Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing.

Megabase-scale mosaic chromosomal alterations (mCAs) in blood are prognostic markers for a host of human diseases. Here, to gain a better understanding of mCA rates in genetically diverse populations, we analyzed whole-genome sequencing data from 67,390 individuals from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program. We observed higher sensitivity with whole-genome sequencing data, compared with array-based data, in uncovering mCAs at low mutant cell fractions and found that individuals of European ancestry have the highest rates of autosomal mCAs and the lowest rates of chromosome X mCAs, compared with individuals of African or Hispanic ancestry. Although further studies in diverse populations will be needed to replicate our findings, we report three loci associated with loss of chromosome X, associations between autosomal mCAs and rare variants in DCPS, ADM17, PPP1R16B and TET2 and ancestry-specific variants in ATM and MPL with mCAs in cis.

The Role of Substance P Receptor Antagonists in Allergic Rhinitis: Ovalbumin-Induced Rat Model.

OBJECTIVE: Substance P is a peptide from the tachykinin family, which is found in peripheral and central nervous systems, causing vasodilation and increased secretion in the nasal mucosa. In this study, we aimed to investigate whether the experimental model of allergic rhinitis will cause allergic changes in the larynx and to compare the effects of aprepitant, a substance P antagonist, on nasal symptoms in allergic rhinitis, and histopathological changes in the nasal and laryngeal mucosa with antihistamine and leukotriene receptor antagonists (LTRA). STUDY DESIGN: An experimental animal study. METHOD: The study was carried out on 34 healthy 8-12 weeks old female Sprague Dawley rats in 5 groups. The rats in which an experimental allergic rhinitis model was created with ovalbumin were scored by observing their nasal symptoms, and nasal and laryngeal mucous membranes included in the study were evaluated histopathologically after medications. RESULTS: As a result of the analysis of the data obtained from the study, antihistamine and LTRA significantly reduced the symptoms of nose scratching and sneezing, while aprepitant did not affect nasal symptoms. In the histopathological examination of the larynx, effects that would make a significant difference were found in the allergy group when compared to the control group. On the larynx, aprepitant reduced pseudostratification significantly compared to the allergy group. CONCLUSION: Aprepitant provides histopathological changes in the treatment of allergic rhinitis, but does not have sufficient effect on nasal symptoms. The effect of aprepitant on the larynx has not been clearly demonstrated. LEVEL OF EVIDENCE: NA Laryngoscope, 133:2891-2897, 2023.

A severe headache due to pigmented villonodular synovitis in a rare location: facial nerve on temporomandibular joint. A case report.

BACKGROUND: Pigmented villonodular synovitis (PVNS) is an infrequent benign tumor-like proliferative lesion developing from the synovial membranes of the joint, tendon sheath, and bursa. CLINICAL PRESENTATION: A 44-year-old woman with numbness on the right side of her face, severe headaches, and swelling in temporomandibular region is presented. On head and neck magnetic resonance imaging, an encapsulated mass approximately 2 cm was detected. The fine-needle aspiration biopsy resulted as suspicion of mesenchymal tumor. A complete resection with the capsule was performed over the temporal branch by monitoring of the facial nerve. The final histopathologic examination resulted as a giant cell tendon sheath tumor. CONCLUSION: Headache is not the main symptom in PVNS, but in severe pain spreading from the temporomandibular region, physical examination should be done carefully for slight swelling, and the possibility of pigmented villonodular synovitis should be considered. Because of the high recurrence rate, en bloc resection is necessary.

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

MOTIVATION: RNA-sequencing (RNA-seq) of tumor tissue is typically only used to measure gene expression. Here, we present a statistical approach that leverages existing RNA-seq data to also detect somatic copy number alterations (SCNAs), a pervasive phenomenon in human cancers, without a need to sequence the corresponding DNA. RESULTS: We present an analysis of 4942 participant samples from 28 cancers in The Cancer Genome Atlas (TCGA), demonstrating robust detection of SCNAs from RNA-seq. Using genotype imputation and haplotype information, our RNA-based method had a median sensitivity of 85% to detect SCNAs defined by DNA analysis, at high specificity (∼95%). As an example of translational potential, we successfully replicated SCNA features associated with breast cancer subtypes. Our results credential haplotype-based inference based on RNA-seq to detect SCNAs in clinical and population-based settings. AVAILABILITY AND IMPLEMENTATION: The analyses presented use the data publicly available from TCGA Research Network (http://cancergenome.nih.gov/). See Methods for details regarding data downloads. hapLOHseq software is freely available under The MIT license and can be downloaded from http://scheet.org/software.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Combination of Sulindac and Bexarotene for Prevention of Intestinal Carcinogenesis in Familial Adenomatous Polyposis.

