Predictive and prognostic biomarkers in gastrointestinal tract tumours

Tumours of the gastrointestinal tract represent nearly a quarter of all newly diagnosed tumours diagnosed in 2019. Various treatment modalities for gastrointestinal cancers exist, some of which may be guided by biomarkers. Biomarkers act as gauges of either normal or pathogenic processes or responses to an exposure or intervention. They come in many forms. This review explores established and potential molecular/immunohistochemical (IHC) predictive and prognostic biomarkers of the gastrointestinal tract.

Macroscopic examination of pathology specimens: a critical reappraisal

Meticulous macroscopic examination of specimens and tissue sampling are crucial for accurate histopathology reporting. However, macroscopy has generally received less attention than microscopy and may be delegated to relatively inexperienced practitioners with limited guidance and supervision. This introductory paper in the minisymposium, Macroscopy Under the Microscope, focuses on issues regarding macroscopic examination and tissue sampling that have been insufficiently addressed in the published literature. It highlights the importance of specimen examination and sampling, discusses some general principles, outlines challenges and suggests potential solutions. It is critical to get macroscopy right the first time as it may not be possible to rectify errors even with expert histological assessment or to retrospectively collect missing data after the specimen retention period. Dissectors must, therefore, receive adequate guidance and supervision until they are proficient in macroscopic specimen examination. We emphasise the importance of the clinical context, optimal specimen fixation, succinct and clinically relevant macroscopic descriptions, macrophotography and judicious tissue sampling. We note that current recommendations based on the number of blocks to be submitted per maximum tumour dimension are ambiguous as the amount of tissue submitted in a cassette is not standardised and it is unclear whether 'block' refers to a tissue block or a paraffin block. Concerns around potential oversampling of 'therapeutic' specimens that could result in overdiagnosis due to detection of incidentalomas are also discussed. We hope that the issues discussed in this paper will engender debate on this clinically critical aspect of pathology practice.

Gastrointestinal Stromal Tumours (GISTs) with KRAS Mutation: A Rare but Important Subset of GISTs

Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the GI tract, usually found in the stomach, jejunum, and ileum. Typically, they are KIT or PDGFR-mutated, allowing for targetable treatments with tyrosine kinase inhibitors such as imatinib. Here, we present two KRAS-mutated wild-type gastrointestinal tumours (GISTs). Both cases occurred in the small bowel of females. Immunohistochemical studies on both tumours showed KIT and DOG-1 positivity, with SDHB retained. Molecular analysis revealed a KRAS G12D mutation and a KRAS G13D mutation, respectively. Wild-type GISTs are extremely uncommon. They typically occur in the stomach or the small bowel. KRAS is one of the genes implicated in this subset of GIST, with KRAS G12D being the most frequently encountered mutation. GIST KRAS mutations can arise alone or in conjunction with KIT, PDFRA, or BRAF mutations. Identification of these rare molecular subtypes is clinically important due to their resistance to imatinib therapy.

Distinguishing Gastric/Esophageal Adenocarcinoma from Pancreatic Adenocarcinoma Using Methylation-Based Droplet Digital PCR

The goal of this study was to develop a methylation-based droplet digital PCR to separate 2 cancer classes that do not have sensitive and specific immunohistochemical stains: gastric/esophageal and pancreatic adenocarcinomas. The assay used methylation-independent primers and methylation-dependent probes to assess a single differentially methylated CpG site; analyses of array data from The Cancer Genome Atlas network showed that high methylation at the cg06118999 probe supports the presence of cells originating from the stomach or esophagus (eg, as in gastric metastasis), whereas low methylation suggests that these cells are rare to absent (eg, pancreatic metastasis). On validation using formalin-fixed paraffin-embedded primary and metastatic samples from our institution, methylation-based droplet digital PCR targeting the corresponding CpG dinucleotide generated evaluable data for 60 of the 62 samples (97%) and correctly classified 50 of the 60 evaluable cases (83.3%), mostly adenocarcinomas from the stomach or pancreas. This ddPCR was created to be easy-to-interpret, rapid, inexpensive, and compatible with existing platforms at many clinical laboratories. We suggest that similarly accessible PCRs could be developed for other differentials in pathology that do not have sensitive and specific immunohistochemical stains.

Long-standing laryngeal rhinoscleroma with rare Mikulicz cells

Rhinoscleroma is an infectious granulomatous disease. It is important to identify pathognomonic Mikulicz cells on microscopy, as these can be rare and the chronic inflammatory infiltrate can appear otherwise nonspecific on biopsies.

Gene of the month: ERG

The ERG gene belongs to the erythroblastosis transformation specific family of transcription factors and encodes for the transcription regulator protein ERG. It is located on chromosome 22q22 and is a nuclear transcription factor. In normal physiology, ERG protein is expressed in endothelial cells and is involved in processes including, but not limited to, angiogenesis and haematopoiesis. Of diagnostic value in clinical practice, ERG immunohistochemistry is a useful marker of endothelial differentiation for both benign and malignant vascular lesions. It is also reliable for identifying ERG gene translocated malignancies such as EWS/FUS::ERG Ewing's sarcoma and TMPSSR2::ERG prostatic carcinoma.

