Small Tissue Biopsies Research Articles

MA08.05 High Concordance in Scoring PD-L1 in NSCLC Using the Roche Digital Pathology uPath system and PD-L1 Assessment Algorithm

Accurate and reproducible assessment of PD-L1 expression is crucial in guiding the use of anti PD-1/PD-L1 immunomodulatory therapy. Interpretation can be challenging and both intra- and inter-pathologist discordance has been shown to be potentially significant in affecting clinical outcomes. Digital pathology and algorithmic assessment tools provide an opportunity to increase accuracy and concordance when making this important assessment in non-small cell lung cancer (NSCLC). Sections of 198 NSCLCs, (84 EBUS aspirates or small tissue biopsies and 114 resections) immunolabelled for PD-L1 using the Roche-Ventana SP263 antibody were scanned with a Roche DP200 digital image scanner and analysed using uPath slide viewer and the Roche PD-L1 interpretative algorithm. Sections were assessed by three ‘blinded’ pathologists for expression of PD-L1 which was given as an absolute percentage, the tumour proportion score (TPS) in four ways; (1) unassisted (by pathologist using conventional microscopy), (2) automated whole slide (unsupervised uPath assessment of whole slide), (3) automated annotated (uPath assessment of slide annotated by pathologist) and (4) assisted (by pathologist using digital image assisted by uPath assessment of annotated slide). The last method of assessment was repeated after a six-week ‘washout’ period. Intraclass correlation co-efficient (ICC) and Cohen’s Kappa (for clinical categories of <1%, 1-49% or ≥50% TPS) were used to compare concordance of scoring assessment methods.Table 1Comparison of TPS scoring methodsTPS assessment methods - Full CohortICCKappap-valueAssisted vs unassisted0.9730.856<0.0001Assisted vs automated whole slide0.9110.475<0.0001Assisted vs automated annotated0.9530.598<0.0001TPS assessment methods - small biopsies/EBUS onlyAssisted vs automated annotated0.9520.836<0.0001 Open table in a new tab Intra-pathologist concordance between repeated assisted reads was very high (ICC 0.991 K 0.989 p<0.0001) as was inter-pathologist concordance for assisted interpretations (ICC 0.986 K 0.910 p<0.0001 respectively) Automated algorithmic assessment guided by pathologists is an accurate approach that helps produce consistent and reliable interpretation of PD-L1 expression in NSCLC by reducing intra- and inter- observer discordance. Digital pathology and automated algorithms are powerful tools that can help optimise the predictive power of PD-L1 expression as a predictor of response to immunomodulatory therapy.

Intraoperative Mass Spectrometry Platform for IDH Mutation Status Prediction, Glioma Diagnosis, and Estimation of Tumor Cell Infiltration.

Surgical tumor resection is the primary treatment option for diffuse glioma, the most common malignant brain cancer. The intraoperative diagnosis of gliomas from tumor core samples can be improved by use of molecular diagnostics. Further, residual tumor at surgical margins is a primary cause of tumor recurrence and malignant progression. This study evaluates a desorption electrospray ionization mass spectrometry (DESI-MS) system for intraoperative isocitrate dehydrogenase (IDH) mutation assessment, estimation of tumor cell infiltration as tumor cell percentage (TCP), and disease status. This information could be used to enhance the extent of safe resection and so potentially improve patient outcomes. A mobile DESI-MS instrument was modified and used in neurosurgical operating rooms (ORs) on a cohort of 49 human subjects undergoing craniotomy with tumor resection for suspected diffuse glioma. Small tissue biopsies (ntotal = 203) from the tumor core and surgical margins were analyzed by DESI-MS in the OR and classified using univariate and multivariate statistical methods. Assessment of IDH mutation status using DESI-MS/MS to measure 2-hydroxyglutarate (2-HG) ion intensities from tumor cores yielded a sensitivity, specificity, and overall diagnostic accuracy of 89, 100, and 94%, respectively (ncore = 71). Assessment of TCP (categorized as low or high) in tumor margin and core biopsies using N-acetyl-aspartic acid (NAA) intensity provided a sensitivity, specificity, and accuracy of 91, 76, and 83%, respectively (ntotal = 203). TCP assessment using lipid profile deconvolution provided sensitivity, specificity, and accuracy of 76, 85, and 81%, respectively (ntotal = 203). Combining the experimental data and using PCA-LDA predictions of disease status, the sensitivity, specificity, and accuracy in predicting disease status are 63%, 83%, and 74%, respectively (ntotal = 203). The DESI-MS system allowed for identification of IDH mutation status, glioma diagnosis, and estimation of tumor cell infiltration intraoperatively in a large human glioma cohort. This methodology should be further refined for clinical diagnostic applications.

Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction

Mass spectrometry (MS) is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across human leukocyte antigen (HLA) allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery driven. Hence, data-dependent tandem MS (MS/MS) acquisition (DDA) is widely used, as it generates high-quality references of peptide fingerprints. However, DDA suffers from the stochastic selection of abundant ions that impairs sensitivity and reproducibility. In contrast, in data-independent acquisition (DIA), the systematic fragmentation and acquisition of all fragment ions within given isolation m/z windows yield a comprehensive map for a given sample. However, many DIA approaches commonly require generating comprehensive DDA-based spectrum libraries, which can become impractical for studying noncanonical and personalized neoantigens. Because the amount of HLA peptides eluted from biological samples such as small tissue biopsies is typically not sufficient for acquiring both meaningful DDA data necessary for generating comprehensive spectral libraries and DIA MS measurements, the implementation of DIA in the immunopeptidomics translational research domain has remained limited. We implemented a DIA immunopeptidomics workflow and assessed its sensitivity and accuracy by matching DIA data against libraries with growing complexity—from sample-specific libraries to libraries combining 2 to 40 different immunopeptidomics samples. Analyzing DIA immunopeptidomics data against a complex multi-HLA spectral library resulted in a two-fold increase in peptide identification compared with sample-specific library and in a three-fold increase compared with DDA measurements, yet with no detrimental effect on the specificity. Furthermore, we demonstrated the implementation of DIA for sensitive personalized neoantigen discovery through the analysis of DIA data with predicted MS/MS spectra of clinically relevant HLA ligands. We conclude that a comprehensive multi-HLA library for DIA approach in combination with MS/MS prediction is highly advantageous for clinical immunopeptidomics, especially when low amounts of biological samples are available.

Characterization of the intestinal mucosal proteome in cats with inflammatory bowel disease and alimentary small cell lymphoma.

BackgroundCurrent tests for diagnosis and differentiation of lymphoplasmacytic enteritis (LPE) and small cell lymphoma (SCL) in cats are expensive, invasive, and lack specificity. The identification of less invasive, more reliable biomarkers would facilitate diagnosis.ObjectivesTo characterize the mucosal proteome in endoscopically obtained, small intestinal tissue biopsy specimens. We hypothesized that differentially expressed proteins could be identified and serve as biomarker candidates for the differentiation of LPE and SCL in cats.AnimalsSix healthy control cats, 6 cats with LPE, and 8 cats with SCL.MethodsThe mucosal proteome was analyzed using 2‐dimensional fluorescence difference gel electrophoresis (2D DIGE) and nanoflow liquid chromatography tandem mass spectrometry. For 5 proteins, results were verified by Western blot analysis.ResultsA total of 2349 spots were identified, of which 9 were differentially expressed with a ≥2‐fold change between healthy cats and cats with LPE and SCL (.01 < P < .001). Eight of these 9 spots were also differentially expressed between cats with LPE and cats with SCL (P .001 < P < .04). However, Western blot analysis for malate dehydrogenase‐1, malate dehydrogenase‐2, apolipoprotein, annexin IV, and annexin V did not confirm significant differential protein expression for any of the 5 proteins assessed.Conclusions and Clinical ImportanceTwo‐D DIGE did not identify potential biomarker candidates in the intestinal mucosa of cats with LPE and SCL. Future studies should focus on different techniques to identify biomarker candidates for cats with chronic enteropathies (CE).

Utilizing single-cell-subtype analysis via advanced microdissection methods and the impact on precision medicine.

