Faculty Bibliography

Background: Mucinous adenocarcinoma is a special type of colorectal cancer (CRC) that has poor response to the treatment, more aggressive behavior and poorer outcome than non-mucinous CRC. Its biological and clinical behavior is largely determined by its molecular genetics. However, the genetics of this group of CRC is yet to be defined. Design: 152 cases of resected CRC with sequencing data generated by Ion AmpliSeq Cancer Hotspot Panel (or 50 genes) in the past two years were retrospectively retrieved from the departmental databases. No neoadjuvant therapy was performed before surgery. CRCs were divided into two groups: 1). Mucinous CRC (MCRC) group (13 mucinous CRC and 19 CRC with at least 20% of mucinous component (n=32) and 2). Non-mucinous CRC (NMCRC) group without mucinous component (n=120). The type and frequency of gene mutations and microsatellite instability (MSI) status defined by immunohistochemistry for mismatch repair proteins were analyzed. Fisher exact test was employed for statistical analysis. Results: In MCRC group, 31 of 32 (97%) were positive for the mutation of either KRAS (15/32), BRAF (15/32) or double mutations (1/32). Only one case showed no mutation for KRAS or BRAF, but TP53. The highest frequent mutations in MCRC group were KRAS (16/32) and BRAF (16/32), PIK3CA (10/32), followed by APC (9/32) and TP53 (8/32). In NMCRC group, 64 of 120 (53%) cases had either KRAS (50/120, 42%) or BRAF (14/120, 12%) mutation, and no double mutations. TP53 mutation (65/120, 54%) is most frequent mutation in this group, followed by KRAS (50/120, 42%), APC (39/120, 33%), PIK3CA (26/120, 22%) and BRAF (14/120, 12%). MSI-high status is more frequently seen in BRAF mutated CRCs in MCRC group (12/15, 80%) than in BRAF mutated NMCRC group (50%) (p<0.05), suggesting that MSI-high status is more commonly related with epigenetic effect in MCRCs. Conclusions: The vast majority of mucinous CRC or CRC with mucinous component have the mutations either in KRAS or BRAF in EGFR signaling pathway, suggesting that dysregulation of EGFR pathway plays a critical role in the development of mucinous CRC or CRC with mucinous component. Poor response to the treatment of mucinous adenocarcinoma may be partially attributable to the unique genetics of this group of CRCs

Background: CRC is a heterogeneous and complex disease, harboring numerous genetic and epigenetic alterations acquired during cancer development. The genetics and epigenetics of CRCs may dictate their histology, biology, and clinical outcome. We reviewed the sequencing data generated from the next generation sequencing technology to analyze the relationship between the quantity of gene mutations and the biology of CRCs Design: 152 cases of resected CRCs without neoadjuvant therapy that have sequencing data generated by Ion AmpliSeq Cancer Hotspot Panel (or 50 genes panel) were retrospectively identified from the department database. These 152 cases also had immunostaining results for mismatch repair proteins (surrogate markers for Microsatellite instability status, or MSI). The CRCs were divided into two groups: hypermutated (3 or more gene mutations) and hypomutated (2 or less gene mutations). Tumor grade, T stage, lymph node metastasis, and MSI status in the two groups were compared and the data analyzed using Fisher's exact test. Results: Of the 152 cases, 93 (61.2%) were classified into the hypomutation group and 59 (38.8%) into the hypermutation groups. In the hypomutation group, 80 (86.0%) were low (well and moderately differentiated) and 13 (14.0%) were high grade (poorly differentiated) CRCs. In the hypermutation group, 37 (62.7%) were diagnosed as low and 22 (37.3%) as high grade CRCs. The hypermutation status is strongly associated with high tumor grade (P=0.0014). High T stages (stage 4) does not correlate with mutation status (25/93 in hypomutation group and 19/59 in hypermutation group, p>0.05). In addition, no correlation between hypermutation and positive lymph nodes or MSI-High was found (54/93 or 20/90 in hypomutation group and 29/59 or 18/57 in hypermutation group, p>0.05). Conclusions: CRCs with hypermutation detected by Ion AmpliSeq Cancer Hotspot Panel are more likely to have high grade of histology, suggesting accumulation of gene mutations leading to worse biological behavior

Background: Over 250,000 breast cancer cases are diagnosed annually in the US, of which 15% (n=37,500) are triple negative breast cancers (TNBC). TNBC has an aggressive clinical course with limited therapeutic options. Some studies estimate that a small proportion of TNBCs defined by immunohistochemical (IHC) stains alone, i.e. estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2)-negative, can, in fact, show HER2 amplification by fluorescent in situ hybridization (FISH) and, therefore, be reclassified as HER2-enriched. If properly classified, these patients can benefit from anti-HER2 therapy. To capture this subset of patients, we performed a now four-year-long prospective study, in which TNBCs were reflexed to HER2 by FISH. Herein, we present our findings with detailed clinicopathologic analysis of the reclassified cases. Design: TNBC cases and ER/PR-positive, HER2-negative breast cancers from 2014 to 2017 with concurrent IHC and FISH results were analyzed. The pathology slides were reviewed by two pathologists. Stromal tumor infiltrating lymphocytes (sTILs) were defined as the percentage of all mononuclear cells within tumor stroma not in direct contact with tumor cells. Results: Of the 253 TNBCs in the past 4 years, 13 tumors (5%) showed HER2 amplification by FISH (6 surgical excisions and 7 core biopsies). Two patients have previously identified BRCA1 mutation. Twelve of 13 tumors (92%) were grade 3. All tumors were invasive ductal carcinoma of no special type. No apocrine morphology was noted. Notably, five tumors had >=50% sTILs, which can be classified as lymphocyte-predominant breast cancer based on some studies. In the same time period, 41 ER/PR-positive/HER2-negative breast cancers were reflexed to HER2 by FISH, none of which showed amplification. All tumors were fixed in formalin for comparable amount of time (6-72 hours). After reclassification, approximately 40% of patients received anti-HER2 therapy. (Table Presented) Conclusions: Pathologists may consider reflexing HER2 evaluation to FISH in TNBCs with grade 3, high ki67 and high sTILs. If 5% of TNBCs can be reclassified as HER2-enriched tumors, based on the national statistics, annually approximately 1875 patients with TNBCs by IHC may actually benefit from anti-HER2 therapy

