No Remdesivir Resistance Observed in the Phase 3 Severe and Moderate COVID-19 SIMPLE Trials

Remdesivir (RDV) is a broad-spectrum nucleotide analog prodrug approved for the treatment of COVID-19 in hospitalized and non-hospitalized patients with clinical benefit demonstrated in multiple Phase 3 trials. Here we present SARS-CoV-2 resistance analyses from the Phase 3 SIMPLE clinical studies evaluating RDV in hospitalized participants with severe or moderate COVID-19 disease. The severe and moderate studies enrolled participants with radiologic evidence of pneumonia and a room-air oxygen saturation of ≤94% or >94%, respectively. Virology sample collection was optional in the study protocols. Sequencing and related viral load data were obtained retrospectively from participants at a subset of study sites with local sequencing capabilities (10 of 183 sites) at timepoints with detectable viral load. Among participants with both baseline and post-baseline sequencing data treated with RDV, emergent Nsp12 substitutions were observed in 4 of 19 (21%) participants in the severe study and none of the 2 participants in the moderate study. The following 5 substitutions emerged: T76I, A526V, A554V, E665K, and C697F. The substitutions T76I, A526V, A554V, and C697F had an EC50 fold change of ≤1.5 relative to the wildtype reference using a SARS-CoV-2 subgenomic replicon system, indicating no significant change in the susceptibility to RDV. The phenotyping of E665K could not be determined due to a lack of replication. These data reveal no evidence of relevant resistance emergence and further confirm the established efficacy profile of RDV with a high resistance barrier in COVID-19 patients.

Late Recurrence of Colorectal Carcinoma in Patients with Malignant Polyp and Risk Factors

Malignant polyps are polypoid lesions that appear benign endoscopically but harbor invasive adenocarcinoma microscopically. Patient with diagnosis of malignant polyp can be managed by surgical resection or endoscopic surveillance. Current literature on long term recurrence is sparse. A total of 76 patients with malignant polyp and follow-up period of over one year are included. Of these, 28 patients underwent endoscopic polypectomy followed by surveillance (group 1). Forty-eight patients underwent segmental colectomy (group 2). In group 1, three patients developed local recurrent pT3 adenocarcinoma (5.9 to 9.7 years) and one patient developed liver metastasis (7.3 years). One patient presented with malignant polyp in another segment of colon (4.0 years). Two of the malignant polyps with local recurrence do not have commonly reported high-risk features, including tumor ≤ 1 mm from resection margin, presence of lymphovascular invasion and high grade tumor, they had invasion depth of >4 mm and harbored a TP53 missense mutation. In group 2, during the follow-up period (1.0-21.8 years, median 9.3 years), none of the patients developed local recurrence. In this study, surveillance group had a local late recurrence rate of 10.7% versus no local recurrence in surgical resection group (0%). Our study shows that depth of invasion of over 4 mm in malignant polyp is a risk factor for late local recurrence if managed by endoscopic surveillance. Further study is needed to explore whether certain molecular alterations, such as TP53 mutation, is a risk factor for late recurrence.

The cytological features of effusions with mesothelioma in situ: A report of 9 cases

INTRODUCTION

The diagnosis of mesothelioma in situ (MIS) is now accepted by the WHO as a pre-invasive neoplastic mesothelial proliferation and considered a diagnosis based on histologic evaluation only. Although the definition of MIS includes recurrent effusions, little is known about the cytologic features of such effusions. Since mesothelioma is usually diagnosed at an advanced stage and has a poor prognosis, early detection of a neoplastic mesothelial population in such effusions can potentially have a positive impact on the management of such a dire disease.

MATERIALS AND METHODS

We reviewed a total of 18 pleural effusions from nine patients with recurrent effusions. Of these, five patients had follow-up biopsies diagnosed as MIS and the remaining four cases had negative radiology and malignant cytology proven by molecular markers (BAP1, MTAP or CDKN2A deletion) and at least 1 year follow-up with no overt mass identified by radiology.

RESULTS

Initial effusions may mimic reactive mesothelial hyperplasia or exhibit atypia. As effusions recur, the cellularity and atypia increase and the mesothelial proliferation becomes morphologically indistinguishable from mesothelioma. Molecular alterations diagnostic of mesothelioma can be detected in these effusions, even in the initial-benign/reactive appearing ones. The cellularity and atypia detected in such effusions surpassed those noted on the biopsies, raising questions regarding the cause of such discrepancy.

CONCLUSION

The diagnosis of MIS can be suspected based on malignant effusion cytology supported by molecular alterations. We propose that the proliferation of neoplastic mesothelial clones represent a clinically silent "liquid phase MIS stage" corresponding to in situ stage in other organs.

High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants

OBJECTIVES

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure.

METHODS

We used a tiered high-throughput SARS-CoV-2 screening program to characterize variants in a supraregional health system over 76 days. Combining targeted reverse transcription-polymerase chain reaction (RT-PCR) and selective sequencing, we screened SARS-CoV-2 reactive samples from all hospitals within our health care system for genotyping dominant and emerging variants.

RESULTS

The median turnaround for genotyping was 2 days using the high-throughput RT-PCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower cycle threshold value, lower age at infection, and increased vaccine-breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach.

CONCLUSIONS

These findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combining RT-PCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.