e15571 Background: Improving the utilization of tumor tissue from diagnostic biopsies is an unmet medical need. This is especially relevant today in the rapidly evolving precision oncology field where tumor genotyping is essential for the indication of many advanced and targeted therapies. National Comprehensive Cancer Network (NCCN) guidelines now mandate molecular testing for clinically actionable targets in certain malignancies. Patients diagnosed with advanced non-small cell lung cancer (NSCLC) are commonly of an older age and have significant co-morbidities. This frequently causes clinical dilemmas regarding the ability to obtain adequate amounts of tissue for tumor genotyping. In these cases, the tumor tissue may have been obtained by an image-guided biopsy, and the diagnosis of NSCLC proper determined via cytology. In certain instances, adequate tissue for tumor genotyping and/or a more advanced mutational analysis to identify oncogenic drivers may not be available. Methods: Following pathology review, formalin fixed paraffin embedded (FFPE) specimens were subjected to advanced immuno-based laser capture microdissection (LCM), DNA was extracted and prepped for droplet digital PCR (ddPCR) and run with a series of positive and negative controls. Results: Utilizing advanced stage lung cancer as an example, an improved genotyping approach for solid tumors is possible. The strategy involves optimization of the microdissection process and analysis of a large number of identical target cells from FFPE specimens sharing similar characteristics, in other words, single-cell subtype analysis. The shared characteristics can include immunostaining status, cell phenotype, and/or spatial location within a histological section. Conclusions: Synergy between microdissection and ddPCR enhances the molecular analysis. We demonstrate a methodology that illustrates genotyping of a solid tumor from a small tissue biopsy sample in a time and cost-efficient manner, using immunostain targeting as an example.

PD-L1 diagnostics in the neoadjuvant setting: implications of intratumoral heterogeneity of PD-L1 expression in triple negative breast cancer for assessment in small biopsies.

PD-L1 expression is a predictive biomarker for anti-PD-L1 immunotherapy in triple negative breast cancer (TNBC). In the neoadjuvant setting, immunohistochemical (IHC) evaluation of PD-L1 expression can only be performed on small tissue biopsies. In our study we investigated heterogeneity of PD-L1 expression in TNBC, and how reliably PD-L1 expression in small tissue samples reflects PD-L1 expression in larger tumor sections in TNBC. Tissue microarrays (TMAs) were constructed from surgical specimens of 110 patients with TNBC. TMAs contained 4 cores (1mm in diameter) per patient. To evaluate PD-L1 expression, TMAs were stained with PD-L1 IHC 22C3 PharmDx. Single-core PD-L1 expression was compared to overall PD-L1 expression of each patient's tumor, to ascertain how often small samples of tumor tissue show the same PD-L1 expression as larger tumor samples. Our study found substantial heterogeneity of PD-L1 expression between different TMA cores from the same patient. Heterogeneity was greater in immune cells (ICs) than in tumor cells, in large part due to the uneven distribution of ICs in the tumor. For IC PD-L1 expression, we found that sensitivity can be as low as 0.81 for detecting PD-L1 expression at the 1% threshold most commonly used in breast cancer. Negative predictive value for ICs was 0.7. There is substantial heterogeneity of PD-L1 expression between small tissue samples from the same TNBC tumor, especially for IC expression. This poses challenges for evaluation of PD-L1 expression in the neoadjuvant setting. Negative biopsies should prompt further investigation, and multiple biopsies might be necessary.

P1.03-11 Molecular Testing of Small Bronchoscopy Specimens Using NanoString Technology

