Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets

The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.

NIPBL::NACC1 Fusion Hepatic Carcinoma

Several reports describing a rare primary liver tumor with histologic features reminiscent of follicular thyroid neoplasms have been published under a variety of descriptive terms including thyroid-like, solid tubulocystic, and cholangioblastic cholangiocarcinoma. Although these tumors are considered to represent histologic variants, they lack classic features of cholangiocarcinoma and have unique characteristics, namely immunoreactivity for inhibin and NIPBL::NACC1 fusions. The purpose of this study is to present clinicopathologic and molecular data for a large series of these tumors to better understand their pathogenesis. We identified 11 hepatic tumors with these features. Immunohistochemical and NACC1 and NIPBL fluorescence in situ hybridization assays were performed on all cases. Four cases had available material for whole-genome sequencing (WGS) analysis. Most patients were adult women (mean age: 42 y) who presented with abdominal pain and large hepatic masses (mean size: 14 cm). Ten patients had no known liver disease. Of the patients with follow-up information, 3/9 (33%) pursued aggressive behavior. All tumors were composed of bland cuboidal cells with follicular and solid/trabecular growth patterns in various combinations, were immunoreactive for inhibin, showed albumin mRNA by in situ hybridization, and harbored the NIPBL::NACC1 fusion by fluorescence in situ hybridization. WGS corroborated the presence of the fusion in all 4 tested cases, high tumor mutational burden in 2 cases, and over 30 structural variants per case in 3 sequenced tumors. The cases lacked mutations typical of conventional intrahepatic cholangiocarcinoma. In this report, we describe the largest series of primary inhibin-positive hepatic neoplasms harboring a NIPBL::NACC1 fusion and the first WGS analysis of these tumors. We propose to name this neoplasm NIPBL:NACC1 fusion hepatic carcinoma.

Deciphering the origin and therapeutic targets of cancer of unknown primary: a case report that illustrates the power of integrative whole-exome and transcriptome sequencing analysis

Cancer of unknown primary (CUP) represents a significant diagnostic and therapeutic challenge, being the third to fourth leading cause of cancer death, despite advances in diagnostic tools. This article presents a successful approach using a novel genomic analysis in the evaluation and treatment of a CUP patient, leveraging whole-exome sequencing (WES) and RNA sequencing (RNA-seq). The patient, with a history of multiple primary tumors including urothelial cancer, exhibited a history of rapid progression on empirical chemotherapy. The application of our approach identified a molecular target, characterized the tumor expression profile and the tumor microenvironment, and analyzed the origin of the tumor, leading to a tailored treatment. This resulted in a substantial radiological response across all metastatic sites and the predicted primary site of the tumor. We argue that a comprehensive genomic and molecular profiling approach, like the BostonGene© Tumor Portrait, can provide a more definitive, personalized treatment strategy, overcoming the limitations of current predictive assays. This approach offers a potential solution to an unmet clinical need for a standardized approach in identifying the tumor origin for the effective management of CUP.

The importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer

Pilocytic astrocytomas are the most common pediatric brain tumors, typically presenting as low-grade neoplasms. We report two cases of pilocytic astrocytoma with atypical tumor progression. Case 1 involves a 12-yr-old boy with an unresectable suprasellar tumor, negative for BRAF rearrangement but harboring a BRAF p.V600E mutation. He experienced tumor size reduction and stable disease following dabrafenib treatment. Case 2 describes a 6-yr-old boy with a thalamic tumor that underwent multiple resections, with no actionable driver detected using targeted next-generation sequencing. Whole-genome and RNA-seq analysis identified an internal tandem duplication in FGFR1 and RAS pathway activation. Future management options include FGFR1 inhibitors. These cases demonstrate the importance of escalating molecular diagnostics for pediatric brain cancer, advocating for early reflexing to integrative whole-genome sequencing and transcriptomic profiling when targeted panels are uninformative. Identifying molecular drivers can significantly impact treatment decisions and improve patient outcomes.

