Specific Subtyping Research Articles

Precision Medicine in Alzheimer’s Disease: Phenotype Investigation, Medication Effects and Variant Analysis in Cell Type Specific Subgroups

AbstractBackgroundAlzheimer’s disease (AD) is characterized by cognitive decline and dementia and has few clinically approved treatments. The clinical and neuropathological heterogeneity of AD suggests the existence of AD subgroups with unique mechanisms and implies the need for cell‐type specific subtyping and treatments. The goal of this project was to investigate the differential effects of medications on cognitive tests in eight previously defined brain cell type‐based polygenic risk scores (PRS).MethodMedication usage information, imputed genotypes, phenotypic data and cognitive test scores were collected for 487,409 participants from the UK Biobank to use in the analysis of the different PRS groups. We determined the characteristics of the PRS used by comparing 16 phenotypes in high and low risk subjects. Association between four cognitive test scores (fluid intelligence, reaction time, prospective memory, and pairs matching) and medication status (treated vs. untreated) was determined using logistic regression. Cognitive scores were rank‐transformed for the analysis, and the logistic regression was performed separately for high‐risk and low‐risk genetic groups. Genome‐wide association studies (GWAS) were used to detect genetic variants linked to medication usage. This analysis was repeated for all, high risk and low risk samples, using only medications that demonstrated a significant association with improved cognitive function during follow up examination.ResultPhenotypic variation was wide among different PRS groups. Genetically different PRS groups shared phenotypic characteristics, suggesting that different underlying mechanisms lead to similar outcomes. Six medications were significantly associated (P<0.05) with improved cognitive function during follow‐up examination. Atenolol, a high blood pressure medication, was associated with the largest gain, with an improvement on the effect of cognitive function by 67% in the high‐risk compared to the low‐risk subjects from an astrocyte genetic subtype (Ast‐M9). The atenolol GWAS focused on the Ast‐M9 high risk group identified two genome wide significant variants at the same locus. These were previously shown to be associated with phenotypes related to blood pressure and were known eQTLs.ConclusionOur findings suggest potential novel implications for genetic subtype‐driven treatment options for AD. Further research is needed to validate these associations that may explain differential effects of medications in AD‐subtypes.

DNA damage response (DDR) variants and effects on the tumor transcriptome and microenvironment in east Asian (EA) prostate cancers (PCa).

75 Background: Aberrations of the DDR pathway have been shown to be prognostic of survival and predictive of PARP inhibition in PCa. We have previously reported on the prevalence of germline DDR mutations based on a 32-gene set in localized PCa in EA men, and observed comparable rates with that of White men. Here, we performed additional analyses investigating for associations between DDR variants to the somatic transcriptome of localized PCa. Methods: We utilized a prospectively recruited cohort of 172 EA patients, with centrally assessed Gleason’s score (GS) by an expert pathologist. Germline profiling was performed by whole exome sequencing (100X) using the Illumina Novaseq (CA). Joint genotyping was performed to annotate variants that were deemed to be pathogenic (P)/likely pathogenic (LP)/conflict of interest pathogenic (CIP) based on the CADD and REVEL scores. Tumor transcriptome was profiled using the Decipher Genomic Classifier (GC, Veracyte, CA) based on the Affymetrix ST array (ThermoFisher, CA). Results: Among the subset of 172 EA men, we observed DDR variants in 26 (15%) patients, which was comparable to the larger cohort of 890 men from the same institution. Among the DDR mutations, 2 (7.7%) were classified as P/LP, while 24 (92.3%) were CIP. Decipher GC scores were comparable between patients with and without DDR mutations (median GC score 0.87 vs 0.53, Mann-Whitney U P=0.10). For luminal-basal subtyping by either the PAM50 and Prostate specific subtyping models, we did not observe a difference for the basal (P=0.48) and luminal subtypes (P=0.21). Interestingly, DNA repair gene-set expression were comparable between patients with DDR mutations versus those without (median score -0.2 vs -0.17). However, we observed microenvironment differences for immune-related genes, where patients harboring DDR mutations manifested a less immune-suppressive environment versus those without (PDL2: -0.15 vs 0.2; Treg: 0.09 vs 0.13; MDSC: 0.03 vs 0.07, respectively). Conclusions: Herein, we report an extension of our previous work (Lua, et al. ASCO GU, 2023), where we show potential linkages between the germline DDR variant status and the tumor transcriptome. Our findings suggest the influence of germline DDR variants that extends beyond tumorigenesis.