Molecular testing for driver variants in oncogenes is crucial for NSCLC management to predict response to targeted therapy. In the majority of cases, NSCLC is diagnosed by trans-thoracic needle aspiration or more commonly bronchoscopy techniques resulting in small diagnostic tissue biopsies or cytological samples. As such specimens may be inadequate for molecular testing, we tested the accuracy of a novel digital molecular barcoding assay to detect actionable mutations in a single-centre cohort. A consecutive cohort of 46 specimens (19 endobronchial biopsy, EnBx; 18 transbronchial biopsy, TBBx; seven bronchoalveolar lavage, BAL; and two transbronchial needle aspirate, TBNA) were obtained ancillary to primary diagnostic specimens from 36 patients undergoing EBUS-guided bronchoscopy at The Prince Charles Hospital. Specimens containing at least 5ng DNA after standard column-based extraction methods were analysed using the NanoString SNV Solid Tumour Panel for testing of 104 somatic variants across 25 genes of clinical significance. NanoString variants calls were compared with routine clinical testing results from the primary diagnostic sample. Agreement analyses for variants common to both methods revealed the positive, negative and overall percentage agreement (PPA, NPA, OPA). One discordant case was validated using droplet digital PCR. Using NanoString, molecular analysis was feasible for 60.1% (28/46) of specimens. At least one variant was identified in 8/28 (28.6%) cases (Table 1). Two (7.1%) cases harboured dual mutations. KRAS mutations were detected in six (21.4%) cases, and EGFR in two (7.1%). Two patients would be eligible for targeted therapy. Agreement analysis for the two methods revealed PPA, NPA and OPA of 100%, 88.9% and 92.3%. In one discordant case, NanoString identified a KRAS G12C mutation and was confirmed by ddPCR with a mutant allele frequency of 5.5%. The mean time for reporting clinical mutation test results was 19.6 days. Of the 18 excluded cases with insufficient DNA, five had routine testing results for comparison however 3/5 cases cited insufficient DNA for reliable EGFR testing.Table 1Clinical and molecular characteristics of bronchoscopy samples used for molecular testingClinical molecular testingNanoStringConcordanceCase no.Sample typeHistological classificationDNA yield (μg)Mutation testing result (MAF)Mutation testing methodTAT to result (days)SNV panel resultAgreement (Yes/No)1BALNo evidence of malignancy2.81Not performedN/AN/AWTNCA2TBNAAC4.39Not performedN/AN/AWTNCA3TBBxSCC0.39Not performedN/AN/AKRAS G12RNCA4TBBxAC1.82EGFR exon 19 (L747_P753>S) del (24%)NGS TruSight21EGFR exon 19 (L747_P753>S) delYes5TBBxNo evidence of malignancy1.24Not performedN/AN/AWTNCA6TBBxNo evidence of malignancy0.62Not performedN/AN/AWTNCA7EnBxAC1.41WT for EGFR, KRAS, NRAS, BRAFNGS TruSight13WTYes8EnBxSCC0.57Not performedN/AN/AWTNCA9TBBxSCC0.53Not performedN/AN/AWTNCA10TBBxAC0.51WT for EGFR, KRAS, NRAS, BRAFNGS TruSight20KRAS G12CNo*11TBBxAC0.31EGFR L858R (12%), EGFR T790M (6%)NGS TruSight13EGFR L858R, EGFR T790MYes12TBBxNo evidence of malignancy0.69Not performedN/AN/AWTNCA13TBBxNSCLC4.26WT for EGFRcastPCR48WTYes14EnBxAC1.37KRAS G12C (10%)NGS TruSight23KRAS G12CYes15EnBxNSCLC19.6KRAS G12A (25%)NGS TruSight20KRAS G12AYes16EnBxCarcinoid1.16Not performedN/AN/AWTNCA17TBBxSCC5.4Not performedN/AN/AWTNCA18EnBxAC4.03WT for EGFR, KRAS, NRAS, BRAFNGS TruSight19WTYes19EnBxSCC2.12Not performedN/AN/AWTNCA20TBBxAC3.85WT for EGFRcastPCR14KRAS G12C, NRAS Q61KNCA21EnBxSCC6.4Not performedN/AN/AWTNCA22TBBxAC1.63WT for EGFRcastPCR20KRAS G12CNCA23EnBxAC0.234WT for EGFR, KRAS, NRAS, BRAFNGS TruSight16WTYes24BALAC0.871BRAF G466V (12%)NGS TruSight24WTYes25TBBxAC0.0918BRAF G466V (12%)NGS TruSightN/AWTYes26TBBxAC0.893WT for EGFRcastPCR13WTYes27TBBxSCC0.66Not performedN/AN/AWTNCA28EnBxAC4.4WT for EGFRcastPCR10WTYesMean2.5819.6 Open table in a new tab The performance of the NanoString platform for SNV characterisation was highly concordant with alternate clinical testing methods for those with sufficient DNA. Advantages of NanoString include its multiplex capacity, high sensitivity, low nucleic acid input, reduced turn-around time (<24hr) compared to alternate testing methods. The NanoString platform is a robust method for identification of actionable variants in NSCLC where at least 5ng of DNA is available.

Abstract 2989: An all-in-one transcriptome-based assay to identify therapy-related biomarkers in lung cancer

