HAVOC: Small-scale histomic mapping of cancer biodiversity across large tissue distances using deep neural networks

Intratumoral heterogeneity can wreak havoc on current precision medicine strategies because of challenges in sufficient sampling of geographically separated areas of biodiversity distributed across centimeter-scale tumor distances. To address this gap, we developed a deep learning pipeline that leverages histomorphologic fingerprints of tissue to create "Histomic Atlases of Variation Of Cancers" (HAVOC). Using a number of objective molecular readouts, we demonstrate that HAVOC can define regional cancer boundaries with distinct biology. Using larger tumor specimens, we show that HAVOC can map biodiversity even across multiple tissue sections. By guiding profiling of 19 partitions across six high-grade gliomas, HAVOC revealed that distinct differentiation states can often coexist and be regionally distributed within these tumors. Last, to highlight generalizability, we benchmark HAVOC on additional tumor types. Together, we establish HAVOC as a versatile tool to generate small-scale maps of tissue heterogeneity and guide regional deployment of molecular resources to relevant biodiverse niches.

Leveraging personalized circulating tumor DNA (ctDNA) for detection and monitoring of molecular residual disease in high-risk melanoma

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Background: High-risk melanoma has variable prognosis. Adjuvant immuno- (IO) and targeted therapy (TT) are approved for stage III-IV resected disease. However, a significant proportion of patients (pts) are cured by local treatment alone or relapse despite adjuvant therapy. Liquid biopsy with ctDNA assays have been used to predict response to treatment and identify pts at higher risk of progression/death. Personalized ctDNA assays are a highly sensitive approach that may enhance upfront risk stratification and early detection of relapse. Methods: Serial ctDNA Monitoring as a predictive Biomarker in advanced neoplAsms (SAMBA) is a Princess Margaret prospective ctDNA kinetics study (NCT03702309) in high-risk melanoma pts. Plasma is collected pre-op (pre-local treatment, if feasible), post-op (after surgery), and every 3-6 months (m) until radiological progressive disease (rPD). Personalized amplicon based NGS assays by Inivata (RaDaR) were used to detect somatic variants in ctDNA identified through whole-exome sequencing of matched tumor tissue. Progression free survival (PFS) and overall survival (OS) from the time of surgery were estimated with the Kaplan Meier and compared with the log-rank test. Results: As of December 2021, 82 of 100 planned pts have been enrolled. A total of 191 samples from 47 pts have been analyzed. Median age was 66 years (27-87), 33 were male (70%). Seven (15%), 30 (64%) and 10 (21%) were stage II/III/IV respectively. All pts had surgery and 8 (17%) adjuvant radiation. No systemic therapy was given to 11 pts (23%); 30 (64%) had IO and 6 (13%) TT. rPD occurred in 13 pts (28%). Median follow up was 24 months. A median of 48 variants were included in the personalized ctDNA panel design (35-52). ctDNA was detected (ctDNA+) at any time point in 12/47 pts (26%), of which 5/12 (42%) were BRAF and NRAS wt on tissue. Median PFS was 4.9 months (m) for ctDNA+ pts and not reached (NR) for ctDNA- pts at post-op (HR = 2.71 CI 0.60-12.31, p = 0.179). Median OS was 23.1 m vs NR in ctDNA+ vs ctDNA- pts (HR = 8.9, CI 1.45-54.77, p = 0.004). Two ctDNA+ pts had neoadjuvant IO and became ctDNA- before surgery. One, free of disease after 12 m, had ctDNA- in 4 follow up samples. The other pt was ctDNA+ in the post-op sample and relapsed within 3 m. Four of 45 (9%) pts had ctDNA+ at post-op. Two of them, including a pt who had neoadjuvant IO, did not receive adjuvant therapy and had rPD within 3 m. The other 2 pts received adjuvant IO; ctDNA cleared and pts remain free of disease at 12 and 34 m. Three pts with rising ctDNA over time experienced rPD after a median of 4 m (2-7). Conclusions: Personalized ctDNA analysis with RaDaR may improve risk of death stratification and selection of pts who could benefit from adjuvant treatment. Detection of ctDNA may precede rPD. Follow-up will continue in pts with rising ctDNA who have not yet had rPD. Pts accrual and sample collection are ongoing, and additional data will be presented. Clinical trial information: NCT03702309.

Diagnosis of the origin of an epibulbar melanocytic tumor with molecular genomics

BACKGROUND

Uveal melanoma (UM) and conjunctival melanoma (CM) are distinct entities with different etiologies and genetic background. We present a case of an atypical subconjunctival melanoma arising from a blue nevus.

