Jay Bowen

Protocol for the Examination of Specimens From Pediatric Patients With Hepatoblastoma

Authors Milton J. Finegold, MD* Department of Pathology, Texas Children’s Cancer Center at Baylor College, Houston, Texas Jay Bowen, MS Center for Childhood Cancer, Columbus Children’s Research Institute, Columbus, Ohio Dolores Lopez-Terrada, MD, PhD Department of Pathology, Texas Children’s Cancer Center at Baylor College, Houston, Texas M. Kay Washington, MD, PhD Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee D. Ashley Hill, MD Department of Pathology, Children’s National Medical Center, Washington DC Joseph Khoury, MD† Department of Pathology, Quest Diagnostics, Las Vegas, Nevada For the Members of the Cancer Committee, College of American Pathologists

Protocol for the examination of specimens from patients with neuroblastoma and related neuroblastic tumors.

Authors Jason A. Jarzembowski, MD, PhD* Department of Pathology, Children’s Hospital of Wisconsin, Milwaukee, Wisconsin Miguel Reyes-Mugica, MD Department of Pathology, Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania Erin R. Rudzinski, MD Department of Laboratories, Seattle Children’s Hospital, Seattle, Washington Neil Sebire Histopathology, Greater Ormond Street Hospital, London, United Kingdom Hiroyuki Shimada, MD, PhD† Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California For the Members of the Cancer Committee, College of American Pathologists

DNA defects, epigenetics, and gene expression in cancer-adjacent breast: a study from The Cancer Genome Atlas

Recurrence rates after breast-conserving therapy may depend on genomic characteristics of cancer-adjacent, benign-appearing tissue. Studies have not evaluated recurrence in association with multiple genomic characteristics of cancer-adjacent breast tissue. To estimate the prevalence of DNA defects and RNA expression subtypes in cancer-adjacent, benign-appearing breast tissue at least 2 cm from the tumor margin, cancer-adjacent, pathologically well-characterized, benign-appearing breast tissue specimens from The Cancer Genome Atlas project were analyzed for DNA sequence, copy-number variation, DNA methylation, messenger RNA (mRNA) sequence, and mRNA/microRNA expression. Additional samples were also analyzed by at least one of these genomic data types and associations between genomic characteristics of normal tissue and overall survival were assessed. Approximately 40% of cancer-adjacent, benign-appearing tissues harbored genomic defects in DNA copy number, sequence, methylation, or in RNA sequence, although these defects did not significantly predict 10-year overall survival. Two mRNA/microRNA expression phenotypes were observed, including an active mRNA subtype that was identified in 40% of samples. Controlling for tumor characteristics and the presence of genomic defects, this active subtype was associated with significantly worse 10-year survival among estrogen receptor (ER)-positive cases. This multi-platform analysis of breast cancer-adjacent samples produced genomic findings consistent with current surgical margin guidelines, and provides evidence that extratumoral RNA expression patterns in cancer-adjacent tissue predict overall survival among patients with ER-positive disease.

The effects of frozen tissue storage conditions on the integrity of RNA and protein.

Abstract Unfixed tissue specimens most frequently are stored for long term research uses at either −80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5–12 years at −80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for −80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at −80° C compared to those stored in VPLN. Long term storage of human research tissues at −80° C provides at least the same quality of RNA and protein as storage in VPLN.

The Role of Tumor Banking and Related Informatics

The majority of this book deals with the diagnostic and research applications of molecular or tissue array technologies with regard to expression profiling of tumors. These efforts (1) will only be successful with the logical application of tumor banking and its associated informatics systems as the translational bridge linking new molecular information to its clinical significance. The design of tumor banks should be such that significant effort is devoted to obtaining data on clinical outcomes (2)which permits investigators to know that such data are available for analysis as they pursue their molecular studies on bank-derived specimens. Tumor banking and its associated inventory informatics have been recognized for over a decade (3,4) as necessary tools to advance the science of molecular testing; however, it has only been in the last 2 to 3 yr that the linkage to clinical outcomes has been seen as crucial to achieving this goal (3) It is estimated that by the year 2005 (5), as much as 10% of clinical laboratory tests will be based on RNA or DNA analysis.

Protocol for the Examination of Specimens From Pediatric and Adult Patients With Extragonadal Germ Cell Tumors

The College of American Pathologists offers these protocols to assist pathologists in providing clinically useful and relevant information when reporting results of surgical specimen examinations. The College regards the reporting elements in the ‘‘Surgical Pathology Cancer Case Summary (Checklist)’’ portion of the protocols as essential elements of the pathology report. However, the manner in which these elements are reported is at the discretion of each specific pathologist, taking into account clinician preferences, institutional policies, and individual practice. The College developed these protocols as an educational tool to assist pathologists in the useful reporting of relevant information. It did not issue the protocols for use in litigation, reimbursement, or other contexts. Nevertheless, the College recognizes that the protocols might be used by hospitals, attorneys, payers, and others. Indeed, effective January 1, 2004, the Commission on Cancer of the American College of Surgeons mandated the use of the checklist elements of the protocols as part of its Cancer Program Standards for Approved Cancer Programs. Therefore, it becomes even more important for pathologists to familiarize themselves with these documents. At the same time, the College cautions that use of the protocols other than for their intended educational purpose may involve additional considerations that are beyond the scope of these documents.