Rectal cancer–specific subtyping using transcriptomics datasets derived from treatment-naive patients to assess novel prognostic signatures and key differences to CMS-based subtyping.

235 Background: Molecular subtyping in colorectal cancer provided novel insights into tumour heterogeneity and delivered new prognostic signatures. Existing methods (such as CMS-based subtyping) were generated without much consideration of differences in expression profiles between colon and rectal cancer tissues. Moreover, stage 2 and 3 rectal cancer patients often receive neo-adjuvant radio-chemotherapy which may impact on gene expression when determined from resection samples. Methods: We investigated possible differences between treatment-naive colon and rectal cancers at the molecular level. We collected mRNA expression profiles for rectal and colon cancer samples available from Gene Expression Omnibus (GEO) database (n=2139) and applied batch-effect correction using ComBat. Results: To explore whether CMS subtypes changed after neoadjuvant chemoradiation in rectal cancers, we analysed rectal tumour samples from 40 patients where both pre-operative biopsies and resections after chemoradiotherapy were available. More than half of samples shifted from CMS1-3 to CMS4 after patients received chemoradiotherapy. We therefore focused our further analysis on treatment-naive rectal cancers. We observed that CMS-based subtyping showed different prognostic potential in treatment-naïve colon vs. rectal cancers. Rectal cancers had significantly better disease-free survival (DFS) when assigned to CMS 2 or 4 compared to colon cancers. This suggested differences in disease biology that were not captured by CMS subtyping. We next aimed to identify molecular subtypes in rectal cancers, and identified three prevalent rectal-specific subtypes (RSS) by applying hierarchical clustering in 182 untreated rectal cancer samples. We used gene co-expression network analysis to define functional gene modules to identify these subtypes. Based on the gene modules’ signatures, we built a classifier to predict our new subtypes in different transcriptomics datasets (n=692). We observed that RSS1 had better disease-free survival (DFS), whereas RSS2 exhibited worse short-term DFS (less than 3 years) and RSS3 showed worse long-term DFS (3+ years). We discovered the deactivation of EGFR, MAPK and WNT pathways on RSS3 as well as high CD8+ infiltration and low CD4+ counts in these tumours. RSS2 exhibits low plasma cell and regulatory T-cell abundance and high activations of TGF-β, NF-κB, and TNF-α. We also observed high EMT, angiogenesis and inflammatory response in this subtype. Lastly, RSS1 showed high expression on MYC target and low activity on angiogenesis genes. Moreover, the immune and inflammatory responses were also lower than in the other subtypes. Conclusions: Rectal-specific subtypes are of prognostic importance and provide new insight into molecular disease pathways and potential targets.

Abstract 1722: Novel multiplex liquid biopsy detection of ALK and ROS1 rearrangements and intratumoral heterogeneity in lung cancer using circulating tumor cells (CTCs) isolated from NSCLC patient bloods and TR-CytoTrapNanoTM technology

