Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell.

Double strand break (DSB) repair primarily occurs through 3 pathways: non-homologous end-joining (NHEJ), alternative end-joining (Alt-EJ), and homologous recombination (HR). Typical methods to measure pathway usage include integrated cassette reporter assays or visualization of DNA damage induced nuclear foci. It is now well understood that repair of Cas9-induced breaks also involves NHEJ, Alt-EJ, and HR pathways, providing a new format to measure pathway usage. Here, we have developed a simple Cas9-based system with validated repair outcomes that accurately represent each pathway and then converted it to a droplet digital PCR (ddPCR) readout, thus obviating the need for Next Generation Sequencing and bioinformatic analysis with the goal to make Cas9-based system accessible to more laboratories. The assay system has reproduced several important insights. First, absence of the key Alt-EJ factor Pol θ only abrogates ∼50% of total Alt-EJ. Second, single-strand templated repair (SSTR) requires BRCA1 and MRE11 activity, but not BRCA2, establishing that SSTR commonly used in genome editing is not conventional HR. Third, BRCA1 promotes Alt-EJ usage at two-ended DSBs in contrast to BRCA2. This assay can be used in any system, which permits Cas9 delivery and, importantly, allows rapid genotype-to-phenotype correlation in isogenic cell line pairs.

Examining the prevalence of homologous recombination repair defects in ER+ breast cancers.

PURPOSE: Homologous recombination deficiency (HRD) is well characterized in triple-negative breast cancer (TNBC), but its prevalence in the hormone-receptor-positive breast cancer subtypes is not as clearly defined. It is estimated that around 50-60% of TNBC cases are deficient in HR. We sought to identify HRD cases in ER+/Her2- patients using various mutational HRD signatures. METHODS: We abstracted published HRD genomic signatures from the Pan-Cancer Analysis of Whole Genomes (PCAWG) database and compared the prevalence of HRD in ER+/Her2- breast cancer, comparing this to the control of set of triple-negative breast cancers. RESULTS: In 78 patients with ER+/Her2- breast cancer, 13 patients have over a 70% probability of being HRD as measured by HRDetect, while 18 qualify as HRD based on HRD score, with an approximate prevalence of HRD ranging between 14 and 20% of cases. CONCLUSION: Our analyses suggest that 14% of ER+/Her2- patients may be HRD and therefore potentially eligible for treatments with HRD-directed therapies such as platinum agents and PARP inhibitors. As the ER+/Her2- subtype is the most common breast cancer subtype, this group of HRD patients is likely more sizable than that of HRD TNBC patients.

DNA characterization reveals potential operon-unit packaging of extracellular vesicle cargo from a gut bacterial symbiont.

Extracellular vesicles (EVs) are lipid bilayer-bound entities secreted by cells across all domains of life, known to contain a range of components, including protein complexes, RNA, and DNA. Recent studies on microbial extracellular vesicles indicate that these virus-sized nanoparticles, 40-90nm in diameter, readily cross the epithelial barrier and reach systemic circulation, can be detected in tissues throughout the body in mice and that 1mL of plasma from healthy humans contains up to one million bacterial EVs. They have been recently recognized for their biologically functional roles, including modulation of bacterial physiology and host-microbe interactions, hence their gain in the microbiome research community's attention. However, the exact understanding of their functionality is still a subject of active research and debate. Here, we employ long-read DNA sequencing on purified extracellular vesicles from a common mammalian gut symbiont, Parabacteroides goldsteinii, to characterize the genomic component within EV cargos. Our findings challenge the notion of DNA packaging into EVs as a stochastic event. Instead, our data demonstrate that the DNA packaging is non-random. Here, we suggest a novel hypothesis of selective EV-DNA packaging, potentially arranged in operon units, hence providing new insights into our understanding of its genetic makeup and its potential role, underlining the importance of our findings in microbial community dynamics.

High Specificity of HPV Cell-Free DNA Tests in Persons With HIV for the Detection of HPV-Related Cancer.

