Discovering fragment length signatures of circulating tumor DNA using Non-negative Matrix Factorization

Sequencing of cell-free DNA (cfDNA) is currently being used to detect cancer by searching both for mutational and non-mutational alterations. Recent work has shown that the length distribution of cfDNA fragments from a cancer patient can inform tumor load and type. Here, we propose non-negative matrix factorization (NMF) of fragment length distributions as a novel method to study fragment lengths in cfDNA samples. Using shallow whole-genome sequencing (sWGS) of cfDNA from a cohort of patients with metastatic castration-resistant prostate cancer (mCRPC), we demonstrate how NMF accurately infers the true tumor fragment length distribution as an NMF component - and that the sample weights of this component correlate with ctDNA levels (r=0.75). We further demonstrate how using several NMF components enables accurate cancer detection on data from various early stage cancers (AUC=0.96). Finally, we show that NMF, when applied across genomic regions, can be used to discover fragment length signatures associated with open chromatin.

Rationalizing the pathway to personalized neoadjuvant immunotherapy: the Lombard Street Approach

Neoadjuvant chemo(radio)therapy is part of the established standard of care in cancer treatment; neoadjuvant application of immunotherapy, however, is only performed within recent trials. Combination of programmed cell death protein 1 and cytotoxic T lymphocyte antigen 4 blockade shows promising results with high pathologic response rates in the neoadjuvant setting and a very low relapse rate in the responding patients. In addition, neoadjuvant administration allows direct determination of treatment efficacy within the individual patient, and offers easy access to paired tumor material, both pretherapy and post-therapy, thus facilitates the rational development of new combinations driven by preclinical analyses. Patient-derived human tumor explant systems such as a recently developed human patient-derived tumor fragment platform can provide an additional tool to further rationalize the development of new treatment combinations. We will discuss neoadjuvant immunotherapy as a unique opportunity for rational trial design, the development of immune signatures for non-responding patients to steer clinical trial development, and the use of patient-derived ex vivo models to identify new personalized immunotherapy combinations. In this context, we propose the ‘Lombard Street Approach’, a back and forth approach of characterizing non-responders on neoadjuvant immunotherapy combinations, identifying promising new combinations for this group in the tumor fragment platform, and performing subsequently signature-driven small proof-of-concept combination trials. Repeating this approach with smaller and smaller groups of non-responders will step by step increase the percentage of patients benefiting from neoadjuvant immunotherapy in a rational and fast manner.

Establishment and characteristic of an orthotopic implantation model of human hepatocellular carcinoma with Luc-GFP-labeled in nude mice

AimTo construct Luc-GFP-labeled human hepatocellular carcinoma (HCC) cell line with high metastatic potential. And to establish a spontaneous metastasis and conveniently monitored orthotopic model of hepatocellular carcinoma in nude mice. Methods: HCCLM3-Luc-GFP cell line stably expressing luciferase (Luc) and green fluorescent protein (GFP) was constructed by lentivirus transfection. The orthotopic xenograft model was established though cell suspension injection method and tumor fragment implanted method. The growth and metastasis of the tumors were observed by in vivo imaging and pathology. Results: HCCLM3-Luc-GFP, a highly metastatic HCC cell line with GFP expression and Luc activity, was obtained. The tumorigenic rates both of two approaches were 100%, but the lung metastatic rate was higher the former than the latter. Conclusion: The orthotopic model of highly metastatic and Luc-GFP-labeled HCC in nude mice was successfully established by above approaches, called as cell suspension injection method and tumor fragment implanted method, respectively. This study provides a new and effective means to monitor the growth of tumors in vivo and to evaluate the efficacy of anti-metastatic drugs against HCC.

Recurrence of cardiac myxoma. Clinical and morphological aspects

Aim: to conduct a one-center retrospective research of heart myxoma relapses in a large group of patients. Materials and methods. Since 1992 to 2016 115 surgical removal of sporadic cardiac myxoma was performed (44 male, 71 female).Results. Two (1.7%) patients had recurrence of sporadic myxoma of the left atrium. One patient had the tumor returned due to inadequate removal of the tumor. Myxoma was removed without excising the place of fi xation to the interatrial septum. The second patient possibly had recurrence of myxoma due to the conservation of a small tumor fragment in another part of the interatrial septum that was not diagnosed during the removal of the primary tumor. Conclusion. Recurrence of sporadic myxoma of the left atrium is rare. The reasons for the recurrence may be different but usually it is due to non-radical removal of the tumor. The results of our research show that even removal of the myxoma together with the interatrial septum does not fully guarantee the prevention of recurrence. The recurrence of sporadic cardiac myxoma is possibly associated with minor formations that are not diagnosed during surgery. We cannot exclude the possibility of forming myxoma denovo also.

An Advanced Orthotopic Ovarian Cancer Model in Mice for Therapeutic Trials

A nude mouse received subcutaneous injection of human ovarian cancer cells HO-8910PM to form a tumor, and then the tumor fragment was surgically transplanted to the ovary of a recipient mouse to establish an orthotopic cancer model. Tumors occurred in 100% of animals. A mouse displayed an ovarian mass, ascites, intraperitoneal spread, and lung metastasis at natural death. The mean survival time was34.1±17.2days, with median survival time of 28.5 days. The findings indicated that the present mouse model can reflect the biological behavior of advanced human ovarian cancers. This in vivo model can be used to explore therapeutic means against chemoresistance and metastasis, and an effective treatment would prolong the survival time.

Diagnostic problems with follicular thyroid cancer – case study

The diagnosis of follicular thyroid cancer is based on postoperative histopathology assessment. In its minimally invasive form, the signs of vascular invasion and capsular infiltration may sometimes be seen only in a small tumor fragment; hence, the diagnosis should be based on multiple histopathology specimens. This case study is a report on a 70-year-old female who was diagnosed with spinal metastasis of follicular thyroid cancer. This diagnosis was established 5 years after partial strumectomy due to goiter and there were no signs of thyroid cancer in postoperative histopathology assessment. Based on this case and literature reports, the authors conclude that the diagnosis of follicular thyroid cancer, especially its minimally invasive forms, may pose a diagnostic problem even when based on postoperative histopathology.