Abstract Introduction: ALK and ROS1 rearrangements are common gene alterations found in subsets of patients with NSCLC. Identification of ALK and ROS1 rearrangement in NSCLC is critical for highly active targeted therapies aiming for these two main tumorigenic drivers. Due to the similarity of tyrosine kinase domains between ALK and ROS1, many ALK inhibitors are also functional in treatment of ROS1 subtype NSCLC. For example, crizotinib, which is a standard therapy for advanced ALK-rearranged NSCLC is highly effective in advanced ROS1-rearranged genotype NSCLC patients. The mutational analysis of these genes requires serial tumor biopsying from primary lesions, which requires high risk clinical procedures. Further, the current tissue-based diagnostics, such as fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are known to be challenging technically with limited sensitivity, subjective interpretation and inaccuracy in monitoring the current tumor status. The TR-CytoTrapNanoTM CTC technology is a blood-based assay to utilize CTCs as a biosource for mRNA extraction to detect genetic alteration or gene expression profiles including ALK and ROS1 gene rearrangements. In this study, we determined the variant specific expression of ALK fusion transcripts (EML4-ALK, KIF-ALK, and TGF-ALK) and ROS1 fusion transcripts (EZR-ROS1, SDC4-ROS1, TPM3-ROS1, LRIG3-ROS1, GOPC-ROS1, CD74-ROS1, and SLC34A2-ROS1) using multiplex digital droplet polymerase chain reaction(ddPCR) technology. Method: The Peripheral Blood Mononuclear Cells isolated from NSCLC patient bloods run through the TR-CytoTrapNanoTM microfluidic system. The CTCs are enriched and captured on the chip surface conjugated with Anti-EpCAM targeting antibody, which specifically binds to CTCs of epithelial origin. Following lysis step facilitate total RNA release from trapped CTCs and then pure mRNAs are isolated using oligo-dT conjugated magnetic beads. The mRNAs are used for following ALK and ROS1 specific reverse transcription reaction to make cDNAs for either ALK or ROS1 fusion transcripts. The specific subtyping of ALK and ROS1 rearrangement are then validated using ddPCR. Results and Conclusion: We tested several liquid biopsies from ALK and ROS1 rearrangement positive patients and corresponding positive data to FISH assays using solid tumor biopsies. Interestingly, some of the CTCs harboring ALK and ROS1 rearrangement has shown high intratumor heterogeneity in the subtypes of fusion partners. we envision that our novel TR-CytoTrapNanoTM CTC ALK/ROS1 rearrangement Assay to monitor treatment response and recurrence in NSCLC patients will be used to monitor treatment response and disease recurrence following treatment with Tyrosine Kinase Inhibitors (TKIs). Note: This abstract was not presented at the meeting. Citation Format: sangjun lee. Novel multiplex liquid biopsy detection of ALK and ROS1 rearrangements and intratumoral heterogeneity in lung cancer using circulating tumor cells (CTCs) isolated from NSCLC patient bloods and TR-CytoTrapNanoTM technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1722. doi:10.1158/1538-7445.AM2017-1722

P3.01-020 Evolving Trends in Lung Cancer Pathology: Topic: Morphology

The Danish Lung Cancer Registry has since 2003 reported all cases of lung cancer in Denmark including the pathology. We present the trends over time in the distribution of subgroups of pathology. All Danish lung cancer patients are ascertained based on coded information in the National Patient Register. Supplementary information for each patient is obtained from the clinical units as well as from the National Pathology Register (NPR). Based on SNOMED coding the patients is categorized in 12 subgroups of lung cancer. Figure 1Trends in lung cancer pathology (%)View Large Image Figure ViewerDownload Hi-res image Download (PPT) The increased number of lung cancer falls mainly in the adenocarcinoma group. Moreover, there is a significant relative increase of adenocarcinomas corresponding with a decrease of patients with NOS and NSCC. The occurrences of the other categories, including small cell carcinoma and squamous carcinoma, have remained largely unchanged. The trend of adenocarcinoma as the predominate type of lung cancer is in accordance with the global evolution. The high frequency is partly due to the need for specific subtyping and the agreement of diagnostic criteria which has resulted in a shift from NOS and NSCC categories to adenocarcinoma.

Identifying Specific Clinical Symptoms of Behavioral Variant Frontotemporal Dementia Versus Differential Psychiatric Disorders in Patients Presenting With a Late-Onset Frontal Lobe Syndrome.

