNS

The post-mortem brains and spinal cords of 20 juvenile ceroid-lipofuscinosis (JC-L) cases from 1973 to 1987 were investigated. Clinical course of the disease was characterized by impaired vision from the age of 5-8 years, progressive dementia, seizures, somatic retardation, and early death (16-29 years of age). Microscopy showed classic intracytoplasmic autofluorescent lipopigment in the nerve cells throughout the CNS and viscera. Immunoperoxidase staining for glial fibrillary acidic protein (GFAP) showed marked gliosis with enlarged reactive astrocytes mainly in the superficial layers of the cerebral cortex. Calcifications of the nervous system principally along the outer and inner brain surfaces were demonstrated by X-ray, macroscopic examination and microscopy. We suggest that the calcifications are secondary to a suspected generalized metabolic error.

Resolution of acute renal failure in toxoplasmic encephalitis despite continuance of sulfadiazine

A patient with AIDS and toxoplasmic encephalitis treated with pyrimethamine and sulfadiazine became hypovolemic and developed acute renal failure. Diagnostic sulfadiazine crystals were abundant in the urine, and ultrasound examination demonstrated sludge and stones, presumably due to sulfadiazine. Renal failure resolved rapidly with hydration and administration of alkali, despite continued administration of sulfadiazine. The relatively old literature concerning crystalluria and renal failure due to sulfonamides is reviewed briefly, since complications due to use of poorly soluble sulfonamides probably will become more widespread as toxoplasmic encephalitis becomes more prevalent.

Open trial of cefepime (BMY 28142) for infections in hospitalized patients

The safety and efficacy of cefepime, a new broad-spectrum, semisynthetic parenteral cephem antibiotic, were evaluated in an open trial at a single hospital. Seventy patients were treated with cefepime: 44 had lower respiratory tract infections, 4 had urinary tract infections, and 22 had skin or soft tissue infections. Of 65 clinically evaluable patients, 64 (98%) had satisfactory responses. No mortality or superinfections occurred. Of 57 respiratory and urinary tract pathogens, 54 (95%) were eradicated and 3 (5%) persisted after therapy. Five bacteremias (two with Streptococcus pneumoniae and one each with Staphylococcus aureus, Proteus mirabilis, and a coagulase-negative staphylococcus) were eradicated. MICs ranged from 1 to 8 micrograms/ml for 13 S. aureus and 9 Pseudomonas aeruginosa isolates and were less than or equal to 0.125 micrograms/ml for 10 streptococcal isolates. Adverse effects occurred in two patients: transient diarrhea and Clostridium difficile toxin in the stool in one patient and loose bowel movements and increased transaminases in the other patient. Cefepime appeared to be well tolerated in humans and was effective against a wide range of isolates, including S. aureus and P. aeruginosa.

Current recommendations and future prospects in the treatment of toxoplasmosis

Toxoplasma infection is highly prevalent throughout the world and causes disease in diverse populations. Effective treatment regimens are available for each clinical entity of toxoplasma, but problems of incomplete clinical efficacy, drug potency, drug safety, and length of treatment remain. No well-controlled clinical trials in humans have been performed to evaluate the efficacy and safety of treatment. Primary treatment of toxoplasmosis is with the synergistic combination of pyrimethamine and sulphonamide. This is considered the treatment of choice for severe disease, disease in immunocompromised patients, and congenital toxoplasmosis. Spiramycin, a macrolide antibiotic, is frequently used alone or alternately with pyrimethamine and sulphonamide for pregnant women with the acute acquired infection to prevent congenital toxoplasmosis. Clindamycin is used frequently to treat acute flares of toxoplasmic chorioretinitis and as second-line therapy for toxoplasmic encephalitis in patients with the acquired immunodeficiency syndrome (AIDS). Inadequacies in the treatment of toxoplasmosis in immunosuppressed patients, exemplified by experience with AIDS patients, should provide the impetus for well-designed trials to find and evaluate more potent and better-tolerated agents. Classes of new drugs that have been investigated and show some promise include: (a) macrolides (roxithromycin, azithromycin); (b) folic acid antagonists (piritrexim and trimetrexate), and (c) purine analogues (arprinocid). Immunomodulators have attracted interest, and interferon-gamma alone and in combination with roxithromycin is effective in murine models. Interleukin-2 is also effective in the murine model.

Morphology of tracheal scar after resection with CO2-laser and high-frequency cutting loop. A study in normal pigs

In 6 pigs a bronchoscopical resection of the tracheal mucosa was performed using CO2-laser on one side, and an electric high-frequency cutting loop (ECL) on the other. The pigs were sacrificed 3 months later. On macroscopic examination the tracheal mucosa appeared almost normal on the laser-resected side, while severe deformation was seen after ECL treatment. Microscopically the respiratory epithelium had regenerated irrespective of the instrument used. After laser resection the subepithelial tissue had a normal width and consisted of collagen fibrils with few vessels and sparse fragmented elastic tissue. The cartilage showed necrosis and pericellular fibrosis. The scar tissue after ECL was a broad cellular and richly vascularized connective tissue. The content of elastic fibres was markedly greater than after laser resection. The cartilage showed small irregular necroses lined by pyknotic nuclei. In neither case had the gland regenerated. Both CO2-laser and ECL caused severe (but not identical) damage to the tissue, clearly visible after 3 months. However, the deformation caused by ECL was not seen at the laser-resected sites, which makes the laser technique seem preferable--where economy permits.