Abstract Background. In the past decade, treatment of advanced stage lung cancer patients guided by somatic aberrations has become routine practice. Different molecular tests are being applied to detect all targetable mutations and fusions. However, in most cases tissue biopsies are small, hampering multiple independent diagnostic tests. To optimize diagnostic testing we developed an all-in-one transcriptome-based assay. Methods. We have developed a targeted next generation sequencing protocol that uses total RNA as input and is based on the Single Primed enrichment Technology (SPET). We included 11 cell lines, four frozen biopsies, 12 pleural effusion samples and 32 FFPE samples with in total 41 known mutations (including EGFR n=15; KRAS n=11; BRAF n=2; PIK3CA n=3 ), 21 fusion genes (including ALK n=15; ROS n=3) and 3 cases of MET exon14 skipping. Results. We confirmed presence of 32 out of 41 mutations, 19 out of 23 fusions and all three cases of exon skipping by our assay. Besides confirming the fusions, we were also able to identify the fusion gene partner for all detected fusion transcripts. For the samples for which we failed to detect the mutations or fusions, the read depth of the target region was less than four, indicating low expression, low tumor content or insufficient unique reads. Independent RNA-based ddPCR on six unconfirmed mutations were all positive, albeit with low numbers of mutant droplets in some cases. One of three undetected fusions was positive in a NanoString fusion gene detection assay. For one of two negative cases, the fusion was most likely false positive by FISH, as this patient was FISH-break positive for both ALK and RET, which is never reported before. Conclusions. This study proved feasibility of this targeted all-in-one transcriptome-based assay for simultaneous detection of mutations and fusions even in relatively small FFPE tissue biopsies. Moreover, we were able to detect the fusion partner genes in all positive cases. We expect that for routine diagnostic testing using an enrichment for tumor cell-rich areas of recently prepared FFPE blocks, the success rate of the all-in-one transcriptome approach will reach similar sensitivity as currently used diagnostic tests. Citation Format: Klaas Kok, Jiacong Wei, Anna A. Rybczynska, Pei Meng, Martijn M. Terpstra, Anthonie J. van der Wekken, Jeroen T. Hiltermann, Ed Schuuring, Harry J. Groen, Anke van den Berg. An all-in-one transcriptome-based assay to identify therapy-related biomarkers in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2989.

Preclinical Modelling of PDA: Is Organoid the New Black?

Pancreatic ductal adenocarcinoma (PDA) is a malignancy of the exocrine pancreas with the worst prognosis among all solid tumours, and soon to become the second leading cause of cancer-related deaths. A more comprehensive understanding of the molecular mechanisms underlying this disease is crucial to the development of diagnostic tools as well as to the identification of more effective therapies. High-frequency mutations in PDA occur in “undruggable” genes, and molecular subtyping based on bulk transcriptome analysis does not yet nominate valid therapeutic intervention strategies. Genome-wide sequencing studies have also demonstrated a considerable intra- and inter-patient’s genetic heterogeneity, which further complicate this dire scenario. More than in other malignancies, functionalization of the PDA genome and preclinical modelling at the individual patient level appear necessary to substantially improve survival rates for pancreatic cancer patients. Traditional human PDA models, including monolayer cell cultures and patient-derived xenografts, have certainly led to valuable biological insights in the past years. However, those model systems suffer from several limitations that have contributed to the lack of concordance between preclinical and clinical studies for PDA. Pancreatic ductal organoids have recently emerged as a reliable culture system to establish models from both normal and neoplastic pancreatic tissues. Pancreatic organoid cultures can be efficiently generated from small tissue biopsies, which opens up the possibility of longitudinal studies in individual patients. A proof-of-concept study has demonstrated that patient-derived PDA organoids are able to predict responses to conventional chemotherapy. The use of this three-dimensional culture system has already improved our understanding of PDA biology and promises to implement precision oncology by enabling the alignment of preclinical and clinical platforms to guide therapeutic intervention in PDA.

Biofabrication of tissue-specific extracellular matrix proteins to enhance the expansion and differentiation of skeletal muscle progenitor cells

Skeletal muscle precursor cells (MPCs) are considered key candidates for cell therapy in the treatment of skeletal muscle dysfunction due to injury, disease, or aging. However, expansion of a sufficient number of functional skeletal muscle cells in vitro from a small tissue biopsy has been challenging due to changes in the phenotypic expression of these cells under nonnatural microenvironmental or traditional culture conditions. This review provides an overview of recent progress in the design and biofabrication of advanced tissue-specific extracellular matrix (ECM) proteins for use in the enhancement of expansion and differentiation of MPCs for cell therapy and 3D bioprinting. We start with a brief introduction about the existing progress, drawbacks, and emerging challenges in the culture and maintenance of long term primary human MPCs for cell therapy. With regard to MPC proliferation, elongation, fusion, and differentiation into mature myofibers, we systematically summarize the benefits and limitations of recent progress. The importance of tissue-specific ECM in skeletal muscle regeneration is discussed, in particular, the mechanisms, rationale, strategy, and methodologies for using tissue-specific ECM proteins for myogenesis in 2D and 3D culture environments. Furthermore, perspectives on the challenges in developing tissue-specific ECM proteins for cell therapy using human MPCs are described. Finally, we propose potential strategies for overcoming the challenges in the development of advanced tissue-specific ECM proteins for promoting cell therapy with human skeletal muscle cells.