Abstract 2149: A whole genome sequencing classifier of homologous recombination deficiency

Homologous recombination deficiency (HRd) is a DNA repair defect prevalent in but not exclusive to breast and ovarian cancer most commonly associated with BRCA1 or BRCA2 alterations. HRd results in accumulation of small and large scale genetic alterations across the genome, including allele specific copy number alterations (aCNAs), small nucleotide variants (SNVs), deletions, and structural variants (SVs). Detection of HRd in tumors predicts response to genotoxic drugs such as PARP inhibitors and platinum.

Genome wide aCNAs such as large state transitions (LST), loss of heterozygosity (LOH), and telomeric allelic imbalances (TAI) in conjunction with BRCA1/2 mutation detection have been implemented in routine diagnostic testing to identify HRd in tumors. However, these features represent a subset of the genetic signatures predictive of HRd, and we hypothesize that a significant portion of tumors with HRd are missed using these existing assays.

Whole genome sequencing (WGS) enables the detection of the full spectrum of genetic lesions that arise in an HRd tumor in a single assay. To demonstrate the added value of WGS to identify HRd, we trained and validated a pan-cancer classifier of HRd. A tumor/normal matched cohort of 321 cancer patients sequenced by WGS was assembled and analyzed as part of a retrospective study, representing 62 tumor types. An unbiased analysis of HRd associated SV signatures revealed the top quartile of samples harboring tandem duplications (Dups) and deletions (Dels) in the size range of 1-10kbp were enriched with BRCA1, BRCA2, and RAD51C/D alterations. Through curating Dels, Dups, HRd SNV/InDel signatures, and alteration of HRd associated genes, 37 unique patients were found to have high confidence HRd, out of which 13% had no alterations in BRCA1, BRCA2, or other HRd genes. We then trained a random forest classifier to identify HRd tumors. The most important predictive features were WGS-specific, namely small deletions with microhomology, SV Dels, and SV Dups. The HRd classifier was validated using an independent cohort of 556 samples from the Pan-Cancer Analysis of Whole Genomes (PCAWG) study. Of 46 samples with biallelic BRCA1/2 alterations, the classifier achieved high areas under receiver-operator characteristic (AUROC, 0.99) and precision recall curves (AUPRC, 0.96). The aCNA score, the number of segments harboring LST, LOH, and TAI, had similar AUROC (0.96) but lower AUPRC (0.87). There were 11 BRCA1/2 non-altered cases predicted to be HRd with the classifier which were not identified by CNA scores, in which 10 had at least 1 alteration in an HRd gene, including RAD51C, CHEK2 biallelic alterations and SVs in PALB2, Fanconi pathway genes, and ATM/ATR. We conclude that a classifier incorporating the additional mutational features which can only be detected using WGS can achieve superior precision in identifying HRd tumors and, in the future, uncover additional patients for therapeutic options.

Citation Format: Kevin Hadi, Gunes Gundem, Max F. Levine, Aditya Deshpande, Minal Patel, Stan Skzrypczak, Majd Al Assaad, Juan Miguel Mosquera, Olivier Elemento, Andrew L. Kung, Juan S. Medina-Martínez, Elli Papaemmanuil. A whole genome sequencing classifier of homologous recombination deficiency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2149.

Use of a navigable interface for integrated whole genome and transcriptome sequencing as a platform for pursuit of therapeutic targets in advanced prostate cancers