INTRODUCTION: Persons with HIV (PWH) experience high rates of human papillomavirus (HPV)-associated cancers compared with the general population. Plasma HPV cell-free DNA (cfDNA) tests are sensitive in patients with known HPV-associated cancers. It is not known whether these tests can screen for invasive cancers in populations with high burdens of nonmalignant HPV disease such as PWH. It was not known whether HPV infection and/or noninvasive anal high-grade squamous intraepithelial lesions (HSIL) alone in this population would result in detectable HPV cfDNA, which would result in a high number of false positives if HPV cfDNA is used to screen for invasive cancers. METHODS: We conducted a prospective study of PWH in 2 cohorts: 20 without anal HSIL and 20 with anal HSIL. We tested anal and vaginal swabs for HPV infection, and HPV genotyped the biopsies of anal HSIL. Finally, we performed HPV cfDNA droplet digital polymerase chain reaction to test for HPV16/18/33 from plasma samples. RESULTS: In the combined cohorts, the median age was 56 years, 12.5% were cisgender women, and none had detectable HIV. In total, 84.6% had prevalent anovaginal HPV infection, including 10 participants with HPV16, 13 with HPV18, and 2 with HPV33 infections. Five and 2 participants had HPV16 and HPV33 detected in anal HSIL, respectively. Despite the high prevalence of HPV infection and anal HSIL, no participant had HPV16/18/33 detectable cfDNA by droplet digital polymerase chain reaction. CONCLUSIONS: These results provide a strong rationale for investigating the use of HPV cfDNA in a screening setting for suspected HPV-related invasive cancers in PWH.

Effect of interproximal home oral hygiene on clinical parameters and inflammatory biomarkers in patients receiving periodontal maintenance.

BACKGROUND: The purpose of this 6-week, single-blinded, randomized clinical trial was to determine if the use of an interproximal brush, with or without a tracking device, is more effective than an oral irrigator in improving interproximal probing depth (PD), clinical attachment level (CAL), plaque index (PI), gingival index (GI), bleeding on probing (BOP), and inflammatory markers. METHODS: Seventy-six patients with Stages III-IV, Grade B periodontitis and a 5-7 mm posterior interproximal PD with BOP were randomized: (1) interproximal brush alone (IB; n = 26), (2) interproximal brush with tracking device (TD; n = 23), (3) oral irrigator (OI; n = 27). Participants used devices once daily for 6 weeks. Clinical measurements (PD, CAL, PI, BOP, GI) and gingival crevicular fluid (GCF) samples were collected at baseline and 6 weeks. RESULTS: All groups showed a significant reduction in PD and CAL (≥1.1 mm, p < 0.0001) and improvement in BOP (≥56%, p < 0.0001) and GI (≥82%, p < 0.001) at the experimental site with no differences among groups. The IB and IB+TD groups showed a significant reduction in PI (≥0.9, p ≤ 0.01). Interleukin (IL)-1ß was reduced in all groups (p = 0.006), but IB+TB more than OI (p ≤ 0.05). IL-10 was reduced among all groups (p = 0.01), while interferon-gamma significantly increased (p = 0.01) in all groups. CONCLUSIONS: IB and OI improved clinical parameters of PD and CAL and reduced inflammatory markers (BOP, GI, GCF IL-1ß). IB had better interproximal plaque reduction. Tracking did not significantly improve clinical parameters compared with the IB and OI groups, suggesting future modifications are needed.

Novel Escherichia coli-Infecting Bacteriophages Isolated from Uganda That Target Human Clinical Isolates.

