Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics.

The analysis of cell-free DNA (cfDNA) in plasma provides information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue of origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.

Liquid biopsy reveals collateral tissue damage in cancer.

Cancer inflicts damage to surrounding normal tissues, which can culminate in fatal organ failure. Here, we demonstrate that cell death in organs affected by cancer can be detected by tissue-specific methylation patterns of circulating cell-free DNA (cfDNA). We detected elevated levels of hepatocyte-derived cfDNA in the plasma of patients with liver metastases originating from different primary tumors, compared with cancer patients without liver metastases. In addition, patients with localized pancreatic or colon cancer showed elevated hepatocyte cfDNA, suggesting liver damage inflicted by micrometastatic disease, by primary pancreatic tumor pressing the bile duct, or by a systemic response to the primary tumor. We also identified elevated neuron-, oligodendrocyte-, and astrocyte-derived cfDNA in a subpopulation of patients with brain metastases compared with cancer patients without brain metastasis. Cell type-specific cfDNA methylation markers enabled the identification of collateral tissue damage in cancer, revealing the presence of metastases in specific locations and potentially assisting in early cancer detection.

Cholangiocarcinoma: An Emerging Target for Molecular Therapy.

BACKGROUND: Cholangiocarcinoma has been traditionally considered a tumor with poor prognosis. Until now, surgical treatment has been the only more or less effective approach. SUMMARY: Over 10 years, chemotherapy with a combination of gemcitabine and cisplatin remains the standard first-line therapy for patients with locally advanced or metastatic cholangiocarcinoma, which leads to a median overall survival of 11.7 months. Several inhibitors of HER (ERBB), HGF/c-MET, Hedgehog, KRAS-BRAF-MEK-ERK, and PI3K/AKT/mTOR signaling pathways did not show their superiority to standard chemotherapy. The rise of hope is associated with the emergence of novel fibroblast growth factor receptors and isocitrate dehydrogenase inhibitors as well as immune checkpoint inhibitors.

ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin.

Cell-free DNA (cfDNA) in human plasma provides access to molecular information about the pathological processes in the organs or tumors from which it originates. These DNA fragments are derived from fragmented chromatin in dying cells and retain some of the cell-of-origin histone modifications. In this study, we applied chromatin immunoprecipitation of cell-free nucleosomes carrying active chromatin modifications followed by sequencing (cfChIP-seq) to 268 human samples. In healthy donors, we identified bone marrow megakaryocytes, but not erythroblasts, as major contributors to the cfDNA pool. In patients with a range of liver diseases, we showed that we can identify pathology-related changes in hepatocyte transcriptional programs. In patients with metastatic colorectal carcinoma, we detected clinically relevant and patient-specific information, including transcriptionally active human epidermal growth factor receptor 2 (HER2) amplifications. Altogether, cfChIP-seq, using low sequencing depth, provides systemic and genome-wide information and can inform diagnosis and facilitate interrogation of physiological and pathological processes using blood samples.

Splicing Factor Transcript Abundance in Saliva as a Diagnostic Tool for Breast Cancer.

Breast cancer is the second leading cause of death in women above 60 years in the US. Screening mammography is recommended for women above 50 years; however, 22% of breast cancer cases are diagnosed in women below this age. We set out to develop a test based on the detection of cell-free RNA from saliva. To this end, we sequenced RNA from a pool of ten women. The 1254 transcripts identified were enriched for genes with an annotation of alternative pre-mRNA splicing. Pre-mRNA splicing is a tightly regulated process and its misregulation in cancer cells promotes the formation of cancer-driving isoforms. For these reasons, we chose to focus on splicing factors as biomarkers for the early detection of breast cancer. We found that the level of the splicing factors is unique to each woman and consistent in the same woman at different time points. Next, we extracted RNA from 36 healthy subjects and 31 breast cancer patients. Recording the mRNA level of seven splicing factors in these samples demonstrated that the combination of all these factors is different in the two groups (p value = 0.005). Our results demonstrate a differential abundance of splicing factor mRNA in the saliva of breast cancer patients.