Pathologic Examination of Pancreatic Specimens Resected for Treated Pancreatic Ductal Adenocarcinoma: Recommendations From the Pancreatobiliary Pathology Society

Currently, there are no internationally accepted consensus guidelines for pathologic evaluation of posttherapy pancreatectomy specimens. The Neoadjuvant Therapy Working Group of Pancreatobiliary Pathology Society was formed in 2018 to review grossing protocols, literature, and major issues and to develop recommendations for pathologic evaluation of posttherapy pancreatectomy specimens. The working group generated the following recommendations: (1) Systematic and standardized grossing and sampling protocols should be adopted for pancreatectomy specimens for treated pancreatic ductal adenocarcinoma (PDAC). (2) Consecutive mapping sections along the largest gross tumor dimension are recommended to validate tumor size by histology as required by the College of American Pathologists (CAP) cancer protocol. (3) Tumor size of treated PDACs should be measured microscopically as the largest dimension of tumor outer limits that is bound by viable tumor cells, including intervening stroma. (4) The MD Anderson grading system for tumor response has a better correlation with prognosis and better interobserver concordance among pathologists than does the CAP system. (5) A case should not be classified as a complete response unless the entire pancreas, peripancreatic tissues, ampulla of Vater, common bile duct, and duodenum adjacent to the pancreas are submitted for microscopic examination. (6) Future studies on tumor response of lymph node metastases, molecular and/or immunohistochemical markers, as well as application of artificial intelligence in grading tumor response of treated PDAC are needed. In summary, systematic, standardized pathologic evaluation, accurate tumor size measurement, and reproducible tumor response grading to neoadjuvant therapy are needed for optimal patient care. The criteria and discussions provided here may provide guidance towards these goals.

New Kids on the Block

CONTEXT.—

With the increasing development and use of iatrogenic agents, pathologists are encountering more novel foreign materials in retrieved gastrointestinal specimens. These colorful and unusual-appearing foreign materials can pose a diagnostic dilemma to those unaware of their morphology, especially if the relevant clinical history is lacking.

OBJECTIVE.—

To discuss the histopathologic features, clinical scenarios and significance, and differential diagnosis of relatively recently described, yet quickly expanding, family of iatrogenic agents that can present as foreign materials in gastrointestinal specimens-pharmaceutical fillers (crospovidone and microcrystalline cellulose), submucosal lifting agents (Eleview and ORISE), lanthanum carbonate, hydrophilic polymers, OsmoPrep, yttrium 90 microspheres (SIR-Sphere and TheraSphere), and resins (sodium polystyrene sulfonate, sevelamer, and bile acid sequestrants).

DATA SOURCES.—

We collate the findings of published literature, including recently published research papers, and authors' personal experiences from clinical sign-out and consult cases.

CONCLUSIONS.—

Correct identification of these iatrogenic agents is important because the presence of some novel agents can explain the histopathologic findings seen in the background specimen, and specific novel agents can serve as diagnostic clues to prompt the pathologist to consider other important and related diagnoses. Awareness of even biologically inert agents is important for accurate diagnosis and to avoid unnecessary and expensive diagnostic studies.

Preoperative Helicobacter pylori Screening and Treatment in Patients Undergoing Laparoscopic Sleeve Gastrectomy

BACKGROUND

The role of preoperative screening and treatment of Helicobacter pylori (HP) in asymptomatic patients undergoing laparoscopic sleeve gastrectomy (LSG) remains unclear. This study aims to define the preoperative prevalence and management of HP and their effect on postoperative outcomes at our institution.

MATERIALS AND METHODS

We reviewed the medical records and surgical specimens of all LSG performed at an academic centre in Toronto, ON between 2010 and 2017.

RESULTS

Review of our institutional database identified 222 patients that underwent LSG, of which 200 had preoperative HP screening: 18% tested positive and 15% were treated. Seven surgical specimens were HP-positive (3.2%). No association was found between preoperative HP status, treatment or HP-positive specimen and postoperative complications at 1 year.

CONCLUSION

Although preoperative screening and treatment likely reduce the prevalence of HP in LSG specimens, our findings suggest that they may be of limited clinical value in LSG as they have little influence on surgical morbidity.

Histologic and Cost-Benefit Analysis of Laparoscopic Sleeve Gastrectomy Specimens Performed for Morbid Obesity

CONTEXT.—

Laparoscopic sleeve gastrectomy (LSG) has quickly become the bariatric surgical procedure of choice for patients with obesity who have failed medical management. Laparoscopic sleeve gastrectomy results in a gastric remnant that is routinely subject to pathologic examination.

OBJECTIVE.—

To perform a histologic and cost-benefit analysis of gastric remnants post-LSG.

DESIGN.—

All LSG cases performed at University Health Network, Toronto, Ontario, Canada, between 2010 and 2019 were reviewed. Specimens that underwent routine histopathologic assessment and ancillary immunohistochemical analysis were analyzed. Baseline patient characteristics and surgical outcomes were obtained from our internal database. The total cost of specimen gross preparation, examination, sampling, and producing and reporting a hematoxylin-eosin slide was calculated.

RESULTS.—

A total of 572 patients underwent LSG during the study period and had their specimens examined histologically. A mean of 4.87 blocks generating 4 hematoxylin-eosin slides was produced. The most common histologic findings reported in LSG specimens ranged from no pathologic abnormalities identified together with proton pump inhibitor-related change. A minority of cases demonstrated clinically actionable histologic findings, of which Helicobacter pylori infection was the most common. The total cost for the complete pathologic analysis of these cases amounted to CaD $66 383.10 (US $47 080.21) with a mean of CaD $116.05 (US $82.40) per case. A total of CaD $62 622.75 (US $44 413.30) was spent on full examination of cases that had no further postoperative clinical impact.

CONCLUSIONS.—

There is a broad spectrum of pathologic findings in LSG specimens, ranging from clinically nonactionable to more clinically actionable. The vast majority of histologic findings had no clinical impact, with only a minority of cases being clinically significant. This study therefore recommends that LSG specimens be subject to gross pathologic examination in the vast majority of cases. However, sections should be submitted for microscopic analysis if grossly evident lesions are present and if there is a clinical/known history of clinically actionable findings.

Gene of the month: TLE 1

TLE 1 is the human homologue belonging to a family of four genes and is located on chromosome 9q21. It consists of 19 exons. Although it does not bind directly to DNA, it acts as a repressor of several signalling pathways via transcription factors. TLE1 protein has several physiological roles in embryogenesis, haematopoiesis, general differentiation, and both neuronal and eye development. Much attention was focused on its expression in the tumour cell nuclei of synovial sarcoma (SS). However, several other soft tissue tumours that do and do not share morphological similarity with SS also display nuclear immunoreactivity for TLE1; hence, caution in interpretation is advocated.

