2011 NYU NMVB Report NYU Dept of Cardiothoracic Surgery NYU Dept of Pathology Monday November 7 th, 2011

NYU Dept. Pathology Audrey Sorensen, RN (Research Nurse Coordinator) Harvey Pass, MD (Surgeon, NYU Steering Committee Member & PI) Dept. Cardiothoracic Surgery Ryan Harrington (Lab Technician, Thoracic Lab) Angela Pittman (Research Project Coordinator) Ruth Pe Benito (Bioresource Manager) Jonathan Melamed, MD (Pathologist, NYU Steering Committee Member) Monica Gorman (Research Coordinator) Rachel Ruoff (Lab Technician, Pathology Lab)

NYU MVB IRB Amendment Approval Amendment to IRB (approved on 10/27 /11) Amendment includes the following statement in the consent: “The NYU School of Medicine is collaborating with the University of Pittsburgh to create and maintain the Mesothelioma Virtual Bank (MVB). Clinical information and biologic samples that are free of any personal health identifiers are shared in accordance with HIPAA standards. This data is used to advance the scientific understanding of Mesothelioma. “

SPECIMENS COLLECTED CATEGORY SerumPlasma Buffy Coat PaxgeneMonoCPTTumorNormalEffusion Mesothelioma Follow-up (n=4) Mesothelioma New (n=7) NYU Additions to MVB 2011

Year Retrospective Cases Prospective Cases Overall Total Total:239 NYU MVB Biospecimen Accrual

YearNew cases collected Collection Method Frozen tissue only Paraffin + Frozen tissue Paraffin tissue only Emphasis on accruing extrapleural pneumonectomy cases NYU MVB tissue accrual

NYU MVB Paraffin TMA 1 NYU MVB Paraffin TMA 1 NYU MVB Paraffin TMA 1 2 identical TMA Blocks 37 cases - arrayed over 2 blocks 37 Tumor + 4 Control 8 Cell lines Supplementary TMA 9 Cases (additional cores for TMA1) 9 Tumor +1 Control Block A Block B

Map for Paraffin TMA ORIENTATION CORES MVB 2230MVB 2213MVB 2197MVB 2211MVB 2212 MVB 2179MVB 2180MVB 2187 MVB 2230MVB 2213MVB 2197MVB 2211MVB 2212 MVB 2215MVB 2186MVB 2199MVB 2190MVB 2181 MVB 2219MVB 2222MVB 2163 MVB 2215MVB 2186MVB 2199MVB 2190MVB 2181 MVB 2167MVB 2191MVB 2189MVB 2214MVB 2203 MVB 2170MVB 2231MVB 2229 MVB 2167MVB 2191MVB 2189MVB 2214MVB 2203 MVB 2207MVB 2202MVB 2174MVB 2168MVB 2161 MVB 2227MVB 2217MVB 2228 MVB 2180 MVB 2207MVB 2202MVB 2174MVB 2168MVB 2161 MVB 2162MVB 2165MVB 2176 MVB 2174 (2890) MVB 2160 MVB 2190MVB 2221MVB 2160 MVB 2174 MVB 2162MVB 2165MVB 2176MVB 2174MVB 2160 Cell Line 1 Cell Line 2 Cell Line 3 Cell Line 4 Cell Line 5 Cell Line 6 Cell Line 7 Cell Line 8 ORIENTATION CORES MVB 2230MVB 2213MVB 2197MVB 2211MVB 2212 MVB 2179MVB 2180MVB 2187 MVB 2230MVB 2213MVB 2197MVB 2211MVB 2212 MVB 2215MVB 2186MVB 2199MVB 2190MVB 2181 MVB 2219MVB 2222MVB 2163 MVB 2215MVB 2186MVB 2199MVB 2190MVB 2181 MVB 2167MVB 2191MVB 2189MVB 2214MVB 2203 MVB 2170MVB 2231MVB 2229 MVB 2167MVB 2191MVB 2189MVB 2214MVB 2203 MVB 2207MVB 2202MVB 2174MVB 2168MVB 2161 MVB 2227MVB 2217MVB 2228 MVB 2180 MVB 2207MVB 2202MVB 2174MVB 2168MVB 2161 MVB 2162MVB 2165MVB 2176MVB 2174MVB 2160 MVB 2190MVB 2221MVB 2160 MVB 2174 MVB 2162MVB 2165MVB 2176MVB 2174MVB 2160 MN 05/16/07 Mesothelioma Specimens Normal Cell Lines Orientation Cores (Liver) Core Size = 0.6mm