Background: The antimicrobial resistance catastrophe is a growing global health threat and predicted to be worse in developing countries. Phages for Global Health (PGH) is training scientists in these regions to isolate relevant therapeutic phages for pathogenic bacteria within their locality, and thus contributing to making phage technology universally available. Materials and Methods: During the inaugural PGH workshop in East Africa, samples from Ugandan municipal sewage facilities were collected and two novel Escherichia coli lytic phages were isolated and characterized. Results: The phages, UP19 (capsid diameter ∼100 nm, contractile tail ∼120/20 nm) and UP30 (capsid diameter ∼70 nm, noncontractile tail of ∼170/20 nm), lysed ∼82% and ∼36% of the 11 clinical isolates examined, respectively. The genomes of UP19 (171.402 kb, 282 CDS) and UP30 (49.834 kb, 75 CDS) closely match the genera Dhakavirus and Tunavirus, respectively. Conclusion: The phages isolated have therapeutic potential for further development against E. coli infections.

Templated Insertions Are Associated Specifically with BRCA2 Deficiency and Overall Survival in Advanced Ovarian Cancer.

Cancer cells defective in homologous recombination (HR) are responsive to DNA-crosslinking chemotherapies, PARP inhibitors, and inhibitors of polymerase theta (Pol θ), a key mediator of the backup pathway alternative end-joining. Such cancers include those with pathogenic biallelic alterations in core HR genes and another cohort of cases that exhibit sensitivity to the same agents and harbor genomic hallmarks of HR deficiency (HRD). These HRD signatures include a single-base substitution pattern, large rearrangements, characteristic tandem duplications, and small deletions. Here, we used what is now known about the backup pathway alternative end-joining (Alt-EJ) through the key factor Pol θ to design and test novel signatures of polymerase theta-mediated (TMEJ) repair. We generated two novel signatures; a signature composed of small deletions with microhomology and another consisting of small, templated insertions (TINS). We find that TINS consistent with TMEJ repair are highly specific to tumors with pathogenic biallelic mutations in BRCA2 and that high TINS genomic signature content in advanced ovarian cancers associate with overall survival following treatment with platinum agents. In addition, the combination of TINS with other HRD metrics significantly improves the association of platinum sensitivity with survival compared with current state-of-the-art signatures. IMPLICATIONS: Small, templated insertions indicative of theta-mediated end-joining likely can be used in conjunction with other HRD mutational signatures as a prognostic tool for patient response to therapies targeting HR deficiency.

Inhibition of the RNA Regulator HuR by SRI-42127 Attenuates Neuropathic Pain After Nerve Injury Through Suppression of Neuroinflammatory Responses.

Microglial activation with the production of pro-inflammatory mediators such as IL-6, TNF-α, and IL-1ß, is a major driver of neuropathic pain (NP) following peripheral nerve injury. We have previously shown that the RNA binding protein, HuR, is a positive node of regulation for many of these inflammatory mediators in glia and that its chemical inhibition or genetic deletion attenuates their production. In this report, we show that systemic administration of SRI-42127, a novel small molecule HuR inhibitor, attenuates mechanical allodynia, a hallmark of NP, in the early and chronic phases after spared nerve injury in male and female mice. Flow cytometry of lumbar spinal cords in SRI-42127-treated mice shows a reduction in infiltrating macrophages and a concomitant decrease in microglial populations expressing IL-6, TNF-α, IL-1ß, and CCL2. Immunohistochemistry, ELISA, and qPCR of lumbar spinal cord tissue indicate suppression of these cytokines and other inflammatory mediators. ELISA of plasma samples in the acute phase also shows attenuation of inflammatory responses. In summary, inhibition of HuR by SRI-42127 leads to the suppression of neuroinflammatory responses and allodynia after nerve injury and represents a promising new direction in the treatment of NP.

Human papillomavirus (HPV) and Merkel cell polyomavirus (MCPyV) in non small cell lung cancer.