Implementation of a precision medicine thoracic (PREDICT) service using reflex testing in a large academic-community practice network

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Background: Broad genomic testing is necessary for treatment of patients with stage IV non-small cell lung cancer (NSCLC). This quality improvement initiative aims to implement a precision medicine service for NSCLC patients at a hybrid academic-community practice oncology network. Methods: Following IRB approval, network tumor registries were queried for retrospective newly diagnosed stage IV NSCLC from 01/2016 through 12/2018. PREDICT was implemented in 08/2021. It consists of: 1) system-wide reflex testing of newly diagnosed stage IV NSCLC patients by an in-house solid tumor focused assay (hybrid DNA/RNA next-generation sequencing (NGS) panel previously reported) and PD-L1 testing, 2) PREDICT navigator, 3) molecular tumor board (MTB), 4) integrated information portal for real-time updates on samples processing, results and treatment recommendations by the MTB. We compared prospective data (08/2021 through 01/2022) after PREDICT with retrospective practice assessment. Comparisons between the groups were conducted using independent samples t-test / Wilcoxon rank sum test for continuous variables and Chi-square test/Fisher’s exact test for categorical variables. Results: Of 861 retrospective patients identified in the compiled registry of stage IV NSCLC, 626 were eligible. Since PREDICT launch in 08/2021, 103 eligible prospective patients have been identified. Prospective patients are slightly older (mean age 70.9 vs 68 years old; p = 0.013), with no other significant demographic or clinical differences identified. Rates of NGS testing obtained within 90 days of biopsy date (BxD) increased significantly (94.1% vs 60.8%; p < 0.0001) after PREDICT. Turnaround times (TAT) from BxD to test results were significantly shorter for both NGS (12 vs 18 days; p < 0.0001) and PD-L1 (7 vs 10 days; p = 0.007) after PREDICT. A trend towards higher rates of actionable alterations (EGFR, ALK, ROS1, RET, BRAF, MET14 skipping, NTRK1/2/3) was noted: 19.6% vs 13% (p = 0.071). Targeted therapy use increased from 6.8% to 15.6% (p = 0.002) in the overall cohort. No differences in time to treatment initiation (TTI) after PREDICT have been identified to this point, with a median of 34 and 35 days for the prospective and retrospective groups, respectively. Conclusions: Implementing a precision medicine service for thoracic oncology patients has led to significantly higher rates of NGS testing for patients with stage IV NSCLC in a large hybrid academic-community practice network. Launching of this initiative resulted in significantly shorter TAT for both NGS and PD-L1 test results. A trend towards higher rates of actionable alterations has been identified. Targeted therapy use has increased significantly overtime, potentially due to higher availability of precision medicine drugs in the current era.

Flow Cytometric Findings in Clonal Cytopenia of Undetermined Significance

OBJECTIVES

To examine flow cytometric (FCM) findings in clonal cytopenia of undetermined significance (CCUS) in relation to variant allele fraction (VAF) and mutation risk.

METHODS

Nine FCM parameters, including 5 FCM metrics (Meyerson-Alayed scoring scheme [MASS] parameters) we previously used to identify myelodysplastic syndromes (MDS), were compared among 96 CCUS samples, 100 low-grade MDS samples and 100 samples from patients without somatic alterations (controls).

RESULTS

FCM findings did not differ between CCUS samples with less than 20% VAF and controls. CCUS samples with more than 20% VAF (CCUS >20% VAF) demonstrated more than 1 abnormal FCM parameter at a frequency between MDS and controls. Abnormalities in CCUS with high-risk alterations (CCUS(hi)) were similar to MDS, with no statistical difference in the percentage of cases with more than 1 FCM abnormality or a positive MASS score. The positive predictive value (PPV) for clinically significant myeloid processes; MDS, CCUS(hi), and CCUS >20% VAF compared with other CCUS samples and controls was 94.8%, with 96.5% specificity and 61% sensitivity using a modified MASS score. A subset of MDS (43%) was distinguished from CCUS(hi) and CCUS >20% VAF using 3 parameters, with a 93.5% PPV and 83.3% specificity.

CONCLUSIONS

FCM abnormalities can distinguish high-risk CCUS based on VAF or alteration type from low-risk CCUS and MDS in many cases. The findings are of potential utility in the evaluation of patients with cytopenias.

Deep Convolutional Neural Networks Implementation for the Analysis of Urine Culture

BACKGROUND

Urine culture images collected using bacteriology automation are currently interpreted by technologists during routine standard-of-care workflows. Machine learning may be able to improve the harmonization of and assist with these interpretations.

METHODS

A deep learning model, BacterioSight, was developed, trained, and tested on standard BD-Kiestra images of routine blood agar urine cultures from 2 different medical centers.

RESULTS

BacterioSight displayed performance on par with standard-of-care-trained technologist interpretations. BacterioSight accuracy ranged from 97% when compared to standard-of-care (single technologist) and reached 100% when compared to a consensus reached by a group of technologists (gold standard in this study). Variability in image interpretation by trained technologists was identified and annotation "fuzziness" was quantified and found to correlate with reduced confidence in BacterioSight interpretation. Intra-testing (training and testing performed within the same institution) performed well giving Area Under the Curve (AUC) ≥0.98 for negative and positive plates, whereas, cross-testing on images (trained on one institution's images and tested on images from another institution) showed decreased performance with AUC ≥0.90 for negative and positive plates.

CONCLUSIONS

Our study provides a roadmap on how BacterioSight or similar deep learning prototypes may be implemented to screen for microbial growth, flag difficult cases for multi-personnel review, or auto-verify a subset of cultures with high confidence. In addition, our results highlight image interpretation variability by trained technologist within an institution and globally across institutions. We propose a model in which deep learning can enhance patient care by identifying inherent sample annotation variability and improving personnel training.

Molecular detection of fowl adenovirus 7 from slaughtered broiler chickens in Iran: the first report

Background

Fowl adenoviruses (FAdVs) are responsible for a variety of clinical symptoms, with an increasing significance in the poultry industry throughout the world. Typical diseases caused by FAdVs include inclusion body hepatitis (IBH), hepatitis-hydropericardium syndrome (HHS), gizzard erosion (GE), respiratory disease, and hemorrhage in muscles and organs.