PATIENTS AND METHODS

A 61-year-old female presented with a partially melanocytic epibulbar mass with surrounding episcleral pigmented spots. The lesion was detached from the overlying conjunctiva without an intraocular component. Excisional biopsy revealed a predominantly epithelioid melanoma, that was suggested to be metastasic, although there was no evidence of a primary melanoma elsewhere.

RESULTS

Molecular analysis identified GNAQ and BAP1 pathogenic variants, which strongly suggested the diagnosis as a primary epibulbar melanoma arising from episcleral blue nevus.

CONCLUSION

This case demonstrates the value of tumor molecular analysis using Next Generation Sequencing (NGS) for differentiating the origin of an unusually located ocular melanoma.

Early Pilomatrix Carcinoma: A Case Report With Emphasis on Molecular Pathology and Review of the Literature

Pilomatrix carcinoma is a rare adnexal tumor with origin from the germinative matrical cells of the hair follicle. Clinically, it presents as a solitary lesion commonly found in the head and neck region and upper back. The tumors cannot be distinguished by their clinical appearance only and frequently are mistaken for cysts. Histopathologic examination provides the definitive diagnosis in most cases. Such carcinomas are aggressive neoplasms with a high probability of local recurrence and distant metastasis. Assessment of the Wnt signaling pathway components such as β-catenin, lymphoid enhancer-binding factor 1 (LEF-1) and caudal-related homeobox transcription factor 2 (CDX-2) potentially can be used for diagnostic purposes and targeted therapy. Herein, we report a rare and unique case of early pilomatrix carcinoma with intralesional melanocytes. We also review the molecular pathology and pathogenesis of these carcinomas as well as the significance of early diagnosis in their management.

BRAF testing timelines and impact on the starting of systemic treatment

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Background: Targeted therapy with BRAF and MEK inhibitors constitute part of the standard treatment for BRAF V600 mutated melanoma. Timely detection of BRAF mutation is necessary for clinicians and patients to make treatment decisions. We aimed to map the BRAF testing timelines from the time of request until the reported result in order to assess obstacles to timely BRAF reporting in our community, and its impact on the initiation of systemic therapy. Methods: In this single-center retrospective study, we included adult patients referred to the Medical Oncology Department at the Princess Margaret Cancer Centre (PM) from January 2019 to August 2019 with histologically confirmed cutaneous or mucosal melanoma and BRAF molecular testing performed in 2019. The Log-Rank method was applied to detect differences in BRAF turnaround time and time to treatment initiation in specified subgroups. A p value < 0.05 was considered statistically significant. Results: Sixty-six cases were identified. The median age was 64 (24-88), and 42 (64%) were male. At the time of BRAF request, 10 (15%) patients had stage II, 33 (50%) had stage III, and 23 (35%) had stage IV disease. Twenty-eight (43%) were positive for the BRAF V600E/K mutation by ARMS assay and 4 (6%) for other variants by NGS test. Thirty-three (50%) patients had the BRAF test available at their first PM Medical Oncology visit. Median time between BRAF request and result was 17 days; when a reflex BRAF test was ordered by the Pathology Department, the median turnaround time was 12 days (95% CI 8-15), compared to 20 days (95% CI 16-23) if the order was requested by another specialist ( p < 0.001). Median time to transfer samples between institutions was 6 days. If the BRAF test was processed within the institution where the biopsy was performed, the BRAF median turnaround time was 13 days (95% CI 6-19) compared to 19 days (95% CI 16-21) if a sample was transferred to another institution ( p = 0.02). In total, 49 patients had systemic therapy. Median time between the first visit with Medical Oncology and treatment initiation was 29 days and was not statistically different if the BRAF result was available or not (28 vs. 34 days; p = 0.09). In the subgroup with stage IV disease (Table), 20 patients received systemic therapy; the median time to treatment initiation was 24 days and differed with BRAF result availability (20 vs. 31 days, p = 0.03). Conclusions: The current BRAF testing timeline at the PM varies from days to weeks. A major factor impacting this timeline is transfer time, which can be streamlined by pathology reflex testing. Delays in turnaround time appears to impact subsequent timing and type of therapeutic interventions, especially in patients with stage IV disease.[Table: see text]

Preliminary results of BEAVER: An investigator-initiated phase II study of binimetinib and encorafenib for the treatment of advanced solid tumors with non-V600E BRAF mutations (mts)

