Overproduction, purification, and transcriptional activity of recombinant Acinetobacter baylyi ADP1 RNA polymerase holoenzyme.

Acinetobacter baylyi is an interesting model organism to investigate bacterial metabolism due to its vast repertoire of metabolic enzymes and ease of genetic manipulation. However, the study of gene expression in vitro is dependent on the availability of its RNA polymerase (RNAp), an essential enzyme in transcription. In this work, we developed a convenient method of producing the recombinant A. baylyi ADP1 RNA polymerase holoenzyme (RNApholo) in E. coli that yields 22 mg of a >96% purity protein from a 1-liter shake flask culture. We further characterized the A. baylyi ADP1 RNApholo kinetic profile using T7 Phage DNA as template and demonstrated that it is a highly transcriptionally active enzyme with an elongation rate of 24 nt/s and a termination efficiency of 94%. Moreover, the A. baylyi ADP1 RNApholo has a substantial sequence identity (∼95%) with the RNApholo from the human pathogen Acinetobacter baumannii. This protein can serve as a source of material for structural and biological studies towards advancing our understanding of genome expression and regulation in Acinetobacter species.

Primary Fallopian Tube Mullerian Adenosarcoma With Sarcomatous Overgrowth and a Previously Unreported MEIS1-NCOA2 Gene Fusion.

Extrauterine Mullerian adenosarcomas (MA) are rare and often associated with endometriosis. We report a 55-yr-old patient seen in consultation for abdominal pain and bloating. Imaging was suggestive of a left adnexal mass and "peritoneal carcinomatosis". Pathological examination of the specimen revealed a MA arising in the left fallopian tube, with sarcomatous overgrowth, diffuse peritoneal involvement and omental "caking". Next-generation sequencing identified a MEIS1-NCOA2 gene fusion, previously unreported in MA.

The effect that pathologic and radiologic interpretation of invasive and non-invasive areas in lung adenocarcinoma has on T-stage and treatment.

Lung adenocarcinoma is currently staged based on invasive tumor size, excluding areas of lepidic (in situ) growth. Invasive tumor size may be determined by pathologic assessment of a surgical specimen or radiographic assessment on computerized tomography (CT) scan. When invasive tumor size is the primary stage determinate, radiographic-pathologic discordance or discordant interpretation among pathologists may alter tumor stage and treatment. We reviewed 40 cases of non-mucinous pulmonary adenocarcinoma in which tumor size was the only stage-determinant. We determined the inter-observer variability when microscopically assessing architectural patterns and its effect on pathologic stage and treatment. Additionally, we correlated pathologic and radiographic assessment of invasive tumor size and its effect on tumor stage and treatment. The intraclass correlation among three pathologists was 0.9879; all three pathologists agreed on T-stage in 75% of cases. Four cases of pathologic disagreement had the potential to alter therapy. Intraclass correlation between the pathologists and invasive tumor size determined by CT scan was 0.8482. In 23 cases (57.5%) the pathologic T-stage differed (it increased >90% of the time) from clinical T-stage (determined by CT scan) based on invasive tumor size. Five of the radiographically-pathologically discrepant cases resulted in a stage change that had the potential to alter adjuvant therapy. Our findings suggest the stage differences in pathologic staging are prognostically relevant, but unlikely to impact routine selection of adjuvant therapy, and the observed variability in clinical stage tends to select against overuse of neoadjuvant therapy when invasive tumor size is the primary stage-determinant.

Vascular tumors of bone.

Vascular tumors of the bone represent a variety of neoplasms, ranging from benign hemangiomas and epithelioid hemangiomas to intermediate grade hemangioendotheliomas to frankly malignant angiosarcomas. Over the years, there has been considerable debate concerning the aggressivity, nomenclature, and mere existence of various nosologic entities, due to morphologic similarities and uncertainty regarding biologic behavior. Such debate has led to confusion among pathologists and clinicians, thus diminishing the prognostic implications in the diagnosis of these lesions. Here we review the current knowledge concerning the primary vascular neoplasms of the bone and correlate clinicopathologic features with tumor behavior.

Breast cancer: assessing response to neoadjuvant chemotherapy by using US-guided near-infrared tomography.