SWI/SNF-deficient cancers of the Gastroenteropancreatic tract: an in-depth review of the literature and pathology

The SWItch Sucrose non-fermentable (SWI/SNF) complex is a large, multi-subunit ATP-dependent nucleosome remodeling complex that acts as a tumor suppressor by modulating transcription. Mutations of SWI/SNF subunits have been described in relation to developmental disorders, hereditary SWI/SNF deficiency syndromes, as well as malignancies. In this review we summarize the current literature in regards to SWI/SNF-deficient tumors of the luminal gastrointestinal tract (GIT) and pancreas. As a group they range from moderately to undifferentiated tumors composed of monotonous anaplastic cells, prominent macronucleoli and a variable rhabdoid cell component. Deficiency of a SWI/SNF subunit is typified by complete loss of nuclear staining by immunohistochemistry for respective subunit.

Minimalist approaches to cancer tissue-of-origin classification by DNA methylation

Classification of cancers by tissue-of-origin is fundamental to diagnostic pathology. While the combination of clinical data, tissue histology, and immunohistochemistry is usually sufficient, there remains a small but not insignificant proportion of difficult-to-classify cases. These challenging cases provide justification for ancillary molecular testing, including high-throughput DNA methylation array profiling, which promises cell-of-origin information and compatibility with formalin-fixed specimens. While diagnostically powerful, methylation profiling platforms are costly and technically challenging to implement, particularly for less well-resourced laboratories. To address this, we simulated the performance of "minimalist" methylation-based tests for cancer classification using publicly-available and internal institutional profiling data. These analyses showed that small and focused sets of the most informative CpG biomarkers from the arrays are sufficient for accurate diagnoses. As an illustrative example, one classifier, using information from just 53 out of about 450,000 available CpG probes, achieved an accuracy of 94.5% on 2575 fresh primary validation cases across 28 cancer types from The Cancer Genome Atlas Network. By training minimalist classifiers on formalin-fixed primary and metastatic cases, generally high accuracies were also achieved on additional datasets. These results support the potential of minimalist methylation testing, possibly via quantitative PCR and targeted next-generation sequencing platforms, in cancer classification.

Gene of the month: TFE 3

Transcription factor enhancer 3 (TFE3), on the short arm of chromosome Xp11.23 and its protein, belongs to the microphthalmia transcription family (MiTF) of transcription factors. It shares close homology with another member of the family, MiTF which is involved in melanocyte development. When a cell is stressed and/or starved, TFE3 protein translocates into the nucleus. TFE3 gene fusions with multiple different partner genes occur in several tumours with resultant nuclear expression of TFE3 protein. The main tumours associated with TFE3 gene fusions are: renal cell carcinoma, alveolar soft part sarcoma, a subset of epithelioid haemangioendotheliomas (EHE), some perivascular epithelioid cell tumours and rare examples of ossifying fibromyxoid tumour and malignant chondroid syringoma. TFE3 immunohistochemistry is of use in routine diagnostic practice with the aforementioned tumours harbouring TFE3 fusions leading to nuclear staining. In addition, there are tumours lacking TFE3 fusions but also display TFE3 nuclear immunolabeling, and these include: granular cell tumour, solid pseudopapillary neoplasm of the pancreas and ovarian sclerosing stromal tumour.

Gene of the month: GLIS1-3

The GLIS 1-3 genes belong to a family of transcription factors, the Krüppel-like zinc finger proteins. The GLIS proteins function primarily as activators of transcription (GLIS 1 and 3), while GLIS 2 functions as a repressor. Collectively, the GLIS proteins are involved in a variety of diseases in several organs ranging from Alzheimer's disease, facial dysmorphism, neonatal diabetes mellitus, breast and colon cancers and leukaemia. In particular, loss-of-function mutations in GLIS2 are responsible for an autosomal recessive cystic kidney disease called nephronophthisis, which is characterised by tubular atrophy, interstitial fibrosis and corticomedullary cysts.Of diagnostic value in current practice are the presence of GLIS 3 and 1 fusions with PAX8 in almost 100% of hyalinising trabecular tumours of the thyroid gland. This enables its separation from papillary thyroid cancer.

Use of whole slide imaging (WSI) for distance teaching

BACKGROUND

Time, travel and financial constraints have meant that traditional visiting teaching engagements are more difficult to accomplish. This has been exacerbated with the advent of the COVID-19 pandemic. The use of digital pathology and whole slide imaging (WSI) as an educational tool for distance teaching is underutilised and not fully exploited. This paper highlights the utility and feedback on the use of WSI for distance education/teaching.

MATERIALS AND METHODS

Building on an existing relationship with the University of the West Indies (UWI), pathologists at University Health Network, Toronto, provided distance education using WSI, a digitised slide image hosting repository and videoconferencing facilities to provide case-based teaching to 15 UWI pathology trainees. Feedback was obtained from residents via a questionnaire and from teachers via a discussion.

RESULTS

There was uniform support from teachers who felt that teaching was not hampered by the 'virtual' engagement. Comfort levels grew with each engagement and technical issues with sound diminished with the use of a portable speaker. The residents were very supportive and enthusiastic in embracing this mode of teaching. While technical glitches marred initial sessions, the process evened out especially when the slide hosting facility, teleconferencing and sound issues were changed.

CONCLUSIONS

There was unanimous endorsement that use of WSI was the future, especially for distance teaching. However, it was not meant to supplant the use of glass slides in their current routine, daily practice.

Establishment of a remote diagnostic histopathology service using whole slide imaging (digital pathology)

BACKGROUND

Whole slide imaging (WSI) has diverse applications in modern pathology practice, including providing histopathology services to remote locations.