Biomarker-Driven Therapy in Metastatic Gastric and Esophageal Cancer: Real-Life Clinical Experience.

BACKGROUND: Precision treatment of cancer uses biomarker-driven therapy to individualize and optimize patient care. OBJECTIVE: To evaluate real-life clinical experience with biomarker-driven therapy in metastatic gastric and esophageal cancer in Israel. PATIENTS AND METHODS: This multicenter retrospective cohort study included patients with metastatic gastric or esophageal cancer who were treated in the participating institutions and underwent biomarker-driven therapy. Treatment was considered to have a benefit if the ratio between the longest progression-free survival (PFS) post biomarker-driven therapy and the last PFS before the biomarker-driven therapy was ≥1.3. The null hypothesis was that ≤15% of patients gain such benefit. RESULTS: The analysis included 46 patients (61% men; median age, 58 years; 57% with poorly-differentiated tumors). At least one actionable (i.e., predictive of response to a specific therapy) biomarker was identified for each patient. Immunohistochemistry was performed on all samples and identified 1-8 (median: 3) biomarkers per patient (most commonly: low TS, high TOPO1, high TOP2A). Twenty-eight patients received therapy after the biomarker analysis (1-4 lines). In the 1st line after biomarker analysis, five patients (18%) achieved a partial response and five (18%) stable disease; the median (range) PFS was 129 (12-1155) days. Twenty-four patients were evaluable for PFS ratio analysis; in seven (29.2%), the ratio was ≥1.3. In a one-sided exact binomial test vs. the null hypothesis, p = 0.019; therefore, the null hypothesis was rejected. CONCLUSIONS: Our findings demonstrated that implementing biomarker-driven analysis is feasible and could provide clinical benefit for a considerable proportion (~30%) of patients with metastatic gastric or esophageal cancer.

Treatment inferred from mutations identified using massive parallel sequencing leads to clinical benefit in some heavily pretreated cancer patients.

Molecular portraits of numerous tumors have flooded oncologists with vast amounts of data. In parallel, effective inhibitors of central pathways have shown great clinical benefit. Together, this promises potential clinical benefits to otherwise end-stage cancer patients. Here, we report a clinical service offering mutation detection of archived samples using the ion Ampliseq cancer panel coupled with clinical consultation.A multidisciplinary think tank consisting of oncologists, molecular-biologists, genetic counselors, and pathologists discussed 67 heavily pretreated, advanced cancer patient cases, taking into account mutations identified using ion Ampliseq cancer panel, medical history, and relevant literature.The team generated a treatment plan, targeting specific mutations, for 41 out of 64 cases. Three patients died before results were available. For 32 patients, the treating oncologists chose not to include the panel recommendation in the treatment plan for various reasons. Nine patients were treated as recommended by the panel, 5 with clinical benefit, and 4 with disease progression.This study suggests that routine use of massive parallel tumor sequencing is feasible and can judiciously affect treatment decisions when coupled with multidisciplinary team-based decision making. Administration of personalized based therapies at an earlier stage of disease, expansion of genetic alterations examined, and increased availability of targeted therapies may lead to further improvement in the clinical outcome of metastatic cancer patients.

Molecular Profiling-Selected Therapy for Treatment of Advanced Pancreaticobiliary Cancer: A Retrospective Multicenter Study.

This multicenter cohort study assessed the impact of molecular profiling (MP) on advanced pancreaticobiliary cancer (PBC). The study included 30 patients treated with MP-guided therapy after failing ≥ 1 therapy for advanced PBC. Treatment was considered as having benefit for the patient if the ratio between the longest progression-free survival (PFS) on MP-guided therapy and the PFS on the last therapy before MP was ≥ 1.3. The null hypothesis was that ≤ 15% of patients gain such benefit. Overall, ≥ 1 actionable (i.e., predictive of response to specific therapies) biomarker was identified/patient. Immunohistochemistry (the most commonly used method for guiding treatment decisions) identified 1-6 (median: 4) actionable biomarkers per patient. After MP, patients received 1-4 (median: 1) regimens/patient (most commonly, FOLFIRI/XELIRI). In a decision-impact analysis, of the 27 patients for whom treatment decisions before MP were available, 74.1% experienced a treatment decision change in the first line after MP. Twenty-four patients were evaluable for clinical outcome analysis; in 37.5%, the PFS ratio was ≥ 1.3. In one-sided exact binomial test versus the null hypothesis, P = 0.0015; therefore, the null hypothesis was rejected. In conclusion, our analysis demonstrated the feasibility, clinical decision impact, and potential clinical benefits of MP-guided therapy in advanced PBC.