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Background: Recurring oncogenic non-V600E BRAF mts have been identified in many cancer types. Preclinical data indicate that some BRAF non-V600E mts can be targeted with BRAF + MEK inhibitors. BEAVER is an investigator-initiated study designed to test the safety and efficacy of binimetinib and encorafenib (B+E) in patients (pts) with non-V600E BRAF mts. Methods: Key eligibility criteria are: pts with advanced solid tumors with BRAF non-V600E activating (class 1 and 2) or inhibitory (class 3) mts, and no prior BRAF/MEK inhibitors. Pts receive binimetinib (45mg PO BID) and encorafenib (450mg PO daily) on a 28-day cycle until intolerable toxicity or progression. The primary objective is OR rate (ORR) as per RECIST 1.1. In this Simon 2-stage trial, ≥1 of 7 pts need to have an objective response (OR) before commencing second stage of study (26 pts total). Secondary objectives include: safety, DCR, PFS, and OS. Exploratory objectives include: genomic profiling of tumors, evaluating circulating tumor DNA dynamics and development of patient derived xenograft (PDX) models. Results: From June 2019 to Feb 2021, 12 pts were screened and 9 pts enrolled; 9 are evaluable for safety and 8 for efficacy. Tumor types were melanoma and colon (n=2 each), as well as gallbladder, lung, breast and uterine cancers (n=1 each). Median age was 62 yrs (range 40-72). Median number of prior treatments was 2 (range 0-6). 1 pt had a class 1, 3 pts had class 2, and 5 pts had class 3, non-V600E BRAF mts. The median number of cycles was 2 (range: 1-7). Common treatment-related adverse events were mostly grade ≤ 2, and included: Blurred vision (78%), fatigue (67%), nausea (44%), vomiting (33%), and rash (33%). Dose reductions were required in 4/9 pts (44%) due to: blurred vision (22%), central serous retinopathy (11%), malaise (11%) and increased lipase (11%). Drug-related grade 3 AEs occurred in 2/9 pts and included: malaise (11%), confusion (11%), fatigue (11%) and increased lipase (11%). All eye toxicities were reversible with dose interruption. ORR was 12.5% (1/8) with one unconfirmed PR in a melanoma pt (BRAF G469S), treated for 6.5 months. One gallbladder cancer pt (BRAF D594N) had SD, and 6 pts had PD as best response. Genomic profiling was performed on archival tumors for 8 pts. Two PDX models were established. Responses to B+E in PDX models mirrored responses in 2 corresponding pts who had PD. Genomic and molecular profiling of pt tumors and corresponding PDXs identified multiple potential mechanisms of B+E resistance including: activation of EGFR and Akt pathways and inactivation of NF1 and Rb1. Conclusions: Preliminary data confirmed the safety of B+E and showed preliminary evidence of anti-tumor activity in advanced cancer pts with non-V600E BRAF mts. This study met the criterion for advancing to stage 2. Enrolment in the BEAVER trial and correlative biomarker analyses are ongoing. Clinical trial information: NCT03839342.

Genomic Landscape of Malignant Peripheral Nerve Sheath Tumor‒Like Melanoma

Malignant peripheral nerve sheath tumor (MPNST)-like melanoma is a rare malignancy with overlapping characteristics of both neural sarcoma and melanoma. Although the genomics of cutaneous melanoma has been extensively studied, those of MPNST-like melanoma have not. To characterize the genomic landscape of MPNST-like melanoma, we performed a single-center, retrospective cohort study at a tertiary academic cancer center. Consecutive patients with a confirmed histologic diagnosis of MPNST-like melanoma were screened, and those whose tissues were locally available were included in this analysis. Archival tissue from six patients (eight samples) was submitted for whole-exome and transcriptome sequencing analysis. We compared these data with available genomic studies of cutaneous melanoma and MPNST. NF1 was altered (mutated, deleted, or amplified) in 67% of patients. Genes related to cell cycle regulation were frequently altered, with frequent deletion of ZNF331, which, to the best of our knowledge, has not been previously described in cutaneous melanoma. The serine protease inhibitor SERPINB4 was deleted in 100% of the patients. We show that MPNST-like melanoma presents overlapping genomic features with cutaneous melanoma and MPNST, but it is unique by the frequency of loss of function of ZNF331 and SERPINB4.

Biologic subtypes of melanoma predict survival benefit of combination anti-PD1+anti-CTLA4 immune checkpoint inhibitors versus anti-PD1 monotherapy

Purpose

Anti-programmed cell death protein 1 (PD1)±anti-cytotoxic T-lymphocyte associated protein 4 (CTLA4) immune checkpoint inhibitors (ICIs) are standard therapeutic options for metastatic melanoma. We assessed whether biologic subtype according to primary tumor type or genomic subtype can function as predictive biomarkers for anti-PD1±anti-CTLA4 ICI in patients with advanced melanoma.

