Predicting A/B compartments from histone modifications using deep learning.

The three-dimensional organization of genomes plays a crucial role in essential biological processes. The segregation of chromatin into A and B compartments highlights regions of activity and inactivity, providing a window into the genomic activities specific to each cell type. Yet, the steep costs associated with acquiring Hi-C data, necessary for studying this compartmentalization across various cell types, pose a significant barrier in studying cell type specific genome organization. To address this, we present a prediction tool called compartment prediction using recurrent neural networks (CoRNN), which predicts compartmentalization of 3D genome using histone modification enrichment. CoRNN demonstrates robust cross-cell-type prediction of A/B compartments with an average AuROC of 90.9%. Cell-type-specific predictions align well with known functional elements, with H3K27ac and H3K36me3 identified as highly predictive histone marks. We further investigate our mispredictions and found that they are located in regions with ambiguous compartmental status. Furthermore, our model's generalizability is validated by predicting compartments in independent tissue samples, which underscores its broad applicability.

Adapting the Voicing My CHOiCES Advance Care Planning Communication Guide for Australian Adolescents and Young Adults with Cancer: Appropriateness, Acceptability, and Considerations for Clinical Practice.

Background: Adolescents and young adults (AYAs) with life-threatening illnesses need support to discuss and voice their end-of-life choices. Voicing My CHOiCES (VMC) is a research-informed American advanced care planning guide designed to help facilitate these difficult discussions. This multi-perspective study aimed to evaluate its appropriateness, acceptability, and clinical considerations for Australian AYAs with cancer. Procedure: Forty-three participants including AYAs who were either undergoing or recently completed cancer treatment, their parents, and multidisciplinary health professionals assessed the acceptability of each VMC section quantitatively (appropriateness-yes/no, helpfulness and whether content caused stress-1 = not at all, to 5 = very) and qualitatively (sources of stress). AYAs also assessed the benefit and burden of completing several sections of the document, to inform clinical considerations. We conducted a mixed-methods analysis to obtain descriptive statistics and to identify prominent themes. Results: In terms of acceptability, almost all participants (96%) rated VMC as appropriate overall. Perceived helpfulness to their situation (to themselves/their child/their patients), to others, and stressfulness were rated, on average, as 4.1, 4.0, and 2.7/5, respectively. Stress was attributed to individual and personal factors, as well as interpersonal worries. All sections were considered more beneficial than burdensome, except for the Spiritual Thoughts section (Section 6). Conclusions: While VMC is an acceptable advance care planning guide for AYAs with cancer, changes to the guide were suggested for the Australian context. Health professionals implementing VMC will need to address and mitigate anticipated sources of stress identified here. Future research evaluating the impact of a new culturally adapted Australian VMC guide is an important next step. Finally, the clinical implications of the present study are suggested.

The association between migraine and hospital readmission due to pain after surgery: A hospital registry study.

BACKGROUND: Migraine has been identified as a risk factor of 30-day hospital readmission after surgery. We aimed to further characterize this association examining pain as a potentially migraine-associated, preventable reason for readmission. HYPOTHESIS: Compared to patients with no migraine, surgical patients with migraine are at increased risk of 30-day hospital readmission with an admitting diagnosis specifying pain. METHODS: This hospital registry study examined 150,710 patients aged 18 years and above, who underwent surgery with general anesthesia and mechanical ventilation between 2007 and 2015 at a tertiary care center and two affiliated community hospitals in Massachusetts, USA. RESULTS: Migraine was associated with an increased risk of 30-day pain-related readmission after surgery (adjusted odds ratio 1.42 [95% confidence interval 1.15-1.75]). The association was stronger for migraine with aura (compared to migraine without aura: Adjusted odds ratio 1.69 [95% confidence interval 1.06-2.70]; compared to no migraine: Adjusted odds ratio 2.20 [95% confidence interval 1.44-3.37]). The predicted adjusted risk of pain-related 30-day readmissions was 9.1 [95% confidence interval 5.3-13.0] in 1000 surgical patients with migraine with aura and 5.4 [95% confidence interval 4.2-6.6] in 1000 patients with migraine without aura, compared to 4.2 [95% confidence interval 3.8-4.5] in 1000 patients with no migraine. Furthermore, migraine was associated with an increased risk of postsurgical 30-day readmission due to a priori defined migraine-related pain (headache or abdominal pain) (adjusted odds ratio 1.55 [95% confidence interval 1.20-2.00]). CONCLUSION: Patients with migraine undergoing surgery are at increased risk of 30-day hospital readmission due to pain.