Programmed Cell Death Ligand 1 Immunohistochemistry: A Concordance Study Between Surgical Specimen, Biopsy, and Tissue Microarray

BackgroundThe immunohistochemical analysis of programmed cell death ligand 1 (PD-L1) expression in tumor tissue of non–small-cell lung cancer patients has now been integrated in the diagnostic workup. Analysis is commonly done on small tissue biopsy samples representing a minimal fraction of the whole tumor. The aim of the study was to evaluate the correlation of PD-L1 expression on biopsy specimens with corresponding resection specimens. Materials and MethodsIn total, 58 consecutive cases with preoperative biopsy and resected tumor specimens were selected. From each resection specimen 2 tumor cores were compiled into a tissue microarray (TMA). Immunohistochemical staining with the antibody SP263 was performed on biopsy specimens, resection specimens (whole sections), as well as on the TMA. ResultsThe proportion of PD–L1-positive stainings were comparable between the resection specimens (48% and 19%), the biopsies (43% and 17%), and the TMAs (47% and 14%), using cutoffs of 1% and 50%, respectively (P > .39 all comparisons). When the resection specimens were considered as reference, PD-L1 status differed in 16%/5% for biopsies and in 9%/9% for TMAs (1%/50% cutoff). The sensitivity of the biopsy analysis was 79%/82% and the specificity was 90%/98% at the 1%/50% cutoff. The Cohens κ value for the agreement between biopsy and tumor. was 0.70 at the 1% cutoff and 0.83 at the 50% cutoff. ConclusionThe results indicate a moderate concordance between the analysis of biopsy and whole tumor tissue, resulting in misclassification of samples in particular when the lower 1% cutoff was used. Clinicians should be aware of this uncertainty when interpreting PD-L1 reports for treatment decisions.

The utilization of cytologic and small biopsy samples for ancillary molecular testing.

There has recently been an increased emphasis on the utilization of cytologic samples and small biopsies for not only diagnostic purposes but also for ancillary testing. In some instances, the ancillary tests contribute to the diagnosis and in other scenarios, they provide prognostic and theranostic information for the management of patients with advanced stage cancer. These ancillary tests include immunohistochemical biomarker analysis, molecular mutation analysis, and cytogenetic tests. Despite the finite nature of the cellular material procured in cytologic and small tissue biopsies, pathologists are tasked with ordering an increasing number of tests using these limited samples. This requires the pathologists to utilize and triage these samples in an optimal fashion so that as much information can be gleaned from a given specimen. This review will focus on the pre-analytic requirements for ancillary molecular and cytogenetic tests in the context of a discussion of the various preparation methods for cytologic and small biopsy specimens. The goal will be to provide the reader with the necessary concepts that can be utilized to develop optimal specimen selection and triage strategies to maximize the chances of effectively utilizing these samples for comprehensive diagnostic and relevant ancillary testing purposes.

The challenges of evaluating predictive biomarkers using small biopsy tissue samples and liquid biopsies from non-small cell lung cancer patients

The list of theranostic biomarkers for the care of patients with advanced stage or metastatic non-small cell lung cancer has lengthened considerably these last few years. Moreover, the advances in therapeutics will certainly increase the number and complexity of these tests performed in laboratories in the near future. In addition, the methods for investigation of biomarkers that require access to biological tissue are less and less invasive with the consequential increase in the use of small-sized tissue biopsies and cytological and blood samples. Thus, each laboratory must master the management of the biological samples according to the number and type of tests to be performed. This review will provide an update of the difference challenges facing pathologists and biologist in responding to the issues related to new treatments. These challenges concern: (I) the management of the pre-analytical phase; (II) the appropriate choice of the technological approach; (III) the performance of quality control; (IV) the mastering of the delay in obtaining the results; and (V) the economic model of the laboratory.

Personalized Hydrogels for Engineering Diverse Fully Autologous Tissue Implants.