Early differentiation between psychiatric disorders and behavioral variant frontotemporal dementia (bvFTD) is of paramount importance in patients with the late-onset frontal lobe syndrome. As bvFTD in patients will deteriorate, psychiatric disorders are treatable. To date, misdiagnosis often occurs due to an overlap of symptoms and lack of specific biomarkers. The aim of our study was to investigate whether specific symptoms could separate bvFTD from psychiatric disorders. In a naturalistic, prospective, multicenter study, 137 patients (aged 45-75 years, 72% male) with a late-onset frontal lobe syndrome were included based on their scores on the Frontal Behavioral Inventory (FBI) and the Stereotypy Rating Inventory (SRI) from April 2011 to June 2013. In a multidisciplinary consensus meeting, diagnoses were established based on elaborate neuropsychological testing, magnetic resonance imaging, fludeoxyglucose F 18 positron emission tomography, cerebrospinal fluid biomarkers, and clinical examination by a neurologist and a psychiatrist based on the International bvFTD Criteria Consortium for bvFTD and DSM-IV-TR criteria for psychiatric disorders. Forty-four subjects (32.8%) were diagnosed with a psychiatric disorder, 10 (7.3%) with possible bvFTD, and 45 (32.8%) with probable bvFTD. A logistic regression analysis was performed with "psychiatry or bvFTD" as dependent variable and clinical variables (Montgomery-Asberg Depression Rating Scale [MADRS], SRI, FBI) and demographics as independent variables. A positive history of psychiatric illness, male gender, lower SRI scores and higher MADRS scores were predictive of psychiatric disorders, explaining 65.2% of the variance in diagnosis of psychiatry versus bvFTD (χ²₅ = 60.04, P < .001). On the FBI, symptom level verbal apraxia/aphasia and impulsivity were predictive of bvFTD, whereas irritability was predictive of psychiatric disorders. In daily clinical practice, specific subtyping of clinical symptoms in patients with late-onset frontal lobe syndrome may aid in differentiating bvFTD patients from psychiatric patients and may provide guidance in patient management.

Diagnostic concordance of non-small cell lung carcinoma subtypes between biopsy and cytology specimens obtained during the same procedure.

The objectives of this study were: 1) to determine the diagnostic concordance of non-small cell lung carcinoma (NSCLC) subtypes in cytology and biopsy specimens taken during the same procedure and evaluate the causes of discordance; and 2) to determine the frequency of immunohistochemistry (IHC) use for subtyping NSCLC. Biopsy and cytology specimens that were obtained at the same procedure and diagnosed as NSCLC between January 2011 and December 2014 at the McGill University Health Center were identified (n = 226 pairs). The diagnostic concordance between the 2 methods was evaluated. The slides from discordant cases were reviewed, and final diagnoses were made based on IHC, resection specimens, or pathologist discussion. Concordance in subtype diagnosis was perfect (adeno-adeno or squamous-squamous) in 66.2% of cases and was partial (adeno or squamous vs non-small cell) in 23%; discordance (adeno vs squamous) was observed in 7.8%. Although subtyping was not possible (ie, the final diagnosis was NSCLC, not otherwise specified) in 12.8% of biopsy specimens and 16.3% of cytology specimens, specific subtyping was not achieved in only 3% of cases when both modalities were considered. IHC was used in 47% of biopsy cases and 13% of cytology cases. Subtyping of NSCLC can be achieved in most cases (97%) by considering findings in both biopsy and cytology specimens, and concordance in subtyping between cytology and biopsy specimens can be reached in a high percentage of cases (89.2%). Cancer Cytopathol 2016;124:737-43. © 2016 American Cancer Society.

A single EBUS-TBNA procedure can support a large panel of immunohistochemical stains, specific diagnostic subtyping, and multiple gene analyses in the majority of non–small cell lung cancer cases

