The genomic and evolutionary landscapes of anaplastic thyroid carcinoma

Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.

Validation and implementation of Aperio LV1 remote live view telepathology system for intraoperative frozen section diagnosis

Introduction

Telepathology (TP) allows for remote slide review with performance comparable to traditional light microscopy. Use of TP in the intraoperative setting allows for faster turnaround and greater user convenience by obviating the physical presence of the attending pathologist. We sought to perform a practical validation of an intraoperative TP system using the Leica Aperio LV1 scanner in tandem with Zoom teleconferencing software.

Methods

A validation was performed in accordance with recommendations from CAP/ASCP, using a retrospectively identified sample of surgical pathology cases with a 1 year washout period. Only cases with frozen-final concordance were included. Validators underwent training in the operation of the instrument and conferencing interface, then reviewed the blinded slide set annotated with clinical information. Validator diagnoses were compared to original diagnoses for concordance.

Results

60 slides were chosen for inclusion. 8 validators completed the slide review, each requiring 2 h. The validation was completed in 2 weeks. Overall concordance was 96.4%. Intraobserver concordance was 97.3%. No major technical hurdles were encountered.

Conclusion

Validation of the intraoperative TP system was completed rapidly and with high concordance, comparable to traditional light microscopy. Institutional teleconferencing implementation driven by the COVID pandemic facilitated ease of adoption.

Prospective study evaluating dynamic changes of cell-free HPV DNA in locoregional viral-associated oropharyngeal cancer treated with induction chemotherapy and response-adaptive treatment

BACKGROUND

Human papillomavirus (HPV)-associated oropharyngeal cancer (OPC) has a favorable prognosis which has led to efforts to de-intensify treatment. Response-adaptive de-escalated treatment is promising, however improved biomarkers are needed. Quantitative cell-free HPV-DNA (cfHPV-DNA) in plasma represents an attractive non-invasive biomarker for grading treatment response and post-treatment surveillance. This prospective study evaluates dynamic changes in cfHPV-DNA during induction therapy, definitive (chemo)radiotherapy, and post-treatment surveillance in the context of risk and response-adaptive treatment for HPV + OPC.

METHODS

Patients with locoregional HPV + OPC are stratified into two cohorts: High risk (HR) (T4, N3, [Formula: see text] 20 pack-year smoking history (PYH), or non-HPV16 subtype); Low risk (LR) (all other patients). All patients receive induction chemotherapy with three cycles of carboplatin and paclitaxel. LR with ≥ 50% response receive treatment on the single-modality arm (minimally-invasive surgery or radiation alone to 50 Gy). HR with ≥ 50% response or LR with ≥ 30% and < 50% response receive treatment on the intermediate de-escalation arm (chemoradiation to 50 Gy with cisplatin). All other patients receive treatment on the regular dose arm with chemoradiation to 70 Gy with concurrent cisplatin. Plasma cfHPV-DNA is assessed during induction, (chemo)radiation, and post-treatment surveillance. The primary endpoint is correlation of quantitative cfHPV-DNA with radiographic response.

DISCUSSION

A de-escalation treatment paradigm that reduces toxicity without compromising survival outcomes is urgently needed for HPV + OPC. Response to induction chemotherapy is predictive and prognostic and can select candidates for de-escalated definitive therapy. Assessment of quantitative cfHPV-DNA in the context of response-adaptive treatment of represents a promising reliable and convenient biomarker-driven strategy to guide personalized treatment in HPV + OPC.

TRIAL REGISTRATION

This trial is registered with ClinicalTrials.gov on October 1st, 2020 with Identifier: NCT04572100 .

Risk and response adapted de-intensified treatment for HPV-associated oropharyngeal cancer: Optima paradigm expanded experience

BACKGROUND

Favorable prognosis for Human papillomavirus-associated (HPV+) oropharyngeal cancer (OPC) led to investigation of response-adaptive de-escalation, yet long-term outcomes are unknown. We present expanded experience and follow-up of risk/response adaptive treatment de-intensification in HPV+ OPC.

METHODS

A phase 2 trial (OPTIMA) and subsequent cohort of sequential off-protocol patients treated from September 2014 to November 2018 at the University of Chicago were reviewed. Eligible patients had T3-T4 or N2-3 (AJCC 7th edition) HPV+ OPC. Patients were stratified by risk: High-risk (HR) (T4, ≥N2c, or >10PYH), all others low-risk (LR). Induction chemotherapy (IC) included 3 cycles of carboplatin and nab-paclitaxel (OPTIMA) or paclitaxel (off-protocol). LR with ≥50% response received low-dose radiotherapy (RT) alone to 50 Gy (RT50). LR with 30-50% response and HR with ≥50% response received intermediate-dose chemoradiotherapy (CRT) to 45 Gy (CRT45). All others received full-dose CRT to 75 Gy (CRT75).