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Background: Metastatic, castration-resistant prostate cancer (mCRPC) is commonly the deadly form of PC. Among these, a subset of tumors are androgen-indifferent with the most aggressive often manifesting variant histology, including neuroendocrine or small cell changes. Neuroendocrine PC can be de novo (NEPC) or develop in response to therapy as treatment emergent (CRPC-NE). Currently effective durable treatments for NEPC are lacking. Hence, we sought to identify additional targets in CRPC/NEPC using an integrative platform of whole genome (WGS) and transcriptome sequencing (RNAseq). Methods: WGS was performed on55 tumor/normal pairs (CRPC-Ad, n= 32; CRPC-NE, n=13; de novo NEPC, n=7; metastatic hormone naïve, PC n=3) from 48 patients. RNAseq data was available in a subset of 21 samples. We employed the Isabl GxT analytic platform and manually curated single base substitution (SBS, COSMIC v3) molecular signatures and structural variants (SV) that involved tumor suppressor genes and oncogenes. Results: We observed 184 events in cancer-associated genes and targets in 38 cases. Non-canonical ETS fusions were identified in 2 CRPC-Ad patients ( MSMB-ERG and YWHAE-ETV4). Other rare events included SVs affecting ALK ( SLC45A3-ALK) and FGFR1 amplification in 1 patient each. Pathogenic germline alterations in 15% of patients with equal frequency in each clinicopathological state. These variants included genes such as BRCA1, BRCA2, and ATM, and other genes of uncertain relevance for prostate cancer ( e.g., PPM1D and MUTYH). SBS genomic signatures associated with homologous recombination deficiency (HRD) were observed in 15% of the patients (7 cases): 3 harbored germline BRCA1/2mutations, 2 with somatic BRCA2 mutations, and 2 without alteration in BRCA1/2 (1 of these CRPC-Ad had a complex SV disrupting RAD51B) without apparent enrichment for any histology, and a majority of both histologies were enriched in Mismatch repair (MMR)-associated SBS. One subject CRPC-NE and amphicrine character, which displayed a complete response to immune checkpoint blockade, harbored driver mutations in AR and CTNNB1, and homozygous loss of MSH2/6. Further, molecular signatures of potential clinical relevance were detected at varying contributions and included CDK12-type genomic instability (CRPC-Ad, n=2) (4%) and MMR deficiency with POLD1 proofreading (CRPC-Ad) who also experienced a durable response to pembrolizumab. Conclusions: WGS/RNAseq in CRPC and NEPC elucidates genomic signatures associated with HRD and MMR, complex SVs in oncogenes, and non-canonical ETS fusions. Expansion of our analysis is underway with enhanced integration of clinical metadata and RNAseq for rational trial design for aggressive variant CRPC and NEPC.

GLI1 -Rearranged Enteric Tumor : Expanding the Spectrum of Gastrointestinal Neoplasms With GLI1 Gene Fusions

GLI1 encodes a transcription factor that targets cell cycle regulators affecting stem cell proliferation. GLI1 gene fusions were initially described in pericytomas with a t[7;12] translocation and more recently in gastric plexiform fibromyxomas and gastroblastomas. This study describes the clinicopathologic, immunohistochemical, and molecular features of three intestinal-based neoplasms harboring GLI1 gene fusions. We studied three unique mesenchymal small bowel tumors. Paraffin embedded tumor tissues from these cases and 62 additional tumor samples that included a plexiform fibromyxoma were sequenced using a targeted RNAseq method to detect fusion events. The study patients included two women and one man who were 52, 80, and 22 years of age at the time of diagnosis. The tumors involved the submucosa and muscularis propria of the duodenum, jejunum, and ileum. All 3 tumors contained a proliferation of monotonous oval or spindle cells with scattered, somewhat dilated vessels. Two cases showed epithelioid structures such as glands, tubules, or nests. Immunohistochemical analysis revealed cytokeratin expression in the epithelioid components of both tumors displaying these features, and variable numbers of mesenchymal cells. Diffuse CD56 positivity was seen in the mesenchymal component of 2 tumors and desmin and smooth muscle actin staining in the other tumor. Immunostains for S-100 protein, DOG-1, and CD117 were negative in all cases. GLI1 fusions with different partner genes were detected in all tumors, and in the plexiform fibromyxoma, used as a control. Validation by fluorescence in situ hybridization was performed. None of the tumors have recurred or metastasize after surgery. We describe novel GLI1 fusions in 3 mesenchymal neoplasms of the small intestine, including 2 with biphenotypic features. Thus far, all cases have pursued indolent clinical courses. We propose the term " GLI1 -rearranged enteric tumor" to encompass this group of unique neoplasms of the small intestine that harbor GLI1 gene fusions and expand the spectrum of gastrointestinal neoplasms with these alterations.

