Hierarchical Classification System for Breast Cancer Specimen Report (HCSBC) -- an end-to-end model for characterizing severity and diagnosis

Automated classification of cancer pathology reports can extract information from unstructured reports and categorize each report into structured diagnosis and severity categories. Thus, such system can reduce the burden for populating tumor registries, help registration for clinical trial as well as developing large dataset for deep learning model development using true pathologic ground truth. However, the content of breast pathology reports can be difficult for categorize due to the high linguistic variability in content and wide variety of potential diagnoses >50. Existing NLP models are primarily focused on developing classifier for primary breast cancer types (e.g. IDC, DCIS, ILC) and tumor characteristics, and ignore the rare diagnosis of cancer subtypes. We then developed a hierarchical hybrid transformer-based pipeline (59 labels) - Hierarchical Classification System for Breast Cancer Specimen Report (HCSBC), which utilizes the potential of the transformer context-preserving NLP technique and compared our model to several state of the art ML and DL models. We trained the model on the EUH data and evaluated our model's performance on two external datasets - MGH and Mayo Clinic. We publicly release the code and a live application under Huggingface spaces repositor

Prognostic biomarkers in patients with human immunodeficiency virusâ positive disease with head and neck squamous cell carcinoma

BackgroundWe examined the prognostic value of a panel of biomarkers in patients with squamous cell carcinoma of the head and neck (SCCHN) who were human immunodeficiency virus (HIV) positive (HIVâ positive head and neck cancer) and HIV negative (HIVâ negative head and neck cancer).MethodsTissue microarrays (TMAs) were constructed using tumors from 41 disease siteâ matched and ageâ matched HIVâ positive head and neck cancer cases and 44 HIVâ negative head and neck cancer controls. Expression of tumor biomarkers was assessed by immunohistochemistry (IHC) and correlations examined with clinical variables.ResultsExpression levels of the studied oncogenic and inflammatory tumor biomarkers were not differentially regulated by HIV status. Among patients with HIVâ positive head and neck cancer, laryngeal disease site (P = .003) and Clavienâ Dindo classification IV (CD4) counts <200 cells/μL (P = .01) were associated with poor prognosis. Multivariate analysis showed that p16 positivity was associated with improved overall survival (OS; P < .001) whereas increased expression of transforming growth factorâ beta (TGFâ β) was associated with poor clinical outcome (P = .001).ConclusionDisease site has significant effect on the expression of biomarkers. Expression of tumor TGFâ β could be a valuable addition to the conventional risk stratification equation for improving head and neck cancer disease management strategies.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139994/1/hed24911.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139994/2/hed24911_am.pd

Unusual Presentation of Anaplastic Large Cell Lymphoma with Clinical Course Mimicking Fever of Unknown Origin and Sepsis: Autopsy Study of Five Cases

Aim To describe a subset of cases with the unusual clinical and histomorphological presentation of anaplastic large cell lymphoma (ALCL) mimicking fever of unknown origin (FUO) and sepsis. Methods A pathology database was searched using full term Systematized Nomenclature of Medicine codes for ALCL to identify 23ALCL cases from the period 1999-2006. Of those, five cases that did not have a correct premortem diagnosis were further analyzed to elucidate the reasons for delayed and incorrect pre-mortem diagnosis. The analyzed data included clinical presentation, duration of symptoms, duration of hospital stay, premortem presumed cause of death, white blood cell count, platelet count, anion gap and blood pH, liver enzymes (alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, alkaline phosphatase), lactate, coagulation tests (prothrombin time, partial thromboplastin time, fibrinogen, D-dimers), microbiology cultures, and radiology and surgical pathology reports. Autopsy reports were reviewed for description of major gross findings, initial clinical diagnosis, and cause of death. Results Five fatal and pre-mortem unrecognized ALCL cases were characterized by rapid decline, with histologic findings showing predominantly extranodal involvement, intravascular lymphomatosis, and hemophagocytosis. The cases were also characterized by unusual clinical manifestations including a FUO, sepsis, and disseminated intravascular coagulation-like picture, lactic acidosis, hepatosplenomegaly, and absence of significant peripheral adenopathy. Conclusions There is a distinct group of ALCLs with unique and specific clinical, gross autopsy, and histopathologic findings. Recognition of this clinical variant may facilitate early detection and potentially timely diagnosis and therap

Pilot study of markers for high-grade anal dysplasia in a southern cohort from the Women's Interagency HIV Study (WIHS)

Background: Anal cancer rates have increased in HIV+ women. Factors associated with anal cancer precursor high-grade squamous intraepithelial lesions (HSIL) in HIV+ and at-risk-HIV- women were assessed. Methods: HIV+ and HIV- women from the Atlanta WIHS cohort were enrolled in a cross-sectional pilot study. All anal (AS) and cervical (CS) swab samples were analyzed for HPV-genotyping (Linear-Array® HPV-Genotyping Test, LA-HPVGT) and FAM19A4 and microRNA-124-2 promoter methylation. All women underwent high resolution anoscopy with biopsy of suspicious lesions and anal cytology (AC) collection. Logistic regression was conducted with anal HSIL histology (A-HSIL) as the dependent variable. Results: 75 women were enrolled: 52(69%) were HIV+ with 3/4 having undetectable viral load, 64(86%) Black, with mean age 49. 44(59%) AC samples were ASCUS/+hrHPV or higher, 38(51%) of all AS were +hrHPV by LA-HPVGT.13 anal biopsies were confirmed A-HSIL. 69(95%) AS and 19(26%) CS tested positive for hypermethylation, respectively. A-HSIL model included ASCUS/+hrHPV or greater on AC and cervical hypermethylation as covariates (Table 1). AS hypermethylation was not associated with A-HSIL. Conclusions: Our results suggest AC with hrHPV testing and/or cervical gene promoter hypermethylation measurements as promising non-invasive screening strategies for A-HSIL in both HIV+ and HIV- women. Lack of association between AS hypermethylation and A-HSIL may reflect characteristics of the anal milieu and warrants further investigation