RESULTS

91 patients consented and 90 patients were treated, of which 31% had >10PYH, 34% had T3/4 disease, and 94% had N2b/N2c/N3 disease. 49% were LR and 51% were HR. Overall response rate to induction was 88%. De-escalated treatment was administered to 83%. Median follow-up was 4.2 years. Five-year OS, PFS, LRC, and DC were 90% (95% CI 81,95), 90% (95% CI 80,95), 96% (95% CI 90,99), and 96% (88,99) respectively. G-tube placement rates in RT50, CRT45, and CRT75 were 3%, 33%, and 80% respectively (p < 0.05).

CONCLUSION

Risk/response adaptive de-escalated treatment for an inclusive cohort of HPV+ OPC demonstrates excellent survival with reduced toxicity with long-term follow-up.

The impact of site-specific digital histology signatures on deep learning model accuracy and bias

The Cancer Genome Atlas (TCGA) is one of the largest biorepositories of digital histology. Deep learning (DL) models have been trained on TCGA to predict numerous features directly from histology, including survival, gene expression patterns, and driver mutations. However, we demonstrate that these features vary substantially across tissue submitting sites in TCGA for over 3,000 patients with six cancer subtypes. Additionally, we show that histologic image differences between submitting sites can easily be identified with DL. Site detection remains possible despite commonly used color normalization and augmentation methods, and we quantify the image characteristics constituting this site-specific digital histology signature. We demonstrate that these site-specific signatures lead to biased accuracy for prediction of features including survival, genomic mutations, and tumor stage. Furthermore, ethnicity can also be inferred from site-specific signatures, which must be accounted for to ensure equitable application of DL. These site-specific signatures can lead to overoptimistic estimates of model performance, and we propose a quadratic programming method that abrogates this bias by ensuring models are not trained and validated on samples from the same site.

Molecular trait of follicular-patterned thyroid neoplasms defined by MALDI-imaging

In the field of thyroid neoplasms, the most interesting recent change regards the introduction of a new terminology for follicular-patterned thyroid tumors, named Noninvasive Thyroid Neoplasm with Papillary-like Nuclear Features (NIFTP). This pre-malignant tumor is considered to be the putative precursor of invasive carcinoma. However, given that several issues are still unresolved, the application of ancillary tools, based on omics-techniques, may improve the clinical management of these challenging cases. The present paper highlights the proteomic profiles of a series of NIFTPs submitted to Fine Needle Aspirations (FNAs) and analysed by MALDI-imaging in order to confirm the heterogeneous phenotype of nodules included in the present NIFTP terminology and to underline the necessity of more accurate biomarkers that can be used for their characterization. Ethical and economic implications in terms of healthcare costs, operative risks, morbidity, as well as the potential need for lifelong hormone replacement therapy, seem to be significant reasons to approach the characterization of NIFTPs using alternative tools such as MALDI-MSI.

Pediatric Chondrosarcoma of the Sternum Resected with Thorascopic Assistance

Background:

Chondrosarcomas are a heterogeneous group of malignant neoplasms that arise from bones, cartilage or other soft tissues that produce cartilage and are commonly seen in the middle decades of life. Despite being the most common primary bone sarcoma in adults, chondrosacromas are rare in pediatric patients.

Case Report:

We report the case of a six-year-old child with a painless enlarging sternal mass of which biopsy was consistent with low-grade surface chondrosarcoma. This is the first reported case of a chest wall chondrosarcoma in a young child. This unusual location in a young patient presented challenges to treatment. Resection of the manubrium was performed by a multidisciplinary team of orthopaedic oncology and pediatric general surgery. The patient underwent a wide resection of the sternal mass from an anterior approach performed by the orthopaedic oncology team using an oscillating saw under video-assisted thoracoscopic surgery to ensure adequate mass resection without injury to nearby structures. The patient was followed with quarterly physical exams and radiographs for 18 months postoperatively and did not have any pain or evidence of recurrence.

Conclusion:

Clinicians should consider utilizing multidisciplinary approaches to treat patients with chondrosarcomas of the chest wall.

