Aviad Zick

Background: Colorectal cancer is the third most commonly diagnosed cancer in the world. Liver metastases are frequent, adversely affecting patient prognosis. We compared progression-free survival and overall survival in colorectal cancer patients with liver metastasis treated with surgical resection or stereotactic body radiotherapy. No previous study had shown superiority of one treatment option over the other. Methods: We conducted a retrospective cohort study of 40 colorectal cancer patients with liver metastasis treated with surgical resection or stereotactic body radiotherapy at the Hebrew University-Hadassah Medical Center. Patient demographics, tumor characteristics, treatment details, and survival outcomes were analyzed. Kaplan–Meier curves and log-rank tests were used for survival analysis. Results: The median overall survival for the entire cohort was 44 months (95% CI 29–59 months). In patients treated with surgical resection, the median overall survival was 51 months (95% CI: 36–67 months), while in patients treated with stereotactic body radiotherapy the median overall survival was 32 months (95% CI: 21–43 months), a non-statistically significant result (p = 0.306). The number of lobes involved did not significantly impact overall survival (p = 0.214). Additionally, it did not significantly affect progression-free survival (p = 0.41). Liver metastases located in the left lobe led to considerably worse progression-free survival compared to other regions involved, specifically in the patients who underwent surgery. Conclusions: Our findings underscore the importance of personalized treatment strategies tailored to the distinct characteristics of colorectal cancer patients with liver metastasis. Currently, surgical resection remains the standard of care. Further research is warranted to address the possibility of extending SBRT to first-line treatment in selected unresectable patients.

BACKGROUND: Small-cell lung cancer (SCLC) is an aggressive malignancy with a poor prognosis and marked transcriptional heterogeneity that may drive distinct therapeutic vulnerabilities. Clinical translation of molecular subtyping has been limited by restricted access to tumor biopsies, particularly at relapse. METHODS: We applied chromatin immunoprecipitation of cell-free nucleosomes carrying active histone modifications followed by sequencing (cfChIP-seq) to 441 plasma samples from individuals with advanced SCLC, other neuroendocrine carcinomas, or non-SCLC cancers, as well as from healthy controls. Plasma cfChIP-seq profiles were integrated with matched tumor transcriptomes from 73 samples, including 41 time-matched pairs. RESULTS: cfChIP-seq captured the epigenetic and transcriptional landscape of tumor-derived cell-free DNA (cfDNA), including SCLC tissue- and cell-of-origin signatures. A quantitative cfChIP-seq–derived SCLC score tracked radiographic tumor burden and was associated with prognosis. Signals at promoters of lineage-defining transcription factor genes, including ASCL1 , NEUROD1 , POU2F3 , and ATOH1 , correlated strongly with matched tumor RNA expression and supported noninvasive inference of SCLC transcriptional subtypes directly from plasma. CONCLUSION: Plasma cfChIP-seq provides a practical liquid biopsy platform for real-time assessment of tumor burden, tumor state, and molecular subtype in SCLC. These findings support further development of cfChIP-seq for precision monitoring and subtype-informed therapeutic stratification in SCLC. TRIAL REGISTRATION: ClinicalTrials.gov NCT02484404, NCT02487095, NCT02769962, NCT03554473, NCT03896503, and NCT02146170. FUNDING: Center for Cancer Research; Intramural Program of the NCI (ZIA BC 011793); European Research Council (ERC) (Adg no. 101019560 “cfChIP”).

Liquid biopsy using ultra-low-pass whole-genome sequencing (ULP-WGS, ∼0.25x coverage) is a promising tool to detect circulating tumor DNA (ctDNA) for cancer management, and the use of the native Oxford Nanopore (ONT) sequencing platform adds DNA methylation to the set of detectable features. Here, we test the performance of methylation-based cell-type deconvolution in ULP-WGS samples from diverse epithelial malignancies and investigate several new computational strategies using our CelFiE-ISH deconvolution framework. We find that incorporating larger numbers of markers restricted to the epithelial cell lineage can reduce the cancer fraction limit of detection down to 1.7-3.1%, matching or exceeding the 3% floor of established copy-number alteration (CNA) benchmarks. Our study provides a useful strategy for analysis of ULP-WGS ONT data and indicates that marker selection remains a key challenge for analyzing methylation-based cancer datasets.