Aims

During 2020, broiler chickens from the north of Iran showed ecchymotic and petechial hemorrhages in thigh and breast muscles at the slaughterhouse. Hemorrhages were observed in 10% to 60% (with an average of 20-30%) of chicks per flock. To find out the etiology of these lesions, the present study was conducted.

Methods

Different environmental factors were investigated, and FAdV, infectious bursal disease virus (IBDV), and chicken infectious anemia virus (CIAV) were detected using molecular assays.

Results

Among the viruses tested, FAdV was detected by polymerase chain reaction (PCR), and sequence analysis clustered the virus into species E, serotype 7.

Conclusion

This is the first report on FAdV-7 existence among poultry in Iran. Effective screening of the chicks at slaughtering age should be performed from the whole country.

Molecular characterization of circulating avian metapneumovirus, subgroup B, in broiler chickens, Iran, 2016-2018

Background

Avian metapneumovirus (aMPV) infection has significant economic impacts on the poultry industry all around the world.

Aims

The aim of this study is molecular investigations of different types of aMPV in broiler farms in different provinces of Iran from 2016 to 2018.

Methods

Tracheal and oropharyngeal swabs were collected from two hundred broiler chickens with respiratory signs in ten provinces of Iran, including Kurdistan, West Azerbaijan, Semnan, Esfahan, Sistan and Baluchistan, Qazvin, Khuzestan, Fars, Gilan, and Khorasan Razavi from February 2016 to December 2018. After RNA extraction, the presence of aMPV was confirmed using N gene special primers. Then, subtype-specific primers were utilized to differentiate the specific subtype. All positive samples were sequenced.

Results

As a general trend, the percentage of aMPV positive chickens increased gradually over time. All samples were clustered together and placed in the subtype B aMPV group. Although 2 samples from 2016 and 2 samples from 2018 were placed in a separate branch, most of the current study samples of 2016, 2017, and 2018 revealed six segregated sub-branches, and they were placed close to other isolates of 2011 and 2013 from Iran.

Conclusion

The current field study indicated the presence of aMPV in a considerable number of areas in Iran. Thus, the role of this virus in broiler respiratory complex should not be neglected.

Clinical Utility of Targeted Next-Generation Sequencing in the Evaluation of Low-Grade Lymphoproliferative Disorders

OBJECTIVES

We investigated the usefulness of a custom-designed 31-gene next-generation sequencing (NGS) panel implemented on a routine basis for the evaluation of low-grade lymphoproliferative disorders (LPDs).

METHODS

In total, 147 blood, bone marrow, and tissue specimens were sequenced, including 81% B-cell, 15% T-cell, and 3% natural killer (NK)-cell neoplasms.

RESULTS

Of the cases, 92 (63%) of 147 displayed at least one pathogenic variant while 41 (28%) of 147 had two or more. Low mutation rates were noted in monoclonal B-cell lymphocytoses and samples with small T- and NK-cell clones of uncertain significance. Pathogenic molecular variants were described in specific disorders and classified according to their diagnostic, prognostic, and potential therapeutic value. Diagnostically, in addition to confirming the diagnosis of 15 of 15 lymphoplasmacytic lymphomas, 10 of 12 T large granular lymphocytic leukemias, and 2 of 2 hairy cell leukemias (HCLs), the panel helped resolve the diagnosis of 10 (62.5%) of 16 challenging cases lacking a specified diagnosis based on standard morphology, phenotype, and genetic analysis.

CONCLUSIONS

Overall, implementation of this targeted lymphoid NGS panel as part of regular hematopathology practice was found to be a beneficial adjunct in the evaluation of low-grade LPDs.

Molecular Profiling of Pediatric and Adult Glioblastoma

OBJECTIVES

Although glioblastoma (GBM) is rare in the pediatric population, it is the most common cause of death among children with central nervous system neoplasms. Recent molecular profiling of these neoplasms has demonstrated distinct differences in comparison to their adult counterparts. Moreover, many pediatric GBMs occur within the context of cancer predisposition syndromes, such as constitutional mismatch repair deficiency syndrome (CMMRD). Children with CMMRD who develop GBM exhibit a high tumor mutational burden and may benefit from treatment with immune checkpoint inhibitors.

METHODS

We performed next-generation sequencing and immunohistochemistry for mismatch repair proteins in our cohort of pediatric and adult GBMs to further characterize the molecular profiles of these groups.

RESULTS

We examined a total of 11 pediatric and 11 adult GBMs. Pediatric patients had a higher number of alterations compared to their adult counterparts. They also had a higher frequency of alterations in the mismatch repair genes, which can be detected by immunohistochemistry (IHC). We also identified one pediatric patient with CMMRD syndrome.

CONCLUSIONS

Our study highlighted the distinct molecular differences between pediatric and adult GBM. We also demonstrated that pediatric patients have a higher frequency of alterations in the mismatch repair genes, which may render them susceptible to treatment with immune checkpoint inhibitors. These alterations can be detected using routine IHC and should be performed on all pediatric GBM.

Clonal cytopenia of undetermined significance (CCUS) with dysplasia is enriched for MDS-type molecular findings compared to CCUS without dysplasia

OBJECTIVES

Although morphologic dysplasia is not typically considered a feature of CCUS, we have consistently observed low-level bone marrow (BM) dysplasia among CCUS patients. We sought to determine whether sub-diagnostic BM dysplasia in CCUS patients is associated with other clinico-pathologic findings of myelodysplastic syndrome (MDS).