Methods

We performed a single-center retrospective cohort analysis of patients who received anti-PD1±anti-CTLA4 ICI for advanced melanoma between 2012 and 2019. Primary tumor type, BRAF and NRAS mutation status, and other covariates were abstracted from chart review. Log-rank tests and multivariable Cox regression models were used to assess differences in clinical progression-free (cPFS) and overall survival (OS).

Results

We identified 230 patients who received 249 lines of anti-PD1±anti-CTLA4 ICI for unresectable or metastatic disease. Of these patients, 74% were cutaneous, 11% mucosal, 8% unknown primary and 7% acral. BRAF and NRAS mutations were identified in 35% and 28% of patients, respectively. In multivariable analyses of the entire cohort, acral or mucosal primary tumor type, >3 metastatic sites, elevated LDH were predictive of shorter cPFS and OS. Combination ICI therapy was associated with longer cPFS (HR 0.57, 95% CI 0.38 to 0.86, p=0.007) and OS (HR 0.42, 95% CI 0.28 to 0.65, p<0.001). Combination ICI was significantly associated with longer OS in unknown primary and mucosal melanoma. There was a non-significant trend toward longer OS with anti-PD1+anti-CTLA4 in cutaneous melanoma, but not in acral melanoma. In multivariable analyses, combination ICI was associated with longer OS in NRAS (HR 0.24, 95% CI 0.10 to 0.62, p=0.003, n=69) and BRAF V600E/K (HR 0.47, 95% CI 0.24 to 0.90, p=0.024, n=86) mutant melanoma but not BRAF/NRAS wild-type (n=94) melanoma.

Conclusions

In our cohort, primary melanoma tumor type and genomic subtype were independent predictive markers of cPFS and OS for patients with metastatic melanoma receiving anti-PD1 ICI. Primary tumor type and genomic subtype—including NRAS—should be further evaluated in prospective clinical trials to determine their value as predictive markers. Biologic subtypes may facilitate clinical decision-making when recommending combination ICI treatment (anti-PD1±anti-CTLA4) versus anti-PD1 alone for patients with metastatic melanoma.

Cauda equina syndrome as the initial presentation of uveal melanoma metastasis

PURPOSE

Uveal melanoma extension to the central nervous system (CNS) is exceedingly rare, and can occur through optic nerve invasion. We report a rare clinical case that presented with cauda equina syndrome as the initial manifestation of metastasis of choroidal melanoma, and showed neurotropic extension by histopathology. Our patient did not demonstrate any evidence of systemic metastasis otherwise.

OBSERVATIONS

A 60-year-old male patient with treated choroidal melanoma in his right eye, with presumed clinical control, developed radiation-induced neovascular glaucoma refractory to medical therapy. The eye required enucleation for pain control. One month post-enucleation, he presented to the emergency department with severe abdominal pain, urine retention, constipation, and leg weakness. Magnetic resonance imaging (MRI) of the spine showed extensive leptomeningeal involvement along the entire spinal cord and the cauda equina. On further inquisition, the patient noted prior visual field defect in the contralateral eye. Brain MRI revealed intracranial metastasis with chiasmal involvement. The patient underwent radiotherapy for the brain and spine to improve his symptoms, and was ultimately transferred to palliative care.

CONCLUSION AND IMPORTANCE

Optic nerve invasion in uveal melanoma may lead to neurotropic spread of melanoma cells with risk of intracranial and spinal cord metastasis. Neurological symptoms should raise the suspicion of clinicians regarding this complication, which is associated with increased melanoma-related mortality.

Metastatic aneurysmal fibrous histiocytoma in a 20-year-old woman: A rare case report with review of the literature and discussion of its genomic features

Aneurysmal fibrous histiocytoma is an uncommon variant of cutaneous fibrous histiocytomas with a local recurrence rate of 19%. We present a case of aneurysmal fibrous histiocytoma in a 20-year-old female with a regional lymph node metastasis and subsequent satellite nodule. The patient initially presented with a 1-month history of two palpable nodules in left lower anterior shoulder and left axilla. Needle core biopsies from both lesions revealed an atypical spindle cell neoplasm with a differential diagnosis of aneurysmal fibrous histiocytoma and angiomatoid fibrous histiocytoma. The axillary dissection confirmed a metastatic deposit in 1 out of 22 lymph nodes. At 6 months a satellite nodule arose between the resection scar and the axilla histopathologically demonstrating a cellular spindle cell nodule at the dermis subcutaneous junction with large, blood-filled pseudovascular spaces lined by histiocytes. The periphery of the lesion showed collagen trapping without a lymphoplasmacytic infiltrate. The lesional cells were diffusely positive for CD10 and focally for CD68 and Illumina RNA fusion panel sequencing was negative. Herein we present this case of metastatic aneurysmal fibrous histiocytoma with review of the literature and discussion of biology, cytogenetic alterations, and differential diagnosis.