Characterization of the T-cell receptor repertoire and immune microenvironment in patients with locoregionally advanced squamous cell carcinoma of the head and neck

3080

Background: Immunotherapy with checkpoint blockade was recently approved for patients with recurrent/metastatic SCCHN, however it has not been investigated in the curative-intent setting yet. In this study, we investigated the T-cell receptor repertoire and the immune microenvironment in tumor tissues of SCCHN patients with locoregionally advanced disease. Methods: T-cell receptor sequencing and polymerase chain reaction for immune-related genes of tumor tissues from 44 patients with locoregionally advanced SCCHN prior to treatment with definitive chemoradiotherapy were conducted. T-cell receptor clonality and the mRNA expression levels of immune-related genes were correlated with various clinicopathological parameters. Results: In patients with locoregionally advanced SCCHN, tumor infiltrating T-cells clonally expand and GRZB mRNA levels were associated significantly with longer progression-free survival (PFS) (p = 0.003) independent of HPV status, tumor and nodal stage. The TCR-β DI was significantly lower in HPV-negative compared to HPV-positive tumors (p = 0.002), signifying more clonal T-cell expansion in HPV-negative tumors. A higher percentage of HPV-negative tumors expressed HLA-A protein compared to HPV-positive tumors (p = 0.049), suggesting that the greater T-cell clonal expansion might be due to more robust antigen presentation by HPV-negative tumors. Conclusions: This study suggests the pre-existence of clonally expanded T-cells in patients with locoregionally advanced SCCHN prior to treatment, and provides rationale to introduce immunotherapy in the curative-intent setting. The association of high GRZB mRNA levels with favorable PFS independent of HPV-status, tumor and nodal stage supports that the pre-existence of an intrinsically inflamed microenvironment enhances chemoradiotherapy effects. Finally, in HPV-positive tumors, the T-cell infiltrate seemed to be more diverse which could be secondary to virally-induced defective expression of HLA class I molecules.

The Incidence and Survival of Rare Cancers of the Thyroid, Parathyroid, Adrenal, and Pancreas

PURPOSE

With the exception of papillary and follicular thyroid cancer, malignant cancers of the thyroid, parathyroid, adrenal, and endocrine pancreas are uncommon. These rare malignancies present a challenge to both the clinician and patient, because few data exist on their incidence or survival. We analyzed the incidence and survival of these rare endocrine cancers (RECs), as well as the trends in incidence over time.

METHODS

We used the NCI's SEER 18 database (2000-2012) to investigate incidence and survival of rare cancers of the thyroid, parathyroid, adrenal, and endocrine pancreas. Cancers were categorized using the WHO classification systems. We collected data on incidence, gender, stage, size, and survival. Time trends were evaluated from 2000-2002 to 2010-2012.

RESULTS

We identified 36 types of rare cancers in the endocrine organs captured in the SEER database. RECs of the thyroid had the highest combined incidence rate (IR8.26), followed by pancreas (IR 3.24), adrenal (IR 2.71), and parathyroid (IR 0.41). The incidence rate for all rare endocrine organs combined increased 32.4 % during the study period. The majority of the increase was attributable to rare cancers of thyroid, which increased in not only microcarcinomas, but in all sizes. The mean 5-year survival for RECs is 59.56 % (range 2.49–100 %).

CONCLUSIONS

This study is a comprehensive analysis ofthe incidence and survival for rare malignant endocrine cancers. There has been an increase in incidence rate of almost all RECs and their survival is low. We hope that our data will serve as a source of information for clinicians as well as bring awareness regarding these uncommon cancers.

Acute appendicitis secondary to a granular cell tumor of the appendix in a 19-year-old male

INTRODUCTION

Granular cell tumors are rare, usually benign, neoplasms presenting as solitary small nodules in the skin or subcutaneous tissue. Involvement of the gastrointestinal tract is unusual, particularly of the appendix, and it is characterized by indolent, submucosal lesions usually diagnosed as an incidental finding.

CASE REPORT

We describe the rare case of acute appendicitis secondary to a granular cell tumor of the appendix in a 19-year-old male.

Epigenetic attenuation of mitochondrial superoxide dismutase 2 in pulmonary arterial hypertension: a basis for excessive cell proliferation and a new therapeutic target

BACKGROUND

Excessive proliferation and impaired apoptosis of pulmonary artery (PA) smooth muscle cells (PASMCs) contribute to vascular obstruction in patients and fawn-hooded rats (FHRs) with PA hypertension (PAH). Expression and activity of mitochondrial superoxide dismutase-2 (SOD2), the major generator of H(2)O(2), is known to be reduced in PAH; however, the mechanism and therapeutic relevance of this are unknown.