METHODS

We identified 49 CCUS patients, 25 with sub-diagnostic dysplasia (CCUS-D), and 24 having no dysplasia (CCUS-ND). We compared the clinical, histologic, and laboratory findings of CCUS-D and CCUS-ND patients to 49 MDS patients, including blood cell counts, BM morphology, flow cytometry, cytogenetics, and results of next-generation sequencing.

RESULTS

No statistically significant differences were observed between CCUS-D and CCUS-ND patients in the degree of cytopenias, BM cellularity, myeloid-to-erythroid ratio, or the presence of flow cytometric abnormalities. However, compared to CCUS-ND, CCUS-D patients exhibited increased mutations in myeloid malignancy-associated genes, including non-TET2/DNMT3A/ASXL1 variants, spliceosome (SF3B1, SRSF2, ZRSR2, or U2AF1) variants, and IDH2/RUNX1/CBL variants. CCUS-D patients were also enriched for higher variant allele frequencies and co-mutation of TET2/DNMT3A/ASXL1 with other genes.

CONCLUSIONS

CCUS-D patients exhibit a molecular (but not clinical) profile more similar to MDS patients than CCUS-ND, suggesting CCUS-D may represent a more immediate precursor to MDS and may warrant closer clinical follow-up.

Tiny but mighty: use of next generation sequencing on discarded cytocentrifuged bile duct brushing specimens to increase sensitivity of cytological diagnosis

Bile duct brushing (BDB) is used to evaluate pancreatobiliary lesions as it widely samples lesions with a low complication rate. Cytological evaluation of BDB is a specific but insensitive test. There is limited literature on the use of post-cytocentrifuged (PCC) samples, which are usually discarded, for next-generation sequencing (NGS) as an adjunct to cytological diagnosis of BDB. In this study we investigate whether molecular analysis by NGS of PCC specimens improves the sensitivity of diagnosis. PCC samples from 100 consecutive BDB specimens spanning 93 unique patients were retained. DNA was extracted and mutational analysis was performed agnostic of morphologic or clinical findings. Each BDB specimen was characterized as negative, atypical or positive based on morphological analysis by trained cytopathologists. Performance characteristics for mutational profiling and morphological analysis were calculated on the basis of clinicopathologic follow-up. There was sufficient clinicopathologic follow-up to classify 94 of 100 cases as either malignant (n = 43) or benign (n = 51). Based on morphologic analysis of cytology, these 94 cases were classified as either benign (n = 55), atypical (n = 18), or as at least suspicious or positive for malignancy (n = 21). Morphologic analysis of cytology showed a sensitivity of 49% and a specificity of 100% if atypical cases were considered negative. NGS revealed oncogenic alterations in 40/43 (93%) of malignant cases based on clinicopathologic follow-up. The most common alterations were in KRAS and TP53, observed in 77% and 49% of malignant cases respectively. No alterations were observed in the 51 benign cases classified based on clinicopathologic follow-up. Supplementing cytomorphologic analysis with molecular profiling of PCC by targeted NGS analysis increased the sensitivity to 93% and maintained specificity at 100%. This study provides evidence for the utility of NGS molecular profiling of PCC specimens to increase the sensitivity of BDB cytology samples, although studies with larger cohorts are needed to verify these findings.

Use of cytology centrifuged supernatants improves cost and turnaround time for targeted next generation sequencing

BACKGROUND

Molecular testing is an essential step in providing patients with advanced non-small-cell lung cancer (NSCLC), the most appropriate front-line targeted therapies. We recently implemented targeted NGS on previously discarded cytology centrifuged supernatant (CCS).

METHODS

In this study, we reviewed our implementation process to evaluate its performance. Performance and turnaround time (TAT) of molecular testing on all cytology NSCLC cases submitted for targeted NGS from June 2018 to September 2019 were evaluated, which included 46 and 62 cytology cases before and after implementation of CCS, respectively. Associated cost savings using CCS was also analyzed.

RESULTS

The mean TAT defined as the time of collection to time of reporting was 8.5 ± 1.8 days in CCS cohort (range 5-13) as compared with 12.2 ± 5.3 days in the (FFPE) cell block (CB) cohort (range: 6-27). The success rate of sequencing was similar for both cohorts (100% in CCS and 96% in FFPE CB).

CONCLUSION

Our results demonstrate that NGS using CCS improves TAT, preserves FFPE CB for other testing, and results in cost savings of $50 per case.

Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases

OBJECTIVES

To report methods and findings of 2 autopsies with molecular evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals.

METHODS

Postmortem examination was completed following Centers for Disease Control and Prevention public guidelines. Numerous formalin-fixed paraffin-embedded (FFPE) tissue types from each case were surveyed for SARS-CoV-2 RNA by quantitative reverse transcription polymerase chain reaction (qRT-PCR). SARS-CoV-2 viral genome was sequenced by next-generation sequencing (NGS) from FFPE lung tissue blocks.

RESULTS

Postmortem examinations revealed diffuse alveolar damage, while no viral-associated hepatic, cardiac, or renal damage was observed. Viral RNA was detected in lungs, bronchi, lymph nodes, and spleen in both cases using qRT-PCR method. RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation.

CONCLUSIONS

SARS-CoV-2 testing and viral sequencing can be performed from FFPE tissue. Detection and sequencing of SARS-CoV-2 in combination with morphological findings from postmortem tissue examination can aid in gaining a better understanding of the virus's pathophysiologic effects on human health.

The emergence of Q1 genotype of avian infectious bronchitis virus in Iran, 2019: the first report

BACKGROUND

Avian infectious bronchitis (IB) is an infectious viral disease of chickens. The effective protection of chickens against many different infectious bronchitis virus (IBV) variants is not achieved unless the circulating genotypes in the region are identified and the cross-protection of the potential of vaccines in use is assessed.