Background: Isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) is an aggressive, heterogeneous brain tumor with limited treatment options. This study employs DNA methylation-based deconvolution of GBM to define its cellular composition and its association with patient outcomes. Methods: We generated oligodendroglial precursor cells at various developmental stages from enriched human neural progenitor cultures and used their DNA methylation signatures, along with published signatures of brain tumor cell types and the tumor microenvironment, to deconvolve 263 adult GBMs (Heidelberg cohort). An independent cohort of 199 GBMs from The Cancer Genome Atlas (TCGA) and GEO, all treated with standard-of-care therapy, was similarly deconvolved. Kaplan-Meier survival analysis was used to assess the prognostic value of the neoplastic components. Results: GBM deconvolution uncovered distinct cellular compositions that differed between the neoplastic and non-neoplastic component. The neoplastic fractions averaged 70% of the tumor bulk and were predominantly composed of oligodendrocyte-like (43%) cell populations, in addition to oligodendrocyte precursor-like (27%), astrocyte-like (19%), and mesenchymal stem cell-like (11%) populations. The non-neoplastic fractions were enriched for macrophages, vascular cells, and immune cell populations. A higher oligodendrocyte-like signature was linked to poorer survival (median survival 14.3 vs. 15.3 months; P = .017), while a higher astrocyte-like signature correlated with improved survival (15.3 vs. 13.4 months; P = .044). Further, a higher astrocyte-to-oligodendrocyte ratio was associated with significantly longer survival (15.8 vs. 11.9 months; P < .00011). Conclusions: The methylation-based deconvolution data and analyses provided insight into GBM heterogeneity and highlighted the prognostic potential of the astrocyte-to-oligodendrocyte ratio and its application in personalized treatment strategies.

Background: —Synovial sarcoma is a rare soft tissue sarcoma. Treatment of synovial sarcoma includes surgery, radiation, pazopanib, and chemotherapy. Targeted therapies, such as B-Raf proto-oncogene, serine/threonine kinase (BRAF) inhibitors, are emerging as a potential treatment option. We describe the sixth case of a BRAFV600E synovial sarcoma, the first extra-thoracic case. This case is the first to show a complete pathological response to BRAF & mitogen-activated protein kinase kinase (MEK) inhibitors. Case description: —We treated a 22-year-old male with a left groin BRAFV600E synovial sarcoma with doxorubicin, Ifosphamide & Sodium 2-Mercaptoethanesulfonate. When we identified BRAFV600E in the tumor, the BRAFV600E and MEK inhibitors (dabrafenib & trametinib) were initiated, followed by surgery, with a complete pathological response. Nine months after the surgery, a local recurrence prompted the resumption of dabrafenib & trametinib followed by radiotherapy, resulting in complete radiological response and the development of hemophagocytic lymphohistiocytosis treated with corticosteroids with resolution of symptoms. Conclusion: —Panel sequencing of synovial sarcoma can identify targetable mutations. Treatment of BRAFV600E synovial sarcoma with dabrafenib & trametinib can lead to complete pathological response and prolonged radiological response, as well as the rare adverse event of hemophagocytic lymphohistiocytosis. Prospective clinical trials are needed to evaluate the efficacy and safety of BRAFV600E & MEK inhibitors as a therapeutic approach in BRAFV600E synovial sarcoma.

TP53 pathogenic variants cause Li-Fraumeni syndrome (LFS), with some variants causing an attenuated phenotype. Herein, we describe the clinical phenotype and genetic characteristics of carriers of NM_000546.6 (TP53): c.541C > T, (p.Arg181Cys) treated at Hadassah Medical Center. We retrospectively examined our genetic databases to identify all carriers of TP53 p.Arg181Cys. We reached out to carriers and their relatives and collected clinical and demographic data, lifestyle factors, carcinogenic exposures as well as additional blood samples for genetic testing and whole exome sequencing. Between 2005 and 2022 a total of 2875 cancer patients underwent genetic testing using genetic panels, whole exome sequencing or targeted TP53 assays. A total of 30 cancer patients, all of Arab-Muslim descent, were found to be carriers of TP53 p.Arg181Cys, the majority from Jerusalem and Hebron, two of which were homozygous for the variant. Carriers were from 24 distinct families of them, 15 families (62.5%) met updated Chompret criteria for LFS. Median age of diagnosis was 35 years-old (range 1–69) with cancers characteristic of LFS (16 Breast cancer; 6 primary CNS tumors; 3 sarcomas) including 4 children with choroid plexus carcinoma, medulloblastoma, or glioblastoma. A total of 21 healthy carriers of TP53 p.Arg181Cys were identified at a median age of 39 years-old (range 2–54)—19 relatives and 2 additional pediatric non-cancer patients, in which the finding was incidental. We report a shared haplotype of 350kb among carriers, limited co-morbidities and low BMI in both cancer patients and healthy carriers. There were no demographic factors or carcinogenic exposures unique to carriers who developed malignancy. Upon exome analysis no other known pathogenic variants in cancer predisposing genes were identified. TP53 p.Arg181Cys is a founder pathogenic variant predominant to the Arab-Muslim population in Jerusalem and Hebron, causing attenuated-LFS. We suggest strict surveillance in established carriers and encourage referral to genetic testing for all cancer patients of Arab-Muslim descent in this region with LFS-associated malignancies as well as family members of established carriers.