METHODS AND RESULTS

SOD2 expression in PASMCs is decreased in PAH patients and FHRs with PAH. FHR PASMCs have higher proliferation and lower apoptosis rates than Sprague-Dawley rat PASMCs. Moreover, FHR PASMCs have hyperpolarized mitochondria, low H(2)O(2) production, and reduced cytoplasmic and mitochondrial redox state. Administration of SOD2 small interfering RNA to normal PASMCs recapitulates the FHR PAH phenotype, hyperpolarizing mitochondria, decreasing H(2)O(2), and inhibiting caspase activity. Conversely, SOD2 overexpression in FHR PASMCs or therapy with the SOD-mimetic metalloporphyrin Mn(III)tetrakis (4-benzoic acid) porphyrin (MnTBAP) reverses the hyperproliferative PAH phenotype. Importantly, SOD-mimetic therapy regresses PAH in vivo. Investigation of the SOD2 gene revealed no mutation, suggesting a possible epigenetic dysregulation. Genomic bisulfite sequencing demonstrates selective hypermethylation of a CpG island in an enhancer region of intron 2 and another in the promoter. Differential methylation occurs selectively in PAs versus aortic SMCs and is reversed by the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine, restoring both SOD2 expression and the ratio of proliferation to apoptosis. Expression of the enzymes that mediate gene methylation, DNA methyltransferases 1 and 3B, is upregulated in FHR lungs.

CONCLUSIONS

Tissue-specific, epigenetic SOD2 deficiency initiates and sustains a heritable form of PAH by impairing redox signaling and creating a proliferative, apoptosis-resistant PASMC. SOD augmentation regresses experimental PAH. The discovery of an epigenetic component to PAH may offer new therapeutic targets.

Abstract 2176: Vascular endothelial growth factor receptor-2 (VEGFR-2) gene variations in bronchioloalveolar cell carcinoma (BAC)

Background VEGF receptor-2 (VEGFR-2) is a key receptor in VEGF-mediated angiogenesis. It plays a significant role in tumor growth and development of metastases. A few studies suggested the angiogenic feature of bronchioalveolar cell carcinoma (BAC), a rare subtype of adenocarcinoma. However the biology of VEGFR-2 in BAC has not been clearly characterized, probably due to its rarity. We sought to determine whether differences in VEGFR-2 expression and microvessel density (MVD) in adenocarcinoma with BAC features (AWBF) might be due to heritable genetic variation in the VEGFR-2 gene. Differences in VEGFR-2 expression and MVD between the pure BAC component of tumor and AWBF, and their comparison with adjacent normal tissue, were also investigated.

Methods DNA was extracted from 46 formalin-fixed paraffin embedded AWBF tissues. Four single-nucleotide polymorphisms (SNPs) and four in/dels were genotyped in all tumors. Tissue microarrays (TMAs) were constructed with tumor tissue (pure BAC component and AWBF component for each tumor) and paired adjacent normal lung tissue. TMAs were stained with anti-VEGFR-2 and anti-phosphorylated-VEGFR-2 (pVEGFR-2) antibodies (scoring: 0-9). MVD was determined by staining with an antibody against CD105, and 95% of the samples had either diffused high or focal high staining.

Results The −271G&gt;A genotype showed a clear gene-dosage effect on pVEGFR-2 expression (GG&gt;GA&gt;AA, p=0.04, linear trend analysis) in AWBF but not in BAC (p&gt;0.1). The −271G&gt;A genotype does not affect the MVD in both BAC and AWBF (linear trend analysis and Kruskal-Wallis, p&gt;0.1). The other SNPs and in/dels did not show any significant association with VEGFR-2, pVEGFR-2, and MVD (p&gt;0.1). VEGFR-2 and pVEGFR-2 expression in tumor (AWBF and pure BAC) was more than 10 times higher the paired normal tissue (p&lt;0.001, Wilcoxon matched pairs test). A trend for higher VEGFR-2 expression in AWBF compared to pure BAC (mean score 4.2 vs. 3.8, p=0.08, Wilcoxon matched pairs test) was observed, while no difference was observed for pVEGFR-2 (p&gt;0.1). For MVD, although the proportion of diffused high staining was higher in BAC (60%) vs. AWBF (47%), this difference is not statistically significant (p&gt;0.1, Fisher's exact test).

Discussion Our study shows that heritable gene variation of −271G&gt;A in VEGFR-2 might reduce the expression of VEGFR-2 in AWBF. This is consistent with the effect of −271G&gt;A in a luciferase assay (Ye et al., AACR 2007), as well as its effect on VEGFR-2 and pVEGFR-2 staining in breast cancer (Cerri et al., SABCS 2009, abstract #904). Although our data are suggestive of different pattern of angiogenesis between pure BAC and AWBF, our sample size is too small to draw any definitive conclusions. Additional studies are ongoing to replicate these findings that will establish the role of genetic variation as a determinant of VEGFR-2 expression in BAC, and the biology of angiogenesis in this rare tumor.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2176.