AIMS

In a monitoring program of IBVs, a new genotype was identified in the north of Iran, 2019. This work was conducted to isolate and characterize this new IBV genotype.

METHODS

Tracheal tissues were collected from chickens showing signs of respiratory involvement. Specimens were homogenized and inoculated to the allantoic fluid of embryonated specific pathogen-free (SPF) eggs. Infectious bronchitis virus was detected using real time-polymerase chain reaction (RT-PCR). The hypervariable region of the IBV S1 gene was amplified for sequencing.

RESULTS

Positive samples were phylogenetically analyzed, and both positive isolates were clustered with Q1 IBV strains.

CONCLUSION

This is the first report of the Q1 outbreak in Iran. More investigations are needed to find the role of Q1 IBV in the respiratory disease complex of chickens.

Genotyping of avian infectious bronchitis virus in Afghanistan (2016-2017): the first report

BACKGROUND

Avian infectious bronchitis (IB) is a highly contagious viral disease which affects the poultry industry. The virus exists in a wide variety of genotypes, and phylogenetic analysis has been used to classify infectious bronchitis virus (IBV) strains.

AIMS

The object of the study is a molecular characterization of circulating IBV in Afghanistan as a first study.

METHODS

The tracheal tissue specimens from 100 different commercial broiler flocks with respiratory distress in Afghanistan were collected during 2016-2017. After real-time reverse transcriptase-polymerase chain reaction (RRT-PCR), IBV-positive samples were further characterized. A 390 bp hypervariable spike glycoprotein gene segment was amplified using Nested PCR, sequenced, and analyzed.

RESULTS

The results of real-time RT-PCR showed that 45/100 of the mentioned flocks were IBV positive. Phylogenetic analysis of all positive samples revealed that IBV strains were clustered into two distinct genotypes: LX4 (GI-19) (9/45) and IS-1494 like (GI-23) (34/45). Also, 2 of the 45 samples remained uncharacterized.

CONCLUSION

It is the first study focusing on the molecular epidemiology of IBV in Afghanistan, extending our understanding of IB in the region. These results showed the high rate of IB infection in Afghanistan broiler farms and confirm the continuing monitoring of IBVs to modify the vaccination program.

Molecular and pathologic characterization of AML with double Inv(3)(q21q26.2)

The inv(3)(q21q26.2) altering a single chromosome 3 homolog is an established myeloid malignancy-associated entity. Comparatively, double inv(3) cases involving both homologs are exceedingly rare with 13 reports across AML, CML and MDS. This scarcity was confirmed by finding only 2 new cases out of 34,898 bone marrows collected during a 55 year period at a large medical center (0.0005%). The double inv(3) was detected by karyotype and confirmed by FISH on both homologs in a 41 year old female and a 72 year old male with AML. In the latter case, a 2.26-fold increase in MECOM RNA level was found using an NGS myeloid gene panel. Chromosomal microarray analysis identified segmental copy-neutral loss-of-heterozygosity (CN-LOH) at 3q21 extending to near the q-arm terminus. This is the third report of distal 3q CN-LOH, substantiating that the double inv(3) arises through somatic repair of acquired segmental LOH. Long term clinical and genetic evaluation revealed no discernible morphologic difference between single and double inv(3) cases, conventional chemotherapy resistance and rapid dominance of the double inv(3) clone. The two new cases are consistent with relatively longer survival of double inv(3) patients in the absence of concurrent chromosome 7 loss compared to those with both abnormalities. Importantly, the first known outcome data of bone marrow transplantation in double inv(3) AML is also presented.

Clinical utility of reflex testing using focused next-generation sequencing for management of patients with advanced lung adenocarcinoma

AIMS

The growing number of genomically targeted therapies has made genomic testing an important part of the care for patients with non-small cell lung cancer. However, limited tissue availability, cost and long turnaround times can create barriers to efficient genomic testing and subsequent treatment. Effective approaches to reduce these barriers are needed.

METHODS

302 advanced lung adenocarcinomas from consecutive patients seen at University Hospitals Cleveland Medical Center (UHCMC) were tested inhouse using a hybrid DNA/RNA next-generation sequencing (NGS) panel. Sample testing was reflexed from pathology for all stage III or IV tumours. Genomic alterations were tiered according to their clinical relevance and reported with guideline-recommended therapies. Clinical implications of genomic testing results were assessed by manual chart review.

RESULTS

With a sample cohort consisting of 64% biopsies, 16% excisions/resections and 20% fine needle aspirations, the assay was reliable with a 95% success rate. The average turnaround time from receipt of unstained formalin-fixed paraffin embedded slides to reporting was 4.8±2.1 days, half of the recommended 10 days and similar to single-gene testing. Alterations with Food and Drug Administration-approved or the National Cancer Center Network guideline-recommended targeted therapies were found in 18% of cases. Within this group, 60% of patients went on genomically driven therapies.

CONCLUSIONS

We found our reflexed inhouse NGS assay to be reliable, cost-effective and efficient. Incorporation of reflex testing with our NGS assay led to an expansion of successful genomic profiling for all guideline-recommended alterations, and by including an expanded number of alterations within our panel we obtained clinically useful information outside the guidelines without changing cost or efficiency. This approach has enabled UHCMC clinicians to efficiently initiate genomically driven therapies for patients with lung adenocarcinoma.