Case report: Metastatic urothelial cancer with an exceptional response to immunotherapy and comprehensive understanding of the tumor and the tumor microenvironment

Although immune checkpoint inhibitors (ICIs) are increasingly used as second-line treatments for urothelial cancer (UC), only a small proportion of patients respond. Therefore, understanding the mechanisms of response to ICIs is critical to improve clinical outcomes for UC patients. The tumor microenvironment (TME) is recognized as a key player in tumor progression and the response to certain anti-cancer treatments. This study aims to investigate the mechanism of response using integrated genomic and transcriptomic profiling of a UC patient who was part of the KEYNOTE-045 trial and showed an exceptional response to pembrolizumab. Diagnosed in 2014 and receiving first-line chemotherapy without success, the patient took part in the KEYNOTE-045 trial for 2 years. She showed dramatic improvement and has now been free of disease for over 6 years. Recently described by Bagaev et al., the Molecular Functional (MF) Portrait was utilized to dissect genomic and transcriptomic features of the patient's tumor and TME. The patient's tumor was characterized as Immune Desert, which is suggestive of a non-inflamed microenvironment. Integrated whole-exome sequencing (WES) and RNA sequencing (RNA-seq) analysis identified an ATM mutation and high TMB level (33.9 mut/mb), which are both positive biomarkers for ICI response. Analysis further revealed the presence of the APOBEC complex, indicating the potential for use of APOBEC signatures as predictive biomarkers for immunotherapy response. Overall, comprehensive characterization of the patient's tumor and TME with the MF Portrait revealed important insights that could potentially be hypothesis generating to identify clinically useful biomarkers and improve treatment for UC patients.

Prevalence of programmed death ligand-1 in patients diagnosed with non-small cell lung cancer in Lebanon

Introduction

Programmed death ligand-1 expression has been shown to be a good predictor of response to cancer therapy with checkpoint inhibitors. Its expression varies among different tumor types and among non-small cell lung cancer patients with different clinical and demographic characteristics. The prevalence and determinants of programmed death ligand-1 expression have been previously reported from various regions of the world, but data from Lebanon are lacking. This study examines the prevalence and the clinical, demographic and pathological predictors of programmed death ligand-1 expression in patients diagnosed with non-small cell lung cancer in Lebanon.

Methods

Medical records of 180 patients diagnosed with primary non-small cell lung cancer at our institution and tested for programmed death ligand-1 expression were reviewed. Clinical, demographic and pathological information were collected and correlated with programmed death ligand-1 expression using the chi-square test and logistic regression.

Results

One hundred eleven of the 180 non-small cell lung cancer tumor samples tested positive for programmed death ligand-1 expression (61.7%). 27.2% of those tumor samples expressed programmed death ligand-1 in 1%-49% of tumor cells, while 34.4% of tumor samples expressed programmed death ligand-1 in 50% or more of their cells. Squamous histology and advanced stage were significant predictors of programmed death ligand-1 expression (odds ratio = 2.79, 95% confidence interval [1.13-6.90], p = 0.012 and odds ratio = 2.48, 95% confidence interval [1.23-4.99], p = 0.044, respectively).

Conclusion

Similar to reports from other populations, our results suggest that programmed death ligand-1 expression in non-small cell lung cancer is highly prevalent in the Lebanese population, especially in patients with advanced stage at diagnosis or squamous cell carcinoma histology. Because of the small sample size, while more that 60% of the patients are Lebanese, the results of this article cannot be extrapolated to the Middle Eastern and the Levantine population.