Targeted therapies for pulmonary adenocarcinoma (ACA) necessitate specific subtyping and molecular testing of non-small cell lung carcinomas (NSCLC). However, endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has decreased the tissue available for these assessments. While EBUS-TBNA specimens have previously been reported to successfully subtype NSCLC, allow immunohistochemistry (IHC), and support molecular diagnostics, no studies have documented the extent to which all objectives are possible in a single sample. Of 107 consecutive EBUS-TBNA specimens that were eligible for molecular testing, 98.8% had enough tissue for IHC, 80.2% received a definitive subtype, and 71.0% had both sufficient tissue to attempt molecular testing and technical success on multigene next-generation sequencing and ALK fluorescence in situ hybridization assays. Both subtyping and molecular diagnostics were possible in 57.9% of patients. The mean number of immunostains performed did not differ between patients with or without successful molecular testing (4.4 versus 4.6, P = .88). Only 40% of patients with insufficient tissue underwent repeat sampling. These findings indicate that a majority of EBUS-TBNA specimens provide sufficient tissue for subtyping pulmonary NSCLC, performing IHC, and completing multiple gene analyses. Although priorities must be assessed for each case individually, performance of IHC does not detract from completion of molecular diagnostics in general. Because most patients never undergo repeat sampling, the tissue yield of EBUS-TBNA should be improved to maximize evaluation for targeted therapies.

Muscle Tension Dysphonia: A Rationale for Symptomatic Subtypes, Expedited Treatment, and Increased Therapy Compliance

This article will briefly identify the variable nature of muscle tension dysphonia (MTD). Causes such as psychogenicity and maladaptive “vocal posture” will be described and questioned. Special Interest Group (SIG) 3 members may benefit from identification of the strengths and weaknesses of an ongoing movement towards a symptomatically generic “MTD.” More specific subtyping of MTD into 9 categories will be proposed, as well as description of associated therapy methods. Increased patient awareness that some subtypes may be self-correctable could simplify intervention, increase compliance, and improve clinician and researcher effectiveness.

A prospective study of soft tissue tumors histocytopathology correlation.

Background. Soft tissue tumors are defined as nonepithelial extraskeletal tissue of the body exclusive of the reticuloendothelial system, glia, and supporting tissue of various parenchymal organs. The absence of recognizable tissue architectural patterns in cytological preparation makes diagnosis by FNAC more difficult. Aims. To assess the utility of FNAC in diagnosing soft tissue tumors and to determine their patterns compared with with the respective histopathology results. Materials and Methods. 150 cases of soft tissue tumors were included in this study for cytologic and histologic correlation. FNAC air dried smears were stained with Giemsa stain and 95% ethanol fixed smears were stained with Papanicolaou stain. The smears were studied for cytological diagnosis and were categorized as benign, suspicious of malignancy, and malignant along with specific subtyping of the lesion. All diagnostic FNAC results were compared for diagnostic concordance using histology results as the “gold standard.” Results. The sensitivity, specificity, positive predictive value, negative predictive value, and efficiency were 70%, 100%, 97.90%, 100%, and 98%, respectively. P value was <0.0001 which shows statistically extreme significant correlation. Conclusion. FNAC is a very important preliminary diagnostic tool in palpable soft tissue lumps with high degree of correlation with the final histopathology report.

Suitability of Computed Tomography-Guided Biopsy Specimens for Subtyping and Genotyping of Non–Small-Cell Lung Cancer

IntroductionRecent advances in the treatment of NSCLC highlight the importance of distinguishing NSCLC subtypes and genotypes. We aimed to determine whether histological specimens obtained from computed tomography (CT)-guided biopsy are suitable for specific subtyping and epidermal growth factor receptor (EGFR) analyses of NSCLC. Patients and MethodsThe clinicohistological data of 332 consecutive patients undergoing 352 CT-guided biopsies for lung lesions between January 2007 and December 2011 were retrospectively analyzed. Additionally, NSCLC specimens were examined for the suitability of EGFR mutational testing. ResultsOf 209 specimens diagnosed as NSCLC, 197 (94.3%) were specifically subtyped into adenocarcinoma (n = 164; 78.5%), squamous cell carcinoma (n = 27; 12.9%) and other subtypes (n = 6; 2.9%). The rate of NSCLC not otherwise specified (NOS) was 5.7%, and the diagnosis of NSCLC-NOS was significantly associated with the poor differentiation of cancer (adjusted odds ratio, 6.17; 95% confidence interval, 1.62-23.55; P = .008). Of 134 histological tumor specimens submitted for EGFR molecular testing, 132 (98.5%) were suitable for analyses, and 130 of them (98.5%) showed conclusive results, revealing 59.8% (n = 79) with EGFR exon mutation(s). The sensitivity, specificity, and positive and negative predictive values of CT-guided biopsy in patients with malignancy were 92.2%, 100%, 100%, and 74.1%, respectively. Six percent (n = 21) of total lung biopsies led to pneumothorax requiring chest drainage, and no procedure-related fatality was observed. ConclusionSmall tumor specimens obtained with CT-guided needle lung biopsy are suitable for specific subtyping and EGFR analyses of NSCLC, thus providing critical information for personalized therapy.