MATERIALS AND METHODS

Utilising an existing contractual partnership with a Northern Ontario group of hospitals, the feasibility of using WSI for primary diagnostic services from Toronto was explored by the dedicated working group. All aspects explored from information technology (IT), laboratory information system (LIS) integration, scanning needs, laboratory workflow and pathologist needs and training, were taken into account in the developing the rationale and business case.

RESULTS

The financial outlay for a scanner was $CA180K (approximately £105.6 k) after discounts. There were no human resource requirements as staff were reorganised to cater for slide scanning. Additional IT/LIS costs were not incurred as existing connectivity was adapted to allow two site groups (gastrointestinal and skin) to pilot this study. Scanned slides were available for pathologist review 24-96 hours sooner than glass slides; there was a 2-day improvement for final authorised cases, and per annum savings were: $CA26 000 (£15.2 k) in courier costs, $CA60 000 (£35.2 k) travel and $CA45 000 (£26.4 k) in accommodation, meals and car rental expense.

CONCLUSION

WSI is a viable solution to provide timely, high-quality and cost efficient histopathology services to underserviced, remote areas.

Review of pathological findings in laparoscopic sleeve gastrectomy specimens performed for morbid obesity

BACKGROUND

Bariatric surgical procedures are employed when there is a failure of lifestyle modification in arresting obesity. Laparoscopic sleeve gastrectomy (LSG) is quickly becoming the bariatric surgical procedure of choice. LSG results in a gastric remnant that is subject to pathological examination. The objective of this paper is to review the literature in regard to histological findings identified in gastric remnants post-LSG and identify the most pertinent histological findings.

MATERIALS AND METHODS

A literature search was performed to identify relevant case series. Data gathered from relevant case series then underwent statistical analysis.

RESULTS

The most common histological findings in an LSG specimen were clinically indolent findings such as no pathological abnormalities identified followed by non-specific gastritis. A minority of cases demonstrated clinically actionable findings for which Helicobacter pylori represented the majority of these findings.

CONCLUSION

There is a broad spectrum of pathological findings in LSG specimens, ranging from clinically indolent to clinically actionable. The most common histological findings are clinically indolent and only a small portion are of clinical significance and, hence, actionable.

SMARCA family of genes

The SMARCA subgroup of genes belong to the SWI1/SNF1 family that are responsible chromatin remodelling and repair. Inactivating mutations in the main SMARCA genes A2 and A4 lead to loss of expression of their respective proteins within the nucleus and, as such have characterised a set of malignancies that are underpinned by SMARCA-deficiency.The morphology of these tumours ranges from small to large epithelioid cells, giant cells and rhabdoid cells. The rhabdoid cells are frequently present in these tumours but are not a sine qua non for the diagnosis. Most of these tumours are undifferentiated or dedifferentiated, high-grade pleomorphic carcinomas. Focally, areas of better differentiation can be seen. The initial description of a SMARCA4-deficient malignancy was the small cell carcinoma of the ovary, hypercalcaemic type. Subsequently, tumours fitting this characteristic morphology and immunophenotype have been described in the lung, thoracic cavity, endometrium and sinonasal tract, gastrointestinal tract and kidney. Immunohistochemical loss of SMARCA2 and SMARCA4 may occur concomitantly or independently of each other.SMARCA-deficient malignant tumours represent a unique subset of tumours with typical morphological and immunohistochemical findings.

Multiple sclerosing pneumocytomas: a review

Sclerosing pneumocytoma (SP) is a rare benign low-grade tumour of the lung, and typically presents as single discrete coin lesions on imaging. Multiple SP is an exceedingly rare entity and thus reported sparingly. We review the literature on multiple SP, their clinical presentations, histopathology, relevant differential diagnoses and molecular histogenesis of this entity. SP has a predilection for East Asian origin females who have never smoked. Patients are either asymptomatic or have symptoms such as cough, haemoptysis that may be persistent, chest pain if involving the pleura and presents as discrete coin lesion on chest X-ray. Histologically, they are papillary, solid, angiomatoid or sclerotic, or combinations of these four basic patterns. Multiple lesions have the same or slightly different histological patterns. They can be distributed in either lung, in any lobe and can even be bilateral. AKT-1 molecular pathways are pivotal in their molecular pathogenesis. In this review, we further propose a classification based on five types of distribution of multiple SP.

A reappraisal of sclerosing nodular and/or polypoid lesions of the gastrointestinal tract rich in IgG4-positive plasma cells

AIMS

To describe additional cases of nodular and polypoid sclerosing lesions of the gastrointestinal tract (GIT) that are associated with numerous IgG4-positive plasma cells, review the pertinent literature to ascertain the relationship with systemic IgG4-related disease, and provide a reporting framework for such lesions.

METHODS AND RESULTS

Five new cases of sclerosing polyps or nodules were collected over a 10-year period, occurring in four females and one male ranging in age from 32 years to 56 years (mean, 41.6 years). Patients were asymptomatic or had epigastric pain, and one had rectal bleeding. None had autoimmune or other obvious IgG4-related disease, and serum IgG4 levels were normal. All were solitary nodules in the stomach (two cases), ileum, caecum, and rectum. Four lesions were submucosal and one was subserosal; all were well circumscribed, composed of hyalinised, keloidal fibrous tissue with lymphoplasmacytic inflammation. Obliterative phlebitis was not seen. Lineage-specific immunomarkers were negative. In excess of 10 IgG4-positive plasma cells per high-power field were seen, and the IgG4/IgG ratios were >0.4.

CONCLUSIONS

Very few IgG4-related lesions in the tubular GIT are associated with disease at other sites and/or elevated serum IgG4 levels. The majority may represent a lesion in the spectrum of IgG4-related disease. The use of the term 'IgG4-positive nodule or polyp with probable histological features of IgG4-related disease' is advocated for nodular and/or polypoid lesions in the GIT with ≥10 IgG4-positive plasma cells in a high-power field and an IgG/IgG4 ratio of >0.4.