Management of Inguinal Involvement of Peritoneal Surface Malignancies by Cytoreduction and HIPEC with Inguinal Perfusion.

BACKGROUND: Achieving complete cytoreduction of peritoneal surface malignancies (PSM) can be challenging. In most cases, delivery of heated intra-peritoneal chemotherapy (HIPEC) is straightforward. However, using the closed technique in some cases may be technically challenging; for example, in patients requiring abdominal closure using a large synthetic mesh. In cases where groin hernias are present, it is imperative to resect the hernia sac, since it may contain tumor deposits. In cases with major inguinal involvement where disease may spread out of the hernia sac or in cases where a hernia repair was performed while disease is present, inguinal perfusion should be considered. AIM: To describe our experience with combined intra-peritoneal and inguinal perfusion of HIPEC following cytoreductive surgery. PATIENTS AND METHODS: This is a retrospective review of all patients who underwent cytoreductive surgery (CRS) and HIPEC at our institution. A prospectively maintained database containing data of patients treated by CRS and HIPEC (n=122) was reviewed. All patients with macroscopic inguinal involvement by PSM with complete cytoreduction perfused by HIPEC were included. RESULTS: We identified five cases who underwent CRS and combined intraperitoneal and inguinal perfusion after resection of large inguinal tumor deposits (n=4) or after a recent hernia repair with hernial sac involvement by mucinous adenocarcinoma (n=1). All five patients were successfully perfused using an additional outflow catheter placed in the groin. DISCUSSION: In cases of inguinal involvement by PSM, complete cytoreduction should be achieved and perfusion of the involved groin considered as it is feasible and safe.

An observational cohort study of bevacizumab and chemotherapy in metastatic colorectal cancer patients: safety and efficacy with analysis by age group.

Bevacizumab improves survival when added to chemotherapy in metastatic colorectal cancer (mCRC). We assessed the safety and efficacy of bevacizumab in mCRC patients ≥70 years old (YO) vs. those <70 YO. mCRC patients treated from 2005-2012 who received chemotherapy (physician's choice) plus bevacizumab were included. The primary end point was safety; secondary objectives were progression-free survival (PFS) and overall survival (OS). Data was collected retrospectively. Three-hundred eight patients (92 ≥70 YO, 216 <70 YO) with 20.5 month median follow-up were included. Of the patients, 1.9 % died due to bevacizumab-related adverse effects; all were <70 YO. Grades 3-5 adverse events of interest for bevacizumab in patients ≥70 YO included hypertension (37.0 %), venous thromboembolism (6.5 %), wound-healing complications (5.4 %), bleeding (7.6 %), fistula (4.3 %), arterial thromboembolism (3.3 %), congestive heart failure (2.2 %), and proteinuria (grades 1-2 only, 14.1 %). Treatment was stopped due to adverse effects in 6.0 % of older patients. Older patients had significantly more ischemic heart disease and hypertension at baseline, and were treated less with FOLFOX and more with 5FU/LV monotherapy; nevertheless, OS and PFS were similar in younger and older patients. Compared to younger patients, in older patients, rates of proteinuria (all grades 1-2) were significantly higher (14.1 vs. 5.6 %, p=0.012) and rates of treatment-related hypertension (grades 3-5) were marginally higher (37 vs. 25.9 %, p=0.053); rates of other adverse events were similar in the two groups. In our patient population, bevacizumab was safe and effective in older as well as younger patients.