Chordoid glioma is a rare brain tumor thought to arise from specialized glial cells of the lamina terminalis along the anterior wall of the third ventricle. Despite being histologically low-grade, chordoid gliomas are often associated with poor outcome, as their stereotypic location in the third ventricle makes resection challenging and efficacious adjuvant therapies have not been developed. Here we performed genomic profiling on 13 chordoid gliomas and identified a recurrent D463H missense mutation in PRKCA in all tumors, which localizes in the kinase domain of the encoded protein kinase C alpha (PKCα). Expression of mutant PRKCA in immortalized human astrocytes led to increased phospho-ERK and anchorage-independent growth that could be blocked by MEK inhibition. These studies define PRKCA as a recurrently mutated oncogene in human cancer and identify a potential therapeutic vulnerability in this uncommon brain tumor.

The presence of tumor-induced systemic immune suppression, including lymphopenia, has been recognized in adult patients with glioblastoma for several decades, and pre-treatment neutrophil-to-lymphocyte count ratio (NLCR) is associated with inferior clinical outcome in patients with glioblastoma. Whether tumor-induced systemic immune suppression is also present in children with malignant brain tumors is not known. We performed a retrospective analysis of pretreatment neutrophil and lymphocyte counts in pediatric patients with medulloblastoma (MB) compared to a control group of children with posterior fossa pilocytic astrocytoma (PA). Compared to the control group, we observed statistically significantly lower absolute lymphocyte counts (ALCs) and higher NLCRs in the medulloblastoma group. Our findings suggest the presence of tumor-induced systemic immune suppression in MB patients already present at the time of diagnosis, with potential implications for the development of immune therapies in this population.

BACKGROUND:Extraneural metastases are relatively rare manifestations of medulloblastoma. CASE PRESENTATION/METHODS:We present the case of a young boy with group three MYCN-amplified medulloblastoma. He received multimodal chemotherapy consisting of gross total resection followed by postoperative craniospinal radiation and adjuvant chemotherapy. The patient developed extraneural metastases 4 months after the end of therapy. Literature review identifies the poor prognosis of MYCN-amplified medulloblastomas as well as extraneural metastases; we review the current limitations and future directions of medulloblastoma treatment options. CONCLUSION/CONCLUSIONS:To the best of our knowledge, this is the first molecularly characterized report of extraneural metastases of medulloblastoma in a child.

Accurate histopathologic diagnosis is essential for providing optimal surgical management of pediatric brain tumors. Current methods for intraoperative histology are time- and labor-intensive and often introduce artifacts that limit interpretation. Stimulated Raman histology (SRH) is a novel label-free imaging technique that provides intraoperative histologic images of fresh, unprocessed surgical specimens. Here we evaluate the capacity of SRH for use in the intraoperative diagnosis of pediatric type brain tumors. SRH revealed key diagnostic features in fresh tissue specimens collected from 33 prospectively enrolled pediatric type brain tumor patients, preserving tumor cytology and histoarchitecture in all specimens. We simulated an intraoperative consultation for 25 patients with specimens imaged using both SRH and standard hematoxylin and eosin histology. SRH-based diagnoses achieved near-perfect diagnostic concordance (Cohen's kappa, kappa > 0.90) and an accuracy of 92-96%. We then developed a quantitative histologic method using SRH images based on rapid image feature extraction. Nuclear density, tumor-associated macrophage infiltration, and nuclear morphology parameters from 3337 SRH fields of view were used to develop and validate a decision-tree machine-learning model. Using SRH image features, our model correctly classified 25 fresh pediatric type surgical specimens into normal versus lesional tissue and low-grade versus high-grade tumors with 100% accuracy. Our results provide insight into how SRH can deliver rapid diagnostic histologic data that could inform the surgical management of pediatric brain tumors.

In this chapter, we describe the use of Illumina® Infinium® HD Assay in conjunction with Illumina's EPIC Methylation 8-sample array platform to obtain glioblastoma molecular profiles. The procedure spans four days, and can be performed by a single laboratory technician. Starting with as little as 250 ng of DNA input, this method allows the flexibility to begin with DNA derived from either formalin-fixed, paraffin-embedded (FFPE) or fresh tissue and is compatible with an Illumina iScan or HiScan system.