Detection of SARS-CoV-2 in formalin-fixed paraffin-embedded tissue sections using commercially available reagents.

Coronavirus Disease-19 (COVID-19), caused by the coronavirus SARS-CoV-2, was initially recognized in Wuhan, China and subsequently spread to all continents. The disease primarily affects the lower respiratory system, but may involve other organs and systems. Histopathologic evaluation of tissue from affected patients is crucial for diagnostic purposes, but also for advancing our understanding of the disease. For that reason, we developed immunohistochemical (IHC) and in situ hybridization (ISH) assays for detection of the. virus. A total of eight autopsy lungs, one placenta, and ten kidney biopsies from COVID-19 patients were stained with a panel of commercially available antibodies for IHC and commercially available RNA probes for ISH. Similarly, autopsy lungs, placentas and renal biopsies from non-COVID-19 patients were stained with the same antibodies and probes. All eight lungs and the placenta from COVID-19 patients stained positive by IHC and ISH, while the kidney biopsies stained negative by both methodologies. As expected, all specimens from non-COVID-19 patients were IHC and ISH negative. These two assays represent a sensitive and specific method for detecting the virus in tissue samples. We provide the protocols and the list of commercially available antibodies and probes for these assays, so they can be readily implemented in pathology laboratories and medical examiner offices for diagnostic and research purposes.

Effect of chemotherapy on cancer stem cells and tumor-associated macrophages in a prospective study of preoperative chemotherapy in soft tissue sarcoma.

BACKGROUND: Cancer stem cells (CSC) may respond to chemotherapy differently from other tumor cells. METHODS: This study examined the expression of the putative cancer stem cell markers ALDH1, CD44, and CD133; the angiogenesis marker CD31; and the macrophage marker CD68 in soft tissue sarcomas (STS) before and after 4 cycles of chemotherapy with doxorubicin and ifosfamide in 31 patients with high-grade soft tissue sarcoma in a prospective clinical trial. RESULTS: None of the markers clearly identified CSCs in STS samples. Macrophages represented a prominent component in viable tumor areas in pre-treatment STS biopsies, ranging from < 5 to > 50%. Furthermore, macrophages expressed CD44 and ALDH1. Macrophage density correlated with baseline maximum standardized uptake value (SUVmax) on fluoro-deoxyglucose positron emission tomography (PET) imaging. Pre-chemotherapy CD68 staining correlated positively with the baseline SUVmax, and negatively with the percent of viable tumor cells in post-chemotherapy resection samples. In particular, cases with more CD68-positive cells at biopsy had fewer viable tumor cells at resection, suggesting a better response to chemotherapy. CONCLUSIONS: In conclusion, ALDH1, CD44, and CD133 are not likely to be useful markers of CSCs in STS. However, our observation of infiltrating macrophages in STS specimens indicates that these immune cells may contribute significantly to STS biology and response to chemotherapy, and could provide a potential target of therapy. Future studies should investigate macrophage contribution to STS pathophysiology by cytokine signaling.

Fluorescence in situ hybridization for the diagnosis of NPHP1 deletion-related nephronophthisis on renal biopsy.

Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy that is a leading genetic etiology of end-stage renal disease in children and young adults. Approximately 60% of patients with a known genetic etiology of nephronophthisis are due to homozygous deletion of the NPHP1 gene. We identified a total of 45 renal biopsies from young patients with chronic kidney disease of undetermined etiology and analyzed them for the possibility of nephronophthisis due to NPHP1 deletion using interphase fluorescence in situ hybridization and/or polymerase chain reaction. Homozygous NPHP1 deletion was identified in 9 patients (20%). In cases with adequate tissue, both assays were performed and showed 100% agreement. Blinded histopathologic analysis was then performed and identified 6 lesions that were significantly more common in biopsies from patients with NPHP1 deletion-proven nephronophthisis than chronic kidney injury of other known etiologies. Many of the classically described nephronophthisis biopsy lesions such as tubular basement membrane duplication, presence of cysts, and mononuclear interstitial inflammation were not significantly associated with this disease when compared with biopsies from patients with chronic kidney injury due to other etiologies. There were, however, morphologic lesions that were strongly associated with NPHP1 deletion including tubular abnormalities such as diverticulum, florets, and macula densa-like change as well as interstitial Tamm-Horsfall aggregates, periglomerular fibrosis, and the absence of arteriosclerosis. Awareness of the histopathologic pattern of injury in nephronophthisis combined with testing for NPHP1 deletion enables renal pathologists to provide a definitive pathologic and genetic diagnosis in a subset of patients with this disease.