Review of pathology and cost benefit analysis of hernia sacs processed over a 19-year period

AIM

Hernia sacs with pathological evaluation over a 19-year period were analysed with regards to pathological diagnoses, full costing and the impact on patient management.

MATERIALS AND METHODS

The database of the Department of Pathology were searched over the study period (2001 to 2019 inclusive) for hernia sacs. The total cost of complete pathology examination was calculated on average numbers and rates of pay that existed over the study period.

RESULTS

A total of 3619 hernia sacs from the abdominal, hiatus/diaphragmatic, inguinal and femoral hernias were retrieved. Of these 3592 cases (99.25%) had sections taken for histological evaluation. A total of 3437 cases representing 95.7% of all hernia sacs did not show any pathological abnormality. If non-neoplastic clinically insignificant lesions seen in hernia sacs is included, then 3552 of 3592 (98.9%) hernia sacs underwent full pathological evaluation for no patient benefit.On average two blocks or tissue sections per case were processed incurring a technical cost of $53 175.00. The total pathologist cost in reporting the 3592 cases was approximately $39 870.00 and rose to $40 410.00 when interpretation of ancillary tests was factored in. $95 328.90 (average $26.90 per specimen with a yearly average total cost of $5 017.31) was spent over the 19-year period in full pathological examination of 3592 hernia sacs.

CONCLUSION

Given the low return on investment and the difficult to quantify time savings and reallocation, we do not advocate the routine sampling of hernia sacs. Gross examination will suffice in 99% of the cases. Selective cases may be sampled if clinically indicated.

Agrin in the Muscularis Mucosa Serves as a Biomarker Distinguishing Hyperplastic Polyps from Sessile Serrated Lesions

PURPOSE

Sessile serrated lesions (SSL) are precursors to colon carcinoma, and their distinction from other polyps, in particular hyperplastic polyps (HP), presents significant diagnostic challenges. We evaluated expression patterns in colonic polyps of previously identified colon carcinoma-associated extracellular matrix (ECM) proteins to identify markers distinguishing SSLs from other polyps.

EXPERIMENTAL DESIGN

Gene-expression analyses of ECM proteins were performed using publicly available data on preneoplastic colonic polyps. In parallel, we evaluated by IHC the expression of agrin (AGRN) in over 400 colonic polyps, including HP, SSL with and without dysplasia, traditional serrated adenomas (TSA), and tubular adenomas (TA), and compared the consistency of standard histologic diagnosis of SSLs by experienced gastrointestinal pathologists with that of AGRN IHC.

RESULTS

Differential gene expression analysis and IHC identified AGRN, serine peptidase inhibitor (SERPINE2), and TIMP metallopeptidase inhibitor 1 (TIMP1) elevated in SSLs and HPs but decreased in TAs and absent in normal colon. AGRN-positive basal laminae were noted in all TA, TSA, HP, and SSL in distinguishable patterns, whereas other polyps and normal mucosa were negative. SSL with or without dysplasia consistently showed IHC staining for AGRN in the muscularis mucosae, which was absent in HP, TSA, TA, and other polyps. In contrast, histologic evaluation showed only weak interobserver agreement (kappa value = 0.493) in distinguishing SSLs.

CONCLUSIONS

Muscularis mucosae-based AGRN immunostaining is a novel biomarker to distinguish SSL from HP, TSA, and TA, with a specificity of 97.1% and sensitivity of 98.9% and can assist in diagnosis of morphologically challenging colonic polyps.

Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Morphological classification of pancreatic ductal adenocarcinoma that predicts molecular subtypes and correlates with clinical outcome

INTRODUCTION

Transcriptional analyses have identified several distinct molecular subtypes in pancreatic ductal adenocarcinoma (PDAC) that have prognostic and potential therapeutic significance. However, to date, an indepth, clinicomorphological correlation of these molecular subtypes has not been performed. We sought to identify specific morphological patterns to compare with known molecular subtypes, interrogate their biological significance, and furthermore reappraise the current grading system in PDAC.

DESIGN

We first assessed 86 primary, chemotherapy-naive PDAC resection specimens with matched RNA-Seq data for specific, reproducible morphological patterns. Differential expression was applied to the gene expression data using the morphological features. We next compared the differentially expressed gene signatures with previously published molecular subtypes. Overall survival (OS) was correlated with the morphological and molecular subtypes.

RESULTS

We identified four morphological patterns that segregated into two components ('gland forming' and 'non-gland forming') based on the presence/absence of well-formed glands. A morphological cut-off (≥40% 'non-gland forming') was established using RNA-Seq data, which identified two groups (A and B) with gene signatures that correlated with known molecular subtypes. There was a significant difference in OS between the groups. The morphological groups remained significantly prognostic within cancers that were moderately differentiated and classified as 'classical' using RNA-Seq.

CONCLUSION

Our study has demonstrated that PDACs can be morphologically classified into distinct and biologically relevant categories which predict known molecular subtypes. These results provide the basis for an improved taxonomy of PDAC, which may lend itself to future treatment strategies and the development of deep learning models.

Gene of the month: GLI-1

The Glioma-associated homologue-1 (GLI-1) gene was first discovered to be amplified in glioblastoma multiforme. It encodes for a zinc-finger transcription factor in the Kruppel family of proteins and is important in the sonic hedgehog signalling pathway. GLI-1 also plays a role in several other pathways and is important for proliferation, migration, invasion, growth and angioinvasion, and cancer stem cell self-renewal in a variety of malignancies. GLI-1 is amplified in several malignancies, including an epithelioid, pericytomatous soft tissue neoplasm that can exhibit malignant behaviour. More recently, GLI-1 fusions with other partner genes have been found in three rare tumours: a pericytomatous tumour with a t(7;12) translocation, where it partners with Actin beta 1, and gastroblastoma and plexiform fibromyxoma, where the partner gene is metastasis-associated lung adenocarcinoma transcript 1, respectively.