Hypertension as a predictive biomarker in bevacizumab treatment for colorectal cancer patients.

Bevacizumab treatment is associated with an increased risk of hypertension (HTN), a potential marker for effectiveness. We aimed to assess whether grades 2-3 HTN during bevacizumab treatment was associated with increased overall survival (OS) or progression-free survival (PFS). One hundred and eighty-one patients with metastatic colorectal cancer (CRC), who were treated in our Department from January 2009-February 2011 were included. Bevacizumab was administered jointly with standard first- or second-line chemotherapy protocols. Blood pressure was measured before each treatment. HTN was graded using common toxicity criteria. There were 181 CRC patients. Grades 2-3 HTN developed in 81 patients (44.75 %) but not in 100 patients (55.25 %); no patient developed grades 4-5 HTN. Median follow-up was 15.2 months. HTN was associated with better OS in HTN-positive versus HTN-negative patients (median not reached vs. 36.8 months, p = 0.029) and better PFS (29.9 vs. 17.2 months, p = 0.024, respectively). Bevacizumab-related HTN may represent a biomarker for clinical benefit in metastatic colorectal cancer patients.

Absence of founder BRCA1 and BRCA2 mutations in cutaneous malignant melanoma patients of Ashkenazi origin.

INTRODUCTION: Several epidemiologic studies have provided suggestive evidence of a link between coetaneous malignant melanoma (CMM) and breast cancer. The Breast Cancer Linkage Consortium (BCLC) reported approximately 2.6-fold increase in the risk for CMM among BRCA2 carrier families. METHODS: To evaluate the role of BRCA1/2 mutations in CMM, we screened 92 Jewish patients of Ashkenazi origin diagnosed with CMM for the three Ashkenazi founder mutations: 185delAG and 5382insC in the BRCA1 and 6174delT in the BRCA2 gene. Information about personal demography, family history of cancer, and occupational and lifestyle history was collected. RESULTS: Thirty-seven of 92 (40.2%) CMM patients reported a family history of cancer in a first-degree relative. In 14 patients, history of breast cancer (BC) was recorded; however, no family had features associated with BRCA carrier status (i.e., young age at BC onset, history of several BC cases or ovarian cancer in the family). None of the patients were found to carry any of these three mutations. CONCLUSION: Our results suggest a limited role for the three Ashkenazi BRCA founder mutations in CMM risk among the Ashkenazi Jewish population. Therefore, screening patients with CMM for these BRCA1/2 mutations is not warranted.

Treatment of pathological humeral shaft fractures with unreamed humeral nail.

PURPOSE: The purpose of this study is to analyze the results of intramedullary fixation of pathological humeral shaft fractures using an unreamed humeral nail (UHN). PATIENTS & METHODS: Twenty-one consecutive patients with 24 humeri fractured secondary to metastatic disease were retrospectively reviewed. The primary tumors included carcinomas of breast (11), kidney (2), multiple myeloma (2), colon (2), prostate (1), thyroid (1), lymphoma (1) and unknown origin (1). All fractures were stabilized with antegrade unreamed humeral nailing. Cemented technique was performed in 5 procedures. The mean age was 64 (range, 40-86), male to female ratio 6:15. RESULTS: Blood loss was unremarkable in 19 patients (22 procedures). Two patients who underwent fixation of additional pathological fractures during the same operation were given a total of 3 units of PC perioperatively. Mean postoperative hospitalization period due to one UHN procedure alone was 3 days (range, 2-7 days). Two patients died of their disease within 3 weeks of surgery. The remaining 19 patients returned to nearly normal function within 6 weeks after nailing. One patient developed postoperative local wound cellulitis. Relief of pain was rated as good in all but one patient. Adjuvant therapy was given in 20 procedures. Bony union was achieved in 88% (15/17) of all the cases where the patient had survived a minimum of 3 months. CONCLUSION: Unreamed humeral nailing of the pathological humeral shaft fractures provides immediate stability and pain relief, minimum morbidity and early return of function to the extremity.