Genetic testing of complement and coagulation pathways in patients with severe hypertension and renal microangiopathy.

A diagnosis of thrombotic microangiopathy on kidney biopsy in a patient presenting with hypertensive emergency has historically elicited the diagnosis of malignant hypertension-associated thrombotic microangiopathy. Recent studies, however, have raised awareness that a number of these patients may actually represent atypical hemolytic uremic syndrome. To further investigate this premise, we performed next-generation sequencing to interrogate the coding regions of 29 complement and coagulation cascade genes associated with atypical hemolytic uremic syndrome in 100 non-elderly patients presenting with severe hypertension, renal failure and a kidney biopsy showing microangiopathic changes limited to the classic accelerated hypertension-associated lesion of arterial intimal edema ('mucoid intimal hyperplasia') in isolation and without accompanying glomerular microthrombi. No pathogenic or likely pathogenic variants were identified in any of the genes analyzed, although 13 patients had rare variants of uncertain significance predicted to be deleterious by all in-silico prediction methods utilized. Accordingly, this large patient cohort showed no definitive burden of disease secondary to genetic variants involving complement or coagulation pathways, which contrasts sharply with the high frequency of similar mutational events reported for atypical hemolytic uremic syndrome. Our results also inform recent data by suggesting that patients who present with severe or malignant hypertension and renal thrombotic microangiopathy may be at higher risk for atypical hemolytic uremic syndrome only if the biopsy shows more active disease that includes glomerular fibrin thrombi.

Complete and sustained response of adult medulloblastoma to first-line sonic hedgehog inhibition with vismodegib.

Medulloblastoma is an aggressive primitive neuroectodermal tumor of the cerebellum that is rare in adults. Medulloblastomas fall into 4 prognostically significant molecular subgroups that are best defined by experimental gene expression profiles: the WNT pathway, sonic hedgehog (SHH) pathway, and subgroups 3 and 4 (non-SHH/WNT). Medulloblastoma of adults belong primarily to the SHH category. Vismodegib, an SHH-pathway inhibitor FDA-approved in 2012 for treatment of basal cell carcinoma, has been used successfully in the setting of chemorefractory medulloblastoma, but not as a first-line therapy. In this report, we describe a sustained response of an unresectable multifocal form of adult medulloblastoma to vismodegib. Molecular analysis in this case revealed mutations in TP53 and a cytogenetic abnormality, i17q, that is prevalent and most often associated with subgroup 4 rather than the SHH-activated form of medulloblastoma. Our findings indicate that vismodegib may also block alternate, non-canonical forms of downstream SHH pathway activation. These findings provide strong impetus for further investigation of vismodegib in clinical trials in the first-line setting for pediatric and adult forms of medulloblastoma.

Prevalence and organ distribution of leukocyte chemotactic factor 2 amyloidosis (ALECT2) among decedents in New Mexico.

Leukocyte chemotactic factor 2 (LECT2) amyloidosis is one of the most recently described types of amyloidosis. Since its description, it has been found to be one the most common types of amyloidosis in large series of amyloid cases involving the kidney and liver in the United States, where it primarily affects patients of Hispanic ethnicity. We sought to investigate the prevalence of this disease among Hispanic adult decedents who had an autopsy performed at the New Mexico Office of the Medical Investigator and determine the organ distribution of amyloid deposition. LECT2 amyloid deposits were identified within the kidney in 3.1% of Hispanic decedents. It was consistently deposited in the liver, spleen, adrenals, and lungs but did not involve the myocardium or brain. LECT2 amyloidosis is likely not rare among Hispanics in the Southwest United States and could represent an important but under-recognized etiology of chronic kidney disease in this population.

Detection of PAX2 deletions and duplications using multiplex ligation-dependent probe amplification.