PURPOSE: To assess initial breast tumor hemoglobin (Hb) content before the initiation of neoadjuvant chemotherapy, monitor the Hb changes at the end of each treatment cycle, and correlate these findings with tumor pathologic response. MATERIALS AND METHODS: The HIPAA-compliant study protocol was approved by the institutional review boards of both institutions. Written informed consent was obtained from all patients. Patients who were eligible for neoadjuvant chemotherapy were recruited between December 2007 and May 2011, and their tumor Hb content was assessed by using a near-infrared imager coupled with an ultrasonography (US) system. Thirty-two women (mean age, 48 years; range, 32-82 years) were imaged before treatment, at the end of every treatment cycle, and before definitive surgery. The patients were graded in terms of their final pathologic response on the basis of the Miller-Payne system as nonresponders and partial responders (grades 1-3) and near-complete and complete responders (grades 4 and 5). Tumor vascularity was assessed from total Hb (tHb), oxygenated Hb (oxyHb), and deoxygenated Hb (deoxyHb) concentrations. Tumor vascularity changes during treatment were assessed from percentage tHb normalized to the pretreatment level. A two-sample two-sided t test was used to calculate the P value and to evaluate statistical significance between groups. Bonferroni-Holm correction was applied to obtain the corrected P value for multiple comparisons. RESULTS: There were 20 Miller-Payne grade 1-3 tumors and 14 grade 4 or 5 tumors. Mean maximum pretreatment tHb, oxyHb, and deoxyHb levels were significantly higher in grade 4 and 5 tumors than in grade 1-3 tumors (P = .005, P = .008, and P = .017, respectively). The mean percentage tHb changes were significantly higher in grade 4 or 5 tumors than in grade 1-3 tumors at the end of treatment cycles 1-3 (P = .009 and corrected P = .009, P = .002 and corrected P = .004, and P < .001 and corrected P < .001, respectively). DISCUSSION: These findings indicate that initial tumor Hb content is a strong predictor of final pathologic response. Additionally, the tHb changes during early treatment cycles can further predict final pathologic response.

Genomic and Molecular Characteristics of Ovarian Carcinosarcoma.

Ovarian carcinosarcoma (OCS) is a rare malignancy with a poor prognosis. It is a biphasic tumor with malignant epithelial and mesenchymal components. A few mutations commonly seen in cancer have been identified in OCS, including TP53, PIK3CA, c-myc, ZNF217, ARID1A, and CTNNB1. Some OCS tumors have shown vascular endothelial growth factor positivity and limited HER2 expression. There is evidence of homologous recombination deficiency in OCS. This malignancy can be categorized as copy number high but has not been shown to have a high tumor mutational burden. There are mixed findings regarding the presence of biomarkers targeted by immune checkpoint inhibitors in OCS. For treatments other than systemic chemotherapy, the data available are largely based on in vitro and in vivo studies. In addition, there are case reports citing the use of poly-ADP ribose polymerase inhibitors, vascular endothelial growth factor inhibitors, and immunotherapy with varying degrees of success. This review paper will discuss the molecular and genomic characteristics of OCS, which can guide future treatment strategies.

Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA.

Malignant peripheral nerve sheath tumor (MPNST), an aggressive soft-tissue sarcoma, occurs in people with neurofibromatosis type 1 (NF1) and sporadically. Whole-genome and multiregional exome sequencing, transcriptomic, and methylation profiling of 95 tumor samples revealed the order of genomic events in tumor evolution. Following biallelic inactivation of NF1, loss of CDKN2A or TP53 with or without inactivation of polycomb repressive complex 2 (PRC2) leads to extensive somatic copy-number aberrations (SCNA). Distinct pathways of tumor evolution are associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumors with H3K27me3 loss evolve through extensive chromosomal losses followed by whole-genome doubling and chromosome 8 amplification, and show lower levels of immune cell infiltration. Retention of H3K27me3 leads to extensive genomic instability, but an immune cell-rich phenotype. Specific SCNAs detected in both tumor samples and cell-free DNA (cfDNA) act as a surrogate for H3K27me3 loss and immune infiltration, and predict prognosis. SIGNIFICANCE: MPNST is the most common cause of death and morbidity for individuals with NF1, a relatively common tumor predisposition syndrome. Our results suggest that somatic copy-number and methylation profiling of tumor or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. This article is highlighted in the In This Issue feature, p. 517.

Chordoma.