Comparison of targeted next generation sequencing (NGS) versus isolated BRAF V600E analysis in patients with metastatic melanoma

Molecular testing on advanced metastatic melanoma is critical for guiding targeted therapy. Traditionally, this analysis has relied on isolated BRAF V600E analysis; however, more recently targeted next generation sequencing (NGS) is being utilized. The clinical utility of BRAF V600E allele-specific PCR and targeted NGS were compared for metastatic melanoma samples sent to UHCMC pathology during a two and half year span. In two thirds of cases, negative for BRAF V600E, additional mutations were detected that may stratify patients for potential or approved targeted therapies. Targeted-NGS testing is feasible and cost-affordable and provides additional potentially actionable information for patients with BRAF V600E/K negative metastatic melanoma. Based on this analysis, we have adopted to screen patients with advanced melanoma with allele-specific V600E/K PCR and reflex negative cases for targeted NGS to maximize patient benefit.

Epigenetic re-expression of HIF-2α suppresses soft tissue sarcoma growth

In soft tissue sarcomas (STS), low intratumoural O2 (hypoxia) is a poor prognostic indicator. HIF-1α mediates key transcriptional responses to hypoxia, and promotes STS metastasis; however, the role of the related HIF-2α protein is unknown. Surprisingly, here we show that HIF-2α inhibits high-grade STS cell growth in vivo, as loss of HIF-2α promotes sarcoma proliferation and increases calcium and mTORC1 signalling in undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma. We find that most human STS have lower levels of EPAS1 (the gene encoding HIF-2α) expression relative to normal tissue. Many cancers, including STS, contain altered epigenetics, and our findings define an epigenetic mechanism whereby EPAS1 is silenced during sarcoma progression. The clinically approved HDAC inhibitor Vorinostat specifically increases HIF-2α, but not HIF-1α, accumulation in multiple STS subtypes. Vorinostat inhibits STS tumour growth, an effect ameliorated by HIF-2α deletion, implicating HIF-2α as a biomarker for Vorinostat efficacy in STS.

Acinic cell carcinoma of breast: morphologic and immunohistochemical review of a rare breast cancer subtype

Acinic cell carcinoma of breast is a rare subtype of triple-negative breast carcinoma and demonstrates extensive morphologic overlap with acinic cell carcinoma of the salivary gland. In this study, we perform a detailed morphologic and immunohistochemical description of 2 cases of this rare entity and undertake a comprehensive review of all reported cases of breast acinic cell carcinoma in the English language literature to date. One-third of reported cases of breast acinic cell carcinoma have been associated with the presence of a ductal carcinoma not otherwise specified component, which is frequently poorly differentiated. Breast acinic cell carcinoma can demonstrate focal morphologic features similar to microglandular adenosis; these areas are frequently negative for collagen IV and laminin on immunohistochemistry. The true relationship between these 2 entities remains unclear, but we advocate that microglandular adenosis-like areas at the periphery of a breast acinic cell carcinoma should be considered part of the carcinomatous process and re-excised if this process extends to the initial surgical margins.

Malignant round cell tumor of bone with EWSR1-NFATC2 gene fusion

Gene rearrangements involving the Ewing sarcoma breakpoint region 1 (EWSR1) gene are seen in a broad range of sarcomas and some nonmesenchymal neoplasms. Ewing sarcoma is molecularly defined by a fusion of the EWSR1 gene (or rarely the related FUS gene) to a member of the E26 transformation-specific (ETS) family of transcription factors, frequently the EWSR1-FLI1 fusion. More recently, EWSR1 gene fusion to non-ETS family members, including the nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 2 (NFATC2) gene, has been reported in a histological variant of Ewing sarcoma. Here, we report a malignant round cell tumor of bone with an EWSR1-NFATC2 fusion gene. This report builds upon the unusual morphological and clinical presentation of bone neoplasms containing an EWSR1-NFATC2 fusion gene.

Hypoxia-dependent modification of collagen networks promotes sarcoma metastasis

Intratumoral hypoxia and expression of hypoxia-inducible factor-1α (HIF-1α) correlate with metastasis and poor survival in patients with sarcoma. We show here that hypoxia controls sarcoma metastasis through a novel mechanism wherein HIF-1α enhances expression of the intracellular enzyme procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2). We show that loss of HIF-1α or PLOD2 expression disrupts collagen modification, cell migration, and pulmonary metastasis (but not primary tumor growth) in allograft and autochthonous LSL-Kras(G12D/+); Trp53(fl/fl) murine sarcoma models. Furthermore, ectopic PLOD2 expression restores migration and metastatic potential in HIF-1α-deficient tumors, and analysis of human sarcomas reveals elevated HIF1A and PLOD2 expression in metastatic primary lesions. Pharmacologic inhibition of PLOD enzymatic activity suppresses metastases. Collectively, these data indicate that HIF-1α controls sarcoma metastasis through PLOD2-dependent collagen modification and organization in primary tumors. We conclude that PLOD2 is a novel therapeutic target in sarcomas and successful inhibition of this enzyme may reduce tumor cell dissemination.

SIGNIFICANCE

Undifferentiated pleomorphic sarcoma (UPS) is a commonly diagnosed and particularly aggressive sarcoma subtype in adults, which frequently and fatally metastasizes to the lung. Here, we show the potential use of a novel therapeutic target for the treatment of metastatic UPS, specifi cally the collagen-modifying enzyme PLOD2.