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor tumor cellularity and extensive genomic instability. To address this, a dataset of whole genomes and transcriptomes was generated from purified epithelium of primary and metastatic tumors. Transcriptome analysis demonstrated that molecular subtypes are a product of a gene expression continuum driven by a mixture of intratumoral subpopulations, which was confirmed by single-cell analysis. Integrated whole-genome analysis uncovered that molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and GATA6. By mapping tumor genetic histories, tetraploidization emerged as a key mutational process behind these events. Taken together, these data support the premise that the constellation of genomic aberrations in the tumor gives rise to the molecular subtype, and that disease heterogeneity is due to ongoing genomic instability during progression.

Adult-onset autoimmune-type enteropathy: potential relationship to an adverse drug reaction

Objective

To describe an example of adult-onset autoimmune enteropathy (AIE) that coincided with drug-induced reaction.

Design

A 54-year-old patient was presented with Stevens-Johnson syndrome after a course of quinolones. This was followed shortly thereafter by epigastric pain, diarrhoea and weight loss. She also developed an autoimmune neutropenia.

Results

Several biopsies were performed from the upper and lower gastrointestinal tract (GIT). The duodenal biopsies showed intraepithelial lymphocytosis; therefore, coeliac disease was considered. However, confirmatory serology was negative and the patient did not respond to a gluten-free/gliadin-free diet. Both upper and lower GIT biopsies consistently showed an absence of goblet cells resembling the changes of an AIE.

Conclusion

This is an unusual case of autoimmune-pattern enteropathy in an adult that was potentially drug-induced.

Unique MLH1 mutations in colonic adenomas in an obligate germline Lynch syndrome carrier

BACKGROUND

An obligate germline Lynch syndrome carrier had four colonic adenomas removed.

MATERIALS AND METHODS

The adenomas were evaluated for grade of dysplasia, MLH1, PMS2, MSH2 and MSH6 protein expression, microsatellite instability (MSI), BRAF, methylation status and a next-generation sequencing (NGS) panel of 52 cancer genes.

RESULTS

There were four tubular or tubulovillous adenomas from the hepatic flexure, rectosigmoid and rectum; one with low-grade and high-grade dysplasia, one with high-grade dysplasia only and two with low-grade dysplasia. All four adenomas showed retention of MLH1, MHS2 and MSH6 but complete loss of PMS2 in both low-grade and high-grade dysplasia areas.Two of the four adenomas were MSI-high, BRAF V600E wild type and were not MLH1 methylated. NGS identified an MLH1 germline variant: NM_000249.3: c.1558+1 G>A, p.(?) in all tissue (adenomas and normal), which likely explains the pathophysiology of Lynch syndrome in this patient. Other variants were also detected in MLH1 and MSH6 in all four adenomas tested; these being reported previously in somatic colorectal cancers.

CONCLUSION

We highlight an MLH1 variant in the colonic adenomas in an obligate Lynch syndrome carrier that resulted in PMS2 protein loss in the absence of mutations of the PMS2 gene.

Traditional serrated adenoma: an overview of pathology and emphasis on molecular pathogenesis

Objective

To provide an overview of the pathology and molecular pathogenesis of traditional serrated adenomas (TSA).

Design

Describe the morphology and molecules that play a role in their pathogenesis.

Results

These exuberant polypoid lesions are typified by tall cells with deeply eosinophilic cytoplasm, elongated nuclei bearing delicate chromatin, ectopic crypt foci, deep clefting of the lining mucosa and an overall resemblance to small bowel mucosa.

Broadly, TSAs arise via three mechanisms. They may be BRAF mutated and CpG island methylator phenotype (CIMP)-high: right sided, mediated through a microvesicular hyperplastic polyp or a sessile serrated adenoma, may also have RNF43 mutations and result in microsatellite stable (MSS) colorectal cancers (CRC). The second pathway that is mutually exclusive of the first is mediated through KRAS mutation with CIMP-low TSAs. These are left-sided TSAs, are not associated with another serrated polyp and result in MSS CRC. These TSAs also have RSPO3, RNF43 and p53 mutations together with aberrant nuclear localisation of β-catenin. Third, there is a smaller group of TSAs that are BRAF and KRAS wild type and arise by as yet unknown molecular events. All TSAs show retention of mismatch repair proteins.

Conclusion

These are characteristic unusual polyps with a complex molecular landscape.

Sclerosing Tumors of the Gastrointestinal Tract: A Systematic Approach

Some lesions in the gastrointestinal tract have a propensity for sclerosis such that it may mask the actual true nature of the lesion. The purpose of this review is to highlight those lesions of the gastrointestinal tract that can be attended by sclerosis. The sclerosis can mask the cellularity of the lesion; hence, knowledge of the key lesions that are known to have sclerosis will be aid the diagnostic pathologist.

Gut-associated lymphoid tissue or so-called “dome” carcinoma of the colon: Review

AIM

To present a comprehensive review of the etiology, clinical features, macroscopic and pathological findings, and clinical significance of Gut-associated lymphoid tissue or “dome” carcinoma of the colon.

METHODS

The English language medical literature on gut- or gastrointestinal-associated lymphoid tissue (GALT) or “dome” carcinoma of the colon was searched and appraised.

RESULTS

GALT/dome-type carcinomas of the colon are thought to arise from the M-cells of the lymphoglandular complex of the intestine. They are typically asymptomatic and have a characteristic endoscopic plaque- or “dome”-like appearance. Although the histology of GALT/dome-type carcinomas displays some variability, they are characterized by submucosal localization, a prominent lymphoid infiltrate with germinal center formation, tumor-infiltrating lymphocytes, absence of desmoplasia, and dilated glands lined by columnar epithelial cells with bland nuclear features and cytoplasmic eosinophilia. None of the patients reported in the literature with follow-up have developed metastatic disease or local recurrence.