CONTEXT.­: Chordomas are uncommon malignant neoplasms with notochordal differentiation encountered by neuropathologists, bone/soft tissue pathologists, and general surgical pathologists. These lesions most commonly arise in the axial skeleton. Optimal therapy typically involves complete surgical resection, which is often technically difficult owing to the anatomic location, leading to a high rate of recurrence. Lesions have been generally resistant to radiation and chemotherapy; however, experimental studies involving targeted therapy and immunotherapy are currently underway. OBJECTIVE.­: To summarize the clinical and pathologic findings of the various types of chordoma (conventional chordoma, dedifferentiated chordoma, and poorly differentiated chordoma), the differential diagnosis, and recent advances in molecular pathogenesis and therapeutic modalities that are reliant on accurate diagnosis. DATA SOURCES.­: Literature review based on PubMed searches containing the term "chordoma" that address novel targeted and immunomodulatory therapeutic modalities; ongoing clinical trials involved in treating chordoma with novel therapeutic modalities identified through the Chordoma Foundation and ClinicalTrials.gov; and the authors' practice experience combined with various authoritative texts concerning the subject. CONCLUSIONS.­: Chordoma is a clinically and histologically unique malignant neoplasm, and numerous diagnostic considerations must be excluded to establish the correct diagnosis. Treatment options have largely been centered on surgical excision with marginal results; however, novel therapeutic options including targeted therapy and immunotherapy are promising means to improve prognosis.

Navigation-assisted resection of tumoral calcinosis of the lumbosacral spine: illustrative case.

BACKGROUND: Tumoral calcinosis is an uncommon disease resulting from dystrophic calcium phosphate crystal deposition, with only 7% of cases involving the spine, and it may diagnostically mimic neoplasms. OBSERVATIONS: In this case, a 54-year-old woman with history of systemic scleroderma presented with 10 months of progressive left lumbosacral pain. Imaging revealed an expansile, 4 × 7-cm, well-circumscribed mass in the lumbosacral spine with L5-S1 neuroforaminal compression. Because intractable pain and computed tomography (CT)-guided needle biopsy did not entirely rule out malignancy, operative management was pursued. The patient underwent L4-S2 laminectomies, left L5-S1 facetectomy, L5 and S1 pediculectomies, and en bloc resection, performed under stereotactic CT-guided intraoperative navigation. Subsequently, instrumented fusion was performed with L4 and L5 pedicle screws and S2 alar-iliac screws. Pathological examination was consistent with tumoral calcinosis, with multiple nodules of amorphous basophilic granular calcified material lined by histiocytes. There was no evidence of recurrence or neurological deficits at 5-month follow-up. LESSONS: Because spinal tumoral calcinosis may mimic neoplasms on imaging or gross intraoperative appearance, awareness of this clinical entity is essential for any spine surgeon. A review of all case reports of lumbosacral tumoral calcinosis (n = 14 from 1952 to 2016) was additionally performed. The case featured in this report presents the first known case of navigation-assisted resection of lumbosacral tumoral calcinosis.

PAX8 Expression in Breast Cancer.

PAX8 expression is frequently detected in renal, thyroidal, and Müllerian carcinomas, and PAX8 immunohistochemistry is often used to confirm the origin of these tumors. Tumors metastatic to the breast may masquerade as primary breast lesions. PAX8 is strongly expressed in tumors of Müllerian origin and largely negative in breast primaries, but an immunohistochemical expression of PAX8 in breast cancer has not been systematically evaluated in a large series. We analyzed 266 cases of invasive carcinoma of the breast on tissue microarrays and whole tissue sections with a PAX8 monoclonal antibody. Both the extent (focal or diffuse) and intensity (weak, moderate, or strong) of nuclear staining were assessed in the tumor cells. In total, 16 cases (6.02%) were positive for PAX8 (12 with weak and 4 with moderate staining). Expression was diffuse in 7 cases and focal in 9 cases. All 16 PAX8-positive tumors were histologic grade III invasive ductal carcinomas, 13 of these were triple-negative, 2 were HER2-positive, only and 1 was progesterone receptor-positive only. Strong PAX8 nuclear expression was not seen in any of the cases. PAX8 was negative in breast tumors with neuroendocrine features. Our study demonstrated a low rate of PAX8 expression in breast cancer. When present, PAX8 expression was only seen in high-grade invasive ductal carcinomas, mostly triple-negative. The presence of PAX8 immunoreactivity alone cannot exclude mammary origin, especially when only weak to moderate staining is observed, so the correlation with available clinical and pathologic data helps to ensure an accurate diagnosis.