BACKGROUND: Renal coloboma syndrome (RCS) is a rare inherited disorder caused by mutations in the PAX2 gene. Clinical testing is currently performed by bidirectional Sanger sequencing of all 12 coding exons of the PAX2 gene, which detects point mutations or small insertion/deletion mutations. Large genomic deletions of PAX2 have been identified in 3/90 known RCS families, accounting for approximately (3%) of RCS cases. In these cases, the deletion was detected by cytogenetic techniques such as G-banding or array comparative genomic hybridization. While these methods would be sufficient to identify whole gene deletions, they may not be able to identify smaller rearrangements affecting single exons. Similarly, such deletions would not be detected by Sanger sequencing. AIM: The aim of this study was to determine whether mutation-negative RCS probands harbor a genomic deletion or duplication involving one or more exons of the PAX2 gene. We evaluated this hypothesis in 46 patients with a clinical suspicion of RCS in whom no mutations were identified. RESULTS: We developed a multiplex ligation-dependent probe amplification assay to detect gene deletion/duplication in all 12 exons of the PAX2 gene. Of the 46 PAX2 mutation-negative samples tested, none demonstrated deletions or duplications in the PAX2 gene. This suggests that deletions or duplications in PAX2 are unlikely to significantly contribute to the pathogenesis of RCS, beyond the known 3% of cases that have been attributed to whole gene deletions. Given these results, we hypothesize that other genes and/or locus control regions regulating PAX2 may be involved in the pathogenesis of PAX2 mutation-negative cases of RCS.

Selective forelimb impairment in rats expressing a pathological TDP-43 25 kDa C-terminal fragment to mimic amyotrophic lateral sclerosis.

Pathological inclusions containing transactive response DNA-binding protein 43 kDa (TDP-43) are common in several neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). TDP-43 normally localizes predominantly to the nucleus, but during disease progression, it mislocalizes to the cytoplasm. We expressed TDP-43 in rats by an adeno-associated virus (AAV9) gene transfer method that transduces neurons throughout the central nervous system (CNS). To mimic the aberrant cytoplasmic TDP-43 found in disease, we expressed a form of TDP-43 with mutations in the nuclear localization signal sequence (TDP-NLS). The TDP-NLS was detected in both the cytoplasm and the nucleus of transduced neurons. Unlike wild-type TDP-43, expression of TDP-NLS did not induce mortality. However, the TDP-NLS induced disease-relevant motor impairments over 24 weeks. We compared the TDP-NLS to a 25 kDa C-terminal proaggregatory fragment of TDP-43 (TDP-25). The clinical phenotype of forelimb impairment was pronounced with the TDP-25 form, supporting a role of this C-terminal fragment in pathogenesis. The results advance previous rodent models by inducing cytoplasmic expression of TDP-43 in the spinal cord, and the non-lethal phenotype enabled long-term study. Approaching a more relevant disease state in an animal model that more closely mimics underlying mechanisms in human disease could unlock our ability to develop therapeutics.

Occurrence of extensive spherical amyloid deposits in a prolactin-secreting pituitary macroadenoma: a radiologic-pathologic correlation.

Pituitary adenomas are the most common tumors of the sellar region, but the occurrence of spherical amyloid deposits in a pituitary adenoma is rare. We describe the clinical features, radiologic characteristics, and pathologic findings of 45-year-old man who presented with galactorrhea, hypogonadism, and hyperprolactinemia who had a pituitary adenoma with extensive spherical amyloid deposits. Approximately 30 cases have been reported, almost exclusively in patients with prolactinomas. Treatment with dopaminergic agonists will result in the expected reduction in prolactin levels; however, in most cases, macroadenomas with spherical amyloid deposits fail to decrease in size. The source of the amyloid deposits in prolactinomas is not clearly defined but may be due to abnormal processing of prolactin or its prohormone. These adenomas with spherical amyloid have a characteristic appearance on magnetic resonance imaging with low or heterogeneous intensity on T1 and low intensity on T2-weighted images. Following infusion of gadolinium, there is enhancement of the periphery but not most of the tumor mass. These magnetic resonance imaging characteristics are different than those of typical pituitary adenomas. These differences should alert clinicians to the possibility of extensive spherical amyloid deposits in a prolactin-secreting pituitary adenoma, which may have important clinical implications. In this report, we correlate the radiologic finds with the pathology and compared them with other sellar and parasellar lesions.

Primary amebic meningoencephalitis deaths associated with sinus irrigation using contaminated tap water.