Subclassification of lymphoproliferative disorders in serous effusions

Rare studies have reported the application of multiple ancillary tests to the diagnosis of lymphoproliferative disorder in serous effusions. In the current study, the authors evaluated the effectiveness of using an algorithm for the triage of serous effusions and the contribution of ancillary studies to achieve a specific subtype of lymphoproliferative disorder. Serous effusion samples that had a final diagnosis of lymphoproliferative disorder or suspicious for lymphoma were selected from cases that were diagnosed between 2001 and 2010. Data were collected on patient and sample characteristics as well as results from immunophenotype and molecular studies. In total, 168 serous effusions were identified from 110 patients. The most common site of involvement was the pleural cavity (n = 133) followed by the peritoneal cavity (n = 30) and pericardial cavity (n = 5). The volume of serous effusions ranged from 2 mL to 1000 mL (mean, 238 mL). In 42 patients (38.2%), serous effusions were the primary source of diagnosis. In 129 patients who had a diagnosis of LPD, either generic (n = 82) or specific (n = 47) ancillary tests were performed as a single test in 58 samples (67.4%) or as a combination of multiple studies in 19 samples (23.2%). Immunophenotyping was successful in almost all samples that had a specific subtype with 16 B-cell and 4 T-cell lymphomas being diagnosed. More samples with a specific subtype of lymphoma underwent molecular tests compared with those who had a generic diagnosis (19.1% vs 13.4%). Successful, specific subtyping of lymphoproliferative disorders was achieved in approximately 33% of cases that were tested for ancillary studies following an approach for the triage and aliquoting of serous effusion samples.

Metastatic non-small-cell lung cancer (NSCLC): ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up

Metastatic non-small-cell lung cancer (NSCLC): ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up

Personalized medicine for lung cancer: new challenges for pathology

Recent advances in non-small-cell lung cancer (NSCLC) therapy mean the relatively simple discrimination between small-cell and 'non-small-cell' carcinoma is insufficient to determine the best treatment for individual patients. Safety, efficacy and prescribing requirements mandate more specific subtyping of NSCLC for several new drugs: practice made difficult by the tumour heterogeneity combined with the paucity of tissue in most diagnostic samples. Immunohistochemical approaches have emerged as accurate predictors of probable tumour histotype. P63 and/or cytokeratins 5 and 6 and thyroid transcription factor 1 (TTF1) are among the best predictors, respectively, of squamous and adenocarcinoma histology. Molecular characteristics may predict response to both newer molecular targeted agents and traditional cytotoxic agents. Specific mutations in the epidermal growth factor receptor (EGFR) gene as predictors of response to EGFR tyrosine kinase inhibitors (erlotinib, gefitinib) is the first example of markers which predict response to targeted agents. Actual drug targets [e.g. thymidilate synthase (TS) - pemetrexed] or markers of the tumour's ability to repair cytotoxic drug-induced damage [e.g. excision repair cross-complementation group 1 (ERCC1) - cisplatin] may well also complement NSCLC diagnosis. This extended diagnostic requirement from increasingly limited material provided by minimally invasive biopsy techniques poses major challenges for pathology.