Granulomatous inflammatory pseudotumor of the spleen: association with Epstein-Barr virus.

A 74-year-old woman with a clinical history of invasive ductal carcinoma of the breast was found to have a splenic mass during a routine radiographic survey. Splenectomy revealed a 3-cm well-demarcated lesion, which on histopathologic examination consisted of heterogeneous inflammatory cells. A striking feature of the lesion was the presence of innumerable well-formed non-necrotizing granulomas. Immunohistochemical studies confirmed the lesion to be composed mainly of mixed T and B lymphocytes, histiocytes, and plasma cells. No spindle cell component was evident on light microscopic examination or by immunohistochemical staining for smooth muscle actin, anaplastic lymphoma kinase, or follicular dendritic cell markers CD21 and CD35. Interestingly, Epstein-Barr virus-encoded RNA and latent membrane protein were detected by in situ hybridization and immunohistochemistry in numerous lymphohistiocytic cells within the lesion, but not in surrounding uninvolved splenic tissue. To our knowledge, this case represents a rare example of splenic inflammatory pseudotumor with exuberant granulomatous reaction in association with Epstein-Barr viral infection.

Detection of human papillomavirus-related squamous cell carcinoma cytologically and by in situ hybridization in fine-needle aspiration biopsies of cervical metastasis: a tool for identifying the site of an occult head and neck primary.

BACKGROUND: Fine-needle aspiration (FNA) biopsy often is the first diagnostic procedure performed in patients with head and neck masses. When squamous cell carcinoma (SCC) is diagnosed, proper management and improved prognosis depends on identification of the primary tumor. Recent studies have indicated that human papillomavirus (HPV) infection is associated closely with oropharyngeal SCC and that these tumors have a distinct nonkeratinizing morphology. In this study, the authors explored the value of identifying HPV-related tumors in neck metastases to determine the origin of occult primary head and neck squamous cell carcinoma (HNSCC). METHODS: Thirty FNA biopsies of neck metastases from patients with HNSCC were recovered from the authors' files from 2004 to 2005. The primary sites included 13 oropharynx, 13 oral cavity, and 4 larynx/hypopharynx. All patients had corresponding tissue samples from the neck mass and the primary carcinoma. The FNA specimens and corresponding tissue samples were classified as either nonkeratinizing SCC (NKSCC) or keratinizing SCC (KSCC). In situ hybridization for HPV (HPV-ISH) was performed using ethanol-fixed, Papanicolaou-stained smears. A positive signal was defined as dark blue or black nuclear dots. Corresponding formalin-fixed, paraffin-embedded tissue sections also were processed for HPV-ISH. RESULTS: Twenty of the 30 FNA specimens were KSCC, and 10 were NKSCC. Eight of the 10 NKSCCs originated in the oropharynx, and 2 had nonoropharyngeal origin. HPV was detected in 7 of 10 NKSCCs. Ten of 30 (33%) FNA biopsies were positive for HPV, and 9 of those biopsies were metastatic from the oropharynx. Nonkeratinzing morphology or HPV-positive ISH in FNA samples significantly predicted oropharyngeal origin (P < .0069 and P < .0004, respectively). CONCLUSIONS: NKSCC in metastatic cervical lymph nodes predicted positive HPV-ISH and was strongly suggestive of an oropharyngeal primary tumor.

Histologic identification of human papillomavirus (HPV)-related squamous cell carcinoma in cervical lymph nodes: a reliable predictor of the site of an occult head and neck primary carcinoma.