Hypoxia-inducible factors: mediators of cancer progression; prognostic and therapeutic targets in soft tissue sarcomas

Soft-tissue sarcomas remain aggressive tumors that result in death in greater than a third of patients due to either loco-regional recurrence or distant metastasis. Surgical resection remains the main choice of treatment for soft tissue sarcomas with pre- and/or post-operational radiation and neoadjuvant chemotherapy employed in more advanced stage disease. However, in recent decades, there has been little progress in the average five-year survival for the majority of patients with high-grade soft tissue sarcomas, highlighting the need for improved targeted therapeutic agents. Clinical and preclinical studies demonstrate that tumor hypoxia and up-regulation of hypoxia-inducible factors (HIFs) is associated with decreased survival, increased metastasis, and resistance to therapy in soft tissue sarcomas. HIF-mediated gene expression regulates many critical aspects of tumor biology, including cell survival, metabolic programming, angiogenesis, metastasis, and therapy resistance. In this review, we discuss HIFs and HIF-mediated genes as potential prognostic markers and therapeutic targets in sarcomas. Many pharmacological agents targeting hypoxia-related pathways are in development that may hold therapeutic potential for treating both primary and metastatic sarcomas that demonstrate increased HIF expression.

Proximal-type Epithelioid Sarcoma of the Head and Neck (HN): A Study with Immunohistochemical and Molecular Analysis of SMARCB1

Proximal-type epithelioid sarcoma is an aggressive variant of epithelioid sarcoma most often occurring in soft tissues of the proximal limbs, characterized by polygonal cells, marked nuclear atypia, and varied rhabdoid features. Malignant rhabdoid tumor is an aggressive, well characterized entity typically with rhabdoid morphology and involving the kidney of pediatric patients. Rarely, tumors with morphologic and biologic features identical to those in kidney occur in extra-renal sites and are regarded as an extrarenal presentation of the same entity in kidney, named malignant extra-renal rhabdoid tumor. Morphologic and immunophenotypical similarities between proximal-type epithelioid sarcoma and malignant rhabdoid tumor pose a diagnostic challenge and may suggest a relationship between the two. Both tumors are characterized by loss of SMARCB1 (INI1/BAF47/SNF5) expression; however, the molecular events involved differ. Here we describe the immunohistochemical and molecular analysis of three head and neck tumors with morphologic features shared by proximal-type epithelioid sarcoma and malignant rhabdoid tumor. All tumors showed loss of SMARCB1expression. Direct sequencing of the promoter and nine coding exons of SMARCB1, multiplex ligation-dependent probe amplification, and whole genome single nucleotide polymorphism array were performed on the two adult cases and showed only a heterozygous deletion of chromosome 22 in a minority of cells in one of the cases. Though rare, proximal-type epithelioid sarcoma could occur in the head and neck and should be differentiated from other epithelioid tumors by the loss of SMARCB1 expression. The lack of detectable genetic alteration in the SMARCB1 locus in head and neck proximal-type epithelioid sarcoma warrants further investigation into the molecular mechanism underlying loss of SMARCB1 expression.

mRNA decay factor AUF1 maintains normal aging, telomere maintenance, and suppression of senescence by activation of telomerase transcription

Inflammation is associated with DNA damage, cellular senescence, and aging. Cessation of the inflammatory cytokine response is mediated in part through cytokine mRNA degradation facilitated by RNA-binding proteins, including AUF1. We report a major function of AUF1-it activates telomerase expression, suppresses cellular senescence, and maintains normal aging. AUF1-deficient mice undergo striking telomere erosion, markedly increased DNA damage responses at telomere ends, pronounced cellular senescence, and rapid premature aging that increases with successive generations, which can be rescued in AUF1 knockout mice and their cultured cells by resupplying AUF1 expression. AUF1 binds and strongly activates the transcription promoter for telomerase catalytic subunit Tert. In addition to directing inflammatory cytokine mRNA decay, AUF1 destabilizes cell-cycle checkpoint mRNAs, preventing cellular senescence. Thus, a single gene, AUF1, links maintenance of telomere length and normal aging to attenuation of inflammatory cytokine expression and inhibition of cellular senescence.

AUF1 is involved in splenic follicular B cell maintenance

BACKGROUND

The adenosine/uridine-rich element (ARE)-binding protein AUF1 functions to regulate the inflammatory response through the targeted degradation of cytokine and other mRNAs that contain specific AREs in their 3' noncoding region (3' NCR). To investigate the role of AUF1 in the immune system, we characterized the lymphoid compartments of AUF1-deficient mice.

RESULTS

Mice lacking AUF1 exhibit an altered proportion and size of splenic B cell subsets. We show prominent apoptosis in splenic B cell follicles and reduced expression of Bcl-2, A1, and Bcl-XL correlate with increased turnover and significant reduction in the number and proportion of splenic FO B cells in AUF1-deficient mice. In addition, AUF1-deficient mice exhibit a sharp decrease in splenic size and lymphocyte cellularity. Bone marrow transfer studies demonstrate that AUF1 deficiency induces cell-autonomous defects in mature B cell subsets but not in the overall number of splenocytes. Reconstitution of irradiated adult AUF1-deficient mice with wild-type bone marrow restores the proportion of FO and marginal zone (MZ) B cells, but does not rescue the decrease in the number of splenocytes. Functionally, AUF1-deficient mice mount an attenuated response to T cell-independent (TI) antigen, which correlates with impaired MZ B cell function.

CONCLUSION

These data indicate that AUF1 is important in the maintenance of splenic FO B cells and adequate humoral immune responses.

Similar regulation of human inducible nitric-oxide synthase expression by different isoforms of the RNA-binding protein AUF1

The ARE/poly-(U) binding factor 1 (AUF1), a protein family consisting of four isoforms, is believed to mediate mRNA degradation by binding to AU-rich elements (ARE). However, evidence exists that individual AUF1 isoforms may stabilize ARE-containing mRNAs. The 3'-untranslated region of the human inducible nitric-oxide synthase (iNOS) contains five AREs, which promote RNA degradation. We have recently shown that the RNA-binding protein KSRP is critically involved in the decay of the iNOS mRNA. In this study we examined the effects of the individual AUF1 isoforms on iNOS expression. Overexpression of each AUF1 isoform reduces iNOS expression on mRNA and protein levels to the same extent by modulation of mRNA stability. Accordingly, knockdown of all or individual AUF1 isoforms by an RNA interference approach enhances iNOS expression. The AUF1 effect on iNOS expression is dependent on the iNOS 3'-untranslated region sequence, as demonstrated in transfection experiments with a reporter mRNA. Binding studies showed that all AUF1 isoforms interact with the same AU-rich region in the iNOS-3'-untranslated region. Cytokine stimulation altered intracellular AUF1 binding activities. These data demonstrate that AUF1 is an important factor that promotes iNOS mRNA degradation. Furthermore, all individual AUF1 isoforms act in a similar manner.