Evaluation for presence of tissue and sampling accuracy based on tumor (9 of 37 cases missing across the two TMAs – added in supplementary block) IHC stain to evaluate antigenicity of tissue: WT-1, Calretinin ORIENTATION CORES ATTTT TTA ATTTT TATTT TTA TATAT TBTTT AAT TTTTT TBTTT ABTATAATT ATAAA BBBBTATTA ATTTTATTTTTTTTAA BTTTT TTT TTTB TTTTT TTT TATTT TTTTT ABT BTTTT TAABT TTTATATTA ATTT BBTBTTTTB QA Steps for TMA (slide A) B- Benign Tissue T-Tumor A- Missing Core MVB # Cores on TMA out of 8 Tumor/Benign Tumor Tumor Tumor Tumor Benign Tumor Possible Tumor 2170 None Tumor/ 2 Benign

MVB # Cores on TMA Blocks out of possible 8 Tumor/Normal Tumor Tumor Tumor Tumor Normal Tumor Possible Tumor 2170 None Tumor/ 2 Normals QA Table for TMA

LiverMVB 2230MVB 2186MVB 2160MVB 2187MVB 2163MVB 2180MVB 2230MVB LiverMVB 2202MVB 2162MVB 2231MVB 2170MVB 2231MVB 2170MVB 2202MVB 2162MVB LiverMVB 2160MVB 2230MVB 2180MVB 2187MVB 2163MVB 2231MVB 2160MVB Liver 4 MVB 2230MVB 2186MVB 2187MVB 2163MVB 2230MVB LiverMVB 2202MVB 2162MVB 2170MVB 2231MVB 2202MVB 2162MVB LiverMVB 2160MVB 2230MVB 2180MVB 2187MVB 2160MVB LiverMVB 2162MVB 2163MVB 2170MVB 2162 Map for Supplementary Paraffin TMA

Frozen TMA Normal lung tissue Tumor tissue (mesothelioma) MVB #s indicate distinct patients N=13 pts mvb22 21 mvb21 89 mvb22 15 mvb22 19 mvb21 89 mvb22 15 mvb22 19 mvb21 90 mvb21 91 mvb21 97 mvb21 90 mvb21 91 mvb21 97 mvb22 17 mvb22 14 mvb21 99 mvb22 17 mvb22 14 mvb21 99 mvb22 03 mvb22 11 mvb22 13 mvb22 03 mvb22 11 mvb22 13 mvb22 12

High Density Frozen TMA: Construction Frozen Array mold Oil

Ischemia-Fixation TMA Pre-analytic variables in FFPE Varied duration from devascularization to preservation: ISCHEMIA time (minutes to hours) Varied duration of fixation: hours Varied tissue processor protocols across institutions Design: Timed experiment with varied ischemia/fixation times of tissue –constituted into TMA (n = 3+) Outcome: TMA slides for 1) investigators to measure preservation of marker of interest against different pre-analytic variables 2) NMVB biospecimen science – to determine biomarkers that reflect early ischemic effects for rating of core preservation on NMVB TMAs.

Ischemia-Fixation Meso TMA Time Delay (hr) Case 1Case 2Case 3 Cell Line Time Fixation (hr)

Diagnostic marker durability: Necrosis, ischemia, overfixation (WT-1, Calretinin) (autopsy vs biopsy material) Impact of preanalytic variables: Tissue expression of current serum /pleural fluid biomarkers: Tools: Frozen TMA & Ischemia/Fixation TMA Biospecimen Science