BACKGROUND: Naegleria fowleri is a climate-sensitive, thermophilic ameba found in the environment, including warm, freshwater lakes and rivers. Primary amebic meningoencephalitis (PAM), which is almost universally fatal, occurs when N. fowleri-containing water enters the nose, typically during swimming, and N. fowleri migrates to the brain via the olfactory nerve. In 2011, 2 adults died in Louisiana hospitals of infectious meningoencephalitis after brief illnesses. METHODS: Clinical and environmental testing and case investigations were initiated to determine the cause of death and to identify the exposures. RESULTS: Both patients had diagnoses of PAM. Their only reported water exposures were tap water used for household activities, including regular sinus irrigation with neti pots. Water samples, tap swab samples, and neti pots were collected from both households and tested; N. fowleri were identified in water samples from both homes. CONCLUSIONS: These are the first reported PAM cases in the United States associated with the presence of N. fowleri in household plumbing served by treated municipal water supplies and the first reports of PAM potentially associated with the use of a nasal irrigation device. These cases occurred in the context of an expanding geographic range for PAM beyond southern tier states with recent case reports from Minnesota, Kansas, and Virginia. These infections introduce an additional consideration for physicians recommending nasal irrigation and demonstrate the importance of using appropriate water (distilled, boiled, filtered) for nasal irrigation. Furthermore, the changing epidemiology of PAM highlights the importance of raising awareness about this disease among physicians treating persons showing meningitislike symptoms.

Congenital megaconial myopathy due to a novel defect in the choline kinase Beta gene.

OBJECTIVES: To describe the first American patient with a congenital muscle dystrophy characterized by the presence in muscle of gigantic mitochondria displaced to the periphery of the fibers and to stress the potential origin and effects of the mitochondrial changes. DESIGN: Case report and documentation of a novel mutation in the gene encoding choline kinase beta (CHKB). SETTING: Collaboration between 2 tertiary care academic institutions. PATIENT: A 2-year-old African American boy with weakness and psychomotor delay. INTERVENTIONS: Detailed clinical and laboratory studies, including muscle biopsy, biochemical analysis of the mitochondrial respiratory chain, and sequencing of the CHKB gene. MAIN OUTCOME MEASURES: Definition of unique mitochondrial changes in muscle. RESULTS: This patient had the same clinical and laboratory features reported in the first cohort of patients, but he harbored a novel CHKB mutation and had isolated cytochrome c oxidase deficiency in muscle. CONCLUSIONS: Besides confirming the phenotype of CHKB mutations, we propose that this disorder affects the mitochondria-associated membrane and the impaired phospholipid metabolism in the mitochondria-associated membrane causes both the abnormal size and displacement of muscle mitochondria.

Genetic alterations in colorectal cancer.

Colorectal cancer (CRC) is the third most common cancer in men and the second most common cancer in women worldwide. Both genetic and epigenetic alterations are common in CRC and are the driving force of tumorigenesis. The adenoma-carcinoma sequence was proposed in the 1980s that described transformation of normal colorectal epithelium to an adenoma and ultimately to an invasive and metastatic tumor. Initial genetic changes start in an early adenoma and accumulate as it transforms to carcinoma. Chromosomal instability, microsatellite instability and CpG island methylator phenotype pathways are responsible for genetic instability in colorectal cancer. Chromosomal instability pathway consist of activation of proto-oncogenes (KRAS) and inactivation of at least three tumor suppression genes, namely loss of APC, p53 and loss of heterozogosity (LOH) of long arm of chromosome 18. Mutations of TGFBR and PIK3CA genes have also been recently described. Herein we briefly discuss the basic concepts of genetic integrity and the consequences of defects in the DNA repair relevant to CRC. Epigenetic alterations, essential in CRC tumorigenesis, are also reviewed alongside clinical information relevant to CRC.

Occult tumors presenting with negative imaging: analysis of the literature.

OBJECT: Some patients presenting with neurological symptoms and normal findings on imaging studies may harbor occult brain tumors that are undetectable on initial imaging. The purpose of this study was to analyze the cases of occult brain tumors reported in the literature and to determine their modes of presentation and time to diagnosis on imaging studies. METHODS: A review of the literature was performed using PubMed. The authors found 15 articles reporting on a total of 60 patients with occult tumors (including the authors' illustrative case). RESULTS: Seizures were the mode of initial presentation in a majority (61.7%) of patients. The initial imaging was CT scanning in 55% and MRI in 45%. The mean time to diagnosis for occult brain tumors was 10.3 months (median 4 months). The time to diagnosis (mean 7.5 months, median 3.2 months) was shorter (p = 0.046) among patients with seizures. Glioblastoma multiforme (GBM) was found more frequently among patients with seizures (67.6% vs 34.8%, p = 0.013). The average time to diagnosis of GBM was shorter than the time to diagnosis of other tumors; the median time to diagnosis was 3.2 months for GBM and 6 months for other tumors (p = 0.04). There was no predilection for side or location of occult tumors. In adult patients, seizures may be predictive of left-sided tumors (p = 0.04). CONCLUSIONS: Based on the results of this study, the authors found that in patients with occult brain tumors, the time to diagnosis is shorter among patients with seizures and also among those with GBM.