Certain types of human papillomavirus (HPV) induce cancers, especially cervical cancers in women. A meta-analysis of the literature suggests that HPV is also associated with 20%-25% of non small cell lung carcinoma (NSCLC). Merkel cell Polyomavirus (MCPyV) causes most Merkel cell carcinomas in immunocompromised hosts, and is associated with some squamous carcinomas of skin in immunocompetent individuals. Since both oncogenic viruses appear to involve the tonsils and, therefore, have clear access to the lungs, we examined that the possible association of HPV and MCPyV infections with lung cancers, especially, NSCLC. DNAs were extracted from 51 frozen tissues from 30 lung cancer patients, and examined for the presence of HPV and MCPyV by PCR and DNA sequencing analysis. Clinical data was correlated with the viral status. HPVs were only detected in 5 adenocarcinomas (16.7% of all lung cancers examined). Three were positive for HPV-16, 1 for HPV-11 and 1 had an unknown HPV type DNA. None was identified in benign tissue. MCPyV DNA was detected in 5 NSCLCs (16.7%). Three of the 5 were identified in squamous carcinomas, 1 in adenocarcinoma, and 1 in an unspecified NSCLC. Two additional samples were positive for MCPyV DNA within benign adjacent lung tissue only. In one adenocarcinoma, HPV-11 was identified in an adenocarcinoma, and MCPyV DNA was detected in the adjacent "benign" tissue. HPV and MCPyV were directly associated with 33.3% of NSCLC. Further studies are necessary to determine if polyomavirus and papillomavirus are necessary risk factors for some cases of NSCLC.

Glomus tumor of the ovary masquerading as granulosa cell tumor: case report.

A solid right adnexal mass in a 73-year-old woman bled profusely with mobilization mimicking a granulosa cell tumor. There was almost complete replacement of the ovary by a circumscribed, 4.0 cm tumor with a hemorrhagic, solid cut surface. Morphologic and phenotypic correlation supported a diagnosis of glomus tumor. Large gaping vessels and small sinusoidal-type vessels formed an anastomotic vascular network with an inner endothelial lining (CD31+/CD34+) and an outer layer of glomocytes (actin+/desmin-/inhibin-). The hemangiopericytoma-like vasculature accounted for bleeding during surgery.

Presentation of renal cell carcinoma as cervical polyp metastasis.

Secondary cervical adenocarcinomas are most commonly seen owing to the extension of a primary endometrial adenocarcinoma. Metastatic tumors from other sites are rather uncommon and, when seen, are most frequently from the ovaries, gastrointestinal tract, or breast. We report a case of metastatic renal cell carcinoma, clear cell variant, to the cervix, which presented as a cervical polyp in a postmenopausal female. To our knowledge, this is the fourth reported case of renal cell carcinoma metastatic to the cervix. This case is only the third in which the cervical metastasis was the presenting sign of renal cell carcinoma and the first in which the clinical presentation was as a cervical polyp.

Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.

Hepatitis C: experiencing stigma.

The purpose of this study was to identify and categorize stigmas associated with hepatitis C. This article will address the qualitative analysis of participants' written narratives describing stigmatic events. These narratives were in response to a question that incorporated a functional definition of stigma. The sample consisted of 39 participants who completed a survey during support group meetings. Of the participants, 84.6% experienced hepatitis C-related stigma. With the qualitative data saturated, a total of five themes and 16 concepts were found. The idea that ignorance precedes all stigmas was refuted with the finding that some concepts may not involve ignorance, as defined in this study, about hepatitis C. This notion was further applied to existing theories concerning disease-related stigma. The findings in this study expand our current knowledge of the complexity of stigma. Implications for nursing practice will include comprehensive structural and institutional application of policy. Furthermore, population and peer education about hepatitis C and against stigma will be a worthy opponent to the problem at hand.

Embryonal rhabdomyosarcoma of the uterine cervix in a 41-year-old woman treated with radical hysterectomy and adjuvant chemotherapy.

BACKGROUND: Cervical embryonal rhabdomyosarcoma (ERMS) mostly affects young girls. The current treatment protocols are based on trials done on patients under 21 years old. ERMS in women over 40 is rare, and studies on treatment and outcome are limited. CASE: We report a case of a 41 year-old woman with cervical ERMS who was treated with radical hysterectomy followed by chemotherapy. She is currently disease-free. CONCLUSION: Cervical ERMS in women over the age of 40 can be treated using protocols established for the pediatric population.