Rapid species specific identification and subtyping of Yersinia enterocolitica by MALDI-TOF Mass spectrometry

Yersinia enterocolitica are Gram-negative pathogens and known as important causes of foodborne infections. Rapid and reliable identification of strains of the species Y. enterocolitica within the genus Yersinia and the differentiation of the pathogenic from the non-pathogenic biotypes has become increasingly important. We evaluated here the application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid species identification and subtyping of Y. enterocolitica. To this end, we developed a reference MS database library including 19 Y. enterocolitica (non-pathogenic biotype 1A and pathogenic biotypes 2 and 4) as well as 24 non-Y. enterocolitica strains, belonging to eleven different other Yersinia spp. The strains provided reproducible and unique mass spectra profiles covering a wide molecular mass range (2000 to 30,000Da). Species-specific and biotype-specific biomarker protein mass patterns were determined for Y. enterocolitica. The defined biomarker mass patterns (SARAMIS SuperSpectrum™) were validated using 117 strains from various Y. enterocolitica bioserotypes in a blind-test. All strains were correctly identified and for all strains the mass spectrometry-based identification scheme yielded identical results compared to a characterization by a combination of biotyping and serotyping. Our study demonstrates that MALDI-TOF-MS is a reliable and powerful tool for the rapid identification of Y. enterocolitica strains to the species level and allows subtyping of strains to the biotype level.

Meta-review of depressive subtyping models

Increasing dissatisfaction with the non-specificity of major depression has led many to propose more specific depressive subtyping models. The present meta-review seeks to map dominant depressive subtype models, and highlight definitions and overlaps. A database search in Medline and EMBASE of proposed depressive subtypes, and limited to reviews published between 2000 and 2011, was undertaken. Of the more than four thousand reviews, 754 were judged as potentially relevant and provided the base for the present selective meta-review. Fifteen subtype models were identified. The subtypes could be divided into five molar categories of (1) symptom-based subtypes, such as melancholia, psychotic depression, atypical depression and anxious depression, (2) aetiologically-based subtypes, exemplified by adjustment disorders, early trauma depression, reproductive depression, perinatal depression, organic depression and drug-induced depression, (3) time of onset-based subtypes, as illustrated by early and late onset depression, as well as seasonal affective disorder, (4) gender-based (e.g. female) depression, and (5) treatment resistant depression. An overview considering definition, bio-psycho-social correlates and the evidence base of treatment options for each subtype is provided. Despite the large data base, this meta-review is nevertheless narrative focused. Subtyping depression is a promising attempt to overcome the non-specificity of many diagnostic constructs such as major depression, both in relation to their intrinsic non-specificity and failure to provide treatment-specific information. If a subtyping model is to be advanced it would need, however, to demonstrate differential impacts of causes and treatments.

Specific subtyping of influenza A virus using a recombinant hemagglutinin protein expressed in baculovirus

Influenza A viruses are subtyped according to antigen characterization of hemagglutinin (HA) and neuraminidase surface glycoproteins. The hemagglutination inhibition (HI) assay using reference antiserum is currently applied to serologic screening of subtype-specific antibodies in sera. The reference antiserum is made by injecting chickens with live or inactivated whole virus preparations. Nonspecific inhibitors of antisera prepared by the conventional method may affect the specificity of HI assay. In this study, highly pure recombinant proteins generated using baculovirus expression vector system based on full-length of HA (HAF) and antigenic region of HA(1) genes of H9 subtype, and also inactivated whole virus were used to immunization of chickens. Measurable antibody titers were present for treated birds after 3 weeks and generally increased after each boost. The performance of the prepared antisera was evaluated by testing a panel of known standard strains of influenza virus representing five HA subtypes. Relative to the conventional method using whole virus immunization and recombinant HAF protein, the antiserum prepared by recombinant HA(1) had a specificity of 100% for all tested subtypes. The antiserum prepared by expression of HA1 protein in baculovirus has the potential for rapid and specific HA subtyping of influenza viruses without producing antibodies specific to other viral proteins.