Despite incremental improvements in the field of tissue engineering, no technology is currently available for producing completely autologous implants where both the cells and the scaffolding material are generated from the patient, and thus do not provoke an immune response that may lead to implant rejection. Here, a new approach is introduced to efficiently engineer any tissue type, which its differentiation cues are known, from one small tissue biopsy. Pieces of omental tissues are extracted from patients and, while the cells are reprogrammed to become induced pluripotent stem cells, the extracellular matrix is processed into an immunologically matching, thermoresponsive hydrogel. Efficient cell differentiation within a large 3D hydrogel is reported, and, as a proof of concept, the generation of functional cardiac, cortical, spinal cord, and adipogenic tissue implants is demonstrated. This versatile bioengineering approach may assist to regenerate any tissue and organ with a minimal risk for immune rejection.

Tissue metabolite profiles for the characterisation of paediatric cerebellar tumours

Paediatric brain tumors are becoming well characterized due to large genomic and epigenomic studies. Metabolomics is a powerful analytical approach aiding in the characterization of tumors. This study shows that common cerebellar tumors have metabolite profiles sufficiently different to build accurate, robust diagnostic classifiers, and that the metabolite profiles can be used to assess differences in metabolism between the tumors. Tissue metabolite profiles were obtained from cerebellar ependymoma (n = 18), medulloblastoma (n = 36), pilocytic astrocytoma (n = 24) and atypical teratoid/rhabdoid tumors (n = 5) samples using HR-MAS. Quantified metabolites accurately discriminated the tumors; classification accuracies were 94% for ependymoma and medulloblastoma and 92% for pilocytic astrocytoma. Using current intraoperative examination the diagnostic accuracy was 72% for ependymoma, 90% for medulloblastoma and 89% for pilocytic astrocytoma. Elevated myo-inositol was characteristic of ependymoma whilst high taurine, phosphocholine and glycine distinguished medulloblastoma. Glutamine, hypotaurine and N-acetylaspartate (NAA) were increased in pilocytic astrocytoma. High lipids, phosphocholine and glutathione were important for separating ATRTs from medulloblastomas. This study demonstrates the ability of metabolic profiling by HR-MAS on small biopsy tissue samples to characterize these tumors. Analysis of tissue metabolite profiles has advantages in terms of minimal tissue pre-processing, short data acquisition time giving the potential to be used as part of a rapid diagnostic work-up.

Abstract 2701: Proteogenomic analysis of endoscopy biopsy identifies alterations in apoptotic pathways in trastuzumab-resistant gastric cancers

Abstract Although the combination of trastuzumab with cisplatin and fluoropyrimidine is standard therapy for metastatic HER2-positive gastric cancers, predictive biomarkers for this therapy need to be further refined. Given the multifactorial nature of clinical trastuzumab resistance, we performed nano-liquid chromatography (LC)-tandem mass spectrometry (MS/MS) proteomic analyses on 13 pairs of frozen HER2-positive tumors and adjacent normal tissue counterparts collected from patients who were treated with trastuzumab in combination with cisplatin and fluoropyrimidine (TCF). We quantified &amp;gt;6,000 protein groups per tumor on the average, and this number was almost comparable to those obtained by NCI's Clinical Proteomic Tumor Analysis Consortium projects, which characterized resected tumors using similar nano-LC-MS/MS technologies. Nano-LC-MS/MS data for differentially expressed proteins were successfully validated by our immunostaining analyses. When we correlated proteomic data with clinical outcome, underexpression of apoptosis pathway proteins was the prominent proteomic signature in TCF-resistant tumors, as compared with TCF-sensitive tumors. Proapoptotic proteins in FAS signaling and mitochondrial apoptosis pathways were less abundant in TCF-resistant tumors than in sensitive tumors. When iTRAQ reporter ion ratios were compared between pretreatment and acquired-resistant tumors from clinical responders, apoptosis pathways were significantly enriched in proteins that were overexpressed in the acquired-resistant tumors. Assuming that the pretreatment tumors of clinical responders were mostly composed of chemosensitive clones, these antiapoptotic proteins may confer survival advantage on resistant clones, resulting in the repopulation of resistant clones overexpressing these antiapoptotic proteins. For the first time to our knowledge, therefore, our proteogenomic study of frozen endoscopic biopsy samples revealed that alterations in apoptotic pathway proteins were most significantly associated with clinical trastuzumab resistance. Our study is also the first to demonstrate that nano-LC-MS/MS technology can be applied to small biopsy tissue samples for precision medicine research. Citation Format: Jeong Won Kang, Il Ju Choi, Hark Kyun Kim. Proteogenomic analysis of endoscopy biopsy identifies alterations in apoptotic pathways in trastuzumab-resistant gastric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2701.