OBJECTIVE: Patients with head and neck squamous cell carcinoma (SCC) often present with cervical lymph node metastasis. Occasionally the primary tumor site remains unknown even after thorough investigation. Management of such cases is problematic and may result in over-treatment and consequent increased morbidity. High risk HPV has been advocated recently as an important etiologic factor for a subset of head and neck SCC. These are believed to have a special predilection for the oropharyngeal tonsils and are characterized by nonkeratinizing basaloid morphology, and a strong reactivity to p16 immunostain. Identifying HPV-related SCC in the lymph nodes may thus provide a means for localizing the primary tumor site. DESIGN: Ninety-three cases of SCC metastatic to the neck from known primary tumors were classified morphologically into conventional keratinizing SCC (KSCC) and non-keratinizing SCC (NKCa). In situ hybridization (ISH) for high risk HPV as well as immunostaining for p16 were performed on all metastsatic and primary tumors. RESULTS: Of the 93 cases of metastatic carcinomas 32 were oropharyngeal, 35 oral, and 26 arose in the laryx/hypopharynx. Twenty-three cases were found to be HPV+ by ISH, of which 22/23 had oropharyngeal origin (P < 0.0001), with 95.7% sensitivity and 85.7% specificity. Twenty-one of these HPV+ oropharyngeal tumors were NKCa (P < 0.0001). The remaining case showed overlapping NKCa/KSCC hybrid morphology. All NKCa were HPV+ and stained diffusely and strongly with p16 antibodies. CONCLUSION: We have demonstrated that HPV status of the lymph node metastasis can be assessed not only by ISH and p16 immunoreactivity but also histomorphologically. In addition, a positive microscopic identification of HPV-related carcinoma is a reliable predictor of oropharyngeal origin.

Expression of mucins, SIMA, villin, and CDX2 in small-intestinal adenocarcinoma.

Expression of gastrointestinal biomarkers MUC1, MUC2, MUC5AC, small-intestinal mucin antigen (SIMA), villin, and CDX2 has been studied in colorectal adenocarcinoma (CRC). Little is known, however, about their expression in small-intestinal adenocarcinoma (SIA). We immunohistochemically compared 30 SIAs with 48 CRCs for the expression of these biomarkers. The results showed that all 6 proteins were variably expressed in SIA, but the frequencies of expression were significantly lower than those for CRC with the exception of MUC1. Specifically, positive staining for MUC1, MUC2, MUC5AC, SIMA, villin, and CDX2 was observed in 16 (53%), 17 (57%), 12 (40%), 15 (50%), 20 (67%), and 18 (60%) of SIAs and 25 (52%), 43 (90%), 39 (81%), 45 (94%), 47 (98%), and 47 (98%) of CRCs, respectively. In addition, SIAs more frequently exhibited a focal staining pattern for MUC2, MUC5AC, SIMA, and villin, whereas more diffuse immunoreactivity was evident in CRCs. Focal staining for MUC1 and diffuse staining for CDX2 were common for SIAs and CRCs. Furthermore, poorly differentiated SIAs tended to express MUC1 more frequently when compared with well- and moderately differentiated SIAs. These observations further support the notion that SIA is immunophenotypically distinct from CRC despite their morphologic similarity.

Immunohistochemical investigation of tumorigenic pathways in small intestinal adenocarcinoma: a comparison with colorectal adenocarcinoma.

Small intestinal adenocarcinoma is an uncommon neoplasm morphologically similar to or indistinguishable from colorectal adenocarcinoma. Although much has been learned about genetic pathways critical to colorectal tumorigenesis, little is known about molecular alterations involved in the development of small intestinal adenocarcinoma. In this study, we immunohistochemically compared non-ampullary small intestinal adenocarcinomas with sporadic colorectal adenocarcinomas for the expression of several proteins known to serve pivotal roles in colorectal tumorigenesis. These included adenomatous polyposis coli and beta-catenin involved in the Wnt signaling pathway, and DNA mismatch repair enzymes hMLH1, hMSH2 and hMSH6 involved in the microsatellite instability pathway. The expression of two important tumor suppressors, p53 and RB, was also examined. The results show that complete loss of adenomatous polyposis coli immunoreactivity, presumably resulting from its gene mutations, was observed in eight of 26 (31%) small intestinal adenocarcinomas and 36 of 51 (71%) colorectal adenocarcinomas (P = 0.0008). Nuclear localization of beta-catenin, an indirect evidence of deregulated Wnt signaling pathway, was observed in 5 (19%) small intestinal adenocarcinomas and 36 (71%) colorectal adenocarcinomas (P<0.0001). Total lack of nuclear staining for one or more of the DNA mismatch repair enzymes occurred in a similar low frequency in both small intestinal and colorectal adenocarcinomas, seen in two of 25 (8%) and 10 of 47 (21%) cases, respectively (P = 0.1958). The frequencies of aberrant p53 and RB expression were also similar between small intestinal and colorectal adenocarcinomas. These observations indicate that defects in the Wnt and microsatellite instability pathways occur in over 90% of colorectal adenocarcinomas, but in only 40% of small intestinal adenocarcinomas. Small intestinal tumorigenesis appears to follow a distinct, yet unidentified, molecular pathway(s) from its colorectal counterpart despite their morphologic similarity.