Familial adenomatous polyposis (FAP) is a hereditary colorectal cancer syndrome, which results in the development of hundreds of adenomatous polyps carpeting the gastrointestinal tract. NSAIDs have reduced polyp burden in patients with FAP and synthetic rexinoids have demonstrated the ability to modulate cytokine-mediated inflammation and WNT signaling. This study examined the use of the combination of an NSAID (sulindac) and a rexinoid (bexarotene) as a durable approach for reducing FAP colonic polyposis to prevent colorectal cancer development. Whole transcriptomic analysis of colorectal polyps and matched normal mucosa in a cohort of patients with FAP to identify potential targets for prevention in FAP was performed. Drug-dose synergism of sulindac and bexarotene in cell lines and patient-derived organoids was assessed, and the drug combination was tested in two different mouse models. This work explored mRNA as a potential predictive serum biomarker for this combination in FAP. Overall, transcriptomic analysis revealed significant activation of inflammatory and cell proliferation pathways. A synergistic effect of sulindac (300 µmol/L) and bexarotene (40 µmol/L) was observed in FAP colonic organoids with primary targeting of polyp tissue compared with normal mucosa. This combination translated into a significant reduction in polyp development in ApcMin/+ and ApcLoxP/+-Cdx2 mice. Finally, the reported data suggest miRNA-21 could serve as a predictive serum biomarker for polyposis burden in patients with FAP. These findings support the clinical development of the combination of sulindac and bexarotene as a treatment modality for patients with FAP. PREVENTION RELEVANCE: This study identified a novel chemopreventive regimen combining sulindac and bexarotene to reduce polyposis in patients with FAP using in silico tools, ex vivo, and in vivo models. This investigation provides the essential groundwork for moving this drug combination forward into a clinical trial.

The Transcriptomic Landscape of Mismatch Repair-Deficient Intestinal Stem Cells.

Lynch syndrome is the most common cause of hereditary colorectal cancer and is secondary to germline alterations in one of four DNA mismatch repair (MMR) genes. Here we aimed to provide novel insights into the initiation of MMR-deficient (MMRd) colorectal carcinogenesis by characterizing the expression profile of MMRd intestinal stem cells (ISC). A tissue-specific MMRd mouse model (Villin-Cre;Msh2 LoxP/LoxP ) was crossed with a reporter mouse (Lgr5-EGFP-IRES-creERT2) to trace and isolate ISCs (Lgr5+) using flow cytometry. Three different ISC genotypes (Msh2-KO, Msh2-HET, and Msh2-WT) were isolated and processed for mRNA-seq and mass spectrometry, followed by bioinformatic analyses to identify expression signatures of complete MMRd and haplo-insufficiency. These findings were validated using qRT-PCR, IHC, and whole transcriptomic sequencing in mouse tissues, organoids, and a cohort of human samples, including normal colorectal mucosa, premalignant lesions, and early-stage colorectal cancers from patients with Lynch syndrome and patients with familial adenomatous polyposis (FAP) as controls. Msh2-KO ISCs clustered together with differentiated intestinal epithelial cells from all genotypes. Gene-set enrichment analysis indicated inhibition of replication, cell-cycle progression, and the Wnt pathway and activation of epithelial signaling and immune reaction. An expression signature derived from MMRd ISCs successfully distinguished MMRd neoplastic lesions of patients with Lynch syndrome from FAP controls. SPP1 was specifically upregulated in MMRd ISCs and colocalized with LGR5 in Lynch syndrome colorectal premalignant lesions and tumors. These results show that expression signatures of MMRd ISC recapitulate the initial steps of Lynch syndrome carcinogenesis and have the potential to unveil novel biomarkers of early cancer initiation. SIGNIFICANCE: The transcriptomic and proteomic profile of MMR-deficient intestinal stem cells displays a unique set of genes with potential roles as biomarkers of cancer initiation and early progression.

Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types.

Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities ("B allele" frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the "B allele" frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.

Pathologist-performed palpation-guided fine needle aspiration cytology of lingual actinomycosis: A case report and review of literature.

"Lingual actinomycosis" is an uncommon, suppurative inflammation of lingual mucosa, caused by Actinomyces. Infectious oral lesions can mimic benign or malignant neoplasms and fine needle aspiration cytology (FNAC) is a simple, minimally invasive procedure for the assessment of patients with such lesions. Here, we describe the case of a 28-year old patient presented with an asymptomatic, submucosal nodular mass of the tongue. Then, FNAC was performed by an experienced fine needle aspiration (FNA) pathologist (* ) in our pathology department and the lesion diagnosed with actinomycosis. We also report a detailed review of cases in the literature, with clinical findings.