Association of common variants in the human eyes shut ortholog (EYS) with statin-induced myopathy: evidence for additional functions of EYS.

INTRODUCTION: Of the nearly 38 million people in the USA who receive statin therapy, 0.1-0.5% experience severe or life-threatening myopathic side effects. METHODS: We performed a genome-wide association study (GWAS) in a group of patients with severe statin myopathy versus a statin-tolerant group to identify genetic susceptibility loci. RESULTS: Replication studies in independent groups of severe statin myopathy (n = 190) and statin-tolerant controls (n = 130) resulted in the identification of three single-nucleotide polymorphisms (SNPs), rs9342288, rs1337512, and rs3857532, in the eyes shut homolog (EYS) on chromosome 6 suggestive of an association with risk for severe statin myopathy (P = 0.0003-0.0008). Analysis of EYS cDNA demonstrated that EYS gene products are complex and expressed with relative abundance in the spinal cord as well as in the retina. CONCLUSION: Structural similarities of these EYS gene products to members of the Notch signaling pathway and to agrin suggest a possible functional role in the maintenance and regeneration of the structural integrity of skeletal muscle.

Juvenile xanthogranuloma in an adult lumbar spine: a case report.

STUDY DESIGN: Case report. OBJECTIVE: To report a very rare case of juvenile xanthogranuloma (JXG) of the spine in an adult. SUMMARY OF BACKGROUND DATA: JXG is very rare in the spine, with only five prior reports in infants and children. To the best of our knowledge, this tumor has never been reported in an adult spine. METHODS: The patient is a 47-year-old woman who presented with bowel and bladder incontinence. Magnetic resonance imaging showed a very large lesion arising from the L2 vertebral body, with massive extension into the retroperitoneum with extensive intradural involvement. She had decreased rectal tone, had 4/5 strength in the right hip flexor, and had diminished sensation in her anterior right thigh and perineal region. She was otherwise neurologically intact. After preoperative embolization, a decompressive laminectomy was performed and the tumor was resected through a posterolateral transpedicular approach, followed by stabilization. Because of extensive involvement of retroperitoneum, complete resection was not possible. RESULTS: After pathologic evaluation of the specimen, a diagnosis of JXG was made. Patient underwent postoperative radiation therapy, and her neurologic examination improved significantly over the next several months. CONCLUSIONS: To the best of our knowledge, this is the first reported case of JXG in an adult spine. Although complete resection of the tumor was not possible, decompression of the dural sac followed by postoperative radiation led to an excellent clinical outcome.

Primary bone diffuse large B-cell lymphoma: clinicopathologic study of 21 cases and review of literature.

Primary bone diffuse large B-cell lymphomas (PB-DLBCL) are uncommon extranodal lymphomas. Herein, we report the clinical, pathologic, immunohistochemical, and molecular features of 21 cases of PB-DLBCL. The mean age of the patients was 54 years (range: 13 to 85 y). The male and female ratio was 1.6:1. The tumors consisted of diffuse sheets of large atypical cells or a polymorphous mixture of small-to-large cells with large multilobated nuclei, fine chromatin, and inconspicuous to prominent nucleoli. Twelve (57%) cases were non-germinal center B (GCB) and 9 (43%) were GCB subtype based on immunohistochemical classification. B-cell lymphomas (BCL)-2 was positive in 17/21 (81%), TP53 in 11/21 (52%) positive and the mean MIB-1 index was 57%. Polymerase chain reaction showed 10 cases with immunoglobulin heavy-chain (IGH) and 4 cases with IGH/BCL-2 gene rearrangement. The fluorescence in-situ hybridization analyses showed 14% of cases with BCL-6, 19% of cases with BCL-2, and 9% of cases with C-MYC gene rearrangement. Age <60 years and complete response to initial treatment were significant predictors of survival outcome (P< or =0.05). Even though no association was observed between the subtype of PB-DLBCL (GCB vs. non-GCB), BCL2, TP53, MIB1 index and overall survival (P>0.05), due to small sample size, and variability in treatment received, this analysis may be interpreted with caution.