CONCLUSION

Increased awareness amongst histopathologists of this variant of colorectal adenocarcinoma is likely to lead to the recognition of more cases.

Neurotrophic tropomyosin or tyrosine receptor kinase (NTRK) genes

The neurotrophic tropomyosin or tyrosine receptor kinase (NTRK) genes (1-3) are proto-oncogenes that when activated are encountered in a wide array of tumours. The recent advent of very specific and selective inhibitors of their gene fusions makes the NRTK gene fusions actionable. NRTK gene fusions are very characteristic of specific tumours: salivary mammary analogue secretory carcinoma, breast secretory carcinoma, infantile fibrosarcoma and congenital mesoblastic nephroma. Over 90% of these tumours bear NTRK gene fusions. While next-generation sequencing is the current platform of choice for the detection of NTRK fusions, immunohistochemistry also shows great promise. Immunohistochemical localisation of the fusion protein to the nucleus, cytoplasm, nuclear membrane and cell membrane is indicative of specific gene fusions involving the NTRK genes.

Neoadjuvant chemoradiation and rectal cancer

Neoadjuvant chemoradiation (NACR) is now standard of care in stage II and III rectal cancer. The advent of this modality of treatment has impacted on the way the pathological evaluation of resection specimens that have been subjected to preoperative chemoradiation is conducted. The gross description, sectioning and microscopic examination have had to be adapted to accommodate the changes induced by NACR. Attempts at introducing a uniform approach to the gross triaging and reporting of these specimens have been met with muted response. There still exists much variation in approach. The purpose of this overview is to highlight some of the newer developments and issues around NACR-treated rectal cancers from a pathological point of view. The NACR-treated resection specimens should be handled in a consistent manner, at least within individual institutions, if not universally. There should be generous sampling with multiple sections taken as tumour is often sequestered deep in the bowel wall. Microscopic examination should be extra vigilant as residual cancer can be present as single cells or small clusters, often deep in the muscularis propria or serosa. Acellular pools of mucin or non-viable tumour cells in mucin within the bowel wall or lymph nodes are not regarded as positive and do not upstage the tumour. The issue of grading of regression has been the subject of much debate, and several approaches have been published. It is recommended that a system that has clinical meaning and use to oncologists be used. Lymph node counts will be reduced after NACR, but reasonable attempts to accrue 12 nodes should be made.

Heterogenous loss of mismatch repair (MMR) protein expression: a challenge for immunohistochemical interpretation and microsatellite instability (MSI) evaluation

Immunohistochemistry (IHC) for mismatch repair (MMR) proteins is used to identify MMR status: being diffusely positive (intact/retained nuclear staining) or showing loss of nuclear tumour staining (MMR protein deficient). Four colonic adenocarcinomas and a gastric adenocarcinoma with associated dysplasia that displayed heterogenous IHC staining patterns in at least one of the four MMR proteins were characterised by next‐generation sequencing (NGS). In order to examine a potential molecular mechanism for these staining patterns, the respective areas were macrodissected, analysed for microsatellite instability (MSI) and investigated by NGS and multiplex ligation‐dependent probe amplification (MLPA) analysis of MLH1, MSH2, MSH6 and PMS2 genes, including MLH1 methylation analysis. One colonic adenocarcinoma showed heterogenous MSH6 IHC staining and molecular analysis demonstrated increasing allelic burden of two MSH6 frameshift variants (c.3261delC and c.3261dupC) in areas with MSH6 protein loss compared to areas where MSH6 was retained. Two colonic adenocarcinomas with heterogenous MLH1 staining showed no differences in sequence variants. In one of these cases, however, MLH1 was hypermethylated in the area of MLH1 loss. Another colon carcinoma with heterogenous PMS2 staining (but with retained MSH6) showed both MSH6 c.3261dupC and 3260_3261dupCC where PMS2 protein was lost and only c.3261dupC where PMS2 was retained. The gastric carcinoma showed complete loss of MSH6 in dysplastic foci, while the underlying invasive carcinoma showed retention of MSH6. Both these areas, however, were MSI‐high and showed the same MSH6 variant: c.3261delC. The gastric dysplasia additionally showed MSH6 c.3261dupC. In four of the five cases where MMR protein was lost, these areas were MSI‐high. Heterogenous MMR IHC (focal and/or zonal within the same tumour or between invasive and dysplastic preinvasive areas) is not always due to artefact and is invariably related to MSI‐high status in the areas of loss. An interesting aspect to this study is the presence of MSH6 somatic mutations irrespective of whether MSH6 IHC staining was intact or lost.

Apoptotic colopathy: a pragmatic approach to diagnosis

‘Apoptotic colopathy’ is an umbrella term signifying a pattern of injury where the gastrointestinal biopsy shows a colitic picture with apoptosis as the predominant histological feature. Although the entities within apoptotic colopathy share a common histological feature— ‘apoptosis’, there is a list of varied clinical differential diagnoses that produce this similar histological pattern of injury. These include graft-versus-host disease, drug-induced injury due to multiple drugs (in particular, mycophenolate mofetil, check point inhibitor therapy and some others), infections (particularly cytomegalovirus, adenovirus and some others), immune disorders and other miscellaneous causes. However, the management of these varied differentials is strikingly different, thus necessitating an algorithmic approach for accurate diagnosis and optimal patient management. A definitive diagnosis requires interpretation of varied histological findings in the appropriate clinical context including clinical history, drug history and laboratory findings. This review will focus on the histopathological findings of varied entities that can manifest as ‘apoptotic colopathy’ on assessment of colonic biopsies.

Cutaneous epithelioid angiomatous nodule: a report of a series including a case with moderate cytologic atypia and immunosuppression

BACKGROUND

Cutaneous epithelioid angiomatous nodule (CEAN) is a very rare and relatively recently recognized vascular proliferation characterized usually by minimal cytological atypia and accompanying mitotic activity. As such, CEAN represents an important diagnostic pitfall, which could lead to significant misdiagnosis and unnecessary treatment.