Subtyping of Undifferentiated Non-small Cell Carcinomas in Bronchial Biopsy Specimens

The emergence of treatments for non-small cell lung carcinoma (NSCLC) with differential efficacy and toxicity between subtypes has highlighted the importance of specific pathologic NSCLC subtyping. Most NSCLCs are inoperable, and pathologic diagnosis is made only on small tissue samples that are prone to diagnostic inaccuracy. In a substantial proportion of cases, standard morphology cannot specifically subtype the tumor, necessitating a diagnosis of NSCLC-not otherwise specified (NOS). Histochemical staining for mucin and immunohistochemical (IHC) identification of NSCLC subtype-associated markers could help predict the final subtype of resected NSCLCs diagnosed as NSCLC-NOS on preoperative bronchial biopsy samples. Paraffin sections of 44 bronchial biopsy samples diagnosed as NSCLC-NOS were stained for mucin (Alcian blue/periodic acid Schiff) and thyroid transcription factor 1 by IHC-(markers of adenocarcinoma), and for S100A7, cytokeratin 5/6, high molecular weight cytokeratins, and p63 proteins-markers of squamous cell carcinoma. A predictive staining panel was derived from statistical analysis after comparing staining profiles with the final postsurgical NSCLC subtype. This panel was prospectively applied to 82 small biopsy samples containing NSCLC. True NSCLC subtype of undifferentiated NSCLC samples was best predicted using Alcian blue/periodic acid Schiff plus p63 and thyroid transcription factor 1 IHC, allowing specific subtyping in 73% of NSCLC-NOS cases with 86% accuracy. When applied prospectively, this staining panel showed 100% concordance with specific NSCLC morphologic subtyping in small biopsies. This approach can facilitate treatment selection by accurately predicting the subtype in undifferentiated NSCLC biopsies, reducing to 7% the proportion of cases without a definite or probable histologic subtype.

Development of a multiplex real-time PCR assay using SYBR Green 1 chemistry for simultaneous detection and subtyping of H9N2 influenza virus type A

Avian influenza viruses are pathogens of economical and public health concerns. However, infections caused by low pathogenic avian influenza particularly H9N2 subtype are not associated with clear clinical features. Hence, rapid detection and subtyping of the virus will enable immediate measures to be implemented for preventing widespread transmission. This study highlights the development of a multiplex real-time reverse-transcriptase polymerase chain reaction (RRT-PCR) assay using SYBR Green 1 chemistry for universal detection of avian influenza viruses and specific subtyping of H9N2 isolates based on melting temperatures ( T m) discriminations. Three melting peaks generated simultaneously at temperatures 85.2 ± 1.0, 81.9 ± 0.9 and 78.7 ± 0.9 °C represent NP, H9 and N2 gene products, respectively. The RRT-PCR assay was about 10–100-fold more sensitive when compared to the conventional RT-PCR method using reference H9N2 isolate. In addition, the RRT-PCR assay was 100% sensitive as well as 92% specific according to the standard virus isolation method in detecting experimentally infected specific-pathogen-free (SPF) chickens.

Addison's disease presenting in four adolescents with type 1 diabetes

Primary adrenocortical insufficiency (Addison's disease) is a potentially fatal condition that often develops insidiously and can be easily overlooked. Although rare in the general population, it is more common in patients with type 1 diabetes mellitus (T1DM). The combination of Addison's disease with T1DM and/or autoimmune thyroid disease is known as autoimmune polyendocrine syndrome type-2 (APS-2). T1DM commonly precedes the development of adrenocortical insufficiency in most patients with APS-2. We, in this study, present four cases of Addison's disease developing in adolescents with pre-existing T1DM. Risk factors for Addison's disease in this population include a history of other organ-specific autoimmunity, particularly thyroid, and a positive family history. In addition to the 'classic' Addisonian features, the development of unexplained recurrent hypoglycemia, reduction in total insulin requirement, improvement in glycemic control, or abnormal pigmentation should arouse suspicion of adrenocortical insufficiency. Adrenal antibodies have been proposed as a screening tool for Addison's disease in the T1DM population, but doubts remain about their specificity and sensitivity. The addition of specific HLA DRB1 subtyping has been proposed to improve predictive value.