Clinical time course of the neglected giant sebaceous gland carcinoma.

In this report, we discussed the progression from the initial presentation until surgical intervention, clinical course, and devastating outcome of a neglected giant sebaceous gland carcinoma of the eyelid in a poorly compliant elderly patient. A 79-year-old woman was referred for treatment of a giant ulcero-nodular lesion in the right upper eyelid. Nine months before, an orange lesion arising from the tarsal conjunctiva in the upper eyelid was observed in her examination undergone in the healthcare center where she initially presented, and the cornea appeared transparent. Surgical excision was recommended, which she declined. The examination three months before in the same center revealed that the lesion invaded the globe and anterior segment architecture could not be visualized. She was then recommended surgical removal of the eyeball, which she also refused. Radiological imaging demonstrated a 33x35 mm mass lesion in the superior lateral of orbit with exophytic growth and invasion of the globe and no systemic metastases were found. Total orbital exenteration surgery was immediately planned and performed. Histopathological examination revealed sebaceous gland carcinoma. Elderly patients with poor compliance should discuss their condition with a psychiatrist and should be managed by a multidisciplinary approach. This way, patients with eyelid malignancies can be encouraged to undergo surgery and receive early treatment, decreasing the need for exenteration, improving clinical outcomes, and reducing the risk of morbidity and mortality.

Comparison of the Diagnostic Utility of Manual Screening and the ThinPrep Imaging System in Liquid-Based Cervical Cytology.

OBJECTIVE: To compare the diagnostic results of the ThinPrep manual method (TPMM) and ThinPrep automated method (TPAM) in liquid-based cytology and present the advantages and disadvantages of both methods. MATERIAL AND METHOD: A total of 1.500 randomized ThinPrep Pap tests that were screened manually and archived in 2015 were reviewed by a blinded researcher manually and by the ThinPrep automatic method. RESULTS: There was a 83.3% increase in the detection of ASCUS (Atypical squamous cells of undetermined significance) with the TPAM compared to the TPMM, and with respect to the reference results, the accuracy was higher for the TPAM than for the TPMM. We also noted a 33.3% increase in the rate of LSIL (Low grade squamous intraepithelial lesion) and 20% increase in the rate of HSIL (High grade squamous intraepithelial lesion) by the TPAM. Concordance was best between the TPAM and reference cytologic diagnoses. The sensitivity was higher for the TPAM and the specificity was similar for both methods. The false positive rate was higher for the TPAM than the TPMM but the false negative rate was higher for the TPMM. We determined a 30% gain in screening time per smear by the TPAM. However, rejection of many samples by the system, especially because of air bubbles, was a limitation of the TPAM. CONCLUSION: The TPAM has advantages over the TPMM as well as disadvantages such as limiting features and a high false positive rate. The TPAM should be supported by the manual method to decrease the false positive rate.

What does the Data of 354,725 Patients from Turkey Tell Us About Cervical Smear Epithelial Cell Abnormalities? - The Epithelial Cell Abnormality Rate is Increasing - Quality Control Studies and Corrective Activity are Musts.

OBJECTIVE: There is no other screening program close to the success rate of PAP test. Cervical cytology constitutes a large workload so that quality control in cervical cytology is important for the quality assurance of pathology laboratories. MATERIAL AND METHOD: In this study, we collected the cervical cytology results from all over Turkey and discussed the parameters influencing the quality of the PAP test. The study was conducted with Turkish gynaecopathology working group and 38 centers (totally 45 hospitals) agreed to contribute from 24 different cities. The study was designed to cover the cervical cytology results during 2013. The results were evaluated from the data based on an online questionnaire. RESULTS: The total number of Epithelial Cell Abnormality was 18,020 and the global Epithelial Cell Abnormality rate was 5.08% in the total 354,725 smears and ranging between 0.3% to 16.64% among centers. The Atypical squamous cells /Squamous intraepithelial lesion ratios changed within the range of 0.21-13.94 with an average of 2.61. When the centers were asked whether they performed quality assurance studies, only 14 out of 28 centers, which shared the information, had such a control study and some quality parameters were better in these centers. CONCLUSION: There is an increase in the global Epithelial Cell Abnormality rate and there are great differences among centers. Quality control studies including the Atypical squamous cells/Squamous intraepithelial lesion ratio are important. Corrective and preventive action according to quality control parameters is a must. A cervical cytology subspecialist in every center can be utopic but a dedicated pathologist in the center is certainly needed.