METHODS

The clinicopathologic findings of 5 cases of CEAN were reviewed including a unique case with typical findings but also moderate cytologic atypia and brisk mitotic activity in a patient on immunosuppression.

RESULTS

The cases were in 3 women and 2 men ranging in age from 18 to 61 years with lesions in the neck (2 cases), upper arm, back and shoulder. In 4 of the cases, the patients did not have any relevant potentially contributory clinical history, and in 1 case the patient was on immunosuppressive treatment. All 5 cases were superficially located within the dermis, well-circumscribed and similarly composed of epithelioid cells displaying minimal (in 4 cases) and moderate (1 case) atypia. The mitotic count ranged from 1 to 3 per 10 high power fields (HPF) in 4 cases and up to 9 per 10 HPF in the immunosuppressed patient. Atypical mitoses were not encountered in any of the cases. Two lesions that were incompletely excised recurred, but none of the patients showed distant metastases.

CONCLUSION

While cytologically alarming, CEAN has a characteristic microscopic appearance and if completely excised follows an indolent course.

p16

The p16 gene belongs to INK4 family of genes and is made up of four members: p16 ^INK4A , p15 ^INK4B , p18 ^INK4C and p19 ^INK4D , all of which share biological properties, namely, inhibition of cell growth and tumour suppression. After p53, p16 is the second most common tumour suppressor gene. It has been regarded as the familial melanoma gene. Immunohistochemistry for p16 has a well-defined role in distinct pathological scenarios. It is used to distinguish desmoplastic melanoma from reactive fibrous proliferation, with former showing strong nuclear positivity. In other types of melanoma, p16 protein expression is lost. Spitz nevi show retention of nuclear staining for p16. Benign mesothelial proliferations tend to retain nuclear p16 immunoreactivity, while malignant mesotheliomas lose expression. However, p16 fluorescent in-situ hybridisation analysis is recommended in the workup of malignant mesothelioma. Another common application of p16 immunohistochemistry is as an indicator for human papillomavirus (HPV) infection and p16 protein is overexpressed in HPV-associated tumours. In this context, p16 immunopositivity should be strong, diffuse, nuclear or nuclear and cytoplasmic in location. Another use for p16 is demonstration of p16 immunopositivity in well-differentiated and dedifferentiated liposarcoma.

Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin-based peri-operative chemotherapy in patients with esophageal adenocarcinoma

Oxaliplatin-based chemotherapy is used to treat patients with esophageal adenocarcinoma (EAC), but no biomarkers are currently available for patient selection. We performed a prospective, clinical trial to identify potential biomarkers associated with clinical outcomes. Tumor tissue was obtained from 38 patients with resectable EAC before and after 2 cycles of oxaliplatin-fluorouracil chemotherapy. Pre-treatment mRNA expression of 280 DNA repair (DNAR) genes was tested for association with histopathological regression at surgery, disease-free survival (DFS) and overall survival (OS). High expression of 13 DNA damage repair genes was associated with DFS less than one year (P < 0.05); expression of 11 DNAR genes were associated with worse OS (P < 0.05). From clinical associations with outcomes, two genes, ERCC1 and EME1, were identified as candidate biomarkers. In cell lines in vitro, we showed the mechanism of action related to repair of oxaliplatin-induced DNA damage by depletion and knockout of protein binding partners of the candidate biomarkers, XPF and MUS81 respectively. In clinical samples from the clinical trial, pre-treatment XPF protein levels were associated with pathological response, and MUS81 protein was associated with 1-year DFS. XPF and MUS81 merit further validation in prospective clinical trials as biomarkers that may predict clinical response of EAC to oxaliplatin-based chemotherapy.

Smad4/DPC4

Smad4 or DPC4 belongs to a family of signal transduction proteins that are phosphorylated and activated by transmembrane serine-threonine receptor kinases in response to transforming growth factor beta (TGF-β) signaling via several pathways. The gene acts as a tumour suppressor gene and inactivation of smad4/DPC4 is best recognised in pancreatic cancer. However, smad4/DPC4 is also mutated in other conditions and cancers such as juvenile polyposis syndrome with and without hereditary haemorrhagic telangiectasia, colorectal and prostate cancers.Immunohistochemistry for smad4/DPC4 protein is most useful in separating benign/reactive conditions from pancreatic cancer in needle/core biopsies. In normal and reactive states, the protein is localised to the cytoplasm and nucleus, while the protein is lost in high-grade pancreatic intraepithelial neoplasia/carcinoma in situ and pancreatic cancer.

Immune checkpoint inhibitor-induced gastrointestinal and hepatic injury: pathologists' perspective

Immune checkpoint inhibitors (CPIs) are a relatively new class of 'miracle' dugs that have revolutionised the treatment and prognosis of some advanced-stage malignancies, and have increased the survival rates significantly. This class of drugs includes cytotoxic T lymphocyte antigen-4 inhibitors such as ipilimumab; programmed cell death protein-1 inhibitors such as nivolumab, pembrolizumab and avelumab; and programmed cell death protein ligand-1 inhibitors such as atezolizumab. These drugs stimulate the immune system by blocking the coinhibitory receptors on the T cells and lead to antitumoural response. However, a flip side of these novel drugs is immune-related adverse events (irAEs), secondary to immune-mediated process due to disrupted self-tolerance. The irAEs in the gastrointestinal (GI) tract/liver may result in diarrhoea, colitis or hepatitis. An accurate diagnosis of CPI-induced colitis and/or hepatitis is essential for optimal patient management. As we anticipate greater use of these drugs in the future given the significant clinical response, pathologists need to be aware of the spectrum of histological findings that may be encountered in GI and/or liver biopsies received from these patients, as well as differentiate them from its histopathological mimics. This present review discusses the clinical features, detailed histopathological features, management and the differential diagnosis of the luminal GI and hepatic irAEs that may be encountered secondary to CPI therapy.