The Great Imposter: A Confusing Case of a Rare Renal Cell Carcinoma.

We report a 61-year-old male with sarcomatoid renal cell carcinoma (sRCC) in the context of multiple paraneoplastic syndromes, including thrombocytosis, leukemoid reaction, and paraneoplastic hepatopathy (Stauffer syndrome). The patient's clinical course was complicated by multiple medical challenges, extensive metastases, and persistent infection. This confusing presentation of a rare subtype of renal cell carcinoma (RCC) highlights the diverse and often misleading manifestations of this aggressive malignancy. Clinicians should be aware of the association between RCC, multiple paraneoplastic syndromes, and its propensity to present with systemic, non-renal symptoms.

Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs.

The Genomics of Malignant Peripheral Nerve Sheath Tumor (GeM) Consortium is an international collaboration focusing on multi-omic analysis of malignant peripheral nerve sheath tumors (MPNSTs), the most aggressive tumor associated with neurofibromatosis type 1 (NF1). Here we present a summary of current knowledge gaps, a description of our consortium and the cohort we have assembled, and an overview of our plans for multi-omic analysis of these tumors. We propose that our analysis will lead to a better understanding of the order and timing of genetic events related to MPNST initiation and progression. Our ten institutions have assembled 96 fresh frozen NF1-related (63%) and sporadic MPNST specimens from 86 subjects with corresponding clinical and pathological data. Clinical data have been collected as part of the International MPNST Registry. We will characterize these tumors with bulk whole genome sequencing, RNAseq, and DNA methylation profiling. In addition, we will perform multiregional analysis and temporal sampling, with the same methodologies, on a subset of nine subjects with NF1-related MPNSTs to assess tumor heterogeneity and cancer evolution. Subsequent multi-omic analyses of additional archival specimens will include deep exome sequencing (500×) and high density copy number arrays for both validation of results based on fresh frozen tumors, and to assess further tumor heterogeneity and evolution. Digital pathology images are being collected in a cloud-based platform for consensus review. The result of these efforts will be the largest MPNST multi-omic dataset with correlated clinical and pathological information ever assembled.

Anti-miRNA Oligonucleotide Therapy for Chondrosarcoma.

Chondrosarcoma is a highly aggressive primary malignant bone tumor mostly occurring in adults. There are no effective systemic treatments, and patients with this disease have poor survival. miR-181a is an oncomiR that is overexpressed in high-grade chondrosarcoma and promotes tumor progression. Regulator of G-protein signaling 16 (RGS16) is a target of miR-181a. Inhibition of RGS16 expression by miR-181a enhances CXC chemokine receptor 4 signaling, which in turn increases MMP1 and VEGF expression, angiogenesis, and metastasis. Here, we report the results of systemic treatment with anti-miRNA oligonucleotides (AMO) directed against miR-181a utilizing a nanopiece delivery platform (NPs). NPs were combined with a molecular beacon or anti-miR-181a oligonucleotides and are shown to transfect chondrosarcoma cells in vitro and in vivo Intratumoral injection and systemic delivery had similar effects on miR-181a expression in nude mice bearing chondrosarcoma xenografts. Systemic delivery of NPs carrying anti-miR-181a also restored RGS16 expression, decreased expression of VEGF and MMP1, MMP activity, and tumor volume by 32% at day 38, and prolonged survival from 23% to 45%. In conclusion, these data support that systemic delivery of AMO shows promise for chondrosarcoma treatment.

PET/CT Helps Downgrade an Aggressive-Appearing Rib Mass to a Probable Benign Lesion in a 9-Year-Old Girl.

We present a case of a 9-year-old girl with no significant medical history who developed acute onset of shortness of breath and upper chest pain during cheerleading practice. Laboratory results and physical examination were unremarkable. Chest radiograph and chest CT showed an expansile lytic aggressive-appearing mass within the left sixth rib. Subsequent F-FDG PET/CT showed a left sixth rib lesion that was not hypermetabolic and appeared benign. Biopsy yielded a diagnosis of enchondroma, a benign intramedullary tumor that accounts for 24% of all bone tumors in children as well as adolescents.

Epithelioid Schwannomas: An Analysis of 58 Cases Including Atypical Variants.