Carumonam versus ceftazidime for urinary tract infections

Carumonam is a new monobactam antibiotic with potent activity against gram-negative aerobes. To study the efficacy and safety of carumonam for treatment of complicated and uncomplicated urinary tract infections, 54 patients were randomized to therapy with either carumonam or ceftazidime. Of 42 patients who could be evaluated, 82% of the carumonam-treated patients and 80% of the ceftazidime-treated patients were cured clinically. At 5 to 9 days posttherapy, microbiologic criteria indicated that 13 carumonam-treated patients (48%) and 8 ceftazidime-treated patients (53%) were cured. Patients with indwelling bladder catheters at the end of therapy had a markedly worse microbiologic outcome than those without catheters. Enterococcus sp. reinfection was common in both groups. Possible adverse clinical and laboratory reactions occurred in six carumonam-treated patients (21%) and four ceftazidime-treated patients (27%). Most reactions occurred at the end of therapy and resolved with discontinuation of the study drug. In this small study, carumonam appeared as safe and as effective as ceftazidime for the treatment of complicated and uncomplicated urinary tract infections.

Lafora's disease and brain calcifications

The brain from a 22-year-old man with progressive myoclonal epilepsy (Lafora's disease) was examined. Besides widespread inclusion bodies in the nerve cells calcifications were seen on the inner and outer surface of the brain. No gliosis was present but the astrocytes were enlarged. They were unrelated to the inclusion bodies, as demonstrated in combined stainings with glial fibrillary acidic protein (GFAP)-PAS or GFAP-Bodian. A transport of an abnormal metabolic product is suggested.

Astrocytes in the prenatal central nervous system. From 5th to 28th week of gestation. An immunohistochemical study on paraffin-embedded material

The CNS from 30 normal fetuses aged 5-28 weeks were studied in GFAP stained paraffin-embedded material. The technique of preparation, autopsy and fixation is described in details. GFAP reacting glial cells developed first in the spinal cord at 7 weeks, and appeared in all regions of CNS during fetal life in a systematic way but with a temporal variation. The supporting and guiding properties of the fibrillary astrocytes are stressed.

Isolation of Gardnerella vaginalis in pure culture from the uterine cavity of patients with irregular bleedings

Hysterectomy was performed in three patients because of persistent irregular vaginal bleeding. Before the operation samples were taken from the cervical os for cultivation of Gardnerella vaginalis, yeasts, viruses, Chlamydia trachomatis, and aerobic and anaerobic bacteria. Immediately after the operation, the uterus was opened under sterile conditions and samples obtained from the isthmus and fundus of the uterine cavity were examined microbiologically. In all three patients G. vaginalis was grown in pure culture from the fundus. Serum antibody titres against G. vaginalis were significantly raised in all three patients, and histology revealed mononuclear cells in the endometrium. The isolation of G. vaginalis from the endometrium of patients with clinical and histological signs of inflammation and with antibodies to G. vaginalis in serum indicates that the organism may play a causative role in endometritis.

Schwartz-Bartter's syndrome and mesencephalic astrocytoma

A case of an astrocytoma arising in the mesencephalon is reported. The patient was first treated at the age of 11 years. He led a normal life for almost 20 years and survived for 25 years in spite of a recurrence 14 years after the initial operation. The last couple of years he developed various neurological disorders and a Schwartz-Bartter's syndrome. The clinical picture is explained by the growth of the tumor along the neuraxis to the hypothalamus.

Laryngeal papillomas: classification and course

Seventy-one cases of laryngeal papillomas have been reviewed. Based on differences in age at presentation, female: male ratio and multiple versus solitary papillomas, the cases were classified into 4 groups: multiple juvenile papillomas, solitary juvenile papillomas, multiple and solitary adult papillomas. The clinical course in the groups is described. The authors do not support the common opinion that juvenile papillomas are influenced by puberty.

Herpes zoster ophthalmicus and the mesencephalic nucleus. A neuropathological study

The ganglion Gasseri and the brainstem were examined in three old patients with herpes zoster without predisposing diseases with special reference to the mesencephalic trigeminal nucleus. The primary lesions in the semilunar ganglion vary with the length of the course. Secondary changes in the brainstem were as expected from pons to the second cervical segment of the cord. Besides, we observed degeneration, inflammation and glial nodules in the mesencephalic trigeminal nucleus in two patients. According to Brodal this nucleus presumably corresponds to the semilunar and spinal ganglia. As herpes zoster virus is prone to attack the sensory nuclei our findings support this hypothesis.

A new vaginal operation for recurrent and large rectocele using dermis transplant

A new operation for large rectocele is described. The operation combines the method of posterior colporrhaphy with the principles of ventral hernia surgery using a submucosal dermis graft to reinforce the vaginal wall. Fifteen postmenopausal women were examined one to four years after treatment for rectocele with this method. All fifteen patients were cured of their symptoms. Only in one case was the anatomical result less perfect. On proper indications this operation is a good alternative to the existing methods of treating rectocele. The method is not difficult to perform for the surgeon familiar with colporrhaphy, and the operation it no more onerous for the patient than is a simple colporhaphy.

Plasminogen activator in vaginal smears during the menstrual cycle

A cytologic staining technique in which the reaction produces an insoluble colored precipitate at the site of trypsin-like proteolysis was applied to human vaginal smears, taken daily over six menstrual cycles. The day of urinary LH surge for each cycle was determined. The enzyme action, namely hydrolysis by plasminogen activator, is confined mainly to intermediate squamous cells. The number of cells stained by the enzyme method reaches a maximum three days prior to the LH surge, whereas the maximum in karyopyknosis occurs close to or at the day of LH surge. The enzyme staining method can thus be used when anticipation of ovulation by about 4 days is needed. No immediate fixation is required prior to the enzyme staining.