Update in nonneoplastic lung diseases

CONTEXT

Nonneoplastic lung diseases include a wide range of pathologic disorders from asthma to interstitial lung disease to pulmonary hypertension. Recent advances in our understanding of the pathophysiology of many of these disorders may ultimately impact diagnosis, therapy, and prognosis. It is important for the practicing pathologist to be aware of this new information and to understand how it impacts the diagnosis, treatment, and outcome of these diseases.

OBJECTIVE

To update current progress toward elucidating the pathophysiology of pulmonary alveolar proteinosis, idiopathic pulmonary hemosiderosis, and pulmonary arterial hypertension, as well as to present classification systems for pulmonary hypertension, asthma, and interstitial lung disease and describe how these advances relate to the current practice of pulmonary pathology.

DATA SOURCES

Published literature from PubMed (National Library of Medicine) and primary material from the authors' institution.

CONCLUSIONS

Improved understanding of the pathophysiology of pulmonary alveolar proteinosis, pulmonary hypertension, and idiopathic hemosiderosis may impact the role of the surgical pathologist. New markers of disease may need to be assessed by immunohistochemistry or molecular techniques. The classification systems for interstitial lung disease, asthma, and pulmonary hypertension are evolving, and surgical pathologists should consider the clinicopathologic context of their diagnoses of these entities.

Comparison of routine and unprepped CT colonography augmented by low fiber diet and stool tagging: a pilot study

BACKGROUND

We performed a pilot study examining the feasibility of a new unprepped CT colonography (CTC) strategy: low fiber diet and tagging (unprepped) vs. low fiber diet, tagging and a magnesium citrate cleansing preparation (prepped). Prior reports of tagging were limited in that the residual stool was neither measured and stratified by size nor did prior reports subjectively evaluate the ease of interpretation by a reader experienced in interpreting CTC examinations.

METHODS

Prospective randomized to unprepped n = 14 and prepped n = 14. Colonic segments were subjectively evaluated for residual stool that would potentially interfere with interpretation. Scores were given in the following categories: percentage of residual stool that was touching or nearly touching mucosa, the largest piece of retained stool, effectiveness of tagging, height of residual fluid, degree of distention, ease of interpretation, and reading time.

RESULTS

Ease of the CT read (scale where 4 = optimal read) averaged 1.3 for the unprepped group and 2.3 for the prepped group. The mean read time averaged 17.5 min for unprepped and 17.9 min for prepped. The degree of distention (scale where 4 = well distended) averaged 3.7 for unprepped and 3.6 for prepped. Supine and prone images combined, the unprepped group had 160 segments with stool; prepped group had 58 segments. The amount of stool covering the mucosa in all segments averaged 1.6 (33%-66% coverage) in the unprepped group and 0.35 (<33% mucosal coverage) in the prepped group. The mean size of the largest piece of stool was 33.67 mm for unprepped and 4.01 mm for prepped. Percentage of tagged stool was not significantly different between the groups (range of 94-98%). The height of residual fluid averaged 8.37 mm for unprepped and 13.4 mm for prepped. Three polyps in three patients were found during optical colonoscopy (OC) in the unprepped group (5, 6, and 10 mm), none of which were prospectively detected at CTC. Three polyps in three patients were detected during OC in the prepped group (5, 10, and 15 mm), two of which were prospectively detected at CTC. Two false-positive lesions were observed at CTC in one patient in the prepped group.

CONCLUSION

There was more stool in the unprepped group and while this factor did not slow down the reading time, it made the examination subjectively harder to interpret and likely caused the three polyps in this group to be missed. We conclude that a truly unprepped strategy that leaves significant residual stool, even if well tagged, is not desirable.

A one-million-year-old Homo cranium from the Danakil (Afar) Depression of Eritrea

One of the most contentious topics in the study of human evolution is that of the time, place and mode of origin of Homo sapiens. The discovery in the Northern Danakil (Afar) Depression, Eritrea, of a well-preserved Homo cranium with a mixture of characters typical of H. erectus and H. sapiens contributes significantly to this debate. The cranium was found in a succession of fluvio-deltaic and lacustrine deposits and is associated with a rich mammalian fauna of early to early-middle Pleistocene age. A magnetostratigraphic survey indicates two reversed and two normal magnetozones. The layer in which the cranium was found is near the top of the lower normal magnetozone, which is identified as the Jaramillo subchron. Consequently, the human remains can be dated at approximately 1 million years before present.