The histologic features and outcome of 58 cases of epithelioid schwannoma were studied to determine the significance of atypical histologic features. Cases were retrieved from personal consultation files from 1999 to 2013. Patients (31 male and 26 female patients) ranged in age from 14 to 80 years (median, 38 y). Two patients had schwannomatosis 1. Tumors developed in the dermis/subcutis (n=56) or muscle (n=2) of the upper extremity (34.5%), lower extremity (34.5%), thorax/abdomen/back (18%), and less common anatomic locations including the scalp, neck, lip, and breast. They ranged in size from 0.25 to 4.5 cm (median, 2.0 cm). Typically circumscribed and surrounded by a perineurium, they comprised single or small groups of epithelioid schwann cells with a moderate amphophilic cytoplasm and occasional nuclear pseudoinclusions. Stroma varied from myxoid to hyalinized, often with thick-walled vessels (55 cases). Mitotic rate ranged from 0 to 9 mitoses/10 high-power field (HPF) (2.37 mm) in the most active areas (mean, 2 to 3 mitoses/10 HPFs). Thirteen cases (22%) were "atypical," defined by a high mitotic rate (≥3 mitoses per 10 HPFs) and nuclear size variation (≥3:1). All (56/56) expressed S100 protein; type IV collagen invested groups or individual cells (16/17). Melanoma markers were negative, except for melan A (1 case). Follow-up in 39 patients (median, 78 mo; range, 6 to 174 mo) indicated that 31 (79%) were alive without disease (including 9/13 atypical cases; median, 78 mo), 7 (18%) were alive with unknown status, and 1 patient had died of unrelated causes. One tumor recurred, but none metastasized. Epithelioid schwannomas, even those with atypical features, are benign and do not constitute a histologic continuum with epithelioid malignant peripheral nerve sheath tumors, which typically occur in deep soft tissues and have more anaplastic features.

A case of recurrent desmoplastic malignant melanoma presenting as empyema with underlying lung mass.

Desmoplastic malignant melanoma (DMM) is an extremely rare subtype of cutaneous melanoma that has diverse clinical presentations. We describe the unique case of a 57-year-old man presenting with empyema secondary to vascular occlusion from metastatic DMM. Only two other cases of DMM presenting as a lung mass have been previously reported in the literature. This report highlights potential insidious pathology of DMM, which requires a high clinical suspicion to properly diagnose and manage.

IMP3 immunocytochemical staining increases sensitivity in the routine cytologic evaluation of biliary brush specimens.

Biliary brush cytology is an important diagnostic tool in the evaluation of biliary strictures. Here, we evaluated 64 patients with biliary strictures who underwent endoscopic retrograde cholangiopancreatography with bile duct brushings. We assessed the utility of combining routine Papanicolaou-stained cytologic evaluation with immunocytochemical expression of insulin-like growth factor mRNA-binding protein-3 (IMP3). Definitive diagnoses were obtained via tissue resection/autopsy, biopsy, fine needle aspiration, or clinical progression of disease. Thirty-nine of the 64 patients were ultimately diagnosed with malignancy. The sensitivity of routine cytology for the detection of malignancy was 33.3%, immunocytochemical-IMP3 expression was 64.1%, and the combined sensitivity was 71.8%. The specificity of each method was 100%. The sensitivity of IMP3 immunocytochemical staining in the detection of malignancy in biliary brushings was superior to routine PAP-stained cytologic evaluation. Moreover, the combined use of biliary brushing cytology and IMP3 immunohistochemistry proved superior to the use of either method alone.

Epithelioid angiosarcoma: a brief diagnostic review and differential diagnosis.

Epithelioid angiosarcoma is a highly aggressive endothelial cell malignancy, most commonly arising in the deep soft tissues, but a variety of primary sites, including the adrenals, thyroid, skin, and bone, are encountered. On hematoxylin-eosin-stained sections, the pathologist encounters sheets of large, mildly to moderately pleomorphic epithelioid cells, with abundant eosinophilic cytoplasm, vesicular nuclei, and prominent nucleoli. Obvious vasoformative foci may not be present, creating confusion with metastatic carcinomas, malignant mesothelioma, melanoma, anaplastic lymphoma, epithelioid peripheral nerve sheath malignancies, and epithelioid sarcoma. Moreover, malignancies with apparent vascular differentiation must be distinguished from less aggressive vascular neoplasms, including epithelioid hemangioendothelioma. Given the range of clinical presentation, the diversity of primary sites, and the nonspecific initial histopathologic appearance, here we review the histologic findings and immunohistochemical profiles of epithelioid angiosarcoma and neoplasms in its differential diagnosis.