Biotin-rich intranuclear inclusions: have you checked your immunohistochemical controls?

Intranuclear biotin interacts with avidin-biotin-complex used for viral immunoperoxidase detection giving false-positive results.

Epidermalization of cervix and vagina: an unsolved dilemma.

BACKGROUND: Epidermoid metaplasia of the uterine cervix and vagina has previously been described, yet few well-documented cases exist. The tendency of the cervical and vaginal epithelium to undergo reactive changes as, for example, adenosis, squamous hyperplasia, hyperkeratosis, and parakeratosis is well known. Such changes can be secondary to uterine prolapse or to other causes that produce continuous irritation. The presence of ectodermal appendages (e.g., sebaceous glands and/or hair follicles), on the other hand, is less common. This is an interesting phenomenon, specially taken into consideration that the embryologic origin of the cervix and upper third of the vagina is from the mullerian duct. CASE: We present and discuss the case of a 70-year-old patient that, on routine gynecologic examination, showed whitish areas on the upper vagina and cervix. Biopsies from such areas demonstrated melanin pigment in the basal squamous epithelium, hyperkeratosis, and hair follicles with associated sebaceous glands. CONCLUSIONS: The presence of ectodermal structures in the cervix and upper vagina can be seen and is still an unresolved issue. To the authors, this phenomenon probably represents metaplastic changes instead of a developmental abnormality.

Hepatitis C: studying stigma.

The purpose of this study was to examine hepatitis C-related stigma within a population of liver disease support group attendees. In total, 39 participants completed a quantitative/qualitative survey during support group meetings. This article reports on the quantitative data. Data collected included the source and location of stigma and stigma's effects on health-seeking behavior and disclosure practices (DISCs). Of the participants, 84.6% experienced hepatitis C-related stigma. All who were Hispanic or older than 65 years experienced stigma. The most common source of stigma was healthcare professionals. More participants reported a decrease in DISCs than in health-seeking behavior. A small portion of participants reported increases in both. Those persons who were stigmatized by healthcare professionals were significantly more likely to subsequently decrease their health-seeking behavior. Of those who reported decreases in DISCs after being stigmatized, more than half (54.5%) were stigmatized by healthcare professionals. The most common location for stigmatization was in the home setting. The findings hold important implications for learning needs of healthcare professionals.

Differential expression of cdk inhibitors p16, p21cip1, p27kip1, and cyclin E in cervical cytological smears prepared by the ThinPrep method.

Our objective was to correlate p16, p21cip1, p27kip1, and cyclin E protein expression with the degree of dysplasia on ThinPrep Papanicolaou (Pap) smears using a modified immunoperoxidase staining. Smears read as normal, atypical squamous cells of undetermined significance (ASC-US), low-grade squamous intraepithelial lesion (LSIL), or high-grade SIL (HSIL) were identified and tested for high-risk human papillomavirus (HR-HPV). Additional smears were processed for immunoperoxidase for p16, p21cip1, p27kip1, and cyclin E. Thirty-four smears were satisfactory for study. The p16 was positive in all nine HSIL, in four of nine LSIL, and in one of seven ASC-US. The p27kip1 was positive in all nine HSIL, in eight of nine LSIL, and in one of seven ASC-US. The p21cip1 was positive in all nine HSIL, in one of nine LSIL, and in one of seven ASC-US. Cyclin E was positive in seven of nine HSIL and in one of nine LSIL and in none of the ASC-US smears. Normal smears were negative for all the antigens. There was poor correlation of protein expression and HR-HPV infection. We concluded that p16, p21cip1, p27kip1, and cyclin E can be demonstrated on Pap smears and they are expressed differentially in dysplastic cells, with highest expression in HSIL. The p21cip1 and cyclin E showed the greatest correlation with HSIL.