Prognostic indicators of survival in patients with small-cell lung cancer at a tertiary care center in Lebanon

Objective:

Small-cell lung cancer is a very aggressive tumor associated with high invasiveness and ease of metastasis and therefore poor prognosis. In the literature, several demographical, clinical as well as pathological factors including age, stage, gender and smoking were cited as independent prognosticators of survival.

Material and Methods:

This is a retrospective cohort study that includes 222 patients diagnosed with small-cell lung cancer between 2010 and 2019. Clinical and demographic data were extracted from their medical records. The Kaplan–Meier and logistic regression models of statistical analysis were used to evaluate the association of these variables with survival.

Results:

Forty-five percent of patients were found to be alive at the time of data collection. The median survival of patients with small-cell lung cancer was found to be 14 months. On univariate analysis, increasing age as well as stage (extensive disease) were found to be significantly associated with decreased survival at 3 years. On the contrary, both gender and smoking status at diagnosis were not shown to significantly influence survival. On multivariate analysis, both age as well as stage remained significantly associated with survival.

Conclusion:

Limited data exist in the literature regarding the prognostic indicators of survival in small-cell lung cancer, especially from the Middle East area. In our study, both age and stage at the time of diagnosis were found to significantly influence survival. Further studies are needed to assess the association of other factors with survival.

Neoadjuvant chemotherapy and Avelumab in early stage resectable nonsmall cell lung cancer

Multiple randomized studies have shown that combination of chemotherapy and immune checkpoint inhibitors (ICIs) leads to better response rates and survival as compared to chemotherapy alone in the advanced stage of NSCLC. Data suggesting a benefit to using ICIs in the neoadjuvant therapy of patients with early stage NSCLC are emerging. Eligible subjects were treatment naïve patients with stage IB, II, and resectable IIIA NSCLC. Patients received three cycles of neoadjuvant chemotherapy with four doses of avelumab every 2 weeks. Patients with squamous cell cancer received cisplatin or carboplatin on day 1 and gemcitabine on days 1 and 8 of each cycle of chemotherapy. Patients with nonsquamous histology received cisplatin or carboplatin with pemetrexed on day 1 of each cycle. Patients then proceeded to their planned surgery. Out of 15 patients accrued as part of stage 1 of the study, four had a radiologic response (1 complete response), lower than the minimum of six responses needed to continue to phase 2 of the study. The study was therefore terminated. Majority had adenocarcinoma histology and stage IIIA disease. The treatment was well tolerated with no unexpected side effects. Four patients (26.7%) had grade III/IV CTCAE toxicity. This study confirms that the preoperative administration of chemotherapy and avelumab is safe. There was no indication of increased surgical complications. The benefit of adding immunotherapy to chemotherapy did not appear to enhance the overall response rate of patients in the neoadjuvant setting in patients with resectable NSCLC because this study failed to meet its primary endpoint.

Association of various dietary habits and risk of lung cancer: an updated comprehensive literature review

Lung cancer remains the leading cause of cancer death in both men and women worldwide. Tobacco smoking remains the single most important factor. Recent research has focused on the role of nutrition and dietary habits on lung tumorigenesis. With many individual reports on separate dietary aspects, no single review is available in the literature that summarizes the updated studies. To our knowledge, this is the first review that comprehensively reviews the updated literature on the effect of dietary habits on lung cancer. This review was concluded in February 2019 and included all meta-analyses, systematic reviews, and literature reviews. Thirty studies were retrieved in total. Items in the diet that offer a protective effect on lung parenchyma are fruits, vegetables, fish, nuts, soy, B vitamins, vitamin D, vitamin E, vitamin C, and zinc. Changing dietary habits to decrease the risk of lung cancer can be performed in parallel with smoking cessation programs. There is a need for future studies with large sample sizes to accurately evaluate some aspects of nutrition and their effect on lung cancer risk. Physicians are encouraged to provide nutritional advice to their patients.

A long-lived cuprous bis-phenanthroline complex for the photodynamic therapy of cancer

An earth-abundant cuprous bis-phenanthroline photosensitizer showed potential use in the photodynamic therapy of cancer.