Members of the NuRD chromatin remodeling complex interact with AUF1 in developing cortical neurons

Chromatin remodeling plays an important role in coordinating gene expression during cortical development, however the identity of molecular complexes present in differentiating cortical neurons that mediate the process remains poorly understood. The A + U-rich element-binding factor 1 (AUF1) is a known regulator of messenger RNA stability and also acts as a transcription factor upon binding to AT-rich DNA elements. Here we show that AUF1 is specifically expressed in subsets of proliferating neural precursors and differentiating postmitotic neurons of the developing cerebral cortex. Moreover, AUF1 is coexpressed with histone deacetylase 1 (HDAC1) and metastasis-associated protein 2 (MTA2), members of the nucleosome remodeling and histone deacetylase complex. AUF1 specifically and simultaneously binds to HDAC1, MTA2, and AT-rich DNA element, its gene regulatory function is modulated by the extent of histone acetylation and in animals lacking AUF1, the composition of the complex is modified. These results suggest that AUF1 is involved in integrating genetic and epigenetic signals during cortical development through recruiting HDAC1 and MTA2 to AT-rich DNA elements.

Endotoxic shock in AUF1 knockout mice mediated by failure to degrade proinflammatory cytokine mRNAs

Excessive production of proinflammatory cytokines, particularly tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta), plays a critical role in septic shock induced by bacterial endotoxin (endotoxemia). Precise control of cytokine expression depends on rapid degradation of cytokine mRNAs, mediated by an AU-rich element (ARE) in the 3' noncoding region and by interacting ARE-binding proteins, which control the systemic inflammatory response. To understand the function of the ARE-binding protein AUF1, we developed an AUF1 knockout mouse. We show that AUF1 normally functions to protect against the lethal progression of endotoxemia. Upon endotoxin challenge, AUF1 knockout mice display symptoms of severe endotoxic shock, including vascular hemorrhage, intravascular coagulation, and high mortality, resulting from overproduction of TNFalpha and IL-1beta. Overexpression of these two cytokines is specific, and shown to result from an inability to rapidly degrade these mRNAs in macrophages following induction. Neutralizing antibodies to TNFalpha and IL-1beta protect AUF1 knockout mice against lethal endotoxic shock. These and other data describe a novel post-transcriptional mechanism whereby AUF1 acts as a crucial attenuator of the inflammatory response, promoting the rapid decay of selective proinflammatory cytokine mRNAs following endotoxin activation. Defects in the AUF1 post-transcriptionally controlled pathway may be involved in human inflammatory disease.

Assembly of AUF1 with eIF4G-poly(A) binding protein complex suggests a translation function in AU-rich mRNA decay

An AU-rich element (ARE) located in the 3'-untranslated region of many short-lived mRNAs functions as an instability determinant for these transcripts. AUF1/hnRNP D, an ARE-binding protein family consisting of four isoforms, promotes rapid decay of ARE-mRNAs. The mechanism by which AUF1 promotes rapid decay of ARE-mRNA is unclear. AUF1 has been shown to form an RNase-resistant complex in cells with the cap-initiation complex and heat shock proteins Hsp70 and Hsc70, as well as other unidentified factors. To understand the function of the AUF1 complex, we have biochemically investigated the association of AUF1 with the components of the translation initiation complex. We used purified recombinant proteins and a synthetic ARE RNA oligonucleotide to determine the hierarchy of protein interactions in vitro and the effect of AUF1 binding to the ARE on the formation of protein complexes. We demonstrate that all four AUF1 protein isoforms bind directly and strongly to initiation factor eIF4G at a C-terminal site regardless of AUF1 interaction with the ARE. AUF1 is shown to directly interact with poly(A) binding protein (PABP), both independently of eIF4G and in a complex with eIF4G. AUF1-PABP interaction is opposed by AUF1 binding to the ARE or Hsp70 heat shock protein. In vivo, AUF1 interaction with PABP does not alter PABP stability. Based on these and other data, we propose a model for the molecular interactions of AUF1 that involves translation-dependent displacement of AUF1-PABP complexes from ARE-mRNAs with possible unmasking of the poly(A) tail.

An integrated stress response regulates amino acid metabolism and resistance to oxidative stress

Eukaryotic cells respond to unfolded proteins in their endoplasmic reticulum (ER stress), amino acid starvation, or oxidants by phosphorylating the alpha subunit of translation initiation factor 2 (eIF2alpha). This adaptation inhibits general protein synthesis while promoting translation and expression of the transcription factor ATF4. Atf4(-/-) cells are impaired in expressing genes involved in amino acid import, glutathione biosynthesis, and resistance to oxidative stress. Perk(-/-) cells, lacking an upstream ER stress-activated eIF2alpha kinase that activates Atf4, accumulate endogenous peroxides during ER stress, whereas interference with the ER oxidase ERO1 abrogates such accumulation. A signaling pathway initiated by eIF2alpha phosphorylation protects cells against metabolic consequences of ER oxidation by promoting the linked processes of amino acid sufficiency and resistance to oxidative stress.