Genomic landscape of malignant peripheral nerve sheath tumor (MPNST)-like melanoma

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Background: Malignant Peripheral Nerve Sheath Tumor (MPNST)-like melanoma is a rare entity wherein cutaneous melanoma mimics histomorphological features of MPNST. The genomic landscape of MPNST-like melanoma has not been previously described. We report the genomic findings of 6 patients diagnosed with MPNST-like melanoma. Methods: We identified consecutive patients with confirmed histological diagnosis of MPNST-like melanoma. Archival tissue was submitted for whole exome and transcriptome sequencing analysis and genomic findings were compared to publicly available data on the genomic landscape of both melanoma and limited genetic descriptions of MPNST. Results: Six patients diagnosed with MPNST-like melanoma between November 2002 and July 2018 had archival tissue available (8 samples). Mean age at diagnosis was 60.5 years (38-74). The mean tumor mutational burden (TMB) was 35.72 mutations/exon coding megabase, ranging from 4.27 to 86.36. NF1 alterations were found in 4 (67%) of cases: one had 3 truncating mutations (W696 + X1870_splice + R1590C) associated with NF1 amplification, one had a deep deletion and another two had truncating mutations (I1908L and W696 + A1530V). Two tumors had non-V600 BRAF mutations that predict alteration in kinase function. We observed deletions of cell cycle regulators: CDKN2A and CDKN2B in 33%; and ZNF331 (19q13.42) in 83% of cases. SERPINB4 (18q21.3), described previously as a tumor suppressor in oral squamous cell carcinomas, was deleted in all samples. The patient with NF1 amplification and truncating mutations received immunotherapy due to metastatic disease and achieved a complete response; his tumor had a TMB of 72.6. Another patient who died of metastatic melanoma, treated with chemotherapy in the pre-immunotherapy era, lacked any NF1 mutation but had a Q61K NRAS mutation; the tumor had a TMB of 15. The remaining patients were treated with surgical resection alone and continue on follow-up. Conclusions: MPNST-like melanoma shares some frequently altered genes in cutaneous melanoma but possesses an excess of NF-1 mutations or deletions, in keeping with its neural-like phenotype. The high frequency of SERPINB4 alterations suggests a critical tumor suppressor role in this subtype of melanoma, warranting further investigation. Additionally, cell cycle dysregulation caused by deletion of ZNF331 and CDKN2A/B may be important in MPNST-like melanoma carcinogenesis.

Non-infectious granulomatous conditions of the skin: a clinicopathological approach to diagnosis

Granulomatous disorders of the skin are diverse and include infectious and non-infectious conditions. They are a source of confusion to many dermatologists and pathologists, including even the most experienced dermatopathologists. Correlation with clinical picture, serology, microbiology and careful morphological examination is essential for accurate diagnosis. Most cases require ancillary histopathological studies to reach a final diagnosis. This review discusses important non-infectious granulomatous conditions of the skin and presents a practical approach when confronted with such entities.

Microcystic variant malignant mesothelioma presenting as a localized paraspinal mass

A 58-year-old man presented with productive cough and fever. Computed tomography (CT) scan of the chest showed an upper right paraspinal mass. CT-guided fine-needle aspiration biopsy showed lobules of vacuolated cells against a background of myxoid material. The cells demonstrated moderate to severe nuclear atypia and occasional mitoses. Immunohistochemistry revealed tumor cells to be immunoreactive for calretinin, WT-1, D2-40, cytokeratin (CK) 7, AE1/AE3, high molecular weight keratin, vimentin and epithelial membrane antigen, and negative for thyroid transcription factor-1, Ber-EP4, carcinoembryonic antigen, S100 protein, CK20, and CDX2. The combined morphologic and immunohistochemical findings confirmed the diagnosis of microcystic variant of localized malignant mesothelioma. The subsequent lung resection showed a pleural-based mass in the right upper lobe and confirmed the diagnosis. Awareness of the existence of unusual morphologic variants and localized forms of mesothelioma are necessary to avoid misdiagnosis of fine needle biopsy samples. Recognition of characteristic cytomorphologic features along with optimal use of panel of immunohistochemistry studies is crucial for making a specific diagnosis.