Diagnostic Approach for Classic Compared With Localized Whipple Disease

BackgroundWhipple disease (WD), a rare systemic infection caused by Tropheryma whipplei, can be a diagnostic challenge due to its variable presentation. The role of T. whipplei polymerase chain reaction (PCR) is unclear as small bowel biopsy with Periodic acid-Schiff (PAS) staining remains the diagnostic gold standard. Individualized diagnostic approaches based on variable clinical manifestations are underutilized. We investigated the methodologies employed at our institution to diagnose WD.MethodsWe retrospectively collected all cases of WD diagnosed from 1994 to 2016. Microbiology laboratory and anatomic pathology databases were queried. Case characteristics and disease clinical phenotypes (classical, localized WD arthritis, and localized central nervous system [CNS] disease) were described. The diagnostic approach and testing yield were analyzed and reported.ResultsThirty-three cases of WD were diagnosed (18 classic WD [CWD], 9 localized WD arthritis [LWD], 6 CNS WD). Misdiagnosis and delay in diagnosis were frequent. Diagnostic approach and test yield differed by classical vs localized WD involvement. Small bowel tissue biopsy PAS stain/PCR was overwhelmingly positive (86%/92%) in CWD, yet seldom positive (12%/42%) in LWD (P < .001). Affected joint synovial fluid PCR was frequently positive in both CWD (100%, 3/3) and LWD (85%, 6/7).ConclusionsThese results support the role of small bowel biopsy PAS stain/PCR in the diagnosis of CW, though this approach may be of limited utility in LWD or CNS WD without gastrointestinal symptoms. Affected joint synovial fluid or cerebrospinal fluid PCR was frequently positive in both CWD and LWD, supporting its diagnostic usefulness.

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

BackgroundEvolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA sequencing (RNASeq) into more frequent use. However, known biases associated with small RNASeq, compounded by low RNA inputs, have been both a significant concern and a hurdle to widespread adoption. As RNASeq is becoming a viable choice for the discovery of small RNAs in low input samples and more labs are employing it, there should be benchmark datasets to test and evaluate the performance of new sequencing protocols and operators. In a recent publication from the National Institute of Standards and Technology, Pine et al., 2018, the investigators used a commercially available set of three tissues and tested performance across labs and platforms.ResultsIn this paper, we further tested the performance of low RNA input in three commonly used and commercially available RNASeq library preparation kits; NEB Next, NEXTFlex, and TruSeq small RNA library preparation. We evaluated the performance of the kits at two different sites, using three different tissues (brain, liver, and placenta) with high (1 μg) and low RNA (10 ng) input from tissue samples, or 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma. As there has been a lack of robust validation platforms for differentially expressed miRNAs, we also compared low input RNASeq data with their expression profiles on three different platforms (Abcam Fireplex, HTG EdgeSeq, and Qiagen miRNome).ConclusionsThe concordance of RNASeq results on these three platforms was dependent on the RNA expression level; the higher the expression, the better the reproducibility. The results provide an extensive analysis of small RNASeq kit performance using low RNA input, and replication of these data on three downstream technologies.

Recent Advances in the Diagnosis of Malignant Mesothelioma: Focus on Approach in Challenging Cases and in Limited Tissue and Cytologic Samples.

Mesothelial proliferations can be diagnostically challenging in small specimens, such as body fluid cytology and small tissue biopsies. A great morphologic challenge for pathologists is the separation of benign reactive mesothelial proliferations from malignant mesotheliomas. Reactive mesothelial proliferations may have histologic features that resemble malignancy including increased cellularity, cytologic atypia, and mitoses. Recent advances in mesothelioma genetics resulted in identification of BAP1 mutations and p16 deletions as features of malignant mesotheliomas. Hence, BAP1 immunohistochemistry and fluorescence in situ hybridization for p16 emerged as 2 most common diagnostically helpful ancillary studies used on limited samples when the question is whether the proliferation is malignant or benign. In contrast, separation of mesothelioma from other malignancies is relatively straight forward using morphology and immunohistochemical stains. The choice of antibody panel to be applied in an individual case is driven by morphology, either epithelioid or sarcomatoid. This brief review will focus on morphology and ancillary testing of mainly pleural mesothelial proliferations.

A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics.

ABSTRACTAnimals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from the blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2678 proteins, including many of interest for further functional studies.This article has an associated First Person interview with the first author of the paper.